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Integral equation theory of molecular liquids based on statistical mechanics is quite promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. Beginning with a molecular interaction…

Soft Condensed Matter · Physics 2015-10-23 A. Kovalenko

The authors present a study of the non equilibrium statistical properties of a one dimensional hard-rod fluid dissipating energy via inelastic collisions and subject to the action of a Gaussian heat bath, simulating an external driving…

Materials Science · Physics 2009-11-13 Umberto Marini-Bettolo-Marconi , Pedro Tarazona , Fabio Cecconi

We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics of crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away…

Materials Science · Physics 2009-11-07 Weinan E , Zhongyi Huang

A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…

Statistical Mechanics · Physics 2009-10-31 I. P. Omelyan , I. M. Mryglod , R. Folk

Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…

This paper focuses on multiscale dynamics occurring in steam supply systems. The dynamics of interest are originally described by a distributed-parameter model for fast steam flows over a pipe network coupled with a lumped-parameter model…

Dynamical Systems · Mathematics 2023-05-15 Hikaru Hoshino , Yoshihiko Susuki , Takashi Hikihara

Encoding the electronic structure of molecules using 2-electron reduced density matrices (2RDMs) as opposed to many-body wave functions has been a decades-long quest as the 2RDM contains sufficient information to compute the exact molecular…

Chemical Physics · Physics 2022-08-11 David Pekker , Chungwen Liang , Sankha Pattanayak , Swagatam Mukhopadhyay

We introduce the "selPT" perturbative approach, based on ab initio molecular dynamics (AIMD), for computing accurate finite-temperature properties by efficiently using correlated wave-function methods. We demonstrate the power of the method…

Materials Science · Physics 2019-05-01 Dario Rocca , Anant Dixit , Michael Badawi , Sébastien Lebègue , Tim Gould , Tomáš Bučko

Molecular dynamics simulations are powerful tools to extract the microscopic mechanisms characterizing the properties of soft materials. We recently introduced machine learning surrogates for molecular dynamics simulations of soft materials…

Soft Condensed Matter · Physics 2021-10-29 J. C. S. Kadupitiya , Nasim Anousheh , Vikram Jadhao

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…

Artificial Intelligence · Computer Science 2018-09-07 Tristan Aumentado-Armstrong

Learning interpretable representations of neural dynamics at a population level is a crucial first step to understanding how observed neural activity relates to perception and behavior. Models of neural dynamics often focus on either…

Machine Learning · Statistics 2025-01-13 Noga Mudrik , Yenho Chen , Eva Yezerets , Christopher J. Rozell , Adam S. Charles

The spectral features of water clusters provide important information on their structure and dynamics and can assist in deciphering the nature of the local environment of aqueous solutions in a variety of different conditions. Accurately…

Computational Physics · Physics 2026-03-11 T. Baird , R. Vuilleumier , S. Bonella

The application of molecular dynamics (MD) simulations to the interpretation of Raman scattering spectra is hindered by inability of atomistic simulations to account for the dynamic evolution of electronic polarizability, requiring the use…

Materials Science · Physics 2023-04-18 Atanu Paul , Anthony Ruffino , Stefan Masiuk , Jonathan Spanier , Ilya Grinberg

Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…

Biomolecules · Quantitative Biology 2025-08-07 Mhd Hussein Murtada , Z. Faidon Brotzakis , Michele Vendruscolo

Among the many additive manufacturing (AM) processes for metallic materials, selective laser melting (SLM) is arguably the most versatile in terms of its potential to realize complex geometries along with tailored microstructure. However,…

Applied Physics · Physics 2019-05-08 Christoph Meier , Ryan W. Penny , Yu Zou , Jonathan S. Gibbs , A. John Hart

We introduce a translational and rotational invariant local representation for vector fields, which can be employed in the construction of machine-learning energy models of solids and molecules. This allows us to describe, on the same…

Materials Science · Physics 2022-08-09 Michelangelo Domina , Matteo Cobelli , Stefano Sanvito

Pre-trained Language Models have emerged as promising tools for predicting molecular properties, yet their development is in its early stages, necessitating further research to enhance their efficacy and address challenges such as…

Machine Learning · Computer Science 2023-10-24 Eduardo Soares , Akihiro Kishimoto , Emilio Vital Brazil , Seiji Takeda , Hiroshi Kajino , Renato Cerqueira

Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…

Soft Condensed Matter · Physics 2024-02-21 Marcel Mokbel , Dominic Mokbel , Susanne Liese , Christoph A. Weber , Sebastian Aland

Simulation-based inference provides a powerful framework for cryo-electron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via learned latent representations. This latent space represents a…

Quantitative Methods · Quantitative Biology 2025-09-05 Luke Evans , Octavian-Vlad Murad , Lars Dingeldein , Pilar Cossio , Roberto Covino , Marina Meila

Simulating and predicting dynamics of quantum many-body systems is extremely challenging, even for state-of-the-art computational methods, due to the spread of entanglement across the system. However, in the long-wavelength limit, quantum…

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