scholarly journals Correction: Implicit-solvent coarse-grained modeling for polymer solutions via Mori–Zwanzig formalism

Soft Matter ◽  
2019 ◽  
Vol 15 (38) ◽  
pp. 7733-7733 ◽  
Author(s):  
Shu Wang ◽  
Zhen Li ◽  
Wenxiao Pan
Keyword(s):  
Soft Matter ◽  
Polymer Solutions ◽  
Coarse Grained ◽  
Implicit Solvent

Correction for ‘Implicit-solvent coarse-grained modeling for polymer solutions via Mori–Zwanzig formalism’ by Shu Wang et al., Soft Matter, 2019, DOI: 10.1039/c9sm01211g.

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.

Introduction to molecular simulations in soft matter

2017 ◽  
Author(s):  
J.-L. Barrat ◽  
J. J. de Pablo
Keyword(s):  
Phase Space ◽  
Numerical Methods ◽  
Theoretical Basis ◽  
Soft Matter ◽  
Relevant Literature ◽  
Coarse Grained ◽  
Soft Interfaces ◽  
Molecular Scale ◽  
Soft Matter Physics ◽  
The Continuum

We describe the main features of the coarse-grained models that are typically useful in modelling soft interfaces, from force fields to the continuum descriptions involving density fields. We explain the theoretical basis of the main numerical methods that are used to explore the phase space associated with these models. Finally, three recent examples, illustrating the spirit in which relatively simple simulations can contribute to solving pending problems in soft matter physics, are briefly described. Clearly, a short series of lectures can offer, at best, a biased and restricted view of the available approaches. Our aim here will be to provide the reader with such an overview, with a focus on methods and descriptions that ‘bridge the scale’ between the molecular scale and the continuum or quasi-continuum one. The objective to present a guide to the relevant literature—which has now to a large extent appeared in the form of textbooks.

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
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