Related papers: Multiple timescales in a model for DNA denaturatio…
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…
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…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
We present detailed molecular dynamics results for the displacement autocorrelation spectra of the Peyrard-Bishop model of thermal DNA denaturation. As the phase transition is approached, the spectra depend on whether the wavelength is…
A discrete nonlinear Schrodinger (NLS) model with long-range dispersive interactions describing the dynamical structure of DNA is proposed. Dispersive interactions of two types: the power dependence $r^{-s}$ and the exponential dependence…
We study the unzipping of a double stranded DNA (dsDNA) by applying an external force on a single strand while leaving the other strand free. We find that the dsDNA can be unzipped to two single strands if the external force exceeds a…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
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…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
In Ref. [1] the author has recently established sharp large deviation principles for cumulative rewards associated with a discrete-time renewal model, supposing that each renewal involves a broad-sense reward taking values in a separable…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…
Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to…
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…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
Two-time correlations are a crucial tool to probe the dynamics of many-body systems. We use these correlation functions to study the dynamics of dissipative quantum systems. Extending the adiabatic elimination method, we show that the…