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Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences…

Biomolecules · Quantitative Biology 2025-03-19 Shuqi Lu , Xiaohong Ji , Bohang Zhang , Lin Yao , Siyuan Liu , Zhifeng Gao , Linfeng Zhang , Guolin Ke

In this paper we show how a two dimensional fluid model can be used to interpret data obtained from an inclined Mach-probe or a Gundestrup probe. We use an analytical approximation of the solution of the differential equations describing…

Plasma Physics · Physics 2009-11-10 Peter Peleman , Stefan Jachmich , Michael Van Schoor , Guido Van Oost

In this paper, we present a new model to simulate the formation, evolution, and break up of a thin film of fluid flowing over a curved surface. Referred to as the discrete droplet method (DDM), the model captures the evolution of thin fluid…

Fluid Dynamics · Physics 2022-10-20 Anand S Bharadwaj , Joerg Kuhnert , Stephane P. A. Bordas , Pratik Suchde

Measurement of the absolute value of the applied pressure in high-pressure muon and neutron experiments is a complicated task. It requires both the presence of a calibration material inside the sample volume as well as additional time for…

Simulations of large-scale plasma systems are typically based on a fluid approximation approach. These models construct a moment-based system of equations that approximate the particle-based physics as a fluid, but as a result lack the…

Plasma Physics · Physics 2022-03-25 Brecht Laperre , Jorge Amaya , Sara Jamal , Giovanni Lapenta

In the present paper we are concerned with a numerical algorithm for the approximation of the two-dimensional neural field equation with delay. We consider three numerical examples that have been analysed before by other authors and are…

Numerical Analysis · Mathematics 2015-11-04 Pedro M. Lima , Evelyn Buckwar

A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…

Materials Science · Physics 2022-10-17 Jiayuwen Qi , Christian Oberdorfer , Emmanuelle A. Marquis , Wolfgang Windl

Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…

Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…

Soft Condensed Matter · Physics 2024-02-20 B. Rusen Argun , Yu Fu , Antonia Statt

We present results of LAMMPS Molecular Dynamics simulations of 2D gravity-driven flows of 30,000 soft uniform spheres through a vertical silo. We vary the gravitational field (g), elastic modulus of the particles (E), and silo outlet…

Soft Condensed Matter · Physics 2025-06-30 Abigail Tadlock , Lori McCabe , Kerstin Nordstrom

We have given theoretical expressions for the forces exerted on a quasi-2D flat and smooth solid plate immersed into a liquid pool of a simple liquid. All forces given by the theory, the local forces on the top, the contact line and the…

Chemical Physics · Physics 2020-08-26 Yuta Imaizumi , Takeshi Omori , Hiroki Kusudo , Carlos Bistafa , Yasutaka Yamaguchi

We present numerical simulation of 2D turbulent flow using a new model for the subgrid scales which are computed using a dynamic equation linking the subgrid scales with the resolved velocity. This equation is not postulated, but derived…

Fluid Dynamics · Physics 2009-11-07 J. -P. Laval , B. Dubrulle , S. Nazarenko

Arc plasmas have promising applications in many fields. To explore their property is of interest. This paper presents detailed pressure-based finite volume simulation of argon arc. In the modeling, the whole cathode region is coupled to…

Plasma Physics · Physics 2022-01-17 Xiaoliang Wang

Despite the modern level of development of computational chemistry methods and techno-logical progress, fast and accurate determination of solvation free energy remains a huge problem for physical chemists. In this paper, we describe two…

Chemical Physics · Physics 2021-05-18 N. N. Kalikin , Y. A. Budkov , A. L. Kolesnikov , D. V. Ivlev , M. A. Krestyaninov , M. G. Kiselev

Non-ideal MHD effects are thought to be a crucial component of the star-formation process. Numerically, several complications render the study of non-ideal MHD effects in 3D simulations extremely challenging and hinder our efforts of…

Astrophysics of Galaxies · Physics 2025-02-12 E. Agianoglou , A. Tritsis , K. Tassis

Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…

Chemical Physics · Physics 2026-04-30 Felipe Silva Carvalho , Steven Ramsey , Tom Kurtzman , Tyler Luchko

The evolution of three-dimensional, large-scale, magnetic fields, in a galactic disk is investigated numerically. The N-body simulations of galactic dynamics are incorporated into the kinematic calculations of induction equations to study…

Astrophysics · Physics 2007-05-23 K. Otmianowska-Mazur , S. von Linden , H. Lesch , G. Skupniewicz

Our ability to numerically model and understand the complex flow behavior of solid-bearing suspensions has increased significantly over the last couple of years, partly due to direct numerical simulations that compute flow around individual…

Computational Physics · Physics 2019-03-21 Zhipeng Qin , Kali Alison , Jenny Suckale

We present an elegant method of determining the eigensolutions of the induction and the dynamo equation in a fluid embedded in a vacuum. The magnetic field is expanded in a complete set of functions. The new method is based on the…

Instrumentation and Methods for Astrophysics · Physics 2015-05-14 M. Schrinner , D. Schmitt , J. Jiang , P. Hoyng

For the Edwards-Anderson model we introduce an integral representation for the surface pressure (per unit surface) in terms of a quenched moment of the bond-overlap on the surface. We find upper and lower bounds uniformly in the volume and…

Mathematical Physics · Physics 2009-11-10 Pierluigi Contucci , Sandro Graffi
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