Related papers: Visualizing Poloidal Orientation in DNA Minicircle…
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…
The dynamics of polymer translocation through a pore has been the subject of recent theoretical and experimental works. We have considered theoretical estimates and performed computer simulations to understand the mechanism of DNA uptake…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
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…
Using Brownian dynamics simulations, we investigate the dynamics of colloids confined in two-dimensional narrow channels driven by a non-uniform force F(y). We considered linear-gradient, parabolic and delta-like driving-force profiles.…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Freezing of charged colloids on square or triangular two-dimensional periodic substrates has been recently shown to realize a rich variety of orientational orders. We propose a theoretical framework to analyze the corresponding structures.…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation…
The chirality-induced spin selectivity (CISS), demonstrated in diverse chiral molecules by numerous experimental and theoretical groups, has been attracting extensive and ongoing interest in recent years. As the secondary structure of DNA,…
In this short note, a correction is made to the recently proposed solution [1] to a 1D biased diffusion model for linear DNA translocation and a new analysis will be given to the data in [1]. It was pointed out [2] by us recently that this…
DNA in sperm cells must undergo an extreme compaction to almost crystalline packing levels. To produce this dense packing, DNA is condensed by protamine, a positively charged protein that loops the DNA into a toroid. Our goal is to…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
Suspensions of anisotropic Brownian particles are commonly encountered in a wide array of applications such as drug delivery and manufacturing of fiber-reinforced composites. Technological applications and fundamental studies of small…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In…
Colloids self-assemble into various organized superstructures determined by particle interactions. There is a tremendous progress in both the scientific understanding and applications of self-assemblies of single-type identical particles.…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
The bias-dependent transport properties of short poly(G)-poly(C) A-DNA strands attached to Au electrodes are investigated with first principles electronic transport methods. By using the non- equilibrium Green's function approach combined…