Related papers: Electrodynamic forces driving DNA-protein interact…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
Based on generalized quantum Langevin equations for the tight-binding wave function amplitudes and lattice displacements, electron and phonon quantum transport are obtained exactly using molecular dynamics (MD) in the ballistic regime. The…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
We present a theoretical analysis of the environment effects on charge transport in double-stranded synthetic poly(G)-poly(C) DNA molecules attached to two ideal leads. Coupling of the DNA to the environment results in two effects: (i)…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
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 consider voltage-driving DNA translocation through a nanopore in the present study. By assuming the DNA is coaxial with the cylindrical nanopore, a hydrodynamic model for determining effective force on a single DNA molecule in a nanopore…
Strong influence of water molecules on the transport and magnetic properties of DNA, observed in this study, opens up real opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules…
Two models for energy and charge transport and storage in biomolecules are considered. A model based on the discrete nonlinear Schrodinger equation with long-range dispersive interactions (LRI's) between base pairs of DNA is offered for the…
Many-electron wavepacket dynamics based on time-dependent configuration interaction (TDCI) is a numerically rigorous approach to quantitatively model electron-transfer across molecular junctions. TDCI simulations of cyanobenzene…
We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences.…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
We analyze the effects of electron-electron and electron-phonon interactions in the dynamics of a system of two or three electrons that can be trapped to a localized state and detrapped to ab extended band states of a quantum dot using a…
The issue of retarded long-range resonant interactions between two molecules with oscillating dipole moments is reinvestigated within the framework of classical electrodynamics. By taking advantage of a theorem in complex analysis, we…
Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is…
The unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ is studied using Monte Carlo simulations. We obtain the dynamical order parameter, $Q$, defined as…