Preamble: this conjecture relates to Topic III. Gravitational Cycles & Induced Torque Into the Cell, and IV: Asymmetry in the Cell Nucleus as a Means for Driving Torque, and VI: Molecular Precession, Gravitation, and Circadian Rhythms. This discussion will be transferred to the site in the next few weeks. The preliminary outline is placed below, but please visit us again soon for a more complete discussion.

Hypothesis: helicity, chirality, and torque are critical characteristics of cell dynamics. Our intent is to look for a mechanism that can link and manipulate the rotational states of separated elements within the cell. Such a mechanisms would allow for the energy states between separated elements to be coupled and their motion subject to group tendencies established by their coherence. A prime candidate for this mechanism is the H-bond network that forms between water molecules. Hydrogen bonds have been shown to form low-energy spin networks and manifolds that can extend well beyond the 1-2 angstroms of the O-H or H-H bond. This tendency allows for water to re-configure its fine-scale bonding structure over intervals as short as picosecond timeframes in search of an extended structure that will lower the global energy state of the fluid. It has been demonstrated in computer simulations that when such an extended structure breaks, torque is conveyed along the manifold. It has also been shown that once broken, the manifold quickly seeks out alternative routes that will accommodate another low energy configuration. This is particularly advantageous for modeling torque transmission within the cytosol, for, although the cell is comprised of roughly 70% water, the impurity and thermal agitation introduced by organelles and other particulates likely prevent the form of any specific spin network to be sustained for long timespans.

H-bond spin networks in water:
Helicity, and chirality are well establish aspects of cellular biology. However, it has also been demonstrated that nuclear spin has also been identified as playing a critical role in the bonding patterns of water; expressed by the observation of very different behavior between ‘ortho-water’ (spin parallel) and para-water (spin anti-parallel). However, we want to focus here on studies made on larger patterns of coordinated spin and clustering in water – facilitated by the H-bond. In the words of Frank Keutch (Harvard) & Richard Saykally (Berkeley):
[Link: http://www.pnas.org/content/98/19/10533.full]

“Although it is clear that the hydrogen bond network and its fluctuations and re-arrangement dynamics determine the properties of the liquid, no experimental studies exist that reveal detailed information on a molecular level without considerable interpretation….A principal obstacle to resolving these issues is that of correctly describing the many-body, or cooperative nature of the hydrogen bonding interactions among a collection of (water) molecules.”

“quantum tunneling processes…rearrange the H-bond on time scales ranging from about 1 μs to 1 ps.”

• “sharp rotation-tunneling structures (have been) measured for (D2O)2.”

And, one quote from: T. Miyake and M. Aida, Hydrogen Bonding Patterns in Water Clusters, 2003.

“Although hydrogen bonds are weaker than covalent bonds, they can form long–lived structures of water clusters.”


Why is this potentially so exciting from a biological perspective? Well – with a little artistic license - we have a cell comprised of roughly 70% water that can wind and unwind itself into energetically preferential clusters. Torsional manifolds or spin networks that are of a scale that can link proteins and organelles separated in the cytoplasm - the tin can and string phone line between molecules. These spin networks might also allow for the cytosol to act as a bank for angular momentum – one that can either be harvested by local proteins, stashed away for use later, or exported out of the cell. Since any change in angular momentum in one region must be balanced by an opposite change in another region, spin manifolds can provide a means for transporting rotations around the cell. Keutch, Saykally, and other researches have found that when water clusters ‘break’, the bonds do so in an unwinding spiral pattern - much like the image we’ve all seen when a carefully placed row of dominoes is laid out in a circle and one is tipped over.We might imagine how, when the hypersensitive bonding structure of these manifolds is broken, two opposing rotations are induced into the cytosol and sent swirling in opposite directions at pico-second time intervals. If we’re looking to move stuff around in the cell, this seems like a pretty good mechanism. Think nano-scaled hurricanes or tornados - but rather that sucking up sofas and rooftops, maybe these spin networks can be modeled to plow proteins around?

Perhaps equally critical, is a geometrical link: water clusters are modeled to form torsional manifolds with diameters as large as 30 angstroms, but larger manifolds have also been modeled. By coincidence, when DNA is packaged as a nucleosome, wound around a series of histones such as the one modeled at the left, each histone has a core that is roughly the same diameter ~ 50 angstroms. Clearly, from looking at the histone structure, the protein group is intimately connected with rotations with a very précised geometry: “147 base pairs of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn”. If we’re looking for a means by which DNA might be connected in a nonlinear cooperative way directly to torsional manifolds and spin networks in the cytosol – one that also requires a precise geometry for clustering - then here’s our link. (More later).

Histone:

[Note: a more appropriate title for this section would have been: Biologically Controlled H-bond Spin Networks in Water. However, in an ironic catch-22, similar to the situation where astrophysicists try to model something they can’t see (dark-matter), we find ourselves trying to model the activity of water whose molecular structure cannot be directly imaged either… (high energy X-rays typically blow apart the H-bond structure (though some evidence for structure has been identified in water nanodrops), and NMR–MDQ images depend very much on the mathematical models that are fed into it - which, for water, are clearly yet to be understood.) Accordingly, we understand that the model here rests on foundations that are as solid as the one supporting the notion of WIMPS. That will not keep us from working with the hypothesis that at least part of the biological activity within the cell is directed towards forming and controlling H-bond spin networks.]

All that said, it is still natural to speculate about how the histone structure shown above might be combined with solved clustering geometry such as this icosahedral cluster of 280 hydrogen-bonded water molecules. In this structure each water molecule is involved in four H-bonds, two as donors and two as acceptors. The network is based on the regular arrangement of 20 slightly flattened tetrahedral 14-molecule units as shown here:

[Ref:Chaplin:http://www1.lsbu.ac.uk/water/clusters_overview.html]
or, From Chem Phys. Letters: http://www.sciencedirect.com/science/article/pii/0009261488872725]

The modeling of large H-bonded molecules and spin manifolds and clusters becomes a many-body problem that quickly exceeds the level of accuracy of computer simulation. Solutions to larger, more complex manifolds are sure to be found. Most proteins have accessible hydrogen with the potential to link to such manifolds. While we don’t envision that the icosahedral cluster above would be the form of water manifold to link with a histone, it is interesting to overlay their images and imagine how the cluster might be altered to bond with the histone structure.

 


The image below illustrates how such water manifolds might link histones when DNA is in its chromatin form.

Since the H-bonds that comprise such manifolds are constantly breaking and re-forming – testing or probing the cytosol for any configuration that might provide a spin advantage – one can imagine how spin tributaries might branch off like limbs of a tree connecting to any molecule that has similar rotational characteristics. One can also envision how such manifolds might tap those molecules for rotational energy and transfer it through its network. (See Topic about molecular wrenches).

See Topic XII: ATP and Gravitational Potential Energy?

Microtubules

Methylation


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