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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 …
Coarse-graining auto-encoders for molecular dynamics
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of
condensed-phase materials and, as a predictive tool, enable computational design of new …
condensed-phase materials and, as a predictive tool, enable computational design of new …
Advances in coarse-grained modeling of macromolecular complexes
Highlights•Coarse-grained models are reduced representations of all-atom models that aim
to retain the essential molecular aspects for the system of interest.•Coarse-grained …
to retain the essential molecular aspects for the system of interest.•Coarse-grained …
Statistically optimal force aggregation for coarse-graining molecular dynamics
Machine-learned coarse-grained (CG) models have the potential for simulating large
molecular complexes beyond what is possible with atomistic molecular dynamics. However …
molecular complexes beyond what is possible with atomistic molecular dynamics. However …
Utilizing machine learning to greatly expand the range and accuracy of bottom-up coarse-grained models through virtual particles
PG Sahrmann, TD Loose… - Journal of Chemical …, 2023 - ACS Publications
Coarse-grained (CG) models parametrized using atomistic reference data, ie,“bottom up”
CG models, have proven useful in the study of biomolecules and other soft matter. However …
CG models, have proven useful in the study of biomolecules and other soft matter. However …
Navigating protein landscapes with a machine-learned transferable coarse-grained model
NE Charron, F Musil, A Guljas, Y Chen… - ar**: Coarse-grained electronic property distributions using heteroscedastic Gaussian processes
JC Maier, NE Jackson - The Journal of Chemical Physics, 2022 - pubs.aip.org
We employ deep kernel learning electronic coarse-graining (DKL-ECG) with approximate
Gaussian processes as a flexible and scalable framework for learning heteroscedastic …
Gaussian processes as a flexible and scalable framework for learning heteroscedastic …
Adversarial-residual-coarse-graining: Applying machine learning theory to systematic molecular coarse-graining
We utilize connections between molecular coarse-graining (CG) approaches and implicit
generative models in machine learning to describe a new framework for systematic …
generative models in machine learning to describe a new framework for systematic …