Abstract DNA-type systems

DOI10.1088/0951-7715/19/3/003MaRDI QIDQ3376402zbMATH OpenOpenAlexWikidataFDO

Authors Diederik Aerts, Marek Czachor

Publication date 23 March 2006

Published in Nonlinearity (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0411031

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Dynamical systems in biology (37N25) Interacting random processes; statistical mechanics type models; percolation theory (60K35) Biophysics (92C05) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Abstract: An abstract DNA-type system is defined by a set of nonlinear kinetic equations with polynomial nonlinearities that admit soliton solutions associated with helical geometry. The set of equations allows for two different Lax representations: A von Neumann form and a Darboux-covariant Lax pair. We explain why non-Kolmogorovian probability models occurring in soliton kinetics are naturally associated with chemical reactions. The most general known characterization of soliton kinetic equations is given and a class of explicit soliton solutions is discussed. Switching between open and closed states is a generic behaviour of the helices. The effect does not crucially depend on the order of nonlinearity (i.e. types of reactions), a fact that may explain why simplified models possess properties occuring in realistic systems. We explain also why fluctuations based on Darboux transformations will not destroy the dynamics but only switch between a finite number of helical structures.

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Cited in

(3)

• Helices for mathematical modelling of proteins, nucleic acids and polymers
• Systems, environments, and soliton rate equations: toward realistic modeling
• Two-State Dynamics for Replicating Two-Strand Systems

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