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We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…

Quantitative Methods · Quantitative Biology 2021-02-24 Sheenam Khuttan , Solmaz Azimi , Joe Z. Wu , Emilio Gallicchio

Fluid-particle systems are very common in many natural processes and engineering applications. However, accurately and efficiently modelling fluid-particle systems with complex particle shapes is still a challenging task. Here, we present a…

Fluid Dynamics · Physics 2023-03-22 Pei Zhang , Ling Qiu , S. A. Galindo-Torres , Yilin Chen , A. Scheuermann , Ling Li

The birth of the lattice Boltzmann method (LBM) fulfils a dream that simple arithmetic calculations can simulate complex fluid flows without solving complicated partial differential flow equations. Its power and potential of resolving more…

Computational Engineering, Finance, and Science · Computer Science 2019-01-10 Jian Guo Zhou

Hydrogen bonding is modeled in terms of virtual exchange of protons between water molecules. A simple lattice model is analyzed, using ideas and techniques from the theory of correlated electrons in metals. Reasonable parameters reproduce…

Soft Condensed Matter · Physics 2009-11-11 Daniel W. Hone , P. A. Pincus

Electrical charging of parallel plates confining a model ionic liquid down to nanoscale distances yields a variety of charge-induced changes in the structural features of the confined film. That includes even-odd switching of the structural…

Materials Science · Physics 2015-06-23 R. Capozza , A. Vanossi , A. Benassi , E. Tosatti

We demonstrate a machine learning-based approach which predicts the properties of crystal structures following relaxation based on the unrelaxed structure. Use of crystal graph singular values reduces the number of features required to…

Materials Science · Physics 2024-02-15 Ethan P. Shapera , Dejan-Krešimir Bučar , Rohit P. Prasankumar , Christoph Heil

Since the 1950s, soft ionic devices have evolved from individual components to an expanding library of sensors, actuators, signal transmitters, and processors. However, integrating these components into complex, multi-functional systems…

Soft Condensed Matter · Physics 2024-10-17 Max Tepermeister , Meredith N. Silberstein

This paper outlines an energy-minimization finite-element approach to the modeling of equilibrium configurations for nematic liquid crystals in the presence of internal and external electric fields. The method targets minimization of system…

Computational Physics · Physics 2014-07-14 J. H. Adler , T. J. Atherton , T. R. Benson , D. B. Emerson , S. P. MacLachlan

In this contribution we review a series of simple one dimensional lattice models that with an appropriate choice of parameters can account for various anomalous features of the behaviour of complex systems such as water. In particular, we…

Statistical Mechanics · Physics 2015-03-13 Enrique Lomba

Much of our understanding of the physical properties of raft domains in biological membranes, and some insight into the mechanisms underlying their formation stem from atomistic simulations of simple model systems, especially ternary…

Soft Condensed Matter · Physics 2023-03-07 Tanmoy Sarkar , Oded Farago

Chemical potential is an effective way to drive phase transition or express wettability. In this letter, we present a chemical-potential-based lattice Boltzmann model to simulate multiphase flows. The nonideal force is directly evaluated by…

Computational Physics · Physics 2017-06-21 Binghai Wen , Xuan Zhou , Bing He , Chaoying Zhang , Haiping Fang

A novel thermodynamic integration (TI) scheme is presented to compute the crystal-liquid interfacial free energy ($\gamma_{\rm cl}$) from molecular dynamics simulation. The scheme is applied to a Lennard-Jones system. By using extremely…

Soft Condensed Matter · Physics 2015-06-19 Ronald Benjamin , Jürgen Horbach

State-of-the-art lattice QCD studies of hot and dense strongly interacting matter currently rely on extrapolation from zero or imaginary chemical potentials. The ill-posedness of numerical analytic continuation puts severe limitations on…

High Energy Physics - Lattice · Physics 2022-04-06 Szabolcs Borsanyi , Zoltan Fodor , Matteo Giordano , Sandor D. Katz , Daniel Nogradi , Attila Pasztor , Chik Him Wong

First-principles based lattice models allow the modeling of ab initio thermodynamics of crystalline mixtures for applications such as the construction of phase diagrams and the identification of ground state atomic orderings. The recent…

We study NaCl ion-pair dissociation in a dilute aqueous solution using computer simulations both for the full system with long range Coulomb interactions and for a well chosen reference system with short range intermolecular interactions.…

Chemical Physics · Physics 2021-10-13 Dedi Wang , Renjie Zhao , John D. Weeks , Pratyush Tiwary

By trapping cold polarizable atoms in periodic potentials created by crossed laser beams, it is now possible to experimentally create "clean" lattice systems. Experimentalists have successfully engineered local and nearest-neighbor…

High Energy Physics - Lattice · Physics 2012-02-09 Y. Meurice

We introduce a nonequilibrium off--lattice model for anisotropic phenomena in fluids. This is a Lennard--Jones generalization of the driven lattice--gas model in which the particles' spatial coordinates vary continuously. A comparison…

Statistical Mechanics · Physics 2016-08-16 M. Díez--Minguito , P. L. Garrido , J. Marro

Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…

Soft Condensed Matter · Physics 2025-08-12 Mahdi Tavakol , Kislon Voïtchovsky

Machine Learning (ML) techniques are revolutionizing the way to perform efficient materials modeling. Nevertheless, not all the ML approaches allow for the understanding of microscopic mechanisms at play in different phenomena. To address…

Materials Science · Physics 2022-06-22 Udaykumar Gajera , Loriano Storchi , Danila Amoroso , Francesco Delodovici , Silvia Picozzi

We present and study lattice and off-lattice microscopic models in which particles interact via a local anisotropic rule. The rule induces preferential hopping along one direction, so that a net current sets in if allowed by boundary…

Statistical Mechanics · Physics 2007-05-23 M. Diez-Minguito , P. L. Garrido , J. Marro