Related papers: Efficiency of DNA replication in the Polymerase Ch…
We develop a diffusion approximation for systems subject to fast random resetting by small amplitudes. Equivalently, this describes systems with frequent but small catastrophes. We demonstrate the validity of the approximation by computing…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
A density-dependent branching process is a particle system in which individuals reproduce independently, but in a way that depends on the current population size. This feature can model a wide range of ecological interactions at the cost of…
DNA supercoils are generated in genome regulation processes such as transcription and replication, and provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and…
Does quantum dynamics play a role in DNA replication? What type of tests would reveal that? Some statistical checks that distinguish classical and quantum dynamics in DNA replication are proposed.
An important problem of reconstruction of diffusion network and transmission probabilities from the data has attracted a considerable attention in the past several years. A number of recent papers introduced efficient algorithms for the…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
Reaction dynamics involving subdiffusive species is an interesting topic with only few known results, especially when the motion of different species is characterized by different anomalous diffusion exponents. Here we study the reaction…
Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then `unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
We study a variation of the trapping reaction, A+B->A, in which both the traps (A) and the particles (B) undergo diffusion, and the traps upon meeting react according to A+A->0 or A. This two-species reaction-diffusion system is known to…
Aim of this note is to analyse branching Brownian motion within the class of models introduced in the recent paper [4] and called chemical diffusion master equations. These models provide a description for the probabilistic evolution of…
The opening of the Y-fork - the first step of DNA replication - is shown to be a critical phenomenon under an external force at one of its ends. From the results of an equivalent delocalization in a non-hermitian quantum-mechanics problem…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
The step-growth polymerisation of a mixture of arbitrary-functional monomers is viewed as a time-continuos random graph process with degree bounds that are not necessarily the same for different vertices. The sequence of degree bounds acts…
Replicability analysis aims to identify the findings that replicated across independent studies that examine the same features. We provide powerful novel replicability analysis procedures for two studies for FWER and for FDR control on the…
A theory of diffusion-controlled intramolecular reactions of polymer chain in dilute solution is formulated. Our model is based on the widely used diffusion-reaction formalism of Wilemski and Fixman (J. Chem. Phys. 60, 866 (1974). Our model…
We replicate a renewal process at random times, which is equivalent to nesting two renewal processes, or considering a renewal process subject to stochastic resetting. We investigate the consequences on the statistical properties of the…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…