Efficient amino acid conformer search with Bayesian optimization

L Fang, E Makkonen, M Todorovic… - Journal of chemical …, 2021 - ACS Publications
Finding low-energy molecular conformers is challenging due to the high dimensionality of
the search space and the computational cost of accurate quantum chemical methods for …

High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning

OT Unke, D Koner, S Patra, S Käser… - … Learning: Science and …, 2020 - iopscience.iop.org
An overview of computational methods to describe high-dimensional potential energy
surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy …

Generating transition states of isomerization reactions with deep learning

L Pattanaik, JB Ingraham, CA Grambow… - Physical Chemistry …, 2020 - pubs.rsc.org
Lack of quality data and difficulty generating these data hinder quantitative understanding of
reaction kinetics. Specifically, conventional methods to generate transition state structures …

Molecular force fields with gradient-domain machine learning (GDML): Comparison and synergies with classical force fields

HE Sauceda, M Gastegger, S Chmiela… - The Journal of …, 2020 - pubs.aip.org
Modern machine learning force fields (ML-FF) are able to yield energy and force predictions
at the accuracy of high-level ab initio methods, but at a much lower computational cost. On …

Dynamical strengthening of covalent and non-covalent molecular interactions by nuclear quantum effects at finite temperature

HE Sauceda, V Vassilev-Galindo, S Chmiela… - Nature …, 2021 - nature.com
Nuclear quantum effects (NQE) tend to generate delocalized molecular dynamics due to the
inclusion of the zero point energy and its coupling with the anharmonicities in interatomic …

Machine learning in nano-scale biomedical engineering

AAA Boulogeorgos, SE Trevlakis… - … , Biological and Multi …, 2020 - ieeexplore.ieee.org
Machine learning (ML) empowers biomedical systems with the capability to optimize their
performance through modeling of the available data extremely well, without using strong …

Dual-level training of Gaussian processes with physically inspired priors for geometry optimizations

C Teng, Y Wang, D Huang, K Martin… - Journal of Chemical …, 2022 - ACS Publications
Gaussian process (GP) regression has been recently developed as an effective method in
molecular geometry optimization. The prior mean function is one of the crucial parts of the …

Enhancing the Quality and Reliability of Machine Learning Interatomic Potentials through Better Reporting Practices

T Maxson, A Soyemi, BWJ Chen… - The Journal of Physical …, 2024 - ACS Publications
Recent developments in machine learning interatomic potentials (MLIPs) have empowered
even nonexperts in machine learning to train MLIPs for accelerating materials simulations …

High-fidelity molecular dynamics trajectory reconstruction with bi-directional neural networks

L Winkler, KR Müller, HE Sauceda - Machine Learning: Science …, 2022 - iopscience.iop.org
Molecular dynamics (MD) simulations are a cornerstone in science, enabling the
investigation of a system's thermodynamics all the way to analyzing intricate molecular …

Automatic identification of chemical moieties

J Lederer, M Gastegger, KT Schütt… - Physical Chemistry …, 2023 - pubs.rsc.org
In recent years, the prediction of quantum mechanical observables with machine learning
methods has become increasingly popular. Message-passing neural networks (MPNNs) …