lördag 7 november 2009

Macroscopic quantum coherence, photosynthesis

Is living systems quantum systems? And is consciousness too? Quantum effects cannot be significant in length and time scales involved and there is absolutely no evidence for them, says classic QM? Is it really so?

Sension 2007; Biophysics: Quantum path to photosynthesis, says: Knowing how plants and bacteria harvest light for photosynthesis so efficiently could provide a clean solution to mankind's energy requirements. The secret, it seems, may be the coherent application of quantum principles.

"After all, living systems look very quantal and we experience directly what could be called free will. We should rely on what we directly experience and ability to think rationally rather than authorities and be ready to question also the existing view about quantum physics. If the standard quantum physics does not allow the needed macroscopic quantum phases, we must modify the quantum physics. Even quantum consciousness theorists have usually adopted the view that wave mechanics is enough for understanding of living matter. Penrose has been an exception since he proposes that quantum gravity could be important." This from Pitkänens blog.

So wavelengths and quantum gravity is the answer. That is locality and non-locality. The problem is gravity is so difficult to explore, because we are all swimming in it. Gravity is dark energy/matter. Fröhlich talked of a quantum superfluid.

Pitkänens interpretion is with new physics. "There is a lot of indirect experimental evidence for the quantum view (the strange findings about the functioning of cell membrane, the effects of ELF em fields on vertebrate brain,...) This involves the identification of dark energy and dark matter in terms of macroscopic quantum phases with non-standard large value of Planck constant, the new view about space-time and about the relationship between experienced time and time of physicists, new view about quantum states based on zero energy ontology, etc.. Also p-adic physics is essential in the proposed view about correlates of cognition and intention." Zero energy ontology and vacuum energy is the same thing.

Photosynthesis in bacterias
To what extent do photosynthetic organisms use quantum mechanics to optimize the capture and distribution of light, asks Fleming 2004. The first law of photosynthetic economics is: "A photon saved is a photon earned."

...tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke 'hopping' of excited-state populations along discrete energy levels, say Fleming. And he continues. ...obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum (sulfurbact.) FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path."

And in an earlier article of the same team:...the fundamental cause of electronic and vibrational dynamics—the coupling between the different energy levels involved—is usually inferred only indirectly. Two-dimensional femtosecond infrared spectroscopy based on the heterodyne detection of three-pulse photon echoes has recently allowed the direct mapping of vibrational couplings, yielding transient structural information...we extend the approach to the visible range and directly measure electronic couplings in a molecular complex, the photosynthetic light-harvesting protein...the conversion of light into chemical energy is driven by electronic couplings that ensure the efficient transport of energy from light-capturing antenna pigments to the reaction centre. We monitor this process as a function of time and frequency and show that excitation energy does not simply cascade stepwise down the energy ladder. We find instead distinct energy transport pathways that depend sensitively on the detailed spatial properties of the delocalized excited-state wavefunctions of the whole pigment–protein complex.

Remarkably long lived electronic quantum coherence is claimed to be present. Authors propose that quantum computation like process - quantum random walk -could be in question. Quantum collapse is a non-deterministic process and if it selects the path in this particular case it can select any path with some probability, not always the shortest one, is Pitkänens wiev.

Convergence curve of the 'blind' optimization (target: to maximize IC/ET) with free phase and amplitude shaping. The inset shows the optimal pulse autocorrelation (I(t)) with its wavelength resolution, that is, the second harmonic generation (SHG) frequency resolved optical gating (FROG) trace, from Herek et al 2002.

Light-harvesting complexes 2 (LH2) are the accessory antenna proteins in the bacterial photosynthetic apparatus.

Herek et al., 2002: Coherent light sources have been widely used in control schemes that exploit quantum interference effects to direct the outcome of photochemical processes. The adaptive shaping of laser pulses is a particularly powerful tool in this context: experimental output as feedback in an iterative learning loop refines the applied laser field to render it best suited to constraints set by the experimenter. This approach has been experimentally implemented to control a variety of processes but the extent to which coherent excitation can also be used to direct the dynamics of complex molecular systems in a condensed-phase environment remains unclear. Here we report feedback-optimized coherent control over the energy-flow pathways in the light-harvesting antenna complex LH2 from Rhodopseudomonas acidophila, a photosynthetic purple bacterium. We show that phases imprinted by the light field mediate the branching ratio of energy transfer between intra- and intermolecular channels in the complex's donor–acceptor system. This result illustrates that molecular complexity need not prevent coherent control, which can thus be extended to probe and affect biological functions.

This year Read et al. (Flemings group) says, Despite their common function, the pigment-protein complexes that make up antenna systems in different types of photosynthetic organisms exhibit a wide variety of structural forms. Some individual organisms express different types of complexes depending on growth conditions. For example, purple photosynthetic bacteria Rp. palustris preferentially synthesize light-harvesting complex 4 (LH4), a structural variant of the more common and widely studied LH2, when grown under low-light conditions. Here, we investigate the ultrafast dynamics and energy level structure of LH4 using two-dimensional (2D) electronic spectroscopy in combination with theoretical simulations. The experimental data reveal dynamics on two distinct time scales, consistent with coherent dephasing within approximately the first 100 fs, followed by relaxation of population into lower-energy states on a picosecond time scale. We observe excited state absorption (ESA) features marking the existence of high-energy dark states, which suggest that the strongest dipole-dipole coupling in the complex occurs between bacteriochlorophyll transition dipole moments in an in-line geometry.

New tools
Photon echo studies of photosynthetic light harvesting, by Read & Fleming this year. I glue from the article.

The broad linewidths in absorption spectra obscure information related to their structure and function. Photon echo techniques scans interactions normally hidden under broad linewidths with sufficient time resolution to follow the fastest energy transfer events in light harvesting. Approach and applications of two types of photon echo experiments: the photon echo peak shift and two-dimensional (2D) Fourier transform photon echo spectroscopy. Photon echo peak shift spectroscopy can be used to determine the strength of coupling between a pigment and its surrounding environment including neighboring pigments and to quantify timescales of energy transfer. Two-dimensional spectroscopy yields a frequency-resolved map of absorption and emission processes, allowing coupling interactions and energy transfer pathways to be viewed directly. Both classes of experiments can be used to probe the quantum mechanical nature of photosynthetic light-harvesting: peak shift experiments allow quantification of correlated energetic fluctuations between pigments, while 2D techniques measure quantum beating directly, both of which indicate the extent of quantum coherence over multiple pigment sites in the protein complex.

Upon irradiation by a laser pulse, the system begins to oscillate between quantum energy levels. An analogy can be drawn to a collection of springs, set into motion by the external perturbation (the pulse). Imagine that each of the springs oscillates with a slightly different frequency, analogous to inhomogeneous broadening wherein the electronic transition frequencies of a collection of chromophores vary. The result of this distribution of frequencies is that the “springs,” oscillating in phase immediately after interaction with the pulse, become gradually less synchronized over time. This is known as dephasing. Imagine then that at some later instant, the motion of the springs is simultaneously reversed by another perturbing pulse. As long as each of the springs maintains its original oscillation frequency and changes only its direction, the overall dephasing is reversed also. When this reverse dephasing or rephasing process occurs not with springs but with a collection of chromophores interacting with laser pulses, the effect is for the sample to emit a light pulse “echoing” the input pulse at the instant when the oscillators are once more in phase.
The appearance of a photon echo signal depends on each of the springs remembering its initial oscillation frequency and phase. If, on the other hand, the frequencies are individually modified or the phases shifted (as can occur through coupling to vibrational motions of the pigments or proteins), the collective motion of the springs devolves into random noise; the constructive interference—rephasing—is never realized, and a photon echo signal is not emitted. Thus, the signal is uniquely sensitive to the coupling between the electronic transitions on the pigments and the nuclear motions of the “bath” (motions of the pigments themselves and of the surrounding protein). The detailed pigment–protein interactions in photosynthesis play an important role in controlling energy flow through the complexes. Furthermore, photon echo signals track energy transfer between the electronic states of neighboring chromophores.

Pigments in photosynthetic pigment–protein complexes are often closely packed and form an excitonically coupled system, and the reaction center can have three distinct absorption bands. However, the excitonically coupled states contain the properties of electronic states from different molecules, and they are correlated to some extent. The more correlation between the states, the larger the peak shift signal generated with this new technique. Photon echo experiments afford control over multiple frequency and time “handles” (i.e., pulse color and duration of time periods T and τ). The frequency domain and the time domain are both used in the measurement of dynamics.

Spectra for FMO from Pelodictyon phaeum. The cross-peak specific spectrum reveals off-diagonal features obscured by the diagonal peaks in the conventional 2D spectrum. Both spectra are colored to emphasize smaller features, and the cross-peak specific coloration is inverted to facilitate direct visual comparison of the cross peaks to those in the conventional 2D spectrum. Diagonal peaks (DPi) are shown with squares while cross peaks (CPij) are denoted with circles. The shape of the edge of the cross peak regions agrees between the spectra, but significant additional structure is visible in the cross peak specific spectrum. Figure from Read et al. (2007)

Photon echo-based experiments may be designed to probe a number of aspects of photosynthetic light-harvesting complexes in detail, including coupling among pigments, coupling between pigments and the surrounding protein environment, contributions to spectral broadening, dynamical time scales, and mechanisms of energy transfer in light harvesting. Perhaps most exciting at this juncture is the recently realized capability of photon echo techniques to directly probe the quantum mechanical underpinnings of ultrafast energy transfer in photosynthesis, first discussed over 50 years ago but elusive of direct experimental observation until now. Coming years will likely see rapid expansion of experimental methods related to those described here.

The data in an earlier study of the group, revealed long-lasting coherence between two electronic states that are formed by mixing of the bacteriopheophytin and accessory bacteriochlorophyll excited states. This coherence can only be explained by strong correlation between the protein-induced fluctuations in the transition energy of neighboring chromophores. Our results suggest that correlated protein environments preserve electronic coherence in photosynthetic complexes and allow the excitation to move coherently in space, enabling highly efficient energy harvesting and trapping in photosynthesis. Quantum coherences between excitonic states play an important role in the dynamics of energy transfer in photosynthetic complexes—i.e., the energy transfer is described by wavelike coherent motion instead of incoherent hopping.

And new physics
From TGD: "The sole problem is to understand how macroscopic quantum coherence is possible in the length scales considered. In TGD framework the hierarchy of Planck constants suggests that both macroscopic quantum coherence and very low dissipation rate are due to the large value of hbar for electrons. Estimate is that dissipation rate should reduce by a factor 1/5 and coherence times and lengths should increase by a factor 5. The electron Compton length is scaled up by a factor 2 to so that it corresponds to the p-adic length scale L(149)=5 nm. This would scale up the fundamental bio-time scale of .1 seconds predicted by TGD to be the time scale assignable to causal diamond of electron."

The reduced Compton wavelength of the electron is one of a trio of related units of length, the other two being the Bohr radius and the classical electron radius. Any one of these three lengths can be written in terms of any other using the fine structure constant, says wikipedia. Studies on p-adic length scale by Carlos Castro 2005, Wikipedia, Andrew Baker 2009, and Hartmut Muller, etc..

Macroscopic quantum coherence and quantum metabolism as different sides of the same coin
"If Planck constant can have arbitrarily large values, the situation becomes possible since Compton lengths and other quantum scales are proportional to Plancks constant. Dark matter is excellent candidate for large Planck constant phases. Quantum classical correspondence suggests the identification of space-time sheets identifiable as quantum coherence regions. Since they can have arbitrarily large sizes, phases with arbitrarily large quantum coherence lengths and arbitrarily long decoherence times seem to be possible in TGD Universe.

Hierarchy of Plancks constants
The interaction is associated with some kind of interface between the systems, perhaps join along boundaries connecting the space-time sheets associated with systems possessing gravitational masses. Also a large space-time sheet carrying the mutual classical gravitational field could be in question.
" And from his blog: "Since bosons are bound states of positive and negative energy fermions at opposite wormhole throats it seems that vector super field must correspond to an operator slashed between positive and negative energy super-fields rather than ordinary vector super-field.

- Even ordinary condensed matter could be "partially dark" in many-sheeted space-time. The realization of hierarchy of Planck constants leads to a considerably weaker notion of darkness. The notion of darkness is relative. For instance, classical interactions and photon exchanges involving a phase transition changing the value of Plancks constant of photon are possible.
- The increase of Plancks constant would make the fine structure constant alpha in question small.
- States behaving in some respects like mini black holes (are maybe found) explained as color flux tubes forming a highly entangled state and identifiable as stringy black holes of strong gravitation and carry a quantum coherent color glass condensate, and would be characterized by a large value of Plancks constant naturally resulting in confinement phase with a large value of alpha's. This condensate would be present also in ordinary black-holes and the blackness of black-hole would be darkness.

Water as a coherence medium would perhaps act just like this. With a collapsing of the fine structure constant in a phase transition and breaking of a strong hydrogen bond giving protons and electrons.

"Besides hydrogen carbon dioxide serves as the basic raw material of these molecules. The covalent double bonds between carbon and oxygen are reduced in the process. The photons excite in the reaction center of photosystem I electron pairs transferred to NADP+ to give NADPH which transfers electrons and metabolic energy to where they are needed. Photosystem II draws electron pairs from water and feeds them to the photo-system I to compensate the electrons lost in the generation of NADPH. As water molecules lose two electrons, oxidation happens which means the generation of O2 molecules. Photonic energy is storde temporally by transforming ADP molecules to ATP molecules."

Photosynthesis in TGD
"p-Adic length scale hypothesis gives very strong quantitative guidelines in the attempt to understand photosynthesis in many-sheeted space-time, and one ends up to a general view about how Bose-Einstein condensates store metabolic energy as zero point kinetic energy and how this energy is utilized by remote metabolism (by generating negative energy MEs = 'a need'). After the light is transmitted to chlorophylls it excites electron pairs in turn transferred between pigments.

Model in TGD:
- The presence of electronic super-conductivity (cause of electronpairs driving the mechanism).
- Dropping k = 137 -> 139 of single proton in ATP synthesis (for ATPase).
- Electron Cooper pairs decay at k = 148 space-time sheet and then drop to k = 151 spacetime sheet (electron shell?).
- The BE-condensate residing at k = 151 cell membrane spacetime sheet is a fundamental electronic Cooper pair BE condensate. That ground state spacetime sheets correspond to different p-adic primes would guarantee that photosystems I and II are separate even when they have (apparent) spatial overlap.
- Antenna pigments could generate MEs transferring the photonic energy to the reaction center as Bose-Einstein condensed photons.
- Chlorofyll transition is certainly responsible for the absorption of quantum and the whole spectrum of visible light is involved. The excited chlorophyll system generates ME bridges?
- For water is suggested that collective effects are of importance, perhaps Bose-Einstein condensates of H, protonic and electronic Cooper pairs, H2, O, and O2 at larger space-time sheets might be partly involved. The model for sol-gel phase transition already led to the tentative idea that Bose-Einstein condensates of free hydrogen atoms could be present in the cellular water. Only a small fraction would reside at larger space-time sheets.
- Bose-Einstein condensates might perhaps make water some kind of liquid crystal structure.

The first thing to notice is that the upper bound .5 eV for IR energies corresponds to the nominal value of the metabolic energy quantum identified as the energy liberated as proton drops from the atomic space-time sheet with k=137 to a very large space-time sheet or the same process for electron Cooper at k=149 space-time sheet. If Cooper pairs are involved, the latter process would occur in the length scale defined by the thickness of the lipid layer of the cell membrane (5 nm). The lower bound corresponds to a metabolic energy quantum assignable to k= 139 for protons and k=151 transition for electrons (thickness of cell membrane).

Second point to notice is that TGD predicts a fractal hierarchy of spectra of metabolic energy quanta. The zero point kinetic energy .125 eV of H atoms in turn correspond to the energy needed to carry doubly charged ion such as Mg2+ or Ca2+ through the cell membrane. ionic pumps are based on remote metabolism, that is sending of negative energy MEs inducing the dropping of H, H2 and possibly 2p from k = 169 space-time sheet or dropping of electronic Cooper pair from k = 149 and electron from k = 151 space-time sheet.

A.H.J. Fleming 2004.
"Planck’s constant comes directly from electromagnetic self-field theory (EMSFT) and its application to the hydrogen atom. Empirically the value of Plancks constant is calculated from the solution of the Bohr radius and the resonant frequency of hydrogen atom. Obviously this raises an issue at the heart of quantum theory.

Where does the self-energy of the system come from? EMSFT theory suggests that photons supply the energy to the electron and the proton and vice-versa. That discrete quanta of Planck’s energy are involved in the particle-field interactions strongly implicate the photon as the energy provider/mediator for the atomic system. This suggests two interfacing systems of motion at differing scales each supplying the other’s energy; two interfacing inhomogeneous systems of equations. The stability of the field/particle system, may also be reflected in a similar equation as seen from the perspective of the photon, hence a state of balance between the motions and interactions of the proton, electron and photons may exist...the source terms of the E- and H-fields of the electron are indeed photons as is the case for quantum field theory... the motion of the electron (and proton) can be written as source terms for the photons if they were written as the particles. The ‘fields’ and ‘particles’ are thus interchangeable in the mathematics of EMSFT. EMSFT is not a classical field theory, but like quantum field theories.

More discussions about Plancks constant and different hierarchias later.

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