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Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
Simulation frameworks such as Isaac Sim have enabled scalable robot learning for locomotion and rigid-body manipulation; however, contact-rich simulation remains a major bottleneck for deformable object manipulation. The continuously…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
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…
Turbulent flows and fluid-structure interactions (FSI) are ubiquitous in scientific and engineering applications, but their accurate and efficient simulation remains a major challenge due to strong nonlinearities, multiscale interactions,…
Deformable elastic bodies in viscous and viscoelastic media constitute a large portion of synthetic and biological complex fluids. We present a parallelized 3D-simulation methodology which fully resolves the momentum balance in the solid…
Objective: We developed a hybrid volume surface integral equation (VSIE) method based on domain decomposition to perform fast and accurate magnetic resonance imaging (MRI) simulations that include both remote and local conductive elements.…
To reduce the carbon footprint of computing and stabilize electricity grids, there is an increasing focus on approaches that align the power usage of IT infrastructure with the availability of clean energy. Unfortunately, research on…
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…
We propose a computational framework for vascular fluid-structure interaction (FSI), focusing on biomechanical modeling, geometric modeling, and solver technology. The biomechanical model is constructed based on the unified continuum…
The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical…
In VLSI physical design, many algorithms require the solution of difficult combinatorial optimization problems such as max/min-cut, max-flow problems etc. Due to the vast number of elements typically found in this problem domain, these…
The dynamics of compressible liquid-vapor flow depends sensitively on the microscale behavior at the phase boundary. We consider a sharp-interface approach, and propose a multiscale model to describe liquid-vapor flow accurately, without…
Algorithmic formulations of GPU programs provide a high-level alternative to device-specific code by expressing computations as compositions of well-defined parallel primitives (e.g., map, sort, reduce), rather than through handcrafted GPU…
Vlasiator is a space plasma simulation code which models near-Earth ion-kinetic dynamics in three spatial and three velocity dimensions. It is highly parallelized, modeling the Vlasov equation directly through the distribution function,…
Earth system models (ESM) demand significant hardware resources and energy consumption to solve atmospheric chemistry processes. Recent studies have shown improved performance from running these models on GPU accelerators. Nonetheless,…
Solid-On-Solid (SOS) computer simulations are employed to investigate the sublimation of surfaces. We distinguish three sublimation regimes: layer-by-layer sublimation, free step flow and hindered step flow. The sublimation regime is…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Implicit solvation is an effective, highly coarse-grained approach in atomic-scale simulations to account for a surrounding liquid electrolyte on the level of a continuous polarizable medium. Originating in molecular chemistry with finite…