Related papers: Bubble propagation in a helicoidal molecular chain
We investigate the dynamics of correlation propagation in the one-dimensional Fermi-Hubbard model with SU($N$) symmetry when the replusive-interaction strength is quenched from a large value, at which the ground state is a Mott-insulator…
The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the…
The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
We explore breather propagation in the damped oscillatory chain with essentially nonlinear (non-linearizable) nearest-neighbour coupling. Combination of the damping and the substantially nonlinear coupling leads to rather unusual two-stage…
We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the…
After photo-excitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we…
We developed a low-energy model that can be used at any time to describe the dynamics of DNA bubbles at temperatures below the melting point. The Schr\"odinger equation associated with this problem is solved in imaginary time with a quantum…
The conformational behavior of a giant DNA mediated by condensing agents in the bulk solution has been investigated through experimental and theoretical approaches. Experimentally, a pronounced conformational hysteresis is observed for…
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
We study the size fluctuations of a local denaturation zone in a DNA molecule in the presence of proteins that selectively bind to single-stranded DNA, based on a (2+1)-dimensional master equation. By tuning the physical parameters we can…
We study the nonlinear dynamics of a completely inhomogeneous DNA chain which is governed by a perturbed sine-Gordon equation. A multiple scale perturbation analysis provides perturbed kink-antikink solitons to represent open state…
Motivated by a question about the sensitivity of knots' diffusive motion to the actual sequence of nucleotides placed on a given DNA, here we study a simple model of a sequence-reading diffusion on a stretched chain with a frozen sequence…
Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…