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The unprecedented amount of data generated from experiments, field observations, and large-scale numerical simulations at a wide range of spatio-temporal scales have enabled the rapid advancement of data-driven and especially deep learning…

Computational Physics · Physics 2024-06-19 Suraj Pawar , Omer San , Aditya Nair , Adil Rasheed , Trond Kvamsdal

Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for…

Chemical Physics · Physics 2021-03-16 Michael Gastegger , Jörg Behler , Philipp Marquetand

Hybrid particle-field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. Here, we introduce a…

Computational Physics · Physics 2020-07-06 Sigbjørn Løland Bore , Michele Cascella

Coarse-grained (CG) models provide an effective route to reducing the complexity of molecular simulations (MD), but conventional approaches depend heavily on long all-atom MD trajectories to adequately sample configurational space. This…

Chemical Physics · Physics 2025-10-28 Maximilian Stupp , P. S. Koutsourelakis

Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…

Chemical Physics · Physics 2025-06-03 Ademola Soyemi , Khagendra Baral , Tibor Szilvasi

State-of-the-art AI deep potentials provide ab initio-quality results, but at a fraction of the computational cost of first-principles quantum mechanical calculations, such as density functional theory. In this work, we bring AI deep…

Distributed, Parallel, and Cluster Computing · Computer Science 2026-02-03 Andong Hu , Luca Pennati , Stefano Markidis , Ivy Peng

Diffusion models provide expressive priors for forecasting trajectories of dynamical systems, but are typically unreliable in the sparse data regime. Physics-informed machine learning (PIML) improves reliability in such settings; however,…

Machine Learning · Computer Science 2026-01-30 Kaiyuan Tan , Kendra Givens , Peilun Li , Thomas Beckers

We describe how the fast quasi-centroid molecular dynamics (f-QCMD) method can be applied to condensed phase systems by approximating the quasi-centroid potential of mean force as a sum of inter- and intra-molecular corrections to the…

Chemical Physics · Physics 2023-10-20 Joseph E. Lawrence , Annina Z. Lieberherr , Theo Fletcher , David E. Manolopoulos

In molecular simulations, neural network force fields aim at achieving \emph{ab initio} accuracy with reduced computational cost. This work introduces enhancements to the Deep Potential network architecture, integrating a message-passing…

Computational Physics · Physics 2024-04-09 Ruiqi Gao , Yifan Li , Roberto Car

This work introduces a novel deep learning-based architecture, termed the Deep Belief Markov Model (DBMM), which provides efficient, model-formulation agnostic inference in Partially Observable Markov Decision Process (POMDP) problems. The…

Machine Learning · Computer Science 2025-03-18 Giacomo Arcieri , Konstantinos G. Papakonstantinou , Daniel Straub , Eleni Chatzi

Predictions of hydrologic variables across the entire water cycle have significant value for water resource management as well as downstream applications such as ecosystem and water quality modeling. Recently, purely data-driven deep…

Machine Learning · Computer Science 2023-01-11 Dapeng Feng , Jiangtao Liu , Kathryn Lawson , Chaopeng Shen

We introduce an unsupervised clustering algorithm to improve training efficiency and accuracy in predicting energies using molecular-orbital-based machine learning (MOB-ML). This work determines clusters via the Gaussian mixture model (GMM)…

Chemical Physics · Physics 2023-03-28 Lixue Cheng , Jiace Sun , Thomas F. Miller

Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…

Computational Physics · Physics 2021-01-11 Zun Wang , Chong Wang , Sibo Zhao , Shiqiao Du , Yong Xu , Bing-Lin Gu , Wenhui Duan

Physiologically Based Pharmacokinetic (PBPK) modeling is a cornerstone of model-informed drug development (MIDD), providing a mechanistic framework to predict drug absorption, distribution, metabolism, and excretion (ADME). Despite its…

Machine Learning · Computer Science 2026-02-24 Shunqi Liu , Han Qiu , Tong Wang

Modeling the time-dependent evolution of electron density is essential for understanding quantum mechanical behaviors of condensed matter and enabling predictive simulations in spectroscopy, photochemistry, and ultrafast science. Yet, while…

Computational Physics · Physics 2025-09-03 Yuan Chiang , Youngsoo Choi , Daniel Osei-Kuffuor

We present an investigation into data selection methods for the efficient sampling of configuration space as applied to the development of inter-atomic potentials for scale bridging in molecular dynamics (MD) simulations. This investigation…

Computational Physics · Physics 2021-08-04 Jan Finkbeiner , Samuel Tovey , Christian Holm

We present a benchmark designed to evaluate the predictive capabilities of universal machine learning interatomic potentials across systems of varying dimensionality. Specifically, our benchmark tests zero- (molecules, atomic clusters,…

Materials Science · Physics 2025-08-22 Giulio Benedini , Antoine Loew , Matti Hellstrom , Silvana Botti , Miguel A. L. Marques

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…

Computational Physics · Physics 2016-01-11 Endre Somogyi , Andrew Abi Mansour , Peter J. Ortoleva

We show how machine learning techniques based on Bayesian inference can be used to reach new levels of realism in the computer simulation of molecular materials, focusing here on water. We train our machine-learning algorithm using…

Materials Science · Physics 2013-02-25 Albert P. Bartok , Michael J. Gillan , Frederick R. Manby , Gabor Csanyi

We present a highly accurate and transferable parameterization of water using the atomic cluster expansion (ACE). To efficiently sample liquid water, we propose a novel approach that involves sampling static calculations of various ice…

Materials Science · Physics 2024-06-21 Eslam Ibrahim , Yury Lysogorskiy , Ralf Drautz