Wave Genetics

Neighbouring nucleotide bonds nonlinearity influence on the dynamics of of conformation perturbations in the DNA molecules.
Berezin A.A, Gariaev P.P.,Maslov M.J,Reshetniak S.A.,Shaitan K.V..,Scheglov V.A.
Abstract.
The shugar-phosphate bonds nonlinearity in the chain of nucleotides on the dynamics on the conformative perturbations propagation process in the DNA molecule has been studied. The initial conditions for displaying considerable difference of behavior of the proposed model for linear and nonlinear bonds have been defined. Biosoliton laser hypothesis has been discussed.

In [1] there has been suggested a model describing the rotating-oscillatory perturbations in the chains of nucleotides for explaining experimental results on the hydrogen-tritium exchange in the DNA molecule. In accordance with this model the open states in a form of localized diclocations of soliton type can be generated and can propagate through DNA chain. The model of [1] (and [2,3]) describes interaction between neighboring nucleotides within the framework of linear potential. In our paper (differ from [1-3]) a principally new case is being considered, when this potential is nonlinear.
Well known that a DNA molecule represents a helix containing of adenine(A), thiamin(T), guanine(G), cytosine(C). Nucleotides in the chains display a certain genetic order and the coupling between the chains is realized through the hydrogen bonds between the complementary pairs (A T,G C).
In our study we simulate the DNA helix by an array of rovibrational (from the words rotation and vibration) vibrators, hanging on the weightless and stretchless rod. For simplify the spirality of the chain is not taken into account and the rovibrational degrees of freedom are considered "frozen".
In the considered case the hamiltonian for an "active" chain looks in the following way:
(1)
where: is the number of base pairs in a chain; is the hamiltonian, describing the own oscillations of the monomers ( rotation angles of nucleotides in a chain, moment of inertia of the basis), is the hamiltonian, characterizing nonlinear-periodical coupling between oscillators ( the elasticity constant of the chain, ), is the hamiltonian, describing the nonlinear coupling between the "active" and "frozen" ( ) chains of DNA molecule ( is the elasticity constant of the hydrogen bonds between complementary bases, coefficients in Eq. (1) are defined according to the following rule: for A T and T A pairs, for G C and C G pairs; is the parameter defined in [4] and obtained on the basis of the Sine-Gordon model and experimental data).
One should mention that at small values of the hamiltonian , which coinsides with the corresponding part of the hamiltonian, used in [2,3]. In this case the equations of motions for , obtained from (1), looks like this:
(2)
where the substitute has made.
In the case when , the system (2) can be transformed into dimensionless Sine-Gordon equation:
(3)
which represents a ”continuous analogue” of the system (2). The Eq.(3) has soliton solutions, in particular one-soliton solution, or kink, describing the dislocation propagation dynamics in the chain.
According to (1) nonlinear equations system can be given as follows:
(4)
As it can be seen, the systems (2) and (4) are considerably different. However we should mention that the numerical study of the (2) and (4) dynamics showed the following: if to take as initial conditions the single soliton solution of its "continuous analogue" (3) kink [2], one can see a similarity in the character of the solutions of (2) and (4). But when the initial conditions were taken like this
(5)
( is the ”step” function having the height of the step equal to and the inclining angle A),
the difference in the dynamics of both systems has been revealed as it can be seen in Fig.1 and Fig.2,3. Both systems (2) and (4) were integrated by the Runge-Kutta method of the 4-th power with the initial conditions looking like (5) in the interval with a step . Boundary conditions were "quasicyclic":

(poly-A-sequence). Parameter of the system . Parameter A was in variance (the inclination of the step function ).
The numerical study of the system (2) showed (Fig. 1) that the solution represents two solitary waves, moving from the right to the left at a constant velosity. The first wave has a quasikink form and the second has quasibreather form (breather is a double-soliton solution of Sine-Gordon equation). The first wave propagates faster then the second one. Both waves due to the ''quasicyclic" boundary conditions when reach the left end appear on the right end without changing their form. Quasikink propagating along the chain of pendula changes the co-ordinate of every pendulum by the angle (a pendulum makes a full turn). So passing the closed chain of pendula К times, it changes the co-ordinate of every pendulum by angle That explains the "shelf" form of the graph (Fig.1).
Fig.2 shows the results of integrating the system (4) under the same conditions. The graph displays same two solitary waves quasikink and quasibreather. Howewer it differs from already considered case. The difference is that at the very beginning the kink moves at negative accelerations wich results in its lower speed to compare with the quasibreather's one. Worth mentioning that the simulation has been done for done for homogenious poly-A-sequence so that the change of quasikink’s velocity can’t be explained by the influence if inhomogenity of the chain. This effect probably appears due to the nonlinear interaction between its monomers.
Fig. 3 illustrates the results of integrating the system (4) under the same conditions with the eonly exclusion that A=2. This time only quasikink is the case and it's negative acceleration results in reversing of the direction of it's motion. The system (2) being integrated under the same conditions results also in quasikink. Its velosity doesn't change to compare with the case shown in Fig.1.
Summing up, we would like to pay attention to the following circumstance. As it has been mentioned above in the systems of DNA type the overexcited rovibrotional states can arise. In quantum language it means that under certain conditions the overexited dynamics rotational states of nucleotides in one or both chains of the DNA molecule can be realized. A hypothesis can be put forward that there exists a principal possibility of creation a biosoliton laser on the DNA molecule. We partially proved it both experimentally and theoretically in our research on the biophoton excited luminecence of laser type in genetic strustures [5-10]). However the problem of dissipation in biopolimers makes the idea of developing a biolaser pretty problematic. At least to prove it we must fulfill the necessary conditions: where and are the width and the velosity of soliton correspondingly, is the dissipation time. If to take and (sound velosity), we'll have the following evaluation . It should be mentioned that the characteristic dissipation time due to the water hydrodynamic forces and the interenal molecular time of dissipation ( [13]).
So the dissipation effect plays a certain role in the act of dislocation forming process along the DNA molecule and it has been already considered as a viscosity parameter in DNA molecules, which depend on the presence of the structured water in the DNA molecule itself and in its microsurrounding (the dissipation magnitude) under consideration were taken 0.1 and 1 [3]. The dislocations are formed or not formed having no dependence on the values and only the ranges of parameters were taken into account. Under large values of the dislocation are being formed slower then under big ones. Much more essential point is influence of the DNA behavior through the other parameter and namely through the spirality step of the polynucleotide. As it follows from our model the change of concentration water molecules leads not only o the superspirality of the biopolimer but to the local decoupling of the DNA helix [3].
This work done on the financial support RFFI (projects N 96-02-18855 - a and N 95-04-12197 -a).

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The fifth level is a chromosomal-holographic level. A genome possesses a holographic memory [37] which in nature is a typically-distributed (non-local) associative memory. At this and the next level non-locality obtains a new feature - a dualistic substantially-wave character, since electromagnetic and/or acoustic fields, bringing out geno-wave information outside chromosome matter, “read” holograms as a substance. A physical field (or fields), marking organism’s prospective space (calibration), comes on scene. Brain crust’s holographic memory, establishing mental, semantic and image spaces calibrating potential actions of higher biosystems, is likely to belong to this category. That’s the way of realizing social and genetic processes.
The sixth level is a genome quantum non-locality. At the levels of up to 6th, genetic information non-locality is realized in an organism’s space. The 6th level is of a special nature, since it acquires a new quality. It’s manifested within the frames of one of the quantum non-locality forms, namely, in permissive form we postulate in the current paper. In this case, non-locality is realized both by biosystem space and by its own, shrinkable to zero, time. Geno-wave programs, instantly spreading in such a way, simultaneously operate in an organism “here and there” and therefore, the semantic construction “now and then” loses its meaning. And this is a strategic factor and a vital evolutionary achievement of multicellular biosystems. Billions of organism’s cells have to instantly “know” a lot of information about each other. Without the “wave information instancy” phenomenon, a giant multicellular continuum of higher biosystems won’t be able to completely coordinate a metabolic process and its physiological and other functions. The intercellular diffusion of signal substances and nerve processes are too inert for this purpose. Even if to assume, that sign electromagnetic fields are involved in an intercellular transfer process passing with a speed of light (this assumption is quite reasonable), it’s not enough. A quantum non-locality mechanism, applicable to genetic apparatus and which can act as an instantly-distributed quantum (wave) object isomorphous with substantial chromosomes, is required. Using non-locality, genetic apparatus of higher biosystems creates an unparalleled phenomenon, when in certain periods of time the “here and there” and “now and then” structures operate within the biosystems’ “closed” space and time as a continuity providing the organism with intrinsic super-coherence, information overredundance, a super-informativity and a linkage and, as a result, proper integrity (survival). The ability of lower organisms’ (hydros, worms, amphibian, lizards, crustaceans) tissues and organs to regenerate (people have lost this ability in large) is a manifestation of this phenomenon. But, considering the biosystems wave self-organization principles we are developing, it can be re-activated. The world’s first successful adaptation of donor tissues implanted to a blind man, which helped to return a sight to the patient, is a good example of regeneration. The ideology of this surgical operation and regeneration processes is described in [33-35].
At the same time, theoretical and experimental researches in this field are just emerging and need further physical and mathematical understanding and development.
Possible mechanism of recording information on laser mirrors
Now, let’s return to some features of the phenomenon of a long-term recording of dynamic photon-polarization-radio wave information on laser mirrors. We think this is linked with the phenomenon of photon fields localization (compression) in the system of correlated dispersers of laser mirrors. Given that the disperser material possesses a low radiation absorption ability, the external light field is capable to retain in the system within a long time without the dissipation in other forms of energy. The reason of localization is connected with the interference of many times diffracted waves. An external electromagnetic signal (in our case, it’s a laser beam modulated by polarization, for instance, by a DNA preparation) is localized (“recorded”) in the system of non-uniform laser mirrors. Later, the signal can be “read” without a significant loss of information in the form of isomorphously (in relation to photons) polarized radio waves. Theoretical researches on a strain state of localized photons [12, 14-19, 24] say in favor of these thoughts. If this opinion is correct, then a chromosomal apparatus may also be considered as a fractal medium of localized photons accumulation, creating a coherent continuum with a quantum-illocally-distributed polarization radio wave genetic information. To some extent, this is in correspondence with our idea of genome quantum non-locality existence in one of its forms - ref. to [8, 34, 37]. It’s possible that the apoptose phenomenon, which is likely to be involved in the regulation of multicellular creatures’ life time, is connected with an abnormal compression of photons by a nuclei of a cell, which are accumulated to a maximal value and then destroy the nuclei. The background principle of gene operation (including anti-oncogenes) may be another supplemental apoptose regulation mechanism. For instance, an anti-oncogene coding the p53 protein could be controlled through the introduction of the DNA artificial flanking contexts from 3’-and 5’-ends of the p53 gene.
Analysis of experimental evidences of gene wave forms existence
We are unaware (with some exceptions, of course) of modern publications on wave genes theory and practice, available in the disclosed scientific journals. In the 1920-1940s, A.G.Gurvich, A.A.Lyubitchev and V.N.Beklemishev, who developed the first theoretical models, were the pioneers in this field; their ideas are described in detail in [32, 33]. In this paper, we are trying to produce more developed opinions of some possible synthesis mechanisms and functions of wave genetic structures, attributable to higher biosystems, as well as of the methods applicable for simulation of sign wave processes in chromosomes and model units simulating chromosome field functions and transferring wave genes. A publication and a patent, granted for the development of a device for the transfer of wave genes from a donor biosystem to an accepting one, are worth mentioning as an example of a rarely-appearing event. The said researches were carried out by Yu.V.Dzang Kangeng [39, 40]. Kangeng’s device for a directed wave transmission of oncologic, including genetic, information to change hereditary characteristics of a biological accepting object is of a special interest. Unfortunately, there’s no theoretical interpretation of the device operation principles. Kangeng’s device has some common functional features with the equipment we developed and whose operation is based on similar principles. Kangeng’s device includes space elements (forms) which enable to split the radiation of a high-frequency SHF electromagnetic field generator into two orthogonally-polarized beams which repeatedly, as in our installation (in our case, it’s a laser beam transforming into radio waves), were passing through a donor biosystem and an accepting biosystems. Dzang Kangeng used a hexahedron, a cone, a sphere and a parabolic-reflector aerial as a kind of special forms. These forms provide a specific spinning (polarization) of the SHF field electromagnetic vectors. In our laser design, one of the mirrors used also had the form of a parabolic-reflector aerial directed to a resonator. During numerous repeated passes through an optically-active (an electromagnetic wave polarization rotating plane) hetero-mesomorphic donor biosystem, organism’s tissues modulate the radiation (in our case, this is laser-radio wave radiation) by polarization, which is strengthen owing to repeated passes and is repeatedly and over a long time delivered to the accepting biosystem. In this process, the generator electromagnetic field, “stored” the donor biosystem gene-sign polarization modulations in its “memory”, resonantly interacts with gene-sign polarizations polarization of the accepting biosystem electromagnetic fields. If the donor biosystem is at an early morphogenesis stage accompanied with an intensive fission of cells, it can’t be excluded that the supposing polarization resonances are also of a holographic nature. Many times-amplified signal, carrying the wave information that was “read” from the donor biosystem chromosome continuum, passes through a substantially-wave structure of the accepting biosystem and makes it execute new polarization-gene-wave programs by means of the variation of their differential polarization structure. Change in the accepting biosystem polarization-gene-wave structure induced by the donor in the process of the field integration (“wave heterosis”) leads to a restructuring of its morphologic (genetic and phenotypic) characteristics. Shear wave correlations of polarization angles during the donor-accepting mixture of physical waves, resulted in acquiring new morpho-genetic and biological properties from the accepting organism, are one of the most important quantum-electrodynamics events of the “wave hybridization” process. This fact allows Dzang Kangeng with the help of the wave method to transfer genetic information from ducks to hens, for instance. Hybrid chickens of hens have got typical features of a duck - a flat beak, an elongated neck, increased internal organs (a hard, a liver, a stomach, and a bowels). A weight of a one-year-old hen-duck hybrid is 70% higher, than a weight of hens grown up from irradiated eggs. The second generation of the hen-duck hybrids saved all changes, which were obtained in the first generation, even without further re-radiation. A wave transfer of peanuts’ features to sunflower seeds resulted in the change of a form, taste and odor of a hybrid plant, which became similar to those of peanuts. Productivity grew by 1.8-fold; new features are transferred from one generation to another even without further re-radiation.
Let’s highlight some common features of the experiments Dzang Kangeng and we independently carried out; they demonstrate the possibility of genetic information existence in a wave form. This similarity is in the polarization modulation of the radiation orthogonal beams with intensity re-distribution in primary orthogonal beams with a frequency secured in the radio wave spectrum we register, by a donor organism. The spinning polarization planes here act as gene-semiotic structures whose biological meanings are identified and coded by angular and intensity shifts by a frequency spectrum. Similarly-polarized waves are known to be able to interfere, while orthogonally-polarized waves do not interfere at all. Waves with a partially-coincided polarization produce, dependent on their polarization coincidence degree, a more or less contrast interference picture. In other words, an angle cosine of each vector in relation to their registration plane or to the wave interference plane is a crucial factor.
Biology, including genetics and embryology, has already come to a turning point in its development, which is similar to the period when physics first admitted an idea that the properties of waves and particles didn’t contradict each other and even were compatible in quantum objects. A huge number of facts and scientific research outcomes available in modern molecular biology, genetics and embryology, can’t be understood without such a definition as physical fields, for instance, or without the application of quantum electrodynamics principles. The idea of lingual attributes of higher biosystems’ genome is a kind of humanitarian counterweight to an apparently excessive physical interpretation of Life functioning basic phenomena. Paces this idea is admitted by society are not high, and this idea faces furious resistance. Current situation is easy to explain: the issue of Life existence is too complicated. Nevertheless, time has come. If we are late with the understanding of wave gene-sign functions of biosystems including the human one, then such diseases as cancer and HIV we’ll destroy our society. We’ll lose an opportunity of a mighty jump in biotechnology and biocomputing. In the end, we’ll also lose an opportunity to purposefully, rationally and positively influence sociogenetic and demographic processes. Following the above-described logic, we are coming to the conclusion that human speech structures, which provide the major information influx for the mankind, possess fractally-scaled supergenetic properties. Evolution of the society is similar to organism’s morphogenesis. Books, libraries, movies, computer memory and people’s live speech in the end are the functional analogues of a cell chromosomal apparatus. The aim of these chromosomes is to control the creation of the society space (houses, roads, oil- and gas pipelines, telephony, the Internet) and to arrange relationships among people inside it. Chromosomal sign properties, which have a lot in common with organisms’, have a substantionally-wave nature. For instance, a movie showing an ideal model of a social structure and people’s relations within its frames is a substantional formation (video tapes). However, it uses a mentally-wave method to input information (light, sound, speech, idea, image). That’s the method chromosomes apply. The latter produce marking and calibration fields to arrange organism’s space and also control information & metabolic relations, using, in particular, quasi-speech methods (let’s remind context orientations in the protein synthesis and functions of oncogenes and HIV). Therefore, people are worth carefully studying the operation principle of their own genetic apparatus and the “tricks” HIVs play to “mislead” our chromosomes. Such kind of a study is especially crucial today when Russia, and not only Russia, could face a demographic and social collapse within the next 5 to 10 years. We have declared the theoretical approach to describe the logic of sign speech-wave relationships between HIV genomes and a master cell as well as the oncogene behavior logic. However, it’s not enough. We must get a set of key tools which would enable us to follow up at least the simplest wave command biocomputing functions of our chromosomes1 and the reprogramming of our chromosomes by nucleotide sequences of HIVs and oncogenes. We have already developed this set of tools - it’s a laser uniquely reflecting coherent polarization-laser-radio wave (PLRW) quantum-non-local sign processes in chromosomes. Physico-mathematical formalism characterizing the PLRW-quantum processes in such appliances is presented in our research2. PLRW-spectroscopy is the basis of wave information record to laser mirrors - the phenomenon we have discovered. We have also managed to record information from specially prepared mesomorphic DNA matrixes, to broadcast it in a waveform at a distance of 1 m and to introduce it in accepting biosystems. As an accepting biosystem, we took plant seeds. Using this phenomenon, we effected a “wave reparation” of a genome of radioactively-damaged old seeds of Athaliana gathered in the Chernobyl Nuclear Power Plant area in 1987, and initiated drastic changes in stem and tuber phenotype in the second generation of the Solanum tuberosum plant. These biological influences don’t have the nature of mutations, they only have a sense meaning and are just another evidence that genetic information can exist in the form of electromagnetic field. Not less important that genetic information can be recorded, stored, read, transmitted and introduced in accepting biosystems. Here, two vital factors emerge. The first one is that the record of vast information volumes, including the genetic one, is an unparalleled event which confirms that it’s possible to develop principally new carriers of the dynamic super-capacity analog memory (images, texts). This is rather important for future biocomputing. The second factor is that owing to the PLRW phenomenon we enter a huge area of genetico-metabolic wave sign processes. Numerous and unclear events of distant “recognition” of the pairs antigene  antibody and transmission RNA anticodon  information RNA codon, as well as complementary mutual recognitions of DNA single chains, self-construction of ribosomes, recognition sites of ferments, careful piloting and landing of transposons in the DNA and so on, are also embraced within the frames of these processes. Nothing of these phenomena can be explained by only Brownian movement and adjacent angstrom van der Waals, ion, hydrogen and electrostatic interactions. And finally, the most important thing for us in the context of the ideas we propose is a wave and sign behavior of viruses, HIV or influenza, for instance. Viruses can be considered as “orphaned” cells which retained minimum of chromosomal information required for a wave search of a site of landing on a master cell and exact place to cut-in own DNA as a transposon in the master cell’s DNA with consequent possible precise re-transpositions. Wave “languages”, which viruses use during the information contact with a cell’s surface and its genome, are the most vulnerable parts of a virus. Viruses use these “languages” to enter semantic space of a cell and then to “mislead” the cell; after that, they undergo mimicry and are reprogrammed, reproduced and thus survive in the end. Cells are likely to be able to “mislead” viruses as well, creating a kind of “wave immunity”. That’s why certain balance of powers in the fight exists; the said balance can shift in favor of a virus - for instance, in favor of influenza virus if the temperature starts fluctuating. Cooling of a blood circulation in nose mucosa capillaries changes the temperature of liquid crystals in chromosome blood cells. At the same time, protective wave programs recorded on high topologies of chromosome mesomorphic phases can only be slightly distorted. As a result, the “cold temperature information breach” appears and is used by influenza virus to reproduce. As a response to this action, a compensatory reaction is evolving in the organism, i.e. the body temperature goes up to a sub-lethal level of 41° C. As we think, this reaction is designed to “submelt” mesomorphic phases of the virus nucleic acid and, therefore, to produce noise or completely erase virus wave programs which it needs to attack organism’s wave semantic space and to kill the growing number of it’s cells. Virus genome acoustic fields tightly linked with photon ones might act as wave bioprograms. Using method of correlative laser spectroscopy, we demonstrated drastic changes in acoustic performance of the DNA liquid crystals in vitro at temperatures of 40-41° C; the results obtained partially confirmed our suppositions. And that’s only an example of wave sign processes in the relationship influenza virus  human organism. Similar sense relationships exist between HIV and man’s cells, and the same issues raise - how to correctly find a site of landing on a cell’s surface and precisely build-in the DNA (reverse transcriptasal copy of a viral RNA) as a mimicrying transposon into the master cell DNA. Thereafter, the task is to get accurately re-transposed in a proper place of a chromosome and to detect and realize itself as a reproducing pathogen. Now we can initially list the bottlenecks of HIV wave programs and name countermeasures to eliminate the problems:
1. Searching and recognition of HIV on a landing site (by altering the radiation nature of a virus and/or sites of landing on a cell, it’s necessary to distort the system of resonance-wave recognition mechanisms).
2. Searching and recognition of a viral DNA on the site of landing to the master cell’s DNA (altering the radiation nature of a virus and/or sites of the landing on the cell’s DNA, it’s necessary to distort the system of resonance-wave recognition mechanisms).
3. Searching and mutual recognition of protein iRNA: HIVHIV RNA (wave distortion of this process).
Any violation of even small wave sign resonances in this triad will result in the loss of infection ability of HIV and other viruses, and the Nature has created an example. As it was already mentioned, it’s an organism’s temperature mode. In a way similar to the one found by the Nature it’ll become possible to design a simple “wave” vaccine against HIV and other viruses and bacteria. Our goal is to study “alphabet” and “grammar” of wave “languages” of viruses’ genome. And the foundation for this study has already been laid. A laser capable to “read” PLRW-wave genetico-metabolic information has been developed. However, the research in this field is rather difficult due to intrinsically natural inertia of the material understanding of genetic and metabolic information. Technical issues also exist. The laser we use generates only red photons, while the chromosomal apparatus of human beings and viruses uses a wide spectrum of coherent radiation ranged from 250 nm to 800 nm. Therefore, it’s necessary to design lasers which function in a full span of the spectrum visible area. This aim is technically feasible, but significant investments are needed to achieve it. In our point of view, all attempts to produce a material vaccine or other drugs to fight against HIV or influenza virus will fail. Viruses continuously change its antigenic composition and thus bury all attempts of immunologists engaged in the vaccine development. Efforts to chemically block certain stages of virus morphogenesis are inefficient and only poison human organisms. Wave vaccine is a reality. This vaccine provides non-invasivity and environment friendliness, since it touches a narrow area of wave sign relations between a virus and a cell.
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