The structure of polyelectrolytes is highly sensitive to small changes in interactions between their monomers. In particular, interactions mediated by counterions play a significant role and are affected by both specific molecular effects and generic concentration effects. The ability of coarse-grained models to reproduce the structural properties of an atomic model is thus a challenging task. Our present study compares the ability of different kinds of coarse-grained models: (i) to reproduce the structure of an atomistic model of a polyelectrolyte (the sodium polyacrylate) and (ii) to reproduce the variations of this structure with the number of monomers and with the concentration of different species. We show that adequate scalings of the gyration radius of the polymer with the number of monomers and with the box size are only obtained, first, if the monomer charges and the counterions are explicitly described and, second, if an attractive Lennard-Jones contribution is added to the interaction between distant monomers. Also, we show that implicit ion models are relevant only to the high electrostatic screening regime.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.jpcb.9b09725 | DOI Listing |
J Phys Chem A
January 2025
Computer Modelling Group, 3710 33 St NW, Calgary, Alberta T2L 2M1, Canada.
Coarse-grained molecular dynamics simulation is widely accepted for assessment of a large complex biological system, but it may also lead to a misleading conclusion. The challenge is to simulate protein structural dynamics (such as folding-unfolding behavior) due to the lack of a necessary backbone flexibility. This study developed a standard coarse-grained model directly from the protein atomic structure and amino acid coarse-grained FF (such as MARTINI FF v2.
View Article and Find Full Text PDFCurr Opin Struct Biol
January 2025
Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA. Electronic address:
Machine-learning methods have gained significant attention in the computational chemistry community as a viable approach to molecular modeling and analysis. Recent successes in utilizing neural networks to learn atomistic force-fields which 'coarse-grain' electronic structure have inspired similar applications to the thermodynamic coarse-graining of chemical and biological systems. In this review, we discuss the current viability and challenges in using machine-learning methods to represent coarse-grained force-fields, as well as the utility of machine-learning in various aspects of coarse-grained modeling.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125.
Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. , for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of this metabolic flexibility, we developed a coarse-grained mathematical framework coupling redox chemistry with principles of cellular resource allocation.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Rio de Janeiro, Brazil.
Background: The apolipoprotein ε4 (ApoE4) allele is a major risk factor for sporadic Alzheimer's disease (AD) and was shown to promote amyloid-β (Aβ) accumulation and mediate pathophysiological processes in AD. Although the molecular interaction between Aβ and ApoE is acknowledged, the precise nature of this interaction remains unclear. This study aims to explore the biophysical and biochemical nature of the interaction between Aβ and ApoE in the ε3 and ε4 isoforms.
View Article and Find Full Text PDFSci Rep
January 2025
School of Railway Engineering, Hunan Technical College of Railway High-Speed, Hengyang, 421002, China.
Research on the evolutionary behavior of the particle breakage processes in coarse-grained soil under the action of train load is of practical significance for subgrade construction and maintenance. However, existing studies have not addressed the prediction of particle size distribution evolution. In this paper, the MTS loading system is used to simulate the dynamic train load effect on coarse-grained soil fillers.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!