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Collective molecular orbitalsand the theory of multilevel self-organization

Ivan Denisov

Федеральное государственное автономное образовательное учреждение высшего профессионального образования

«СИБИРСКИЙ ФЕДЕРАЛЬНЫЙ УНИВЕРСИТЕТ»Институт фундаментальной биологии и биотехнологии

Кафедра биофизики

“Bioluminescent biotechnology” 2013 Krasnoyarsk

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Plan

1. The problem with computational models for biology

2. Multilevel approach for biological systems modeling

3. The collective orbitals in nanodiamond

4. The multilevel model of microtubules dynamics

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The problem with computational models for biology

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Genotype → Phenotype Mapping

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Genotype → Phenotype Mapping

A testable genotype-phenotype map: Modeling evolution of RNA molecules. In: Lässig, M. and Valleriani, A., editors, Biological Evolution and Statistical Physics, pp. 56–83. Springer-Verlag, Berlin, 2002

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The Whole-Cell Computational Model

J. R. Karr, J. C. Sanghvi, D. N. Macklin, M. V. Gutschow, J. M. Jacobs, B. Bolival, N. Assad-Garcia, J. I. Glass, and M. W. Covert, “A whole-cell computational model predicts phenotype from genotype,” Cell, vol. 150, no. 2, pp. 389–401, Jul. 2012.

7Idea was taken from F.A. Kondrashov lecturehttp://elementy.ru/video?pubid=431332

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Biological hierarchy

A. Pavé, “Biological and Ecological Systems Hierarchical Organisation,” in Hierarchy in Natural and Social Sciences, vol. 3, D. Pumain, Ed. Berlin/Heidelberg: Springer-Verlag, 2006, pp. 39–70.

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Biological hierarchy

A. Pavé, “Biological and Ecological Systems Hierarchical Organisation,” in Hierarchy in Natural and Social Sciences, vol. 3, D. Pumain, Ed. Berlin/Heidelberg: Springer-Verlag, 2006, pp. 39–70.

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Self-organization in cells

Micelles and liposomes

Microtubules

Lipid rafts

Viruses envelopes

George K.S., Wu S. Lipid raft: A floating island of death or survival. // Toxicology and applied pharmacology. Elsevier B.V., 2012. Vol. 259, № 3. P. 311–319.

Protein folding

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Cells are multilevel & selfassembled

For making the whole-cell models we need:

1. Describe the interaction between objects in several organization levels with known properties of all objects

2. Find the objects properties in each level from character lows of physics, chemistry and biology for each level

Lodish, 2003

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Multilevel approach for biological systems modeling

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Bioparticles & Object of organization

● Quasi-particle approach common used in physics for solve many body problems.

● The object of organization for modeling degrees of freedom reorganization.

Pollack G.H. The fourth phase of water: beyond solid, liquid, and vapor. Seattle, WA: Ebner and Sons, 2013.

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Is there a way to introduce standard model for multilevel self-organized systems?

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Classical mechanics and algorithmics

Algorithmic functions — trigger function and successor functions.

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Chemical bond model

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Structured enthropy storage in organisation objects

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Multilevel systems organisation

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Collective orbitals in nanodiamond

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3. NanodiamondCollective states in nanodiamond: theoretical explanation of experiment.

Atomic orbitals → collective molecular orbitals → collective supramolecular orbitals → biopolimers

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Compression of surface

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Subsurface states in diamondoids

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New spherical system resemble hydrogenic wavefunctions

Properties recursion in Nature!

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Multilevel model of microtubules dynamics

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4. Microtubules multilevel self-assembly

Desai A., Mitchison T.J. Microtubule polymerization dynamics // Annual review of cell and developmental biology. 1997. Vol. 13, № 1. P. 83–117.

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One microtubule

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500 microtubules without diffusion

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900 microtubules with diffusion

Comparision

Воробьев И.А., Малый И.В. Об отношении длины и динамики микротрубочек: краевой эффект и свойства протяженной радиальной сети // Цитология. 2008. т. 50, № 6. С. 477–486.

Bimodal distribution

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Conclusion

1. Suggested multilevel approach for modeling can be used to study the biological systems through several levels of organization

2. The subsurface localization of collective orbitals can explain magnetic properties of nanodiamond

3. Multilevel model of microtubules is describing experimental effects better than single-level model

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Acknowledgement

The Genomic Research and Educational Center of SibFU

Peter I. BelobrovAndrey A. Zimin

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Tamm's states gave the ideato look on the collective states

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Subsurface states in 1D model

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L + 2 level

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One MT experimentalM

icro

t ubule

length

(m

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Time (min)

Assembly

Rescue

Disassembly

Catastrophe

60 90 0

50

10

20

30

40

30

μ