Multiscale Simulation of Liquid Water Using a Four-to-One Mapping for Coarse-Graining

2013 ◽  
Vol 9 (11) ◽  
pp. 5168-5175 ◽  
Author(s):  
Anu Nagarajan ◽  
Christoph Junghans ◽  
Silvina Matysiak
Keyword(s):  
Liquid Water ◽  
Coarse Graining ◽  
Multiscale Simulation

Coarse-Graining Parameterization and Multiscale Simulation of Hierarchical Systems. Part I

2010 ◽  
pp. 13-34 ◽  
Author(s):  
Steve Cranford ◽  
Markus Buehler
Keyword(s):  
Coarse Graining ◽  
Multiscale Simulation ◽  
Hierarchical Systems

scholarly journals 1P-038 Coarse graining methodology for the multiscale simulation of complex biological systems(The 46th Annual Meeting of the Biophysical Society of Japan)

2008 ◽  
Vol 48 (supplement) ◽  
pp. S26
Author(s):  
Kei Moritsugu ◽  
Jeremy C. Smith ◽  
Akinori Kidera
Keyword(s):  
Annual Meeting ◽  
Biological Systems ◽  
Coarse Graining ◽  
Multiscale Simulation ◽  
Biophysical Society

Coarse-Graining Parameterization and Multiscale Simulation of Hierarchical Systems. Part II

2010 ◽  
pp. 35-68
Author(s):  
Steve Cranford ◽  
Markus Buehler
Keyword(s):  
Coarse Graining ◽  
Multiscale Simulation ◽  
Hierarchical Systems

Systematic Coarse Graining of Biomolecular and Soft-Matter Systems

MRS Bulletin ◽  
2007 ◽  
Vol 32 (11) ◽  
pp. 929-934 ◽  
Author(s):  
Gary S. Ayton ◽  
Will G. Noid ◽  
Gregory A. Voth
Keyword(s):  
High Resolution ◽  
Soft Matter ◽  
Coarse Graining ◽  
Multiscale Simulation ◽  
Atomic Scale ◽  
Coarse Grained ◽  
Statistical Mechanical ◽  
Transfer Of Information ◽  
Very High

AbstractCoarse-grained modeling is a key component in the field of multiscale simulation. Many biomolecular and otherwise complex systems require the characterization of phenomena over multiple length and time scales in order to fully resolve and understand their behavior. These different scales range from atomic to near macroscopic dimensions, and they are generally not independent of one another, but instead coupled. That is, phenomena occurring at atomic length scales have an effect at macroscopic dimensions and vice versa. Systematic transfer of information between these different scales represents a core challenge in the field of multiscale simulation. Coarse-grained modeling works at an intermediate resolution that can bridge the very high resolution (atomic) scale to the very low resolution (macroscopic) scale. As such, a significant challenge is the development of a systematic methodology whereby coarse-grained models can be derived from their high-resolution atomistic-scale counterpart. Here, a systematic theoretical and computational methodology will be described for developing coarse-grained representations of biomolecular and other soft-matter systems. At the heart of the methodology is a variational statistical mechanical algorithm that uses forcematching of atomistic molecular dynamics data to a coarse-grained representation. A theoretical analysis of the coarse-graining methodology will be presented, along with illustrative applications to membranes, peptides, and carbohydrates.

Multiscale Polarizable Coarse-graining Water Models on Cluster-level Electrostatic Dipoles

2021 ◽  
Author(s):  
Min Li ◽  
John Z.H. Zhang
Keyword(s):  
Force Field ◽  
Liquid Water ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Water Model ◽  
Biological Processes ◽  
Water Models ◽  
Cluster Level

The development of coarse-grained (CG) water model is increasingly important in CG studies of biological processes. In this work, we developed a generic CG force field of liquid water on...

scholarly journals Coarse Graining Methodology for the Multiscale Simulation of Complex Biological Systems

2009 ◽  
Vol 96 (3) ◽  
pp. 404a ◽  
Author(s):  
Kei Moritsugu ◽  
Jeremy C. Smith ◽  
Akinori Kidera
Keyword(s):  
Biological Systems ◽  
Coarse Graining ◽  
Multiscale Simulation

Ultra-coarse-graining modeling of liquid water

2021 ◽  
Vol 154 (22) ◽  
pp. 224506
Author(s):  
Min Li ◽  
WenCai Lu ◽  
John ZengHui Zhang
Keyword(s):  
Liquid Water ◽  
Coarse Graining
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