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2 - Open quantum system approaches to biological systems
- from Part I - Introduction
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- By Alireza Shabani, University of California, Masoud Mohseni, Google, Seogjoo Jang, University of New York, Akihito Ishizaki, University of California Berkeley, Martin Plenio, Universität Ulm, Patrick Rebentrost, Harvard University, Alan Aspuru-Guzik, Harvard University, Jianshu Cao, Massachusetts Institute of Technology, Seth Lloyd, Massachusetts Institute of Technology, Robert Silbey, Massachusetts Institute of Technology
- Edited by Masoud Mohseni, Yasser Omar, Gregory S. Engel, University of Chicago, Martin B. Plenio, Universität Ulm, Germany
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- Book:
- Quantum Effects in Biology
- Published online:
- 05 August 2014
- Print publication:
- 07 August 2014, pp 14-52
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- Chapter
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Summary
Quantum biology, as introduced in the previous chapter, mainly studies the dynamical influence of quantum effects in biological systems. In processes such as exciton transport in photosynthetic complexes, radical pair spin dynamics in magnetoreception, and photo-induced retinal isomerization in the rhodopsin protein, a quantum description is a necessity rather than an option. The quantum modelling of biological processes is not limited to solving the Schrödinger equation for an isolated molecular structure. Natural systems are open to the exchange of particles, energy or information with their surrounding environments that often have complex structures. Therefore the theory of open quantum systems plays a key role in dynamical modelling of quantum-biological systems. Research in quantum biology and open quantum system theory have found a bilateral relationship. Quantum biology employs open quantum system methods to a great extent while serving as a new paradigm for development of advanced formalisms for non-equilibrium biological processes.
In this chapter, we overview the basic concepts of quantum mechanics and approaches to open quantum system (or decoherence) dynamics. Here, we do not intend to discuss all aspects of about a century-old theory of open quantum systems that dates back to the original work of Paul Dirac on atomic radiative emission and absorption (Dirac, 1927). Instead, we mainly focus on the integro-differential equations that are commonly used for modelling quantum-biological systems. Interested readers can learn more about open quantum systems in various books and review articles in both physics and chemistry literature, including the references (Kraus, 1983; Breuer and Petruccione, 2002; Kubo et al., 2003; Weiss, 2008; May and Kühn, 2011).
3 - Generalized Förster resonance energy transfer
- from Part I - Introduction
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- By Seogjoo Jang, University of New York, Hoda Hossein-Nejad, University College London, Gregory D. Scholes, University of Toronto
- Edited by Masoud Mohseni, Yasser Omar, Gregory S. Engel, University of Chicago, Martin B. Plenio, Universität Ulm, Germany
-
- Book:
- Quantum Effects in Biology
- Published online:
- 05 August 2014
- Print publication:
- 07 August 2014, pp 53-81
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- Chapter
- Export citation
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Summary
Introduction
Decades of effort in structural biology and ultrafast spectroscopy have elucidated many details of natural photosynthesis (Blankenship, 2002; Hu et al., 2002), and it is now a well-established fact that the initial light-harvesting process that leads up to the collection of energy at reaction centres, where charge transfer reaction occurs, is a process with almost perfect efficiency. The mechanism underlying the energy migration in a photosynthetic system is a fundamentally quantum-mechanical one, known as excitation energy transfer (EET) or resonance energy transfer (RET) (Silbey, 1976; Agranovich and Galanin, 1982; Scholes, 2003; May and Kühn, 2011; Olaya-Castro and Scholes, 2011).
Resonance energy transfer is ubiquitous, and had been observed as sensitized luminescence long before modern quantum-mechanical understanding of molecular systems was established (Agranovich and Galanin, 1982). Normally, when a molecule becomes excited electronically by absorbing a photon, it luminesces by emitting another photon, within about a nanosecond, if it is fluorescence, or much later for phosphorescence. However, when another molecule with similar excitation energy is present within a distance of tens of nanometres, it can swap its excitation with the molecule as follows:
D∗ + A → D + A∗,
where D∗ (D) is the excited (ground) state donor of the energy and A (A∗) is the ground (excited) state acceptor. Thus, the excitation of D sensitizes that of A.
Clear and sensible understanding of the RET process had been beyond the reach of classical mechanics as had any other molecular processes involving matter–radiation interaction.