Related papers: Bio-Polymer Hairpin Loops Sustained by Polarons
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We study numerically self-trapped (polaron) states of quasiparticles (electrons, holes or excitons) in a deformable nanotube formed by a hexagonal lattice, wrapped into a cylinder (carbon- and boron nitride-type nanotube structures). We…
Conjugated polymers exhibit unique spin-dependent phenomena arising from weak yet critical hyperfine interactions. Understanding these spin effects, particularly the spin-dependent formation and decay of correlated spin pairs, is important…
Formation of a pseudoknot in the conserved RNA core domain in the ribonucleoprotein human telomerase is required for function. In vitro experiments show that the pseudoknot (PK) is in equilibrium with an extended hairpin (HP) structure. We…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
The behavior of charge carriers in polar materials is governed by electron-phonon interactions, which affect their mobilities via phonon scattering and may localize carriers into self-induced deformation fields, forming self-trapped…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics.…
We provide a unified theory for the high force elasticity of biopolymers solely in terms of the persistence length, $\xi_p$, and the monomer spacing, $a$. When the force $f>\fh \sim k_BT\xi_p/a^2$ the biopolymers behave as Freely Jointed…
We analyze the probability of a single loop formation in a long flexible polymer chain in disordered environment in $d$ dimensions. The structural defects are considered to be correlated on large distances $r$ according to a power law $\sim…
We consider electron(hole)-phonon coupling in crystalline organic semiconductors, using naphthalene for our case study. Employing a first-principles approach, we compute the changes in the self-consistent Kohn-Sham potential corresponding…
Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…
By considering a metal/polymer/metal structure within a tight-binding one-dimensional model, we have investigated the polaron formation in the presence of an electric field. When a sufficient voltage bias is applied to one of the metal…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We…
Polymers are a primary building block in many biomaterials, often interacting with anisotropic backgrounds. While previous studies have considered polymer dynamics within nematic solvents, rarely are the the effects of anisotropic viscosity…
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
Using data from contact maps of the DNA-polymer of $E. Coli$ (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain.…