Related papers: Revisiting FPGA Acceleration of Molecular Dynamics…

Recent hardware acceleration advances have enabled powerful specialized accelerators for finite element computations, spiking neural network inference, and sparse tensor operations. However, existing approaches face fundamental limitations:…

Implementing an application on a FPGA remains a difficult, non-intuitive task that often requires hardware design expertise in a hardware description language (HDL). High-level synthesis (HLS) raises the design abstraction from HDL to…

The use of Field Programmable Gate Arrays (FPGAs) to accelerate computational kernels has the potential to be of great benefit to scientific codes and the HPC community in general. With the recent developments in FPGA programming…

Machine learning (ML)-based steering can improve the performance of ensemble-based simulations by allowing for online selection of more scientifically meaningful computations. We present DeepDriveMD, a framework for ML-driven steering of…

This research delves into sophisticated neural network frameworks like Convolutional Neural Networks (CNN), Recurrent Neural Networks (RNN), Long Short-Term Memory Networks (LSTMs), and Deep Belief Networks (DBNs) for improved analysis of…

Particle accelerator modeling is an important field of research and development, essential to investigating, designing and operating some of the most complex scientific devices ever built. Kinetic simulations of relativistic, charged…

Space missions increasingly deploy high-fidelity sensors that produce data volumes exceeding onboard buffering and downlink capacity. This work evaluates FPGA acceleration of neural networks (NNs) across four space use cases on the AMD…

Implementing Machine Learning (ML) models on Field-Programmable Gate Arrays (FPGAs) is becoming increasingly popular across various domains as a low-latency and low-power solution that helps manage large data rates generated by continuously…

The current over-provisioned heterogeneous multi-cores require effective run-time optimization strategies, and the run-time power monitoring subsystem is paramount for their success. Several state-of-the-art methodologies address the design…

Molecular dynamics (MD) simulates the time evolution of atomic systems governed by interatomic forces, and the fidelity of these simulations depends critically on the underlying force model. Classical force fields (CFFs) rely on fixed…

Mass spectrometry (MS) is essential for protein analysis but faces significant challenges with large datasets and complex post-translational modifications, resulting in difficulties in spectral identification. Open Modification Search (OMS)…

Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…

Heterogeneous embedded systems, with diverse computing elements and accelerators such as FPGAs, offer a promising platform for fast and flexible ML inference, which is crucial for services such as autonomous driving and augmented reality,…

Recent trends in business and technology (e.g., machine learning, social network analysis) benefit from storing and processing growing amounts of graph-structured data in databases and data science platforms. FPGAs as accelerators for graph…

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…

In high-energy physics, the increasing luminosity and detector granularity at the Large Hadron Collider are driving the need for more efficient data processing solutions. Machine Learning has emerged as a promising tool for reconstructing…

There is a large body of legacy scientific code written in languages like Fortran that is not optimised to get the best performance out of heterogeneous acceleration devices like GPUs and FPGAs, and manually porting such code into parallel…

With their widespread availability, FPGA-based accelerators cards have become an alternative to GPUs and CPUs to accelerate computing in applications with certain requirements (like energy efficiency) or properties (like fixed-point…

Large Language Models (LLMs) with Mixture-of-Expert (MoE) architectures achieve superior model performance with reduced computation costs, but at the cost of high memory capacity and bandwidth requirements. Near-Memory Processing (NMP)…

Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…