Related papers: Statistical Mechanics of DNA Mutation using SUSY Q…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
The denaturation of double-stranded DNA as function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 piconewtons of below a…
The exactly solvable eigenproblems in Schr\"odinger quantum mechanics typically involve the differential "shift operators". In the standard supersymmetric (SUSY) case, the shift operator turns out to be of first order. In this work, I…
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is…
The method of multidimensional SUSY Quantum Mechanics is applied to the investigation of supersymmetrical N-particle systems on a line for the case of separable center-of-mass motion. New decompositions of the superhamiltonian into…
We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
We study the tautomeric transitions in base pairs of DNA considering elastic properties of DNA as classical and tunneling of protons as quantum, and show that the dynamics of the transitions admits of soliton like solutions whose shape and…
In addition to the usual supersymmetric (SUSY) continuous symmetry transformations for the general N = 2 SUSY quantum mechanical model, we show the existence of a set of novel discrete symmetry transformations for the Lagrangian of the…
We construct a class of matrix models, where supersymmetry (SUSY) is spontaneously broken at the matrix size $N$ infinite. The models are obtained by dimensional reduction of matrix-valued SUSY quantum mechanics. The potential of the models…
We use supersymmetric (SUSY) methods to study the delocalization transition at zero energy in a one-dimensional tight-binding model of spinless fermions with particle-hole symmetric disorder. Like the McCoy-Wu random transverse-field Ising…
We consider the time-independent Wigner functions of phase-space quantum mechanics (a.k.a. deformation quantization) for a Morse potential. First, we find them by solving the $\ast$-eigenvalue equations, using a method that can be applied…
We consider a model for two types (bath and tracers) of 2D quantum particles in a perpendicular magnetic field. Interactions are short range and inter-species, and we assume that the bath particles are fermions, all lying in the lowest…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
Somatic mutations, or alterations in DNA of a somatic cell, are key markers of cancer. In recent years, mutational signature analysis has become a prominent field of study within cancer research, commonly with Nonnegative Matrix…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
We demonstrate the existence of a novel set of discrete symmetries in the context of N = 2 supersymmetric (SUSY) quantum mechanical model with a potential function f(x) that is a generalization of the potential of the 1D SUSY harmonic…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…