Related papers: Protein sliding and hopping kinetics on DNA
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
Relaxation, <Sz(t)>, of the average spin of a carrier in course of hops over sites hosting random hyperfine fields is studied theoretically. In low dimensions, d = 1, 2, the decay of average spin with time is non-exponential at all times.…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
The dynamics of many glassy systems are known to exhibit string-like hopping motions each consisting of a line of particles displacing one and other. By using molecular dynamics simulations of glassy polymers, we show that these motions…
Motivated by a question about the sensitivity of knots' diffusive motion to the actual sequence of nucleotides placed on a given DNA, here we study a simple model of a sequence-reading diffusion on a stretched chain with a frozen sequence…
The crossover from single-file diffusion, where the mean-square displacement scales as <x^2> ~t^(1/2), to normal Fickian diffusion, where <x^2>~t$, is studied as a function of channel width for colloidal particles. By comparing Brownian…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
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…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Motivated by diverse phenomena in cellular biophysics, including bacterial flagellar motion and DNA transcription and replication, we study the overdamped nonlinear dynamics of a rotationally forced filament with twist and bend elasticity.…
We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops--a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation…
The dynamics of steps on crystal surfaces is considered. In general, the meandering of the steps obeys a subdiffusive behaviour. The characteristic asymptotic time laws depend on the microscopic mechanism for detachment and attachment of…
According to the classical theory of Brownian motion, the mean squared displacement of diffusing particles evolves linearly with time whereas the distribution of their displacements is Gaussian. However, recent experiments on mesoscopic…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
The L\'evy walk process with rests is discussed. The jumping time is governed by an $\alpha$-stable distribution with $\alpha>1$ while a waiting time distribution is Poissonian and involves a position-dependent rate which reflects a…
The motility of eukaryotic cells is strongly influenced by their environment, with confined cells often developing qualitatively different motility patterns from those migrating on simple two-dimensional substrates. Recent experiments,…
Cellular responses often require the fast activation or repression of specific genes, which depends on Transcription Factors (TFs) that have to quickly find the promoters of these genes within a large genome. Transcription Factors (TFs)…