相关论文: Message-Passing Multi-Cell Molecular Dynamics on t…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Machine learning potentials have achieved great success in accelerating atomistic simulations. Many of them relying on atom-centered local descriptors are natural for parallelization. More recent message passing neural network (MPNN) models…
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
Physical phenomena such as chemical reactions, bond breaking, and phase transition require molecular dynamics (MD) simulation with ab initio accuracy ranging from milliseconds to microseconds. However, previous state-of-the-art neural…
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…
Training machine learning models in parallel is an increasingly important workload. We accelerate distributed parallel training by designing a communication primitive that uses a programmable switch dataplane to execute a key step of the…
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
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…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have…
In diffusion-based molecular communication, information is transferred from a transmitter to a receiver using molecular carriers. The low achievable data rate is the main disadvantage of diffusion-based molecular over radio-based…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
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…
A novel adaptive technique for electromagnetic Particle In Cell (PIC) plasma simulations is presented here. Two main issues are identified in designing adaptive techniques for PIC simulation: first, the choice of the size of the particle…
In diffusion-based molecular communication, information transport is governed by diffusion through a fluid medium. The achievable data rates for these channels are very low compared to the radio-based communication system, since diffusion…
Significant inter-symbol interference (ISI) challenges the achievement of reliable, high data-rate molecular communication via diffusion. In this paper, a hybrid modulation based on pulse position and concentration is proposed to mitigate…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
Mode-division multiplexing (MDM) is seen as a possible solution to satisfy the rising capacity demands of optical communication networks. To make MDM a success, fibers supporting the propagation of a huge number of modes are of interest.…