Photosynthesis Research
Springer Netherlands
Molecular dynamics simulations in photosynthesis
Volume: 144, Issue: 2
DOI 10.1007/s11120-020-00741-y

Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.

Keywords dynamics simulations in photosynthesis&author=Nicoletta Liguori,Roberta Croce,Siewert J. Marrink,Sebastian Thallmair,&keyword=Molecular dynamics,Photosynthesis,Light harvesting,Thylakoid membrane,Conformational switch,Coarse-grained,&subject=Original Article,