Related papers: Statistical Mechanics of DNA Mutation using SUSY Q…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
By exploiting the supersymmetric invariant restrictions on the chiral and anti-chiral supervariables, we derive the off-shell nilpotent symmetry transformations for a specific (0 + 1)-dimensional N = 2 supersymmetric quantum mechanical…
We study the large deviations of additive quantities, such as energy or current, in stochastic processes with intermittent reset. Via a mapping from a discrete-time reset process to the Poland-Scheraga model for DNA denaturation, we derive…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
We apply the quantum-mechanics bootstrap to supersymmetric quantum mechanics (SUSY QM) and to its matrix relative, the Marinari-Parisi model, which is conjectured to describe the worldvolume of unstable $D0$ branes. Using positivity of…
In this paper, we analyze Gaussian processes using statistical mechanics. Although the input is originally multidimensional, we simplify our model by considering the input as one-dimensional for statistical mechanical analysis. Furthermore,…
We argue that the freezing transition scenario, previously explored in the statistical mechanics of 1/f-noise random energy models, also determines the value distribution of the maximum of the modulus of the characteristic polynomials of…
We make a detailed study of the first and second-order SUSY partners of a one-dimensional free Hamiltonian with a singular perturbation proportional to a Dirac delta function. It is shown that the second-order transformations increase the…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
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…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The confluent SUSY QM usually involves a second-order SUSY transformation where the two factorization energies converge to a single value. In order to achieve it, one generally needs to solve an indefinite integral, which limits the actual…
Stochastic quantization provides an alternate approach to the computation of quantum observables, by stochastically sampling phase space in a path integral. Furthermore, the stochastic variational method can provide analytical control over…
The strength of the spin-orbit interaction relevant to transport in a low dimensional structure depends critically on the relative geometrical arrangement of current carrying orbitals. Recent tight-binding orbital models for spin transport…
We describe a faster and more accurate algorithm for computing the statistical mechanics of DNA denaturation according to the Poland-Scheraga type. Nearest neighbor thermodynamics is included in a complete and general way. The algorithm…
Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases,…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
Search for SUSY in HEP is of enormous interest for the past few decades. Continuous searches were conducted at LHC regarding SUSY for prompt, non-prompt, R-parity conserving and violating generation and decays. The limits obtained from…