DNA dynamics as a solid-state, quantum represented transition mechanism.
PROGRESSES IN THE THEORY OF UNCONVENTIONAL PROCESSES IN PHYSICS CAN PROVIDE NEW IDEAS ON QUANTUM MEASUREMENT IN BIOLOGY. G. Ciraolo (^)
The relations between biology and fundamental physics have been discussed in the 20th century by a few great scientists such as Schrodinger, Bohr, Heisenberg and Wigner. The debate produced thoughts on the applications of theoretical physics to biology by proposing deductions connected to each other discipline and experience. However, despite speculations coming from these “master actors” of science, biology progressed in a quite autonomous way with respect to physicists’ suggestions, so the successes of biochemistry along the past 60 years, following Crick and Watson’s elucidation of DNA structure, have been so astonishing that no requirement was felt due for an interpretation of the biological world in terms of foundations of physics. Provided that the ultimate nature of biological phenomena is microphysical (especially the writing, replication and transcription of genome), there is full scope but no practical necessity to analyze life processes in terms of quantum meta-principles. Modern biology became totally adult without any explicit reference to general quantum models just as Watson’s classical book on molecular biology summarized in the formula that “chemical links are fully explained by quantum mechanics”. Nothing less, nothing more!
In fact, the need for distinguishing living matter from non living one arises from the fact that life evolves not as a random original process but as the result of “written” constraints, essentially pre-existing rules of selection on equiprobable states of information that minimize systemic degrees of freedom beyond direct links to criteria and theories on physical universe (invariance, conservation, symmetry etc..): this specificity of the living seems in conflict with statements that claim exhaustiveness of information arising from basic chemistry and thermodynamics in biology (1). In fact, the main biological phenomena (including genetic coding, replication and potential for evolution) go beyond laws of motion described by linear expressions like ordinary Schrodinger equation and Master equation. More specifically, some physicists threw further doubt over the assumption that the biological world is totally “supported” by laws of actual fundamental physics (including its paradoxes). Wigner looked as the most popular member of this group: his model compares DNA replication and transcription to the transformation laws of quantum mechanics, but in this case the matrix transfers considered can’t be generalized because the assumptions of the model depend on the way representations are originally formulated (2).
Apart from particular models, the central argument of doubters of physical foundations of biology is that evolution of “coding” in the physical world is a one-to-one process and it is invariant with respect to time direction, while the same phenomenon in hereditary biology shows a non linear and many-to-one reality: moreover, time is never symmetric in the living matter. Despite such peculiarities many scientists, including molecular biologists, tend to dissolve conceptual uncertainties into an experimental complexity of motion of the observed systems without weighing up quantum selection and classification of coded states. In living systems, stationary states transferring hereditary information emerge from complex degrees of freedom that lack in a classical system’s evolution of motion. So, what can become the physics-biology relation?
Biology research is ultimately linked with nanoscale phenomena and technologies, so mathematical physics and molecular biology can be more and more associated with the search for the micro-secrets of life (a possible EPR paradox in biology?). Biological hereditary phenomena are a mixture between microphysics (in the description of quantum stationary states) and quasi-classical level of selection (justifying high reliability of information transfer): living matter seems to relate to its physical origin as microphysical transitions converge into phase coherences. More specifically, biological macromolecules could possess states that transfer matter without dissipation, as superconducting or superfluid systems do. In fact, neither a classical description of observables nor a linear quantum probabilistic wave function seem exhaustive with accounting for the high reliability of the hereditary process and for rarity of mutation rate (10⁻⁸ for each elementary hereditary transmission, while the rate leading to species extinction would be 10⁻⁴). In biology, the storage of information coincides with the path of its transmission (information is its own transmission: in physics we have the case of Majorana fermions that can store and transmit quantum information without being perturbed by external world (3)). Here the process of quantum measurement is the one that can unify description and expression of observables: the initial conditions of a “biological measurement” are unconventional as are those of particular phenomena of solid-state and statistical physics (4).
In unconventional phenomena the order parameter plays a central role as a consequence of cooperative phenomena of non-linearly orientated positions or momenta. In superconductivity, impulsive structures tend to shape stable physical effects, like an un-resisted density of current or a coherent spin orientation. Can similar phenomena be observed in the biological world (5)? Ordered phenomena of orientation or conduction have been detected at room temperatures where mixed properties emerge, for instance electron-hole complexes can produce type I superconductors and currents of spin are involved in type II superconductors that show growing competitive states of magnetic polarization.
Magnetism has effects on biological macromolecules which can particularly observed in cancer chromosomic multipliers. The repeated exposition of cancer cells to magnetic fields of 60 Hz (0.25-0.5 mG) induces loss of at least 10% of chromosomes, according to Héroux and Li (6). The cells exposed to magnetic fields return in three weeks to baseline numbers of chromosomes and become extremely sensitive to further variations of the magnetic field, except for the fact that no effects were observed in a range of field intensity from 100 to 500 nT. Further microcosmic studies have investigated the relation between DNA’s electronic structures and magnetism (7). DNA presents a great range of physical properties regarding meta-stable states and modified magnetism due to uncoupled electrons and hanging bonds.
In molecular biology, the DNA macromolecule has charge complex structures, primarily hydrogen junctions and polarization gaps between complementary bases (1-to-2 rings) (8). Pairs of DNA “coated” with superconducting material (molybdenum and germanium) can form a device which is interfered under a magnetic external field. Another “coat” of DNA and superconducting material has been observed to “purify” carbon nanotubes (including graphene) in an “envelope” that maximizes efficiency of the wires (9)(10). Regarding the natural functions of DNA inside the cell (replication, regulation), “coats” that produce parabolic growth can be distinguished from other complexes that obey to exponential laws: a parabolic growth of nucleotides suggests that cells regulation is active while instead DNA undergoes plastic deformation under exponential growth and no interaction with magnetic fields is permitted.
The various configurations of DNA show transitions between ball-like and helical patterns (or inversely) with ordered emerging phases (singlet to triplet electronic states) and chirality of the disordered molecule becoming 3D symmetry of the same. The double-stranded DNA (with helical symmetry) can show spin polarization (even in case of weak spin-orbit coupling) which single-stranded DNA cannot show (11).
DNA as a transmitter of information to proteins through quantum computation can be represented through 64-dimensional Hilbert spaces (the number of codons of genetic information) for DNA and protein space with no degenerate eigenvalues for DNA and degenerate eigenvalues for the second matrix (relating to protein side as receiver) (12). The vibrational spectrum of DNA seems to indicate a particular kind of “biological” information based on redundancy (90% of the chromosome has no biosynthetic function, as it happens for the units of any language); this “linguistic” function of DNA allows selection of appropriate frequencies and resonances supposable to work through nonlinear, ultra-stable waves of solitons. In fact, soliton waves can preserve information in an efficient and long-term way. Making progresses in the application of solid-state physics to molecular biology will deal with the relation between loss of genetic information and damaged DNA; in a contest of accelerated replication, DNA is inflated by templates’ production and grows exponentially, as if the “words” of its initial language went lost and unknown strings were diffused, “turning off” resonances in the macromolecule.
The “turning signal” in inflating DNA can be chemically given by H-bonds (that are reproduced in nucleotides pairing) through the switching of the proton connecting the two filaments of DNA. The H-bond provides a sort of flip-flop mechanism given the tunneling probability of the proton which can be calculated according to Dirac equivalent equation of electron (13)(14) from the following expression
P = ∑ (1/n²) exp (-(nπE²g/4eђFVf)
where E²g = energy gap for tunneling, F is a uniform electric field, Vf is Fermi velocity
We can evaluate the prospects of repairing a damaged DNA under a “conductance” model of replication. The connection of DNA with superconducting devices has already been observed with proximity effects that suggest a twofold capacity of DNA to interact with “conductors” (including enzymes, oncogenic activators and ligands to suppressor sites): this “duplex” function includes deployment to form electron-hole complexes or to spread along waves of vibrational energy characterized by spin coherence and relaxation.
Spin-dependent transport in DNA molecules has been observed by various researchers (15) particularly when DNA is sandwiched between ferromagnetic devices (Ni and Fe show magnetoresistance factors of 26% and 16%). Depending on currents applied to DNA, this molecule can behave like an insulator or a conducting device, showing non-linear voltage-current characteristics. In the cases of ferromagnetic materials surrounding DNA and having different magnetizations, there are two states permitted of transport as spin alignments have different Fermi velocities: spin-up electrons have a greater probability of scattering between electrodes than spin-down electrons. The currents generated in the DNA molecule are different because parallel spin configuration corresponds to higher intensity of current than antiparallel configurations. Nearing voltages applied of 2 mA, the difference of response in terms of current generated in the two configurations is 0.5 eV in nickel and 0.8 in iron.
Various conjectures are permitted. A complex of mutagenic DNA and graphene-transported superconductors with similar Fermi energy (InAs?) may evolve towards ferromagnetism. In solid-state physics type II superconductivity can differ from type I superconductivity or anti-ferromagnetism; charge-ordered correlations for parallel-aligned spins of DNAs π-electrons can be created (16).
(*) Cert. Math., studying for an open degree at the Open University
(1) “The physical basis of coding and reliability of coding and reliability in biological evolution”, H.H. Pattee, Biophysics Laboratory, Stanford University, Stanford, California, 94305.
(2) “The probability of the existence of a self-reproducing unit”, E.P. Wigner, The Logic of Personal Knowledge, Rouledge and Kegan Paul, London, 1961.
(3) “Teoria simmetrica dell’elettrone e del positrone”, E. Majorana, Nuovo Cimento, 14: 171 (see English translation)
(4) “Focus on quantum dissipation in unconventional environments”, Milena Grifoni and Elisabetta Paladino, New Journal of Physics, 10 115003 doi:10.1088/1367-2630/10/11/115003
(5) “Conformational flexibility of DNA”, Andryi Marko, Vasil Denysenkov, Dominik Margraf, Pavol Cekan, Olav Schiemann, Snorri Th. Sigurdsson, Thomas F. Prisner, Journal of the American Chemical Society, J. Am. Chem. Soc. 2011, 133, 13375–13379
(6) “ELF Magnetic Fields Alter Cancer Cells Through Metabolic Restriction,” Li and Héroux, Electromagnetic Biology and Medicine, posted on the journal’s Web site on August 5.
(7) “The electronic structures, magnetism and meta-stable states of DNA”, Wang Yongjuan et al., Chinese Science Bulletin 2006 Vol.51 No. 14 1666-1672
(8) “Observation of negative differential resistance in DNA molecular junctions”, Ning Kang, Artur Erbe, Elke Scheer, Applied Physics Letters 96, 023701 (2010)
(9) “Evolution of DNA sequences towards recognition of metallic armchair carbon nanotubes”, X. Tu, A.R. Hight Walker, C.Y. Khripin and M. Zheng, J. Am. Chem. Soc.
(10) “ Charge and energy transfer dynamics in single-wall carbon nanotube ensembles”, Jared J. Crochet, Graduate School of Vanderbilt University, December 2007
(11) “Spin-Selective Transport of Electrons in DNA Double Helix”, Ai-Min Guo and Qing-feng Sun, Physical Review Letters, PRL 108, 218102 (2012)
(12) “Quantum mechanical model for information transfer from DNA to protein”, Ioannis G. Karafyllidis
(13) “Tunneling in semiconducting nanotube and graphene nanoribbon p-n junctions”, Jena, D., Fang, T., Zhang,Q., et al. Zener, Appl. Phys. Lett. 93, 112106(2008)
(14) “Graphene, neutrino mass and oscillation”, Zhong-Yue Wang, ArXiv: 0909.1856
(15) “DNA Spintropics”, M. Zwolak and M. Di Ventra, Applied Physics Letters, Volume 81, Number 5.
(16) “π-electrons in a single strand of DNA: a phenomenological approach”, Kazumoto Iguchi, International Journal of Modern Physics B, Vol.18, No.13 (2004) 1845-1910.
Solid-state physics suggests some conjectures on DNA dynamics and evolution
|DNA’s references to other phenomena in condensed matter theory||Dna replicating without stop||Dna replicating as a regulated mechanism||Dna in a double helix stable configuration|
|phenomena of reference||Turns to Z- DNA and relief of torsional strain of B-DNA, chiral-unspecific and final single-stranded structure; random processes, coupling phenomena like in basic solid-state systems (class I superconductors and
|Transition to A-DNA from B-DNA and “good” right-handed chirality; higher strain energy with respect to Z-conformation, there is magnetic polarization (in solid-state physics we have phenomena like class II superconductors, ferromagnetism and ferroelectricity)
|Stabilization on B-DNA conformation (hydrated DNA, relaxed configuration), overlapping of bases, super-helix configuration, lower energy for bending; long-range interactions, suggestion to study links with phenomena of intermediate strength with additional magnetic fields (diamagnetism/paramagnetism)|
|Mechanism of activation||Electron-hole property or drugging, singlet excitation?||Population inversion disorderà order and/or triplet excitation?||multiband structure
very low statistical temperature?
|Main features||Anti-symmetric coupling of π-electrons and proton tunnelling in hydrogen bonds of complementary bases||DNA’s magnetic polarization connected to internal and external magnetic fields, symmetrization of electronic spins, Majorana fermions?||aperiodic solid that stores genetic information through code degeneracy and “stop-to-replicate” triplets of nucleotides|
|quasi-particles diffusion and transport||Dipolar structure and electric polarization of rings of complementary nitrogen bases, waves of polarons and phonons||diode tunnels of proton-coupled electrons with emerging magnetic polarization, soliton waves across DNA filaments||stability of fluxes throughout nuclei, permeability of membranes, charge motion and electron transport|