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We design, implement, and evaluate GPU-based algorithms for the maximum cardinality matching problem in bipartite graphs. Such algorithms have a variety of applications in computer science, scientific computing, bioinformatics, and other…
Solving exactly Combinatorial Optimization Problems (COPs) using a Branch-and-Bound (B&B) algorithm requires a huge amount of computational resources. Therefore, we recently investigated designing B&B algorithms on top of graphics…
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Modeling multimetallic systems efficiently enables faster prediction of desirable chemical properties and design of new materials. This work describes an initial implementation for performing multireference wave function method localized…
Accurate numerical simulations of interaction between fluid and solid play an important role in applications. The task is challenging in practical scenarios as the media are usually highly heterogeneous with very large contrast. To overcome…
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This article presents an optimized algorithm and implementation for calculating resolution-of-the-identity Hartree-Fock (RI-HF) energies and analytic gradients using multiple Graphics Processing Units (GPUs). The algorithm is especially…
The alpha complex, a subset of the Delaunay triangulation, has been extensively used as the underlying representation for biomolecular structures. We propose a GPU-based parallel algorithm for the computation of the alpha complex, which…
Real-world node embedding applications often contain hundreds of billions of edges with high-dimension node features. Scaling node embedding systems to efficiently support these applications remains a challenging problem. In this paper we…
We describe a method for parallelizing the lexicographic enumeration algorithm for the factorization set of an element in a numerical semigroup via bounds. This enables the use of GPU and distributed computing methods. We provide a CUDA…
Particle accelerator modeling is an important field of research and development, essential to investigating, designing and operating some of the most complex scientific devices ever built. Kinetic simulations of relativistic, charged…
Cosmic-ray acceleration processes in astrophysical plasmas are often investigated with fully-kinetic or hybrid kinetic numerical simulations, which enable us to describe a detailed microphysics of particle energization mechanisms. Tracing…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
In this paper we have derived explicitly computable bounds on the error in energy norms for the fully nonlinear Poisson-Boltzmann equation. Together with the computable bounds, we have also obtained efficient error indicators which can…
Molecular Dynamics (MD) simulations play a central role in physics-driven drug discovery. MD applications often use the Particle Mesh Ewald (PME) algorithm to accelerate electrostatic force computations, but efficient parallelization has…
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We develop a GPU-accelerated dynamic programming (DP) method for valuing, operating, and bidding energy storage under multistage stochastic electricity prices. Motivated by computational limitations in existing models, we formulate DP…