Related papers: The URDME manual Version 1.5
ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems Limbach et al., Comput. Phys. Commun. 174,…
BOUT++ is a 3D nonlinear finite-difference plasma simulation code, capable of solving quite general systems of PDEs, but targeted particularly on studies of the edge region of tokamak plasmas. BOUT++ is publicly available, and has been…
Machine learning techniques are powerful tools for construction of emulators for complex systems. We explore different machine learning methods and conceptual methodologies, ranging from functional approximations to dynamical…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
Frequently, the design of physicochemical processes requires screening of large numbers of alternative designs with complex geometries. These geometries may result in conformal meshes which introduce stability issues, significant…
This paper aims to establish a first general error estimate for numerical approximations of the system of reaction-diffusion equations (SRDEs), using reasonable regularity assumptions on the exact solutions. We employ the gradient…
To fully leverage the power of image simulation to corroborate and explain patterns and structures in atomic resolution microscopy (e.g., electron and scanning probe), an initial correspondence between the simulation and experimental image…
A novel method - the Virtual Ring Shear-Slip Mesh Update Method (VR-SSMUM) - for the efficient and accurate modeling of moving boundary or interface problems in the context of the numerical analysis of fluid flow is presented. We focus on…
We propose a new theoretical framework that exploits convolution kernels to transform a Volterra-type path-dependent (non-Markovian) stochastic process into a standard (Markovian) diffusion process. Remarkably, it is also possible to go…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
The microstructure of materials evolves through chemical reactions and mechanical stress, often strongly coupled in phenomena such as pressure solution or crystallization pressure. This article presents MASKE: a simulator to address the…
We introduce Scan2Mesh, a novel data-driven generative approach which transforms an unstructured and potentially incomplete range scan into a structured 3D mesh representation. The main contribution of this work is a generative neural…
This article proposes a universal simulation platform for simulating systems undergoing duress. In other words, this paper introduces a total simulation package which includes a number of methods of simulating the flexibility of a given…
It is desired to equip robots with the capability of interacting with various soft materials as they are ubiquitous in the real world. While physics simulations are one of the predominant methods for data collection and robot training,…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
Decentralized multi-robot motion planning requires each robot to generate collision-free trajectories from local observations, without global sensing or reliable communication. However, most existing planners, whether classical or…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
In the present work we compare reliability of several most widely used reduced detailed chemical kinetic schemes for hydrogen-air and hydrogen-oxygen combustible mixtures. The validation of the schemes includes detailed analysis of 0D and…
Biochemical reactions typically occur at low copy numbers, but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a…
We present a new method for numerical hydrodynamics which uses a multidimensional generalisation of the Roe solver and operates on an unstructured triangular mesh. The main advantage over traditional methods based on Riemann solvers, which…