Introduction to theory-modeling methods in photosynthesisReport as inadecuate




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Photosynthesis Research

, 102:437

First Online: 31 July 2009Received: 03 July 2009Accepted: 13 July 2009

Abstract

Theory and molecular modeling play an increasingly important role in complementing the experimental findings and supporting the interpretation of the data. Owing to the increase in computational power combined with the development of more efficient methods, computer simulations and modeling have emerged as primary ingredients of modern scientific inquiry. Here, we introduce the methods that in our view bring the largest promises in photosynthesis research, indicate how they have already contributed, and can in the near future assume a significant role in this field. Particular emphasis is given to density functional theory and its combination with molecular dynamics simulations. We point out the need for a multi-scale approach in facing the challenging task of describing processes which cover several orders of magnitude both in the time scale and in the size of the systems of interest.

KeywordsDFT Molecular dynamics QMMM Multi-scale simulations Free energy calculations AbbreviationsMDMolecular dynamics

PESPotential energy surface

DFTDensity functional theory

CPMDCar–Parrinello molecular dynamics

QM-MMQuantum mechanics-molecular mechanics

Special issue of Photosynthesis Research -Basics and Applications of Biophysical Techniques in Photosynthesis and Related Processes-.

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Author: Francesco Buda

Source: https://link.springer.com/







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