Journal: Scientific Reports

Article Title: Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

doi: 10.1038/s41598-020-71820-2

Figure Lengend Snippet: Parameter space plots showing changes in the diffusion coefficient and bead velocities with respect to σ and γ (obeying the following conditions: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\upsigma }^{2}=2\upgamma {\mathrm{k}}_{\mathrm{B}}\mathrm{T}$$\end{document} σ 2 = 2 γ k B T ) as well as values of the exponent s (from the weight function of dissipative and random forces), at three values of the conservative repulsion force coefficient. Sub-plots show the diffusion coefficients in real units after time scale calibration based on the average velocities of DPD and coarse-grained MD water beads. The red horizontal line at the sub-plots shows the value of the diffusion coefficient of the target MD system.

Article Snippet: The diffusivity of the simulated system was calculated using the standard equation for the diffusion coefficient in molecular dynamics .

Techniques: Diffusion-based Assay