Optimized CUDA-Based PDE Solver for Reaction Diffusion Systems on Arbitrary Surfaces

Partial differential equation (PDE) solvers are commonly employed to study and characterize the parameter space for reaction-diffusion (RD) systems while investigating biological pattern formation. Increasingly, biologists wish to perform such studies with arbitrary surfaces representing ‘real’ 3D geometries for better insights. In this paper, we present a highly optimized CUDA-based solver for RD equations on triangulated meshes in 3D. We demonstrate our solver using a chemotactic model that can be used to study snakeskin pigmentation, for example. We employ a finite element based approach to perform explicit Euler time integrations. We compare our approach to a naive GPU implementation and provide an in-depth performance analysis, demonstrating the significant speedup afforded by our optimizations. The optimization strategies that we exploit could be generalized to other mesh based processing applications with PDE simulations.

San Antonio Alcohol Safety Action Project - analytic study no. 5-6: analysis of PDE and rehabilitation. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Linear Fractional PDE, Uniqueness of Global Solutions

Mathematics Subject Classification: 26A33, 47A60, 30C15.

Hyperbolic Fibrations and PDE

2010 Mathematics Subject Classification: 35L10, 35L90.

Sub- and Super-solutions of a Nonlinear PDE, and Application to a Semilinear SPDE

2010 Mathematics Subject Classification: 35R60, 60H15, 74H35.

Fast iterative solvers for time-dependent PDE-constrained optimization problems

Otto-von-Guericke-Universität Magdeburg, Fakultät für Mathematik, Kumulative Habilitation, 2016