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 …
[HTML][HTML] Classical molecular dynamics
This issue of JCP highlights both developments in and applications of classical molecular
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …
simulation in 67 articles. A recent issue of JCP focused on electronic structure software …
[HTML][HTML] A microcanonical approach to temperature-transferable coarse-grained models using the relative entropy
Bottom-up coarse-graining methods provide systematic tools for creating simplified models
of molecular systems. However, coarse-grained (CG) models produced with such methods …
of molecular systems. However, coarse-grained (CG) models produced with such methods …
Departures from perfect isomorph behavior in Lennard-Jones fluids and solids
DM Heyes, D Dini, S Pieprzyk… - The Journal of Chemical …, 2023 - pubs.aip.org
Isomorphs are lines on a fluid or solid phase diagram along which the microstructure is
invariant on affine density scaling of the molecular coordinates. Only inverse power (IP) and …
invariant on affine density scaling of the molecular coordinates. Only inverse power (IP) and …
Accelerated calculation of configurational free energy using a combination of reverse Monte Carlo and neural network models: Adsorption isotherm for 2D square and …
AK Ball, S Rana, G Agrahari, A Chatterjee - Computer Physics …, 2023 - Elsevier
We demonstrate the application of artificial neural network (ANN) models to reverse Monte
Carlo based thermodynamic calculations. Adsorption isotherms are generated for 2D square …
Carlo based thermodynamic calculations. Adsorption isotherms are generated for 2D square …
Learning efficient, collective Monte Carlo moves with variational autoencoders
JI Monroe, VK Shen - Journal of Chemical Theory and …, 2022 - ACS Publications
Discovering meaningful collective variables for enhancing sampling, via applied biasing
potentials or tailored MC move sets, remains a major challenge within molecular simulation …
potentials or tailored MC move sets, remains a major challenge within molecular simulation …
Efficiency Comparison of Single-and Multiple-Macrostate Grand Canonical Ensemble Transition-Matrix Monte Carlo Simulations
Recent interest in parallelizing flat-histogram transition-matrix Monte Carlo simulations in the
grand canonical ensemble, due to its demonstrated effectiveness in studying phase …
grand canonical ensemble, due to its demonstrated effectiveness in studying phase …
The kernel-weighted local polynomial regression (KwLPR) approach: an efficient, novel tool for development of QSAR/QSAAR toxicity extrapolation models
A Gajewicz-Skretna, S Kar, M Piotrowska… - Journal of …, 2021 - Springer
The ability of accurate predictions of biological response (biological activity/property/toxicity)
of a given chemical makes the quantitative structure‐activity/property/toxicity relationship …
of a given chemical makes the quantitative structure‐activity/property/toxicity relationship …
Anisotropic coarse-grain Monte Carlo simulations of lysozyme, lactoferrin, and NISTmAb by precomputing atomistic models
We develop a multiscale coarse-grain model of the NIST Monoclonal Antibody Reference
Material 8671 (NISTmAb) to enable systematic computational investigations of high …
Material 8671 (NISTmAb) to enable systematic computational investigations of high …
A structure–dynamics relationship enables prediction of the water hydrogen bond exchange activation energy from experimental data
It has long been understood that the structural features of water are determined by hydrogen
bonding (H-bonding) and that the exchange of, or “jumps” between, H-bond partners …
bonding (H-bonding) and that the exchange of, or “jumps” between, H-bond partners …