Bottom-up coarse-graining: Principles and perspectives
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
Coarse-graining entropy, forces, and structures
JF Rudzinski, WG Noid - The Journal of chemical physics, 2011 - pubs.aip.org
Coarse-grained (CG) models enable highly efficient simulations of complex processes that
cannot be effectively studied with more detailed models. CG models are often parameterized …
cannot be effectively studied with more detailed models. CG models are often parameterized …
OpenMSCG: A software tool for bottom-up coarse-graining
The “bottom-up” approach to coarse-graining, for building accurate and efficient
computational models to simulate large-scale and complex phenomena and processes, is …
computational models to simulate large-scale and complex phenomena and processes, is …
[HTML][HTML] The impact of resolution upon entropy and information in coarse-grained models
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously
facilitate numerical calculations and theoretical analyses of complex phenomena. However …
facilitate numerical calculations and theoretical analyses of complex phenomena. However …
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
Coarse-grained (CG) models provide a computationally efficient method for rapidly
investigating the long time-and length-scale processes that play a critical role in many …
investigating the long time-and length-scale processes that play a critical role in many …
The theory of ultra-coarse-graining. 1. General principles
Coarse-grained (CG) models provide a computationally efficient means to study
biomolecular and other soft matter processes involving large numbers of atoms correlated …
biomolecular and other soft matter processes involving large numbers of atoms correlated …
Coarse-graining methods for computational biology
MG Saunders, GA Voth - Annual review of biophysics, 2013 - annualreviews.org
Connecting the molecular world to biology requires understanding how molecular-scale
dynamics propagate upward in scale to define the function of biological structures. To …
dynamics propagate upward in scale to define the function of biological structures. To …
Temperature and phase transferable bottom-up coarse-grained models
Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the
structural correlations in atomistic simulations, the general use of bottom-up CG methods is …
structural correlations in atomistic simulations, the general use of bottom-up CG methods is …
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
The multiscale coarse-graining (MS-CG) method [S. Izvekov and GA Voth, J. Phys. Chem. B
109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to …
109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to …
Systematic methods for structurally consistent coarse-grained models
WG Noid - Biomolecular Simulations: Methods and Protocols, 2013 - Springer
This chapter provides a primer on theories for coarse-grained (CG) modeling and, in
particular, reviews several systematic methods for determining effective potentials for CG …
particular, reviews several systematic methods for determining effective potentials for CG …