Hydrogen bond and dark matter

The notion of dark N-H atoms leads to a new view about hydrogen bond. For the necessary context see background ideas see this, this, and this. Indeed, the little discovery of this morning was that the hydrogen atoms associated with hydrogen bonds could be actually λ^k-H atoms. This hypothesis has interesting implications and predicts the formula H_1.5O for water in atto-second time scales suggested by neutron diffraction and electron scattering.

1. The formation of hydrogen bond would correspond to a fusion of name and conjugate name between N-H-O-H atom and its conjugate N_c-H-O-H atom (the shorthand notation N_c= λ^k-N will be used. This process would drop one proton to a larger space-time sheet and could transform it to a dark proton. In the original situation water would be chemically like H₂O expect that the water molecules would have fractional positive charges N/λ^k and 1- N/λ^k meaning that water without hydrogen bonds would be positively charged.

2. H-O-(λ^k-H)-O-H pairs obey the chemical formula H₃-O₂. Hence the darkening of protons in the formation of hydrogen bonds would predict the H_1.5O formula suggested by neutron diffraction and electron scattering in atto-second time scale.

3. The mass of (N-H)-O-H molecule would be by N-1 electron masses higher than ordinary water molecule and it would behave like fractionally charged object. The λ^k-hydrogen associated with hydrogen bond would in turn have mass m_p+λ^km_e. For λ≈ 2¹¹≈ m_p/m_e and k=1, this would mean that the mass would be approximately 2m_p instead of m_p.

   On the other hand, the hydrogen bonding in TGD framework yields pairs H-O-(λ^k-H)-O-HH₃O₂== 2H_1.5O rather than pairs H₂O-H...OH₂== 2H₂O. For the favored value λ=2¹¹≈ m_p/m_e of λ and k=1 the mass of a pair of hydrogen bonded molecules in TGD Universe would be nearly the same as the mass for ordinary hydrogen bonded H₂O molecules in the Universe of standard model. This could explain why chemists would have failed to discover that water is not quite what we believe it to be. Be as it may, these are testable predictions and in principle could allow to check whether the model makes sense and if so, also determine the value of λ and k.

4. It is quite possible that most of water is ordinary and an interesting question is whether pH could measure the amount of pairs of (N-H)-O-H atom and its conjugate (N_c-H)-O-H. If pH measures the number of pairs of this kind of molecules, the mass density of water would depend slightly on pH.

5. As discussed here, the stability of negatively charged DNA strand is poorly understood. The presence of fractionally charged (N-H)-O-H water molecules in the vicinity of DNA would have a further stabilizing effect besides the positive fractional charges associated witht the names of DNA nucleotides (in case of single DNA strand).

6. The energy needed to cut hydrogen bond is expected to depend on N-N_c pair characterizing the final state and on the molecular environment where the pair exists and would not thus be a property of hydrogen bond. It is not clear whether this energy can be identified as the energy of hydrogen bond (the value of which varies in water). The letters appearing in the names of molecules would be characterized by the energies needed to produce them, and the N-N_c pair with the minimum energy would dominate in a given environment which could be also macromolecule so that name of the molecule would be dictated by the properties of molecule.

7. Genetic code would reduce at deeper level to the names of DNA nucleotides. It is quite possible that the splitting of DNA double strand gives rise to quantum superposition of N-N_c pairs. This would make possible quantal mechanism of mutations. McFadden has suggested this kind of mechanism but assuming that different DNAs would superpose which to my opinion cannot be the case. Also quantum computations by RNA strands can be imagined if it is possible to achieve the situation that the probabilities of various pairs in superposition are essentially identical.

Universal mechanism of catalytic action and stability of charged polymers

As explained here and here, the idea that dark N-H-atoms could naturally serve as names of bio-molecules, and that molecules labelled by conjugate names could play the role of lock and key in catalytic action. This would mean that the emergence of symbolic representations and "molecular sex" between conjugate named molecules distinguishes bio-chemistry from the ordinary chemistry. Below some further remarks related to this idea.

1. Basic observations

The basic observations are following.

1. Since fine structure constant for the interactions of dark electrons with proton (and any other charge) is scaled down by 1/hbar factor the effective charge of proton plus dark N-electron system is 1-N/λ^k and positive except for full shell of electrons with N=λ^k.

2. The fusion of N-H-atom and its conjugate must liberate proton and decay of λ^k-atom requires that proton is feeded to the system.

The previous observations lead to a detailed model for bio-catalytic action.

1. N-hydrogen atoms have effective charge 1-N/λ^k for N< λ^kso that the binding regions of catalysts and reacting molecules should carry effective fractional surface charge which is always positive: this is a testable prediction.

2. Catalyst in general has several names: one for each reactant molecule. Catalytic action involving the formation of reactants-catalyst complex by fusion of N-H-atoms and their conjugates necessarily involves a temporary liberation of protons, one for each letter of each name of the catalyst.
3. The generation of λ^k-H-atom in the fusion of letter and conjugate letter should correlate with the formation of hydrogen bonds between catalyst and substrate.
4. The liberated protons could drop to a larger space-time sheet and liberate metabolic energy quanta kicking the complex formed by the reacting molecules over the potential wall separating it from the outcome of the reaction. In the transition to the final state the surplus energy would be liberated and kick a protons back to the original space-time sheet and λ^k-atom would decay to N-atom and its conjugate. Also metabolism could kick the dropped protons back to the system so that the catalyst would not be stuck to the product of the reaction.

The fact that the names of bio-molecules carry positive effective charge relates in an interesting manner to the problem of how charged bio-polymers can be stable (I am grateful for Dale Trenary for pointing me the problem and for interesting discussions). For instance, DNA carries a charge of -2 units per nucleotide due to the phosphate backbone. The models trying to explain the stability involve effective binding of counter ions to the polyelectrolyte so that the resulting system has a lower charge density.

The simulations of DNA condensation by Stevens however predict that counter ion charge should satisfy z> 2 in the case of DNA. The problem is of course that protons with z=1 are the natural counter ions. The positive surface charge defined by the dark N-H-atoms attached to the nucleotides of DNA strand could explain the stability. In the case of DNA double strand the combination of names and conjugate names liberates one proton per nucleotide and stability could be guaranteed by these, possibly dark, protons residing at a larger space-time sheet.

For more details see the chapter Crop circles and life at parallel space-time sheets: part I , where a brief overview about living systems as ordinary matter quantum controlled by dark matter is given. If you are too afraid that you neighbor spots you in the middle of act of reading something about crop circles, you might prefer the end of the chapter Many-Sheeted DNA.

A more precise definition of N-atom and dark matter as a matter in wrong place

Earlier I speculated with the notion of dark N-particle (-atom or -molecule) and the possible significance of N-particles for the deeper understanding of lock and key mechanism of bio-catalysis and DNA replication.

Dark N-particles associated with DNA, possibly hydrogen bonds, could serve as names for nucleotides so that the emergence of symbols would distinguish between molecules in vitro and vivo. Dark fermionic N-particle and λ^k-N, particle a would serve as names for DNA nucleotide and its conjugate and their composite would be λ^k-atom analogous to a full electronic shell and therefore highly stable. Quite generally, molecules with conjugate names would be like opposite sexes: sex, symbolic representations, and meaning would emerge already at the molecular level.

1. Objection

There is an obvious objection against dark N-hydrogen atoms as names of DNA nucleotides. λ is in general integer valued and λ ≈ 2¹¹ seems to be favored. This value of λ would however make the mass of N-hydrogen atom or its conjugate quite too high to be physically acceptable.

Somehow it seems that N-hydrogen atom involves only single ordinary proton. In this case however the total electronic charge of the system would be N units of dark electronic charge and one protonic charge, which seems strange. The resolution of the problem is that dark electron-electron Coulomb interaction energy is reduced by 1/λ^k by the scaling down of the dark fine structure constant (proportional to 1/hbar). Hence effectively electronic and protonic charges would compensate each other for λ^k atom whereas for N-atoms the charge would be effectively fractional and 1-N/λ^k units.

2. How to observe N-atoms?

The most elegant definition of dirt is as a matter in wrong place. It would seem that also dark matter is matter in wrong place, but only effectively.

The question is how to observe N-atoms and N-molecules. The key observation is that the transition energies of N-molecules are N times large than corresponding ordinary molecules. This makes them thermally stable under much higher temperatures. The transitions of these molecules give rise to dark N-photons, which can decay to N ordinary photons with same energies as emitted in the transitions of ordinary molecules.

The presence of spectral lines of transitions of atoms or molecules which are not be stable at the temperature of environment, would serve as a signature of dark N-particles. Interestingly, spectral analysis demonstrates the presence water inside sunspots, where the temperature varies in the range 3000-4500 K. The decay of N-photons to ordinary photons emitted by thermally stable N-water molecules with N> 10 would explain the finding. Also the quite recent evidence discovered by M. Moshina that Sun has a solid surface consisting mostly of calcium-ferrite is inconsistent with the fact that photosphere has temperature 5800 K. The explanation of the puzzle would be in terms of dark N-iron and other dark N-elements.

Without exaggerating one can say that the systematic search for the presence of molecules and condensed matter structures in places where it is thermally stable could revolutionize our world view.

3.Plasmoids as life forms?

There is evidence that plasmoids satisfy the basic criteria for primitive living systems (E. Lozneanu and M. Sanduloviciu (2003), Minimal-cell system created in laboratory by self-organization, Chaos, Solitons and Fractals, Volume 18, Issue 2, October, p. 335. See also Plasma blobs hint at new form of life, New Scientist vol. 179 issue 2413 - 20 September 2003, page 16.)

One of the basic ideas of TGD based quantum model of living systems is that plasmoids identified as rotating magnetic systems analogous to Searl device are primitive life forms and predecessors of the molecular life. Rotation generates radial electric field having non-vanishing divergence whose sign depends on the direction of rotation (difficult to understand in Maxwellian ED), which in turn generates radial ohmic current charging the system. The dropping of electrons of this current to larger space-time sheets at the boundaries of rotating system liberates zero point kinetic energy as a usable metabolic energy. This mechanism would define fundamental metabolic energy currencies also in ordinary living matter.

4. Is molecular high-T life possible?

Life based on dark N-molecules could in principle survive at high temperatures. I have already earlier considered half seriously the possibility that Earth interior (say mantle-core boundary) and even solar photosphere could serve as seats of high-T life developed from plasmoids and that the Earth interior would be like the womb of Mother Gaia, where life evolved from simple plasmoids. The basic inspiration came from the evidence that crop circles cannot be fraud. See the chapters Crop circles and life at parallel space-time sheets: part I and II, where a brief overview about living systems as ordinary matter quantum controlled by dark matter is given.

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