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MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
Advancements in computing power have made it possible to numerically simulate large-scale fluid-mechanical and/or particulate systems, many of which are integral to core industrial processes. Among the different numerical methods available,…
Despite significant advances in particle imaging technologies over the past two decades, few advances have been made in particle tracking, i.e. linking individual particle positions across time series data. The state-of-the-art tracking…
Colloidal and other granular media experience a transition to rigidity known as jamming if the fill fraction is increased beyond a critical value. The resulting jammed structures are locally disordered, bear applied loads inhomogenously,…
We introduce a particle-based simulation method for granular material in interactive frame rates. We divide the simulation into two decoupled steps. In the first step, a relatively small number of particles is accurately simulated with a…
Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interations deform vesicle membrane is a fundamental question in biophysics. In this article we developed a fast algorithm to…
Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins…
Diffeomorphic matching (only one of several names for this technique) is a technique for non-rigid registration of curves and surfaces in which the curve or surface is embedded in the flow of a time-series of vector fields. One seeks the…
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are charged spherical particles coated with a polymer brush that…
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…
Interactions govern the flow of information and the formation of correlations in quantum systems, dictating the phases of matter found in nature and the forms of entanglement generated in the laboratory. Typical interactions decay with…
The human neuromuscular system consisting of skeletal muscles and neural circuits is a complex system that is not yet fully understood. Surface electromyography (EMG) can be used to study muscle behavior from the outside. Computer…
Theoretical research into many-body quantum systems has mostly focused on regular structures which have a small, simple unit cell and where a vanishingly small number of pairs of the constituents directly interact. Motivated by advances in…
We describe AMUSE, the Astrophysical Multipurpose Software Environment, a programming framework designed to manage multi-scale, multi-physics simulations in a hierarchical, extensible, and internally consistent way. Constructed as a…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
Simulation has become the evaluation method of choice for many areas of distributing computing research. However, most existing simulation packages have several limitations on the size and complexity of the system being modeled. Fine…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
Creating realistic droplet simulations and animations has long been a formidable challenge for researchers and developers due to the inherent complexity of fluid dynamics. Achieving lifelike droplet splash simulations while managing…