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Agent-based modelling constitutes a versatile approach to representing and simulating complex systems. Studying large-scale systems is challenging because of the computational time required for the simulation runs: scaling is at least…
Optimizing high-performance power electronic equipment, such as power converters, requires multiscale simulations that incorporate the physics of power semiconductor devices and the dynamics of other circuit components, especially in…
Molecular Dynamics simulations can help scientists to gather valuable insights for physical processes on an atomic scale. This work explores various techniques for SIMD vectorization to improve the pairwise force calculation between…
The random phase approximation (RPA) has received a considerable interest in the field of modeling systems where noncovalent interactions are important. Its advantages over widely used density functional theory (DFT) approximations are the…
The impressive progress of the kinetic schemes in the solution of gas dynamics problems and the development of effective parallel algorithms for modern high performance parallel computing systems led to the development of advanced methods…
We have developed an application and implemented parallel algorithms in order to provide a computational framework suitable for massively parallel supercomputers to study the unitary dynamics of quantum systems. We use renowned parallel…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
This paper deals with the problem of simulating dense dispersed systems composed by large numbers of particles undergoing ballistic aggregation. The most classical approaches for dealing with such problems are represented by the so-called…
In this paper, we present a new multibody physics simulation framework that utilizes the subsystem-based structure and the Alternating Direction Method of Multiplier (ADMM). The major challenge in simulating complex high degree of freedom…
Theoretical and experimental investigations of water vapor interaction with porous materials are very needful for various fields of science and technology. Not only studies of the interaction of water vapor and porous material as a…
Numerous applications of Eikonal equations prompted the development of many efficient numerical algorithms. The Heap-Cell Method (HCM) is a recent serial two-scale technique that has been shown to have advantages over other serial…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
We propose a hierarchy of multi-level kinetic Monte Carlo methods for sampling high-dimensional, stochastic lattice particle dynamics with complex interactions. The method is based on the efficient coupling of different spatial resolution…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
We implement a three-body potential to model associative bond swaps, and release it as part of the HOOMD-blue software. The use of a three-body potential to model swaps has been proven to be effective and has recently provided useful…
Stokesian Dynamics (SD) is a numerical framework used for simulating hydrodynamic interactions in particle suspensions at low Reynolds number. It combines far-field approximations with near-field lubrication corrections, offering a balance…
A common strategy today to generate efficient locomotion movements is to split the problem into two consecutive steps: the first one generates the contact sequence together with the centroidal trajectory, while the second one computes the…