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Protein
1.) Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems - Engel et al - Evidence for functional quantum coherence in photosynthetic protein 2.) Coherently wired light-harvesting in photosynthetic marine algae at ambient temperatures - Collini et al - Evidence for room temperature functional quantum coherence in photosynthetic protein. 3.) Dynamics of Light Harvesting in Photosynthesis - Cheng & Fleming - Impact of advances in modelling and spectroscopic techniques on understanding of quantum coherence in photosysnthetic protein. 4.) Genes don't reveal all - based on Michael Snyder, Stanford - Influence of transcription factor proteins on genes 1.) Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems Gregory Engel et al Dept. of Chemistry, University of California Berkeley Nature, vol. 446, pp. 782-6, April 2007 This paper points out that photosynthetic complexes are adapted to capture light, and put its energy into long-term storage. This process has normally been described in classical terms, and quantum coherence has been to a good extent ignored in the traditional analysis. However, the possibility of quantum coherence has been predicted, and in this paper the authors describe evidence for long-lived quantum coherence being involved in energy transfer within photosynthetic systems. The wavelike process is thought to account for the efficiency of the sytem, because it allows the sampling of large areas of phase space, in order to find the most efficient path, or to transfering energy to the area in the lowest energy state. The Engel et al experiment involved electronic spectroscopy to observe the evolution of electronic coherence. Quantum beating was found to last for 660 fs, which was much more than the 250 fs estimated for conventional models. Conventional models had assumed that quantum coherence would be rapidly destroyed, and had therefore not factored it into their models of photosynthetic systems. By contrast, the authors conclude that long-lived quantum coherence must play an active role in photosynthetic systems. A quantum coherent system allows sampling in order to direct energy to the lowest energy state. The system is viewed as performing a quantum computation, in which it senses many states simultaneously and from these selects the correct answer. This is seen as analogous to Grover's algorithm, allowing both the discovery of the lowest energy state and the transfer of coherence. This is more efficent than any classical search engine. Protein is seen as providing the structure in which coherence can be preserved and at the same time modulating the coherence as a result of the local dielectric environment. 2.) ROOM TEMPERATURE QUANTUM COHERENCE IN PROTEIN Coherently wired light-harvesting in photosynthetic marine algae at ambient temperatures Elisabetta Collini, Cathy Wong, Krystyna Wilk, Paul Curmi, Paul Brumer & Gregory Scholes Universities of Toronto, New South Wales and Padua Nature, 463, pp. 644-7, 4 February 2010 doi:10.1038/nature08811 INTRODUCTION: This low-key paper may in time come to be seen as one of the decisive studies of the 21st century. The paper shows that room temperature quantum coherence can occur in biological matter. In 2007, Engel et al had shown that coherence was possible in organic matter, but this was only demonstrated at very low temperatures, whereas the Collini study demonstrates similar activity at ambient temperature. The paper and related commentaries makes no mention of consciousness, although a relevance to quantum computing is suggested, which is a possible step towards discussing consciousness. The main plank of the arguments against quantum consciousness relates to the speed of decoherence in biological matter being too quick for coherence to be relevant to processing, particularly neural processing, in such matter. This argument looks to have been substantially undermined by the recent study. Antenna proteins are an essential part of the photosyntetic process, which absorbs light and transmits the resulting excitation between molecules to a reaction centre. Recent research has concentrated on determining the mechanisms that support a very high level of efficiency in this energy transport. Light-harvesting antennas are comprised of eight pigment-molecules, with different pigments absorbing different frequencies of light. The route the energy takes across the molecule is important in terms of energy efficiency. Studies have documented the fact that light-absorbing molecules in some photosynthetic proteins transfer energy according to quantum mechanical rather than classical laws even at ambient temperature. This contradicts the 20th century dogma that long-range quantum coherence would always decohere in the temperatures found found in biological systems. This paper by Collini et al describes X-ray crystallography studies of two types of marine cryptophyte algae that have long-lasting excitation oscillations and correlations and anti-correlations, symptomatic of quantum coherence even at ambient temperature. Distant molecules within the photosynthetic protein are thought to be connected to quantum coherence, and to produce efficient light-harvesting as a result. The cryptophytes can photosynthesise in low-light conditions suggesting a particularly efficient transfer of energy within protein. According to the traditional theory, this would imply only small separation between chromophores, whereas the actual separation is unusually large. In this study, performed at room temperature, the antenna protein received a laser pulse, which results in a coherent superposition in the protein. The experimental data of the study shows that the superposition persists for 400 femtoseconds and over a distance of 2.5 nanometres. Quantum coherence occurs in a complex mix of quantum interference between electronic resonances, and decoherence caused by interaction with the environment. The authors think that long-lived quantum coherence facilitates efficient energy transfer across protein units. The authors remains uncertain, as to how quantum coherence can persist for hundreds of femtoseconds in biological matter. One suggestion is that the expected rate of decoherence is slowed by shared or correlated motions in the surrounding environment. Where light-harvesting chromophores are covalently bound to the protein backbone, it is suggested that this may strengthen correlated motions between the chromophores and the protein. In the same issue of 'Nature' that published Collinis study, the 'News and Views' section of the journal also comments on her paper. It emphasises that this is the first study in which quantum coherence in photosynthetic proteins has been observed at room temperature. It comments on the remarkable efficiency of energy transfer, between the antennas that guide excitation energy from hundreds of light-absorbing pigment molecules towards the subsequent reaction centres that drive biochemical events. Collini is suggesting that quantum coherence could be a factor in this efficiency. Earlier studies had observed coherent behaviour in green sulphur bacteria, but at very low temperatures. Collini et al observed quantum coherence in the antenna, and found that this persisted over 400 femtoseconds, in contrast to an expectation in traditional theory of only 100 femtoseconds. Coherence was observed between widely separated pigment molecules. This has also been observed in bacterial light-harvesting complexes. However, this was at very low temperatures, while the Collini study was at room temperature. Engel et al, who were responsible for some of the earlier studies, have speculated that quantum coherence allows antennas to search for the lowest energy state of the complex more efficiently, thus enhancing the energy transfer to the reaction centre. Coherence might help excitations to avoid local energy traps or minima, on their way to the reaction centre. Covalent binding to the protein backbone is speculated to make coherence longer lasting. Perhaps the most surprising aspect of this latest paper on coherence in proteins is the speed with which news of the development has made its way to the level of more popular science, in the form of a useful full page summary by Kate McAlpine in the 'New Scientist'. She mentions that Gregory Engel, who was respnsible for the earlier low temperature studies of coherence in bacterial proteins, is enthusiastic about the Collini result. Engel and his group have also performed a study at 4 degrees centigrade, much above previous levels, although below the 21 degrees of the Collini study. Engel is also quoted as saying that this work could have implications for quantum computing, where a core problem has been to operate at the very low temperatures that are usually thought necessary to prevent quantum decoherence. The speed with which this work has been picked up and given prominence in a popular science magazine suggests a background change of attitude to coherence in protein. The vexed question of quantum consciousness is not mentioned, but the suggestion of activities within protein as a model for quantum computing is moving is in that direction. 3.) Dynamics of Light Harvesting in Photosynthesis Cheng, Y. & Fleming, R., University of California, Berkeley Annual Review of Physical Chemistry, 2009, 60: pp. 241-62, doi:10.1146/annurev.physchem.040808.090259 This article discusses recent experimental advances in modelling and spectroscopic techniques, and their application to the study of electronic excitations involved in light harvesting by photosynthetic protein. These advances are connected to the both Engel (2007) and Collini (2010), who have made observations of long-lasting quantum coherence in photosynthetic systems. In photosynthesis, peripheral antenna absorb light, and convert it into electronic excitations that are transferred to the reaction centre of the photosynthetic system. Photosynthetic organisms are characterised by a very high light-to-charge conversion efficiency of over 95%. The antennas and the reaction centres are connected by the Fenna-Matthews-Olson (FMO) complex. This is a trimer that comprises three identical subunits, each containing several tightly packed bacteriochlorophyll (BChl) pigments that support delocalised electronically excited states. In the last decade, evidence has shown that the compact packing of this system means that it cannot be described by traditional classical means. The traditional theory of excitation energy transfer in these proteins did not involve coherence, but this view has proved inadequate, because of the close packing of the pigments. Scholes and Fleming (4.) have shown that excitation energy transfer between blocks of excitationally coupled molecules proceeds via delocalised exciton states. Delocalisation here means that the energy of an electron is spread over an extended region. Their model involves excitations delocalised over a small group of molecules. The photosynthetic complex has dense almost equally spaced exciton levels and strong excitonic coupling. This structure involves the spatial overlap of exciton wave functions, and theory predicts rapid energy transfer between exciton states that have a strong overlap of their wave functions. Ultrafast studies of the antenna complex indicate that equations, known as Redfield equations, are needed to describe the long-lived coherence observed in the Engel et al (2007) experiment. Traditional theories assumed independent fluctuations of energy at different sites, but recent experiments (5.&6.) suggest that correlated energetic fluctuations might be important in pigment-protein complexes. Ultrafast spectroscopic technology involving three laser pulses has been important for studying excitation energy transfer over time scales measured in femtoseconds. These have revealed delocalised excitations and couplings. The 2D form of srpectroscopy employed here is sensitive to the quantum phase evolution of photosynthetic systems. Quantum beats in the 2D spectra are related to the coherence dynamics of the system being studied. These type of quantum beats were observed in the Engel experiment. The spectroscopic studies are sensitive to the transition dipoles of excitons determined by the pigment arrangement, and the redistribution of the transition dipoles due to the electronic couplings. This process cannot be explained by localised molecular excitation, but only by the redistribution of transition dipole moments, due to the delocalisation of the exciton states. The excitonic couplings and site energies of excited states in the FMO complex have been used to describe the dynamics of excitation transfer (Brixner et al, 5). Molecular transition dipole moments are redistributed due to the electronic couplings between BChls, and result in different positions and orientations of the dipoles. Brixner et al showed that the energy transport in the system depends on the spatial properties of the excited wave functions, as predicted by Redfield theory. The spatial/energetic nature of the complex allows the excitation to move to the lowest energy state (minima) in two or at most three steps. Delocalisation states in pigment-protein complexes have been known to exist for some time, but it was only the development of two-dimensional spectroscopy that revealed the relevance of quantum coherence to the function of the complexes. Engel's 2007 study revealed a complex quantum beating pattern at time scales similar to the excitatory energy transfer of the system. It is thus argued that the classical random walk cannot fully describe the dynamics of light harvesting. The strong agreement between the observed beating signal and the beat system predicted from the systems excitonic structure indicates long-lasting quantum coherence. Excitations are shown to move coherently through the FMO complex. On this basis, Engel et al propose that quantum coherence promotes light harvesting. They propose that the FMO complex runs a quantum search algorithm that is more efficient than a classical system. The algorithm enables a rapid and reversible search for the site that connects to the reaction complex (the minima). Reversibility guards against becoming trapped in a secondary minima, which could happen with a classical system. Further to this, Fleming et al (4.) observed long-lasting coherence in a photosynthetic reaction centre. This could only be explained by correlations between protein motions that modulate the transition energies of neighbouring chromophores. This suggests that protein environments work to preserve electronic coherence in photosynthetic complexes and thus optimise excitatory energy transfer. References:- 1.) Collini, Elizabetta et al, (2010) - Coherently wired light harvesting in photosynthetic marine algae at ambient temperature - Nature, 463, pp. 644-7 doi:10.1038/nature08811 2.) Engel, G. et al (2007) - Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems - Nature, 446, pp. 782-6 3.) van Grondelle et al, (2006) - Energy transfer in photosynthesis: experimental insights and quantitative models - Phys. Chem. Phys, 8: pp. 793-807 4.) Scholes, G. & Fleming, R., (2005) - Energy transfer and photosynthetic light harvesting - Adv. Chem. Phys., 132: pp. 57-130 5.) Brixner, T. et al, (2005) - Two-dimensional spectroscopy of electronic couplings in photosynthesis - Nature, 434: 625-628 6.) Lee, H., Cheng, Y. & Fleming, R., (2007) - Coherence dynamics in photosynthesis: protein protection of excitonic coherence - Science, 316: pp. 1462-65 P. 7.) Renger, T. et al, (2007) - Refinement of the structural model of a pigment-protein complex - Journal Phys. Chem. B, 111: pp. 10487-501 4.) Genes don't reveal all P. Based on Michael Snyder, Stanford Center for Genomics P. Focus, 216, June 2010 P. The article says that the assumption that there is a simple relationship between heriditary features and genes is now being challenged. Genes are coming to be seen as only part of the story. Snyder's Stanford team suggest that the other 'non-coding' areas of DNA are more important than genes in creating heriditary differences. Genes are essential as a code for all the proteins that make up the main building blocks of organic life, but not necessarily for the way they are expressed or organised. Scientists looking for the causes of heriditary diseases have not been able to find them in the differences between genes. P. The genes are likened to dimmer switches in that they can be turned up or down. Protein molecules called transcription factors bind to what are here referred to as control areas of the DNA, which boost the genes in their production of proteins. If the transcription doesn't bind, the gene may not produce the protein. If there is a defect in the DNA control area, the transcription factor may fail to bind to the control area, and the gene may fail to function properly. Snyder's research showed that the difference between regulatory regions of DNA in human individuals was 1,000 times greater than the variation in genes. A similar high degree of variability was found in the ability of control DNA to bind a transcription factor related to the regulation of genes involved in the immune system. Snyder argues that we shouldn't be surprised by the importance of the control areas, because organisms might not function at all, if there was a substantial variability in genes. From our point of view, the article is interesting in emphasising the importance of protein in influencing DNA. Protein Dynamics of Light Harvesting in Photosynthesis |
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