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The Stokeslet and stresslet kernels are commonly used in boundary element simulations and singularity methods for slow viscous flow. Evaluating the velocity induced by a collection of Stokeslets and stresslets by direct summation requires…
Finite element methods usually construct basis functions and quadrature rules for multidimensional domains via tensor products of one-dimensional counterparts. While straightforward, this approach results in integration spaces larger than…
We present Fast Approximate Minimum Spanning Tree (FAMST), a novel algorithm that addresses the computational challenges of constructing Minimum Spanning Trees (MSTs) for large-scale and high-dimensional datasets. FAMST utilizes a…
Computing fixed-radius near-neighbor graphs is an important first step for many data analysis algorithms. Near-neighbor graphs connect points that are close under some metric, endowing point clouds with a combinatorial structure. As…
We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism…
A heterogeneous CPU-GPU node is getting popular in HPC clusters. We need to rethink algorithms and optimization techniques for such system depending on the relative performance of CPU vs. GPU. In this paper, we report a performance…
A key scalability challenge in neural solvers for industrial-scale physics simulations is efficiently capturing both fine-grained local interactions and long-range global dependencies across millions of spatial elements. We introduce the…
This work introduces a kernel-independent, multilevel, adaptive algorithm for efficiently evaluating a discrete convolution kernel with a given source distribution. The method is based on linear algebraic tools such as low rank…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
We design and implement HPMC, a scalable hard particle Monte Carlo simulation toolkit, and release it open source as part of HOOMD-blue. HPMC runs in parallel on many CPUs and many GPUs using domain decomposition. We employ BVH trees…
Contour trees offer an abstract representation of the level set topology in scalar fields and are widely used in topological data analysis and visualization. However, applying contour trees to large-scale scientific datasets remains…
Computational experiments are exploited in finding a well-designed processing path to optimize material structures for desired properties. This requires understanding the interplay between the processing-(micro)structure-property linkages…
Gyrokinetic codes in plasma physics need outstanding computational resources to solve increasingly complex problems, requiring the effective exploitation of cutting-edge HPC architectures. This paper focuses on the enabling of ORB5, a…
Current trends in the computer graphics community propose leveraging the massive parallel computational power of GPUs to accelerate physically based simulations. Collision detection and solving is a fundamental part of this process. It is…
The tree method is a widely implemented algorithm for collisionless $N$-body simulations in astrophysics well suited for GPU(s). Adopting hierarchical time stepping can accelerate $N$-body simulations; however, it is infrequently…
Executing quantum algorithms over distributed quantum systems requires quantum circuits to be divided into sub-circuits which communicate via entanglement-based teleportation. Naively mapping circuits to qubits over multiple quantum…
The understanding of the mechanisms driving vascular development is still limited. Techniques to generate vascular trees synthetically have been developed to tackle this problem. However, most algorithms are limited to single trees inside…
Embedding tree-like data, from hierarchies to ontologies and taxonomies, forms a well-studied problem for representing knowledge across many domains. Hyperbolic geometry provides a natural solution for embedding trees, with vastly superior…
We introduce our new binary tree code for neighbour search and gravitational force calculations in an N-particle system. The tree is built in a "top-down" fashion by "recursive coordinate bisection" where on each tree level we split the…
Binary Partition Hierarchies (BPH) and minimum spanning trees are fundamental data structures involved in hierarchical analysis such as quasi-flat zones or watershed. However, classical BPH construction algorithms require to have the whole…