Related papers: Bio-Polymer Hairpin Loops Sustained by Polarons

Nanoscale and microscale confinement of biopolymers naturally occurs in cells and has been recently achieved in artificial structures designed for nanotechnological applications. Here, we present an extensive theoretical investigation of…

SnSe is a layered material that currently holds the record for bulk thermoelectric efficiency. The primary determinant of this high efficiency is thought to be the anomalously low thermal conductivity resulting from strong anharmonic…

Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…

Exact diagonalization calculations show a continuous transition from delocalized to small polaron behavior as a function of intersite electron-lattice coupling. A transition, found previously at Hartree-Fock level [Yonemitsu et al., Phys.…

Cilia and flagella are highly conserved slender organelles that exhibit a variety of rhythmic beating patterns from non-planar cone-like motions to planar wave-like deformations. Although their internal structure, composed of a…

We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are…

While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…

We propose a model Hamiltonian for describing charge transport through short homogeneous double stranded DNA molecules. We show that the hybridization of the overlapping pi orbitals in the base-pair stack coupled to the backbone is…

Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally…

We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…

A single electron in one dimensional lattice is considered within the framework of extended Holstein model at strong-coupling limit. Disordered density-displacement type electron-phonon interaction is proposed. Basic parameters of small…

Polaron and bipolaron formation in the Holstein-Hubbard model with harmonic confinement potential, relevant to quantum dot structures, is investigated in one to three dimensions by means of unbiased quantum Monte Carlo simulations. The…

The nanoscale fluctuation dynamics of semi dilute high molecular weight polymer solutions of Polyethylenoxide (PEO) in D2O under non-equilibrium flow conditions were studied by the neutron spin-echo technique. The sample cell was in…

The formation of a polaron quasiparticle from a bare electron is studied in the framework of the Holstein model of electron-phonon coupling. Using Schr\"{o}dinger's formalism, we calculate the time evolution of the distribution of the…

The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…

We present a simple model which describes elastic response of single-stranded DNA (ssDNA) to stretching, including the regime of very high force (up to 1000 pN). ssDNA is modelled as a discreet persistent chain, whose ground state is a…

We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness of the molecular setup moderately…

We study the dynamics of a double-stranded DNA (dsDNA) segment, as a semiflexible polymer, in a shear flow, the strength of which is customarily expressed in terms of the dimensionless Weissenberg number Wi. Polymer chains in shear flows…

We study a model of "elastic" lattice polymer in which a fixed number of monomers $m$ is hosted by a self-avoiding walk with fluctuating length $l$. We show that the stored length density $\rho_m = 1 - <l>/m$ scales asymptotically for large…

We establish a macroscopic description of the splay--density coupling in semiflexible main-chain nematic polymers with hairpins, using a vectorial continuity constraint for the "recovered" polar order of the chain tangents and introducing…