Biological semiconductors and quantum biology

INTRODUCTION

There are several evidenced examples in biology of processes which involve ultra-fast electron transfer, singlet and triplet spin mechanisms and quantum coherence.

These includes:

  1. Evidence of the solid state photo-CIDNP effect (via singlet and triplet states), ultra-fast electron transfer, and quantum coherence in photosynthesis.
  2. Evidence of the solid state photo-CIDNP effect (via singlet and triplet states) and ultra-fast electron transfer in flavoproteins.  In addition there are widely explored scientific theories of cryptochrome (a flavoprotein) triggering a quantum mechanical effect during ‘magnetoreception’.

There is also evidence of that the redox state of cysteine residues may support singlet and triplet states, and ultra-fast electron transfer in both flavoproteins and photosynthesis.  The coupling between circadian rhythms (providing periodicity) and redox could potentially influence the oxidative interface -consisting mainly of the redox regulation of redox-reactive cysteine residues on proteins. This may provide environmental support for quantum transport.

Consideration is also given to other environments where singlet and triplet states, ultra-fast electron transfer, and quantum coherence can be found – including at higher temperatures. Manifestations of quantum coherence in different solid state systems include semiconductor confined systems, magnetic systems, crystals and superconductors. Ultrafast electron transfer and charge separation is possible in semiconductors A Ayzner 2015, S Gélinas 2014, and work is currently being undertaken on semiconductor spintronic devices operating at room temperature. (N Thanh Tu 2016)

PJ Hore (2016) has pointed out that certain organic semiconductors (OLEDs) exhibit magnetoelectroluminescence or magnetoconductance, the mechanism of which shares essentially identical physics with radical pairs in biology. There are three main types of organic spintronic phenomena.  This includes a magnetic field effect in organic light emitting diodes, where spin mixing between singlet and triplet polaron pairs can be influenced by an external magnetic field leading to organic magnetoresistive effect.  E Ehrenfreund 2011F Geng 2016.   

J Vattay and S A Kaufmann (2015) have also suggested the existence of bio-conductor materials which neither metals nor insulators but new quantum critical materials which have unique material properties.  E Prati (2015) then used their work to explore room temperature solid state quantum devices at the end of chaos for long living quantum states.

The idea of biological semiconductors has been around for some years (e.g see A V Vannikov 1970). Several natural semiconductors have now been identified in biology.  Endogenous bioelectrical signals play critical roles in a near-infinite number of ubiquitous biological processes such as energy harvesting, rapid communications and inter/intra cellular synchronisation.  Specific examples include photosynthesis, vision, carbohydrate metabolism, neurophysiology, wound healing, tissue regeneration and embryonic development.  And several natural semiconductors have already been identified e.g melanin and peptides. Charge transport has been found in a variety of naturally-derived small molecule, semiconducting biological compounds – carotenoids (produced by plants and bacteria).  These include protection against oxidative species, pigmentation, and light havesting for photosynthesis.  The polyconjugated structure of this class of compounds suggests that the natural electronic activity of derivatives could be repurposed as an active semiconductor material for organic electron devices.   M Mukovich 2012.    And there are π-conjugated organic semiconducting materials. C Wang 2011.

It is of interest then that organic molecules that serve as chromophores (of which flavins such as cryptochrome, are examples) consist of extended conjugated π-systems, which allow electronic excitation by sunlight and provide photochemical reactivity. Eukaryotic riboflavin-binding proteins typically bind riboflavin between the aromatic residues of mostly tryptophan- and tyrosine-built triads of stacked aromatic rings…Ultrafast electron transfer mechanisms from an aromatic moiety to a photoexcited flavin are not only observed for riboflavin-binding proteins but for other flavoproteins, like for BLUF (blue light sensing using FAD) domains, cryptochromes, and DNA photolyases.  H Staudt 2011.

Hopping conduction is widely considered the dominant charge transport mechanism in disordered organic semiconductors. A V Nenashev 2015.  And in biology, evidence has been found that the existence of central aromatic acids can serve as stepping stones to support an electron hopping mechanism W Sun 2016, including in flavins.

It may be the case that levels of conductivity could change/adapt within biology.  This is explored in more depth towards the end of this article. Biology could draw on a complex system of interfaces between different types of conductors (from flavins to iron sulphur clusters which are ubiquitous in biology) and insulators, periodic oscillations (biological rhythms), redox systems, and generated magnetism (biological organisms also produce tiny electrical currents exist due to the chemical reactions that occur as part of the normal functions, even in the absence of external electric fields). There will also be responses to changes in the environment (e.g temperature and external magnetic fields).  

For example redox doping could increase the conductivity of a material – and in biology such redox doping could be provided by the biological redox state – including the redox state of cysteine residues.  It might also be the case, that in certain conditions, there could be a transition to superconducting (e.g  E H Halpern 1972.

‘RADICAL PAIRS’ MECHANISMS IN MAGNETORECEPTION AND PHOTOSYNTHESIS

In chemical reactions involving transient radical pairs (singlet and triplet states), quantum effects are proposed to induce a sensitivity to the intensity and/or orientation of external magnetic fields. The governing principle of these phenomena is the magnetic field dependent interconversion between quantum-coherent and often entangled states of electronic spin pairs.

When activated by light, it is theorised that cryptochromes undergo a redox cycle, in the course of which radical pairs are generated during photo-reduction as well as during light-independent re-oxidation. 

In biology a ‘radical pair’ is a short-lived reaction intermediate comprising 2 radicals formed in tandem whose unpaired electron spins may be either antiparallel (↑↓, a singlet state, S) or parallel (↑↑, a triplet state, T). C T Rogers 2008.  It is proposed that in magnetoreception the absorption of a photon raises a receptor molecule into an excited state and leads to a light-activated electron transfer from a donor to an acceptor, thus generating a spin-correlated pair. By interconversion, singlet states radical pairs with an antiparallel spin are transformed into triplet states with parallel spin and vice versa. The singlet/triplet ratio depends on, among other factors, the alignment of the receptor molecule in the external magnetic field and could thus mediate information on magnetic direction. R Wiltschko 2014. 

A well-studied precedent for magnetically sensitive radical pair chemistry is provided by the initial charge separation steps of bacterial photosynthetic energy conversion, which proceed via a series of radical ion pairs formed by sequential electron transfers along a chain of immobilized chlorophyll and quinone cofactors in a reaction center protein complex. Provided subsequent forward electron transfer is blocked, the recombination of the primary radical pair responds to magnetic fields in excess of ≈1 mT. In unblocked reaction centers, spin correlation can be transferred along the electron transport chain from the primary to the secondary radical pair, whose lifetime is also magnetically sensitive. Similar effects occur in plant photosystems. C T Rogers 2008. 

RADICAL PAIR MECHANISMS, ULTRA-FAST ELECTRON TRANSFER, AND QUANTUM COHERENCE IN BIOLOGY

During charge separation in photosynthetic reaction centres, triplet states can react with molecular oxygen generating destructive singlet oxygen. The triplet product yield in bacteria and plants is observed to be reduced by weak magnetic fields.  It has been suggested that this effect is due to ‘solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP), which is an efficient method of creating non-equilibrium polarization of nuclear spins by using chemical reactions, which have radical pairs as intermediates.

A ‘solid-state photo-CIDNP effect’  (J Matysik 2009) has been observed in:

Previously it had been proposed that such effects were a quantum zeno effect.  A T Dellis and I K Kominis, 2009,  Dellis and Kominis 2011  Now Kominis also refers to this as the solid state photo-CIDNP effect (Kominis 2013), but perhaps this effect can be seen as analogous to the quantum zeno effect.

The effect also reduces oxidative stress in bacteria and plants and so offers an important anti-oxidant effect. Marais et al 2015),

It has been noted there seems to be a link between the conditions of occurrence of photo-CIDNP in reaction centres and the conditions of the unsurpassed efficient light-induced electron transfer in reaction centres. J Matysik 2009. Efficiency of electron transfer and the general observability of the solid state photo CIDNP effect have one common feature: the short life time of the radical pair which reflects an optimised reaction channel avoiding side reactions as well as leading to broadening of the excitation held curve of the effect (I F Cespedes-Camacho and J Matysik 2014).  In studies it has been demonstrated that up to three mechanisms are involved to build up CIDNP under continuous illumination – which may run in parallel.  

Supporting Quantum Coherence

Direct evidence for the presence of quantum coherence over appreciable length scales and timescales in the FMO pigment protein complex of the green sulphur bacteria was observed by Engel et al in 2007. They presented the spectroscopic observation, at low temperature (77K), of quantum coherent dynamics (that is, coherent superpositions evolving in time) of an electronic excitation across multiple pigments within the FMO complex. Since that time a huge body of literature has arisen, and further experiments suggest that the coherence is non-negligible even at room temperature, for up to 300fs. N Lambert – ‎2012.  Further evidence of quantum coherence has been found in Rhodobacter sphaeroides pigment protein complex H Lee 2007P Rebentrost. 2009Xian-Ting Liang 2010, and various photosynthetic systems LHC2 (including spinach).

Energy transfer and trapping in the light harvesting antennae of purple photosynthetic bacteria is an ultrafast process, which occurs with a quantum efficiency close to unity.  M Ferretti 2016Rienk van Grondelle has suggested that during photosynthesis, plants use electronic coherence for ultrafast energy and electron transfer and have selected specific vibrations to sustain those coherences. In this way photosynthetic energy transfer and charge separation have achieved their amazing efficiency. At the same time these same interactions are used to photoprotect the system against unwanted byproducts of light harvesting and charge separation at high light intensities.

It has been proposed that light harvesting in chromophores is realised by excitonic system living at the edge of quantum chaos (G Vattay 2014), where energy level distribution becomes semi-poissonian…semiconductor materials are known to also exhibit quantum chaotic conditions. E Prati 2015.

Evidence of ultra-fast electron transfer in flavoproteins.

And beyond ultrafast charge separation in photosynthesis, there are similar dynamics in bond isomerization in sensory photoreceptors and repairing DNA damage.  It should be noted that in the DNA repair enzyme photolyase, it has been found that maximum efficiency was not enhanced by the ultrafast photoinduced process but by the synergistic optimisation of all steps in the complex repair reaction. C Tan 2015.  

Very fast photo-induced electron transfer is feasible along the conserved tryptophan pathway found in flavoproteins of the photolyase/cryptochrome family.  Both cryptochromes and photolayses are flavoproteins that undergo ultrafast charge seperation upon electron excitation of their flavin cofactors.  T Firmino 2016. Dr T Biskup 2011.  Ya-Ting Kao 2008,  D Zhong 2006.

Evidence of the Solid State Photo CIDNP effect in Flavoproteins

A solid state Photo-CIDNP effect has also been demonstrated on the photochemical yield of a flavin-tryptophan radical pair in Escherichia coli photolyase. K B Henbest 2008.

And a solid state photo CIDNP effect has been observed a mutant of the bluelight photoreceptor phototropin (LOV1-C57S from Chlamydomonas reinhardtii). S S Thamarath 2010.

In the same way that photo-CIDNP MAS NMR has provided detailed insights into photosynthetic electron transport in reaction centres, it is anticipated in a variety of applications in mechanistic studies of other photoactive proteins. It may be possible to characterize the photoinduced electron transfer process in cryptochrome in detail. W Xiao-Jie12016.

Until recently solid-state photo-CIDNP effect has required high magnetic fields and cyclic electron transfer, which is reached, for example in RCs of Rb. sphaeroides by reduction or removal of the quinones.  But it has also been speculated that solid-state photo CIDNP effect at earth field plays a role in the magnetoreception of biological systems….Studies have found that the ‘solid-state photo-CIDNP’ effect allows for signal enhancement of factors of several 10000 s. Such strong signal enhancement allows for example selectively observing photosynthetic cofactors forming radical-pairs at nanomolar concentrations in membranes, cells, and even in entire plants. W Xiao-Jie 2016.  Also see G Jeskchke 2011.  

Evidence of that the redox state of cysteine residues supports the radical pair mechanism and ultra-fast electron transfer in both flavoproteins and photosynthesis.

It has been proposed that the side chains of tyrosine and cysteine residues can act as the relay stones of electron transfer in proteins.  The driving forces come from the loss of the active protons (protons link the ring oxygen of the tyrosine and the sulphur of the cysteine) in the appropriate protein environments, which lowers the reduction potentials of these two residues.  An example is the long distance electron transfer of the class I ribonucleotide reductase, involving four tyrosines and a cysteine residue. Additionally, the Giese Group, examined electron transfer along a series of polypeptides and demonstrated that the existence of central aromatic acids can serve as stepping stones to support the electron hopping mechanism. W Sun 2016.   A V Vannikov 1970  noted that ‘assuming an electron or hole in a polypeptide is located on any peptide group, then if the life of this state is comparable with the period of interpeptide vibrations, the distances between all the bonds in the peptide group are changed and stabilised in this state.  Furthermore, in the neighbourhood of this peptide group, the distances between neighbouring peptitdes also becomes different, which changes the probability of transfer from group to group.  It is observed that the proposed mechanism for this is extremely similar to the mechanism of the motion of a polaron in a oxide semiconductor’.

Orf et al 2016 has recently demonstrated that an operative photoprotection mechanism exists in green sulfur bacteria and that this mechanism is activated by oxidation of two cysteine residues.  This new photoprotection mechanism identified by differs from more familiar motifs; the new mechanism employs amino acid residues instead of isomerization of dedicated photoprotective chromophores, such as carotenoids. It also seems to protect against damage from a single excitation (rather than multiple excitations). That is, the mechanism depends on redox potential, not light intensity….The system undergoes intersystem crossing into the triplet state after ~25% of excitations, and the lifetime of the triplet state is between 10-100 μs. The redox-sensitive cysteine residues in the protein,  modulate their redox state between free thiol and thiyl radical form to quench BChl excitations, probably via an electron transfer/ultrafast recombination mechanismOrf 2015.

It has been reported that the side chains of tryptophan residue can speed up electron transfer rates as relay intermediates of long range electron transfer processes in many enzymes including DNA photolyases, where three Trp residues can form an electron transfer wire to facilitate electron hopping. W Sun 2016.  In the complex 1 of the respiratory chain on the inner membrane of the mitrochrondria, electrons are transferred over a cascade of iron-sulphur clusters from a Flavin adenine mononucleotide cofactor to a quinone binding set.  The overall pathway is nearly 10nm long and most likely to involve aromatic amino-acid residues as stepping stones to bridge the gaps between the iron-sulphur clusters.

The extended electron-transfer in animal cryptochromes in mediated by a tetrad of aromatic amino acids.  D Nohr 2016.  Some photoreactive proteins, including those responsive to UV light, utilize characteristic aligned tryptophan residues for electron transfer.  Very fast photo electron transfer (PET) is feasible along the conserved linear tryptophan pathway found in the flavoproteins of the photolyase/cryptochrome family, including Arabidopsis UVR2 and UVR3…starting from the singly reduced (semiquinod) state of FAD, the overall photoreduction process is completed within 30ps, as has been shown by time-resolved optical absorption spectroscopy in E Coli DNA photolyase.  Dr T Biskup 2011.

For FAD in the fully oxidized state, PET generates a sequence of radical pair species. And in flavo-proteins (mutated in order to remove a cysteine residue next to the chromophore), it is possible to form a spin-correlated radical pair. Such radical pairs recombine, generally speaking, from both singlet and triplet states, giving rise to strong solid state-CIDNP. Because of the rigid environment, molecular mobility is strongly restricted; therefore, anisotropic spin interactions come into play and affect the evolution of the radical pairs… Presently, flavoproteins represent the only system, where both liquid state-CIDNP and solid state-CIDNP have been observed (even then, for slightly different flavoproteins).  Denis V. Sosnovsky.  2016. 

Commonalities among flavin-based photo and redox receptors could reflect evolutionary relationships among them.  In the canonical LOV photocycle, a Flavin excited triplet state reacts with the thiol group of a conserved cysteine residue.  Bond formation likely proceeds via a redox process as supported by detection of a transient Flavin neutral semiquinone (NSQ) in C reinhardti phot1 LOV1, by indirect arguments from magnetic resonance experiments and by the general efficacy of Flavin photoreduction in the cysteine-devoid variants. Thus the NSQ is a likely intermediate in generating the adduct.  The BAT-LOV P1988C variant demonstrates that cysteines at the adduct forming position is an effective electron donor to the photo excited Flavin.  LOV signalling through the NSQ state has parallels to signal transduction in other flavin based photoreceptors including cryptochromes and BLUF.  There is strong evidence that the signalling state of cryptochrome involves reduction of the FAD to either NSQ or anionic semiquinone states.  A NSQ state may be populated transiently during the photocycle of a radical pair intermediate between the Flavin and a conserved Try. . E F Yee 2015.  Also see A Hense 2014.   A Czarna2013. R J Kutta 2015 for the role of cysteine residues in the generation of radical pairs in various flavoproteins.

ENVIRONMENTALLY ASSISTED QUANTUM TRANSPORT

Several recent papers have suggested that optimally efficient networks are not purely quantum, but are assisted by some interaction with a ‘noisy’ classical environment. Y Li 2014. An overview of this approach is given in http://qubit-ulm.com/quantum-effects-in-biology/.

An important aspect of biological environments are vibrations which originate from proteins and embedded molecules. At specific frequencies this vibrational motion can be long-lived and interact in highly non-trivial fashion with electronic motion which could give rise to fast transport, molecular recognition or long-lived quantum coherence in biological systems.

Following this approach, if the oscillations of the exciton and the oscillations of the surrounding proteins are the same then when coherence gets knocked out of tune by white noise, it can be knocked back into tune by the protein oscillations….there would be a need to tune surrounding molecular white noise so that it would nudge the off-beat electrons into the same beat, but not too vigorously, or they would be knocked into different rhythms and coherence would be lost. Jim Al-Khalili, ‎- 2014.

Perhaps redox/circadian rhythms could offer this ‘same beat. How the protein environment controls the redox properties of the cofactors is fundamental to the understanding of electron transfers. R Razeghiford and T J Wydrzynski 2005. 

The Coupling of Circadian Rhythms and Redox

Many rhythms can be observed in organisms, some of which are driven by periodic signals from the surrounding environment, such as light and temperature, but others are generated by the organisms themselves.  Such a self sustained rhythm can be observed at single cell levels.  The concentrations of mRNAs and proteins increase and decrease rhythmically with a well defined temporal period in cells. 

Rhythmic environmental cues create a periodic life-strategy that starts from oscillations in metabolism, primarily photosynthesis.  Circadian rhythms affect every aspect of the plant including water up-take and efficient usage, nitrogen metabolism, mineral nutrition, hormonal pathways, carbohydrate biochemistry, disease resistances signalling. FrontiersAN Dodd – ‎2015 and M L. Guerriero et al 2014.   

Expression of the light-harvesting complex protein genes (Lhc) is under the control of a circadian clock. B Piechulla 1998.  In tomatoes, cryptochromes mediate blue light induction of nuclear genes that encode plastid proteins required not only for photosynthesis and other functions of plastids, such as chlorophyll a/b binding, but also for components of the plastid transcription apparatus. (Loredana Lopez 2012). 

The supramolecular organisation of some pigment-protein-complexes e.g in the circadian rhythms of photosynthesis in Gonyaulaz, the supramolecular organisation of the pigment-protein complex has been found to change periodically, providing a demonstration of the power of membranes to generate circadian rhythmicity (possibly together with a cytoplasmic protein). T. Vanden Driessche 1996. And effective quantum yield and non-photochemical quenching have been found to vary with circadian rhythms.   A McMinn 2013.

All elements of photosynthesis are also subject to very specific timings S Lloyd 2011.  and a global clock could help coordinate these.

Recently, it has become apparent that the cellular redox state oscillates in vivo and in vitro, with a period of about one day (circadian). M Putker 2016.

Redox balance is key for molecules utilised in the context of anti-oxidation protection…results strongly suggest that the circadian clockwork is involved in complex cellular programmes that regulate endogenous ROS and also defend the organism against exogenous oxidative challenge. Current evidence seems to support the conclusion that the responses to ROS are mediated both through the regular function of the molecular clockwork and the involvement of the TTFL genes in extra-circadian pathways…. Redox reactions persist in the absence of gene transcription, and that cycles of oxidation and reduction are conserved across all domain of life. These results suggest that non-transcriptional processes such as metabolic state may interact and work in parallel with the canonical genetic mechanisms of keeping circadian time. Redox perturbs circadian rhythms which in turn perturb redox. Although a single model has yet to emerge, studies strongly suggest that redox state may be an oscillation that feeds back upon the TTFL, whereby a cell’s redox state may alter clock gene expression and the clock genes, in turn, regulate redox state.  Lisa Wulund 2015.  A Stangherlin – ‎2013  .  K Nishio 2015 N B Milev 2015.

In  order to understand reactive oxygen species ROS) regulation of signaling pathways it is necessary to understand the mechanism of how ROS alters protein function. The oxidative interface consists mainly of the redox regulation of redox-reactive cysteine residues on proteins by ROS. Findings indicate that the cysteine residues exposed on the surface of proteins are the dominant intracellular thiol and that they may play an important role in intracellular antioxidant defences. R Requejo 2010.  By specific and reversible oxidation of redox-sensitive cysteines, many biological processes sense and respond to signals from the intracellular redox environment. Redox signals are therefore important regulators of cellular homeostasis.  Oxidative modifications result in changes in structure and/or function of the protein.  P D Ray 2012.

Interestingly a disulphide bond between two cysteine residues in CRY 1 weakens its interaction with PER2 whereas a reduced state of CRY1 stabilises the complex and facilitates transcriptional repression.  The atomic interplay could act as a sensor of the metabolic status of the cell.   

It has been noted that photoinduced electron transfer reaction  plays a pivotal role in regulating many lightswitched enzyme activities such as photosynthesis and circadian rhythm… In cryptochrome, the process of electron transfer is pivotal to generate the 24-hour life cycle of circadian rhythm. Ting-fang He 2011. 

But perhaps circadian rhythms/24 hour redox might also have a role in supporting ultra fast electron transfers and quantum coherence in photosynthesis and magnetoreception. 

Circadian rhythms have been modelled in several ways.  This has included as:

One challenge to the above approach is that it is known that circadian rhythms (produced by the transcription translation loop)  are not necessary for magnetoreception in cockroaches (O Bazalova 2016) or drosophila (R Gegear 2008).    

The circadian clock of wild-type D. melanogaster is slowed (longer tau) in constant magnetic fields, in a dose dependent manner, but only in blue light and with a functional cry gene. Interestingly, cry-dependent magnetosensitivity does not require a functioning circadian clock, but it does require a functional cry gene.  cry’s functional requirement for blue light (<420nm) in phase shifting circadian clocks and in altering spatial orientation and taxis in several species relative to gravity, magnetic fields, solar, lunar, and celestial radiation  makes it the most interesting of the genes currently associated with both biological clocks and geotaxis.  D L Clayton 2016.  .

Although TTFL circadian rhythms are not needed for magnetoreception, it may be the case  that like peroxiredoxins,  flavoproteins such as cryptochrome in redox state may be exhibiting a circadian oscillation with a period of about 24 hours.

Peroxiredoxin proteins may not be unique in their ability to undergo circadian redox oscillations since many other proteins are susceptible to oxidation of their cysteine residues by peroxide  S Ray 2016.

So even if the TTFL generated circadian rhythms are not supporting magnetoreception directly, they are likely to be linked in through a redox-circadian system (perhaps supporting an integrated clock and compass (Cryptochrome based) system in animals.

The Cryptochrome protein (CRY) in Arabidopsis, Drosophila, and mouse provide the most direct path by which redox status can interact with the core components of the transcription–translation feedback loop (TTFL). CRY shares homology with a phylogenetically ancient enzyme family that repairs DNA in response to ultraviolent light known as the photolyases, leading to speculation that redox is therefore crucial to CRY function. Indeed, the CRY protein does contain motifs that bind the flavins, a group of organic compounds known for their prominent role in electron transport in many metabolic reactions and also their ability to be reduced by the incidence of light. Lisa Wulund 2015.

In Drosophila it has been proposed that CRY activation involves intramolecular electron transfer and presumably subsequent conformational changes, thus, the cellular redox status also regulates the transfer of photic information and CRY stability.  Results suggests that the cellular redox status and electron transfer modulate the light dependent activation of CRY, which in turn affects the subsequent transmission of the light signal to TIM and the degradation of CRY itself, with subsequent clock setting….In zebrafish cells, the light-induced redox changes stimulating intracellular mitogen- activated protein kinase (MAPK) signaling that transduces photic signals to zCry1a gene transactivation. Importantly, light also drives the production of intracellular ROS, such as H2O2 , that leads to an altered redox status and increases intracellular catalase activity by stimulating catalase transcription, an event which occurs after the maximum expression of the zCry1a gene has been reached. This increased catalase activity diminishes light induced cellular ROS levels, resulting in decreased zCry1a transcription and creating a negative feedback loop. Thus, this altered redox state triggers the transduction of photic signals that regulate and synchronize the circadian clock.  M L Fanjul-Moles 2015. 

It has been found that a reduced magnetic field may affect positive phototaxis and flight capacity of a migratory rice planthopper – potentially acting through an antioxidative stress relatied cryptochrome-circadian clock AKH/AKHR signalling pathway.  Gui-Jun Wan 2016.

WATER AND THE REDOX STATE

Water-protein coupling) is also influenced by the redox state.  With femtosecond resolution, distinct solvation dynamics have been observed in apoflavodoxin and in three redox states of holoflavodoxin. From the apoflavodoxin to oxidized holoflavodoxin (flavin mononucleotide – FMN), similar fast water-network relaxations in 1 ps have been observed, but different waterprotein coupling fluctuations (18.3 vs 25 ps) from the two different structural flexibilities. From the oxidized to semiquinone (FMNH• ) states, the local structure becomes more rigid due to the extra hydrogen-bond formation by the redox switching. The local solvation dynamics significantly slow down to 2.6 and 40 ps, a clear correlation between the local structural rigidity and water-network immobility. From the semiquinone to hydroquinone (FMNH‾ ) states, the solvation relaxations become faster again in 1 and 21 ps with a significant increase in total solvation energy, due to a more polar environment with more mobile water molecules in a looser and larger pocket caused by the negative repulsion between the anionic cofactor and neighboring negatively charged residues.  He, Ting-fang

TEMPERATURE COMPENSATION

One central feature of all circadian rhythms is ‘temperature compensation’ which allows organisms to maintain robust rhythms with a period close to a diel cycle over a broad range of physiological temperatures. 

A 2010 study showed that in drosophila, who protective heat and stress response had been inhibited, the clock hardly shifts with temperature changes, but since the conventional model predicts everything is temperature sensitive, no single pathway should be this influential.  Recent findings suggested that the temperature-induced shifts of the clock involve genetic pathways separate from the molecular cycles of the core clock, but linked to them.   P B. Kidd 2015.  In drosophila, brief noxious heat pulses have been demonstrated to cause dramatic decreases in Per and Tim protein abundance and phase shifts in locomotor disruption of the Per-Tim complex via a Cryptochrome dependent mechanism.  A Bellemer 2015.  Different subsets of clock neurons operate at high and low temperatures to mediate Drosophila clock synchronisation to temperature cycles, suggesting that temperature entrainment is not restricted to measuring the amplitude of such cycles.  Cryptochrome dampens temperature input into the clock and therefore contributes to the integration of different Zeitgebers. C Gentile 2013.  

THE POSSIBLE ROLE OF IRON SULPHUR CLUSTERS COUPLED TO CRYPTOCHROME

Ultra-fast electron transfer (in both photosynthesis and magnetoreception) may also involve interaction with an iron sulphur cluster. 

In 2016, Chinese scientists claimed to have discovered a new magnetoreceptor.  A polymeric protein, dubbed MagR (Drosophila CG8198)  forms a complex with a photosensitive protein called Cryptochrome (Cry).  The MagR/Cry protein complex, the researchers found, has a permanent magnetic moment, which means that it spontaneously aligns in the direction of external magnetic fields.  This is the only known protein complex that has a permanent magnetic moment. Cry likely regulates the magnetic moment of the rod-shaped complex, while the iron-sulfur clusters in the MagR protein are probably what give rise to the permanent magnetic polarity of the structure. S Qin – ‎2016.  Also see images below.

One way to increase the strength of geomagnetic field effects in to use materials with a strong magnetic moment, such as iron oxides (T Ritz 2010).  Cysteine residues associated with iron sulphur clusters could also support a photoinduced ultra-fast electron transfer in magnetoreception.  e.g In the complex 1 of the respiratory chain on the inner membrane of the mitrochrondria, electrons are transferred over a cascade of iron-sulphur clusters from a Flavin adenine mononucleotide cofactor to a quinone binding set.  The overall pathway is nearly 10nm long and most likely to involve aromatic amino-acid residues as stepping stones to bridge the gaps between the iron-sulphur clusters.

Iron sulphur clusters are also found throughout biology, for example CryB in Rhodobacter Sphaeroides (the only bacterial cryptochrome with a currently known biological function) has an iron sulphur cluster and is a member of a group of FeS-BCP proteins. mFeS-BCP (bacterial cryptochromes and photolyases with iron sulphur clusters) have been found in hundreds of bacterial organisms.  CryB in Rhodobacter Sphaeroides has been found to undergo a photoscycle – it does not only affect gene expression in response to blue light illumination, but also in response to singlet oxygen stress conditions. Geisselbrecht – ‎2012Hendrischk et 2009.  S Metz 2012

In photosynthesis, early experiments showed an increase in the relative magnetic field effect in Fe2+ – deleted reaction centre and more recently an experiment by Kirmaier et al, an increase in yield of triplet products was observed in Fe2+ depleted RCs relative to native RCs.  Based on these observations it has been proposed that a mechanism via such an effect could occur – that the high spin Fe2+ ion generates an effective magnetic field, thereby serving the protective function of reducing the triplet production in the purple bacterial RC under conditions where the forward electron transfer is blocked.  Marais et al 2015.

IS BIOLOGY MAKING USE OF SEMI-CONDUCTORS

The above has set out the case for biological semiconductors being ulitised in nature, but it may also be the case that levels of conductivity would change within biological material which forms part of a complex system of conductors, insulators, redox systems, etc – which in turn responds to changes in the environment (e.g temperature and magnetic fields).

Endogenous bioelectrical signals play critical roles in a near-infinite number of ubiquitous biological processes such as energy harvesting, rapid communications and inter/intra cellular synchronisation.  Specific examples include photosynthesis, vision, carbohydrate metabolism, neurophysiology, wound healing, tissue regeneration and embryonic development.   Charge transport has been found in a variety of naturally-derived small molecule, semiconducting biological compounds – carotenoids (produced by plants and bacteria).  These include protection against oxidative species, pigmentation, and light havesting for photosynthesis.  The polyconjugated structure of this class of compounds suggests that the natural electronic activity of derivatives could be repurposed as an active semiconductor material for organic electron devices.   M Mukovich 2012.  

If cryptochrome and/or iron sulphur clusters, were found to be acting like organic semi-conductors, this could provide an explanation for the arising of the radical pair mechanism – together with ultra-fast electron transfer, and potentially quantum coherence. This could include a possible hybridization of semiconductors and magnetism. It should be noted that magnetite (another potential trigger of magnetoreception) is also semiconductor.

But it could also be the case that cryptochrome and/or iron sulphur clusters may be found to be unconventional superconductors.  This could also bring together of the radical pair mechanism, ultra-fast electron transfer and quantum coherence – taking place at room temperature and in proximity to magnetism.

A biological high temperature semi or superconductor might make use interfaces, as interfaces provide an ideal tool to enhance and stabilize conductivity. The possibilities of interfacing between organic semiconductors and biology are currently being considered in organic bioelectronics.

Organic semiconductors and the structure of flavins .

π-conjugated systems exhibit directional preference in the intermolecular connection and demonstrate enhanced energy and/or charge carrier transfer. N Gospodino 2014.  In aromatic and conjugated organic molecules and polymers, the π-orbitals are delocalized along the molecule, giving rise to electronic mobility both along the chain and between adjacent chains via interaction between their π- orbitals. Adding or removing electrons to such material systems may result in a high electronic conductivity. In the form of positively charged polarons and/or bipolarons, electronic charges can thus migrate within and in between different molecules. Depending on electronic structure, density of charge carriers, and morphology, organic electronic materials can exhibit semiconducting, semimetallic, and even metallic conductivity, all of which have been extensively explored in various solid-state electronic devices. Historically, most organic electronic materials are synthetic, but there has always been a parallel interest in naturally occurring organic conducting materials. D T. Simon 2016.  

All organic molecules that serve as chromophores (of which flavins such as cryptochrome, are examples) consist of extended conjugated π-systems, which allow electronic excitation by sunlight and provide photochemical reactivity. 

Semiconductors and radical pairs

The racial pair mechanism can be found in semiconductors. There are three main types of organic spintronic phenomena: (i) magnetic field effect in organic light emitting diodes, where spin mixing between singlet and triplet polaron pairs can be influenced by an external magnetic field leading to organic magnetoresistive effect (ii) magnetoresistance in organic spin valves (OSVs), where spin injection, transport, manipulation, and detection have been demonstrated; and (iii) magnetoelectroluminescence bipolar OSVs or spin-OLEDs, where spin polarized electrons and holes are simultaneously injected into the organic semiconductor layer, leading to the dependence of electroluminescence intensity on relative magnetization of the electrodes. F Geng 2016.

Triplet-pair reactions impact on the operation of organic light-emitting diodes as well as photovoltaic devices. Conventional models for triplet pairs assume they interact only weakly, but recently, using electron spin resonance,long-lived, strongly interacting triplet pairs in an organic semiconductor, have been observed generated via singlet fission. L R Weiss (2016) , C Keong Yong 2016 .

A model for a hybrid system of semiconductor and photosynthetic protein has already been put forward by Younghye Kim 2014.  Biological semiconductors already exist and in a biological semiconductors, water could potentially act as a gating medium. D T Simon 2016.

Photoinduced ultra fast electron transfer in Semiconductors

Comprehensive studies of photoinduced electron transfer from semiconducting (conjugated) polymers to buckminsterfullerene have demonstrated ultrafast, long lived photoinduced electron transfer. Comparative studies with different semiconducting polymers as donors demonstrate that in degenerate ground state polymers, soliton excitations form before the electron transfer can occur; thereby inhibiting charge transfer and charge separation. In non-degenerate ground state systems, photoinduced electron transfer occurs in less than 10−12s, quenching the photoluminescence as well as the intersystem crossing into the triplet manifold. N S Sariciftc 1994.  

In the case of photoinduced phase transition, light induces drastic phase changes such as insulator-metal transition, photoinduced superconductivity, structural phase transition, magnetic phase transition and dielectric phase transition.. ultrafast dynamics for a purely electronic phase transition associated with the ferroelectric charge ordering in a two-dimensional organic material α-(bis(ethylenedithio)-tetrathiafulvalene)2I3 (α-(BEDT-TTF)2I3), has been observed by probing a pulse SHG intensity from a sample excited by a pump light pulse. M Aihara 2008.  

Photoinduced Electron Transfer in Biology. 

Photoinduced electron transfer reaction plays a pivotal role in regulating many light-switched enzyme activities such as photosynthesis and circadian rhythm. In the biological system, the donor-acceptor distance may vary from a few angstroms to tens of angstroms…In experiments with  flavodoxin, by altering the critical redox-sensitive residues, different redox potentials for the acceptor to convert from oxidized to one-electron reduced, and from one-electron reduced to two-electron reduced states are generated. From such a great variety of driving forces, results shows a strong correlation between the rates of electron transfer and the reaction energy.  He, Ting-fang 2011. 

THEORIES OF BIOLOGICAL SUPERCONDUCTORS

London speculated that superconductivity might exist in certain biological systems and specifically in the aromatic organic long-chain molecules which have conjugated double bonds containing itinerant electrons (π electrons).  Utilising this speculation of London and BSC theory of coupled electrons Little postulated the existence of an organic polymer that might be a superconductor at room temperature. Ladik et al discussed the possibility of superconductivity in DNA molecules at room temperature.  Ginzburg discussed the problem of high temperature superconductivity in terms of exciton mechanisms and described a thin film sandwich of a metallic superconductor between organic dielectrics, and Gamble and McConnel talked about exciton mechanisms for organics and metallic codeposited and as films for enhancement effects of the critical temperature ….. A  A Wolf developed a thermodynamic relation between the crucial temperature and the ratio of the internal energy (U) and the entropy (S).  This was represented by the equation = Tc = U*/S (U* is net internal energy of the superconducting material). This implies that if the entropy of a superconducting material is reduced and if the internal energy of a material is increased consistent with the maintenance of the electron pairing, one could raise the critical temperature of the superconducting material E H Halpern 1972. 

The coupling of circadian rhythms (modelled as dissipative structures) could have a key role to play in this – as dissipative structures with access to free energy will reduce internal entropy and thus become more ordered by externalising entropic output to the environment.   

The search for organic superconductors had been boosted in the 1960s by the idea that conductive polymer chains with polarizable molecular groups may provide for electrons running along the polymer chains a highly effective Cooper pair coupling by means of an energy exchange via localized excitons  Since the first discovery of an organic superconductor in 1980  Tc >10 K has been achieved.  However, the origin of superconductivity has turned out to be far from the suggested excitonic mechanism. Electric conduction stems here from π- electrons in stacked aromatic rings forming one-dimensional or two-dimensional (2D) delocalized electron systems. This restriction of the effective dimensionality and strong Coulomb repulsion effects push the systems toward metal-insulator, magnetic, and SC transitions. R Hott 2011

Frohlich proposed a theory in which biomolecules with higher electric dipole moment lie up along the actin filaments immediately beneath the cell membrane, and electric dipole oscillators propagate along each filament as coherent waves without thermal loss – just as in the case of superconducting media.  H Frohlich 1968, 1970 and 1975.

It has also been extreme sensitivity of some organisms to weak magnetic fields  may relate to the superconductive junction phenomena  in these biological systems. A weak magnetic field effect on probable Josephson junctions have been observed in carbon films at 25.  Electron tunnelling through these junctions take place in response to the very small magnetic fields.  Freeman W Cope 1979.   Freeman W Cope 1975 reviewed the evidence for solid state physical processes in diverse biological systems. He found that  semiconduction of electrons across the enzyme particles as the rate-limiting process in cytochrome oxidase is evidenced by the peculiar kinetic patterns of this enzyme and by microwave Hall effect measurements. PN junction conduction of electrons is suggested by kinetics of photobiological free radicals in eye and photosynthesis. Superconduction at physiological temperatures may be involved in growth and nerve. Phonons and polarons seem likely to be involved in mitochondrial phosphorylation.  

E D Giudice 1989 also made the proposal of coherent electromagnetic processes as the engine for biological dynamics suggests that Josephson effects could be present in living cells and claimed that there was evidence for this. And it has been proposed that the quantum like transition that realizes the stable state of living matter at room temperature is similar to the non conventional BCS-like transition as seen in high Tc superconductors. N Poccia 2009. 

The Josephson effect describes tunneling of Cooper pairs through a barrier – a Josephson junction is a contact between two superconductors separated from each other by a thin dielectric tunnel barrier. 

The relationship between protein dynamics and function is a subject of considerable contemporary interest.  It has been found that the quantum mechanical hydrogen tunneling associated with enzymatic C-H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. J P Klinman 2013.  

A variety of transport properties of biological materials, such as hemoglobin, amino acids, proteins, polypeptides, and so on, have been investigated as potential natural conductors, started with the pioneering works by Eley et al. Most of them are insulating except cytochrome-c3. In recent studies on biomolecular conductors, DNA is one of the most active target molecules, and numerous experiments concerning the transport properties of DNA molecule have been carried out. In the double-stranded DNA molecules, nucleobases establish a one-dimensional p-stacking structure which was proposed to be an efficient charge conduction path within DNA. This past decade has seen numerous controversial studies regarding electrical conduction of DNA. Some reported high conductivity  or even superconducting properties (A Y Kasumov 2001), while others claimed that the carefully deionized DNA molecules are insulating. The controversy seems to have settled on a wide consensus that, apart from ionic conduction by the sodium gegenions, double-stranded DNA is an electrical insulator. G Saito 2012.

Similarities between the structures of biological materials and unconventional semiconductors and superconductors.

A. Flavoproteins

Eukaryotic riboflavin-binding proteins typically bind riboflavin between the aromatic residues of mostly tryptophan- and tyrosine-built triads of stacked aromatic rings.  Mechanistically, fast electron transfer from the aromatic moiety to the riboflavin has been proposed to quench the excited state of riboflavin by building a couple of a positively charged amino acid radical and a negatively charged flavin semiquinone. 

Above is the structure of riboflavin.  Below is the structure of an organic superconductor.

Ultrafast electron transfer mechanisms from an aromatic moiety to a photoexcited flavin are not only observed for riboflavin-binding proteins but for other flavoproteins, like for BLUF (blue light sensing using FAD) domains, cryptochromes, and DNA photolyases.  H Staudt 2011. 

All organic molecules that serve as chromophores (of which flavins such as cryptochrome, are examples) consist of extended conjugated π-systems, which allow electronic excitation by sunlight and provide photochemical reactivity  . 

Extended electron-transfer in animal cryptochromes is mediated by a tetrad of aromatic amino acids.  D Nohr 2016.  

Organic semiconductors that are crystalline in nature can also hold a charge and be used to create memory. Crystal structures have been determined in several members of the photolyase/cryptochrome superfamily in various species: CPD photolyase (Escherichia coli, Synechococcus sp. and Thermus thermophilus), CRY-DASH (Synechocystis sp), and a plant cryptochrome (the PHR region of Arabidopsis CRY1), and the CryB crystal in rhodobacter sphaeroides.   See theorised dCRY structure and reactivity – set out below.

It is therefore interesting to note some of the emerging findings on the role that cryptochrome plays in animal memory. Recent results indicate a key role of cryptochrome proteins in time and place learning(TPL) and confirm the limited role of the SCN in TPL. It is thought that TPL involves the hippocampus, and reflects an episodic-like memory task, but due to its functional nature, also entail the translation of experienced episodes into semantic rules acquired by training. CK Mulder 2016 . Mice deficient in cryptochrome exhibit impaired recognition memory, increased anxiety, and lack of time-place associations. A Malik 2015.  Normal ongoing brain activity can be disrupted by magnetic stimulation.  Further implications of these findings are explored in another post- click here to find out more.

B. Iron Sulphur Clusters

Their most common oxidation states are paramagnetic and present significant challenges for understanding the magnetic properties of mixed valence systems . Charge distribution in the clusters depends on coordination number of the metals and the extent of the magnetic coupling between them- with ferromagnetic coupling favouring charge doclocalisation, and anti-ferromagnetic coupling appearing to give rise to charge localisation.

Although in most magnetotactic microorganisms, the geomagnetic field is detected by magnetic particles with a permanent magnetic moment, a magnetic iron-sulphur crystals have also been found in microorganisms. The magnetosomes are found in planar groups inside the cytoplasm of each cell in the aggregate.  M Farina 1990.  Ferrimagnetic greigite (Fe3S4) occurred in all types of sulfide-producing magnetotactic bacteria examined.  Mackinawite (tetragonal FeS) and, tentatively, sphalerite-type cubic FeS were also identified. Mackinawite converted to greigite over time within the bacteria that were deposited on electron microscope grids and stored in air.  Orientation relationships between the two minerals indicate that the cubic-close-packed S substructure remains unchanged during the transformation; only the Fe atoms rearrange. Neither mackinawite nor cubic FeS are magnetic, and yet they are aligned in chains such that when converted to magnetic greigite, the probable easy axis of magnetization, is parallel to the chain direction. The resulting chains of greigite are ultimately responsible for the magnetic dipole moment of the cell. Both greigite and mackinawite magnetosomes can contain Cu, depending on the sampling locality.  M Posfai 1998.  T Kasama 2006 . 

Up to now, at least four structure types of iron-based superconductors have been developed, including the discovering of superconductivity in tetragonal FeS  (mackinawite-type FeS, is now confirmed as a superconductor and not a magnetic semiconductor) although its Tc is only 5K, it is seen to provide a new platform to realise high temperature superconductors. It has been found that the substantial difference in magnetic and superconducting behaviour in different FeS phases is directly tied to the crystal structure details and compositions. S J Kuhn 2016.  E E Rodriguez 2016.   Results both indicate the existence of strong itinerant spin fluctuations in mackinawite, and mackinawite exhibits the magnetic characteristics of the high temperature Fe-based superconductors with which it is isostructural. If strong spin fluctuations are the mediators of electron pairing in these Fe-based superconductors. Mackinawite may be one of the simplest Fe-based superconductors.  K D Kwon 2011.  Unlike its heavier analogs FeSe and FeTe, however, mackinawite is metastable and therefore cannot be synthesized from their respective elements using solid state methods, unless it is alloyed with significant amounts of Co, Ni, or Cu.  C K H Borg 2016.

The Fe-S cluster is capable of transferring electrons in electron transfer chains (for photosynthesis and respiration) and of catalysing redox reactions.  Additionally Fe-S Clusters act as catalytic centres, regulators of gene expression and sensors off iron and oxygen.  The simplest Fe/S clusters are of the (2Fe-2S and 4Fe-4S) types which contain either ferrous or ferric iron and sulphide and which are usually integrated into proteins via coordination of iron ions by cysteine or histidine residues.  John H. Golbeck 1993.

Superconductors and singlet and triplet states   

It is fascinating to consider what relationship/interaction radical pairs might have with cooper pairs. The pairing mechanism responsible for the high−Tc superconductivity in some organic superconductors remains one of the most challenging problems of current Solid State Physics.

Radical pairs.  It is proposed that in magnetoreception the absorption of a photon raises a receptor molecule into an excited state and leads to a light-activated electron transfer from a donor to an acceptor, thus generating a spin-correlated pair. By interconversion, singlet states radical pairs with an antiparallel spin are transformed into triplet states with parallel spin and vice versa. The singlet/triplet ratio depends on, among other factors, the alignment of the receptor molecule in the external magnetic field and could thus mediate information on magnetic direction. R Wiltschko 2014. 

Cooper pairsUsually, the Cooper pairs form in a singlet state, where the electrons have opposite spins, so that the Cooper pairs have zero spin overall. On rarer occasions, Cooper pairs to form in a triplet state with parallel spins. Due to the Pauli exclusion principle, which requires that the pairing wave function is antisymmetric upon exchanging the electrons, the singlet state has even parity and the triplet state has odd parity

However some materials of significant theoretical and practical interest, such as high temperature cuprates and heavy fermion compounds, are beyond BCS theory. This is explored further below.

Photoinduced ultra fast electron transfer in Superconductors

Ultrafast electron dynamics has also been evidenced in superconducting Bi2Sr2CaCu2O8+δ (Bi-2212), and photoexcited  MoS2/WS2  heterostructures. X Hong 2015

Superconductors and antioxidant effect

Graphene has recently been found to transition to superconductivity and may be an example of a p-wave (spin triplet) superconductor. Treated particles of graphene derived from carbon nanotubes have demonstrated potential as antioxidants. Graphene based materials are shown to protect against a variety of molecular targets from oxidation by reactive oxygen species, and to be highly effective as hydroxyl-radical scavengers.  When hydroxyl radical is produced photolytically, the overall antioxidant effect is a combination of preventative antioxidant activity (UV absorption) and OH radical scavenging.  Y Qiu 2014.

Superconductors and magnetism 

When a material makes the transition from normal to superconducting state, it actively excludes magnetic fields from its interior; this is called the Meissner Effect. In superconductors it would be expected that due to their spin, electrons would orientate in a magnetic field in a manner analogous to a compass needle. C C Agosta 2016.

However in an unconventional superconductor, it is possible to have a combination of magnetism and quantum coherence in the same system.  The most important classes of superconductors have been found in proximity to magnetism, including not only heavy-fermion superconductors, but also organic superconductors, cuprates, and iron-based superconductors. All of them have similar phase diagrams, in which, either by pressure or chemical substitution, a magnetic phase is suppressed, giving rise to a superconducting phase. This has led to the suggestion that an effective search strategy for discovering new superconductors is to identify a stoichiometric phase that is magnetic, and then find a way to hinder magnetism. Following such an approach, a team led by Jin-Guang Cheng at the Beijing National Laboratory, China, reported the discovery of the first superconductor based on manganese, an element whose magnetism was thought to be too strong to allow superconductivity. By suppressing magnetism with a large applied pressure, the authors found that manganese phosphide ( MnPMnP) can become superconducting at a critical temperature. R M Norman 2015. 

It has been proposed that a complete synergy between superconducting and magnetic orders is possible through the creation of spin-triplet pairs, which are generated at carefully engineered superconductor interfaces with ferromagnetic materials. J Linder 2015. 

However it has also been recognised that the microscopic theory about the coexistence of magnetism and superconductivity in strongly interacting heavy electrons is either too complex or insufficiently developed to describe the complicated behaviour, although there have been attempts to explain this e.g  RG Cai – ‎2014.   Also see Xian-Hui Ge 2016.   If holographic duality yields increasingly accurate predictions about the behaviour of cuprates and other strongly correlated materials, these materials can be conceived as, essentially, being black holes in higher dimensions.  Holographic superconductors are explored in more depth below.

Patterns in Type II superconductors.

Vortices control the current carrying ability of all superconductors.

Related to this, are patterns found in semiconductors and  superconductors, which resemble Turing patterns.  Turing patterns can include stripes,  hexagonal arrangement of spots, and hexagonal superlattices (Y Lang 2006).  Overall 7 patterns of morphogenesis have been evidenced. N Tompkins 2014. 

Electrons involved in superconductivity can form patterns, stripes or checkerboards, and exhibit different symmetries – aligning preferentially along one direction. These patterns and symmetries have important consequences for superconductivity – they can compete, coexist or possibly even enhance superconductivity.

Stripes formation occurs in type I superconducting film. In two gap superconductors, superconducting vortices accommodate themselves by forming striped flux patterns. (J Guiterrez Royo 2012).  In type II superconductor systems , a magnetic field can penetrate a sample in a tube-like configuration.  The magnetic flux (superconducting vortices) arrange in the lattice with hexagonal symmetry.  Competition between superconducting and non superconducting phases can result in a formation of a hexagonal pattern. (Y Holovatch 2015).

As in the case of the reaction diffusion modelling – periodical oscillations may play a role in this. Applied magnetic fields may produce interesting effects in nanostructured superconductors e.g they may induce different types of periodic responses. In hybrid superconducting/non superconducting system commensurability effects between the vortex lattice and the artificial non-superconducting array generate well defined period features in the magnetic and transport properties, at temperatures close to the superconducting critical temperature.  A Gómez Gutiérrez – ‎2014.

Reaction diffusion type patterning may offer the most efficient shapes for conduction and phase masks/holography. The following shows a generated reaction diffusion pattern (black and white).  Next to it is a superconducting disk.  It is also interesting to note that microtubules (underneath the disk) have been evidenced to be generated through reaction diffusion. N Glade 2004.   Superconductor patterning also includes dendrite fluxes

Patterns in reaction diffusion (self organising) modelling might assist with understanding semi and superconducting system.  Similar wave patterns to those found in the BZ  model appear in many other reaction diffusion systems having the same dynamic behaviour.  For some values of the parameters, the BZ reaction (which includes a negative feedback loop via organic free radicals) and PP models also behave as excitable systems.  The main feature of this kind of system is the way they respond to perturbations.  There exists a threshold value, such as if the perturbation goes above it, the system reaches the fixed point only after a long excursion in the phase space… The propagation of the excitation through neighboring points, coupled diffusively, generates traveling pulses. In two dimensions there are circular propagating waves. M Cecini 2003.   Vortices in a flow have significant effect on front propagation, in particular a moving vortex tends to pin and drag a front.  If a chain of vortices oscillates periodically (e.g forced by an external perturbation) mode locking often occurs.  Mode locked results in faceted fronts that line up along the general direction of the underlying vortex array. J R Boehmer 2008.

In addition, the relationship between reaction diffusion patterning and superconducting may be related to the finding that a map of entanglement entropy of a superconducting qubit that, over time, comes to strongly resemble that of classical dynamics—the regions of entanglement in the quantum map resemble the regions of chaos on the classical map. The islands of low entanglement in the quantum map are located in the places of low chaos on the classical map. “And, it turns out that thermalization is the thing that connects chaos and entanglement. It turns out that they are actually the driving forces behind thermalization’. S Fernandez 2016.  

It has been proposed that light harvesting in chromophores is realised by excitonic system living at the edge of quantum chaos (G Vattay 2014), where energy level distribution becomes semi-poissonian…semiconductor materials are known to also exhibit quantum chaotic conditions. E Prati 2015.

HOLOGRAPHIC SUPERCONDUCTORS

Some materials of significant theoretical and practical interest, such as high temperature cuprates and heavy fermion compounds, are beyond BCS theory. There are indications that the involving physics is in strongly coupled regime, so one needs a departure from the quasi-particle paradigm of Fermi liquid theory.  Anti-de Sitter/Conformal Field Theory(AdS/CFT) correspondence remains to be understood from first principles, this duality creating an interface between gravitational theory and dynamics of quantum field theory provides an invaluable source of physical intuition as well as computational power. In particular, in a “large N and large λ” limit, the gravity side can be well described by classical general relativity, while the dual field theory involves the dynamics with strong interaction. It is often referred to as “holography” since a higher dimensional gravity system is described by a lower dimensional field theory without gravity, which is very reminiscent of an optical hologram…. It has been shown that the AdS/CFT correspondence can indeed provide solvable models of strong coupling superconductivity. Rong-Gen Cai 2015.

EMERGENCE

In some materials, the strong electron-electron correlations to other degrees of freedom with the complex many body quantum system lead to new, emergent properties that are controlled by a competition of correlations and fluctuation effects, characterized by phase transitions at a critical temperature, where correlations lead to coordination with a macroscopic region – resulting in the breaking of a symmetry of the system.  Below the transition temperature, a new broken-symmetry ground state is found, which can possess a variety of novel, emergent properties that are macroscopically observable. In condensed-matter physics, the complex interaction of many degrees of freedom such as electrons, ions and spins lead to the formation of properties such superconditivity, magnetism, charge density waves and orbitally ordered states, etc. L Rettig 2012. 

Exploring Dissipative Dynamics through Classical-Quantum Correspondence.

The above findings could potentially be explored using classical-quantum correspondence. 

The equivalence of the Agarwal equation with the Redfield theory shows they satisfy a surprising level of classical-quantum correspondence. (1) The harmonic oscillator master equation derived from Redfield theory, in the limit of a classical bath, is identical to the Agarwal master equation. (2) Following Agarwal, the Agarwal master equation can be transformed to phase space, and differs from the classical FP equation only by a zero point energy in the diffusion coefficient. D Kohen, (1997).

The FKPP equation could be used to explore correspondence – see bullet points below. 

  • The FKPP equation describes the propagation of unstable non linear wave fronts/population dynamics. Pulled fronts are extremely sensitive to noise in the leading edge. Fluctuations arise when the underlying physical substrate consists of discrete constituents interacting on a lattice (intrinsic noise), or when there are external environmental perturbations (extrinsic noise). P Bressloff. 2011.
  • Dynamo theory and the azimuthal magnetic field can be reduced to the FKPP equation. S Fedotov et al 2003.  
  • If the classical treatment of the FKPP equation due to Freidlin is expanded  to include the phenomenon of anisotropic diffusion with a finite velocity, in the long-time large-distance asymptotic limit the Hamiltonian dynamical system associated with the anisotropic reaction–diffusion equation has a structure identical to that of general relativity theory. The function determining the position of the reaction front and its speed is nothing else but the action functional for a particle in both gravitational and electromagnetic fields….. It is well known that the macroscale equations for turbulent heat/mass transport involve effective anisotropic transport processes with a finite velocity S Fedotov  et al 2000. The evolution of hadronic scattering amplitudes at fixed impact parameter in the regime where nonlinear parton saturation effects become sizable has been shown to be similar to the time evolution of a system of classical particles undergoing reaction-diffusion processes.
  • The same FKPP (reaction diffusion) type of equation appears in various fields of statistical physics and, recently, in the domain of Quantum Chromodynamics (QCD), the interaction theory of quarks and gluons, where it models the evolution of the gluon momenta in the wave-function of a hadron or a nucleus when the energy increases..
  • Higher order corrections to the Colour Glass Condensate evolution equations, include the BK and JIMWLK equations (the BK equation lies in the university class of the FKPP equation and correspondences to a spin glass phase of FKPP). The correspondence between the BK and FKPP equations, clarifies the properties of saturation fronts in QCD in analogy with known properties of reaction–diffusion processes. A crucial property is the emergence of traveling waves. Reaction–diffusion processes exhibit an extreme sensitivity to particle number fluctuations, generated by gluon splittings, which produce correlations among pairs of gluons.  F Gleis 2010.   Also see Robi Peschanski 2008Charles R. Doering, and H Weigert 2004.

CONCLUSION

If room temperature semiconducting and superconducting is being utilised in biology, this could open a whole new world up to us – one of where we also understand:

  • The quantum mechanisms of photosynthesis to create solar power cells  (at 100% efficiency),and how to substantially increase crop yields.
  • How to revolutionise our use of energy and create technologies to address climate change
  • How to harness clean nuclear energy, as high temperature superconductors can be used to create the magnetic field to contain the fusion plasma.
  • Effective treatment for neurological, immunological and other forms of disease and disorder.
  • How to develop more powerful computing and artificial intelligence.
  • How to take major steps towards almost unimaginable discoveries such as utilising quantum tunnelling.
  • That all natural systems are ultimately open, and looking at something in isolation (in a laboratory) has major limitations. If we understand this, then discovery never needs to end.

Ethical Issues

Understanding biological mechanisms and translating them into technologies could radically change the way we live. So it would be easy to get carried away and feel that all the drive should be towards validating the existence of these mechanisms and the creating associated technologies.

However, we should remember that science takes place within a wider society. Science has responsibilities within this broader societal framework.

It is questionable whether the biological mechanisms themselves (either individually or in combination) could be patented, particularly in those countries that are resistant to such patents.

Who, for example, could be said to own a patent for biological organic semiconductors or  superconductors – or copyright the idea of quantum biology? For many people have published on these subjects and contributed towards understanding them.

As a recent study produced by the LSE and Havard stated “New ideas and technologies are not the product of a few far-sighted geniuses but arise through societies and social networks acting as ‘collective brain”:

In addition, emerging quantum (and quantum-classical) biology may reveal mechanisms that are fundamental to life – so how could any human being claim to own them?

If the biological mechanisms cannot patented, the question remains over the ethics of holding the ownership of associated technologies. If one company, or country, owned such technologies, it would cause a great imbalance in the world.

If the mechanisms themselves cannot be patented and various scientists across the world had open access to them, then there is a greater likelihood that the technologies would emerged in a relatively balanced way across different companies and countries. Opportunities would also arise for partnership between the owners of those different technologies.

Competition and commercialism can offer the impetus to produce new technologies quickly and efficiency (and at decreasing cost which increases levels of access). But competition and commercialism can also emphasis individualism.

The degree of change we may face cannot take place in a world of individuals that merely compete with each other. We must better understand how we can make best use of that “collective brain” to promote positive outcomes for all. Bioethics offers a starting point, but it can only be meaningful if those engaging in the debate have some awareness of what it means to be part of a self-organised system – where everything is connected to everything else and the idea of the individual (as we currently understand it) has been recognised as illusion.

This would reflect a world where quantum mechanics had become as accepted and integrated into social thinking (and acting) as classical mechanics. This would be a world where so many things we had thought impossible would become possible- because we would have stopped seeing them as impossible.

If such awareness existed, it would facilitate the start of a debate by a true community. 

The alternative is that the human race makes the choice of  suppressing such technology in order to avoid social and economic upheaval – but this would ignore the fact that the world is currently experiencing low growth, increasingly levels of inequality, and widespread war and poverty.  And developing such technologies to support power hording and the creation of new weaponry is likely to lead to further tensions and war.  Do we really have this choice if we think beyond ourselves and our immediate group? 

October 2016. This article merely joins up other peoples work into an overall system.  These works have been referenced so it is clear that others have provided the individual pieces of evidence that have been used to shape a specific systems approach.    

 

 

 

 

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