Coarse-grained computer simulation of dynamics in thylakoid membranes: methods and opportunities.
Coarse-grained simulation is a powerful and well-established suite of computational methods for studying structure and dynamics in nanoscale biophysical systems. As our understanding of the plant photosynthetic apparatus has become increasingly nuanced, opportunities have arisen for coarse-grained simulation to complement experiment by testing hypotheses and making predictions. Here, we give an overview of best practices in coarse-grained simulation, with a focus on techniques and results that are applicable to the plant thylakoid membrane-protein system. We also discuss current research topics for which coarse-grained simulation has the potential to play a key role in advancing the field.
Biophysics Graduate Group, University of California Berkeley, CA, USA ; Department of Chemistry, University of California Berkeley, CA, USA.
Anna R
AR
Schneider
Department of Chemistry, University of California Berkeley, CA, USA ; Chemical Sciences and Physical Biosciences Divisions, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
Phillip L
PL
Geissler
Brownian dynamics; Monte Carlo; coarse-grained modeling; nanoscale; photosystem; simulation; thylakoid membrane