Biological Spintronic Semiconductors: Frontiers

Spintronics

Spintronics is an emerging field of basic and applied research in physics and engineering.  Spintronics, meaning “spin transport electronics”, exploits the intrinsic spin of electrons, in addition to their electronic charge, in solid-state devices like sensors.

Spintronic devices make use of spin properties instead of, or in addition to electron charge to carry information, thereby offering opportunities for novel micro‐ and nano‐electronic devices. These devices are expected to become the ideal memory media for computing and main operating media for future quantum computing..  In spintronics the spin of an electron is controlled by an external magnetic field and polarize the electrons. These polarized electrons are used to control the electric current. The goal of spintronics is to develop a semiconductor that can manipulate the magnetism of an electron…  External magnetic fields can be applied so that the spins are aligned (all up or all down), allowing a new way to store binary data in the form of one’s (all spins up) and zeroes (all spins down).

Biological materials are being investigated in spintronics as in the face of continued miniaturization of components and circuitry in microelectronics, conventional semiconductor microelectronics is rapidly approaching its useful miniaturization limits… For an alternative approach…. biological molecules are known to self‐assemble with nanometer scale resolution and possess some unique qualities that might be crucial for nanoscale fabrication.  A Fakhar 2008.

Biological Semiconductors

The concept of biological semiconductors has been around for some years (e.g A V Vannikov 1970. Bioelectrical signals play critical roles in many 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.

Biological semiconductors already identified include melanin and peptides. Charge transport has also been found in a variety of naturally-derived small molecule, semiconducting biological compounds including carotenoids (produced by plants and bacteria), which offer protection against oxidative species, pigmentation, and light harvesting for photosynthesis. M Mukovich 2012.  

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.  It has been 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 an oxide semiconductor’. L I. Boguslavskii – 2013.

Spintronics, Spin Chemistry and Quantum Biology 

Spin chemistry is an older field of science than spintronics.  It has been drawn upon by those attempting to explain room temperature quantum mechanical effects in photosynthesis and (possibly) magnetoreception (N Lambert 2013).

Very recently it has been recognised that the fields of spin chemistry and spintronics  are working on very similar areas of science and there is a strong argument for drawing the two fields together.

 J Matysik (2017)  has provided an initial ontology that describes the similarities and differences  between the findings of each field.  It might also be useful to turn this into a semantic web ontology to assist in research, and also connect in other fields including quantum biology, and broader biology.  It is important that there is more communication between chemistry, physics and biology around spin in biological materials.

There are various theories relating to quantum biology, but it is hoped that with the drawing together of scientific disciplines, the exact mechanisms will become clearer.

Quantum Biology as Biological Spintronic Semiconductors.

There are several evidenced examples in biology of processes which involve ultra-fast electron transfer, singlet and triplet spin mechanisms and quantum coherence (taking place at room temperature).

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

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.

Radical pairs in Quantum Biology: Magnetoreception and Photosynthesis

Certain organic semiconductors (OLEDs) exhibit magnetoelectroluminescence or magnetoconductance, the mechanism of which shares essentially identical physics with radical pairs in biology”. PJ Hore (2016).

  1. 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.
  2. In the case of organic semiconductors photoexcitation or electrical excitation results in strongly bound electron–hole pairs, so-called excitons. Depending on the relative orientation of the electron and hole spin, the exciton may be of an overall singlet or triplet spin state.  A Kohler 2009.

Magnetoreception

The two mechanisms theorised to enabled magnetoreception are (1) the radical pair mechanism (taken from spin chemistry) utilising a flavoprotein called ‘cryptochrome’, and (2) Magnetite. Some researchers have looked at each mechanism separately, while others have considered whether the two mechanisms could be coupled together in some way.

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

It is proposed that 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.

Photosynthesis

The initial charge separation steps of bacterial photosynthetic energy conversion proceeds 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 Pairs and Ultra-Fast Electron Transfer

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 Marais – ‎2016

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

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, I F Cespedes-Camacho and J Matysik 2014. 

Photosystem II reaction centre (RC) in higher plants share many structural and functional features with the bacterial RC, reflecting evolution from a common ancestral RC, Amongst these similarities is an Fe2+ ion, a spin-2 iron ion, positioned between the two ubiquinone molecules in both types of RCs. The ion has been postulated to play a structural and/or energetic role in electron transfer.  It has also been proposed that it plays a role in the photo-CIPNP effect – reducing oxidative stress in bacteria and plants and so offers an important anti-oxidant effect. (Marais et al 2015)

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.  J Matysik 2009.

Until now, no CIDNP phenomenon has been observed in spintronics, although the possibility of obtaining such effects has been mentioned : “If nuclear spin resonance is
found to have an impact on the spin-dependent electron transport due to the hyperfine interaction, ultimately the opposite process may become possible: storing electronic spin information in the nuclear spin.”   J Matysik (2017).

But the photo-CIDNP effect also has implications for quantum biology and thus for increased understanding of biology, for example it has been found that cryptochrome plays a role in animal memory. CK Mulder 2016 , A Malik 2015.

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 (77 K), 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 300 fs. 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 2016.

Rienk 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.

Ultra-Fast Electron Transfer in Flavoproteins

Beyond ultrafast charge separation in photosynthesis, there are similar dynamics in bond isomerization in sensory photoreceptors and repairing DNA damage.  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.

The Solid State Photo CIDNP Effect in the Photolyase/Cryptochrome Family.

A solid state Photo-CIDNP effect has been demonstrated in

  • The photochemical yield of a flavin-tryptophan radical pair in Escherichia coli photolyase. K B Henbest 2008.
  • 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. W Xiao-Jie 2016.  Also see G Jeskchke 2011.  

Flavins: Extended Conjugated π-Systems and Stacked Aromatic rings.

Aromatic compounds with extended π-conjugated system have attracted attention because of their potential utilization in organic electronic materials, including organic semi-conductors. π conjugation in most organic semiconductors for OFETs is extended through 1D condensation of aromatic rings. Xin Shi 2016.

The intrinsic optoelectronic activity of many types of biologically-derived soft matter is attributed to aromatic components. M Mukovich 2012.  

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.

The Redox State of Cysteine Residues, Radical Pairs and Ultra-fast Electron Transfer

Hopping Mechanisms in Organic Semiconductors

Hopping conduction is widely considered the dominant charge transport mechanism in disordered organic semiconductors. A V Nenashev 2015.

In organic semiconductors, 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. 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.  

The conductivity of organic semiconductors can be increased, and the barriers to charge-carrier injection from other materials can be reduced, by the use of highly reducing or oxidizing species to n- or p-dope, respectively, the semiconductor. Molecular species with well-defined redox chemistry which form stable cations or anions provide one such approach. S Barlow

Electron Hopping Mechanisms in Biology

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 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. W Sun 2015. 

Multi-step tunnelling (or hopping) is required for functional charge transport in many redox enzymes (examples include ribonucleotide reductase photosystem II DNA photolyase, MauG, and cytochrome c peroxidase.  It has been proposed that many such enzymes, most especially those that generate high-potential intermediates during turnover, could be irreversibly damaged if the intermediates are not inactivated in some way.  But appropriately placed tyrosine (Tyr) and/or tryptophan (Trp) residues could prevent such damage by rapid reduction of the intermediates followed by transfer of the oxidizing equivalent to less harmful sites or out of the protein altogether. J R Winkler 2015.

Electron Hopping in Photosynthesis

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 mechanism.  Orf 2015.

It has been 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.  Orf et al 2016

Electron Hopping in Flavoproteins

  • 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.
  • Very fast photo electron transfer (PET) is feasible along the conserved linear tryptophan pathway found in the flavoproteins of the photolyase/cryptochrome familyDr T Biskup 2011.  He, Ting-fang 2011.  Cryptochromes are probably the evolutionary descendents of DNA photolyases.
  • The extended electron-transfer in animal cryptochromes in mediated by a tetrad of aromatic amino acids.  D Nohr 2016.
  • 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… LOV signalling through the Flavin neutral semiquinone (NSQ) state has parallels to signal transduction in other flavin based photoreceptors including cryptochromes and BLUF.  E F Yee 2015.  LOV domains are involved with control of phototropism chloroplast relocation, stomatal opening, rapid inhibition of stem growth, and gametogenesis, for higher plants, and circadian temporal regulation in bacteria and fungi… H Zhou 2017.

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. Denis V. Sosnovsky.  2016.  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.

Protein Complex with a Permanent Magnetic Moment

In 2016, Chinese scientists claimed to have discovered a new magnetoreceptor.

In this case a polymeric protein, dubbed MagR (Drosphila CG8198) forms a complex with a photosensitive protein called cryptochrome.

The MagR/Cry protein complex 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.

It is thought that 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.

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).

Iron Sulphur clusters 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. H Beinert – ‎1997.

Fe-S clusters are 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.

Cysteine residues associated with iron sulphur clusters  might support a photoinduced ultra-fast electron transfer in magnetoreception.  For example 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 found throughout biology e.g mFeS-BCP (bacterial cryptochromes and photolyases with iron sulphur clusters) have been found in hundreds of bacterial organisms.  One of this bacterial cryptochromes (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. Crystal structures have been determined in several members of the photolyase/cryptochrome superfamily in various species including CryB crystal in rhodobacter sphaeroides.

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.

It seems possible that this might relate to the fact that the Cryptochrome protein (CRY) in Arabidopsis, Drosophila, and the mouse provide the most direct path by which redox status can interact with the core components of the transcription–translation feedback loop (TTFL) of the biological clock.   Lisa Wulund 2015.

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.

Circadian Rhythms

Circadian rhythms are a key type of biological oscillations and perhaps can be seen as a global clock which ensures that timing throughout an organism is optimally co-ordinated and aligned with its environment. Rhythmic environmental cues create a periodic life-strategy.

Cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. They also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (UV-A) light in plants.  C Lin 2005. 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.  .

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. 

Circadian rhythms affect every aspect of a plant physiology, including

  • Prime resistance to the oxidation reactions that occur during light harvesting, water up-take and efficient usage, nitrogen metabolism, mineral nutrition, hormonal pathways, carbohydrate biochemistry, disease resistances signalling. FrontiersAN Dodd – ‎2015   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 T. Vanden Driessche 1996.
  • Effective quantum yield and non-photochemical quenching, which has been found to vary with circadian rhythms.   A McMinn 2013.

All elements of photosynthesis are also subject to very specific timings S Lloyd 2011. 

Similar findings on the importance of circadian rhythms has also been found in the physiology and functioning of a wide range of species spanning across the biological kingdoms, including birds and mammals.

Timing in entities is highly important. For example 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.  

Redox and Circadian Rhythms.

Redox balance is key for molecules utilised in the context of anti-oxidation protection.Current evidence seems to support the conclusion that the responses to reaction oxygen species (ROS) are mediated both through the regular function of the molecular clockwork and the involvement of the Transcription Translation Feedback Loop genes in extra-circadian pathways..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.  Lisa Wulund 2015.  K Nishio 2015,  N B Milev 2015. 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.

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.

The Association Between the Transcription-Translation Feedback Loop and Redox in Cryptochrome.

  • 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. Lisa Wulund 2015.
  • Recently, it has been found that the redox cofactor FAD stabilises the clock protein cryptochrome (CRY), modifying rhythmic clock gene expression. In mice it has been found that:
    • FAD stabilizes Cryptochrome (CRY) proteins by competing with FBXL3. (It has been theorised that the magnetoreceptor function arises from light-induced formation of a radical pair through electron transfer between a flavin cofactor (FAD) and a triad of tryptophan residues).
    • FAD concentration in the nucleus has a daily rhythm
    • FAD lengthens the circadian period
    • In vivo knockdown of Riboflavin kinase (Rfk) alters CRY and PER1 expression rhythms.

    A Harino et al (2017) have concluded that  light-independent mechanisms of FAD regulate CRY and contribute to proper circadian oscillation of metabolic genes in mammals.   However, it is important to consider that such a relationship may not be a simple causative one.  For example there are two negative feedback loops in the BZ reaction – one is via organic free radicals L Hegedu (2000). The circadian clock system can also be modeled on reaction-diffusion and includes negative feedback loops.

  • 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…  In zebrafish cells altered redox state triggers the transduction of photic signals that regulate and synchronize the circadian clock  M L Fanjul-Moles 2015. 

It may be the case that cryptochrome is instrumental in supporting an integrated clock and compass system in many species.

Questions over the Role of Circadian Rhythms in Magnetoreception

Several studies have suggested that circadian rhythms (produced by the transcription translation feedback loop) are not necessary for magnetoreception in cockroaches (O Bazalova 2016) or drosophila (R Gegear 2008).

Interestingly, cry-dependent magnetosensitivity in Drosophila does not require a functioning circadian clock, but it does require a functional cry gene.

Unfortunately there are no current research findings on whether cryptochrome can undergo circadian redox rhythms, in addition to those rhythms produced by the transcription translation feedback loop. This is important as there is the potential for cryptochrome to be producing redox circadian rhythms.

Such rhythms have been found in peroxiredoxin proteins (thought to the be earliest form of biological clock). And 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.

Water and the Redox State

Water is fundamental to biology and 1ater-protein coupling is also influenced by the redox state.  He, Ting-fang

In a biological semiconductors, water could potentially act as a gating medium. D T Simon 2016.

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  P B. Kidd 2015.

Cryptochrome dampens temperature input into the clock and therefore contributes to the integration of different Zeitgebers. C Gentile 2013.  

Models of Circadian Rhythms

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

Is Biology Making Use of Its Own Semiconductors?

The above has set out the case for biological semiconductors being ulitised in nature.

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 and electron hopping mechanisms. These would interact with both the internal (e.g tiny magnetic fields generated by the human body) and external  (e.g external temperature and the Earths magnetic field) environments.

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

Is Biology Also Making Use of Superconductors?

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
  • 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.
  • 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.  It is interesting to note that quantum biology is focused on photosynthesis and magnetoreception (which it is theorised may generate free radicals in the retina).
  • Freeman W Cope 1976 also suggested that 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.   The Josephson effect describes tunneling of Cooper pairs (very similar to radical pairs) through a barrier – a Josephson junction is a contact between two superconductors separated from each other by a thin dielectric tunnel barrier. 
  • E D Giudice 1989 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.
  • N Poccia 2009 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.
  • Various experiments have been carried out on 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. Some studies reported high conductivity  or even superconducting properties (A Y Kasumov 2001), while others claimed that the carefully deionized DNA molecules are insulating.  G Saito 2012.
  • 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.  

NB: I have attempted to reference a wider range of theories in relation to both biological semi-conductors and superconductors at the end of this article*.

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.

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

Superconducting Material in Biology

Materials currently being considered as biological semiconductors may later be found to be biological superconductors e.g this might include a material like MagR.

Certain iron based materials possess fine superconducting properties. The five unbound electrons found in iron — as a result of individual modes of operation, facilitate superconductivity. J C Seamus Davis 2017.

Iron Sulphur Clusters

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.. S J Kuhn 2016.  E E Rodriguez 2016.   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.

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….Both greigite and mackinawite magnetosomes can contain Cu, depending on the sampling locality.  M Posfai 1998.  T Kasama 2006 .

Superconductors: Singlet and Triplet States

It is fascinating to consider what relationship/interaction radical pairs might have with cooper pairs – the pairing mechanism

Usually, 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.

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.

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. 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. 

Patterns in Type II Superconductors.

Vortices control the current carrying ability of all superconductors.

This finding may have a relationship to the patterns found in semiconductors and superconductors, which resemble Turing patterns (which can include stripes, hexagonal arrangement of spots, and hexagonal superlattices Y Lang 2006), N Tompkins 2014.)

Electrons involved in superconductivity can form patterns, stripes or checkerboards, and exhibit different symmetries – aligning preferentially along one direction.

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).

These patterns and symmetries have important consequences for superconductivity – they can compete, coexist or possibly even enhance superconductivity.  J Zaanen (2010) found that that the fractal like arrangement of oxygen atoms in a cooper oxide superconductor appeared to influence the quantum behaviors of electrons and support high temperature superconductivity.

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.

Patterns in reaction diffusion (self organising) modelling might assist with understanding semi and superconducting system. 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 nature, striped arrangements often arise; when they do, they are nearly always the result of an outside external perturbation that induces a directional bias on the actions of the individual. J Tabony – ‎200

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. 

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 (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.   So the FKPP equation could potentially be used to explore classical quantum correspondence. e.g  P Bressloff. 2011, S Fedotov et al 2003,  Fedotov  et al 2000F Gleis 2010.  Robi Peschanski 2008Charles R. Doering, and H Weigert 2004. who set out the various ways in which the FKPP equation is found in both classical and quantum physics.

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
  • 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.
  • If biological superconductors are discovered this might help harness clean nuclear energy, as high temperature superconductors can be used to create the magnetic field to contain the fusion plasma.
  • 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.

Some implications for computing

Magnetic semiconductors  are semiconductor materials that exhibit both ferromagnetism (or a similar response) and useful semiconductor properties. If implemented in devices, these materials could provide a new type of control of conduction.  This could assist with the development of spin transistors  –  essentially the application of electrons set in particular states of spin to store information.

“New information technologies can be envisioned that are based on biological principles and that use biomaterials in the fabrication of devices and components; it is anticipated that these information technologies could enable stored data to be retained for more than 100 years and storage capacity to be 1,000 times greater than current capabilities. These could also facilitate compact computers that will operate with substantially lower power than today’s computers.” Mitra Basu 2017.

Such bio-materials could potentially support biological computers utilising metabolic reactions.

Some scientists currently exploring quantum computing are look at approaches utilising light rather than electricity. Such quantum computers work by isolating spinning electrons inside a new type of semiconductor material. When a laser strikes the electron, it reveals which way it is spinning by emitting one or more quanta, or particles, of light. Those spin states replace the ones and zeros of traditional computing. Potentially a biological semiconductor (which produce a radical pairs reaction) could offer this new type of semiconductor material.

Ethical Issues

When I first started this article I had in mind a rosy view of the world, where any new scientific discovery would be used for the common good.  In retrospect this was naïve of me. Technology can be ‘good, bad or neutral’.

A biological semiconductor or superconductor would not be ‘invented’. Nature will have provided it to us. And I can think of no justifiable argument for patenting of what freely exists in nature. Lets hope we have the capacity to make the best use of it. But I am not going to try and set that vision out myself. Such ethical issues go beyond the views of the individual.

October 2016 (trimmed down in July 2017). 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.    

Additional References

These are articles I have also looked at and may be of relevance, but I felt the above article was already becoming too complex.

  • I K Kominis has looked at the radical pair effect in quantum biology as being a type of quantum zeno effect A T Dellis and I K Kominis, 2009,  Dellis and Kominis 2011 More recently he has referred to this as the solid state photo-CIDNP effect (Kominis 2013).
  • J Vattay and S A Kaufmann (2015) have 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.
  • 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. 1988
  • Semilinear integrodifferential equation that characterizes several dissipative models of Viscoelasticity, Biology and Superconductivity. M De Angelis 2012.
  • A model for a hybrid system of semiconductor and photosynthetic protein has already been put forward by Younghye Kim 2014.
  •  It is 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.   Further implications of these findings are explored in another post- click here to find out more.

Apologies to those who have written articles that are relevant to this post, but which I haven’t been able to locate through searches.

 

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