Related papers: Statistical Mechanics of DNA Mutation using SUSY Q…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
Mutational signatures are powerful summaries of the mutational processes altering the DNA of cancer cells. The usual approach to mutational signature analysis consists of decomposing the matrix of mutation counts from a sample of patients…
Analytical expressions for spectra and wave functions are derived for a Bohr Hamiltonian, describing the collective motion of deformed nuclei, in which the mass is allowed to depend on the nuclear deformation. Solutions are obtained for…
The three-dimensional Schr\"odinger equation with a position-dependent (effective) mass is studied in the framework of Supersymmetrical (SUSY) Quantum Mechanics. The general solution of SUSY intertwining relations with first order…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
We propose a numerical method of estimating various physical quantities in lattice (supersymmetric) quantum mechanics. The method consists only of deterministic processes such as computing a product of transfer matrix, and has no…
This work is aimed at demonstrating the possibility to construct new exactly-solvable stochastic systems by use of the extended supersymmetric quantum mechanics ($N=4 SUSY QM$) formalism. A feature of the proposed approach consists in $N=4…
Within the framework of second order derivative (one dimensional) SUSYQM we discuss particular realizations which incorporate large energy shifts between the lowest states of the spectrum of the superhamiltonian (of Schr\"odinger type). The…
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…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
Chains of first-order SUSY transformations for the spin equation are studied in detail. It is shown that the transformation chains are related with a olynomial pseudo-supersymmetry of the system. Simple determinant formulas for the final…
Some results on the ordered statistics of eigenvalues for one-dimensional random Schr\"odinger Hamiltonians are reviewed. In the case of supersymmetric quantum mechanics with disorder, the existence of low energy delocalized states induces…
Supersymmetrical intertwining relations of second order in the derivatives are investigated for the case of supercharges with deformed hyperbolic metric $g_{ik}=diag(1,-a^2)$. Several classes of particular solutions of these relations are…
The oxidative damage of DNA is a compelling issue in molecular biophysics as it plays a vital role in the epigenetic control of gene expression and is believed to be associated with mutagenesis, carcinogenesis, and ageing. To understand the…
The variance, higher order moments, covariance, and joint moments or cumulants are shown to be special cases of a certain tensor in $V^{\otimes n}$ defined in terms of a collection $X_1,...,X_n$ of $V$-valued random variables, for an…
The Deformation Dependent Mass (DDM) Kratzer model is constructed by considering the Kratzer potential in a Bohr Hamiltonian, in which the mass is allowed to depend on the nuclear deformation, and solving it by using techniques of…
We investigate (pseudo)differential forms in the framework of supergeometry. Definitions, basic properties and Cartan calculus (DeRham differential, Lie derivative, inner product, Hodge operator) are presented; the symplectic supermechanics…
The relativistic finite-difference SUSY Quantum Mechanics (QM) is developed. We show that it is connected in a natural way with the q-deformed SUSY Quantum Mechanics. Simple examples are given.
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
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…