Related papers: tinyMD: A Portable and Scalable Implementation for…
In this paper I describe some results on the use of virtual processors technology for parallelize some SPMD computational programs. The tested technology is the INTEL Hyper Threading on real processors, and the programs are MATLAB scripts…
Scaling up hardware systems has become an important tactic for improving performance as Moore's law fades. Unfortunately, simulations of large hardware systems are often a design bottleneck due to slow throughput and long build times. In…
Synthetic molecular dynamics (synMD) trajectories from learned generative models have been proposed as a useful addition to the biomolecular simulation toolbox. The computational expense of explicitly integrating the equations of motion in…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
This paper presents PICO-TINYML-BENCHMARK, a modular and platform-agnostic framework for benchmarking the real-time performance of TinyML models on resource-constrained embedded systems. Evaluating key metrics such as inference latency, CPU…
Wave packet molecular dynamics (WPMD) has recently received a lot of attention as a computationally fast tool to study dynamical processes in warm dense matter beyond the Born-Oppenheimer approximation. These techniques, typically, employ…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
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…
This paper investigates the effectiveness of small language models (SLMs) for agentic tasks (function/tool/API calling) with a focus on running agents on edge devices without reliance on cloud infrastructure. We evaluate SLMs using the…
We develop a modeling and simulation framework capable of massively parallel simulation of multicellular systems with spatially resolved stochastic kinetics in individual cells. By the use of operator-splitting we decouple the simulation of…
Understanding and modeling human mobility patterns is crucial for effective transportation planning and urban development. Despite significant advances in mobility research, there remains a critical gap in simulation platforms that allow…
We show that efficient simulations of the Kardar-Parisi-Zhang interface growth in 2 + 1 dimensions and of the 3-dimensional Kinetic Monte Carlo of thermally activated diffusion can be realized both on GPUs and modern CPUs. In this article…
Comprehending the performance bottlenecks at the core of the intricate hardware-software interactions exhibited by highly parallel programs on HPC clusters is crucial. This paper sheds light on the issue of automatically asynchronous MPI…
We present a Python extension to the massively parallel HPC simulation toolkit waLBerla. waLBerla is a framework for stencil based algorithms operating on block-structured grids, with the main application field being fluid simulations in…
Task-based programming models have become very popular, as they offer an attractive solution to parallelize serial application code with task and data annotations. They usually depend on a runtime system that schedules the tasks to multiple…
High-performance computing (HPC) applications are increasingly executed in heterogeneous environments, introducing new challenges for programming and software portability. SYCL has emerged as a leading model designed to simplify…
The evolving requirements of Internet of Things (IoT) applications are driving an increasing shift toward bringing intelligence to the edge, enabling real-time insights and decision-making within resource-constrained environments. Tiny…