Related papers: DNA uptake into nuclei: Numerical and analytical r…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
A polymer chain confined in nano-scale geometry has been used to investigate the underlying mechanism of Nuclear Pore Complex (NPC), where transport of cargoes is directional. It was shown here that depending on the solvent quality (good or…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
Protein chains of the (FG)$_n$ ($n \simeq$ 300) type cap the cytoplasmatic side of the nucleopore complex, which connects the nucleus to the remainder of an eukaryotic cell. We study the properties of three fundamental polymer models that…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
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…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
Nanopores -- nanosized holes that can transport ions and molecules -- are very promising devices for genomic screening, in particular DNA sequencing. Both solid-state and biological pores suffer from the drawback, however, that the channel…
The capture and translocation of biomolecules through nanometer-scale pores are processes with a potential large number of applications, and hence they have been intensively studied in the recent years. The aim of this paper is to review…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
During the last decade, the laser trapping technique has been actively applied to elucidate the property of macromolecules, DNA, RNA, cytoskeleton fibres, etc. Due to the inherent difficulty in the direct trapping of single molecules at…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…