Related papers: Pychastic: Precise Brownian Dynamics using Taylor-…
The efficient simulation of models defined in terms of stochastic differential equations (SDEs) depends critically on an efficient integration scheme. In this article, we investigate under which conditions the integration schemes for…
We present a novel open-source Python software package, bfieldtools, for magneto-quasistatic calculations with current densities on surfaces of arbitrary shape. The core functionality of the software relies on a stream-function…
We study the dynamics of Brownian particles in a heterogeneous one-dimensional medium with a spatially-dependent diffusion coefficient of the form $D(x)\sim |x|^c$, at constant temperature. The particle's probability distribution function…
We present a differentiable dynamics solver that is able to handle frictional contact for rigid and deformable objects within a unified framework. Through a principled mollification of normal and tangential contact forces, our method…
The package performs molecular-dynamics-like agent-based simulations for models of aligning self-propelled particles in two dimensions such as e.g. the seminal Vicsek model or variants of it. In one class of the covered models, the…
WaveTrain is an open-source software for numerical simulations of chain-like quantum systems with nearest-neighbor (NN) interactions only. The Python package is centered around tensor train (TT, or matrix product) format representations of…
Differential equations based on physical principals are used to represent complex dynamic systems in all fields of science and engineering. Through repeated use in both academics and industry, these equations have been shown to represent…
Multibody dynamics simulators are an important tool in many fields, including learning and control for robotics. However, many existing dynamics simulators suffer from inaccuracies when dealing with constrained mechanical systems due to…
A new method is proposed for integrating the equations of motion of an elastic filament. In the standard finite-difference and finite-element formulations the continuum equations of motion are discretized in space and time, but it is then…
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…
An elastic rod model for semi-flexible polymers is presented. Theory for a continuum rod is reviewed, and it is shown that a popular discretised model used in numerical simulations gives the correct continuum limit. Correlation functions…
In this work it is shown how the immersed boundary method of (Peskin2002) for modeling flexible structures immersed in a fluid can be extended to include thermal fluctuations. A stochastic numerical method is proposed which deals with…
In several industrial applications, such as crystallization, pollution control, and flow assurance, an accurate understanding of the aqueous electrolyte solutions is crucial. Electrolyte equilibrium calculation contributes with the design…
We introduce a Rigid-Body Fluctuating Immersed Boundary (RB-FIB) method to perform large-scale Brownian dynamics simulations of suspensions of rigid particles in fully confined domains, without any need to explicitly construct Green's…
The transport of self-propelled particles such as bacteria and phoretic swimmers through crowded heterogeneous environments is relevant to many natural and engineering processes, from biofilm formation and contamination processes to…
This paper describes PyOED, a highly extensible scientific package that enables developing and testing model-constrained optimal experimental design (OED) for inverse problems. Specifically, PyOED aims to be a comprehensive Python toolkit…
ergodicity is an open-source Python library for computational work on stochastic dynamics, with particular emphasis on non-ergodicity, time-average behavior, heavy-tailed processes, and decision making under uncertainty. The package brings…
In this paper, by using a Taylor development type formula, we show how it is possible to associate differential operators with stochastic differential equations driven by a fractional Brownian motion. As an application, we deduce that…
There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the…
A thermal analogue of the classical brachistochrone problem, which minimizes the connection time between two equilibrium states of harmonically confined Brownian particles, has recently been solved theoretically. Here we report its…