@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{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={The morphology of conjugated polymer thin films deposited by the resonant infrared matrix-assisted pulsed laser evaporation (RIR-MAPLE) process is related to the emulsion characteristics. However, a fundamental understanding of how...}, 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{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={Understanding protein structure and function relationships in cellulose synthase (CesA), including divergent isomers, is an important goal. Here, we report results from mutant complementation assays that tested the ability of sequence variants of AtCesA7, a secondary wall CesA of Arabidopsis thaliana, to rescue the collapsed vessels, short stems, and low cellulose content of the irx3-1 AtCesA7 null mutant. We tested a catalytic null mutation and seven missense or small domain changes in and near the AtCesA7 FTVTSK motif, which lies near the catalytic domain and may, analogously to bacterial CesA, exist within a substrate “gating loop.” A low-to-high gradient of rescue occurred, and even inactive AtCesA7 had a small positive effect on stem cellulose content but not stem elongation. Overall, secondary wall cellulose content and stem length were moderately correlated, but the results were consistent with threshold amounts of cellulose supporting particular developmental processes. Vibrational sum frequency generation microscopy allowed tissue-specific analysis of cellulose content in stem xylem and interfascicular fibers, revealing subtle differences between selected genotypes that correlated with the extent of rescue of the collapsing xylem phenotype. Similar tests on PpCesA5 from the moss Physcomitrium (formerly Physcomitrella) patens helped us to synergize the AtCesA7 results with prior results on AtCesA1 and PpCesA5. The cumulative results show that the FTVTxK region is important for the function of an angiosperm secondary wall CesA as well as widely divergent primary wall CesAs, while differences in complementation results between isomers may reflect functional differences that can be explored in further work.}, 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={Langmuir–Blodgett (LB) film deposition gives an opportunity to control the packing density and orientation of anisotropic nanoparticles at a monolayer level, allowing accurate characterization of their anisotropic material properties. The uniaxial deposition of rod-shaped cellulose nanocrystals (CNCs) over a macroscopically large area is achieved by aligning the long axis of CNCs on the LB trough with the direction of the maximum drag force within the meniscus during the vertical pulling of the substrate from the LB trough. On the uniaxially-aligned LB films, anisotropic linear and non-linear optical properties of CNCs are obtained using Mueller matrix spectroscopy and sum frequency generation spectroscopy, respectively, and explained with time-dependent density functional theory calculations. Also, the frictional anisotropy of the LB film is measured using atomic force microscopy and explained theoretically. The findings of this study will be valuable for preparation of anisotropic nanoparticle thin films with uniform arrangements and utilization of their anisotropic material properties.}, 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={Fluorine power! The synthesis of densely fluorinated monomers and their copolymerization into water-soluble 19F MRI agents is reported. These copolymers demonstrate improved 19F MRI sensitivity compared to state-of-the-art materials and enable non-invasive quantification of solution oxygenation.}, 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={Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant's hierarchical assembly, and establish a direct correlation between the protein's structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells' color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.}, 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/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} }