Statistical Mechanics of DNA Mutation using SUSY Quantum Mechanics

K. Haritha, K. V. S. Shiv Chaitanya

DOI：: 10.1088/1751-8121/ac0985

英文摘要：

In this paper, we investigate DNA denaturation through Statistical Mechanics and show that exceptional polynomials lead to DNA mutation. We consider a DNA model with two chains connected by Morse potential representing the H bonds, and then we calculate the partition function for this model. The partition function is converted into a Schrödinger like an equation. We exploit the techniques of SUSY quantum mechanics to model DNA mutation. We also compute the thermal denaturation of DNA for each mutated state.

机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。

阅读原文

阅读 PDF ↗

arXiv 页面 ↗HTML 原文 ↗

本文内容

英文摘要相关论文

机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。

继续探索

相关论文

DNA sequence from the unzipping force? : one mutation problem

The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the zipped from the unzipped regions. We propose a comparison method (``differential force microscope'') to detect mutations. Two lattice models are treated as specific examples.

2002-07-17cond-mat.softcond-mat.stat-mechq-bio

DNA Sequence Evolution with Neighbor-Dependent Mutation

We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting well-known methods of nonlinear dynamics. Results are presented for the CpG-methylation-deamination process which dominates point substitutions in vertebrates. The dinucleotide frequencies generated by the model (using empirically obtained mutation rates) match the overall pattern observed in non-coding DNA. A web-based tool has been constructed to compute single…

2003-07-02cond-mat.stat-mechphysics.bio-phphysics.comp-ph

On the role of mismatches in DNA denaturation

In the framework of the Poland Scheraga model of DNA denaturation, we derive a recursion relation for the partition function of double stranded DNA, allowing for mismatches between the two strands. This relation is studied numerically using standard parameters for the stacking energies and loop entropies. For complementary strands (of length 1000), we find that mismatches are significant only when the cooperativity parameter $σ$ is of order one. Since $σ\sim O(10^{-5})$ in DNA, entropic gains from mismatches are overwhelmed by the energetic cost of opening a loop: mismatches are therefore irre…

2003-04-09cond-mat.softcond-mat.stat-mechq-bio

Tautomeric mutation: A quantum spin modelling

A quantum spin model representing tautomeric mutation is proposed for any DNA molecule. Based on this model, the quantum mechanical calculations for mutational rate and complementarity restoring repair rate in the replication processes are carried out. A possible application to a real biological system is discussed.

2006-12-13cond-mat.othercond-mat.stat-mech

On the Selection and Evolution of Regulatory DNA Motifs

The mutation and selection of regulatory DNA sequences is presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we construct an explicit model for the evolution of regulatory sequences, making use of the known biophysics of the binding of regulatory proteins to DNA sequences, under the assumption that fitness of a sequence depends only on its binding affinity to the regulatory protein. The model is confined to the mean field (i.e., infinite population size) limit. Using real…

2003-01-02cond-mat.stat-mechphysics.bio-phq-bio.PE

Analytical study of the effect of recombination on evolution via DNA shuffling

We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the model allows us to obtain a full analytical treatment of both its dynamical and equilibrium properties, for the case of an infinite population. We also briefly discuss finite population size corrections.

2003-03-28cond-mat.stat-mechphysics.bio-phq-bio.PE

更多相关论文收起更多论文

Four-state quantum chain as a model of sequence evolution

A variety of selection-mutation models for DNA (or RNA) sequences, well known in molecular evolution, can be translated into a model of coupled Ising quantum chains. This correspondence is used to investigate the genetic variability and error threshold behaviour in dependence of possible fitness landscapes. In contrast to the two-state models treated hitherto, the model explicitly takes the four-state nature of the nucleotide alphabet into account and allowes for the distinction of mutation rates for the different base substitutions, as given by standard mutation schemes of molecular phylogeny…

2000-08-08cond-mat.stat-mechq-bio