Related papers: Bio-Polymer Hairpin Loops Sustained by Polarons
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
We have considered as a theoretical possibility for the development of a nanobiochip the operation principle of which is based on measuring conductance in single-stranded and double-stranded DNA. Calculations have demonstrated that in the…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
Nanomaterials hold much promise for biological applications, but they require appropriate functionalization to provide biocompatibility in biological environments. For non-covalent functionalization with biocompatible polymers, the polymer…
Exceptionally displaceable ions, evidenced by huge ratios of materials static to high-frequency dielectric constants, enable short-range electron-phonon interactions to stabilize large planar bipolarons. These large bipolarons are compact…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
From the per unit length free energy for DNA under tension, we have calculated an effective contour length dependent persistence length for short DNA. This effective persistence length results from the enhanced fluctuations in short DNA. It…
Entangled ring polymers, along with blends of ring and linear polymers, continue to be a topic of great interest and debate due to the conflicting experimental results in the literature as well as the difficulty of producing entangled…
We study the adsorption of semiflexible polymers such as polyelectrolytes or DNA on planar and curved substrates, e.g., spheres or washboard substrates via short-range potentials using extensive Monte-Carlo simulations, scaling arguments,…
Using analytical approach and Monte-Carlo (MC) simulations, we study the elastic behaviour of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We…
Nanopores in 2D materials are highly desirable for DNA sequencing, yet achieving single-stranded DNA (ssDNA) transport through them is challenging. Using density functional theory calculations and molecular dynamics simulations we show that…
From extensive Monte Carlo simulations of a Larson model of perfectly periodic heteropolymers (PHP) in water a striking stiffening is observed as the period of the alternating hydrophobic and hydrophilic blocks is shortened. At short period…
A simple model is used to analyse published results on large room-temperature diamagnetism for two films of oxidised atactic polypropylene (OAPP) at low magnetic fields. The model involves induced currents expected in circular closed loops…
Polarons, introduced by Davydov to explain energy transport in $\alpha$-helices, correspond to electrons localised on a few lattice sites because of their interaction with phonons. While the static polaron field configurations have been…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…
Dissipative solitons are stable localized coherent structures with linear frequency chirp generated in normal-dispersion mode-locked lasers. The soliton energy in fiber lasers is limited by the Raman effect, but implementation of…
The force-extension relation for a semi-flexible polymer such as DNA confined in a nanoslit is investigated and it is found that both the effective persistence length and the form of the force-extension relation change as the chain goes…
Every smooth closed curve can be represented by a suitable Fourier sum. We show that the ensemble of curves generated by randomly chosen Fourier coefficients with amplitudes inversely proportional to spatial frequency (with a smooth…