Related papers: Moving breathers in bent DNA with realistic parame…
A growing body of literature examines the effects of superdiffusive subballistic movement pre-measurement (ageing or time lag) on observations arising from single-particle tracking. A neglected aspect is the finite lifetime of these…
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…
By means of the Brownian dynamics (BD) method of simulations we have developed, we study dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE), focusing on the relevance of the `defect' concept due to de Gennes in…
The existence and properties of envelope solitary waves on a periodic, traveling wave background, called traveling breathers, are investigated numerically in representative nonlocal dispersive media. Using a fixed point computational…
We report on a theoretical study of point mutations effects on charge transfer properties in the DNA sequence of the tumor-suppressor p53 gene. On the basis of effective single-strand or double-strand tight-binding models which simulate…
The sampling of the configuration space in diffusion Monte Carlo (DMC) is done using walkers moving randomly. In a previous work on the Hubbard model [\href{https://doi.org/10.1103/PhysRevB.60.2299}{Assaraf et al.~Phys.~Rev.~B \textbf{60},…
We study the properties of discrete breathers, also known as intrinsic localized modes, in the one-dimensional Frenkel-Kontorova lattice of oscillators subject to damping and external force. The system is studied in the whole range of…
The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the…
We introduce a model for translational molecular motors to demonstrate that a multivalent catalytic walker with flexible, uncoordinated legs can transform the free energy of surface-bound substrate sites into mechanical work and undergo…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
We probe the electrostatic cost associated with the approach phase of DNA translocation events. Within an analytical theory at the Debye-Huckel level, we calculate the electrostatic free energy of a rigid DNA molecule interacting with a…
We study the motion of long polymers (eg DNA) in a gel under the influence of an external force acting locally on small segments of the polymer. In particular, we examine the dependence of the drift velocity on the position where the force…
Nanoscale molecular systems such as DNA require an atomistic quantum treatment to accurately capture their electrical properties, owing to their small dimensions. A central challenge in modeling transport through these systems is the…
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature…
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively…
We explore an asymmetric two-fermion Hubbard dimer to test the accuracy of the adiabatic approximation of time-dependent density functional theory in modelling time-resolved charge transfer. We show that the model shares essential features…
Quantum transport for DNA conduction has widely studied with interest in application as a candidate in making nanowires as well as interest in the scientific mechanism. In this paper, we review recent works with concerning the electronic…
Numerous experiments on charge transfer in DNA yield a contradictory picture of the transfer: on the one hand they suggest that it is a very slow process and the charge is almost completely localized on one Watson-Crick pair, but on the…