Input and data for "Simulating precursor steps for fibril formation in methylcellulose solutions"

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Persistent link to this item

https://doi.org/10.13020/kkcn-8g83
https://hdl.handle.net/11299/202793

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Keywords

Methylcellulose

fibril formation

simulations

Collection period

2017-11-01
2019-03-20

Date completed

2019-04-24

Date updated

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Source information

Journal Title

Journal ISSN

Volume Title

Title

Input and data for "Simulating precursor steps for fibril formation in methylcellulose solutions"

Published Date

2019-05-08

Authors

Sethuraman, Vaidyanathan

Dorfman, Kevin D

Group

Dorfman Research Group

Author Contact

Dorfman, Kevin D
dorfman@umn.edu

Type

Dataset

Abstract

We 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.

Description

Each folder contains the data corresponding to the figures in the paper. Some of them contain the trajectory files (for visualization) or the .vmd files compatible with VMD software. The links to codes and video repository, a README file for understanding the usage of each codes in code repository (codes_usage/README.pdf), source files utilized for generating color maps (see inside folder Upload_data/Fig_8), and README files for each folder showing how to retrieve the data are present in the .tar file.

Referenced by

Vaidyanathan Sethuraman and Kevin D. Dorfman. (2019). Simulating precursor steps for fibril formation in methylcellulose solutions. Phys. Rev. Materials 3, 055601.
https://doi.org/10.1103/PhysRevMaterials.3.055601

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License

CC0 1.0 Universal
http://creativecommons.org/publicdomain/zero/1.0/

Publisher

Collections

Data Repository for U of M (DRUM)
Dorfman Group Research Data
MRSEC Research Data

Funding information

University of Minnesota Materials Science Research and Engineering Center Award No. DMR-1420013

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Previously Published Citation

Suggested citation

Sethuraman, Vaidyanathan; Dorfman, Kevin D. (2019). Input and data for "Simulating precursor steps for fibril formation in methylcellulose solutions". Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/kkcn-8g83.

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