Related papers: DNA looping provides stability and robustness to t…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
Mixed feedback loops combining transcriptional and post-transcriptional regulations are common in cellular regulatory networks. They consist of two genes, encoding a transcription factor and a small non-coding RNA (sRNA), which mutually…
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…
Molecular noise in gene regulatory networks has two intrinsic components, one part being due to fluctuations caused by the birth and death of protein or mRNA molecules which are often present in small numbers and the other part arising from…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
Positive feedback and cooperativity in the regulation of gene expression are generally considered to be necessary for obtaining bistable expression states. Recently, a novel mechanism of bistability termed emergent bistability has been…
Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and trade-offs of DNA-based storage systems by introducing a new channel model, which we…
We consider a high-$Q$ Duffing oscillator in a weakly non-linear regime with the driving frequency $\sigma$ varying in time between $\sigma_i$ and $\sigma_f$ at a characteristic rate $r$. We found that the frequency sweep can cause…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
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…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
Cell-fate transition can be modeled by ordinary differential equations (ODEs) which describe the behavior of several molecules in interaction, and for which each stable equilibrium corresponds to a possible phenotype (or 'biological…
Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…
This paper is concerned with the problem of robust reliable control for a class of uncertain 2D discrete switched systems with state delays represented by a model of Roesser type. The parameter uncertainties are assumed to be norm-bounded.…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
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…
We analyze the stability and bifurcation structure of steady states in a mechanochemical model of pattern formation in regenerating tissue spheroids. The model couples morphogen dynamics with tissue mechanics via a positive feedback loop:…