Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

2014 ◽  
Vol 141 (7) ◽  
pp. 075101 ◽  
Author(s):  
Manami Nishizawa ◽  
Kazuhisa Nishizawa
Keyword(s):  
Potential Of Mean Force ◽  
The Self ◽  
Coarse Grained ◽  
Force Analysis ◽  
Self Association ◽  
Coarse Grained Simulations

The Role of Amino Acid Sequence in the Self-Association of Therapeutic Monoclonal Antibodies: Insights from Coarse-Grained Modeling

2013 ◽  
Vol 117 (5) ◽  
pp. 1269-1279 ◽  
Author(s):  
Anuj Chaudhri ◽  
Isidro E. Zarraga ◽  
Sandeep Yadav ◽  
Thomas W. Patapoff ◽  
Steven J. Shire ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
The Self ◽  
Coarse Grained ◽  
Self Association ◽  
Therapeutic Monoclonal Antibodies

Coarse-Grained Modeling of the Self-Association of Therapeutic Monoclonal Antibodies

2012 ◽  
Vol 116 (28) ◽  
pp. 8045-8057 ◽  
Author(s):  
Anuj Chaudhri ◽  
Isidro E. Zarraga ◽  
Tim J. Kamerzell ◽  
J. Paul Brandt ◽  
Thomas W. Patapoff ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
The Self ◽  
Coarse Grained ◽  
Self Association ◽  
Therapeutic Monoclonal Antibodies

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>

Coarse-grained simulation of the self-assembly of lipid vesicles concomitantly with novel block copolymers with multiple tails

Soft Matter ◽  
2021 ◽  
Author(s):  
Alexander Kantardjiev
Keyword(s):  
Molecular Dynamics ◽  
Block Copolymers ◽  
Self Assembly ◽  
Lipid Vesicles ◽  
The Self ◽  
Coarse Grained ◽  
Copolymer Concentration ◽  
Copolymer Structure ◽  
Coarse Grained Molecular Dynamics

We carried out a series of coarse-grained molecular dynamics liposome-copolymer simulations with varying extent of copolymer concentration in an attempt to understand the effect of copolymer structure and concentration on vesicle self-assembly and stability.

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

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