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

2010 ◽  
pp. 49-82
Keyword(s):  
Case Studies ◽  
Coarse Graining ◽  
Multiscale Simulation ◽  
Hierarchical Systems

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

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

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

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

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.

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

scholarly journals Computational Multiscale Solvers for Continuum Approaches

Materials ◽  
2019 ◽  
Vol 12 (5) ◽  
pp. 691 ◽  
Author(s):  
Francisco Montero-Chacón ◽  
José Sanz-Herrera ◽  
Manuel Doblaré
Keyword(s):  
Additive Manufacturing ◽  
Multiscale Analysis ◽  
Coarse Graining ◽  
Multiscale Simulation ◽  
Localization Problem ◽  
Numerical Schemes ◽  
Proper Generalized Decomposition ◽  
Coarse Scale ◽  
Algorithmic Treatment ◽  
Technological Interest

Computational multiscale analyses are currently ubiquitous in science and technology. Different problems of interest—e.g., mechanical, fluid, thermal, or electromagnetic—involving a domain with two or more clearly distinguished spatial or temporal scales, are candidates to be solved by using this technique. Moreover, the predictable capability and potential of multiscale analysis may result in an interesting tool for the development of new concept materials, with desired macroscopic or apparent properties through the design of their microstructure, which is now even more possible with the combination of nanotechnology and additive manufacturing. Indeed, the information in terms of field variables at a finer scale is available by solving its associated localization problem. In this work, a review on the algorithmic treatment of multiscale analyses of several problems with a technological interest is presented. The paper collects both classical and modern techniques of multiscale simulation such as those based on the proper generalized decomposition (PGD) approach. Moreover, an overview of available software for the implementation of such numerical schemes is also carried out. The availability and usefulness of this technique in the design of complex microstructural systems are highlighted along the text. In this review, the fine, and hence the coarse scale, are associated with continuum variables so atomistic approaches and coarse-graining transfer techniques are out of the scope of this paper.

scholarly journals Multiscale Simulation of Multiprotein Assemblies: The Challenges of Ultra-Coarse-Graining

2013 ◽  
Vol 104 (2) ◽  
pp. 376a ◽  
Author(s):  
Gregory A. Voth
Keyword(s):  
Coarse Graining ◽  
Multiscale Simulation
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