2012/06/15 by Johan Strümpfer, Klaus Schulten · 1 citation
Physics and Astronomy · Biochemistry, Genetics and Molecular Biology · #Spectroscopy and Quantum Chemical Studies #Photosynthetic Processes and Mechanisms #Advanced Chemical Physics Studies
paper · doi:10.1021/ct3003833
openalex publication_date 2012/06/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/06/24
Calculating the evolution of an open quantum system, i.e., a system in contact with a thermal environment, has presented a theoretical and computational challenge for many years. With the advent of supercomputers containing large amounts of memory and many processors, the computational challenge posed by the previously intractable theoretical models can now be addressed. The hierarchy equations of motion present one such model and offer a powerful method that remained under-utilized so far due to its considerable computational expense. By exploiting concurrent processing on parallel computers the hierarchy equations of motion can be applied to biological-scale systems. Herein we introduce the quantum dynamics software PHI, that solves the hierarchical equations of motion. We describe the integrator employed by PHI and demonstrate PHI's scaling and efficiency running on large parallel computers by applying the software to the calculation of inter-complex excitation transfer between the light harvesting complexes 1 and 2 of purple photosynthetic bacteria, a 50 pigment system.