Browsing by Author "Sethuraman, Vaidyanathan"
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Item Input and data for "Simulating precursor steps for fibril formation in methylcellulose solutions"(2019-05-08) Sethuraman, Vaidyanathan; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research GroupWe use coarse-grained molecular dynamics simulations to study the precursor steps for fibril formation in methylcellulose solutions. Simulations of ring stacking between two collapsed methylcellulose chains demonstrate the existence of a capture radius that is much larger than that predicted by polymer diffusion alone. When two rings are in very close proximity, they stack together to form a fibril precursor. Simulations of stacks of such rings suggest that this structure is metastable. In contrast, chains that are within the capture radius but not in close proximity, as well as for systems containing both ringlike and relaxed chains, fibril-like structures form via a distinctly different mechanism. Irrespective of their initial arrangement, the chains undergo two specific conformational changes: (i) a part of either a ring or a randomly coiled chain splays out and (ii) the splayed chain subsequently engulfs a nearby chain if it is within a certain capture distance. The latter results are consistent with recent experimental measurements of fibril formation by short methylcellulose chains, which suggests the formation of a twisted bundle.Item Simulation data for "Adsorption of Charge Sequence-Specific Polydisperse Polyelectrolytes"(2021-05-28) Sethuraman, Vaidyanathan; Zheng, David; Morse, David C; Dorfman, Kevin D; vsethura@umn.edu; Sethuraman, Vaidyanathan; Dorfman LabSimulation data and codes for reproducing the data in the paper titled "Adsorption of Charge Sequence-Specific Polydisperse Polyelectrolytes".Item Simulation data for "Influence of charge sequence on the adsorption of polyelectrolytes to oppositely-charged polyelectrolyte brushes"(2019-06-20) Sethuraman, Vaidyanathan; McGovern, Michael; Morse, David C; Dorfman, Kevin D; vsethura@umn.edu; Sethuraman, Vaidyanathan; Dorfman GroupWhen a solution of polyanionic chains is placed in contact with a polycationic brush, the polyanions adsorb into the brush. We investigate the influence of the charge sequences of the free and bound species on the thermodynamics of polyelectrolyte adsorption. As model systems, we consider free and brush polyelectrolytes with either block or alternating charge sequences, and study the adsorption process using coarse-grained Langevin dynamics with implicit solvent, explicit counterions, and excess salt. Free energy, internal energy, and entropy of adsorption are computed using umbrella sampling methods. When the number of polyanions exceed the number of polycations, the brush becomes overcharged. Free chains adsorb most strongly when both free and tethered chains have a block charge sequence, and most weakly when both species have an alternating sequence. Adsorption is stronger when the free polyanion has a block sequence and the tethered polycation is alternating than in the reverse case of an alternating free polymer and a tethered block copolymer. Sequence-dependent effects are shown to be largely energetic, rather than entropic, in origin.Item Supporting Data and Codes for Origins of the suppression of fibril formation in grafted methylcellulose solutions(2020-05-22) Sethuraman, Vaidyanathan; Dorfman, Kevin D; vsethura@umn.edu; Sethuraman, Vaidyanathan; Dorfman GroupThe data set consists of the codes used to generate and analyze the molecular dynamics trajectories along with the trajectory restart files and the files containing the data points for the figures in the article. It is released for the faithful reproduction of the data in the article.