scholarly journals Tuning the selective permeability of polydisperse polymer networks

Soft Matter ◽  
2020 ◽  
Vol 16 (35) ◽  
pp. 8144-8154 ◽  
Author(s):  
Won Kyu Kim ◽  
Richard Chudoba ◽  
Sebastian Milster ◽  
Rafael Roa ◽  
Matej Kanduč ◽  
...  
Keyword(s):  
Computer Simulations ◽  
Polymer Networks ◽  
Model Membranes ◽  
Coarse Grained ◽  
Implicit Solvent ◽  
Selective Permeability ◽  
Polydisperse Polymer

We study the permeability and selectivity (‘permselectivity’) of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations.

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 Towards the realistic computer model of precipitation polymerization microgels

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vladimir Yu. Rudyak ◽  
Elena Yu. Kozhunova ◽  
Alexander V. Chertovich
Keyword(s):  
Computer Simulations ◽  
Precipitation Polymerization ◽  
Coarse Grained ◽  
Polymerization Process ◽  
New Horizons ◽  
Experimental Systems ◽  
Structure Factors ◽  
The Subject ◽  
First Time

Abstract In this paper we propose a new method of coarse-grained computer simulations of the microgel formation in course of free radical precipitation polymerization. For the first time, we simulate the precipitation polymerization process from a dilute solution of initial components to a final microgel particle with coarse grained molecular dynamics, and compare it to the experimental data. We expect that our simulation studies of PNIPA-like microgels will be able to elucidate the subject of nucleation and growth kinetics and to describe in detail the network topology and structure. Performed computer simulations help to determine the characteristic phases of the growth process and show the necessity of prolongated synthesis for the formation of stable microgel particles. We demonstrate the important role of dangling ends in microgels, which occupy as much as 50% of its molecular mass and have previously unattended influence on the swelling behavior. The verification of the model is made by the comparison of collapse curves and structure factors between simulated and experimental systems, and high quality matching is achieved. This work could help to open new horizons in studies that require the knowledge of detailed and realistic structures of the microgel networks.

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 Formation of adhesion domains in stressed and confined membranes

Soft Matter ◽  
2015 ◽  
Vol 11 (19) ◽  
pp. 3780-3785 ◽  
Author(s):  
Nadiv Dharan ◽  
Oded Farago
Keyword(s):  
Surface Tension ◽  
Lipid Bilayers ◽  
Computer Simulations ◽  
Molecular Model ◽  
Coarse Grained ◽  
Supported Lipid Bilayers

We use computer simulations of a coarse-grained molecular model of supported lipid bilayers to study the formation of adhesion domains in confined membranes, and in membranes subjected to a non-vanishing surface tension. When the membrane is subjected to compression, the condensation of the adhesion domains triggers membrane buckling.

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