@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"]}, DOI={10.1002/adts.202300411}, abstractNote={Abstract Single‐stranded DNA (ssDNA) plays a pivotal role in both nanotechnology and various biological processes. Many processes and applications can be better understood with enhanced structural characterization of ssDNA; however, the dynamic nature of the molecule makes accurate characterization with atomistic resolution extremely difficult. This study uses a method that integrates experimental small‐angle X‐ray scatter (SAXS) data and molecular modeling data using a genetic algorithm (GA) to predict an all‐atom conformational ensemble of ssDNA. The results of this study also validate the performance of various AMBER force fields and implicit solvent models for ssDNA. Overall, the results are able to determine the most accurate atomistic representation of poly‐Thymine (polyT) in solution to date that closely matches the experimental SAXS observations enabling a better understanding of the behavior of ssDNA in solution.}, journal={ADVANCED THEORY AND SIMULATIONS}, author={Oweida, Thomas J. and Yingling, Yaroslava G.}, year={2023}, month={Sep} }
 @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={Peptide–polymer amphiphiles (PPAs) are tunable hybrid materials that achieve complex assembly landscapes by combining the sequence-dependent properties of peptides with the structural diversity of polymers. Despite their promise as biomimetic materials, determining how polymer and peptide properties simultaneously affect PPA self-assembly remains challenging. We herein present a systematic study of PPA structure–assembly relationships. PPAs containing oligo(ethyl acrylate) and random-coil peptides were used to determine the role of oligomer molecular weight, dispersity, peptide length, and charge density on self-assembly. We observed that PPAs predominantly formed spheres rather than anisotropic particles. Oligomer molecular weight and peptide hydrophilicity dictated morphology, while dispersity and peptide charge affected particle size. These key benchmarks will facilitate the rational design of PPAs that expand the scope of biomimetic functionality within assembled soft materials.}, 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{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} }