@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{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{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={AbstractA comprehensive study is reported on the effect of salt concentration, polyelectrolyte block length, and polymer concentration on the morphology and structural properties of nanoaggregates self‐assembled from BAB single‐strand DNA (ssDNA) triblock polynucleotides in which A represents polyelectrolyte blocks and B represents hydrophobic neutral blocks. A morphological phase diagram above the gelation point is developed as a function of solvent ionic strength and polyelectrolyte block length utilizing an implicit solvent ionic strength method for dissipative particle dynamics simulations. As the solvent ionic strength increases, the self‐assembled DNA network structures shrinks considerably, leading to a morphological transition from a micellar network to worm‐like or hamburger‐shape aggregates. This study provides insight into the network morphology and its changes by calculating the aggregation number, number of hydrophobic cores, and percentage of bridge chains in the network. The simulation results are corroborated through cryogenic transmission electron microscopy on the example of the self‐assembly of ssDNA triblocks.}, 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{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{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{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{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{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{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{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} }