@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{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{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{kim_farmer_yingling_2017, title={Effect of graphene oxidation rate on adsorption of poly-thymine single stranded DNA}, volume={4}, number={8}, journal={Advanced Materials Interfaces}, author={Kim, H. S. and Farmer, B. L. and Yingling, Y. G.}, year={2017} }
 @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{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{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{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{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} }