scholarly journals Minimal Coarse-Grained Modeling toward Implicit Solvent Simulation of Generic Bolaamphiphiles

2020 ◽  
Vol 124 (14) ◽  
pp. 2938-2949
Author(s):  
Somajit Dey ◽  
Jayashree Saha
Keyword(s):  
Coarse Grained ◽  
Implicit Solvent

scholarly journals ‘Martinizing’ the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

2018 ◽  
Vol 114 (3) ◽  
pp. 344a-345a
Author(s):  
Clarisse Gravina Ricci ◽  
Bo Li ◽  
Li-Tien Cheng ◽  
Joachim Dzubiella ◽  
J. Andrew McCammon
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Solvent Method

scholarly journals Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Astrid F. Brandner ◽  
Stepan Timr ◽  
Simone Melchionna ◽  
Philippe Derreumaux ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lattice Boltzmann ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Mesoscopic Scale ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Cellular Compartments ◽  
Biological Entities

Abstract In this work we present the coupling between Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzmann Molecular Dynamics (LBMD) simulation technique in order to include naturally hydrodynamic interactions in implicit solvent simulations of lipid systems. After validating the implementation of the model, we explored several systems where the action of a perturbing fluid plays an important role. Namely, we investigated the role of an external shear flow on the dynamics of a vesicle, the dynamics of substrate release under shear, and inquired the dynamics of proteins and substrates confined inside the core of a vesicle. Our methodology enables future exploration of a large variety of biological entities and processes involving lipid systems at the mesoscopic scale where hydrodynamics plays an essential role, e.g. by modulating the migration of proteins in the proximity of membranes, the dynamics of vesicle-based drug delivery systems, or, more generally, the behaviour of proteins in cellular compartments.

Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent

2009 ◽  
Vol 113 (1) ◽  
pp. 267-274 ◽  
Author(s):  
Yassmine Chebaro ◽  
Xiao Dong ◽  
Rozita Laghaei ◽  
Philippe Derreumaux ◽  
Normand Mousseau
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Coarse Grained ◽  
Replica Exchange ◽  
Implicit Solvent ◽  
Replica Exchange Molecular Dynamics ◽  
Dynamics Simulations

scholarly journals Computational studies of peptide-induced membrane pore formation

2017 ◽  
Vol 372 (1726) ◽  
pp. 20160219 ◽  
Author(s):  
Richard Lipkin ◽  
Themis Lazaridis
Keyword(s):  
Pore Formation ◽  
Coarse Grained ◽  
Future Research ◽  
Implicit Solvent ◽  
Computational Studies ◽  
Membrane Pore ◽  
Membrane Pores ◽  
Solvent Models ◽  
Future Research Directions ◽  
Implicit Solvent Models

A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs. This article is part of the themed issue ‘Membrane pores: from structure and assembly, to medicine and technology’.

scholarly journals “Martinizing” the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins

2017 ◽  
Vol 121 (27) ◽  
pp. 6538-6548 ◽  
Author(s):  
Clarisse G. Ricci ◽  
Bo Li ◽  
Li-Tien Cheng ◽  
Joachim Dzubiella ◽  
J. Andrew McCammon
Keyword(s):  
Free Energy ◽  
Solvation Free Energy ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Solvent Method

Implicit-solvent coarse-grained modeling for polymer solutions via Mori-Zwanzig formalism

Soft Matter ◽  
2019 ◽  
Vol 15 (38) ◽  
pp. 7567-7582 ◽  
Author(s):  
Shu Wang ◽  
Zhen Li ◽  
Wenxiao Pan
Keyword(s):  
Polymer Solutions ◽  
Dynamic Properties ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Bottom Up ◽  
System P

We present a bottom-up coarse-graining (CG) method to establish implicit-solvent CG modeling for polymers in solution, which conserves the dynamic properties of the reference microscopic system.

Sign in / Sign up

Export Citation Format

Share Document