Related papers: The URDME manual Version 1.5
We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar…
In this work, we propose an automatic mesh generation algorithm, FlowMesher, which can be used to generate unstructured meshes for mesh domains in any shape with minimum (or even no) user intervention. The approach can generate high-quality…
Recent developments in vortex particle methods for simulating three-dimensional incompressible flows are presented. A lightweight, dynamic Large-Eddy Simulation model is tested, featuring a dynamic procedure that relies solely on Lagrangian…
Previous efforts have managed to generate production-ready 3D assets from text or images. However, these methods primarily employ NeRF or 3D Gaussian representations, which are not adept at producing smooth, high-quality geometries required…
Multi-color Stochastic Rotation Dynamics (SRDmc) has been introduced by Inoue et al. as a particle based simulation method to study the flow of emulsion droplets in non-wetting microchannels. In this work, we extend the multi-color method…
Robot description models are essential for simulation and control, yet their creation often requires significant manual effort. To streamline this modeling process, we introduce AutoURDF, an unsupervised approach for constructing…
We investigate the potential of numerical algorithms to decipher the kinetic parameters involved in multi-step chemical reactions. To this end we study a dimerization kinetics of protein as a model system. We follow the dimerization…
Involutive MCMC is a unifying mathematical construction for MCMC kernels that generalizes many classic and state-of-the-art MCMC algorithms, from reversible jump MCMC to kernels based on deep neural networks. But as with MCMC samplers more…
This paper summarizes the development of mVEM, a MATLAB software package containing efficient and easy-following codes for various virtual element methods (VEMs) published in the literature. We explain in detail the numerical implementation…
The recently proposed generalized epidemic modeling framework (GEMF) \cite{sahneh2013generalized} lays the groundwork for systematically constructing a broad spectrum of stochastic spreading processes over complex networks. This article…
We present an algorithm for fast generation of quasi-uniform and variable-spacing nodes on domains whose boundaries are represented as computer-aided design (CAD) models, more specifically non-uniform rational B-splines (NURBS). This new…
Dynamical systems are ubiquitous within science and engineering, from turbulent flow across aircraft wings to structural variability of proteins. Although some systems are well understood and simulated, scientific imaging often confronts…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…
The field of photorealistic 3D avatar reconstruction and generation has garnered significant attention in recent years; however, animating such avatars remains challenging. Recent advances in diffusion models have notably enhanced the…
We introduce Pairwise Distance-Diffusion Analysis (PDDA), a geometric framework for estimating the Hurst exponent from distance plots of long-memory stochastic processes. A single construction yields two complementary routes: R/S-PDDA, a…
Intraoperative observation of tissue internal structure is often difficult. Hence, real-time soft tissue deformation is essential for the localization of tumor and other internal structures. We propose a method to simulate the internal…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
Multiscale non-equilibrium physics at large variations of local Knudsen number are encountered in applications of aerospace engineering and micro-electro-mechanical systems, such as high-speed flying vehicles and low pressure of the…
This work outlines a diffuse interface method for the study of fracture and fragmentation in ductile metals at high strain-rates in Eulerian finite volume simulations. The work is based on an existing diffuse interface method capable of…