Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effective potentials

2013 ◽  
Vol 15 (20) ◽  
pp. 7701 ◽  
Author(s):  
Yong-Lei Wang ◽  
Alexander Lyubartsev ◽  
Zhong-Yuan Lu ◽  
Aatto Laaksonen
Keyword(s):  
Ionic Liquids ◽  
Coarse Grained ◽  
Effective Potentials ◽  
Coarse Grained Simulations

Coarse-Grained Simulations of Ionic Liquid Materials: From Monomeric Ionic Liquids to Ionic Liquid Crystals and Polymeric Ionic Liquids

2021 ◽  
Author(s):  
Yonglei Wang ◽  
Bin Li ◽  
Aatto Laaksonen
Keyword(s):  
Ionic Liquid ◽  
Ionic Liquids ◽  
Liquid Crystals ◽  
Physicochemical Properties ◽  
Coarse Grained ◽  
Environmental Applications ◽  
Polymeric Ionic Liquids ◽  
Heterogeneous Structures ◽  
Ionic Liquid Crystals ◽  
Coarse Grained Simulations

Ionic liquid (IL) materials are promising electrolytes with striking physicochemical properties for energy and environmental applications. Heterogeneous structures and transport quantities of monomeric and polymeric ILs are intrinsically intercorrelated and...

Grand-Reaction Method for Simulations of Ionization Equilibria and Ion Partitioning in a Broad Range of pH and Ionic Strength

2019 ◽  
Author(s):  
Jonas Landsgesell ◽  
Oleg Rud ◽  
Pascal Hebbeker ◽  
Raju Lunkad ◽  
Peter Košovan ◽  
...  
Keyword(s):  
Mean Field ◽  
Coarse Grained ◽  
Reactive System ◽  
Acid Base ◽  
Buffer Solution ◽  
Reaction Method ◽  
Ionization Equilibria ◽  
Coarse Grained Simulations ◽  
Ph Range ◽  
Weak Polyelectrolytes

We introduce the grand-reaction method for coarse-grained simulations of acid-base equilibria in a system coupled to a reservoir at a given pH and concentration of added salt. It can be viewed as an extension of the constant-pH method and the reaction ensemble, combining explicit simulations of reactions within the system, and grand-canonical exchange of particles with the reservoir. Unlike the previously introduced methods, the grand-reaction method is applicable to acid-base equilibria in the whole pH range because it avoids known artifacts. However, the method is more general, and can be used for simulations of any reactive system coupled to a reservoir of a known composition. To demonstrate the advantages of the grand-reaction method, we simulated a model system: A solution of weak polyelectrolytes in equilibrium with a buffer solution. By carefully accounting for the exchange of all constituents, the method ensures that all chemical potentials are equal in the system and in the multi-component reservoir. Thus, the grand-reaction method is able to predict non-monotonic swelling of weak polyelectrolytes as a function of pH, that has been known from mean-field predictions and from experiments but has never been observed in coarse-grained simulations. Finally, we outline possible extensions and further generalizations of the method, and provide a set of guidelines to enable safe usage of the method by a broad community of users.<br><br>

scholarly journals Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Laura Orellana ◽  
Ozge Yoluk ◽  
Oliver Carrillo ◽  
Modesto Orozco ◽  
Erik Lindahl
Keyword(s):  
Coarse Grained ◽  
Intermediate States ◽  
Coarse Grained Simulations

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA–star polymer conjugates: a coarse-grained molecular simulation study

Soft Matter ◽  
2017 ◽  
Vol 13 (38) ◽  
pp. 6770-6783 ◽  
Author(s):  
Joshua E. Condon ◽  
Arthi Jayaraman
Keyword(s):  
Molecular Simulation ◽  
Simulation Study ◽  
Coarse Grained ◽  
Star Polymer ◽  
Backbone Flexibility ◽  
Polymer Architecture ◽  
Polymer Conjugates ◽  
Coarse Grained Simulations

Using coarse-grained simulations, we study the effect of varying oligonucleic acid (ONA) backbone flexibility, ONA charge and star polymer architecture on structure and thermodynamics of ONA–star polymer conjugates assembly.

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