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 …
Perspective: Advances, challenges, and insight for predictive coarse-grained models
WG Noid - The Journal of Physical Chemistry B, 2023 - ACS Publications
By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …
computational and conceptual advantages for studying soft materials. In particular, bottom …
A review of advancements in coarse-grained molecular dynamics simulations
SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …
large and complex systems in an efficient and inexpensive manner due to its lowered …
Perspective: Coarse-grained models for biomolecular systems
WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …
grained (CG) models provide significant computational and conceptual advantages with …
Understanding dynamics in coarse-grained models. I. Universal excess entropy scaling relationship
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by
reducing the unnecessary degrees of freedom of the fine-grained (FG) system while …
reducing the unnecessary degrees of freedom of the fine-grained (FG) system while …
Many-body coarse-grained interactions using Gaussian approximation potentials
We introduce a computational framework that is able to describe general many-body coarse-
grained (CG) interactions of molecules and use it to model the free energy surface of …
grained (CG) interactions of molecules and use it to model the free energy surface of …
[HTML][HTML] On the representability problem and the physical meaning of coarse-grained models
In coarse-grained (CG) models where certain fine-grained (FG, ie, atomistic resolution)
observables are not directly represented, one can nonetheless identify indirect the CG …
observables are not directly represented, one can nonetheless identify indirect the CG …
[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 …
Developing and testing of lipid force fields with applications to modeling cellular membranes
The amphipathic nature of the lipid molecule (hydrophilic head and hydrophobic tails)
enables it to act as a barrier between fluids with various properties and to sustain an …
enables it to act as a barrier between fluids with various properties and to sustain an …
Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids
NJH Dunn, WG Noid - The Journal of chemical physics, 2015 - pubs.aip.org
The present work investigates the capability of bottom-up coarse-graining (CG) methods for
accurately modeling both structural and thermodynamic properties of all-atom (AA) models …
accurately modeling both structural and thermodynamic properties of all-atom (AA) models …