Related papers: Bio-Polymer Hairpin Loops Sustained by Polarons
Equilibrium states of a closed semiflexible polymer binding to a cylinder are described. This may be either by confinement or by constriction. Closed completely bound states are labeled by two integers: the number of oscillations, $n$, and…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
We report a single step synthesis of a polyisobutene with a bis-urea moiety in the middle of the chain. In low polarity solvents, this polymer self-assembles by hydrogen bonding to form a combshaped polymer with a central hydrogen bonded…
We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
The formation of polaron and its migration in a DNA chain are studied within a semiclassical Peyrard-Biship-Holstein polaron model. Comparing the energetics of the polaron system found from the quantum chemical and semiclassical…
The Rice-Sneddon model for BaBiO$_3$ is a nice model Hamiltonian for considering the properties of polarons and bipolarons in a three-dimensional oxide crystal. We use exact diagonalization methods on finite samples to study the stability…
Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static, or temporally fluctuating far…
We consider polarons in models of coupled electronic and vibrational degrees of freedom, in the presence of a soft nonlinear inter-particle potential (Morse potential). In particular, we focus on a a bound state of a polaron with a…
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…
The fabrication of hybrid materials consisting of nanoporous hosts with conductive polymers is a challenging task, since the extreme spatial confinement often conflicts with the stringent physico-chemical requirements for polymerization of…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and $B$ represent two different types of base pairs having two- and three-bonds,…
The unique properties of organic semiconductors make them versatile base materials for many applications ranging from light emitting diodes to transistors. The low spin-orbit coupling typical for carbon-based materials and the resulting…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible polymers to…
Following a resurgence of interest in dilute superconductivity in polar semiconductors, we perform a variational calculation to probe the existence of Fr{\"o}hlich bipolarons in these materials. Our solution is capable of interpolating…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
The dynamical behavior of an acoustic polaron in typical non-degenerate conjugated polymer, polydiacetylene, is numerically studied by using Su-Schrieffer-Heeger's model for the one dimensional electron-lattice system. It is confirmed that…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…