Related papers: The URDME manual Version 1.5
A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded…
Reward models (RMs) are essential for aligning large language models (LLM) with human expectations. However, existing RMs struggle to capture the stochastic and uncertain nature of human preferences and fail to assess the reliability of…
We present a versatile open-source pipeline for simulating inhomogeneous reaction-diffusion processes in highly resolved, image-based geometries of porous media with reactive boundaries. Resolving realistic pore-scale geometries in…
Masked Diffusion Models (MDMs) have emerged as a promising approach for generative modeling in discrete spaces. By generating sequences in any order and allowing for parallel decoding, they enable fast inference and strong performance on…
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…
In this paper, we extend the unified kinetic particle (UGKP) method to the frequency-dependent radiative transfer equation with both absorption-emission and scattering processes. The extended UGKP method could not only capture the diffusion…
FLAME is a software package to perform a wide range of atomistic simulations for exploring the potential energy surfaces (PES) of complex condensed matter systems. The range of methods include molecular dynamics simulations to sample free…
The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework, frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical…
This article presents a multi-physics methodology for the numerical simulation of physical systems that involve the non-linear interaction of multi-phase reactive fluids and elastoplastic solids, inducing high strain-rates and high…
As the complexity of robot systems increases, it becomes more effective to simulate them before deployment. To do this, a model of the robot's kinematics or dynamics is required, and the most commonly used format is the Unified Robot…
The purpose of this paper is to propose a time-step-robust cell-to-cell integration of particle trajectories in 3-D unstructured meshes in particle/mesh Lagrangian stochastic methods. The main idea is to dynamically update the mean fields…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
Available algorithms for the initialization of volume fractions typically utilize exact functions to model fluid interfaces, or they rely on computationally costly intersections between volume meshes. Here, a new algorithm is proposed that…
Geometrical Volume-of-Fluid (VoF) methods mainly support structured meshes, and only a small number of contributions in the scientific literature report results with unstructured meshes and three spatial dimensions. Unstructured meshes are…
Designs incorporating kinematic loops are becoming increasingly prevalent in the robotics community. Despite the existence of dynamics algorithms to deal with the effects of such loops, many modern simulators rely on dynamics libraries that…
The current fabrication and assembly of fluidic circuits for soft robots relies heavily on manual processes; as the complexity of fluidic circuits increases, manual assembly becomes increasingly arduous, error-prone, and timeconsuming. We…
This work is an attempt to develop an approximate scheme for estimating the volume-based truncation errors in the finite volume analysis of laminar flows. The volume-based truncation error is the net flow error across the faces of a control…
In this paper we present computational techniques to investigate the solutions of two-component, nonlinear reaction-diffusion (RD) systems on arbitrary surfaces. We build on standard techniques for linear and nonlinear analysis of RD…
We have developed a graphical user interface (GUI) based package $\mu$2mech to perform phase-field simulation for predicting microstructure evolution. The package can take inputs from ab initio calculations and CALPHAD (Calculation of Phase…
Very recently neural implicit rendering techniques have been rapidly evolved and shown great advantages in novel view synthesis and 3D scene reconstruction. However, existing neural rendering methods for editing purposes offer limited…