Related papers: Moving breathers in bent DNA with realistic parame…
A variety of viruses tightly pack their genetic material into protein capsids that are barely large enough to enclose the genome. In particular, in bacteriophages, forces as high as 60 pN are encountered during packaging and ejection,…
Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the…
We study a model for polaron-like charge transport mechanism along DNA molecules with emphasis on the impact of parametrical and structural disorder. Our model Hamiltonian takes into account the coupling of the charge carrier to two…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
Ultrafast charge transfer processes provide a facile way to create interlayer excitons in directly contacted transition metal dichalcogenide (TMD) layers. More sophisticated heterostructures composed of TMD/hBN/TMD enable new ways to…
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…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
We examine the dynamics of strongly localized periodic solutions (discrete breathers) in two-dimensional array of coupled finite one-dimensional chains of oscillators. Localization patterns with both single and multiple localization sites…
A model for anomalous transport of tracer particles diffusing in complex media in two dimensions is proposed. The model takes into account the characteristics of persistent motion that active bath transfer to the tracer, thus the model…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
We study the mean velocity and diffusion constant in three related models of molecular Brownian ratchets. Brownian ratchets can be used to describe translocation of biopolymers like DNA through nanopores in cells in the presence of…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
Breathing solitons are nonlinear waves in which the energy concentrates in a localized and oscillatory fashion. Similarly to stationary solitons, breathers in dissipative systems can form stable bound states displaying molecule-like…
In this paper we investigate the transport of energetic particles in turbulent plasmas. A numerical approach is used to simulate the effect of the background plasma on the motion of energetic protons. The background plasma is in a…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and 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…
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…
This study examines anomalous diffusion and dynamical phase transitions in a nonlinear bouncer model with short-range interactions leading to velocity-dependent (adiabatic) collisions. By varying a control parameter, transitions between…
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…
The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…