Related papers: Statistical Mechanics of DNA Mutation using SUSY Q…
The iteration procedure of supersymmetric transformations for the two-dimensional Schroedinger operator is implemented by means of the matrix form of factorization in terms of matrix 2x2 supercharges. Two different types of iterations are…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we…
We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and…
We present a statistical mechanical model of aggregation in colloidal systems with DNA mediated interactions. We obtain a general result for the two-particle binding energy in terms of the hybridization free energy $\Delta G$ of DNA and two…
For the DNA denaturation transition in the presence of random contact energies, or equivalently the disordered wetting transition, we introduce a Strong Disorder Renewal Approach to construct the optimal contacts in each disordered sample…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
The Transfer-Integral (TI) operator is a powerful method to investigate the statistical physics of 1-dimensional models, like those used to describe DNA denaturation. At the cost of a certain number of approximations, the TI equation can be…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
A model for the information transfer from DNA to protein using quantum information and computation techniques is presented. DNA is modeled as the sender and proteins are modeled as the receiver of this information. On the DNA side, a…
We construct a double degenerate supersymmetry in one dimensional quantum mechanics. Here the energy levels satisfy the conditions $E_{0,1}^{((-)}=0$ and $E_{n,n+1}^{(+)}=E_{n+2,n+3}^{(-)}$.The corresponding SUSY Hamiltonians$(H^{(\pm)}$)…
We give the classification of second-order polynomial SUSY Quantum Mechanics in one and two dimensions. The particular attention is paid to the irreducible supercharges which cannot be built by repetition of ordinary Darboux…
Two-dimensional quantum models which obey the property of shape invariance are built in the framework of polynomial two-dimensional SUSY Quantum Mechanics. They are obtained using the expressions for known one-dimensional shape invariant…
Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
The asymptotic behaviour of the superpotential of general SUSY transformations for a coupled-channel Hamiltonian with different thresholds is analyzed. It is shown that asymptotically the superpotential can tend to a diagonal matrix with an…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…
It is shown by analyzing the $1D$ Schr\"odinger equation that discontinuities in the coupling constant can occur in both the energies and the eigenfunctions. Surprisingly, those discontinuities, which are present in the energies {\it…