Johan Strümpfer and Klaus Schulten.
Open quantum dynamics calculations with the hierarchy equations of
motion on parallel computers.
Journal of Chemical Theory and Computation, 8:2808-2816, 2012.
(PMC: 3480185)
STRU2012A
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.
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