Related papers: The URDME manual Version 1.5
Universal Multimodal Retrieval (UMR) aims to enable search across various modalities using a unified model, where queries and candidates can consist of pure text, images, or a combination of both. Previous work has attempted to adopt…
Reaction-Diffusion (RD) systems provide a computational framework that governs many pattern formation processes in nature. Current RD system design practices boil down to trial-and-error parameter search. We propose a differentiable…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
Diagnoses from histopathology images rely on information from both high and low resolutions of Whole Slide Images. Ultra-Resolution Cascaded Diffusion Models (URCDMs) allow for the synthesis of high-resolution images that are realistic at…
The udkm1Dsim toolbox is a collection of Python classes and routines to simulate the thermal, structural, and magnetic dynamics after laser excitation as well as the according X-ray scattering response in one-dimensional sample structures.…
We propose a new semiparametric approach for modelling nonlinear univariate diffusions, where the observed process is a nonparametric transformation of an underlying parametric diffusion (UPD). This modelling strategy yields a general class…
Despite the rapidly evolving field of computational electromagnetics, few open-source tools have managed to tackle the problem of automatic mesh generation for properly discretizing the problem of interest into a finite set of elements…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
We present the spatial regime conversion method (SRCM), a novel hybrid modelling framework for simulating reaction-diffusion systems that adaptively combines stochastic discrete and deterministic continuum representations. Extending the…
Systems composed of soft matter (e.g., liquids, polymers, foams, gels, colloids, and most biological materials) are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges,…
A new open source tool for fluid simulation of multi-component plasmas is presented, based on a flexible software design that is applicable to scientific simulations in a wide range of fields. This design enables the same code to be…
The high-performance computing resources and the constant improvement of both numerical simulation accuracy and the experimental measurements with which they are confronted, bring a new compulsory step to strengthen the credence given to…
This paper presents a generic framework for the numerical simulation of transformation-diffusion processes in complex volume geometric shapes. This work follows a previous one devoted to the simulation of microbial degradation of organic…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
The multiscale nature of turbulent combustion necessitates accurate and computationally efficient methods for direct numerical simulations (DNS). The field has long been dominated by high-order finite differences, which lack the flexibility…
The reaction-diffusion master equation (RDME) is a lattice stochastic reaction-diffusion model that has been used to study spatially distributed cellular processes. The RDME is often interpreted as an approximation to spatially-continuous…
A biochemical network can be simulated by a set of ordinary differential equations (ODE) under well stirred reactor conditions, for large numbers of molecules, and frequent reactions. This is no longer a robust representation when some…
Approximating partial differential equations for extensive industrial and scientific applications requires leveraging the power of modern high-performance computing. In large-scale parallel computations, the geometrical discretisation…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…