Related papers: Theoretical Models for Tension-Dependent DNA Loopi…
Topological data analysis (TDA) approaches are becoming increasingly popular for studying the dependence patterns in multivariate time series data. In particular, various dependence patterns in brain networks may be linked to specific tasks…
Linear thresholding systems have been used as a model of neural activation and more recently proposed as a model of gene regulation. Here we exhibit linear thresholding systems whose dynamics produce surprisingly long cycles.
We study the non-monotonic force-extension behaviour of helical ribbons using a new model for inextensible elastic strips. Unlike previous rod models our model predicts hysteresis behaviour for low-pitch ribbons of arbitrary material…
DNA minicircles are closed double-stranded DNA (dsDNA) fragments that have been demonstrated to be an important experimental tool to understand supercoiled, or stressed, DNA mechanics, such as nucleosome positioning and DNA-protein…
Measurements of electron transfer rates as well as of charge transport characteristics in DNA produced a number of seemingly contradictory results, ranging from insulating behaviour to the suggestion that DNA is an efficient medium for…
We study the effect of the composition of the genetic sequence on the melting temperature of double stranded DNA, using some simple analytically solvable models proposed in the framework of the wetting problem. We review previous work on…
The macroscopic curvature of double helical DNA induced by regularly repeated adenine tracts is well-known but still puzzling. Its physical origin remains controversial even though it is perhaps the best-documented sequence modulation of…
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…
Single-molecule force-extension experiments have allowed quantitative measurements of the mechanical responses of biomolecules to applied forces explaining their roles in key biological functions. Electrophoretic stretching of charged…
We apply the time-dependent local-spin-density approximation as general theory to describe ground states and spin-density oscillations in the linear response regime of two-dimensional nanostructures of arbitrary shape. For this purpose, a…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
Charge diffusion through desoxyribonucleic acid (DNA) is a physico-chemical phenomenon that on the one hand is being explored for technological purposes, on the other hand is applied by nature for various informational processes in life.…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
Transcriptional pulsing has been observed in both prokaryotes and eukaryotes and plays a crucial role in cell to cell variability of protein and mRNA numbers. The issue is how the time constants associated with episodes of transcriptional…
We simulate the nonlinear dynamic responses in Kirchhoff rod by including the important effects due to inertia and kinematic coupling of tension and torsion. We begin by reviewing a dynamic rod model of a strand (length of cable or DNA) in…
Recent ultrafast experiments have implicated that intrachain base-stacking rather than base-pairing mediate the fate and transport of photoexcited species in DNA chains. Here use an $SU(2)\otimes SU(2)$ lattice model which incorporates both…
It is a standard exercise in mechanical engineering to infer the external forces and torques on a body from its static shape and known elastic properties. Here we apply this kind of analysis to distorted double-helical DNA in complexes with…
Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living…