Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and...

37
1 Collective molecular orbitals and 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

Transcript of Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and...

Page 1: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

1

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

Page 2: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

2

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

Page 3: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

3

1

The problem with computational models for biology

Page 4: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

4

Genotype → Phenotype Mapping

Page 5: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

5

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

Page 6: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

6

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.

Page 7: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

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

Page 8: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

8

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.

Page 9: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

9

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.

Page 10: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

10

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

Page 11: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

11

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

Page 12: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

12

2

Multilevel approach for biological systems modeling

Page 13: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

13

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.

Page 14: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

14

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

Page 15: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

15

Classical mechanics and algorithmics

Algorithmic functions — trigger function and successor functions.

Page 16: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

16

Chemical bond model

Page 17: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

17

Structured enthropy storage in organisation objects

Page 18: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

18

Multilevel systems organisation

Page 19: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

19

3

Collective orbitals in nanodiamond

Page 20: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

20

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

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

Page 21: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

21

Compression of surface

Page 22: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

22

Page 23: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

23

Subsurface states in diamondoids

Page 24: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

24

New spherical system resemble hydrogenic wavefunctions

Properties recursion in Nature!

Page 25: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

25

4

Multilevel model of microtubules dynamics

Page 26: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

26

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.

Page 27: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

27

One microtubule

Page 28: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

28

500 microtubules without diffusion

Page 29: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

29

900 microtubules with diffusion

Page 30: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

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

Page 31: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

31

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

Page 32: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

32

Acknowledgement

The Genomic Research and Educational Center of SibFU

Peter I. BelobrovAndrey A. Zimin

Page 33: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

33

Page 34: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

34

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

Page 35: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

35

Subsurface states in 1D model

Page 36: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

36

L + 2 level

Page 37: Collective molecular orbitals and the theory of multilevel ... · Collective molecular orbitals and the theory of multilevel self-organization Ivan Denisov ... The fourth phase of

37

One MT experimentalM

icro

t ubule

length

(m

)

Time (min)

Assembly

Rescue

Disassembly

Catastrophe

60 90 0

50

10

20

30

40

30

μ