Related papers: GridFF: Efficient Simulation of Organic Molecules …
Accelerating molecular docking -- the process of predicting how molecules bind to protein targets -- could boost small-molecule drug discovery and revolutionize medicine. Unfortunately, current molecular docking tools are too slow to screen…
This paper presents a heterogeneous adaptive mesh refinement (AMR) framework for efficient simulation of moderately stiff reactive problems. This framework features an elaborate subcycling-in-time algorithm along with a specialized…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
The field of plasma physics heavily relies on simulations to model various phenomena, such as instabilities, turbulence, and nonlinear behaviors that would otherwise be difficult to study from a purely theoretical approach. Simulations are…
This article proposes a novel high-performance computing approach for the prediction of the temperature field in powder bed fusion (PBF) additive manufacturing processes. In contrast to many existing approaches to part-scale simulations,…
Magnetohydrodynamic (MHD) simulations based on the ideal MHD equations have become a powerful tool for modeling phenomena in a wide range of applications including laboratory, astrophysical, and space plasmas. In general, high-resolution…
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high…
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving correctly and consistently with, e.g., available…
We present GO-Surf, a direct feature grid optimization method for accurate and fast surface reconstruction from RGB-D sequences. We model the underlying scene with a learned hierarchical feature voxel grid that encapsulates multi-level…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
Commercial graphics processors (GPUs) have high compute capacity at very low cost, which makes them attractive for general purpose scientific computing. In this paper we show how graphics processors can be used for N-body simulations to…
We present a new algorithm to quickly generate high-performance GPU implementations of complex imaging and vision pipelines, directly from high-level Halide algorithm code. It is fully automatic, requiring no schedule templates or…
Machine learning force fields (MLFFs) are gradually evolving towards enabling molecular dynamics simulations of molecules and materials with ab initio accuracy but at a small fraction of the computational cost. However, several challenges…
We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…
Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
COVID-19 has shown the importance of having a fast response against pandemics. Finding a novel drug is a very long and complex procedure, and it is possible to accelerate the preliminary phases by using computer simulations. In particular,…
Simulating large-scale microswimmer dynamics in viscous fluid poses significant challenges due to the coupled high spatial and temporal complexity. Conventional high-performance computing (HPC) methods often address these two dimensions in…
Rapid growth in scientific data and a widening gap between computational speed and I/O bandwidth make it increasingly infeasible to store and share all data produced by scientific simulations. Instead, we need methods for reducing data…
There exists an increasing interest for using immersed boundary methods (IBMs) (Peskin 2000) to model moving objects in computational fluid dynamics. Indeed, this approach is particularly efficient, because the fluid mesh does not require…