Travkin HSPT

Introduction to Hierarchical, Heterogeneous, Multiscale Biology and its Applications

As it is established in HSP-VAT the mathematical formulation, statements, and modeling of physical processes occurring in strongly heterogeneous media results on the whole in the necessity for the particular medium scaled characteristics development, and accordingly, for process governing equations. This is all applicable to the Heterogeneous Scaled nature of assignments within the Biology disciplines.

Among major aims of the HSP-VAT application to Biological/Medicine issues/problems are the following:

1) Provide theoretical derivation of main sets of governing equations (GE) on each level of the hierarchy and estimate feasibility of closure developments.

2) Develop theoretical mechanisms and varieties of closure approaches for each specific biological or/and medicine system hierarchical level.

3) Estimate the feasibility of theoretical procedures for the development of numerical convergent algorithms for solution evaluations of the equations governing the process.

4) That all above finally give the tools, open procedures for Hierarchical Quantitative Scaled modeling of biological substances, objects, and even tissue.

We would like to say that we have been going through the stage of conceptual formulation and development of basics of Heterogeneous (Hierarchical) Scaled (HtS) sub-disciplines and topics in biology as, for example, of cell, cellular culture, tissue modeling, biomimetic design, etc. since approximately 80s.

Most of our findings and conceptual solutions are found to be more rigorous; physically and mathematically are strict while having the base of already developed many subjects in other physical and mathematical sciences. Sorry for my language - many issues are open for arguments and discussion; many are still in a private domain.

Among obvious concepts (obvious for sufficient qualification biologists, physicists and mathematicians) there are the HtS Bacteriology and Virology as the sciences, which utmost functionality are based on the acknowledgment of facts communicated to the existence of the multiscaled collective phenomena, those are beyond of only the orthodox Homogeneous one scale chemical and physical nature.

We would like to make a statement with connection to the nature of these phenomena: there is the possibility of finding the outstandingly more complicated responses and in vivo behavior by the facts communicated to the collective scaled nature of cultures, colonies and/or tissues existence.

That is why we have been applying the known in the HSP-VAT tools while formulating the basic physical and mathematical concepts, models within tasks of/for (HtS) Bacteriology and Virology, Systems Biology, Cell Biology, etc.

What Can not be Explained and Answered by the One Scale Homogeneous Biology

No matter how hard and how clever people have been trying to do this. Few main reasons for that are given in:

"Why is it Different from Homogeneous and other Theories and Methods of Heterogeneous Media Mechanics/(other Sciences) Description?"

where few words on logic and history of the HSP-VAT are spelled in

"Announcements"

along with the fundamental controversial grounds for this currently dominating "theological" physics acting in and on behalf of Biology explained in

"Reductionism and/versus Holism in Physics and Biology - are Both Defective Concepts without Scaleportation "

"What is in use in Continuum Mechanics of Heterogeneous Media as of Through ~1950 - 2005?"

See just small portion of arguments in our scaled solutions and data reduction as in

"Globular Morphology Two Scale Electrostatic Exact Solutions"

and other subsections of this website. Etc., etc.

Here below is just the short first come first appeared list, following the TOC in many Biology Textbooks:

Proteins:

There is no chance correctly provide and model the now important "Protein - to - Protein Interaction" analysis. Thus, the modeling that labs having had right now is also of obsolete 30 years old physics, chemistry base.

These sentences above and below on areas of inability to cover them with the homogeneous one-scale physics and chemistry tools, were written as around ~2002-2003, or even earlier. Just recently I was pointed out to the place where people wrote the similar statements on the features of "Protein - to - Protein" or Macromolecule-to-Macromolecule interactions. Where? - in California, and New York; just we can find that in the web -

"National Center for Dynamic Interactome Research"

where they spell the words -"Current technologies are not suitable to reveal dynamic interactions between macromolecules at sufficient scale, with sufficient reliability or with sufficient sensitivity to keep pace with the genomic revolution brought about by sequencing technologies. The vision of the National Center for Dynamic Interactome Research is to develop innovative and dramatically new approaches for the detection, isolation, and analysis of macromolecular complexes that will enable scientists to realize the full potential of the revolution brought about by genomics, interdisciplinary research, and proteomics technologies."

2013 - Oh, surprise, they deleted the wonderful words above - at least not seen as in previous years in the "Home" page. That means they still read some texts around of their narrow, narrow specializations.

That was good to read in ~ 2009-2011. Meanwhile, we had in ~(2009 - 2011) some ideas to tell about on their own - these teams tools developed and the results obtained with those tools, a few published in "Nature." The tools are still of the one-scale orthodox homogeneous physics. Scrutiny has been uploaded in the below subsections -

"How not to Scale-Down...or -Up.. .. Analysis of Current Studies on Scaled, Collective Phenomena in Biology Fields Presented as the One-Scale Concepts "

"How the Orthodox Homogeneous Physics and Following it Orthodox Mathematics Screwing Biology Now **"

At the same time, it is hard to believe that these particular teams of biologists are able, or really willing to "develop innovative and dramatically new approaches"? The matter of fact is that they have message about their obsolete physics and math attempts to proceed to the upper point in their polyscaling agenda, read in our -

"BOTTOM-UP THEORETICAL, STRUCTURAL, CELLULAR BIOLOGY "MULTISCALING" "

In fact, their way of doing business is restricted by the desire to go only along their own route (after all, these are financial rules) - which they can not accomplish due to insufficient knowledge and scopes of vision, those are within the conventional biology homogeneous one scale paradigm.

Ferments:

Finding the Michaelis-Menten constant K_{m} is the attractive problem, but is an impossible task for Homogeneous Biology, for example. The trouble is with the definition and the method of assessment as for homogeneous matter which is not really of this kind. The current theory and practices reflect those from physics of 30-40 years old, and definitely are obsolete. Students got to the learning procedures that are not strengthening their trust to the methods - homogeneous by nature, and to an accuracy of the experiments. Etc., etc.

Membranes:

Not possible to Model and Simulate correctly the 1D Across Transport, the 2D Surficial Control and Transport, and the 3D Function and Control in Cell and in Tissue. What is used in chromatography right now is the self-appointed alchemistry, skillful anyway, of obsolete knowledge from Fluid Mechanics. Some of the explanations for this statement are given here in

- "Effective Coefficients in Fluid Mechanics"

- "Laminar Flow in Porous Media"

- "Fluid Mechanics"

Etc., etc.

Workers went down the scales to the atomic and protein scales. Nevertheless, this won't help in core to find ways to model the polyscale phenomena in 2D or better 3D cross transport polyscale reality. Why is that read in -

"How not to Scale-Down...or -Up.. .. Analysis of Current Studies on Scaled, Collective Phenomena in Biology Fields Presented as the One-Scale Concepts "

Cells:

No chance to figure out and to model and simulate neither Momentum nor Energy Transport within the cell. Just because the way biologists right now do this conceptual understanding and modeling - is out of touch (the fun to read). They follow the orthodox physics of 30 years old as of the times workers took their physics (atomic) courses. Those Homogeneous medium descriptions are too simplistic, obsolete, and even wrong.

There is no chance to understand the overall energy production, transformation to the other types of energy, and transport even within the singular cell. Those explanations by now on are simply fragmentary and disconnected within the whole picture.

Tissue:

There is no chance to understand, model and simulate the tissue samples, any kind as via the One scale Homogeneous medium approach, theory, even as the one scale heterogeneous tissue taken as a Homogeneous medium. This is the present time scientific understanding and practices in Biology and Health sciences. I wrote on that and studied few types of cell, mostly the muscle tissue cells and the brain cells, and that statement here is the one resulting out of firm outcomes of these continuing studies.

There is no chance to understand correctly and model correctly (not just on a verbal level) the interplay of tissue response and of the nervous system impact.

Nanotechnologies in Biology and Medicine:

There is no chance to understand and model correctly the impact and consequences of nanoscale drug delivery and tissue, organ effect with the Homogeneous one scale methods. We write on this also in - "Nanotechnologies"

Biosystems:

There is no way to find out by using the Homogeneous one scale just many (few) biosystems interconnection, interdependencies, communication between the biosystems if we want to assess with mathematical abilities, to model, and simulate the time dependent biosystems in vivo in their environment(s). What is right now being modeled is just the prehistorically "arithmetic" systems with "wooden" stiff interconnections.

Ecosystems:

There is no way to find out by using the Homogeneous one scale just many (few) species interconnection, interdepedencies, communication, food chain characteristics between the species, in the ecosystem, if we want to assess with mathematical abilities, to model, and simulate the time dependent ecosystems in vivo in their environment(s). What is right now being modeled is, sorry, also just the prehistorically "arithmetic" qualitative models.

Those are the "wooden" unrealistic models. That's impossible to model that kind of system as ecosystems with the Homogeneous one scale biology modeling tools.

Among the reasons explaining why the correct Hierarchical Scaled Biophysics modeling and simulation in Biology and Medicine could not be achieved with reasonable results right now, while actually since the 1990s, we must mention the absence of published theory and models for polyphase polyscale solid and soft solid biomedia elasticity, viscoelasticity theories. To this category should be added the polyscale electrodynamics in biomedia firstly based on the Maxwell-Lorentz type of EM Governing Equations (GE) - those are the approximate one scale GEs; then all over developments for biomedia using the polyscale Scaleportation with the correct Galilean type polyscale Electrodynamics theory with its bio-applications ought to be provided.

Yes, of course, and the Sub-Atomic electrodynamics polyscale phenomena and transport (remember, the Electron Transport in a cell ?..) should be at disposal of biologists and medics.