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 …
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
An overview of computational methods to describe high-dimensional potential energy
surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy …
surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy …
Generating transition states of isomerization reactions with deep learning
Lack of quality data and difficulty generating these data hinder quantitative understanding of
reaction kinetics. Specifically, conventional methods to generate transition state structures …
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
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 …
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
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 …
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 …
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
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 …
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
Recent developments in machine learning interatomic potentials (MLIPs) have empowered
even nonexperts in machine learning to train MLIPs for accelerating materials simulations …
even nonexperts in machine learning to train MLIPs for accelerating materials simulations …
High-fidelity molecular dynamics trajectory reconstruction with bi-directional neural networks
Molecular dynamics (MD) simulations are a cornerstone in science, enabling the
investigation of a system's thermodynamics all the way to analyzing intricate molecular …
investigation of a system's thermodynamics all the way to analyzing intricate molecular …
Automatic identification of chemical moieties
In recent years, the prediction of quantum mechanical observables with machine learning
methods has become increasingly popular. Message-passing neural networks (MPNNs) …
methods has become increasingly popular. Message-passing neural networks (MPNNs) …