Related papers: GPU-accelerated Red Blood Cells Simulations with T…
We present a multi-GPU extension of the 3D Gaussian Splatting (3D-GS) pipeline for scientific visualization. Building on previous work that demonstrated high-fidelity isosurface reconstruction using Gaussian primitives, we incorporate a…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
Monte Carlo (MC) simulation is commonly considered to be the most accurate dose calculation method in radiotherapy. However, its efficiency still requires improvement for many routine clinical applications. In this paper, we present our…
The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…
Numerical solution of reaction-diffusion equations in three dimensions is one of the most challenging applied mathematical problems. Since these simulations are very time consuming, any ideas and strategies aiming at the reduction of CPU…
Monte Carlo simulations of the transport of protons in human tissue have been deployed on graphics processing units (GPUs) with impressive results. To provide a more complete treatment of non-elastic nuclear interactions in these…
Computational fluid dynamics and fluid-structure interaction simulations involving moving and deforming bodies is extremely hard. In this work, we present a graphical processing unit (GPU) optimized implementation of the sharp-interface…
We implemented a fast Reciprocal Monte Carlo algorithm, to accurately solve radiative heat transfer in turbulent flows of non-grey participating media that can be coupled to fully resolved turbulent flows, namely to Direct Numerical…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
This dissertation presents the design, implementation and evaluation of GPU-accelerated simulation frameworks for Evolutionary Spatial Cyclic Games (ESCGs), a class of agent-based models used to study ecological and evolutionary dynamics.…
Computational biology has increasingly turned to agent-based modeling to explore complex biological systems. Biological diffusion (diffusion, decay, secretion, and uptake) is a key driver of biological tissues. GPU computing can vastly…
We introduce a simulator of charge transport in fully-depleted, thick CCDs that include Coulomb repulsion between carriers. The calculation of this long-range interaction is highly intensive computationally, and only a few thousands of…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Within the scope of reacting flow simulations, the real-time direct integration (DI) of stiff ordinary differential equations (ODE) for the computation of chemical kinetics stands as the primary demand on computational resources. Meanwhile,…
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…
The reliability of cardiovascular computational models depends on the accurate solution of the hemodynamics, the realistic characterization of the hyperelastic and electric properties of the tissues along with the correct description of…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
The recent trend of using Graphics Processing Units (GPU's) for high performance computations is driven by the high ratio of price performance for these units, complemented by their cost effectiveness. At first glance, computational fluid…
We introduce a GPU-accelerated implementation of time-dependent density functional theory with the minimal auxiliary basis approach (TDDFT-risp) in GPU4PySCF, together with large system demonstrations carried out using the Tamm--Dancoff…