Molecular dynamics simulations in photosynthesis

Nicoletta Liguori*, Roberta Croce, Siewert Jan Marrink, Sebastian Thallmair*

*Corresponding author for this work

Research output: Contribution to JournalReview articleAcademicpeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)273-295
JournalPhotosynthesis Research
Volume144
Issue number2
DOIs
Publication statusPublished - 15 Apr 2020

Funding

This work is supported by The Netherlands Organization for Scientific Research (NWO), via a Veni Grant to N.L. and via a TOP Grant to R.C. S.T. thanks the European Commission for financial support via a Marie Skłodowska-Curie Actions Individual Fellowship (MicroMod-PSII, Grant Agreement 748895).

FundersFunder number
H2020 Marie Skłodowska-Curie Actions748895
European Commission
Nederlandse Organisatie voor Wetenschappelijk Onderzoek

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    • NWO VENI grant

      Liguori, Nicoletta (Recipient), 2018

      Prize / Grant: GrantAcademic

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