Related papers: JAX, M.D.: A Framework for Differentiable Physics
We present a novel, JAX-powered implementation of a parametric component-separation method for CMB polarization data, explicitly designed to handle spatially varying foreground Spectral Energy Distributions (SEDs). The approach models this…
Accurate and efficient thermal dynamics models of permanent magnet synchronous motors are vital to efficient thermal management strategies. Physics-informed methods combine model-based and data-driven methods, offering greater flexibility…
We introduce microJAX, the first fully differentiable implementation of the image-centered ray-shooting (ICRS) algorithm for gravitational microlensing. Built on JAX and its XLA just-in-time compiler, microJAX exploits GPU parallelism while…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
We introduce JPC, a JAX library for training neural networks with Predictive Coding. JPC provides a simple, fast and flexible interface to train a variety of PC networks (PCNs) including discriminative, generative and hybrid models. Unlike…
We propose the use of automatic differentiation through the programming framework jax for accelerating a variety of analysis tasks throughout gravitational wave (GW) science. Firstly, we demonstrate that complete waveforms which cover the…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
We present jax-cosmo, a library for automatically differentiable cosmological theory calculations. It uses the JAX library, which has created a new coding ecosystem, especially in probabilistic programming. As well as batch acceleration,…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Simulating rigid-body dynamics with contact in a fast, massively vectorizable, and smoothly differentiable manner is highly desirable in robotics. An important bottleneck faced by existing differentiable simulation frameworks is contact…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
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…