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      Molecular dynamics simulations in photosynthesis

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          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.

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          Most cited references171

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          QM/MM methods for biomolecular systems.

          Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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            Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid

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              Perspective: Coarse-grained models for biomolecular systems.

              W Noid (2013)
              By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
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                Author and article information

                Contributors
                n.liguori@vu.nl
                s.thallmair@rug.nl
                Journal
                Photosynth Res
                Photosyn. Res
                Photosynthesis Research
                Springer Netherlands (Dordrecht )
                0166-8595
                1573-5079
                15 April 2020
                15 April 2020
                2020
                : 144
                : 2
                : 273-295
                Affiliations
                [1 ]Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
                [2 ]GRID grid.4830.f, ISNI 0000 0004 0407 1981, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, , University of Groningen, ; Nijenborgh 7, 9747 AG Groningen, The Netherlands
                Author information
                http://orcid.org/0000-0001-5695-4012
                http://orcid.org/0000-0003-3469-834X
                http://orcid.org/0000-0001-8423-5277
                http://orcid.org/0000-0002-3396-5840
                Article
                741
                10.1007/s11120-020-00741-y
                7203591
                32297102
                560f7740-9932-4368-b527-4a077a3d1708
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 11 December 2019
                : 24 March 2020
                Categories
                Original Article
                Custom metadata
                © Springer Nature B.V. 2020

                Plant science & Botany
                molecular dynamics,photosynthesis,light harvesting,thylakoid membrane,conformational switch,coarse-grained

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