Related papers: Computational Tools for Cardiac Simulation -- GPU-…
Performing inference over simulators is generally intractable as their runtime means we cannot compute a marginal likelihood. We develop a likelihood-free inference method to infer parameters for a cardiac simulator, which replicates…
Cardiovascular diseases (CVDs) are the leading causes of mortality worldwide. The contraction and relaxation of left ventricle (LV) is the main driving force of blood circulation. Altered LV hemodynamics is believed to be associated with…
The phase-field method has become a useful tool for the simulation of classical metallurgical phase transformations as well as other phenomena related to materials science. The thermodynamic consistency that forms the basis of these…
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
In this study, we present a comprehensive numerical analysis of blood flow within human left ventricle models, with particular emphasis on optimizing simulation conditions to enhance the realism and computational efficiency of heart flow…
Simulations of systems with quenched disorder are extremely demanding, suffering from the combined effect of slow relaxation and the need of performing the disorder average. As a consequence, new algorithms, improved implementations, and…
Executing large quantum circuits is not feasible using the currently available NISQ (noisy intermediate-scale quantum) devices. The high costs of using real quantum devices make it further challenging to research and develop quantum…
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…
Quantum computing is an emerging technology, promising a paradigm shift in computing, and allowing for speedups in many different problems. However, quantum devices are still in their early stages, most with only a small number qubits. This…
Simulations of physical phenomena are essential to the expedient design of precision components in aerospace and other high-tech industries. These phenomena are often described by mathematical models involving partial differential equations…
The heart is a vital organ that relies on the orchestrated propagation of electrical stimuli to coordinate each heart beat. Abnormalities in the heart's electrical behaviour can be managed with a cardiac pacemaker. Recently, the closed-loop…
We present the meshfree Mixed Collocation Method (MCM) to solve the monodomain model for numerical simulation of cardiac electrophysiology. We apply MCM to simulate cardiac electrical propagation in 2D tissue sheets and 3D tissue slabs as…
We explore how the big-three computing paradigms -- symmetric multi-processor (SMC), graphical processing units (GPUs), and cluster computing -- can together be brought to bare on large-data Gaussian processes (GP) regression problems via a…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
In this paper we describe and demonstrate a C++ code written to determine the trajectory of particles traversing oriented single crystals and a CUDA code written to evaluate the radiation spectra from charged particles with arbitrary…
Current supercomputers often have a heterogeneous architecture using both CPUs and GPUs. At the same time, numerical simulation tasks frequently involve multiphysics scenarios whose components run on different hardware due to multiple…
Computational fluid dynamics (CFD) models of blood flow in the left ventricle (LV) and aorta are important tools for analyzing the mechanistic links between myocardial deformation and flow patterns. Typically, the use of image-based…
In this work, we detail the GPU-porting of an in-house pseudo-spectral solver tailored towards large-scale simulations of interface-resolved simulation of drop- and bubble-laden turbulent flows. The code relies on direct numerical…
The study of thrombosis is crucial to understand and develop new therapies for diseases like deep vein thrombosis, diabetes related strokes, pulmonary embolism etc. The last two decades have seen an exponential growth in studies related to…