Related papers: PULSEDYN - A dynamical simulation tool for studyin…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
PySINDy is a Python package for the discovery of governing dynamical systems models from data. In particular, PySINDy provides tools for applying the sparse identification of nonlinear dynamics (SINDy) (Brunton et al. 2016) approach to…
Automated data-driven modeling, the process of directly discovering the governing equations of a system from data, is increasingly being used across the scientific community. PySINDy is a Python package that provides tools for applying the…
Pulgon-tools is an open-source software package providing building blocks for the analysis and modeling of quasi-one-dimensional (quasi-1D) periodic systems based on line-group theory. While mature libraries exist for space-group detection…
Understanding the interplay between different wave excitations, such as phonons and localized solitons, is crucial for developing coarse-grained descriptions of many-body, near-integrable systems. We treat the Fermi-Pasta-Ulam-Tsingou…
A challenging and fundamental research problem is the better understanding and control of the turbulent transport of heat in present-day tokamak fusion experiments. Recent developments in numerical methods along with enormous gains in…
When modeling complex, hierarchical, and time-dynamic systems, such as biological systems, good computational tools are essential. Current tools, while powerful, often lack comprehensive frameworks for modular model composition,…
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular…
We present a major update to QuSpin, SciPostPhys.2.1.003 -- an open-source Python package for exact diagonalization and quantum dynamics of arbitrary boson, fermion and spin many-body systems, supporting the use of various (user-defined)…
The nonequilibrium dynamics of correlated many-particle systems is of interest in connection with pump-probe experiments on molecular systems and solids, as well as theoretical investigations of transport properties and relaxation…
Nonlinear time series analysis is becoming a more and more reliable tool for the study of complicated dynamics from measurements. The concept of low-dimensional chaos has proven to be fruitful in the understanding of many complex phenomena…
Quantum fluctuation relations provide a microscopic formulation of thermodynamics beyond equilibrium, but experimentally accessing many-body quantum work statistics remains an outstanding challenge. The quantum piston constitutes a…
Since Lorenz's seminal work on a simplified weather model, the numerical analysis of nonlinear dynamical systems has become one of the main subjects of research in physics. Despite of that, there remains a need for accessible, efficient,…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e.,…
Merlin++ is a C++ charged-particle tracking library developed for the simulation and analysis of complex beam dynamics within high energy particle accelerators. Accurate simulation and analysis of particle dynamics is an essential part of…
Important nonlinear dynamics, such as those found in plasma and fluid systems, are typically hard to simulate on classical computers. Thus, if fault-tolerant quantum computers could efficiently solve such nonlinear problems, it would be a…
With the advent of the gyrokinetic formalism, recent developments in low-noise nonlinear $\delta f$ methods, and enormous gains in computing power, large-scale gyrokinetic simulations have become an important tool for improved understanding…
We study the use of the Evans Nonequilibrium Molecular Dynamics (NEMD) heat flow algorithm for the computation of the heat conductivity in one-dimensional lattices. For the well-known Fermi-Pasta-Ulam (FPU) model, it is shown that when the…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…