@article{taussig_ghasemi_han_kwansa_li_keene_woodward_yingling_malliaras_gomez_et al._2024, title={Electrostatic self-assembly yields a structurally stabilized PEDOT:PSS with efficient mixed transport and high-performance OECTs}, volume={7}, ISSN={["2590-2385"]}, DOI={10.1016/j.matt.2023.12.021}, abstractNote={<h2>Summary</h2> Organic electronics and organic electrochemical transistors (OECTs) are gaining importance for their potential to replicate complex biological processes of the human brain. Such devices require polymeric materials to efficiently transport and couple ionic and electronic charges in aqueous media, therefore demanding water-insoluble systems capable of efficient electronic and ionic conductions. This has created a fundamental stability-performance compromise for water-soluble conducting polymers such as poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS), whereby stability has been achieved at the expense of electronic properties. Here, we demonstrate a breakthrough in structural stabilization of PEDOT:PSS through electrostatic self-assembly (ESA) that leads to the formation of an efficient mixed conductor in a hydrated state. Benefiting from the multiscale morphology control provided by ESA, PEDOT:PSS mixed conductors exhibit superior carrier mobility and high volumetric capacitance resulting in a state-of-the-art thin-film OECT figure of merit (<i>μC</i>∗ = 752.5 F/cmVs) in aqueous media, making this approach suitable for creating robust mixed conductors for bioelectronic applications and beyond.}, number={3}, journal={MATTER}, author={Taussig, Laine and Ghasemi, Masoud and Han, Sanggil and Kwansa, Albert L. and Li, Ruipeng and Keene, Scott T. and Woodward, Nathan and Yingling, Yaroslava G. and Malliaras, George G. and Gomez, Enrique D. and et al.}, year={2024}, month={Mar} }
 @article{allen_pinky_beard_calzadilla_gringeri_sanders_knight_yingling_2024, title={Monomer Architecture as a Mechanism to Control the Self-Assembly of Oligomeric Diblock Peptide-Polymer Amphiphiles}, url={https://doi.org/10.26434/chemrxiv-2024-0bhgz}, DOI={10.26434/chemrxiv-2024-0bhgz}, abstractNote={Diblock oligomeric peptide-polymer amphiphiles (PPAs) are biohybrid materials that offer versatile functionality by integrating the sequence-dependent properties of peptides with the synthetic versatility of polymers. Despite their potential as biocompatible materials, the rational design of PPAs for assembly into multi-chain nanoparticles remains challenging due to the complex intra- and intermolecular interactions emanating from the polymer and peptide segments. To systematically explore the impact of monomer architecture on nanoparticle assembly, PPAs were synthesized with a random coil peptide (XTEN2) and oligomeric alkyl acrylates with unique side chains: ethyl, tert-butyl, n-butyl, and cyclohexyl. Experimental characterization using electron and atomic force microscopies demonstrated that tail hydrophobicity impacted accessible morphologies. Moreover, characterization of different assembly protocols (i.e., bath sonication and thermal annealing) revealed that certain tail architectures provide access to kinetically trapped assemblies. All-atom molecular dynamics simulations of micelle structure formation unveiled key interactions and differences in hydration states, dictating PPA assembly behavior. These findings highlight the complexity of PPA assembly dynamics and serve as valuable benchmarks to guide the design of PPAs for a variety of applications including catalysis, mineralization, targeted sequestration, antimicrobial activity, and cargo transportation}, author={Allen, Benjamin and Pinky, Sabila and Beard, Emily and Calzadilla, Nicholas and Gringeri, Abigail and Sanders, Matthew and Knight, Abigail and Yingling, Yaroslava}, year={2024}, month={Apr} }
 @article{allen_pinky_beard_gringeri_calzadilla_sanders_yingling_knight_2024, title={Monomer Architecture as a Mechanism to Control the Self-Assembly of Oligomeric Diblock Peptide-Polymer Amphiphiles}, url={https://doi.org/10.26434/chemrxiv-2024-0bhgz-v2}, DOI={10.26434/chemrxiv-2024-0bhgz-v2}, abstractNote={Diblock oligomeric peptide-polymer amphiphiles (PPAs) are biohybrid materials that offer versatile functionality by integrating the sequence-dependent properties of peptides with the synthetic versatility of polymers. Despite their potential as biocompatible materials, the rational design of PPAs for assembly into multi-chain nanoparticles remains challenging due to the complex intra- and intermolecular interactions emanating from the polymer and peptide segments. To systematically explore the impact of monomer architecture on nanoparticle assembly, PPAs were synthesized with a random coil peptide (XTEN2) and oligomeric alkyl acrylates with unique side chains: ethyl, tert-butyl, n-butyl, and cyclohexyl. Experimental characterization using electron and atomic force microscopies demonstrated that tail hydrophobicity impacted accessible morphologies. Moreover, characterization of different assembly protocols (i.e., bath sonication and thermal annealing) revealed that certain tail architectures provide access to kinetically trapped assemblies. All-atom molecular dynamics simulations of micelle structure formation unveiled key interactions and differences in hydration states, dictating PPA assembly behavior. These findings highlight the complexity of PPA assembly dynamics and serve as valuable benchmarks to guide the design of PPAs for a variety of applications including catalysis, mineralization, targeted sequestration, antimicrobial activity, and cargo transportation}, author={Allen, Benjamin and Pinky, Sabila and Beard, Emily and Gringeri, Abigail and Calzadilla, Nicholas and Sanders, Matthew and Yingling, Yaroslava and Knight, Abigail}, year={2024}, month={Apr} }
 @article{hussein_cannon_hutchison_gorman_yingling_mayer_2024, title={Phosphate-binding protein-loaded iron oxide particles: adsorption performance for phosphorus removal and recovery from water}, volume={3}, ISSN={["2053-1419"]}, url={https://doi.org/10.1039/D4EW00052H}, DOI={10.1039/D4EW00052H}, abstractNote={Adsorbents featuring high-affinity phosphate-binding proteins (PBPs) have demonstrated highly selective and rapid phosphorus removal and recovery.}, journal={ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY}, author={Hussein, Faten B. and Cannon, Andrew H. and Hutchison, Justin M. and Gorman, Christopher B. and Yingling, Yaroslava G. and Mayer, Brooke K.}, year={2024}, month={Mar} }
 @article{kwansa_singh_williams_haigler_roberts_yingling_2024, title={Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods}, volume={1}, ISSN={["1572-882X"]}, DOI={10.1007/s10570-023-05691-x}, journal={CELLULOSE}, author={Kwansa, Albert L. and Singh, Abhishek and Williams, Justin T. and Haigler, Candace H. and Roberts, Alison W. and Yingling, Yaroslava G.}, year={2024}, month={Jan} }
 @article{zhang_pinky_kwansa_ferguson_yingling_stiff-roberts_2023, title={Correlation of Emulsion Chemistry, Film Morphology, and Device Performance in Polyfluorene LEDs Deposited by RIR-MAPLE}, volume={3}, ISSN={["1944-8252"]}, url={https://doi.org/10.1021/acsami.3c03012}, DOI={10.1021/acsami.3c03012}, abstractNote={Thin films of polyfluorene (PFO) were deposited using emulsion-based resonant infrared, matrix-assisted pulsed laser evaporation (RIR-MAPLE). Here, it is shown that properly selected surfactant chemistry in the emulsion can increase crystalline β phase (β-PFO) content and consequently improve the color purity of light emission. To determine the impact of surfactant on the device performance of resulting films, blue light-emitting diodes (LEDs) with PFO as an active region were fabricated and compared. Molecular dynamics (MD) simulations were used to explain the physical and chemical changes in the emulsion properties as a function of the surfactant. The results indicate that the experimental film morphology and device performance are highly correlated to the emulsion droplet micelle structure and interaction energy among PFO, primary solvent, and water obtained from MD simulations. While the champion device performance was lower than other reported devices (luminous flux ∼0.0206 lm, brightness ∼725.58 cd/m2, luminous efficacy ∼0.0548 lm/W, and luminous efficiency ∼0.174 cd/A), deep blue emission with good color purity (CIE chromaticity diagram coordinate of (0.177,0.141)) was achieved for low operating voltages around 3 V. Furthermore, a much higher β-phase content of 21% was achieved in annealed films (without the pinholes typically found in β-PFO deposited by other techniques) by using sodium dodecyl sulfate (SDS) as the surfactant.}, journal={ACS APPLIED MATERIALS & INTERFACES}, author={Zhang, Buang and Pinky, Sabila K. and Kwansa, Albert L. and Ferguson, Spencer and Yingling, Yaroslava G. and Stiff-Roberts, Adrienne D.}, year={2023}, month={Mar} }
 @article{choi_kwansa_yingling_kim_2023, title={DFT-Based Calculation of Molecular Hyperpolarizability and SFG Intensity of Symmetric and Asymmetric Stretch Modes of Alkyl Groups}, volume={127}, ISSN={["1520-5207"]}, url={https://doi.org/10.1021/acs.jpcb.3c03910}, DOI={10.1021/acs.jpcb.3c03910}, abstractNote={Vibrational sum frequency generation (SFG) spectroscopy has been extensively used for obtaining structural information of molecular functional groups at two-dimensional (2D) interfaces buried in the gas or liquid medium. Although the SFG experiment can be done elegantly, interpreting the measured intensity in terms of molecular orientation with respect to the lab coordinate is quite complicated. One of the main reasons is the difficulty of determining the hyperpolarizability tensors of even simple molecules that govern their SFG responses. The single-bond polarizability derivative model has been proposed to estimate the relative magnitude of SFG-active hyperpolarizability by assuming that the perturbation associated to each vibration is negligible. In this study, density functional theory was used to calculate the polarizability and dipole derivative tensors of the CH3 stretch mode of CH3I, CH3CH2I, CH3OH, and CH3CH2OH. Then, the hyperpolarizability tensors of symmetric and asymmetric vibration modes were calculated considering the Boltzmann distribution of representative conformers, which allowed us to theoretically calculate their SFG intensities at all polarization combinations as a function of the tilt angle of the CH3 group with respect to the surface normal direction. Then, the ratios of the calculated SFG intensities for the CH3 symmetric and asymmetric stretch peaks used in experimental studies for the CH3 tilt angle determination were compared. This comparison clearly showed that the effect of vibrational coupling among neighboring functional groups is significant and cannot be assumed to be negligible. This study presents new parameters that can be used in determining the average tilt angle of the CH3 group at the 2D interface with SFG measurements as well as limitations of the method.}, number={39}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Choi, Juseok and Kwansa, Albert L. and Yingling, Yaroslava G. and Kim, Seong H.}, year={2023}, month={Sep}, pages={8456–8467} }
 @article{pinky_kwansa_zhang_stiff-roberts_yingling_2023, title={Effect of solvent on the emulsion and morphology of polyfluorene films: all-atom molecular dynamics approach}, volume={2}, ISSN={["1744-6848"]}, url={https://doi.org/10.1039/D2SM01001A}, DOI={10.1039/D2SM01001A}, abstractNote={Solvent-mediated non-covalent interactions in emulsion are correlated with the morphology of conjugated polymer thin films.}, journal={SOFT MATTER}, author={Pinky, Sabila K. and Kwansa, Albert L. and Zhang, Buang and Stiff-Roberts, Adrienne D. and Yingling, Yaroslava G.}, year={2023}, month={Feb} }
 @article{verma_kwansa_ho_yingling_zimmer_2023, title={Insights into substrate coordination and glycosyl transfer of poplar cellulose synthase-8}, volume={31}, ISSN={["1878-4186"]}, DOI={10.1016/j.str.2023.07.010}, abstractNote={Cellulose is an abundant cell wall component of land plants. It is synthesized from UDP-activated glucose molecules by cellulose synthase, a membrane-integrated processive glycosyltransferase. Cellulose synthase couples the elongation of the cellulose polymer with its translocation across the plasma membrane. Here, we present substrate- and product-bound cryogenic electron microscopy structures of the homotrimeric cellulose synthase isoform-8 (CesA8) from hybrid aspen (poplar). UDP-glucose binds to a conserved catalytic pocket adjacent to the entrance to a transmembrane channel. The substrate's glucosyl unit is coordinated by conserved residues of the glycosyltransferase domain and amphipathic interface helices. Site-directed mutagenesis of a conserved gating loop capping the active site reveals its critical function for catalytic activity. Molecular dynamics simulations reveal prolonged interactions of the gating loop with the substrate molecule, particularly across its central conserved region. These transient interactions likely facilitate the proper positioning of the substrate molecule for glycosyl transfer and cellulose translocation.}, number={10}, journal={STRUCTURE}, author={Verma, Preeti and Kwansa, Albert L. and Ho, Ruoya and Yingling, Yaroslava G. and Zimmer, Jochen}, year={2023}, month={Oct}, pages={1166-+} }
 @article{kwansa_pani_deloach_tieppo_moskala_perri_yingling_2023, title={Molecular Mechanism of Plasticizer Exudation from Polyvinyl Chloride}, volume={6}, ISSN={["1520-5835"]}, url={https://doi.org/10.1021/acs.macromol.2c01735}, DOI={10.1021/acs.macromol.2c01735}, abstractNote={Plasticizers improve polymer material flexibility and durability by lowering glass transition and cold flex temperatures. While many different classes of plasticizers have been synthesized and used in various applications, several classes have been phased out due to concerns over their safety. One of the main problems that hinder the development of a new generation of efficient and safe plasticizers is the plasticizers’ migration and exudation from polymer materials, which leads to a reduction of mechanical properties and premature degradation. Here, we employed multiscale molecular dynamics, validated by experiment, to investigate the molecular mechanism of exudation of an orthophthalate plasticizer (di-2-ethylhexyl phthalate (DEHP)), non-orthophthalate plasticizers (di-n-butyl terephthalate (DnBT) and di-2-ethylhexyl terephthalate (DEHT)), and their blends from polyvinyl chloride (PVC). The results suggest that DnBT acted as an intermediary between PVC and DEHT, improving the compatibility of the plasticizer blend and reducing the degree of exudation. Specifically, it was predicted that the 70:30 wt % DnBT–DEHT blend was on par with the DEHP control system. These results also suggest that plasticizer-PVC compatibility is a stronger determinant of plasticizer exudation than the plasticizer size, diffusivity, and viscosity, given that DnBT is a smaller, more mobile, faster-diffusing, and lower-viscosity plasticizer than DEHT. Overall, our results indicate that the most important parameters that control exudation were Hansen solubility and consequently Flory–Huggins interaction parameters.}, journal={MACROMOLECULES}, author={Kwansa, Albert L. L. and Pani, Rakhee C. C. and DeLoach, Joseph A. A. and Tieppo, Arianna and Moskala, Eric J. J. and Perri, Steven T. T. and Yingling, Yaroslava G. G.}, year={2023}, month={Jun} }
 @article{oweida_yingling_2023, title={Resolving Structure of ssDNA in Solution by Fusing Molecular Simulations and Scattering Experiments with Machine Learning}, volume={9}, ISSN={["2513-0390"]}, url={https://doi.org/10.1002/adts.202300411}, DOI={10.1002/adts.202300411}, abstractNote={Abstract}, journal={ADVANCED THEORY AND SIMULATIONS}, author={Oweida, Thomas J. and Yingling, Yaroslava G.}, year={2023}, month={Sep} }
 @article{peerless_gulyuk_milliken_kim_reid_lee_kim_hendren_choi_yingling_2023, title={Role of Nanoscale Morphology on the Efficiency of Solvent-Based Desalination Method}, volume={1}, ISSN={["2690-0637"]}, url={https://doi.org/10.1021/acsestwater.2c00473}, DOI={10.1021/acsestwater.2c00473}, abstractNote={Brine desalination is important for minimizing the environmental impact of contaminated wastewater, yet current desalination techniques have high energy requirements. Solvent-based desalination (SBD) method, which is the process of extracting fresh water using an organic solvent, has existed for decades, yet has not reached competitive efficiencies. In this work, 10 organic solvents were tested for SBD efficacy via synergetic studies using bench-scale extraction experiments and molecular dynamics (MD) simulations. The SBD effectiveness was correlated to the computationally observed ability of the solvent to form one of the three morphologies in water: ordered, disordered, or partial nanoscale. We correlated that solvents that form ordered and disordered morphologies were not able to clean up the water. Solvents that were able to cause low salinity in water showed computationally observed partial nanoscale phase separation, where nanometer-scale aggregated solvent phases were able to effectively reject salt ions while capturing comparatively large amounts of water molecules. The formation of a partial nanoscale phase is likely driven by the solvent structure with bulky hydrocarbons adjacent to hydrophilic end groups. Our results make a step toward the rational design of solvents that may allow for efficient SBD and thus a low-cost source of fresh water.}, journal={ACS ES&T WATER}, author={Peerless, James S. and Gulyuk, Alexey V and Milliken, Nina J. B. and Kim, Gyu Dong and Reid, Elliot and Lee, Jae Woo and Kim, Dooil and Hendren, Zachary and Choi, Young Chul and Yingling, Yaroslava G.}, year={2023}, month={Jan} }
 @article{mahmood_rizvi_tracy_yingling_2023, title={Solvent Effects in Ligand Stripping Behavior of Colloidal Nanoparticles}, volume={6}, ISSN={["1936-086X"]}, url={https://doi.org/10.1021/acsnano.3c01313}, DOI={10.1021/acsnano.3c01313}, abstractNote={Inorganic colloidal nanoparticle (NP) properties can be tuned by stripping stabilizing ligands using a poor solvent. However, the mechanism behind ligand stripping is poorly understood, in part because in situ measurements of ligand stripping are challenging at the nanoscale. Here, we investigate ethanol solvent-mediated oleylamine ligand stripping from magnetite (Fe3O4) NPs in different compositions of ethanol/hexane mixtures using atomistic molecular dynamics (MD) simulations and thermogravimetric analysis (TGA). Our study elucidates a complex interplay of ethanol interactions with system components and indicates the existence of a threshold concentration of ∼34 vol % ethanol, above which ligand stripping saturates. Moreover, hydrogen bonding between ethanol and stripped ligands inhibits subsequent readsorption of the ligands on the NP surface. A proposed modification of the Langmuir isotherm explains the role of the enthalpy of mixing of the ligands and solvents on the ligand stripping mechanism. A good agreement between the MD predictions and TGA measurements of ligand stripping from Fe3O4 NPs validates the simulation observations. Our findings demonstrate that the ligand coverage of NPs can be controlled by using a poor solvent below the threshold concentration and highlight the importance of ligand-solvent interactions that modulate the properties of colloidal NPs. The study also provides an approach for a detailed in silico study of ligand stripping and exchange from colloidal NPs that are crucial for applications of NPs spanning self-assembly, optoelectronics, nanomedicine, and catalysis.}, journal={ACS NANO}, author={Mahmood, Akhlak U. and Rizvi, Mehedi H. and Tracy, Joseph B. and Yingling, Yaroslava G.}, year={2023}, month={Jun} }
 @article{chatterjee_pratakshya_kwansa_kaimal_cannon_sartori_marmiroli_orins_feng_drake_et al._2023, title={Squid Skin Cell-Inspired Refractive Index Mapping of Cells, Vesicles, and Nanostructures}, volume={1}, ISSN={["2373-9878"]}, DOI={10.1021/acsbiomaterials.2c00088}, abstractNote={The fascination with the optical properties of naturally occurring systems has been driven in part by nature's ability to produce a diverse palette of vibrant colors from a relatively small number of common structural motifs. Within this context, some cephalopod species have evolved skin cells called iridophores and leucophores whose constituent ultrastructures reflect light in different ways but are composed of the same high refractive index material─a protein called reflectin. Although such natural optical systems have attracted much research interest, measuring the refractive indices of biomaterial-based structures across multiple different environments and establishing theoretical frameworks for accurately describing the obtained refractive index values has proven challenging. Herein, we employ a synergistic combination of experimental and computational methodologies to systematically map the three-dimensional refractive index distributions of model self-assembled reflectin-based structures both in vivo and in vitro. When considered together, our findings may improve understanding of squid skin cell functionality, augment existing methods for characterizing protein-based optical materials, and expand the utility of emerging holotomographic microscopy techniques.}, journal={ACS BIOMATERIALS SCIENCE & ENGINEERING}, author={Chatterjee, Atrouli and Pratakshya, Preeta and Kwansa, Albert L. and Kaimal, Nikhil and Cannon, Andrew H. and Sartori, Barbara and Marmiroli, Benedetta and Orins, Helen and Feng, Zhijing and Drake, Samantha and et al.}, year={2023}, month={Jan} }
 @article{xie_li_singh_deshmukh_yingling_2022, title={A Comparison between the Lower Critical Solution Temperature Behavior of Polymers and Biomacromolecules}, url={https://www.mdpi.com/2673-7167/2/1/5}, DOI={10.3390/physchem2010005}, abstractNote={All-atom molecular dynamics (MD) simulations are employed to compare the lower critical solution temperature (LCST) behaviors of poly(N-isopropylacrylamide) (PNIPAM) and elastin-like polypeptides (ELPs) with the canonical Val-Pro-Gly-Val-Gly ((VPGVG)n) sequence over a range of temperatures from 280 K to 380 K. Our simulations suggest that the structure of proximal water dictates the conformation of both the (VPGVG)n ELPs and PNIPAM chains. Specifically, the LCST transition in ELPs can be attributed to a combination of thermal disruption of the network of the proximal water near both hydrophilic and hydrophobic groups in the backbone and side-chain of (VPGVG)n, resulting in a reduction in solvent accessible surface area (SASA). This is accompanied with an increase in the secondary structure above its LCST. In the case of PNIPAM, the LCST transition is a result of a combination of a reduction in the hydrophobic SASA primarily due to the contributions of isopropyl side-chain and less to the backbone and the formation of intra-chain hydrogen bonds between the amide groups on the side-chain above its LCST.}, journal={Physchem}, author={Xie, Yuxin and Li, Nan K. and Singh, Abhishek and Deshmukh, Sanket A. and Yingling, Yaroslava}, year={2022}, month={Mar} }
 @article{mahmood_yingling_2022, title={All-Atom Simulation Method for Zeeman Alignment and DipolarAssembly of Magnetic Nanoparticles br}, volume={18}, ISSN={["1549-9626"]}, url={https://doi.org/10.1021/acs.jctc.1c01253}, DOI={10.1021/acs.jctc.1c01253}, abstractNote={Magnetic nanoparticles (MNPs) can organize into novel structures in solutions with excellent order and unique geometries. However, studies of the self-assembly of smaller MNPs are challenging due to a complicated interplay between external magnetic fields and van der Waals, electrostatic, dipolar, steric, and hydrodynamic interactions. Here, we present a novel all-atom molecular dynamics simulation method to enable detailed studies of the dynamics, self-assembly, structure, and properties of MNPs as a function of core sizes and shapes, ligand chemistry, solvent properties, and external field. We demonstrate the use and effectiveness of the model by simulating the self-assembly of oleic acid ligand-functionalized magnetite (Fe3O4) nanoparticles, with spherical and cubic shapes, into rings, lines, chains, and clusters under a uniform external magnetic field. We found that the long-range electrostatic interactions can favor the formation of a chain over a ring, the ligands promote MNP cluster growth, and the solvent can reduce the rotational diffusion of the MNPs. The algorithm has been parallelized to take advantage of multiple processors of a modern computer and can be used as a plugin for the popular simulation software LAMMPS to study the behavior of small MNPs and gain insights into the physics and chemistry of different magnetic assembly processes with atomistic details.}, number={5}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, publisher={American Chemical Society (ACS)}, author={Mahmood, Akhlak U. and Yingling, Yaroslava G.}, year={2022}, month={May}, pages={3122–3135} }
 @article{du_vandavasi_molloy_yang_massenburg_singh_kwansa_yingling_o'neill_chait_et al._2022, title={Evidence for Plant-Conserved Region Mediated Trimeric CESAs in Plant Cellulose Synthase Complexes br}, volume={8}, ISSN={["1526-4602"]}, url={https://doi.org/10.1021/acs.biomac.2c00550}, DOI={10.1021/acs.biomac.2c00550}, abstractNote={Higher plants synthesize cellulose using membrane-bound, six-lobed cellulose synthase complexes, each lobe containing trimeric cellulose synthases (CESAs). Although molecular biology reports support heteromeric trimers composed of different isoforms, a homomeric trimer was reported for in vitro studies of the catalytic domain of CESA1 of Arabidopsis (AtCESA1CatD) and confirmed in cryoEM structures of full-length CESA8 and CESA7 of poplar and cotton, respectively. In both structures, a small portion of the plant-conserved region (P-CR) forms the only contacts between catalytic domains of the monomers. We report inter-subunit lysine-crosslinks that localize to the small P-CR, negative-stain EM structure, and modeling data for homotrimers of AtCESA1CatD. Molecular dynamics simulations for AtCESA1CatD trimers based on the CESA8 cryoEM structure were stable and dependent upon a small set of residue contacts. The results suggest that homomeric CESA trimers may be important for the synthesis of primary and secondary cell walls and identify key residues for future mutagenic studies.}, journal={BIOMACROMOLECULES}, publisher={American Chemical Society (ACS)}, author={Du, Juan and Vandavasi, Venu Gopal and Molloy, Kelly R. and Yang, Hui and Massenburg, Lynnicia N. and Singh, Abhishek and Kwansa, Albert L. and Yingling, Yaroslava G. and O'Neill, Hugh and Chait, Brian T. and et al.}, year={2022}, month={Aug} }
 @article{nash_manning_gulyuk_kuznetsov_yingling_2022, title={Gold nanoparticle design for RNA compaction}, volume={17}, ISSN={["1559-4106"]}, url={https://doi.org/10.1116/6.0002043}, DOI={10.1116/6.0002043}, abstractNote={RNA-based therapeutics hold a great promise in treating a variety of diseases. However, double-stranded RNAs (dsRNAs) are inherently unstable, highly charged, and stiff macromolecules that require a delivery vehicle. Cationic ligand functionalized gold nanoparticles (AuNPs) are able to compact nucleic acids and assist in RNA delivery. Here, we use large-scale all-atom molecular dynamics simulations to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. The analysis of ammonium binding sites showed that longer ligands that bind deep within the major groove did not cause bending. By limiting ligand length and, thus, excess free volume, we have designed nanoparticles with controlled internal binding to RNA's major groove. NPs that are able to induce RNA bending cause a periodic variation in RNA's major groove width. Density functional theory studies on smaller models support large-scale simulations. Our results are expected to have significant implications in packaging of nucleic acids for their applications in nanotechnology and gene delivery.}, number={6}, journal={BIOINTERPHASES}, author={Nash, Jessica A. and Manning, Matthew D. and Gulyuk, Alexey V. and Kuznetsov, Aleksey E. and Yingling, Yaroslava G.}, year={2022}, month={Nov} }
 @article{allen_wright_taylor_oweida_kader-pinky_patteson_bucci_cox_senthilvel_yingling_et al._2022, title={Mapping the Morphological Landscape of Oligomeric Di-block Peptide-Polymer Amphiphiles**}, volume={1}, ISSN={["1521-3773"]}, url={https://doi.org/10.1002/anie.202115547}, DOI={10.1002/anie.202115547}, abstractNote={Abstract}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, publisher={Wiley}, author={Allen, Benjamin P. and Wright, Zoe M. and Taylor, Hailey F. and Oweida, Thomas J. and Kader-Pinky, Sabila and Patteson, Emily F. and Bucci, Kara M. and Cox, Caleb A. and Senthilvel, Abishec Sundar and Yingling, Yaroslava G. and et al.}, year={2022}, month={Jan} }
 @article{allen_wright_taylor_oweida_kader‐pinky_patteson_bucci_cox_senthilvel_yingling_et al._2022, title={Mapping the Morphological Landscape of Oligomeric Di‐block Peptide–Polymer Amphiphiles**}, url={https://doi.org/10.1002/ange.202115547}, DOI={10.1002/ange.202115547}, abstractNote={Abstract}, journal={Angewandte Chemie}, author={Allen, Benjamin P. and Wright, Zoe M. and Taylor, Hailey F. and Oweida, Thomas J. and Kader‐Pinky, Sabila and Patteson, Emily F. and Bucci, Kara M. and Cox, Caleb A. and Senthilvel, Abishec Sundar and Yingling, Yaroslava G. and et al.}, year={2022}, month={Mar} }
 @article{oweida_kim_donald_singh_yingling_2021, title={Assessment of AMBER Force Fields for Simulations of ssDNA}, volume={17}, ISSN={["1549-9626"]}, url={https://doi.org/10.1021/acs.jctc.0c00931}, DOI={10.1021/acs.jctc.0c00931}, abstractNote={Single-stranded DNA (ssDNA) plays an important role in biological processes and is used in DNA nanotechnology and other novel applications. Many important research questions can be addressed with molecular simulations of ssDNA molecules; however, no dedicated force field for ssDNA has been developed, and there is limited experimental information about ssDNA structures. This study assesses the accuracy and applicability of existing Amber force fields for all-atom simulations of ssDNA, such as ff99, bsc0, bsc1, and OL15, in implicit and explicit solvents via comparison to available experimental data, such as Forster resonance energy transfer and small angle X-ray scattering. We observed that some force fields agree better with experiments than others mainly due to the difference in parameterization of the propensity for hydrogen bonding and base stacking. Overall, the Amber ff99 force field in the IGB5 or IGB8 implicit solvent and the bsc1 force field in the explicit TIP3P solvent had the best agreement with experiment.}, number={2}, journal={JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, publisher={American Chemical Society (ACS)}, author={Oweida, Thomas J. and Kim, Ho Shin and Donald, Johnny M. and Singh, Abhishek and Yingling, Yaroslava G.}, year={2021}, month={Feb}, pages={1208–1217} }
 @article{chandler_minevich_roark_viard_johnson_rizvi_deaton_kozlov_panigaj_tracy_et al._2021, title={Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities}, volume={13}, ISSN={["1944-8252"]}, url={http://dx.doi.org/10.1021/acsami.1c09230}, DOI={10.1021/acsami.1c09230}, abstractNote={Precise control over the assembly of biocompatible three-dimensional (3D) nanostructures would allow for programmed interactions within the cellular environment. Nucleic acids can be used as programmable crosslinkers to direct the assembly of quantum dots (QDs) and tuned to demonstrate different interparticle binding strategies. Morphologies of self-assembled QDs are evaluated via gel electrophoresis, transmission electron microscopy, small-angle X-ray scattering, and dissipative particle dynamics simulations, with all results being in good agreement. The controlled assembly of 3D QD organizations is demonstrated in cells via the colocalized emission of multiple assembled QDs, and their immunorecognition is assessed via enzyme-linked immunosorbent assays. RNA interference inducers are also embedded into the interparticle binding strategy to be released in human cells only upon QD assembly, which is demonstrated by specific gene silencing. The programmability and intracellular activity of QD assemblies offer a strategy for nucleic acids to imbue the structure and therapeutic function into the formation of complex networks of nanostructures, while the photoluminescent properties of the material allow for optical tracking in cells in vitro.}, number={33}, journal={ACS APPLIED MATERIALS & INTERFACES}, publisher={American Chemical Society (ACS)}, author={Chandler, Morgan and Minevich, Brian and Roark, Brandon and Viard, Mathias and Johnson, M. Brittany and Rizvi, Mehedi H. and Deaton, Thomas A. and Kozlov, Seraphim and Panigaj, Martin and Tracy, Joseph B. and et al.}, year={2021}, month={Aug}, pages={39030–39041} }
 @article{li_xie_yingling_2021, title={Insights into Structure and Aggregation Behavior of Elastin-like Polypeptide Coacervates: All-Atom Molecular Dynamics Simulations}, volume={125}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.1c02822}, abstractNote={The stimuli-responsive character of elastin-like polypeptides (ELP) has led to their use in a wide range of applications. The temperature-triggered aggregation, or LCST behavior, of ELPs is a complex and multistep phenomenon, which proposed to include the structural transitions, loss of hydrophobic hydration, expulsion of water molecules and physical association of chains. Thus, the origin and detailed mechanism of LCST in ELPs is difficult to elucidate. Here, to gain insights into structure and dynamics of coacervates, we performed all-atom molecular dynamics simulations of 27 90-mer ELPs in explicit water at 350 K. Two sequences, poly(VGPVG)18 and poly(VPGVG)18, were examined due to their experimentally observed differences in thermal hysteresis albeit identical overall composition but different arrangement of amino acids. The simulation results indicate that surface hydrophobicity of poly(VGPVG) aggregate is less than that of the poly(VPGVG) aggregate, and there are marked changes in torsion angles and the propensities of secondary structural motifs during the aggregation process. Moreover, there are significant differences between structure of a single polypeptide in water and structure within the aggregate. Overall, the aggregation process is driven by the formation of peptide-peptide interactions whereas the average hydration of peptides remains almost the same between dissolved and aggregated states. Even though the aggregation is driven by the hydrophobic interactions, ELP coacervate has no hydrophobic core and contains many water molecules. Overall, our findings provide an insight into the sequence-dependent structure of coacervates and molecular behavior of individual peptides during aggregation.}, number={30}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Li, Nan K. and Xie, Yuxin and Yingling, Yaroslava G.}, year={2021}, month={Aug}, pages={8627–8635} }
 @article{burris_makarem_slabaugh_chaves_pierce_lee_kiemle_kwansa_singh_yingling_et al._2021, title={Phenotypic effects of changes in the FTVTxK region of an Arabidopsis secondary wall cellulose synthase compared with results from analogous mutations in other isoforms}, volume={5}, ISSN={["2475-4455"]}, url={https://doi.org/10.1002/pld3.335}, DOI={10.1002/pld3.335}, abstractNote={Abstract}, number={8}, journal={PLANT DIRECT}, publisher={Wiley}, author={Burris, Jason N. and Makarem, Mohamadamin and Slabaugh, Erin and Chaves, Arielle and Pierce, Ethan T. and Lee, Jongcheol and Kiemle, Sarah N. and Kwansa, Albert L. and Singh, Abhishek and Yingling, Yaroslava G. and et al.}, year={2021}, month={Aug} }
 @article{peerless_kwansa_hawkins_smith_yingling_2021, title={Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with a Machine Learning Model}, volume={61}, ISSN={["1549-960X"]}, url={https://doi.org/10.1021/acs.jcim.0c01204}, DOI={10.1021/acs.jcim.0c01204}, abstractNote={The molecular dynamics (MD) simulation technique is among the most broadly used computational methods to investigate atomistic phenomena in a variety of chemical and biological systems. One of the most common (and most uncertain) parametrization steps in MD simulations of soft materials is the assignment of partial charges to atoms. Here, we apply uncertainty quantification and sensitivity analysis calculations to assess the uncertainty associated with partial charge assignment in the context of MD simulations of an organic solvent. Our results indicate that the effect of partial charge variance on bulk properties, such as solubility parameters, diffusivity, dipole moment, and density, measured from MD simulations is significant; however, measured properties are observed to be less sensitive to partial charges of less accessible (or buried) atoms. Diffusivity, for example, exhibits a global sensitivity of up to 22 × 10-5 cm2/s per electron charge on some acetonitrile atoms. We then demonstrate that machine learning techniques, such as Gaussian process regression (GPR), can be effective and rapid tools for uncertainty quantification of MD simulations. We show that the formulation and application of an efficient GPR surrogate model for the prediction of responses effectively reduces the computational time of additional sample points from hours to milliseconds. This study provides a much-needed context for the effect that partial charge uncertainty has on MD-derived material properties to illustrate the benefit of considering partial charges as distributions rather than point-values. To aid in this treatment, this work then demonstrates methods for rapid characterization of resulting sensitivity in MD simulations.}, number={4}, journal={JOURNAL OF CHEMICAL INFORMATION AND MODELING}, publisher={American Chemical Society (ACS)}, author={Peerless, James S. and Kwansa, Albert L. and Hawkins, Branden S. and Smith, Ralph C. and Yingling, Yaroslava G.}, year={2021}, month={Apr}, pages={1745–1761} }
 @article{lee_stryutsky_mahmood_singh_shevchenko_yingling_tsukruk_2021, title={Weakly Ionically Bound Thermosensitive Hyperbranched Polymers}, volume={37}, ISSN={["0743-7463"]}, DOI={10.1021/acs.langmuir.0c03487}, abstractNote={We synthesized novel amphiphilic hyperbranched polymers (HBPs) with variable contents of weakly ionically tethered thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) macrocations in contrast to traditional covalent linking. Their assembling behavior was studied below and above the lower critical solution temperature (LCST). The HBPs underwent a morphological transition under changing temperature and ionic strength due to the LCST transition of PNIPAM and the reduction in the ionization degree of terminal ionic groups, respectively. We suggest that, in contrast to traditional branched polymers, ionically linked PNIPAM macrocations can reversibly disassociate from the sulfonate groups and form mobile coronas, endowing the dynamic micellar morphologies. In addition, assembly at the air-water interface confined PNIPAM macrocations and resulted in the formation of heterogeneous Langmuir-Blodgett (LB) monolayers with diverse surface morphologies for different peripheral compositions with circular domains formed in the condensed state. The HBPs with 25% PNIPAM showed larger and more stable circular domains that were partially preserved at high compression than those of HBPs with 50% PNIPAM. Moreover, the LB monolayers showed variable surface mechanical and surface charge distribution, which can be attributed to net dipole redistribution caused by the behavior of mobile PNIPAM macrocations and core sulfonate groups.}, number={9}, journal={LANGMUIR}, author={Lee, Hansol and Stryutsky, Alexandr and Mahmood, Akhlak-Ul and Singh, Abhishek and Shevchenko, Valery V. and Yingling, Yaroslava G. and Tsukruk, Vladimir V.}, year={2021}, month={Mar}, pages={2913–2927} }
 @article{chae_ngo_chen_kwansa_chen_meddeb_podraza_yingling_ounaies_kim_2020, title={Anisotropic Optical and Frictional Properties of Langmuir-Blodgett Film Consisting of Uniaxially-Aligned Rod-Shaped Cellulose Nanocrystals}, volume={7}, ISSN={["2196-7350"]}, DOI={10.1002/admi.201902169}, abstractNote={Abstract}, number={9}, journal={ADVANCED MATERIALS INTERFACES}, author={Chae, Inseok and Ngo, Dien and Chen, Zhe and Kwansa, Albert L. and Chen, Xing and Meddeb, Amira Barhoumi and Podraza, Nikolas J. and Yingling, Yaroslava G. and Ounaies, Zoubeida and Kim, Seong H.}, year={2020}, month={May} }
 @article{xiong_singh_yu_zhang_lee_yingling_nepal_bunning_tsukruk_2020, title={Co-assembling Polysaccharide Nanocrystals and Nanofibers for Robust Chiral Iridescent Films}, volume={12}, url={https://doi.org/10.1021/acsami.0c08571}, DOI={10.1021/acsami.0c08571}, abstractNote={Assembling robust chiral biopolymer structures without compromising vivid optical iridescence is a grand challenge for biocomposite materials. Herein, we report a hierarchical nanocellulose nanostructures with a helicoidal organization co-assembled from chiral rigid cellulose nanocrystals (CNC) and amorphous longer nanofibers isolated from the hydrolyzed wood pulp. This resulting highly iridescent chiral nanocellulose material are much tougher than traditional chiral CNC films. We found that the mixed nanocellulose bundles are composed of co-assembled needle-like nanocrystals and very long (up to 800 nm) flexible cellulose nanofibers (CNF). Large-scale molecular simulation indicates that enhanced dynamic hydrogen bonding with labile networking facilitates mechanical reinforcement, owing to increased nanocrystal length, the co-assembly of nanofibrils in mixed bundles, and interchain entanglements. This study provides a novel strategy to transform the wood pulp residues into high-value-added photonic-bound polysaccharide materials. These hierarchical biomaterials can overcome the conflicting trends in designing balanced mechanical and optical performance of chiral biofilms and their conversion to robust chiral photonic materials with enhanced performance.}, number={31}, journal={ACS Applied Materials & Interfaces}, publisher={American Chemical Society (ACS)}, author={Xiong, Rui and Singh, Abhishek and Yu, Shengtao and Zhang, Shuaidi and Lee, Hansol and Yingling, Yaroslava G. and Nepal, Dhriti and Bunning, Timothy J. and Tsukruk, Vladimir V.}, year={2020}, month={Aug}, pages={35345–35353} }
 @article{kim_brown_zauscher_yingling_2020, title={Effect of Octadecylamine Surfactant on DNA Interactions with Graphene Surfaces}, volume={36}, url={https://doi.org/10.1021/acs.langmuir.9b02926}, DOI={10.1021/acs.langmuir.9b02926}, abstractNote={Understanding of how to integrate DNA molecules with graphene materials is important for the development of bio-sensors and biomolecular logic circuits. For some of these applications, controlling DNA structural conformation on the graphene substrate is critically important and can be achieved through the use of self-assembled monolayers. Here, we performed all-atom molecular dynamics simulations to understand how various 1-octadecylamine (ODA) coatings of graphene surface affect the conformation of double-stranded (dsDNA) on the surface. The simulation results demonstrated that dsDNA structures become more stable as ODA concentration increases due to formation of DNA-ODA hydrogen bonds and reduction of DNA - surface interactions, which aid in retaining internal DNA interactions. Specifically, the interaction of ODA molecules with DNA prevents nucleobases from forming pi-pi stacking interactions with the surface. Some dsDNA conformations, such as sharp kinks or unwinding, can happen more frequently in DNA with A-T sequences due to weaker pairing interactions than G-C sequences. Furthermore, our results conclude that both DNA sequence and ODA concentration play an essential role in experimentally observed conformational changes of DNA on the graphene surface.}, number={4}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={Kim, Ho Shin and Brown, Nathanael A. and Zauscher, Stefan and Yingling, Yaroslava G.}, year={2020}, month={Feb}, pages={931–938} }
 @article{singh_kwansa_kim_williams_yang_li_kubicki_roberts_haigler_yingling_2020, title={In silico structure prediction of full-length cotton cellulose synthase protein (GhCESA1) and its hierarchical complexes}, volume={27}, ISSN={0969-0239 1572-882X}, url={http://dx.doi.org/10.1007/s10570-020-03194-7}, DOI={10.1007/s10570-020-03194-7}, number={10}, journal={Cellulose}, publisher={Springer Science and Business Media LLC}, author={Singh, Abhishek and Kwansa, Albert L. and Kim, Ho Shin and Williams, Justin T. and Yang, Hui and Li, Nan K. and Kubicki, James D. and Roberts, Alison W. and Haigler, Candace H. and Yingling, Yaroslava G.}, year={2020}, month={Apr}, pages={5597–5616} }
 @article{jones_yingling_reaney_westerhoff_2020, title={Materials matter in phosphorus sustainability}, volume={45}, ISSN={["1938-1425"]}, DOI={10.1557/mrs.2020.4}, abstractNote={T year marks the 350th anniversary of the discovery of phosphorus by German alchemist Hennig Brandt.1 As element 15 in the periodic table, phosphorus is known to researchers for its luminescent and reactive characteristics in elemental form, as a dopant in semiconductors, as a key constituent in nerve agents and industrial detergents,2 and, most recently, in its two-dimensional (2D) form, phosphorene (a black phosphorus allotrope). However, its role in biology and agriculture has more foundational implications for society.3 It is part of the backbone of DNA. Because of its central role in biological energy transfer processes, phosphorus is also an essential component in fertilizers underpinning the productivity of global food systems, enabling society to sustain Earth’s growing population. Unfortunately, myriad cross-disciplinary challenges pervade the life cycle of phosphorus, from its sources and availability to its application and disposal or reuse.4,5 The challenges around the phosphorus life cycle are so complex that they have been termed a “wicked problem”;6,7 the problems are intractable, contested, and plagued by a high degree of uncertainty. These can be more deeply appreciated by noting that challenges in the phosphorus life cycle span 17 orders of magnitude in length scale—from the atomic scale of elemental phosphorus and the orthophosphate ion to farms and farmers, phosphate mines, and lakes to global economics and public policy (see Figure 1).8,9 These length scales involve diverse stakeholders with sometimes competing priorities.}, number={1}, journal={MRS BULLETIN}, author={Jones, Jacob L. and Yingling, Yaroslava G. and Reaney, Ian M. and Westerhoff, Paul}, year={2020}, month={Jan}, pages={7–10} }
 @article{oweida_mahmood_manning_rigin_yingling_2020, title={Merging Materials and Data Science: Opportunities, Challenges, and Education in Materials Informatics}, volume={3}, url={https://doi.org/10.1557/adv.2020.171}, DOI={10.1557/adv.2020.171}, abstractNote={Since the launch of the Materials Genome Initiative (MGI) the field of materials informatics (MI) emerged to remove the bottlenecks limiting the pathway towards rapid materials discovery. Although the machine learning (ML) and optimization techniques underlying MI were developed well over a decade ago, programs such as the MGI encouraged researchers to make the technical advancements that make these tools suitable for the unique challenges in materials science and engineering. Overall, MI has seen a remarkable rate in adoption over the past decade. However, for the continued growth of MI, the educational challenges associated with applying data science techniques to analyse materials science and engineering problems must be addressed. In this paper, we will discuss the growing use of materials informatics in academia and industry, highlight the need for educational advances in materials informatics, and discuss the implementation of a materials informatics course into the curriculum to jump-start interested students with the skills required to succeed in materials informatics projects.}, journal={MRS Advances}, publisher={Cambridge University Press (CUP)}, author={Oweida, Thomas J. and Mahmood, Akhlak and Manning, Matthew D. and Rigin, Sergei and Yingling, Yaroslava G.}, year={2020}, month={Mar}, pages={1–18} }
 @article{taylor_chung_kwansa_johnson_teator_milliken_koshlap_yingling_lee_leibfarth_2020, title={Partially Fluorinated Copolymers as Oxygen Sensitive(19)F MRI Agents}, volume={26}, ISSN={["1521-3765"]}, DOI={10.1002/chem.202001505}, abstractNote={Abstract}, number={44}, journal={CHEMISTRY-A EUROPEAN JOURNAL}, author={Taylor, Nicholas G. and Chung, Sang Hun and Kwansa, Albert L. and Johnson, Rob R., III and Teator, Aaron J. and Milliken, Nina J. B. and Koshlap, Karl M. and Yingling, Yaroslava G. and Lee, Yueh Z. and Leibfarth, Frank A.}, year={2020}, month={Aug}, pages={9982–9990} }
 @article{umerani_pratakshya_chatterjee_sanchez_kim_ilc_kovacic_magnan_marmiroli_sartori_et al._2020, title={Structure, self-assembly, and properties of a truncated reflectin variant}, volume={117}, ISSN={["1091-6490"]}, DOI={10.1073/pnas.2009044117}, abstractNote={Significance}, number={52}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Umerani, Mehran J. and Pratakshya, Preeta and Chatterjee, Atrouli and Sanchez, Juana A. Cerna and Kim, Ho Shin and Ilc, Gregor and Kovacic, Matic and Magnan, Christophe and Marmiroli, Benedetta and Sartori, Barbara and et al.}, year={2020}, month={Dec}, pages={32891–32901} }
 @article{brabham_singh_stork_rong_kumar_kikuchi_yingling_brutnell_rose_debolt_2019, title={Biochemical and physiological flexibility accompanies reduced cellulose biosynthesis in Brachypodium cesa1S830N}, volume={11}, ISSN={2041-2851}, url={http://dx.doi.org/10.1093/aobpla/plz041}, DOI={10.1093/aobpla/plz041}, abstractNote={Abstract}, number={5}, journal={AoB PLANTS}, publisher={Oxford University Press (OUP)}, author={Brabham, Chad and Singh, Abhishek and Stork, Jozsef and Rong, Ying and Kumar, Indrajit and Kikuchi, Kazuhiro and Yingling, Yaroslava G and Brutnell, Thomas P and Rose, Jocelyn K C and Debolt, Seth}, editor={Jameson, PaulaEditor}, year={2019}, month={Jul} }
 @inbook{deaton_aydin_li_chu_dutt_yingling_2019, place={Singapore}, title={Dissipative Particle Dynamics Approaches to Modeling the Self-Assembly and Morphology of Neutral and Ionic Block Copolymers in Solution}, DOI={10.1007/978-981-33-6639-8_4}, abstractNote={Block copolymer assemblies have demonstrated enormous potentials in a wide variety of applications. Yet, further advances in the theory and computational modeling of block copolymer-based assemblies are needed to boost the development and the application of these materials. This review is intended to present key micellization theory, approaches and recent advances in prediction and modeling self-assembly of block copolymers in solution. Specifically, we examine the current progress in the modeling and simulation of block copolymer-based assemblies utilizing the mesoscale modeling technique Dissipative Particle Dynamics (DPD). We also discuss advantages and limitations of the different approaches in modeling the structural and dynamical properties of neutral and ionic block copolymers using DPD.}, booktitle={Foundations of Molecular Modeling and Simulation: Select Papers from FOMMS 2018}, publisher={Springer Nature}, author={Deaton, Thomas A. and Aydin, Fikret and Li, Nan K. and Chu, Xiaolei and Dutt, Meenakshi and Yingling, Yaroslava}, editor={Maginn, E. and Errington, J.Editors}, year={2019}, pages={75–100} }
 @article{gardinier_kohle_peerless_ma_turker_hinckley_yingling_wiesner_2019, title={High-Performance Chromatographic Characterization of Surface Chemical Heterogeneities of Fluorescent Organic–Inorganic Hybrid Core–Shell Silica Nanoparticles}, volume={13}, ISSN={1936-0851 1936-086X}, url={http://dx.doi.org/10.1021/acsnano.8b07876}, DOI={10.1021/acsnano.8b07876}, abstractNote={In contrast to small-molar-mass compounds, detailed structural investigations of inorganic core-organic ligand shell hybrid nanoparticles remain challenging. The assessment of batch-reaction-induced heterogeneities of surface chemical properties and their correlation with particle size has been a particularly long-standing issue. Applying a combination of high-performance liquid chromatography (HPLC) and gel permeation chromatography (GPC) to ultra-small (<10 nm diameter) poly(ethylene glycol)-coated (PEGylated) fluorescent core-shell silica nanoparticles, we elucidate here previously unknown surface heterogeneities resulting from varying dye conjugation to nanoparticle silica cores and surfaces. Heterogeneities are predominantly governed by dye charge, as corroborated by molecular dynamics simulations. We demonstrate that this insight enables the development of synthesis protocols to achieve PEGylated and targeting ligand-functionalized PEGylated silica nanoparticles with dramatically improved surface chemical homogeneity, as evidenced by single-peak HPLC chromatograms. Because surface chemical properties are key to all nanoparticle interactions, we expect these methods and fundamental insights to become relevant to a number of systems for applications, including bioimaging and nanomedicine.}, number={2}, journal={ACS Nano}, publisher={American Chemical Society (ACS)}, author={Gardinier, Thomas C. and Kohle, Ferdinand F. E. and Peerless, James S. and Ma, Kai and Turker, Melik Z. and Hinckley, Joshua A. and Yingling, Yaroslava G. and Wiesner, Ulrich}, year={2019}, month={Jan}, pages={1795–1804} }
 @article{garcia quiroz_li_roberts_weber_dzuricky_weitzhandler_yingling_chilkoti_2019, title={Intrinsically disordered proteins access a range of hysteretic phase separation behaviors}, volume={5}, ISSN={2375-2548}, url={http://dx.doi.org/10.1126/sciadv.aax5177}, DOI={10.1126/sciadv.aax5177}, abstractNote={Salient nonequilibrium phase separation behaviors in intrinsically disordered proteins dictate phase separation–driven assembly.}, number={10}, journal={Science Advances}, publisher={American Association for the Advancement of Science (AAAS)}, author={Garcia Quiroz, Felipe and Li, Nan K. and Roberts, Stefan and Weber, Patrick and Dzuricky, Michael and Weitzhandler, Isaac and Yingling, Yaroslava G. and Chilkoti, Ashutosh}, year={2019}, month={Oct}, pages={eaax5177} }
 @article{yang_mcmanus_oehme_singh_yingling_tien_kubicki_2019, title={Simulations of Cellulose Synthesis Initiation and Termination in Bacteria}, volume={123}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/acs.jpcb.9b02433}, DOI={10.1021/acs.jpcb.9b02433}, abstractNote={The processivity of cellulose synthesis in bacterial cellulose synthase (CESA) was investigated using molecular dynamics simulations and the hybrid quantum mechanics and molecular mechanics approach. Our results suggested that cellulose synthesis in bacterial CESA can be initiated with H2O molecules. The chain length or degree of polymerization (DOP) of the product cellulose is related to the affinity of the cellulose chain to the transmembrane tunnel of the enzyme. This opens up the possibility of generating mutants that would produce cellulose chains with desired chain lengths that could have applications in the biofuel and textile fields that depend on the DOP of cellulose chains.}, number={17}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Yang, Hui and McManus, John and Oehme, Daniel and Singh, Abhishek and Yingling, Yaroslava G. and Tien, Ming and Kubicki, James D.}, year={2019}, month={Apr}, pages={3699–3705} }
 @article{mcgoorty_singh_deaton_peterson_taliaferro_yingling_castellano_2018, title={Bathophenanthroline Disulfonate Ligand-Induced Self-Assembly of Ir(III) Complexes in Water: An Intriguing Class of Photoluminescent Soft Materials}, volume={3}, ISSN={2470-1343 2470-1343}, url={http://dx.doi.org/10.1021/acsomega.8b02034}, DOI={10.1021/acsomega.8b02034}, abstractNote={Strong evidence of concentration-induced and dissolved electrolyte-induced chromophore aggregation has been universally observed in numerous water soluble bis-cyclometalated Ir(III) photosensitizers bearing the sulfonated diimine ligands bathophenanthroline disulfonate and bathocuproine disulfonate. This new class of aqueous-based soft materials was highly photoluminescent in their aggregated state where detailed spectroscopic investigations of this phenomenon revealed significant blue shifts of their respective photoluminescence emission spectra with concomitant increases in excited-state lifetimes and quantum yields initiating even at micromolar chromophore concentrations in water or upon the addition of a strong electrolyte. A combination of nanoscale particle characterization techniques, static and dynamic photoluminescence spectroscopic studies, along with atomistic molecular dynamics (MD) simulations of these soft materials suggests the formation of small, heterogeneous nanoaggregate structures, wherein the sulfonated diimine ancillary ligand serves as a pro-aggregating subunit in all instances. Importantly, the experimental and MD findings suggest the likelihood of discovering similar aqueous aggregation phenomena occurring in all transition-metal complexes bearing these water-solubilizing diimine ligands.}, number={10}, journal={ACS Omega}, publisher={American Chemical Society (ACS)}, author={McGoorty, Michelle M. and Singh, Abhishek and Deaton, Thomas A. and Peterson, Benjamin and Taliaferro, Chelsea M. and Yingling, Yaroslava G. and Castellano, Felix N.}, year={2018}, month={Oct}, pages={14027–14038} }
 @article{scavuzzo-duggan_chaves_singh_sethaphong_slabaugh_yingling_haigler_roberts_2018, title={Cellulose synthase "class specific regions' are intrinsically disordered and functionally undifferentiated}, volume={60}, ISSN={["1744-7909"]}, url={https://publons.com/wos-op/publon/28057448/}, DOI={10.1111/jipb.12637}, abstractNote={Abstract}, number={6}, journal={JOURNAL OF INTEGRATIVE PLANT BIOLOGY}, publisher={Wiley-Blackwell}, author={Scavuzzo-Duggan, Tess R. and Chaves, Arielle M. and Singh, Abhishek and Sethaphong, Latsavongsakda and Slabaugh, Erin and Yingling, Yaroslava G. and Haigler, Candace H. and Roberts, Alison W.}, year={2018}, month={Jun}, pages={481–497} }
 @article{manning_nash_yingling_2018, title={Design of Histone-Mimic Nanoparticles for DNA and RNA Compaction using Molecular Modeling}, volume={114}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/J.BPJ.2017.11.2010}, DOI={10.1016/J.BPJ.2017.11.2010}, abstractNote={The design of nanoparticles that can induce specific structural transitions in nucleic acids is important for nanotechnology applications including gene delivery and nanoelectronics. It is known that in biological systems, the binding of cationic proteins induces structural changes in DNA or RNA, which can affect gene expression or cause the compaction of DNA into chromatin. The anionic backbone of the nucleic acids DNA and RNA allow for non-specific electrostatic interactions with cationic proteins, nanoparticles, or dendrimers. The interaction of nucleic acids and nanoparticles may be tuned through changes in nanoparticle size, charge, polarity, or shape. However, the factors that affect structural transitions are not fully understood. We performed atomistic molecular dynamics simulations of the binding of nucleic acids to monolayer-protected gold nanoparticles to elucidate structural changes that take place for nanoparticles and DNA upon binding. Results from these simulations were analyzed to determine modes of DNA and RNA bending with nanoparticles. Our simulations show that highly charged nanoparticles cause DNA to bend with little damage to the helix structure, similar to DNA in the nucleosome. Nanoparticle shape as well as charge is shown to affect the wrapping of nucleic acids with the nanoparticle. Low salt concentrations and high nanoparticle charge cause greater disruptions to DNA structure. We find that the roll parameter is the most important base-pair parameter for DNA bending. Requirements for bending differed significantly between DNA and dsRNA. The degree of DNA bending is controlled by the charge of the NPs, but ligand flexibility played a more significant role in dsRNA bending. We have shown that functionalized gold NPs can be designed to wrap and compact both RNA an DNAs with fine control of binding strength through NP charge and ligand chemistry.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Manning, Matthew and Nash, Jessica A. and Yingling, Yaroslava G.}, year={2018}, month={Feb}, pages={362a} }
 @article{gu_oweida_yingling_chilkoti_zauscher_2018, title={Enzymatic Synthesis of Nucleobase-Modified Single-Stranded DNA Offers Tunable Resistance to Nuclease Degradation}, volume={19}, ISSN={1525-7797 1526-4602}, url={http://dx.doi.org/10.1021/acs.biomac.8b00816}, DOI={10.1021/acs.biomac.8b00816}, abstractNote={We synthesized long, nucleobase-modified, single-stranded DNA (ssDNA) using terminal deoxynucleotidyl transferase (TdT) enzymatic polymerization. Specifically, we investigated the effect of unnatural nucleobase size and incorporation density on ssDNA resistance to exo- and endonuclease degradation. We discovered that increasing the size and density of unnatural nucleobases enhances ssDNA resistance to degradation in the presence of exonuclease I, DNase I, and human serum. We also studied the mechanism of this resistance enhancement using molecular dynamics simulations. Our results show that the presence of unnatural nucleobases in ssDNA decreases local chain flexibility and hampers nuclease access to the ssDNA backbone, which hinders nuclease binding to ssDNA and slows its degradation. Our discoveries suggest that incorporating nucleobase-modified nucleotides into ssDNA, using enzymatic polymerization, is an easy and efficient strategy to prolong and tune the half-life of DNA-based materials in nucleases-containing environments.}, number={8}, journal={Biomacromolecules}, publisher={American Chemical Society (ACS)}, author={Gu, Renpeng and Oweida, Thomas and Yingling, Yaroslava G. and Chilkoti, Ashutosh and Zauscher, Stefan}, year={2018}, month={Jul}, pages={3525–3535} }
 @article{manning_kwansa_oweida_peerless_singh_yingling_2018, title={Progress in ligand design for monolayer-protected nanoparticles for nanobio interfaces}, volume={13}, ISSN={1934-8630 1559-4106}, url={http://dx.doi.org/10.1116/1.5044381}, DOI={10.1116/1.5044381}, abstractNote={Ligand-functionalized inorganic nanoparticles, also known as monolayer-protected nanoparticles, offer great potential as vehicles for in vivo delivery of drugs, genes, and other therapeutics. These nanoparticles offer highly customizable chemistries independent of the size, shape, and functionality imparted by the inorganic core. Their success as drug delivery agents depends on their interaction with three major classes of biomolecules: nucleic acids, proteins, and membranes. Here, the authors discuss recent advances and open questions in the field of nanoparticle ligand design for nanomedicine, with a focus on atomic-scale interactions with biomolecules. While the importance of charge and hydrophobicity of ligands for biocompatibility and cell internalization has been demonstrated, ligand length, flexibility, branchedness, and other properties also influence the properties of nanoparticles. However, a comprehensive understanding of ligand design principles lies in the cost associated with synthesizing and characterizing diverse ligand chemistries and the ability to carefully assess the structural integrity of biomolecules upon interactions with nanoparticles.}, number={6}, journal={Biointerphases}, publisher={American Vacuum Society}, author={Manning, Matthew D. and Kwansa, Albert L. and Oweida, Thomas and Peerless, James S. and Singh, Abhishek and Yingling, Yaroslava G.}, year={2018}, month={Dec}, pages={06D502} }
 @article{li_roberts_quiroz_chilkoti_yingling_2018, title={Sequence Directionality Dramatically Affects LCST Behavior of Elastin-Like Polypeptides}, volume={19}, ISSN={1525-7797 1526-4602}, url={http://dx.doi.org/10.1021/acs.biomac.8b00099}, DOI={10.1021/acs.biomac.8b00099}, abstractNote={Elastin-like polypeptides (ELP) exhibit an inverse temperature transition or lower critical solution temperature (LCST) transition phase behavior in aqueous solutions. In this paper, the thermal responsive properties of the canonical ELP, poly(VPGVG), and its reverse sequence poly(VGPVG) were investigated by turbidity measurements of the cloud point behavior, circular dichroism (CD) measurements, and all-atom molecular dynamics (MD) simulations to gain a molecular understanding of mechanism that controls hysteretic phase behavior. It was shown experimentally that both poly(VPGVG) and poly(VGPVG) undergo a transition from soluble to insoluble in aqueous solution upon heating above the transition temperature ( Tt). However, poly(VPGVG) resolubilizes upon cooling below its Tt, whereas the reverse sequence, poly(VGPVG), remains aggregated despite significant undercooling below the Tt. The results from MD simulations indicated that a change in sequence order results in significant differences in the dynamics of the specific residues, especially valines, which lead to extensive changes in the conformations of VPGVG and VGPVG pentamers and, consequently, dissimilar propensities for secondary structure formation and overall structure of polypeptides. These changes affected the relative hydrophilicities of polypeptides above Tt, where poly(VGPVG) is more hydrophilic than poly(VPGVG) with more extended conformation and larger surface area, which led to formation of strong interchain hydrogen bonds responsible for stabilization of the aggregated phase and the observed thermal hysteresis for poly(VGPVG).}, number={7}, journal={Biomacromolecules}, publisher={American Chemical Society (ACS)}, author={Li, Nan K. and Roberts, Stefan and Quiroz, Felipe Garcia and Chilkoti, Ashutosh and Yingling, Yaroslava G.}, year={2018}, month={Apr}, pages={2496–2505} }
 @article{peerless_milliken_oweida_manning_yingling_2018, title={Soft Matter Informatics: Current Progress and Challenges}, volume={2}, ISSN={2513-0390}, url={http://dx.doi.org/10.1002/adts.201800129}, DOI={10.1002/adts.201800129}, abstractNote={Abstract}, number={1}, journal={Advanced Theory and Simulations}, publisher={Wiley}, author={Peerless, James S. and Milliken, Nina J. B. and Oweida, Thomas J. and Manning, Matthew D. and Yingling, Yaroslava G.}, year={2018}, month={Nov}, pages={1800129} }
 @article{xiong_kim_zhang_korolovych_zhang_yingling_tsukruk_2018, title={Wrapping Nanocellulose Nets around Graphene Oxide Sheets}, volume={57}, ISSN={1433-7851}, url={http://dx.doi.org/10.1002/anie.201803076}, DOI={10.1002/anie.201803076}, abstractNote={Abstract}, number={28}, journal={Angewandte Chemie International Edition}, publisher={Wiley}, author={Xiong, Rui and Kim, Ho Shin and Zhang, Lijuan and Korolovych, Volodymyr F. and Zhang, Shuaidi and Yingling, Yaroslava G. and Tsukruk, Vladimir V.}, year={2018}, month={May}, pages={8508–8513} }
 @misc{nash_kwansa_peerless_kim_yingling_2017, title={Advances in Molecular Modeling of Nanoparticle Nucleic Acid Interfaces}, volume={28}, ISSN={["1043-1802"]}, url={https://publons.com/wos-op/publon/28057442/}, DOI={10.1021/acs.bioconjchem.6b00534}, abstractNote={Nanoparticles (NPs) play increasingly important roles in nanotechnology and nanomedicine in which nanoparticle surface chemistry allows for control over interactions with other nanoparticles and biomolecules. In particular, for applications in drug and gene delivery, a fundamental understanding of the NP-nucleic acid interface allows for development of more efficient and effective nanoparticle carriers. Computational modeling can provide insights of processes occurring at the inorganic NP-nucleic interface in detail that is difficult to access by experimental methods. With recent advances such as the use of graphics processing units (GPUs) for simulations, computational modeling has the potential to give unprecedented insight into inorganic-biological interfaces via the examination of increasingly large and complex systems. In this Topical Review, we briefly review computational methods relevant to the interactions of inorganic NPs and nucleic acids and highlight recent insights obtained from various computational methods that were applied to studies of inorganic nanoparticle-nanoparticle and nanoparticle-nucleic acid interfaces.}, number={1}, journal={BIOCONJUGATE CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Nash, Jessica A. and Kwansa, Albert L. and Peerless, James S. and Kim, Ho Shin and Yingling, Yaroslava G.}, year={2017}, month={Jan}, pages={3–10} }
 @article{peerless_bowers_kwansa_yingling_2017, title={Effect of C 60 adducts on the dynamic structure of aromatic solvation shells}, volume={678}, ISSN={0009-2614}, url={http://dx.doi.org/10.1016/j.cplett.2017.04.010}, DOI={10.1016/j.cplett.2017.04.010}, abstractNote={We report herein on the use of all-atom molecular dynamics simulations to investigate the solvation environment of C60 and four C60-derived fullerenes immersed in a variety of aromatic solvents. Utilizing a recently developed solvation shell analysis technique that quantifies the spatial relationships between fullerenes and solvent on a molecular level, we show that the number of fullerene substituents and solvent chemistry are crucial determinants of the solvation shell structure and thus fullerene solvation behavior. Specifically, it is shown for the derivatives investigated that the number of fullerene substituents is more critical to solvation behavior than the substituent chemistry.}, journal={Chemical Physics Letters}, publisher={Elsevier BV}, author={Peerless, James S. and Bowers, G. Hunter and Kwansa, Albert L. and Yingling, Yaroslava G.}, year={2017}, month={Jun}, pages={79–84} }
 @article{kim_farmer_yingling_2017, title={Effect of Graphene Oxidation Rate on Adsorption of Poly-Thymine Single Stranded DNA}, volume={4}, ISSN={2196-7350}, url={http://dx.doi.org/10.1002/admi.201601168}, DOI={10.1002/admi.201601168}, abstractNote={In order to understand how oxidation rate of graphene surfaces affects single‐stranded poly‐thymine, poly(T)20, structure during physisorption, all‐atom molecular dynamics simulations are performed. In aqueous solutions, poly(T)20 is a complex structure with stacked and coiled regions. However, on the graphene surfaces, there are three different regimes for the adsorption process, which heavily depends on the surface oxidation: (1) on pristine graphene or graphene oxide (GO) with low oxygen coverage (GO 5%) the stacked poly(T)20 structure becomes unfolded due to formation of strong π–π interactions with the surface, (2) on graphene oxide with moderate oxygen coverage (GO 10%–25%) the structure of poly(T)20 is well preserved because of the balance between van der Waals and electrostatic interactions, and (3) on graphene oxide with high oxygen content (GO 30%–60%) stacked poly(T)20 structure is locally disrupted due to formation of strong hydrogen bonds with the surface. Moreover, surface roughness due to the presence of oxygen groups plays a pivotal role in structural retention of poly(T)20 by preventing its nucleobases from forming π–π stacking interactions with the surface.}, number={8}, journal={Advanced Materials Interfaces}, publisher={Wiley}, author={Kim, Ho Shin and Farmer, Barry L. and Yingling, Yaroslava G.}, year={2017}, month={Mar}, pages={1601168} }
 @article{li_li_tu_im_mo_han_fuss_carroll_chilkoti_yingling_et al._2017, title={Functional Modification of Silica through Enhanced Adsorption of Elastin-Like Polypeptide Block Copolymers}, volume={19}, ISSN={1525-7797 1526-4602}, url={http://dx.doi.org/10.1021/acs.biomac.7b01307}, DOI={10.1021/acs.biomac.7b01307}, abstractNote={A powerful tool for controlling interfacial properties and molecular architecture relies on the tailored adsorption of stimuli-responsive block copolymers onto surfaces. Here, we use computational and experimental approaches to investigate the adsorption behavior of thermally responsive polypeptide block copolymers (elastin-like polypeptides, ELPs) onto silica surfaces, and to explore the effects of surface affinity and micellization on the adsorption kinetics and the resultant polypeptide layers. We demonstrate that genetic incorporation of a silica-binding peptide (silaffin R5) results in enhanced adsorption of these block copolymers onto silica surfaces as measured by quartz crystal microbalance and ellipsometry. We find that the silaffin peptide can also direct micelle adsorption, leading to close-packed micellar arrangements that are distinct from the sparse, patchy arrangements observed for ELP micelles lacking a silaffin tag, as evidenced by atomic force microscopy measurements. These experimental findings are consistent with results of dissipative particle dynamics simulations. Wettability measurements suggest that surface immobilization hampers the temperature-dependent conformational change of ELP micelles, while adsorbed ELP unimers (i.e., unmicellized block copolymers) retain their thermally responsive property at interfaces. These observations provide guidance on the use of ELP block copolymers as building blocks for fabricating smart surfaces and interfaces with programmable architecture and functionality.}, number={2}, journal={Biomacromolecules}, publisher={American Chemical Society (ACS)}, author={Li, Linying and Li, Nan K. and Tu, Qing and Im, Owen and Mo, Chia-Kuei and Han, Wei and Fuss, William H. and Carroll, Nick J. and Chilkoti, Ashutosh and Yingling, Yaroslava G. and et al.}, year={2017}, month={Dec}, pages={298–306} }
 @article{tu_kim_oweida_parlak_yingling_zauscher_2017, title={Interfacial Mechanical Properties of Graphene on Self-Assembled Monolayers: Experiments and Simulations}, volume={9}, ISSN={1944-8244 1944-8252}, url={http://dx.doi.org/10.1021/acsami.6b16593}, DOI={10.1021/acsami.6b16593}, abstractNote={Self-assembled monolayers (SAMs) have been widely used to engineer the electronic properties of substrate-supported graphene devices. However, little is known about how the surface chemistry of SAMs affects the interfacial mechanical properties of graphene supported on SAMs. Fluctuations and changes in these properties affect the stress transfer between substrate and the supported graphene and thus the performance of graphene-based devices. The changes in interfacial mechanical properties can be characterized by measuring the out-of-plane elastic properties. Combining contact resonance atomic force microcopy experiments with molecular dynamics simulations, we show that the head group chemistry of a SAM, which affects the interfacial interactions, can have a significant effect on the out-of-plane elastic modulus of the graphene-SAM heterostructure. Graphene supported on hydrophobic SAMs leads to heterostructures stiffer than those of graphene supported on hydrophilic SAMs, which is largely due to fewer water molecules present at the graphene-SAM interface. Our results provide an important, and often overlooked, insight into the mechanical properties of substrate-supported graphene electronics.}, number={11}, journal={ACS Applied Materials & Interfaces}, publisher={American Chemical Society (ACS)}, author={Tu, Qing and Kim, Ho Shin and Oweida, Thomas J. and Parlak, Zehra and Yingling, Yaroslava G. and Zauscher, Stefan}, year={2017}, month={Mar}, pages={10203–10213} }
 @article{kim_oweida_yingling_2017, title={Interfacial stability of graphene-based surfaces in water and organic solvents}, volume={53}, ISSN={0022-2461 1573-4803}, url={http://dx.doi.org/10.1007/s10853-017-1893-9}, DOI={10.1007/s10853-017-1893-9}, number={8}, journal={Journal of Materials Science}, publisher={Springer Nature}, author={Kim, Ho Shin and Oweida, Thomas J. and Yingling, Yaroslava G.}, year={2017}, month={Dec}, pages={5766–5776} }
 @article{li_kuang_fuss_zauscher_kokkoli_yingling_2017, title={Macromol. Rapid Commun. 20/2017}, volume={38}, DOI={10.1002/marc.201770066}, abstractNote={Front Cover: The responsiveness of polyelectrolyte block copolymers to ionic strength and/or pH allow for tuning the self-assembly process and the resultant materials properties. As the salt increases, the polymer network can undergo a sharp morphological transition from micellar network to hamburger-shaped aggregate, which is predicted using dissipative particle dynamics (DPD) simulations and cryogenic transmission electron microscopy (cryo-TEM) on the example of the self-assembly of single-stranded DNA triblocks. Further details can be found in article number 1700422 by Yaroslava G. Yingling* and co-workers.}, number={20}, journal={Macromolecular Rapid Communications}, publisher={Wiley-Blackwell}, author={Li, Nan K. and Kuang, Huihui and Fuss, William H. and Zauscher, Stefan and Kokkoli, Efrosini and Yingling, Yaroslava G.}, year={2017}, month={Oct} }
 @article{kim_farmer_yingling_2017, title={Physisorption: Effect of Graphene Oxidation Rate on Adsorption of Poly-Thymine Single Stranded DNA (Adv. Mater. Interfaces 8/2017)}, volume={4}, ISSN={2196-7350}, url={http://dx.doi.org/10.1002/ADMI.201770036}, DOI={10.1002/admi.201770036}, abstractNote={In article number 1601168, Ho Shin Kim, Yaroslava G. Yingling, and co-workers investigate the effect of graphene oxidation on the adsorption of poly-thymine single-stranded DNA (ssDNA) via all-atom molecular dynamics simulations. The cover illustrates the conformational changes of folded ssDNA on graphene and graphene oxide surfaces. This study found that oxidation rate of graphene surface is correlated to the ssDNA structural stability.}, number={8}, journal={Advanced Materials Interfaces}, publisher={Wiley}, author={Kim, Ho Shin and Farmer, Barry L. and Yingling, Yaroslava G.}, year={2017}, month={Apr} }
 @article{li_kuang_fuss_zauscher_kokkoli_yingling_2017, title={Salt Responsive Morphologies of ssDNA-Based Triblock Polyelectrolytes in Semi-Dilute Regime: Effect of Volume Fractions and Polyelectrolyte Length}, volume={38}, ISSN={1022-1336}, url={http://dx.doi.org/10.1002/marc.201700422}, DOI={10.1002/marc.201700422}, abstractNote={Abstract}, number={20}, journal={Macromolecular Rapid Communications}, publisher={Wiley}, author={Li, Nan K. and Kuang, Huihui and Fuss, William H. and Zauscher, Stefan and Kokkoli, Efrosini and Yingling, Yaroslava G.}, year={2017}, month={Sep}, pages={1700422} }
 @article{xiong_kim_zhang_kim_korolovych_ma_yingling_lu_tsukruk_2017, title={Template-Guided Assembly of Silk Fibroin on Cellulose Nanofibers for Robust Nanostructures with Ultrafast Water Transport}, volume={11}, ISSN={1936-0851 1936-086X}, url={http://dx.doi.org/10.1021/acsnano.7b04235}, DOI={10.1021/acsnano.7b04235}, abstractNote={The construction of multilength scaled hierarchical nanostructures from diverse natural components is critical in the progress toward all-natural nanocomposites with structural robustness and versatile added functionalities. Here, we report a spontaneous formation of peculiar "shish kebab" nanostructures with the periodic arrangement of silk fibroin domains along straight segments of cellulose nanofibers. We suggest that the formation of these shish kebab nanostructures is facilitated by the preferential organization of heterogeneous (β-sheets and amorphous silk) domains along the cellulose nanofiber driven by modulated axial distribution of crystalline planes, hydrogen bonding, and hydrophobic interactions as suggested by all-atom molecular dynamic simulations. Such shish kebab nanostructures enable the ultrathin membrane to possess open, transparent, mechanically robust interlocked networks with high mechanical performance with up to 30 GPa in stiffness and 260 MPa in strength. These nanoporous robust membranes allow for the extremely high water flux, up to 3.5 × 104 L h-1 m-2 bar-1 combined with high rejection rate for various organic molecules, capability of capturing heavy metal ions and their further reduction into metal nanoparticles for added SERS detection capability and catalytic functionalities.}, number={12}, journal={ACS Nano}, publisher={American Chemical Society (ACS)}, author={Xiong, Rui and Kim, Ho Shin and Zhang, Shuaidi and Kim, Sunghan and Korolovych, Volodymyr F. and Ma, Ruilong and Yingling, Yaroslava G. and Lu, Canhui and Tsukruk, Vladimir V.}, year={2017}, month={Nov}, pages={12008–12019} }
 @article{nagarajan_rongala_luang_singh_shadiac_hayes_sutton_gilliham_tyerman_mcphee_et al._2016, title={A Barley Efflux Transporter Operates in a Na+-Dependent Manner, as Revealed by a Multidisciplinary Platform}, volume={28}, ISSN={["1532-298X"]}, url={https://publons.com/wos-op/publon/5454554/}, DOI={10.1105/tpc.15.00625}, abstractNote={A barley efflux transporter that is primarily borate-permeable operates as a channel in a Na+-dependent manner. Plant growth and survival depend upon the activity of membrane transporters that control the movement and distribution of solutes into, around, and out of plants. Although many plant transporters are known, their intrinsic properties make them difficult to study. In barley (Hordeum vulgare), the root anion-permeable transporter Bot1 plays a key role in tolerance to high soil boron, facilitating the efflux of borate from cells. However, its three-dimensional structure is unavailable and the molecular basis of its permeation function is unknown. Using an integrative platform of computational, biophysical, and biochemical tools as well as molecular biology, electrophysiology, and bioinformatics, we provide insight into the origin of transport function of Bot1. An atomistic model, supported by atomic force microscopy measurements, reveals that the protein folds into 13 transmembrane-spanning and five cytoplasmic α-helices. We predict a trimeric assembly of Bot1 and the presence of a Na+ ion binding site, located in the proximity of a pore that conducts anions. Patch-clamp electrophysiology of Bot1 detects Na+-dependent polyvalent anion transport in a Nernstian manner with channel-like characteristics. Using alanine scanning, molecular dynamics simulations, and transport measurements, we show that conductance by Bot1 is abolished by removal of the Na+ ion binding site. Our data enhance the understanding of the permeation functions of Bot1.}, number={1}, journal={Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Nagarajan, Yagnesh and Rongala, Jay and Luang, Sukanya and Singh, Abhishek and Shadiac, Nadim and Hayes, Julie and Sutton, Tim and Gilliham, Matthew and Tyerman, Stephen and McPhee, Gordon and et al.}, year={2016}, pages={202–218} }
 @article{nash_tucker_therriault_yingling_2016, title={Binding of single stranded nucleic acids to cationic ligand functionalized gold nanoparticles}, volume={11}, ISSN={["1559-4106"]}, url={https://publons.com/publon/28057454/}, DOI={10.1116/1.4966653}, abstractNote={The interactions of nanoparticles (NPs) with single stranded nucleic acids (NAs) have important implications in gene delivery, and nanotechnological and biomedical applications. Here, the complexation of cationic ligand functionalized gold nanoparticles with single stranded deoxyribose nucleic acid (DNA) and ribonucleic acid (RNA) are examined using all atom molecular dynamics simulations. The results indicated that complexation depends mostly on charge of nanoparticle, and, to lesser extent, sequence and type of nucleic acid. For cationic nanoparticles, electrostatic interactions between charged ligands and the nucleic acid backbone dominate binding regardless of nanoparticle charge. Highly charged nanoparticles bind more tightly and cause compaction of the single-stranded NAs through disruption of intrastrand π–π stacking and hydrogen bonding. However, poly-purine strands (polyA-DNA, polyA-RNA) show less change in structure than poly-pyrimidine strands (polyT-DNA, polyU-RNA). Overall, the results show that control over ssNA structure may be achieved with cationic NPs with a charge of more than 30, but the extent of the structural changes depends on sequence.}, number={4}, journal={BIOINTERPHASES}, author={Nash, Jessica A. and Tucker, Tasha L. and Therriault, William and Yingling, Yaroslava G.}, year={2016}, month={Dec} }
 @article{grant_kim_dupnock_hu_yingling_tsukruk_2016, title={Bionanocomposites: Silk Fibroin-Substrate Interactions at Heterogeneous Nanocomposite Interfaces (Adv. Funct. Mater. 35/2016)}, volume={26}, ISSN={1616-301X}, url={http://dx.doi.org/10.1002/ADFM.201670231}, DOI={10.1002/adfm.201670231}, abstractNote={Silk assembly can be controlled by manipulating substrate chemistry and factors relevant to layer-by-layer assembly, as described by V. V. Tsukruk and co-workers on page 6380. Silk assembles into individual fibrils when sheared on hydrophilic graphene oxide while maintaining its globular solution state morphology on hydrophobic reduced graphene oxide as shown on this cover. Molecular Dynamics simulations and high resolution microscopy are used to probe the non-covalent interactions driving this response.}, number={35}, journal={Advanced Functional Materials}, publisher={Wiley}, author={Grant, Anise M. and Kim, Ho Shin and Dupnock, Trisha L. and Hu, Kesong and Yingling, Yaroslava G. and Tsukruk, Vladimir V.}, year={2016}, month={Sep}, pages={6496–6496} }
 @article{nixon_mansouri_singh_du_davis_lee_slabaugh_vandavasi_o’neill_roberts_et al._2016, title={Comparative Structural and Computational Analysis Supports Eighteen Cellulose Synthases in the Plant Cellulose Synthesis Complex}, volume={6}, ISSN={2045-2322}, url={http://dx.doi.org/10.1038/srep28696}, DOI={10.1038/srep28696}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, publisher={Springer Science and Business Media LLC}, author={Nixon, B. Tracy and Mansouri, Katayoun and Singh, Abhishek and Du, Juan and Davis, Jonathan K. and Lee, Jung-Goo and Slabaugh, Erin and Vandavasi, Venu Gopal and O’Neill, Hugh and Roberts, Eric M. and et al.}, year={2016}, month={Jun} }
 @article{rangnekar_nash_goodfred_yingling_labean_2016, title={Design of Potent and Controllable Anticoagulants Using DNA Aptamers and Nanostructures}, volume={21}, ISSN={["1420-3049"]}, url={https://doi.org/10.3390/molecules21020202}, DOI={10.3390/molecules21020202}, abstractNote={The regulation of thrombin activity offers an opportunity to regulate blood clotting because of the central role played by this molecule in the coagulation cascade. Thrombin-binding DNA aptamers have been used to inhibit thrombin activity. In the past, to address the low efficacy reported for these aptamers during clinical trials, multiple aptamers have been linked using DNA nanostructures. Here, we modify that strategy by linking multiple copies of various thrombin-binding aptamers using DNA weave tiles. The resulting constructs have very high anticoagulant activity in functional assays owing to their improved cooperative binding affinity to thrombin due to optimized spacing, orientation, and the high local concentration of aptamers. We also report the results of molecular dynamics simulations to gain insight into the solution conformations of the tiles. Moreover, by using DNA strand displacement, we were able to turn the coagulation cascade off and on as desired, thereby enabling significantly better control over blood coagulation.}, number={2}, journal={MOLECULES}, publisher={MDPI AG}, author={Rangnekar, Abhijit and Nash, Jessica A. and Goodfred, Bethany and Yingling, Yaroslava G. and LaBean, Thomas H.}, year={2016}, month={Feb} }
 @article{ge_li_mccormick_lichtenberg_yingling_stiff-roberts_2016, title={Emulsion-Based RIR-MAPLE Deposition of Conjugated Polymers: Primary Solvent Effect and Its Implications on Organic Solar Cell Performance}, volume={8}, ISSN={["1944-8252"]}, url={https://publons.com/publon/9429677/}, DOI={10.1021/acsami.6b05596}, abstractNote={Emulsion-based, resonant infrared matrix-assisted pulsed laser evaporation (RIR-MAPLE) has been demonstrated as an alternative technique to deposit conjugated polymer films for photovoltaic applications; yet, a fundamental understanding of how the emulsion target characteristics translate into film properties and solar cell performance is unclear. Such understanding is crucial to enable the rational improvement of organic solar cell (OSC) efficiency and to realize the expected advantages of emulsion-based RIR-MAPLE for OSC fabrication. In this paper, the effect of the primary solvent used in the emulsion target is studied, both experimentally and theoretically, and it is found to determine the conjugated polymer cluster size in the emulsion as well as surface roughness and internal morphology of resulting polymer films. By using a primary solvent with low solubility-in-water and low vapor pressure, the surface roughness of deposited P3HT and PCPDTBT polymer films was reduced to 10 nm, and the efficiency of P3HT:PC61BM OSCs was increased to 3.2% (∼100 times higher compared to the first MAPLE OSC demonstration [ Caricato , A. P. ; Appl. Phys. Lett. 2012 , 100 , 073306 ]). This work unveils the mechanism of polymer film formation using emulsion-based RIR-MAPLE and provides insight and direction to determine the best ways to take advantage of the emulsion target approach to control film properties for different applications.}, number={30}, journal={ACS APPLIED MATERIALS & INTERFACES}, publisher={American Chemical Society (ACS)}, author={Ge, Wangyao and Li, Nan K. and McCormick, Ryan D. and Lichtenberg, Eli and Yingling, Yaroslava G. and Stiff-Roberts, Adrienne D.}, year={2016}, month={Aug}, pages={19494–19506} }
 @article{roark_tan_ivanina_chandler_castaneda_kim_jawahar_viard_talic_wustholz_et al._2016, title={Fluorescence Blinking as an Output Signal for Biosensing}, volume={1}, ISSN={2379-3694 2379-3694}, url={http://dx.doi.org/10.1021/acssensors.6b00352}, DOI={10.1021/acssensors.6b00352}, abstractNote={We demonstrate the first biosensing strategy that relies on quantum dot (QD) fluorescence blinking to report the presence of a target molecule. Unlike other biosensors that utilize QDs, our method does not require the analyte to induce any fluorescence intensity or color changes, making it readily applicable to a wide range of target species. Instead, our approach relies on the understanding that blinking, a single particle phenomenon, is obscured when several QDs lie within the detection volume of a confocal microscope. If QDs are engineered to aggregate when they encounter a particular target molecule, the observation of quasi-continuous emission should indicate its presence. As proof of concept, we programmed DNAs to drive rapid isothermal assembly of QDs in the presence of a target strand (oncogene K-ras). The assemblies, confirmed by various gel techniques, contained multiple QDs and were readily distinguished from free QDs by the absence of blinking.}, number={11}, journal={ACS Sensors}, publisher={American Chemical Society (ACS)}, author={Roark, Brandon and Tan, Jenna A. and Ivanina, Anna and Chandler, Morgan and Castaneda, Jose and Kim, Ho Shin and Jawahar, Shriram and Viard, Mathias and Talic, Strahinja and Wustholz, Kristin L. and et al.}, year={2016}, month={Nov}, pages={1295–1300} }
 @article{zhao_li_yingling_hall_2016, title={LCST Behavior is Manifested in a Single Molecule: Elastin-Like polypeptide (VPGVG)n}, volume={17}, ISSN={["1526-4602"]}, url={https://publons.com/publon/9429675/}, DOI={10.1021/acs.biomac.5b01235}, abstractNote={The physical origin of the lower critical solution temperature (LCST) behavior of a variety of fluids, including elastin-like polypeptides (ELPs), has been studied for the past few decades. As is the case for polymer solutions, LCST behavior of ELPs is invariably reported for large systems of molecules and is considered evidence for collective behavior. In contrast, we find evidence for properties changes associated with LCST behavior in a single molecule by performing long atomic-level molecular dynamics simulation on the ELP sequences (Val-Pro-Gly-Val-Gly)n for four different length peptides over a wide range of temperatures. We observe a sharp transition in the number of hydrogen bonds between peptide and water and in the number of water molecules within the first hydration shell as temperature rises; this is used to locate the transition temperature. The dependence of the transition temperatures of ELPs on their lengths agrees well with experiments in that both have the same power law exponents. Our simulations reveal that the tendency for pentamers (VPGVG) in ELPs of all lengths to lose H-bonds with water or to gain H-bonds with themselves as temperature rises is independent of the length of the chain in which they are embedded. Thus, the transition temperature of ELPs in pure water is determined by two factors: the hydrogen bonding tendency of the pentamers and the number of pentamers per ELP. Moreover, the hydrogen bonding tendency of pentamers depends only on their sequences, not on the ELP chain length.}, number={1}, journal={BIOMACROMOLECULES}, publisher={American Chemical Society (ACS)}, author={Zhao, Binwu and Li, Nan K. and Yingling, Yaroslava G. and Hall, Carol K.}, year={2016}, month={Jan}, pages={111–118} }
 @article{pasquinelli_yingling_2016, title={Molecular Dynamics Simulations of Nano-biomaterials}, DOI={10.1007/978-94-017-9780-1_402}, journal={Encyclopedia of Nanotechnology}, publisher={Springer Netherlands}, author={Pasquinelli, Melissa A. and Yingling, Yaroslava G.}, year={2016}, pages={2260–2269} }
 @article{sethaphong_davis_slabaugh_singh_haigler_yingling_2016, title={Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis}, volume={23}, ISSN={0969-0239 1572-882X}, url={http://dx.doi.org/10.1007/s10570-015-0789-6}, DOI={10.1007/s10570-015-0789-6}, number={1}, journal={Cellulose}, publisher={Springer Science and Business Media LLC}, author={Sethaphong, Latsavongsakda and Davis, Jonathan K. and Slabaugh, Erin and Singh, Abhishek and Haigler, Candace H. and Yingling, Yaroslava G.}, year={2016}, month={Feb}, pages={145–161} }
 @article{kim_huang_yingling_2016, title={Sequence dependent interaction of single stranded DNA with graphitic flakes: atomistic molecular dynamics simulations}, volume={1}, ISSN={2059-8521}, url={http://dx.doi.org/10.1557/adv.2016.91}, DOI={10.1557/adv.2016.91}, abstractNote={In an attempt to understand the structure and dynamics of ssDNA on graphene based surfaces, we performed all-atom implicit solvent molecular dynamics simulations of ssDNA on graphene and graphene oxide (GO) surfaces. Simulations indicate that adsorption of poly(A), poly(T) and poly (AT) have similar mechanisms of adsorption to free standing graphitic flakes, which are governed by a surface oxygen content. Specifically, higher oxygen content of a surface leads to decrease in persistence length of ssDNA. However, the role of DNA sequence on the physisorption mechanism is minimal.}, number={25}, journal={MRS Advances}, publisher={Cambridge University Press (CUP)}, author={Kim, Ho Shin and Huang, Sabrina M. and Yingling, Yaroslava G.}, year={2016}, pages={1883–1889} }
 @article{grant_kim_dupnock_hu_yingling_tsukruk_2016, title={Silk Fibroin-Substrate Interactions at Heterogeneous Nanocomposite Interfaces}, volume={26}, ISSN={["1616-3028"]}, url={https://publons.com/publon/2231504/}, DOI={10.1002/adfm.201601268}, abstractNote={Silk fibroin adsorption at the heterogeneous hydrophobic–hydrophilic surface of graphene oxide (GO) with different degrees of oxidation is addressed experimentally and theoretically. Samples are prepared using various spin‐assisted deposition conditions relevant to assembly of laminated nanocomposites from graphene‐based components, and compared with silicon dioxide (SiO2) as a benchmark substrate. Secondary structure of silk backbones changes as a function of silk fibroin concentration, substrate chemical composition, and deposition dynamics are assessed and compared with molecular dynamic simulations. It is observed that protofibrils form at low concentrations while variance in the deposition speed has little effect on silk secondary structure and morphology. However, balance of nonbonded interactions between electrostatic and van der Waals contributions can lead to silk secondary structure retention on the GO surface. Molecular dynamics simulations of silk fibroin at different surfaces show that strong van der Waals interactions play a pivotal role in losing and disrupting secondary structure on graphene and SiO2 surfaces. Fine tuning silk fibroin structure on heterogeneous graphene‐based surfaces paves the way toward development of biomolecular reinforcement for biopolymer–graphene laminated nanocomposites.}, number={35}, journal={ADVANCED FUNCTIONAL MATERIALS}, publisher={Wiley-Blackwell}, author={Grant, Anise M. and Kim, Ho Shin and Dupnock, Trisha L. and Hu, Kesong and Yingling, Yaroslava G. and Tsukruk, Vladimir V.}, year={2016}, month={Sep}, pages={6380–6392} }
 @article{kim_eom_koo_yingling_2016, title={The effect of imidazolium cations on the structure and activity of the Candida antarctica Lipase B enzyme in ionic liquids}, volume={18}, ISSN={1463-9076 1463-9084}, url={http://dx.doi.org/10.1039/C6CP02355J}, DOI={10.1039/c6cp02355j}, abstractNote={To understand how cations affect the enzyme structure and activity of Candida antarctica Lipase B, we performed MD simulations of CALB in four types of ionic liquids with varying sizes of cations and correlated the results with the experimental data.}, number={32}, journal={Physical Chemistry Chemical Physics}, publisher={Royal Society of Chemistry (RSC)}, author={Kim, Ho Shin and Eom, Doyoung and Koo, Yoon-Mo and Yingling, Yaroslava G.}, year={2016}, pages={22062–22069} }
 @article{when in silico meets in vitro: molecular basis of function of an anion-permeable efflux transporter from barley (hordeum vulgare l.)_2016, url={https://publons.com/wos-op/publon/382040/}, journal={Abstracts of Papers of the American Chemical Society}, year={2016} }
 @article{li_fuss_yingling_2015, title={An Implicit Solvent Ionic Strength (ISIS) Method to Model Polyelectrolyte Systems with Dissipative Particle Dynamics}, volume={24}, ISSN={["1521-3919"]}, url={https://publons.com/publon/9429670/}, DOI={10.1002/mats.201400043}, abstractNote={Herein, a new coarse‐grained methodology for modeling and simulations of polyelectrolyte systems using implicit solvent ionic strength (ISIS) with dissipative particle dynamics (DPD) is presented. This ISIS model is based on mean‐field theory approximation and the soft repulsive potential is used to reproduce the effect of solvent ionic strength. The capability of the ISIS model is assessed via two test cases: dynamics of a single long polyelectrolyte chain and the self‐assembly of polyelectrolyte diblock copolymers in aqueous solutions with variable ionic strength. The results are in good agreement with previous experimental observations and theoretical predictions, which indicates that our polyelectrolyte model can be used to effectively and efficiently capture salt‐dependent conformational features of large‐scale polyelectrolyte systems in aqueous solutions, especially at the salt‐dominated regime.}, number={1}, journal={MACROMOLECULAR THEORY AND SIMULATIONS}, publisher={Wiley-Blackwell}, author={Li, Nan K. and Fuss, William H. and Yingling, Yaroslava G.}, year={2015}, month={Jan}, pages={7–12} }
 @article{lei_singh_bashline_li_yingling_gu_2015, title={CELLULOSE SYNTHASE INTERACTIVE1 Is Required for Fast Recycling of Cellulose Synthase Complexes to the Plasma Membrane in Arabidopsis}, volume={27}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.15.00442}, DOI={10.1105/tpc.15.00442}, abstractNote={Rapid recycling of cellulose synthase in plants under stress is dependent on CELLULOSE SYNTHASE INTERACTIVE1- and clathrin-mediated endocytosis. Plants are constantly subjected to various biotic and abiotic stresses and have evolved complex strategies to cope with these stresses. For example, plant cells endocytose plasma membrane material under stress and subsequently recycle it back when the stress conditions are relieved. Cellulose biosynthesis is a tightly regulated process that is performed by plasma membrane-localized cellulose synthase (CESA) complexes (CSCs). However, the regulatory mechanism of cellulose biosynthesis under abiotic stress has not been well explored. In this study, we show that small CESA compartments (SmaCCs) or microtubule-associated cellulose synthase compartments (MASCs) are critical for fast recovery of CSCs to the plasma membrane after stress is relieved in Arabidopsis thaliana. This SmaCC/MASC-mediated fast recovery of CSCs is dependent on CELLULOSE SYNTHASE INTERACTIVE1 (CSI1), a protein previously known to represent the link between CSCs and cortical microtubules. Independently, AP2M, a core component in clathrin-mediated endocytosis, plays a role in the formation of SmaCCs/MASCs. Together, our study establishes a model in which CSI1-dependent SmaCCs/MASCs are formed through a process that involves endocytosis, which represents an important mechanism for plants to quickly regulate cellulose synthesis under abiotic stress.}, number={10}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Lei, Lei and Singh, Abhishek and Bashline, Logan and Li, Shundai and Yingling, Yaroslava G. and Gu, Ying}, year={2015}, month={Oct}, pages={tpc.15.00442} }
 @article{nash_singh_li_yingling_2015, title={Characterization of Nucleic Acid Compaction with Histone-Mimic Nanoparticles through All-Atom Molecular Dynamics}, volume={9}, ISSN={["1936-086X"]}, url={https://publons.com/publon/5454552/}, DOI={10.1021/acsnano.5b05684}, abstractNote={The development of nucleic acid (NA) based nanotechnology applications rely on the efficient packaging of DNA and RNA. However, the atomic details of NA-nanoparticle binding remains to be comprehensively characterized. Here, we examined how nanoparticle and solvent properties affect NA compaction. Our large-scale, all-atom simulations of ligand-functionalized gold nanoparticle (NP) binding to double stranded NAs as a function of NP charge and solution salt concentration reveal different responses of RNA and DNA to cationic NPs. We demonstrate that the ability of a nanoparticle to bend DNA is directly correlated with the NPs charge and ligand corona shape, where more than 50% charge neutralization and spherical shape of the NP ligand corona ensured the DNA compaction. However, NP with 100% charge neutralization is needed to bend DNA almost as efficiently as the histone octamer. For RNA in 0.1 M NaCl, even the most highly charged nanoparticles are not capable of causing bending due to charged ligand end groups binding internally to the major groove of RNA. We show that RNA compaction can only be achieved through a combination of highly charged nanoparticles with low salt concentration. Upon interactions with highly charged NPs, DNA bends through periodic variation in groove widths and depths, whereas RNA bends through expansion of the major groove.}, number={12}, journal={ACS NANO}, publisher={American Chemical Society (ACS)}, author={Nash, Jessica A. and Singh, Abhishek and Li, Nan K. and Yingling, Yaroslava G.}, year={2015}, month={Dec}, pages={12374–12382} }
 @article{li_fuss_yingling_2015, title={Cover Picture: Macromol. Theory Simul. 1∕2015}, volume={24}, ISSN={1022-1344}, url={http://dx.doi.org/10.1002/MATS.201570001}, DOI={10.1002/mats.201570001}, abstractNote={Cover: Morphological transformations of polyelectrolyte self-assembled structures in aqueous solutions are identified in response to the change in solvent ionic strength, through the application of a newly developed implicit solvent ionic strength (ISIS) model for a dissipative particle dynamics (DPD) method. Further details can be found in the article by N. K. Li, W. H. Fuss, and Y. G. Yingling* on page 7.}, number={1}, journal={Macromolecular Theory and Simulations}, publisher={Wiley}, author={Li, Nan K. and Fuss, William H. and Yingling, Yaroslava G.}, year={2015}, month={Jan}, pages={1–1} }
 @article{effect of np shape and ligand flexibility in the design of nucleic acid wrapping nps_2015, url={https://publons.com/wos-op/publon/28057470/}, journal={Abstracts of Papers of the American Chemical Society}, year={2015} }
 @article{effect of surface polarity on physisorption of biomolecules: molecular modeling_2015, url={https://publons.com/publon/28057471/}, journal={Abstracts of Papers of the American Chemical Society}, year={2015} }
 @article{peerless_bowers_kwansa_yingling_2015, title={Fullerenes in Aromatic Solvents: Correlation between Solvation-Shell Structure, Solvate Formation, and Solubility}, volume={119}, ISSN={["1520-6106"]}, url={https://publons.com/publon/10429550/}, DOI={10.1021/acs.jpcb.5b09386}, abstractNote={In this work, an all-atom molecular dynamics simulation technique was employed to gain insight into the dynamic structure of the solvation shell formed around C60 and phenyl-C61-butyric acid methyl ester (PCBM) in nine aromatic solvents. A new method was developed to visualize and quantify the distribution of solvent molecule orientations in the solvation shell. A strong positive correlation was found between the regularity of solvent molecule orientations in the solvation shell and the experimentally obtained solubility limits for both C60 and PCBM. This correlation was extended to predict a solubility of 36 g/L for PCBM in 1,2,4-trimethylbenze. The relationship between solvation-shell structure and solubility provided detailed insight into solvate formation of C60 and solvation in relation to solvent molecular structure and properties. The determined dependence of the solvation-shell structure on the geometric shape of the solvent might allow for enhanced control of fullerene solution-phase behavior during processing by chemically tailoring the solvent molecular structure, potentially diminishing the need for costly and environmentally harmful halogenated solvents and/or additives.}, number={49}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, publisher={American Chemical Society (ACS)}, author={Peerless, James S. and Bowers, G. Hunter and Kwansa, Albert L. and Yingling, Yaroslava G.}, year={2015}, month={Dec}, pages={15344–15352} }
 @article{gold nanoparticle-nucleic acid modeling using gpu-accelerated molecular dynamics_2015, url={https://publons.com/publon/28057466/}, journal={Abstracts of Papers of the American Chemical Society}, year={2015} }
 @article{yang_zimmer_yingling_kubicki_2015, title={How Cellulose Elongates-A QM/MM Study of the Molecular Mechanism of Cellulose Polymerization in Bacterial CESA}, volume={119}, ISSN={["1520-6106"]}, url={https://publons.com/publon/8660952/}, DOI={10.1021/acs.jpcb.5b01433}, abstractNote={The catalytic mechanism of bacterial cellulose synthase was investigated by using a hybrid quantum mechanics and molecular mechanics (QM/MM) approach. The Michaelis complex model was built based on the X-ray crystal structure of the cellulose synthase subunits BcsA and BcsB containing a uridine diphosphate molecule and a translocating glucan. Our study identified an SN2-type transition structure corresponding to the nucleophilic attack of the nonreducing end O4 on the anomeric carbon C1, the breaking of the glycosidic bond C1-O1, and the transfer of proton from the nonreducing end O4 to the general base D343. The activation barrier found for this SN2-type transition state is 68 kJ/mol. The rate constant of polymerization is estimated to be ∼8.0 s(-1) via transition state theory. A similar SN2-type transition structure was also identified for a second glucose molecule added to the growing polysaccharide chain, which aligned with the polymer 180° rotated compared to the initially added unit. This study provides detailed insights into how cellulose is extended by one glucose molecule at a time and how the individual glucose units align into cellobiose repeating units.}, number={22}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, publisher={American Chemical Society (ACS)}, author={Yang, Hui and Zimmer, Jochen and Yingling, Yaroslava G. and Kubicki, James D.}, year={2015}, month={Jun}, pages={6525–6535} }
 @misc{li_lei_yingling_gu_2015, title={Microtubules and cellulose biosynthesis: the emergence of new players}, volume={28}, ISSN={["1879-0356"]}, url={https://publons.com/wos-op/publon/28057463/}, DOI={10.1016/j.pbi.2015.09.002}, abstractNote={Microtubules determine the orientation of newly formed cellulose microfibrils in expanding cells. There are many hypotheses regarding how the information is transduced across the plasma membrane from microtubules to cellulose microfibrils. However, the molecular mechanisms underlying the co-alignment between microtubules and cellulose microfibrils were not revealed until the recent discovery of cellulose synthase interacting (CSI) proteins. Characterization of CSIs and additional cellulose synthase-associated proteins will greatly advance the knowledge of how cellulose microfibrils are organized.}, journal={CURRENT OPINION IN PLANT BIOLOGY}, publisher={Elsevier BV}, author={Li, Shundai and Lei, Lei and Yingling, Yaroslava G. and Gu, Ying}, year={2015}, month={Dec}, pages={76–82} }
 @article{molecular description of lcst behavior of elastin-like peptides poly(vpgvg) and poly(vgpvg)_2015, url={https://publons.com/publon/28057468/}, journal={Abstracts of Papers of the American Chemical Society}, year={2015} }
 @article{morphological and rheological properties of aqueous micellar network of polyelectrolyte block copolymers_2015, url={https://publons.com/publon/28057469/}, journal={Abstracts of Papers of the American Chemical Society}, year={2015} }
 @article{li_fuss_tang_gu_chilkoti_zauscher_yingling_2015, title={Prediction of solvent-induced morphological changes of polyelectrolyte diblock copolymer micelles}, volume={11}, ISSN={["1744-6848"]}, url={https://publons.com/wos-op/publon/7980728/}, DOI={10.1039/c5sm01742d}, abstractNote={A comprehensive set of data is obtained with the utilization of ISIS DPD model to construct the phase diagram of amphiphilic polyelectrolyte diblock copolymers in aqueous solution.}, number={42}, journal={SOFT MATTER}, publisher={Royal Society of Chemistry (RSC)}, author={Li, Nan K. and Fuss, William H. and Tang, Lei and Gu, Renpeng and Chilkoti, Ashutosh and Zauscher, Stefan and Yingling, Yaroslava G.}, year={2015}, pages={8236–8245} }
 @article{simulations of the self-assembly of polyelectrolyte block copolymers using dissipative particle dynamics with an implicit solvent ionic strength (isis) method_2015, url={https://publons.com/publon/28057467/}, journal={Abstracts of Papers of the American Chemical Society}, year={2015} }
 @article{slabaugh_davis_haigler_yingling_zimmer_2014, title={Cellulose synthases: new insights from crystallography and modeling}, volume={19}, ISSN={1360-1385}, url={http://dx.doi.org/10.1016/j.tplants.2013.09.009}, DOI={10.1016/j.tplants.2013.09.009}, abstractNote={•A crystal structure and a modeled structure of cellulose synthases are examined. •We explore similarities/differences between bacterial and plant cellulose synthase. •Molecular mechanisms for known cellulose synthase missense mutations are proposed. •We predict specific residues putatively involved in glucan translocation in plants. Detailed information about the structure and biochemical mechanisms of cellulose synthase (CelS) proteins remained elusive until a complex containing the catalytic subunit (BcsA) of CelS from Rhodobacter sphaeroides was crystalized. Additionally, a 3D structure of most of the cytosolic domain of a plant CelS (GhCESA1 from cotton, Gossypium hirsutum) was produced by computational modeling. This predicted structure contributes to our understanding of how plant CelS proteins may be similar and different as compared with BcsA. In this review, we highlight how these structures impact our understanding of the synthesis of cellulose and other extracellular polysaccharides. We show how the structures can be used to generate hypotheses for experiments testing mechanisms of glucan synthesis and translocation in plant CelS. Detailed information about the structure and biochemical mechanisms of cellulose synthase (CelS) proteins remained elusive until a complex containing the catalytic subunit (BcsA) of CelS from Rhodobacter sphaeroides was crystalized. Additionally, a 3D structure of most of the cytosolic domain of a plant CelS (GhCESA1 from cotton, Gossypium hirsutum) was produced by computational modeling. This predicted structure contributes to our understanding of how plant CelS proteins may be similar and different as compared with BcsA. In this review, we highlight how these structures impact our understanding of the synthesis of cellulose and other extracellular polysaccharides. We show how the structures can be used to generate hypotheses for experiments testing mechanisms of glucan synthesis and translocation in plant CelS.}, number={2}, journal={Trends in Plant Science}, publisher={Elsevier BV}, author={Slabaugh, Erin and Davis, Jonathan K. and Haigler, Candace H. and Yingling, Yaroslava G. and Zimmer, Jochen}, year={2014}, month={Feb}, pages={99–106} }
 @article{slabaugh_sethaphong_xiao_amick_anderson_haigler_yingling_2014, title={Computational and genetic evidence that different structural conformations of a non-catalytic region affect the function of plant cellulose synthase}, volume={65}, ISSN={1460-2431 0022-0957}, url={http://dx.doi.org/10.1093/jxb/eru383}, DOI={10.1093/jxb/eru383}, abstractNote={Summary Computational modelling of peptide structure, genetic complementation in Arabidopsis thaliana, and confocal microscopy provide evidence that a region between two transmembrane helices may adopt two predominant structural conformations that affect the function of plant cellulose synthase.}, number={22}, journal={Journal of Experimental Botany}, publisher={Oxford University Press (OUP)}, author={Slabaugh, Erin and Sethaphong, Latsavongsakda and Xiao, Chaowen and Amick, Joshua and Anderson, Charles T. and Haigler, Candace H. and Yingling, Yaroslava G.}, year={2014}, month={Sep}, pages={6645–6653} }
 @article{tang_tjong_li_yingling_chilkoti_zauscher_2014, title={Enzymatic Polymerization of High Molecular Weight DNA Amphiphiles That Self-Assemble into Star-Like Micelles}, volume={26}, ISSN={["1521-4095"]}, url={https://publons.com/wos-op/publon/7980721/}, DOI={10.1002/adma.201306049}, abstractNote={High molecular weight ssDNA amphiphiles are synthesized by enzymatic polymerization. These highly asymmetric diblock DNA copolymers self-assemble into "hairy", star-like micelles, shown in the AFM image and the DPD snapshot.}, number={19}, journal={ADVANCED MATERIALS}, publisher={Wiley-Blackwell}, author={Tang, Lei and Tjong, Vinalia and Li, Nan and Yingling, Yaroslava G. and Chilkoti, Ashutosh and Zauscher, Stefan}, year={2014}, month={May}, pages={3050–3054} }
 @article{li_quiroz_hall_chilkoti_yingling_2014, title={Molecular Description of the LCST Behavior of an Elastin-Like Polypeptide}, volume={15}, ISSN={["1526-4602"]}, url={https://publons.com/wos-op/publon/9429682/}, DOI={10.1021/bm500658w}, abstractNote={Elastin-like polypeptides (ELPs) with the repeat sequence of VPGVG are widely used as a model system for investigation of lower critical solution temperature (LCST) transition behavior. In this paper, the effect of temperature on the structure, dynamics and association of (VPGVG)18 in aqueous solution is investigated using atomistic molecular dynamics simulations. Our simulations show that as the temperature increases the ELP backbones undergo gradual conformational changes, which are attributed to the formation of more ordered secondary structures such as β-strands. In addition, increasing temperature changes the hydrophobicity of the ELP by exposure of hydrophobic valine-side chains to the solvent and hiding of proline residues. Based on our simulations, we conclude that the transition behavior of (VPGVG)18 can be attributed to a combination of thermal disruption of the water network that surrounds the polypeptide, reduction of solvent accessible surface area of the polypeptide, and increase in its hydrophobicity. Simulations of the association of two (VPGVG)18 molecules demonstrated that the observed gradual changes in the structural properties of the single polypeptide chain are enough to cause the aggregation of polypeptides above the LCST. These results lead us to propose that the LCST phase behavior of poly(VPGVG) is a collective phenomenon that originates from the correlated gradual changes in single polypeptide structure and the abrupt change in properties of hydration water around the peptide and is a result of a competition between peptide-peptide and peptide-water interactions. This is a computational study of an important intrinsically disordered peptide system that provides an atomic-level description of structural features and interactions that are relevant in the LCST phase behavior.}, number={10}, journal={BIOMACROMOLECULES}, publisher={American Chemical Society (ACS)}, author={Li, Nan K. and Quiroz, Felipe Garcia and Hall, Carol K. and Chilkoti, Ashutosh and Yingling, Yaroslava G.}, year={2014}, month={Oct}, pages={3522–3530} }
 @article{persistence length of single stranded dna: effect of length, sequence and surface_2014, url={https://publons.com/publon/28057474/}, DOI={10.1016/J.BPJ.2013.11.1626}, abstractNote={The knowledge of the DNA persistence length indicates the chain's flexibility which is related to the possible final folded state of DNA and provides the means for understanding DNA's structure in solution and on surfaces. The persistence length of ssDNA depends on the rigidity of the backbone and an intra-chain repulsion due to negatively charged backbone. In order to determine the contributions of rigidity and electrostatics on persistence length of ssDNA we conducted series of molecular dynamics simulations with regular and neutralized DNA of various length and sequences. We found that persistence length is largely determined by the flexibility of the backbone. However the electrostatic contribution to the persistence length is sequence dependent due to differences in base stacking and hydrogen bonding network. To investigate the effect of surface on the structure and dynamics of single stranded DNA (ssDNA) we performed molecular dynamics simulations of surface constrained ssDNA. We observed that surface grafting of ssDNA significantly changes its folding pathway, pi-pi stacking interaction, persistence length, and end to end distance when compared to free ssDNA. Moreover, we found that the number of bases and sequence play an important role in structure and dynamics of ssDNA constrained on the surface. Our research provided atomistic understanding of dynamics and conformational changes of single stranded DNA under various conditions; the length and sequence dependence as well as the effect of surface immobilization.}, journal={Biophysical Journal}, year={2014} }
 @article{li_kim_nash_lim_yingling_2014, title={Progress in molecular modelling of DNA materials}, volume={40}, ISSN={["1029-0435"]}, url={https://publons.com/publon/9429685/}, DOI={10.1080/08927022.2014.913792}, abstractNote={The unique molecular recognition properties of DNA molecule, which store genetic information in cells, are responsible for the rise of DNA nanotechnology. In this article, we review the recent advances in atomistic and coarse-grained force fields along with simulations of DNA-based materials, as applied to DNA–nanoparticle assemblies for controlled material morphology, DNA–surface interactions for biosensor development and DNA origami. Evidently, currently available atomistic and coarse-grained representations of DNA are now at the stage of successfully reproducing and explaining experimentally observed phenomena. However, there is a clear need for the development of atomistic force fields which are robust at long timescales and in the improvement of the coarse-grained models.}, number={10-11}, journal={MOLECULAR SIMULATION}, publisher={Informa UK Limited}, author={Li, Nan K. and Kim, Ho Shin and Nash, Jessica A. and Lim, Mina and Yingling, Yaroslava G.}, year={2014}, pages={777–783} }
 @article{kim_ha_sethaphong_koo_yingling_2014, title={The relationship between enhanced enzyme activity and structural dynamics in ionic liquids: a combined computational and experimental study}, volume={16}, ISSN={["1463-9084"]}, url={https://publons.com/publon/389513/}, DOI={10.1039/c3cp52516c}, abstractNote={Candida antarctica lipase B (CALB) is an efficient biocatalyst for hydrolysis, esterification, and polymerization reactions. In order to understand how to control enzyme activity and stability we performed a combined experimental and molecular dynamics simulation study of CALB in organic solvents and ionic liquids (ILs). Our results demonstrate that the conformational changes of the active site cavity are directly related to enzyme activity and decrease in the following order: [Bmim][TfO] > tert-butanol > [Bmim][Cl]. The entrance to the cavity is modulated by two isoleucines, ILE-189 and ILE-285, one of which is located on the α-10 helix. The α-10 helix can substantially change its conformation due to specific interactions with solvent molecules. This change is acutely evident in [Bmim][Cl] where interactions of LYS-290 with chlorine anions caused a conformational switch between α-helix and turn. Disruption of the α-10 helix structure results in a narrow cavity entrance and, thus, reduced the activity of CALB in [Bmim][Cl]. Finally, our results show that the electrostatic energy between solvents in this study and CALB is correlated with the structural changes leading to differences in enzyme activity.}, number={7}, journal={PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, publisher={Royal Society of Chemistry (RSC)}, author={Kim, Ho Shin and Ha, Sung Ho and Sethaphong, Latsavongsakda and Koo, Yoon-Mo and Yingling, Yaroslava G.}, year={2014}, pages={2944–2953} }
 @article{pani_bond_krishnan_yingling_2013, title={Correlating fullerene diffusion with the polythiophene morphology: molecular dynamics simulations}, volume={9}, ISSN={["1744-6848"]}, url={https://publons.com/publon/11561895/}, DOI={10.1039/c3sm51906f}, abstractNote={Polymer film morphology is known to correlate with the efficient charge transport and device efficiency of the bulk heterojunction solar cell. Further improvements of the performance of organic solar cells require a better understanding of the mechanisms of diffusion and molecular rearrangement. In this paper, we used atomistic molecular dynamics simulations to provide insights into the factors affecting diffusion of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and fullerene (C60) into poly(3-hexylthiophene) (P3HT). We examined the diffusion and interactions of PCBMs in amorphous and around crystalline P3HTs at different temperatures. Simulations showed that fullerene particles tend to aggregate in amorphous P3HTs and on (100) surfaces. However, the diffusion of fullerenes on the (010) surface was mainly attributed to the preferential binding between fullerene cages and aromatic P3HT backbone which led to their directional diffusion on the thiophene backbone. The presence of the functional group in PCBM can be attributed to an increase in the diffusion coefficient by a factor of 1.5 to 2 as compared to C60. Interestingly low regioregularity of P3HTs reduced the diffusion and aggregation of PCBMs.}, number={42}, journal={SOFT MATTER}, publisher={Royal Society of Chemistry (RSC)}, author={Pani, Rakhee C. and Bond, Benjamin D. and Krishnan, Ganesh and Yingling, Yaroslava G.}, year={2013}, pages={10048–10055} }
 @article{modeling polymer/biopolymer and nanoparticle interactions: prediction of materials morphology_2013, url={https://publons.com/publon/28057478/}, journal={Abstracts of Papers of the American Chemical Society}, year={2013} }
 @article{sethaphong_haigler_kubicki_zimmer_bonetta_debolt_yingling_2013, title={Tertiary model of a plant cellulose synthase}, volume={110}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1301027110}, DOI={10.1073/pnas.1301027110}, abstractNote={
            A 3D atomistic model of a plant cellulose synthase (CESA) has remained elusive despite over forty years of experimental effort. Here, we report a computationally predicted 3D structure of 506 amino acids of cotton CESA within the cytosolic region. Comparison of the predicted plant CESA structure with the solved structure of a bacterial cellulose-synthesizing protein validates the overall fold of the modeled glycosyltransferase (GT) domain. The coaligned plant and bacterial GT domains share a six-stranded β-sheet, five α-helices, and conserved motifs similar to those required for catalysis in other GT-2 glycosyltransferases. Extending beyond the cross-kingdom similarities related to cellulose polymerization, the predicted structure of cotton CESA reveals that plant-specific modules (plant-conserved region and class-specific region) fold into distinct subdomains on the periphery of the catalytic region. Computational results support the importance of the plant-conserved region and/or class-specific region in CESA oligomerization to form the multimeric cellulose–synthesis complexes that are characteristic of plants. Relatively high sequence conservation between plant CESAs allowed mapping of known mutations and two previously undescribed mutations that perturb cellulose synthesis in
            Arabidopsis thaliana
            to their analogous positions in the modeled structure. Most of these mutation sites are near the predicted catalytic region, and the confluence of other mutation sites supports the existence of previously undefined functional nodes within the catalytic core of CESA. Overall, the predicted tertiary structure provides a platform for the biochemical engineering of plant CESAs.
          }, number={18}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Sethaphong, L. and Haigler, C. H. and Kubicki, J. D. and Zimmer, J. and Bonetta, D. and DeBolt, S. and Yingling, Y. G.}, year={2013}, month={Apr}, pages={7512–7517} }
 @article{singh_li_yingling_2013, title={Tuning DNA Bending with Charged Nanoparticles: Molecular Simulations}, volume={104}, url={https://publons.com/wos-op/publon/28057475/}, DOI={10.1016/j.bpj.2012.11.196}, abstractNote={The interactions between DNA and charged nanoparticles have transpired into applications from biosensors to DNA-templated metallization. However, the process of non-specific DNA binding with NP is difficult to characterize and is not well understood. We performed molecular dynamics simulations to understand the mechanisms of DNA-NP interactions and observed that the ligand chemistry on the NPs has contrasting impact on the helical structure of DNA. All atom simulations show that uncharged NPs with -CH3 and -NH2 ligand end groups can only bind to the minor groove of DNA through hydrophobic interactions and do not induce a DNA helical distortion. On the other hand, charged NPs (from +6 to +60) can bind to both major and minor grooves of DNA. Moreover, while highly charged NPs wrap the DNA tightly, weakly charged NP can partially denaturate the DNA helix through a collective clustering behavior. Overall, we observed that by tuning the ligand chemistry and its density of GNP we can control the binding modes and the structural mechanics of DNA.}, number={2}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Singh, Abhishek and Li, Nan and Yingling, Yaroslava G.}, year={2013}, month={Jan}, pages={29a} }
 @inproceedings{yi_thakur_sethaphong_yingling_2013, title={X3DBio2: A visual analysis tool for biomolecular structure comparison}, volume={8654}, ISSN={["1996-756X"]}, url={http://dx.doi.org/10.1117/12.2002626}, DOI={10.1117/12.2002626}, abstractNote={A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) biomolecular structures. Investigating these structure relationships is important not only for understanding of functional properties of biologically significant molecules, but also for development of new and improved materials based on naturally-occurring molecules. We developed a new visual analysis tool, X3DBio2, for 3D biomolecular structure comparison and analysis. The tool is designed for elucidation of structural effects of mutations in proteins and nucleic acids and for assessment of time dependent trajectories from molecular dynamics simulations. X3DBio2 is a freely downloadable open source software and provides tightly integrated features to perform many standard analysis and visual exploration tasks. We expect this tool can be applied to solve a variety of biological problems and illustrate the use of the tool on the example study of the differences and similarities between two proteins of the glycosyltransferase family 2 that synthesize polysaccharides oligomers. The size and conformational distances and retained core structural similarity of proteins SpsA to K4CP represent significant epochs in the evolution of inverting glycosyltransferases.}, booktitle={Visualization and Data Analysis 2013}, publisher={SPIE}, author={Yi, Hong and Thakur, Sidharth and Sethaphong, Latsavongsakda and Yingling, Yaroslava G.}, editor={Wong, Pak Chung and Kao, David L. and Hao, Ming C. and Chen, Chaomei and Healey, Christopher G.Editors}, year={2013}, month={Feb} }
 @article{effect of solvent on the interfacial properties between functionalized nanoparticles and polymers_2012, url={https://publons.com/wos-op/publon/28057488/}, journal={Abstracts of Papers of the American Chemical Society}, year={2012} }
 @article{effect of surface immobilization on the dna structure and its mechanical properties_2012, url={https://publons.com/wos-op/publon/28057502/}, journal={Abstracts of Papers of the American Chemical Society}, year={2012} }
 @article{railsback_singh_pearce_mcknight_collazo_sitar_yingling_melechko_2012, title={Gold Nanoparticles: Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation (Adv. Mater. 31/2012)}, volume={24}, ISSN={0935-9648}, url={http://dx.doi.org/10.1002/adma.201290188}, DOI={10.1002/adma.201290188}, abstractNote={On page 4261, A. V. Melechko, Y. G. Yingling, and co-workers show that weakly charged cationic nanoparticles cause structural changes including local denaturing and compaction to DNA under mild conditions. The foreground of the cover image shows molecular dynamics simulations of the collective action of weakly charged cationic nanoparticles, which results in DNA strand separation. In the background is an electrophoresis photograph in which a new band (lower left) appears upon addition of gold nanoparticles capped with a mixed monolayer containing cationic ligands.}, number={31}, journal={Advanced Materials}, publisher={Wiley}, author={Railsback, Justin G. and Singh, Abhishek and Pearce, Ryan C. and McKnight, Timothy E. and Collazo, Ramón and Sitar, Zlatko and Yingling, Yaroslava G. and Melechko, Anatoli V.}, year={2012}, month={Aug}, pages={4221–4221} }
 @article{interactions of gold nanoparticles with dna: interplay of sequence, ligands charge and polarity_2012, url={https://publons.com/wos-op/publon/28057480/}, DOI={10.1016/J.BPJ.2011.11.3474}, abstractNote={DNA template can trigger the self-assembly of metal or semiconductor nanoparticles into programmable molecular architectures. The performance of DNA-nanoparticle system strongly depends on the size and ligand chemistry of nanoparticles. We performed molecular dynamics simulations to investigate the effect of colloidal gold nanoparticle (GNP) ligands charge and polarity on the ability to bind DNA molecules. We tailored the surface of GNP by introducing different terminal functionality to thiolated ligands, such as hydrophobic, polar and charged groups. We found that uncharged GNPs and GNPs with cationic ligand charge density of less than 10% can only bind to the minor groove of DNA. Whereas GNPs with ligands charge density of higher than 10% can bind to major or minor groove. Binding to major groove result in significant distortion and wrapping of DNA around the GNP. The distortions of the DNA helical structure strongly depends on the ligand charge density. Also at higher nanoparticle concentration and low charge densities, the ligand hydrophobicity can disrupt the hydrogen bonding between base pairs of DNA strands and leads to unwinding of DNA helix. We observed that by tuning the cationic charge density and polarity of GNP we can control the binding modes and DNA structural modifications.}, journal={Biophysical Journal}, year={2012} }
 @inbook{pasquinelli_yingling_2012, place={New York}, title={Molecular dynamics simulations of nano-bio materials}, DOI={10.1007/978-90-481-9751-4_402}, booktitle={Encyclopedia of Nanotechnology}, publisher={Springer}, author={Pasquinelli, M.A. and Yingling, Y.G.}, editor={Bhushan, BharatEditor}, year={2012}, pages={1454–1463} }
 @article{pani_yingling_2012, title={Role of Solvent and Dendritic Architecture on the Redox Core Encapsulation}, volume={116}, ISSN={["1520-5215"]}, url={https://publons.com/publon/11561889/}, DOI={10.1021/jp304253g}, abstractNote={Dendrimers with redox cores can accept, donate, and/or store electrons and are used in nanoscale devices like artificial receptors, magnetic resonance imaging, sensors, light harvesting antennae, and electrical switches. However, the dendrimer molecular architectures can significantly alter the encapsulation of the redox core and charge transfer pathways, thereby changing the electron transfer rates. In this study, we used molecular dynamics simulations to investigate the role of solvent and peripheral groups on molecular structure and core encapsulation of iron-sulfur G2-benzyl ether dendrimers in polar and nonpolar solvent. We found that the dendrimer branches collapse in water and swell in chloroform. The presence of the long hydrophobic alkyl groups at the periphery deters the encapsulation of the core in water which may cause an increase in electron transfer rate. However, in chloroform, the dendrimer branches remain in the extended form, which leads to an increased radius of gyration. Our results suggest that peripheral alkyl chains in dendrimers cause steric hindrance, which prevents branches from back folding in chloroform solvent, but in water it reverses the trend. Overall, the presence of a hydrophobic interior and hydrophilic periphery in a dendrimer improves core encapsulation in water while hindering encapsulation in chloroform.}, number={28}, journal={JOURNAL OF PHYSICAL CHEMISTRY A}, publisher={American Chemical Society (ACS)}, author={Pani, Rakhee C. and Yingling, Yaroslava G.}, year={2012}, month={Jul}, pages={7593–7599} }
 @article{structure prediction of a cellulose synthase protein and the effect of mutations_2012, url={https://publons.com/wos-op/publon/28057479/}, DOI={10.1016/J.BPJ.2011.11.1379}, abstractNote={Cellulose synthases (CesAs) are the proteins responsible for the polymerization of cellulose from glucose. They are integral membrane proteins that contain multiple transmembrane helices and a cytoplasmic catalytic domain. Due to the fact that CesAs are found on the membrane and that it is difficult to crystallize such proteins, the structure of CesAs has not been determined and the exact enzymatic mechanism is unknown. We used a combination of protein structure prediction servers and molecular dynamics simulations to predict catalytic domain of cotton CesA. The globular catalytic region from this gene revealed to contain a stretch of beta sheets flanked by a UDP-glucose binding site. The predicted structure explains well the effect of point mutations that generally characterized by dwarfism, reduction in cellulose crystallinity, and reduced root elongation. Moreover, we predicted the overall position of CesA towards the membrane that may be linked to the extrusion of the cellulose from the catalytic region to the exterior of the cell. Supported as a part of the Center of Lignocellulose Structure and Formation under DOE Award DE-SC0001090.}, journal={Biophysical Journal}, year={2012} }
 @article{marlowe_singh_yingling_2012, title={The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study}, volume={32}, ISSN={["1873-0191"]}, url={https://publons.com/wos-op/publon/11561894/}, DOI={10.1016/j.msec.2012.07.044}, abstractNote={Understanding sequence dependent mechanical and structural properties of collagen fibrils is important for the development of artificial biomaterials for medical and nanotechnological applications. Moreover, point mutations are behind many collagen associated diseases, including Osteogenesis Imperfecta (OI). We conducted a combination of classical and steered atomistic molecular dynamics simulations to examine the effect of point mutations on structure and mechanical properties of short collagen fibrils which include mutations of glycine to alanine, aspartic acid, cysteine, and serine or mutations of hydroxyproline to arginine, asparagine, glutamine, and lysine. We found that all mutations disrupt structure and reduce strength of the collagen fibrils, which may affect the hierarchical packing of the fibrils. The glycine mutations were more detrimental to mechanical strength of the fibrils (WT > Ala > Ser > Cys > Asp) than that of hydroxyproline (WT > Arg > Gln > Asn > Lys). The clinical outcome for glycine mutations agrees well with the trend in reduction of fibril's tensile strength predicted by our simulations. Overall, our results suggest that the reduction in mechanical properties of collagen fibrils may be used to predict the clinical outcome of mutations.}, number={8}, journal={MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS}, publisher={Elsevier BV}, author={Marlowe, Ashley E. and Singh, Abhishek and Yingling, Yaroslava G.}, year={2012}, month={Dec}, pages={2583–2588} }
 @article{kim_pani_ha_koo_yingling_2012, title={The role of hydrogen bonding in water-mediated glucose solubility in ionic liquids}, volume={166}, ISSN={["1873-3166"]}, url={https://publons.com/wos-op/publon/11561884/}, DOI={10.1016/j.molliq.2011.11.008}, abstractNote={The restriction of low solubility of glucose in ionic liquids (IL) can be overcome by mixing an aqueous glucose solution into ILs. In this paper, the change in molecular interactions between glucoses in [Emim][TfO] system as a result of the presence of water molecules was explored using all-atoms molecular dynamics simulations. The water molecules initially located around glucose molecule are rapidly uptaken by anions and most of the water shell around glucose is replaced by anions. The presence of monodispersed water at low concentration leads to the increased mobility of the system components and higher solubility of glucose in water-mediated [Emim][TfO] than that in [Emim][TfO]. Our simulations show that water acts as a solubility enhancer which disrupts glucose–glucose interaction and enhances glucose–solvent (water and [TfO]−) interaction, resulting in higher glucose solubility. Hydrogen bonding network between glucose, water and [TfO]− molecules is a key driving force in the dissolution process of glucose in water-mediated ILs.}, journal={JOURNAL OF MOLECULAR LIQUIDS}, publisher={Elsevier BV}, author={Kim, Ho Shin and Pani, Rakhee and Ha, Sung Ho and Koo, Yoon-Mo and Yingling, Yaroslava G.}, year={2012}, month={Feb}, pages={25–30} }
 @article{tuning dna structure and compaction with gold nanoparticles_2012, url={https://publons.com/publon/28057484/}, journal={Abstracts of Papers of the American Chemical Society}, year={2012} }
 @article{railsback_singh_pearce_mcknight_collazo_sitar_yingling_melechko_2012, title={Weakly Charged Cationic Nanoparticles Induce DNA Bending and Strand Separation}, volume={24}, ISSN={["0935-9648"]}, url={https://publons.com/wos-op/publon/5454547/}, DOI={10.1002/adma.201104891}, abstractNote={Weakly charged cationic nanoparticles cause structural changes including local denaturing and compaction to DNA under mild conditions. The charged ligands bind to the phosphate backbone of DNA and the uncharged ligands penetrate the helix and disrupt base pairing. Mobility shifts in electrophoresis, molecular dynamics, and UV-vis spectrophotometry give clues to the details of the interactions.}, number={31}, journal={ADVANCED MATERIALS}, publisher={Wiley-Blackwell}, author={Railsback, Justin G. and Singh, Abhishek and Pearce, Ryan C. and McKnight, Timothy E. and Collazo, Ramon and Sitar, Zlatko and Yingling, Yaroslava G. and Melechko, Anatoli V.}, year={2012}, month={Aug}, pages={4261-+} }
 @article{yi_singh_yingling_2012, title={X3DBio1: A Visual Analysis Tool for Biomolecular Structure Exploration}, volume={8294}, ISSN={["1996-756X"]}, url={https://publons.com/publon/10869587/}, DOI={10.1117/12.906893}, abstractNote={Protein tertiary structure analysis provides valuable information on their biochemical functions. The structure-to-function 
relationship can be directly addressed through three dimensional (3D) biomolecular structure exploration and 
comparison. We present X3DBio1, a visual analysis tool for 3D biomolecular structure exploration, which allows for 
easy visual analysis of 2D intra-molecular contact map and 3D density exploration for protein, DNA, and RNA 
structures. A case study is also presented in this paper to illustrate the utility of the tool. X3DBio1 is open source and 
freely downloadable. We expect this tool can be applied to solve a variety of biological problems.}, journal={VISUALIZATION AND DATA ANALYSIS 2012}, publisher={SPIE}, author={Yi, Hong and Singh, Abhishek and Yingling, Yaroslava G.}, editor={Wong, Pak Chung and Kao, David L. and Hao, Ming C. and Chen, Chaomei and Kosara, Robert and Livingston, Mark A. and Park, Jinah and Roberts, IanEditors}, year={2012} }
 @article{characterization of osteogenesis imperfecta mutations in type i collagen: a molecular dynamics study_2011, url={https://publons.com/publon/28057491/}, DOI={10.1016/J.BPJ.2010.12.1029}, abstractNote={Osteogenesis Imperfecta is a disease characterized by too little collagen in the body, causing brittle bones, permanent disfigurement, and often death. Collagen, the most prevalent protein in the human body, could be used in tissue engineering if the mechanism of mutations is determined. To provide fundamental understanding of the molecular basis of this disease, extensive molecular dynamics simulations were conducted. A Glycine-Proline-Hydroxyproline tropocollagen molecule was used as a building block for a fibril that consists of seven tropocollagen strands. The central tropocollagen molecule was modified to include typical mutations present in the diseased collagen. Specifically, mutations of Glycine to Alanine, Aspartic Acid, Cysteine, and Serine and mutations of Hydroxyproline to Arginine, Asparagine, Glutamine, and Lysine were included in this study. We found that mutations disrupt hydration and the electrostatics pattern of the collagen fiber. Moreover, the fibril diameter increases as a result of mutations of both Glycine and Hydroxyproline amino acids. Steered molecular dynamics was used to determine the binding, shear, and tensile mechanical properties of the affected collagen fibrils. It was determined that the wild type tropocollagen molecule has better mechanical properties, which means that the point mutations weaken the tropocollagen. Our results indicate that the lysine mutation dramatically destabilized tropocollagen chemical and mechanical properties, which explains the high death rate related to this mutation.}, journal={Biophysical Journal}, year={2011} }
 @article{computational prediction of cellulose synthase protein structure_2011, url={https://publons.com/publon/28057492/}, DOI={10.1016/J.BPJ.2010.12.1334}, abstractNote={Cellose synthases (CesAs) are the proteins responsible for the polymerization of cellulose from glucose. They are transmembrane proteins that take their substrate from within the cytosol of the cell and extrude the product to the exterior. Due to the fact that they are found on the membrane and that it is difficult to crystallize such proteins, the structure of CesAs has not been determined. However, the ability of CesAs to form rather large complexes with each other has been observed under optical microscopy.}, journal={Biophysical Journal}, year={2011} }
 @article{singh_sethaphong_yingling_2011, title={Interactions of Cations with RNA Loop-Loop Complexes}, volume={101}, ISSN={["0006-3495"]}, url={https://publons.com/publon/5454556/}, DOI={10.1016/j.bpj.2011.06.033}, abstractNote={RNA loop-loop interactions are essential in many biological processes, including initiation of RNA folding into complex tertiary shapes, promotion of dimerization, and viral replication. In this article, we examine interactions of metal ions with five RNA loop-loop complexes of unique biological significance using explicit-solvent molecular-dynamics simulations. These simulations revealed the presence of solvent-accessible tunnels through the major groove of loop-loop interactions that attract and retain cations. Ion dynamics inside these loop-loop complexes were distinctly different from the dynamics of the counterion cloud surrounding RNA and depend on the number of basepairs between loops, purine sequence symmetry, and presence of unpaired nucleotides. The cationic uptake by kissing loops depends on the number of basepairs between loops. It is interesting that loop-loop complexes with similar functionality showed similarities in cation dynamics despite differences in sequence and loop size.}, number={3}, journal={BIOPHYSICAL JOURNAL}, publisher={Elsevier BV}, author={Singh, Abhishek and Sethaphong, Latsavongsakda and Yingling, Yaroslava G.}, year={2011}, month={Aug}, pages={727–735} }
 @article{molecular dynamics simulation studies on the hybridization events of surface immobilized dna_2011, url={https://publons.com/wos-op/publon/28057490/}, DOI={10.1016/J.BPJ.2010.12.635}, abstractNote={Surfaces functionalized with ssDNAs can be used to uniquely and reversibly bind complimentary DNAs. Such DNA modified materials are used in nanoscale supramolecular assembly, as optical, electrochemical and piezoelectric biosensors. Recognition and recombination pathways of DNA functionalized system are regulated by ssDNA hybridization. We conducted molecular dynamics simulation studies of DNA strands thiolated on the surface and in the presence of duplex and compared their dynamics to the dynamics of the DNA strands in solution. We investigated the optimal ssDNA length, effect of linker type and length to understand the effect of immobilization on subsequent DNA hybridization. Our results indicate that sensitivity and selectivity are directly dependent on the length and sequence of ssDNA strands. The persistence length, folding pathway and time are directly dependent on the hybridization and length of ssDNA. Minimum energy pathways were explored to understand the kinetics of ssDNA folding during the event of hybridization. Simulations suggest that restrained ssDNAs, compared to labile suspensions of free ssDNAs, are more capable of hybridization and hence DNA-based assembly. Our study helps understanding the science associated with the ssDNA hybridization and provides feedback to the associated experiments.}, journal={Biophysical Journal}, year={2011} }
 @article{nucleic acid helical conformation and sequence effects on cationic binding_2011, url={https://publons.com/publon/28057489/}, DOI={10.1016/J.BPJ.2010.12.631}, abstractNote={Conformation dependent molecular recognition has often been more associated with proteins which must be able to sense thousands of different molecules within a cell. Despite lacking as extensive a repertoire, nucleic acids also depend on nuances of structure with their environment to gain specificity for regulating genetic duplication, editing, expression, and suppression. In order to explore this topic further, molecular dynamics simulations of nucleic acid dupelexes of DNA and RNA were performed to examine subtleties with their inherent cation binding behavior. We discovered that despite small differences between chemical moieties of DNA and RNA, stark contrasts in counterion interactions occured. In the presence of either 0.1M Na+ or 0.1M K+, ion dynamics were not significantly altered for a given duplex. However, greater deviations were seen between duplexes of different helical forms. A final inquiry into the role of geometry leads us to conclude that helical geometry is responsible for a greater majority of cationic interactions and diffusive ion binding than can be explained exclusively by electrostatics resulting from chemical moieties alone.}, journal={Biophysical Journal}, year={2011} }
 @article{nucleic acid helical conformation and sequence effects on cationic binding_2011, url={https://publons.com/publon/28057504/}, journal={Abstracts of Papers of the American Chemical Society}, year={2011} }
 @article{singh_yingling_2011, title={Simulations of Stretching Single Stranded DNA}, volume={1301}, ISSN={0272-9172 1946-4274}, url={http://dx.doi.org/10.1557/opl.2011.569}, DOI={10.1557/opl.2011.569}, abstractNote={ABSTRACT}, journal={MRS Proceedings}, publisher={Cambridge University Press (CUP)}, author={Singh, Abhishek and Yingling, Yaroslava G.}, year={2011} }
 @article{singh_eksiri_yingling_2011, title={Theoretical Perspective on Properties of DNA-Functionalized Surfaces}, volume={49}, ISSN={["0887-6266"]}, url={https://publons.com/publon/5454555/}, DOI={10.1002/polb.22349}, abstractNote={Abstract}, number={22}, journal={JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS}, publisher={Wiley-Blackwell}, author={Singh, Abhishek and Eksiri, Hamed and Yingling, Yaroslava G.}, year={2011}, month={Nov}, pages={1563–1568} }
 @article{cationic sequence dependence in nucleic acid structures_2010, url={https://publons.com/wos-op/publon/28057495/}, DOI={10.1016/J.BPJ.2009.12.244}, abstractNote={Nucleic acids require cationic shielding to overcome inherent self-repulsive electrostatics. The cations that take this role are collectively referred to as screening ions and exchange with those in the bulk solution. Here molecular dynamics simulations were performed for a large variety of helical stems to investigate the behavior of cations around nucleic acids. We show that cations have specific affinity with high residence times for polypurine stretches. Polypurine tracts are implicated in viral physiology, ribosomal entry points, and as aptamers for divalent cations. Also the examination of HIV-1 TAR RNA core helix has shown that there is a sequence dependent cationic localization toward the purine-rich run within the TAR duplex. A region of high ion affinity agrees very well with the position of the X-ray determined divalent cations within a fragment from the HIV-1 TAR RNA. We show that a unique sequestration of ions within the core helix occurred independently of a nucleotide bulge and solely based on sequence of the helix. Our results suggest a high propensity toward purine dependent colocalization of one to two cations distinct from those performing phosphate backbone screening.}, journal={Biophysical Journal}, year={2010} }
 @article{singh_snyder_lee_johnston_caruso_yingling_2010, title={Effect of Oligonucleotide Length on the Assembly of DNA Materials: Molecular Dynamics Simulations of Layer-by-Layer DNA Films}, volume={26}, ISSN={["0743-7463"]}, url={https://publons.com/publon/5454528/}, DOI={10.1021/la102762t}, abstractNote={DNA strand length has been found to be an important factor in many DNA-based nanoscale systems. Here, we apply molecular dynamics simulations in a synergistic effort with layer-by-layer experimental data to understand the effect of DNA strand length on the assembly of DNA films. The results indicate that short (less than 10 bases) and long (more than 30 bases) single-stranded DNAs do not exhibit optimal film growth, and this can be associated with the limited accessibility of the bases on the surface due to formation of self-protected interactions that prevent efficient hybridization. Interestingly, the presence of a duplex attached to a single strand significantly alters the persistence length of the polyT strands. Our study suggests that restrained polyT, compared to labile suspensions of free polyT, are more capable of hybridization and hence DNA-based assembly.}, number={22}, journal={LANGMUIR}, publisher={American Chemical Society (ACS)}, author={Singh, Abhishek and Snyder, Stacy and Lee, Lillian and Johnston, Angus P. R. and Caruso, Frank and Yingling, Yaroslava G.}, year={2010}, month={Nov}, pages={17339–17347} }
 @article{singh_sethaphong_yingling_2010, title={Molecular Dynamics and Distribution of Ions in Kissing Loop}, volume={98}, url={https://publons.com/wos-op/publon/28057496/}, DOI={10.1016/j.bpj.2009.12.1439}, abstractNote={RNAs have hierarchical folding of structure which is endowed with abilities to catalyze biochemical reactions, support ligand binding, and proteins recognition. Ionic environment assist RNA to form stable higher order structures. In this study, molecular dynamics simulations were used to analyze the monovalent cationic distributions within RNA loop-loop complexes taken from separate viral species. We demonstrate that cations in show strong preferential distribution around kissing loop region however, ion dynamics do not indicate concrete evidence of specific binding. Cationic spatial localization was observed in a variety of kissing loops. Simulations results reveal the presence of electronegative channels that formed through the major groove of all RNA loop-loop helices and attract and retain the cations. Significant drop of diffusion coefficients was observed for ions inside ionic channels. Effect of sequence on the ion distribution was observed by carrying out mutational studies on the bacterial and viral kissing loops. Molecular dynamics results show strong correlation of ionic propensity regulated by sequence.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Singh, Abhishek and Sethaphong, Latsavongsakda and Yingling, Yaroslava G.}, year={2010}, month={Jan}, pages={264a} }
 @article{marlowe_yingling_2010, title={The Effect of Genetic Mutations on Structural and Mechanical Properties of Collagen: Molecular Dynamics Simulations}, volume={98}, url={https://publons.com/publon/28057505/}, DOI={10.1016/j.bpj.2009.12.3081}, abstractNote={Osteogenesis Imperfecta is a disease characterized by too little collagen in the body, causing brittle bones, permanent disfigurement, and often death. To provide fundamental understanding of the molecular basis of these diseases, extensive molecular dynamics simulations were conducted using the AMBER 10.0 suite. A Glycine-Proline-Hydroxyproline tropocollagen molecule was used as a building block for a fibril. The central tropocollagen molecule was later modified to corresponding mutations. Electrostatic measurements, hydration and ion patterns were determined, garnering an observation of a hydrophobic dipole. Our simulations indicate that the mutations significantly affect binding and mechanical properties of the collagen fibrils. Moreover, we predict that the high death rate related to lysine mutation can be explained by the increase in diameter and significant loss of mechanical properties in collagen fibril.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Marlowe, Ashley E. and Yingling, Yaroslava G.}, year={2010}, month={Jan}, pages={568a} }
 @article{sethaphong_singh_marlowe_yingling_2010, title={The Sequence of HIV-1 TAR RNA Helix Controls Cationic Distribution}, volume={114}, ISSN={["1932-7455"]}, url={https://publons.com/publon/5454532/}, DOI={10.1021/jp906147q}, abstractNote={Sequence dependency of metal ion aggregation around RNA structures is known to be involved in critical functions ranging from processes of molecular recognition to enzymatic chemistry. Ion interactions with an HIV-1 TAR RNA core helix were examined with explicit solvent molecular dynamics simulations. The results have shown that there is a sequence-dependent cationic localization toward the purine-rich run within the TAR helix and other purine-rich duplexes. The behavior is independent of ionic species or a presence of a bulge. A region of high ion affinity agrees very well with the position of the X-ray determined divalent cations within a fragment from the HIV-1 TAR RNA.}, number={12}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, publisher={American Chemical Society (ACS)}, author={Sethaphong, Latsavongsakda and Singh, Abhishek and Marlowe, Ashley E. and Yingling, Yaroslava G.}, year={2010}, month={Apr}, pages={5506–5512} }
 @article{semichaevsky_singh_yingling_2009, title={Computational Discovery Of The Electronegative Channel In RNA Loop-loop Interactions}, volume={96}, ISSN={0006-3495}, url={http://dx.doi.org/10.1016/j.bpj.2008.12.334}, DOI={10.1016/J.BPJ.2008.12.334}, abstractNote={The most common motifs found in nature and used in bionanotechnology are hairpin loops which consist of a helical part and a loop with unpaired residues. The unpaired residues in these elements can lead to further super-assembly of RNA structures via formation of the loop-loop interactions. These loop-loop interactions regulate biological functions in both prokaryotic and eukaryotic organisms such as gene expression in different viruses and are also actively used in bionanotechnology for self-assembly of RNA building blocks into novel nanostructures. It has been observed that the super-assembly of RNA directly depends on the presence and specific concentration of ions. In order to understand the role of ions in loop-loop formation and stability, we conducted a series of explicit solvent atomistic molecular dynamics simulations of distinct kissing loops elements taken from various organisms. In our simulations we varied the concentration of different ions (such as Na+, K+, Mg2+, and Cl−) from zero to 1M solution and examined known destabilizing mutations. We discovered that in most organisms the loop-loop assembly process depends on the presence of electronegative and hydration channel. The properties of this channel are independent of the concentration and the type of ions. The size of this channel and RNA sequence determines the stability. We also examined the formation of the channel during self-assembly and discovered the critical threshold for the channel formation.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Semichaevsky, Andrey and Singh, Abhishek and Yingling, Yaroslava G.}, year={2009}, month={Feb}, pages={83a} }
 @article{kasprzak_yingling_simon_shapiro_2009, title={Computational and Experimental Determination of the tRNA-like Structure in the 3′UTR of the Turnip Crinkle Virus (TCV)}, volume={96}, DOI={10.1016/j.bpj.2008.12.1003}, abstractNote={Turnip crinkle virus (TCV) is a plant virus, which is not capped or polyadenylated. Being one of the smallest plus strand viruses makes it a useful system for studying translation and transcription. Its 3′ proximal region, together with the 5′ UTR, enhances translation. We have employed our massively parallel genetic algorithm, MPGAfold, to predict the secondary structure of the 3′ terminal 195 nt region. Compensatory mutagenesis analyses in vivo and in-line structure probing confirmed the existence of the key predicted features (stem-loop motifs an one H-type pseudoknot) and added another pseudoknot to the model. Based on this information, we employed our 3D molecular modeling software, RNA2D3D, to predict the 3D structure of the core three hairpins and two pseudoknots. Our model structurally resembled a tRNA. Experimental data verified this structure, thus establishing the existence of the first internal tRNA-like structure discovered. Molecular dynamics simulations showed the stability of the entire structure as well as flexibility of some of its elements, in agreement with the in-line structure probing data. The model with its structure-implied functionality has led to further experimental determination of how the interconnected 3′ UTR sequence and structure elements participate in the processes of translation and replication. The structure element was found to bind the 60S ribosomal subunit, and thus act as a translation enhancer. This is the first such interaction in a 3′ UTR with the large subunit discovered. We also found that this tRNA-like element is a major part of a structural switch determining if the viral template is translated or replicated. Similar mechanisms may exist in other viruses and genomes, as the structural elements similar to the tRNA-like structure in the TCV have also been identified in several viruses.}, number={3}, journal={Biophysical Journal}, publisher={Elsevier BV}, author={Kasprzak, Wojciech K. and Yingling, Yaroslava G. and Simon, Anne E. and Shapiro, Bruce A.}, year={2009}, month={Feb}, pages={19a–20a} }
 @article{comp 215-explicit molecular dynamics simulations of kissing loop motif formed between tar-rna element of hiv-1 and aptamer_2008, url={https://publons.com/wos-op/publon/28057500/}, journal={Abstracts of Papers of the American Chemical Society}, year={2008} }
 @article{semichaevsky_marlowe_yingling_2008, title={Comparing Ion Distributions around RNA and DNA Helical and Loop-loop Motifs}, volume={1130}, ISSN={0272-9172 1946-4274}, url={http://dx.doi.org/10.1557/proc-1130-w05-05}, DOI={10.1557/proc-1130-w05-05}, abstractNote={Abstract}, journal={MRS Proceedings}, publisher={Cambridge University Press (CUP)}, author={Semichaevsky, Andrey V and Marlowe, Ashley E and Yingling, Yaroslava G}, year={2008} }
 @inbook{shapiro_bindewald_kasprzak_yingling_2008, title={Protocols for the In Silico Design of RNA Nanostructures}, ISBN={9781934115350 9781597454803}, ISSN={1064-3745 1940-6029}, url={http://dx.doi.org/10.1007/978-1-59745-480-3_7}, DOI={10.1007/978-1-59745-480-3_7}, abstractNote={Recent developments in the field of nanobiology have significantly expanded the possibilities for new modalities in the treatment of many diseases, including cancer. Ribonucleic acid (RNA) represents a relatively new molecular material for the development of these biologically oriented nanodevices. In addition, RNA nanobiology presents a relatively new approach for the development of RNA-based nanoparticles that can be used as crystallization substrates and scaffolds for RNA-based nanoarrays. Presented in this chapter are some methodological shaped-based protocols for the design of such RNA nanostructures. Included are descriptions and background materials describing protocols that use a database of three-dimensional RNA structure motifs; designed RNA secondary structure motifs; and a combination of the two approaches. An example is also given illustrating one of the protocols.}, booktitle={Methods in Molecular Biology™}, publisher={Humana Press}, author={Shapiro, Bruce A. and Bindewald, Eckart and Kasprzak, Wojciech and Yingling, Yaroslava}, year={2008}, pages={93–115} }
 @article{mccormack_yuan_yingling_kasprzak_zamora_shapiro_simon_2008, title={Structural Domains within the 3' Untranslated Region of Turnip Crinkle Virus}, volume={82}, ISSN={0022-538X}, url={http://dx.doi.org/10.1128/jvi.00416-08}, DOI={10.1128/JVI.00416-08}, abstractNote={ABSTRACT}, number={17}, journal={Journal of Virology}, publisher={American Society for Microbiology}, author={McCormack, J. C. and Yuan, X. and Yingling, Y. G. and Kasprzak, W. and Zamora, R. E. and Shapiro, B. A. and Simon, A. E.}, year={2008}, month={Jun}, pages={8706–8720} }
 @article{stupina_meskauskas_mccormack_yingling_shapiro_dinman_simon_2008, title={The 3' proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits}, volume={14}, ISSN={1355-8382}, url={http://dx.doi.org/10.1261/rna.1227808}, DOI={10.1261/RNA.1227808}, abstractNote={During cap-dependent translation of eukaryotic mRNAs, initiation factors interact with the 5′ cap to attract ribosomes. When animal viruses translate in a cap-independent fashion, ribosomes assemble upstream of initiation codons at internal ribosome entry sites (IRES). In contrast, many plant viral genomes do not contain 5′ ends with substantial IRES activity but instead have 3′ translational enhancers that function by an unknown mechanism. A 393-nucleotide (nt) region that includes the entire 3′ UTR of the Turnip crinkle virus (TCV) synergistically enhances translation of a reporter gene when associated with the TCV 5′ UTR. The major enhancer activity was mapped to an internal region of ∼140 nt that partially overlaps with a 100-nt structural domain previously predicted to adopt a form with some resemblance to a tRNA, according to a recent study by J.C. McCormack and colleagues. The T-shaped structure binds to 80S ribosomes and 60S ribosomal subunits, and binding is more efficient in the absence of surrounding sequences and in the presence of a pseudoknot that mimics the tRNA-acceptor stem. Untranslated TCV satellite RNA satC, which contains the TCV 3′ end and 6-nt differences in the region corresponding to the T-shaped element, does not detectably bind to 80S ribosomes and is not predicted to form a comparable structure. Binding of the TCV T-shaped element by 80S ribosomes was unaffected by salt-washing, reduced in the presence of AcPhe-tRNA, which binds to the P-site, and enhanced binding of Phe-tRNA to the ribosome A site. Mutations that reduced translation in vivo had similar effects on ribosome binding in vitro. This strong correlation suggests that ribosome entry in the 3′ UTR is a key function of the 3′ translational enhancer of TCV and that the T-shaped element contains some tRNA-like properties.}, number={11}, journal={RNA}, publisher={Cold Spring Harbor Laboratory}, author={Stupina, V. A. and Meskauskas, A. and McCormack, J. C. and Yingling, Y. G. and Shapiro, B. A. and Dinman, J. D. and Simon, A. E.}, year={2008}, month={Sep}, pages={2379–2393} }
 @article{shapiro_yingling_kasprzak_bindewald_2007, title={Bridging the gap in RNA structure prediction}, volume={17}, ISSN={0959-440X}, url={http://dx.doi.org/10.1016/j.sbi.2007.03.001}, DOI={10.1016/j.sbi.2007.03.001}, abstractNote={The field of RNA structure prediction has experienced significant advances in the past several years, thanks to the availability of new experimental data and improved computational methodologies. These methods determine RNA secondary structures and pseudoknots from sequence alignments, thermodynamics-based dynamic programming algorithms, genetic algorithms and combined approaches. Computational RNA three-dimensional modeling uses this information in conjunction with manual manipulation, constraint satisfaction methods, molecular mechanics and molecular dynamics. The ultimate goal of automatically producing RNA three-dimensional models from given secondary and tertiary structure data, however, is still not fully realized. Recent developments in the computational prediction of RNA structure have helped bridge the gap between RNA secondary structure prediction, including pseudoknots, and three-dimensional modeling of RNA.}, number={2}, journal={Current Opinion in Structural Biology}, publisher={Elsevier BV}, author={Shapiro, Bruce A and Yingling, Yaroslava G and Kasprzak, Wojciech and Bindewald, Eckart}, year={2007}, month={Apr}, pages={157–165} }
 @article{yingling_shapiro_2007, title={Computational Design of an RNA Hexagonal Nanoring and an RNA Nanotube}, volume={7}, ISSN={1530-6984 1530-6992}, url={http://dx.doi.org/10.1021/nl070984r}, DOI={10.1021/nl070984r}, abstractNote={The combination of computer modeling, RNA structure versatility, and siRNA function can be efficiently used to design an all-RNA nanoparticle capable of siRNA delivery. Here, we present a computational design of an RNA nanoring and a nanotube. An RNA nanoring consists of six simple linear building blocks that are assembled together via known noncovalent loop-loop contacts based on RNAI/RNAII inverse sequences. The helical sequences of the building blocks can include siRNAs for drug delivery.}, number={8}, journal={Nano Letters}, publisher={American Chemical Society (ACS)}, author={Yingling, Yaroslava G. and Shapiro, Bruce A.}, year={2007}, month={Aug}, pages={2328–2334} }
 @article{prasad_conforti_garrison_yingling_2007, title={Computational investigation into the mechanisms of UV ablation of poly(methyl methacrylate)}, volume={253}, ISSN={0169-4332}, url={http://dx.doi.org/10.1016/j.apsusc.2007.01.054}, DOI={10.1016/j.apsusc.2007.01.054}, abstractNote={Molecular dynamics simulations with an embedded Monte Carlo based reaction scheme were used to study UV ablation of poly(methyl methacrylate) (PMMA) at 157 nm. We discuss the onset of ablation, the formation and distribution of products in the plume and stress relaxation of the polymer matrix. Laser induced heating and bond-breaks are considered as ablation pathways. We show here that depending on the nature of energy deposition the evolution of ablation plume and yield composition can be quite different. If all of photon energy is converted to heat it can set off ablation via mechanical failure of the material in the heated region. Alternatively, if the photon energy goes towards breaking bonds first, it initiates chemical reactions, polymer unzipping and formation of gaseous products inside the substrate. The ejection of these molecules has a hollowing out effect on the substrate which can lead to ejection of larger chunks. No excessive pressure buildup due to creation of gaseous molecules or entrainment of larger polymer chunks is observed in this case.}, number={15}, journal={Applied Surface Science}, publisher={Elsevier BV}, author={Prasad, Manish and Conforti, Patrick F. and Garrison, Barbara J. and Yingling, Yaroslava G.}, year={2007}, month={May}, pages={6382–6385} }
 @article{conforti_yingling_garrison_2007, title={Computational studies of ultraviolet ablation of poly(methyl methacrylate)}, volume={59}, ISSN={1742-6588 1742-6596}, url={http://dx.doi.org/10.1088/1742-6596/59/1/068}, DOI={10.1088/1742-6596/59/1/068}, abstractNote={The results from our recent molecular dynamics and electronic calculations studies of the interaction of ultraviolet light with poly(methyl methacrylate) are discussed. Molecular dynamics simulations in the photochemical and photothermal regimes demonstrate the delayed onset of ablation due to the slow pressure relaxation in the polymeric material. Electronic structure calculations show the possible wavelength-dependent pathways of exothermic and endothermic release of gaseous and small molecules which could induce the ablation pocess. The results from our studies are the centerpiece for the current development of the mesoscale model of the light irradiation of polymeric material.}, journal={Journal of Physics: Conference Series}, publisher={IOP Publishing}, author={Conforti, P F and Yingling, Y G and Garrison, B J}, year={2007}, month={Apr}, pages={322–327} }
 @article{yingling_garrison_2007, title={Incorporation of chemical reactions into UV photochemical ablation of coarse-grained material}, volume={253}, ISSN={0169-4332}, url={http://dx.doi.org/10.1016/j.apsusc.2007.01.100}, DOI={10.1016/j.apsusc.2007.01.100}, abstractNote={A coarse-grained representation of material can significantly speed up molecular dynamics simulations. The difficulty arises when the simulations need to include chemical reactions. We have developed a methodology for including the effects of chemical reactions in coarse-grained molecular dynamics simulations, namely the Coarse-Grained Chemical Reactions Model (CGCRM). The model adopts physically and experimentally based parameters of a specific material, such as photochemical passways, the probabilities, and the exothermicities of chemical reactions. We have applied this approach to elucidate the effects of photochemical reactions on laser ablation of organic and polymeric materials. We find that the model provides a plausible description of the essential processes.}, number={15}, journal={Applied Surface Science}, publisher={Elsevier BV}, author={Yingling, Yaroslava G. and Garrison, Barbara J.}, year={2007}, month={May}, pages={6377–6381} }
 @article{bindewald_hayes_yingling_kasprzak_shapiro_2007, title={RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign}, volume={36}, ISSN={0305-1048 1362-4962}, url={http://dx.doi.org/10.1093/nar/gkm842}, DOI={10.1093/NAR/GKM842}, abstractNote={We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions. Our database provides a user-friendly way of searching structural elements by PDB code, structural classification, sequence, keyword or inter-helix angles. In addition, the structural data was subjected to energy minimization. This database is useful for analyzing RNA structures as well as for designing novel RNA structures on a nanoscale. The database can be accessed at: http://rnajunction.abcc.ncifcrf.gov/}, number={suppl_1}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Bindewald, Eckart and Hayes, Robert and Yingling, Yaroslava G. and Kasprzak, Wojciech and Shapiro, Bruce A.}, year={2007}, month={Oct}, pages={D392–D397} }
 @article{yingling_shapiro_2007, title={The Impact of Dyskeratosis Congenita Mutations on the Structure and Dynamics of the Human Telomerase RNA Pseudoknot Domain}, volume={24}, ISSN={0739-1102 1538-0254}, url={http://dx.doi.org/10.1080/07391102.2007.10531238}, DOI={10.1080/07391102.2007.10531238}, abstractNote={Abstract The pseudoknot domain is a functionally crucial part of telomerase RNA and influences the activity and stability of the ribonucleoprotein complex. Autosomal dominant dyskeratosis congenita (DKC) is an inherited disease that is linked to mutations in telomerase RNA and impairs telomerase function. In this paper, we present a computational prediction of the influence of two base DKC mutations on the structure, dynamics, and stability of the pseudoknot domain. We use molecular dynamics simulations, MM-GBSA free energy calculations, static analysis, and melting simulations analysis. Our results show that the DKC mutations stabilize the hairpin form and destabilize the pseudoknot form of telomerase RNA. Moreover, the P3 region of the predicted DKC-mutated pseudoknot structure is unstable and fails to form as a defined helical stem. We directly compare our predictions with experimental observations by calculating the enthalpy of folding and melting profiles for each structure. The enthalpy values are in very good agreement with values determined by thermal denaturation experiments. The melting simulations and simulations at elevated temperatures show the existence of an intermediate structure, which involves the formation of two UU base pairs observed in the hairpin form of the pseudoknot domain.}, number={4}, journal={Journal of Biomolecular Structure and Dynamics}, publisher={Informa UK Limited}, author={Yingling, Yaroslava G. and Shapiro, Bruce A.}, year={2007}, month={Feb}, pages={303–319} }
 @article{theoretical investigation of formation and properties of rna nanoparticles_2007, url={https://publons.com/publon/11561857/}, journal={Biophysical Journal}, year={2007} }
 @article{hastings_yingling_chirikjian_shapiro_2006, title={Structural and Dynamical Classification of RNA Single-Base Bulges for Nanostructure Design}, volume={3}, DOI={10.1166/jctn.2006.005}, number={1}, journal={Journal of Computational and Theoretical Nanoscience}, author={Hastings, W.A. and Yingling, Y.G. and Chirikjian, G.S. and Shapiro, B.A}, year={2006}, pages={63–77} }
 @article{structural and dynamical classification of rna single-base bulges for nanostructure design_2006, url={https://publons.com/wos-op/publon/5310277/}, DOI={10.1166/JCTN.2006.3049}, journal={Journal of Computational and Theoretical Nanoscience}, year={2006} }
 @article{yingling_shapiro_2006, title={The Prediction of the Wild-type Telomerase RNA Pseudoknot Structure and the Pivotal Role of a Bulge in its Formation}, volume={25}, url={https://publons.com/publon/11561861/}, DOI={10.1016/j.jmgm.2006.01.003}, abstractNote={In this study, the three-dimensional structure of the wild-type human telomerase RNA pseudoknot was predicted via molecular modeling. The wild-type pseudoknot structure is then compared to the recent NMR solution structure of the telomerase pseudoknot, which does not contain the U177 bulge. The removal of the bulge from the pseudoknot structure results in higher stability and significant reduction of activity of telomerase. We show that the effect of the bulge on the structure results in a significant transformation of the pseudoknot junction region where the starting base pairs are disrupted and unique triple base pairs are formed. We found that the formation of the junction region is greatly influenced by interactions of the U177 bulge with loop residues and rotation of residue A174. Moreover, this is the first study to our knowledge where a structure as complex as the pseudoknot has been solved by purely theoretical methods.}, number={2}, journal={Journal of Molecular Graphics and Modelling}, publisher={Elsevier BV}, author={Yingling, Y.G. and Shapiro, B.A.}, year={2006}, pages={261–274} }
 @article{yingling_garrison_2005, title={Coarse-Grained Model of the Interaction of Light with Polymeric Material: Onset of Ablation}, volume={109}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp0527711}, DOI={10.1021/jp0527711}, abstractNote={A coarse-grained model has been developed for molecular dynamics simulations of the interaction of light with polymeric materials. The photon energy can result in a vibrational excitation (photothermal process) or disruption of a chemical bond (photochemical process) in a polymer. In the latter case, the formation of active radial sites and the occurrence of chemical reactions have to be taken into consideration. The novel feature of this model is the incorporation of chemical reactions into the united atom approximate representation of the polymer structure, which permits the study of laser ablation, degradation, or the effect of various chemical reactions on large time and length scales. The chemical reactions are included in the model in a probabilistic manner as in the kinetic Monte Carlo method. This model adopts physically and experimentally known quantities such as enthalpies and probabilities of reactions. Properties such as laser irradiation time, laser fluence, and wavelength are explicitly included. Moreover, no chemically correct interaction potential is required to incorporate the effects of chemical reactions on the dynamics of the system after energy deposition. We find that the model provides a plausible description of the essential processes. The laser-induced pressure relaxation is the main mechanism responsible for the onset of polymer ablation. Since the pressure relaxation processes are slow, there is a delay in the onset of ablation after the end of the laser pulse as is observed experimentally. The vaporization processes are not efficient for material removal, and the effect is minimal for both photochemical and photothermal processes. A lower fluence is needed for the onset of ablation with photochemical processes than photothermal processes.}, number={34}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Yingling, Yaroslava G. and Garrison, Barbara J.}, year={2005}, month={Sep}, pages={16482–16489} }
 @article{yingling_shapiro_2005, title={Dynamic Behavior of the Telomerase RNA Hairpin Structure and its Relationship to Dyskeratosis Congenita}, volume={348}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/j.jmb.2005.02.015}, DOI={10.1016/j.jmb.2005.02.015}, abstractNote={In this paper, we present the results from a comprehensive study of nanosecond-scale implicit and explicit solvent molecular dynamics simulations of the wild-type telomerase RNA hairpin. The effects of various mutations on telomerase RNA dynamics are also investigated. Overall, we found that the human telomerase hairpin is a very flexible molecule. In particular, periodically the molecule exhibits dramatic structural fluctuations represented by the opening and closing of a non-canonical base-pair region. These structural deviations correspond to significant disruptions of the direct hydrogen bonding network in the helix, widening of the major groove of the hairpin structure, and causing several U and C nucleotides to protrude into the major groove from the helix permitting them to hydrogen bond with, for example, the P3 domain of the telomerase RNA. We suggest that these structural fluctuations expose a nucleation point for pseudoknot formation. We also found that mutations in the pentaloop and non-canonical region stabilize the hairpin. Moreover, our results show that the hairpin with dyskeratosis congenita mutations is more stable and less flexible than the wild-type hairpin due to base stacking in the pentaloop. The results from our molecular dynamics simulations are in agreement with experimental observations. In addition, they suggest a possible mechanism for pseudoknot formation based on the dynamics of the hairpin structure and also may explain the mutational aspects of dyskeratosis congenita.}, number={1}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Yingling, Yaroslava G. and Shapiro, Bruce A.}, year={2005}, month={Apr}, pages={27–42} }
 @article{yingling_garrison_2004, title={Coarse-Grained Chemical Reaction Model}, volume={108}, url={https://publons.com/publon/3366906/}, DOI={10.1021/jp035730i}, abstractNote={We have developed a methodology for including effects of chemical reactions in coarse-grained computer simulations such as those that use the united atom approximation. The new coarse-grained chemical reaction model (CGCRM) adopts the philosophy of kinetic Monte Carlo approaches and includes a probabilistic element to predicting when reactions occur, thus obviating the need for a chemically correct interaction potential. The CGCRM uses known chemical reactions along with their probabilities and exothermicities for a specific material in order to assess the effect of chemical reactions on a physical process of interest. The reaction event in the simulation is implemented by removing the reactant molecules from the simulation and replacing them with product molecules. The position of the product molecules is carefully adjusted to make sure that the total energy change of the system corresponds to the reaction exothermicity. The CGCR model has been applied to simulations of laser irradiation of chlorobenzene...}, number={6}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Yingling, Y.G. and Garrison, B.J.}, year={2004}, pages={1815–1821} }
 @article{yingling_conforti_garrison_2004, title={Theoretical investigation of laser pulse width dependence in a thermal confinement regime}, volume={79}, ISSN={0947-8396 1432-0630}, url={http://dx.doi.org/10.1007/s00339-004-2575-4}, DOI={10.1007/S00339-004-2575-4}, number={4-6}, journal={Applied Physics A}, publisher={Springer Science and Business Media LLC}, author={Yingling, Y.G. and Conforti, P.F. and Garrison, B.J.}, year={2004}, month={Sep}, pages={757–759} }
 @article{garrison_delcorte_zhigilei_itina_krantzman_yingling_mcquaw_smiley_winograd_2003, title={Big molecule ejection—SIMS vs. MALDI}, volume={203-204}, ISSN={0169-4332}, url={http://dx.doi.org/10.1016/s0169-4332(02)00661-x}, DOI={10.1016/S0169-4332(02)00661-X}, abstractNote={Using the results of molecular dynamics (MD) simulations, we discuss the question of whether the observed difference in mass limits in secondary ion mass spectrometry (SIMS) and matrix assisted laser desorption ionization (MALDI) are inherently related to the underlying physics of ejection or rather insufficient experimentation. The simulations show clearly that the physics of large molecule emission in SIMS and MALDI is very different. Consequently, we conclude that larger molecules can be ejected in MALDI than in SIMS.}, journal={Applied Surface Science}, publisher={Elsevier BV}, author={Garrison, B.J. and Delcorte, A. and Zhigilei, L.V. and Itina, T.E. and Krantzman, K.D. and Yingling, Y.G. and McQuaw, C.M. and Smiley, E.J. and Winograd, N.}, year={2003}, month={Jan}, pages={69–71} }
 @article{zhigilei_leveugle_garrison_yingling_zeifman_2003, title={Computer Simulations of Laser Ablation of Molecular Substrates}, volume={34}, DOI={10.1002/chin.200318285}, abstractNote={Abstract}, number={18}, journal={ChemInform}, publisher={Wiley-Blackwell}, author={Zhigilei, Leonid V. and Leveugle, Elodie and Garrison, Barbara J. and Yingling, Yaroslava G. and Zeifman, Michael I.}, year={2003}, month={May} }
 @article{zhigilei_leveugle_garrison_yingling_zeifman_2003, title={Computer Simulations of Laser Ablation of Molecular Substrates}, volume={103}, ISSN={0009-2665 1520-6890}, url={http://dx.doi.org/10.1021/cr010459r}, DOI={10.1021/cr010459r}, abstractNote={ion reactions by primary radicals, for example: C6H5Cl + •Cl f C6H4Cl• + HCl ∆H°rxn ) from -109.3 to -66.4 kJ/mol Radical-radical recombination reactions, for example: Cl• + •Cl f Cl2 ∆H°rxn ) -239.2 kJ/mol C6H5• + •C6H5 f C12H10 ∆H°rxn ) -564.4 to -478.9 kJ/mol Computer Simulations of Laser Ablation of Molecular Substrates Chemical Reviews, 2003, Vol. 103, No. 2 327}, number={2}, journal={Chemical Reviews}, publisher={American Chemical Society (ACS)}, author={Zhigilei, Leonid V. and Leveugle, Elodie and Garrison, Barbara J. and Yingling, Yaroslava G. and Zeifman, Michael I.}, year={2003}, month={Feb}, pages={321–348} }
 @article{zhigilei_yingling_itina_schoolcraft_garrison_2003, title={Molecular dynamics simulations of matrix-assisted laser desorption - connections to experiment}, volume={226}, url={https://publons.com/publon/3366925/}, DOI={10.1016/s1387-3806(02)00962-4}, abstractNote={The molecular dynamics (MD) simulation technique has been applied to investigate fundamental aspects of matrix-assisted laser desorption. In this paper, we focus on direct comparisons of the results from the simulations with experimental data and on establishing links between the measured or calculated parameters and the basic mechanisms of molecular ejection. The results on the fluence dependence of the ablation/desorption yields and composition of the ejected plume are compared with mass spectrometry and trapping plate experiments. Implications of the prediction of a fluence threshold for ablation are discussed. The strongly forward-peaked velocity and angular distributions of matrix and analyte molecules, predicted in the simulations, are related to the experimental distributions. The shapes and amplitudes of the acoustic waves transmitted from the absorption region through the irradiated sample are compared to recent photoacoustic measurements and related to the ejection mechanisms. The conformational changes during plume evolution and the ejection velocities of analyte molecules are studied and the directions for future investigations are discussed. Finally, we demonstrate that the MD simulation technique can be used to model other processes relevant to mass spectrometry applications, such as laser disintegration of aerosol particles and laser ablation in the presence of photochemical reactions.}, number={1}, journal={International Journal of Mass Spectrometry}, publisher={Elsevier BV}, author={Zhigilei, L.V. and Yingling, Y.G. and Itina, T.E. and Schoolcraft, T.A. and Garrison, B.J.}, year={2003}, pages={85–106} }
 @article{yingling_garrison_2003, title={Photochemical ablation of organic solids}, volume={202}, ISSN={0168-583X}, url={http://dx.doi.org/10.1016/s0168-583x(02)01855-4}, DOI={10.1016/s0168-583x(02)01855-4}, abstractNote={We have investigated by molecular dynamics simulations the ablation of material that is onset by photochemical processes. We compare this system with only photochemical processes to a system containing photochemical and photothermal processes. The simulations reveal that ablation by purely photochemical processes is accompanied by the ejection of relatively cold massive molecular clusters from the surface of the sample. The top of the plume exhibits high temperatures whereas the residual part of the sample is cold. The removal of the damaged material through big molecular cluster ejection is consistent with experimental observations of low heat damage of material.}, journal={Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms}, publisher={Elsevier BV}, author={Yingling, Yaroslava G. and Garrison, Barbara J.}, year={2003}, month={Apr}, pages={188–194} }
 @article{yingling_garrison_2002, title={Photochemical induced effects in material ejection in laser ablation}, volume={364}, ISSN={0009-2614}, url={http://dx.doi.org/10.1016/s0009-2614(02)01327-1}, DOI={10.1016/s0009-2614(02)01327-1}, abstractNote={Molecular dynamics simulations are used to investigate the effect of photochemical processes on molecular ejection mechanisms in laser ablation of organic solids. The presence of photochemical decomposition processes and subsequent chemical reactions changes the temporal and spatial energy deposition profile from pure photothermal ablation. A strong and broad acoustic wave propagation results and this pressure wave in conjunction with the temperature increase in the absorbing region causes the ejection of hot massive molecular clusters. These massive clusters later disintegrate in the plume into the smaller clusters and monomers due to ongoing chemical reactions.}, number={3-4}, journal={Chemical Physics Letters}, publisher={Elsevier BV}, author={Yingling, Yaroslava G and Garrison, Barbara J}, year={2002}, month={Oct}, pages={237–243} }
 @article{yingling_zhigilei_garrison_koubenakis_labrakis_georgiou_2001, title={Laser ablation of bicomponent systems: A probe of molecular ejection mechanisms}, volume={78}, ISSN={0003-6951 1077-3118}, url={http://dx.doi.org/10.1063/1.1353816}, DOI={10.1063/1.1353816}, abstractNote={A combined experimental and molecular dynamics simulation study of laser ablation of a model bicomponent system with solutes of different volatility provides a consistent picture of the mechanisms of material ejection. The comparison of the ejection yields shows that there are two distinct regimes of molecular ejection, desorption at low laser fluences, and a collective ejection of a volume of material or ablation at higher fluences. Ejection of volatile solutes dominates in the desorption regime, whereas nonvolatile solutes are ejected only in the ablation regime.}, number={11}, journal={Applied Physics Letters}, publisher={AIP Publishing}, author={Yingling, Yaroslava G. and Zhigilei, Leonid V. and Garrison, Barbara J. and Koubenakis, Antonis and Labrakis, John and Georgiou, Savas}, year={2001}, month={Mar}, pages={1631–1633} }
 @article{yingling_zhigilei_garrison_2001, title={Photochemical fragmentation processes in laser ablation of organic solids}, volume={180}, ISSN={0168-583X}, url={http://dx.doi.org/10.1016/s0168-583x(01)00414-1}, DOI={10.1016/s0168-583x(01)00414-1}, abstractNote={Studies on ultraviolet (UV) laser ablation of molecular solids have received considerable attention due to its proven and potential applications. Despite its active practical use the mechanisms of laser ablation are still being studied and debated. One crucial mechanistic discussion is on the relative importance of direct photodissociation of chemical bonds versus thermal ejection following rapid conversion of light energy into heat in the ablation processes. It is generally believed that these two processes are coupled in UV ablation resulting in difficulty in analyzing the relative importance of the two mechanisms. In the simulations presented here the breathing sphere model is enhanced allowing the photon absorption event to break a bond in the molecule and then have subsequent abstraction and recombination reactions. The initial system to model is chlorobenzene. Chlorobenzene is chosen because of simplicity of its fragmentation, entailing exclusively scission of the carbon–chlorine bond to yield phenyl and chlorine radicals. The results from the simulations allow us to study the photochemical events and their coupling with the thermal processes.}, number={1-4}, journal={Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms}, publisher={Elsevier BV}, author={Yingling, Yaroslava G. and Zhigilei, Leonid V. and Garrison, Barbara J.}, year={2001}, month={Jun}, pages={171–175} }
 @article{yingling_zhigilei_garrison_2001, title={The role of the photochemical fragmentation in laser ablation: a molecular dynamics study}, volume={145}, ISSN={1010-6030}, url={http://dx.doi.org/10.1016/s1010-6030(01)00580-9}, DOI={10.1016/s1010-6030(01)00580-9}, abstractNote={Despite numerous studies, the mechanistic understanding of the role of the photochemical processes and their coupling with the thermal processes in UV laser ablation is still far from being complete. In this work, the effects of the photochemical reactions on the laser ablation mechanism are delineated based on the results of molecular dynamics simulations of 248 nm laser irradiation of solid chlorobenzene. Photochemical reactions are found to release additional energy into the irradiated sample and decrease the average cohesive energy, therefore decreasing the value of the ablation threshold. The yield of emitted fragments becomes significant only above the ablation threshold. Below the ablation threshold only the most volatile photoproduct, HCl, is ejected in very small amounts, whereas the remainder of photoproducts are trapped inside the sample. Results of the simulations are in a good qualitative agreement with experimental data on the ejection of photoproducts in the laser ablation of chlorobenzene.}, number={3}, journal={Journal of Photochemistry and Photobiology A: Chemistry}, publisher={Elsevier BV}, author={Yingling, Yaroslava G. and Zhigilei, Leonid V. and Garrison, Barbara J.}, year={2001}, month={Dec}, pages={173–181} }
 @article{new polyvalent rna nanoparticle comprises rna motifs as building blocks, useful in a drug delivery composition for treating or preventing a disease or disorder, e.g. aids, alzheimer's disease, anemia, cancer, hypertension, or obesity, url={https://publons.com/publon/15543588/} }
 @article{new polyvalent rna nanoparticle, useful for treating or preventing a disease or disorder, e.g. adenoma, aging, aids, alopecia, alzheimer's disease, or anemia, url={https://publons.com/publon/15543587/} }