Related papers: PSDF: Particle Stream Data Format for N-Body Simul…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
We propose a new file format named "H5MD" for storing molecular simulation data, such as trajectories of particle positions and velocities, along with thermodynamic observables that are monitored during the course of the simulation. H5MD…
Scenario-aware dataflow (SADF) is a prominent tool for modeling and analysis of dynamic embedded dataflow applications. In SADF the application is represented as a finite collection of synchronous dataflow (SDF) graphs, each of which…
Nowadays simulations can produce petabytes of data to be stored in parallel filesystems or large-scale databases. This data is accessed over the course of decades often by thousands of analysts and scientists. However, storing these volumes…
GANDALF is a new hydrodynamics and N-body dynamics code designed for investigating planet formation, star formation and star cluster problems. GANDALF is written in C++, parallelised with both OpenMP and MPI and contains a python library…
Stokesian Dynamics (SD) is a powerful computational framework for simulating the motion of particles in a viscous Newtonian fluid under Stokes-flow conditions. Traditional SD implementations can be computationally expensive as they rely on…
Realistic simulation of dynamic scenes requires accurately capturing diverse material properties and modeling complex object interactions grounded in physical principles. However, existing methods are constrained to basic material types…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Hospitals around the world collect massive amounts of physiological data from their patients every day. Recently, there has been an increase in research interest to subject this data to statistical analysis to gain more insights and provide…
Exa-scale simulations are on the horizon but almost no new design for the output has been proposed in recent years. In simulations using individual time steps, the traditional snapshots are over resolving particles/cells with large time…
Palabos-npFEM is a computational framework for the simulation of blood flow with fully resolved constituents. The software resolves the trajectories and deformed state of blood cells, such as red blood cells and platelets, and the complex…
State-space models (SSMs) are a widely used tool in time series analysis. In the complex systems that arise from real-world data, it is common to employ particle filtering (PF), an efficient Monte Carlo method for estimating the hidden…
We present FlowPM, a Particle-Mesh (PM) cosmological N-body code implemented in Mesh-TensorFlow for GPU-accelerated, distributed, and differentiable simulations. We implement and validate the accuracy of a novel multi-grid scheme based on…
Background and Objective: Hemodynamic analysis of blood flow through arteries and veins is critical for diagnosing cardiovascular diseases, such as aneurysms and stenoses, and for investigating cardiovascular parameters, such as turbulence…
Molecular dynamics simulations have been used in different scientific fields to investigate a broad range of physical systems. However, the accuracy of calculation is based on the model considered to describe the atomic interactions. In…
Nauticle is a general-purpose simulation tool for the flexible and highly configurable application of particle-based methods of either discrete or continuum phenomena. It is presented that Nauticle has three distinct layers for users and…
Astrophysical research in recent decades has made significant progress thanks to the availability of various $N$-body simulation techniques. With the rapid development of high-performance computing technologies, modern simulations have been…
Simulating trajectories of dynamical systems is a fundamental problem in a wide range of fields such as molecular dynamics, biochemistry, and pedestrian dynamics. Machine learning has become an invaluable tool for scaling physics-based…
Most existing Dynamic Gaussian Splatting methods for complex dynamic urban scenarios rely on accurate object-level supervision from expensive manual labeling, limiting their scalability in real-world applications. In this paper, we…
In many real-world OpenFlow-based SDN deployments, the ability to program heterogeneous forwarding elements built with different forwarding architectures is a desirable capability. In this paper, we discuss a data plane programming…