@article{wang_wang_hall_2020, title={Development of a coarse-grained lipid model, LIME 2.0, for DSPE using multistate iterative Boltzmann inversion and discontinuous molecular dynamics simulations}, volume={521}, ISSN={["1879-0224"]}, DOI={10.1016/j.fluid.2020.112704}, abstractNote={We suggest an improved version of the intermediate resolution implicit solvent model for lipids, LIME, that was previously developed for use with discontinuous molecular dynamics (DMD) simulations. LIME gets its geometrical and energy parameters between bonded and nonbonded pairs of coarse-grained (CG) sites from atomistic simulations. The improved model, LIME 2.0, uses multiple square wells rather than the single square well used in original LIME to obtain intermolecular interactions that more faithfully mimic those from atomistic simulations. The multi-state iterative Boltzmann inversion (MS-IBI) scheme is used to determine the interaction parameters. This means that a single set of interaction parameters between coarse-grained sites can be used to represent the lipid bilayers at different temperatures. The physical properties of CG DSPE lipid bilayer are calculated using CG simulations and compared to atomistic simulations results to verify the improved model. The phase transition temperature of the lipid bilayer is measured accurately and the lipid translocation phenomenon, “flip-flop” is observed through CG simulation. These results suggest that CG parameterization using multiple square-wells and the MS-IBI scheme is well suited to the study of lipid bilayers across a range of temperatures with DMD simulations.}, journal={FLUID PHASE EQUILIBRIA}, author={Wang, Kye Won and Wang, Yiming and Hall, Carol K.}, year={2020}, month={Oct} }
 @article{wang_hall_2019, title={Characterising the throat diameter of through-pores in network structures using a percolation criterion}, volume={117}, ISSN={["1362-3028"]}, DOI={10.1080/00268976.2019.1654140}, abstractNote={We present a method for measuring the pore throat diameter of a simulated porous material. The pore throat diameter is the size of the narrowest pore that has both an entrance and an exit in a network structure. Knowledge of the pore throat diameter allows estimation of the size of the largest molecules that can travel through a network structure without interruption. In this method, a chain of virtual circles (in 2-dimensions) or spheres (in 3-dimensions) is constructed along a percolated path through the pores in a network. The diameter of the largest circle or sphere for which this is possible is the pore throat diameter. The method is applied to two 2-dimensional models (one where we know the pore throat diameter and one where we do not), and well predicts the pore throat diameters in each case. The pore throat diameter of a 3-dimensional DNA-mediated hydrogel model is also determined. This method is applicable to any porous structure for which molecular coordinate information is available. The ability to predict pore throat diameters in simulation could be useful for determining the size of molecules that can safely be administered by hydrogel drug delivery systems. GRAPHICAL ABSTRACT}, number={23-24}, journal={MOLECULAR PHYSICS}, author={Wang, Kye Won and Hall, Carol K.}, year={2019}, pages={3614–3622} }
 @article{wang_betancourt_hall_2018, title={Computational Study of DNA-Cross-Linked Hydrogel Formation for Drug Delivery Applications}, volume={51}, ISSN={["1520-5835"]}, DOI={10.1021/acs.macromol.8b01505}, abstractNote={We present the results of discontinuous molecular dynamics (DMD) simulations aimed at understanding the formation of DNA-mediated hydrogels and assessing their drug loading ability. Poly(ethylene glycol) (PEG) precursors of four and six arms that are covalently functionalized on all ends with oligonucleotides are cross-linked by a single oligonucleotide whose sequence is complementary to the oligonucleotide conjugated to the precursor. We show that the precursors with large molecular weight and many arms are advantageous in forming a three-dimensional percolated network. Analysis of the percolated networks shows that the pore diameter distribution becomes narrower as the precursor concentration, the number of arms, and the molecular weight increase. The pore throat diameter, the size of the largest molecule that can travel through the hydrogel networks without being trapped, is determined. The percolated network slows the movement of molecules inside the pores. Molecules larger than the pore throat diamet...}, number={23}, journal={MACROMOLECULES}, author={Wang, Kye Won and Betancourt, Tania and Hall, Carol K.}, year={2018}, month={Dec}, pages={9758–9768} }