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This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
Discrete-state, continuous-time Markov models are becoming commonplace in the modelling of biochemical processes. The mathematical formulations that such models lead to are opaque, and, due to their complexity, are often considered…
This paper presents a parallel \PG{implementation} for the Optimal Transportation Meshfree (OTM) method on large CPU clusters. Communications are handled with the Message Passing Interface (MPI). The Recursive Coordinate Bisection (RCB)…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
In this paper, we present a multiple-time-step integration algorithm (MTSA) for particle collisions in particle-resolved simulations. Since the time step required for resolving a collision process is much smaller than that for a fluid flow,…
We present a parallel-scalable method for simulating non-dilute suspensions of deformable particles immersed in Stokesian fluid in three dimensions. A critical component in these simulations is robust and accurate collision handling. This…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
Optimizing metamaterials with complex geometries is a big challenge. Although an active learning algorithm, combining machine learning (ML), quantum computing, and optical simulation, has emerged as an efficient optimization tool, it still…
In this paper, a hardware-optimized approach to emotion recognition based on the efficient brain-inspired hyperdimensional computing (HDC) paradigm is proposed. Emotion recognition provides valuable information for human-computer…
Modeling and predicting the dynamics of complex multiscale systems remains a significant challenge due to their inherent nonlinearities and sensitivity to initial conditions, as well as limitations of traditional machine learning methods…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
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…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
This technical report provides an in-depth evaluation of both established and state-of-the-art methods for simulating constrained rigid multi-body systems with hard-contact dynamics, using formulations of Nonlinear Complementarity Problems…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…