Full Text:   <3249>

CLC number: O324

On-line Access: 2024-08-27

Received: 2023-10-17

Revision Accepted: 2024-05-08

Crosschecked: 0000-00-00

Cited: 0

Clicked: 5659

Citations:  Bibtex RefMan EndNote GB/T7714

-   Go to

Article info.
1. Reference List
Open peer comments

Journal of Zhejiang University SCIENCE A 2007 Vol.8 No.9 P.1401-1407

http://doi.org/10.1631/jzus.2007.A1401


On the stochastic dynamics of molecular conformation


Author(s):  DENG Mao-lin, ZHU Wei-qiu

Affiliation(s):  Department of Mechanics, State Key Laboratory of Fluid Power Transmission and Control, Zhejiang University, Hangzhou 310027, China

Corresponding email(s):   zjudeng@yahoo.com.cn, wqzhu@yahoo.com

Key Words:  Biological macromolecule, Thermal fluctuation, Stationary statistics, Transition time, Stochastic averaging method


DENG Mao-lin, ZHU Wei-qiu. On the stochastic dynamics of molecular conformation[J]. Journal of Zhejiang University Science A, 2007, 8(9): 1401-1407.

@article{title="On the stochastic dynamics of molecular conformation",
author="DENG Mao-lin, ZHU Wei-qiu",
journal="Journal of Zhejiang University Science A",
volume="8",
number="9",
pages="1401-1407",
year="2007",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2007.A1401"
}

%0 Journal Article
%T On the stochastic dynamics of molecular conformation
%A DENG Mao-lin
%A ZHU Wei-qiu
%J Journal of Zhejiang University SCIENCE A
%V 8
%N 9
%P 1401-1407
%@ 1673-565X
%D 2007
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2007.A1401

TY - JOUR
T1 - On the stochastic dynamics of molecular conformation
A1 - DENG Mao-lin
A1 - ZHU Wei-qiu
J0 - Journal of Zhejiang University Science A
VL - 8
IS - 9
SP - 1401
EP - 1407
%@ 1673-565X
Y1 - 2007
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2007.A1401


Abstract: 
An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamiltonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1] Binney, J.J., Dowrick, N.J., Fisher, A.J., Newman, M.E.J., 1992. The Theory of Critical Phenomena, an Introduction to the Renormalization Group. Clarendon Press, Oxford, UK.

[2] Brown, S., Fawzi, N.J., Head-Gordon, T., 2003. Coarse-grained sequences for protein folding and design. Proc. Natl. Acad. Sci. USA, 100(19):10712-10717.

[3] Ebeling, W., Schimansky-Geier, L., Romanovsky, Y.M., 2002. Stochastic Dynamics of Reacting Biomolecules. World Scientific, Singapore, p.28-31.

[4] Frauenfelder, H., Wolynes, P.G., 1985. Rate theories and the puzzles of hemoprotein kinetics. Science, 229:337-345.

[5] Honeycutt, J.D., Thirumalai, D., 1992. The nature of folded states of globular proteins. Biopolymers, 32(6):695-709.

[6] Itô, K., 1951. On stochastic differential equations. Mem. Amer. Math. Soc., 4:289-302.

[7] Khasminskii, R.Z., 1968. On the averaging principle for stochastic differential Itô equation. Kibernetika, 4:260-279 (in Russian).

[8] McCammon, J.A., Harvey, S.C., 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.

[9] Mezić, I., 2006a. On the dynamics of molecular conformation. Proc. Natl. Acad. Sci. USA, 103(20):7542-7547.

[10] Mezić, I., 2006b. Biomolecules as Nonlinear Oscillators: Life-enabling Dynamics. The 2nd International Conference on Dynamics, Vibration and Control. Beijing, China.

[11] Peyrard, M., 2004. Nonlinear dynamics and statistical physics of DNA. Nonlinearity, 17(2):R1-R40.

[12] Tabor, M., 1989. Chaos and Integrability in Nonlinear Dynamics. John Wiley and Sons, New York.

[13] Yakushevich, L.V., 2004. Nonlinear Physics of DNA. Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim.

[14] Zhu, W.Q., 2003. Nonlinear Stochastic Dynamics and Control —A Hamiltonian Theoretical Framework. Science Press, Beijing (in Chinese).

[15] Zhu, W.Q., 2006. Nonlinear stochastic dynamics and control in hamiltonian formulation. ASME Applied Mechanics Reviews, 59(4):230-248.

[16] Zhu, W.Q., Yang, Y.Q., 1997. Stochastic averaging method of quasi-nonintegrable-Hamiltonian systems. ASME J. Appl. Mech., 64:157-164.

[17] Zhu, W.Q., Huang, Z.L., Yang, Y.Q., 1997. Stochastic averaging of quasi-integrable-Hamiltonian systems. ASME J. Appl. Mech., 64:975-984.

[18] Zhu, W.Q., Huang, Z.L., Suzuki, Y., 2002. Stochastic averaging and Lyapunov exponent of quasi-partially-integrable-Hamiltonian system. Int. J. Non-Linear Mech., 37(3):419-437.

Open peer comments: Debate/Discuss/Question/Opinion

<1>

Please provide your name, email address and a comment





Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - 2024 Journal of Zhejiang University-SCIENCE