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Simulating the long-timescale dynamics of biomolecules is a central challenge in computational science. While enhanced sampling methods can accelerate these simulations, they rely on pre-defined collective variables that are often difficult…

Biomolecules · Quantitative Biology 2025-12-01 Aditya Sengar , Jiying Zhang , Pierre Vandergheynst , Patrick Barth

The totally asymmetric simple exclusion process (TASEP) is a paradigmatic lattice model for one-dimensional particle transport subject to excluded-volume interactions. Solving the inhomogeneous TASEP in which particles' hopping rates vary…

Statistical Mechanics · Physics 2023-10-31 Luca Ciandrini , Richmond L. Crisostomo , Juraj Szavits-Nossan

Classical $(1+1)D$ cellular automata, as for instance Domany-Kinzel cellular automata, are paradigmatic systems for the study of non-equilibrium phenomena. Such systems evolve in discrete time-steps, and are thus free of time-discretisation…

Quantum Physics · Physics 2021-04-14 Edward Gillman , Federico Carollo , Igor Lesanovsky

We study confined solutions of certain evolutionary partial differential equations (pde) in 1+1 space-time. The pde we study are Lie-Poisson Hamiltonian systems for quadratic Hamiltonians defined on the dual of the Lie algebra of vector…

solv-int · Physics 2007-05-23 O. B. Fringer , D. D. Holm

Cosmic-ray acceleration processes in astrophysical plasmas are often investigated with fully-kinetic or hybrid kinetic numerical simulations, which enable us to describe a detailed microphysics of particle energization mechanisms. Tracing…

High Energy Astrophysical Phenomena · Physics 2025-02-12 Gabriel Torralba Paz , Artem Bohdan , Jacek Niemiec

We introduce a new approach for the robust control of quantum dynamics of strongly interacting many-body systems. Our approach involves the design of periodic global control pulse sequences to engineer desired target Hamiltonians that are…

Quantum Physics · Physics 2020-07-08 Joonhee Choi , Hengyun Zhou , Helena S. Knowles , Renate Landig , Soonwon Choi , Mikhail D. Lukin

The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…

Computational Physics · Physics 2018-07-04 Jen-Hao Chen , Ren-Chuen Chen , Jinn-Liang Liu

Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…

Machine Learning · Computer Science 2023-08-29 Xiang Fu , Tian Xie , Nathan J. Rebello , Bradley D. Olsen , Tommi Jaakkola

We present a quantum algorithm based on repeated measurement to solve initial-value problems for nonlinear ordinary differential equations (ODEs), which may be generated from partial differential equations in plasma physics. We map a…

Quantum Physics · Physics 2025-04-30 Joseph Andress , Alexander Engel , Yuan Shi , Scott Parker

A method for simulation of elastoplastic solids in multibody systems with nonsmooth and multidomain dynamics is developed. The solid is discretised into pseudo-particles using the meshfree moving least squares method. The particles carry…

Soft Condensed Matter · Physics 2016-11-14 John Nordberg , Martin Servin

Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…

Numerical Analysis · Mathematics 2023-11-01 Igor Ostanin , Vasileios Angelidakis , Timo Plath , Sahar Pourandi , Anthony Thornton , Thomas Weinhart

Hamiltonian particle-based simulations of plasma dynamics are inherently computationally intensive, primarily due to the large number of particles required to obtain accurate solutions. This challenge becomes even more acute in many-query…

Numerical Analysis · Mathematics 2025-06-19 Emmanuel Franck , Laurent Navoret , Vincent Vigon , Raphaël Côte , Guillaume Steimer

Nonlinearities and instabilities in mechanical structures have shown great promise for embedding advanced functionalities. However, simulating structures subject to nonlinearities can be challenging due to the complexity of their behavior,…

Soft Condensed Matter · Physics 2025-10-23 Paul Ducarme , Bart Weber , Martin van Hecke , Johannes T. B. Overvelde

Phase mixing is a fundamental kinetic process that governs dissipation and stability in collisionless plasmas, but its inherent filamentation in velocity space creates major challenges for both high-fidelity simulations and reduced-order…

Plasma Physics · Physics 2025-09-23 Darian Figuera-Michal , Sungpil Yum , Jae-Min Kwon , Eisung Yoon

Quantifying simulation uncertainties is a critical component of rigorous predictive simulation. A key component of this is forward propagation of uncertainties in simulation input data to output quantities of interest. Typical approaches…

Mathematical Software · Computer Science 2015-11-13 E. Phipps , M. D'Elia , H. C. Edwards , M. Hoemmen , J. Hu , S. Rajamanickam

Particle acceleration in collisionless plasma systems is a central question in astroplasma and astroparticle physics. The structure of the acceleration regions, electron-ion energy equilibration, preacceleration of particles at shocks to…

High Energy Astrophysical Phenomena · Physics 2020-02-19 Martin Pohl , Masahiro Hoshino , Jacek Niemiec

A complex (dusty) plasma system is well known as a paradigmatic model for studying the kinetics of solid-liquid phase transitions in inactive condensed matter. At the same time, under certain conditions a complex plasma system can also…

We present initial results regarding the existence, stability and interaction of linear and nonlinear vibrational modes in a system of two coupled, one dimensional lattices with unequal numbers of masses. The effects on these nonlinear…

Biological Physics · Physics 2007-05-23 Kyle Forinash

Discovering the underlying dynamics of complex systems from data is an important practical topic. Constrained optimization algorithms are widely utilized and lead to many successes. Yet, such purely data-driven methods may bring about…

Dynamical Systems · Mathematics 2023-05-17 Nan Chen , Yinling Zhang

The goal of this presentation is to highlight various computational techniques used to study dynamics of quantum many-body systems. We examine the projection and variable phase methods being applied to multi-channel problems of scattering…

Nuclear Theory · Physics 2014-12-22 Alexander Volya
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