Related papers: Statistical Mechanics of DNA Mutation using SUSY Q…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…
The new method based on the SUSY algebra with supercharges of higher order in derivatives is proposed to search for dynamical symmetry operators in 2-dim quantum and classical systems. These symmetry operators arise when closing the SUSY…
We investigate the $h$-deformed quantum (super)group of $2\times 2$ matrices and use a kind of contraction procedure to prove that the $n$-th power of this deformed quantum (super)matrix is quantum (super)matrix with the deformation…
The phase transition of $(PolyA/PolyT)_{100}$ duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat…
We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…
The fundamentals of Statistical Mechanics require a fresh definition in the context of the developments in Classical Mechanics of integrable and chaotic systems. This is done with the introduction of Micro Partitions ; a union of disjoint…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
A mathematical algorithm to describe DNA or RNA sequences of $N$ nucleotides by a string of $2N$ integers numbers is presented in the framework of the so called crystal basis model of the genetic code. The description allows to define a not…
We derive the on-shell as well as off-shell nilpotent supersymmetric (SUSY) symmetry transformations for the N = 2 SUSY quantum mechanical model of a one (0 + 1)-dimensional (1D) free SUSY particle by exploiting the SUSY invariant…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
We revisit the novel symmetries in $\mathcal{N}$ = 2 supersymmetric (SUSY) quantum mechanical (QM) models by considering specific examples of coupled systems. Further, we extend our analysis to a general case and list out all the novel…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
We study the SUSY breaking of the covariant gauge-fixing term in SUSY QED and observe that this corresponds to a breaking of the Lorentz gauge condition by SUSY. Reasoning by analogy with SUSY's violation of the Wess-Zumino gauge, we argue…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
In this manuscript we propose a mathematical framework to couple transcription and translation in which mRNA production is described by a set of master equations while the dynamics of protein density is governed by a random differential…
The number partitioning problem consists of partitioning a sequence of positive numbers ${a_1,a_2,..., a_N}$ into two disjoint sets, ${\cal A}$ and ${\cal B}$, such that the absolute value of the difference of the sums of $a_j$ over the two…
We propose a SUSY variant of the action for a massless spinning particles via the inclusion of twistor variables. The action is constructed to be invariant under SUSY transformations and $\tau$-reparametrizations even when an interaction…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…