@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{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{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{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{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{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{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} }
 @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{kwansa_de vita_freeman_2016, title={Tensile mechanical properties of collagen type I and its enzymatic crosslinks}, volume={214}, ISSN={["1873-4200"]}, DOI={10.1016/j.bpc.2016.04.001}, abstractNote={Collagen type I crosslink type and prevalence can be influenced by age, tissue type, and health; however, the role that crosslink chemical structure plays in mechanical behavior is not clear. Molecular dynamics simulations of ~65-nm-long microfibril units were used to predict how difunctional (deH-HLNL and HLKNL) and trifunctional (HHL and PYD) crosslinks respond to mechanical deformation. Low- and high-strain stress-strain regions were observed, corresponding to crosslink alignment. The high-strain elastic moduli were 37.7, 37.9, 39.9, and 42.4 GPa for the HLKNL, deH-HLNL, HHL, and PYD-crosslinked models, respectively. Bond dissociation analysis suggests that PYD is more brittle than HHL, with deH-HLNL and HLKNL being similarly ductile. These results agree with the tissues in which these crosslinks are found (e.g., deH-HLNL/HLKNL in developing tissues, HHL in mature skin, and PYD in mature bone). Chemical structure-function relationships identified for these crosslinks can aid the development of larger-scale models of collagenous tissues and materials.}, journal={BIOPHYSICAL CHEMISTRY}, author={Kwansa, Albert L. and De Vita, Raffaella and Freeman, Joseph W.}, year={2016}, pages={1–10} }
 @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} }