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Genome Information, Code Evolution, Folding Dynamics and Entropy Production: Several Fundamental Problems in Theoretical Biology |
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Abstract: The rationalization of biology is discussed in an information-centered context. The studies in the field of theoretical biology are reviewed which include the following topics. (1) The formation and construction of the genome recognition code. A set of statistical quantities describing base composition and base correlation can serve as the genome recognition code. (2) The genome evolution direction and the maximum information principle. It is proposed that the quanlity of the function-coding information of a genome grows with time in the course of evolution. It is proposed also that the Shannon information quantity of the local DNA segments obeys the maximum information principle. (3) The adaptive evolution of the genetic code. It is proved that the prevalent standard amino acid code is a mutational deterioration-minimal code of an adaptive evolution and it is demonstrated that the genetic code satisfies both the principles of robust stability and evolvability. (4) The protein folding dynamics based on quantum transition. The protein folding rate formula is deduced based on quantum transition between torsion states by using conformation dynamics. All theoretical results (including the rate and its dependence on chain length, inertia moment and temperature, etc.) are consistent with the updated experimental data. (5) The cell switch and entropy production. The dynamics of lysogenic/lytic transition of lambda phage - the simplest form of the life - is studied from a set of differential equations. The entropy production rate of the typical cell switch is calculated. It is proved that the dynamics of this particular system obeys some topological theorem and thus the obtained results are of general nature.
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Received: 23 November 2009
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Corresponding Authors:
Liao-Fu Luo
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