NERSCPowering Scientific Discovery Since 1974

Jonathan Madsen

Dissertation Announcement
Jonathan R. Madsen Ph.D.
Application Performance Specialist
1 Cyclotron Rd
Berkeley, CA 94720 US


Jonathan Madsen earned his Ph.D. from Texas A&M University in Nuclear Engineering in December 2017 under the supervision of Dr. Ryan G. McClarren and Dr. John Ford and earned his M.S. in Nuclear Engineering (Health Physics) in August 2013 under the supervision of Dr. Gamal Akabani. His doctoral research focused on applying the concepts of compressed sensing to Monte Carlo scoring arrays in an effort to reduce memory allocation and reduce computation time through statistical de-noising during the reconstruction of the solution and his masters research focused on extending the classical Monte Carlo transport approach to utilize a quantum-mechanical description of the electron probability densities

He has been a member of the Geant4 collaboration since 2011 and is currently serving as the Deputy Coordinator of the Run, Event, and Detector Responses Working Group and the Deputy Coordinator of the Geant4 Research and Development Task Force, and is a primary developer for the Geant Exascale Proxy Application with the DOE's Exascale Computing Project.

During his time as a NESAP for Data post-doc on the TomoPy project at NERSC, he implemented two high-fidelity iterative algorithms for tomographic reconstruction on the GPU, which were previously discarded due to inferiority to other algorithms on the CPU, and increased the scientific throughput by a factor exceeding 215x on 8 GPUs vs. the Edison supercomputer. The scientific impact of this result was a reduction of a minimum of ~6.5 hours to reach acceptable tolerance to ~110 seconds.

Research Interests

High-performance computing, parallel computing, multithreading, GPU-offloading, C, C++, Python, CUDA, Monte Carlo transport, deterministic transport, porting scientific software applications to highly-parallel machines, computational physics


  • Madsen, J.R. and G. Akabani, Low-energy cross-section calculations of single molecules by electron impact : a classical Monte Carlo transport approach with quantum mechanical description. Phys Med Biol, 2014. 59(9): p. 2285-305.