Related papers: Statistical Mechanics of DNA Mutation using SUSY Q…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…
New solutions for second-order intertwining relations in two-dimensional SUSY QM are found via the repeated use of the first order supersymmetrical transformations with intermediate constant unitary rotation. Potentials obtained by this…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Along the years, supersymmetric quantum mechanics (SUSY QM) has been used for studying solvable quantum potentials. It is the simplest method to build Hamiltonians with prescribed spectra in the spectral design. The key is to pair two…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
Semiparametric statistics play a pivotal role in a wide range of domains, including but not limited to missing data, causal inference, and transfer learning, to name a few. In many settings, semiparametric theory leads to (nearly)…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Recently, a new quantum model - two-dimensional generalization of the Scarf II - was completely solved analytically by SUSY method for the integer values of parameter. Now, the same integrable model, but with arbitrary values of parameter,…
How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to…
The possible role of quantum effects in transfer of genetic information is studied. It's argued that the nucleotides selection during DNA replication is performed by means of proton tunneling between nucleotide and DNA-polimerase bound by…
We review the higher-order supersymmetric quantum mechanics (H-SUSY QM), which involves differential intertwining operators of order greater than one. The iterations of first-order SUSY transformations are used to derive in a simple way the…
A gauge invariant mathematical formalism based on deformation quantization is outlined to model an $\mathcal{N}=2$ supersymmetric system of a spin $1/2$ charged particle placed in a nocommutative plane under the influence of a vertical…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
In this paper we provide an alternative approach to the works of the physicists S. Cocco and R. Monasson about a model of DNA molecules. The aim is to predict the sequence of bases by mechanical stimulations. The model described by the…