Abstract
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.
Highlights
Photosynthesis spans disparate length and time scales, from femtosecond quantum events to seasonal canopy-scale processes
Many of the key phenomena that regulate the efficiency of lightharvesting and charge separation in the thylakoid membrane occur on intermediate scales—nanometers to microns in space, and milliseconds to minutes in time
The popular biochemical, spectroscopic, and fluorescence microscopy methods are effective for exploring protein behavior within and trafficking between grana and stroma lamellae, but obscure functional distinctions between the many local environments within each membrane region
Summary
Photosynthesis spans disparate length and time scales, from femtosecond quantum events to seasonal canopy-scale processes. Many of the key phenomena that regulate the efficiency of lightharvesting and charge separation in the thylakoid membrane occur on intermediate scales—nanometers to microns in space, and milliseconds to minutes in time In this regime, it has been experimentally challenging to simultaneously probe structure and function. Coarse-grained modeling is powerful and widely applicable, yet, like any scientific technique, requires attention to a host of subtleties if it is to yield meaningful insights (Frenkel, 2013) In this Mini Review, we outline key considerations for building and utilizing coarse-grained models of plant photosynthetic membrane systems, and give examples of research topics in this field where simulation has been or could be a valuable complement to experiment
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