NONLINEAR INDICES ANALYZING METHOD FOR MOLECULAR DYNAMICS OF PROTEIN DYNAMICAL TRANSITION

L. L. Zhang (), Q. Ruan () and L. X. Zhou
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L. L. Zhang: Surface Physics National Key Laboratory, Department of Physics, Fudan University, No. 220, Handan Road, Shanghai 200433, P. R. China
Q. Ruan: Research Center for Nonlinear Science, Institute of Mathematics, Fudan University, No. 220, Handan Road, Shanghai 200433, P. R. China
L. X. Zhou: Surface Physics National Key Laboratory, Department of Physics, Fudan University, No. 220, Handan Road, Shanghai 200433, P. R. China

International Journal of Modern Physics C (IJMPC), 2004, vol. 15, issue 03, 351-361

Abstract: We introduce four kinds of nonlinear indices into the analysis of free energy data produced by protein simulation with molecular dynamics. They are fractional dimension, approximate entropy, Poincare plot indices and predictability index with neural network. In this paper, the 200 K dynamical transition of myoglobin is used as an example, and the free energy data of the simulation is taken as time series to calculate the nonlinear indices. We show that all these indices as a function of temperature allow to indicate the dynamical transition with an obvious turning point, a "valley" or a "peak" around 200 K.

Keywords: Dynamical transition; nonlinear indices; molecular dynamics (search for similar items in EconPapers)
Date: 2004
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DOI: 10.1142/S0129183104005759

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