Related papers: Moving breathers in bent DNA with realistic parame…
Employing the Bethe ansatz approach and numerical simulations of measurements of particles' positions we investigate a post-quench many-body dynamics of attractively interacting bosons on a ring, which in the mean-field approach corresponds…
We illuminate the influence of transition mutations and disorder on charge localization and transfer along B-DNA sequences. Homopolymers are the best for charge transfer (cf. Refs.~ \cite{LVBMS:2018, MLTS:2019}). Hence, we consider as…
Most of the anticancer drugs bind to double-stranded DNA (dsDNA) by intercalative-binding mode. Although experimental studies have become available recently, a molecular-level understanding of the interactions between the drug and dsDNA…
We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site…
Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic…
We study generic aspects of bubble dynamics in DNA under time dependent perturbations, for example temperature change, by mapping the associated Fokker-Planck equation to a quantum time-dependent Schroedinger equation with imaginary time.…
We study kinetics of electrons, scattered by heavy particles undergoing slow diffusive motion. In a three-dimensional space we claim the existence of the crossover region (on the energy axis), which separates the states with fast diffusion…
We investigate the charge transport in synthetic DNA polymers built up from single types of base pairs. In the context of a polaron-like model, for which an electronic tight-binding system and bond vibrations of the double helix are…
We address the relation between long range correlations and charge transfer efficiency in aperiodic artificial or genomic DNA sequences. Coherent charge transfer through the HOMO states of the guanine nucleotide is studied using the…
The Brownian dynamics of a single microorganism coupled by chemotaxis to a diffusing concentration field which is secreted by the microorganism itself is studied by computer simulations in spatial dimensions $d=1,2,3$. Both cases of a…
In this paper, interstitial migration generated by scattering with a mobile breather is investigated numerically in a Frenkel-Kontorova one-dimensional lattice. Consistent with experimental results it is shown that interstitial diffusion is…
We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
Recent research has shown that motile cells can adapt their mode of propulsion depending on the environment in which they find themselves. One mode is swimming by blebbing or other shape changes, and in this paper we analyze a class of…
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…
One-dimensional hopping model is useful to describe the motion of microscopic particle in thermal noise environment, such as motor proteins. Recent experiments about the new generation of light-driven rotary molecular motors found that, the…
The Bose-Hubbard model effectively describes bosons on a lattice with on-site interactions and nearest-neighbour hopping, serving as a foundational framework for understanding strong particle interactions and the superfluid to Mott…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
Motivated by recent experiments on biomimetic membranes exposed to several aqueous phases, we theoretically study the morphology of a membrane in contact with a liquid droplet formed via aqueous phase separation. We concentrate on membranes…
We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that…