Gaussian process regression for materials and molecules

VL Deringer, AP Bartók, N Bernstein… - Chemical …, 2021 - ACS Publications
We provide an introduction to Gaussian process regression (GPR) machine-learning
methods in computational materials science and chemistry. The focus of the present review …

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 …

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 …

Machine learning directed optimization of classical molecular modeling force fields

BJ Befort, RS DeFever, GM Tow… - Journal of Chemical …, 2021 - ACS Publications
Accurate force fields are necessary for predictive molecular simulations. However,
developing force fields that accurately reproduce experimental properties is challenging …

Exploring the role of microbial proteins in controlling environmental pollutants based on molecular simulation

J Wu, J Lv, L Zhao, R Zhao, T Gao, Q Xu, D Liu… - Science of the Total …, 2023 - Elsevier
Molecular simulation has been widely used to study microbial proteins' structural
composition and dynamic properties, such as volatility, flexibility, and stability at the …

[HTML][HTML] Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

AJ Bryer, JS Rey, JR Perilla - Nature Communications, 2023 - nature.com
Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular
research. For large assemblies, ultra coarse models are often knowledge-based, relying on …

Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in …

Y Ge, X Wang, Q Zhu, Y Yang, H Dong… - Journal of Chemical …, 2023 - ACS Publications
Precise regulation of the peptide self-assembly into ordered nanostructures with intriguing
properties has attracted intense attention. However, predicting peptide assembly at atomic …

[HTML][HTML] A machine learning enabled hybrid optimization framework for efficient coarse-graining of a model polymer

Z Shireen, H Weeratunge, A Menzel… - npj Computational …, 2022 - nature.com
This work presents a framework governing the development of an efficient, accurate, and
transferable coarse-grained (CG) model of a polyether material. The framework combines …

Accelerating computational discovery of porous solids through improved navigation of energy-structure-function maps

EO Pyzer-Knapp, L Chen, GM Day, AI Cooper - Science Advances, 2021 - science.org
While energy-structure-function (ESF) maps are a powerful new tool for in silico materials
design, the cost of acquiring an ESF map for many properties is too high for routine …

[HTML][HTML] Recent advances in particle-based simulation of surfactants

T Taddese, RL Anderson, DJ Bray… - Current opinion in colloid & …, 2020 - Elsevier
We review the recent literature on particle-based simulation of surfactants, focusing on key
methodological developments in the areas of surfactant self-assembly, micelle formation …