Related papers: A Model of Sequence Dependent Protein Diffusion Al…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
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)…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the…
The entire T7 bacteriophage genome contains 39937 base pairs (Database NCBI RefSeq N1001604). Here, electrostatic potential distribution around double helical T7 DNA was calculated by Coulomb method using the computer program of Sorokin…
Proteins often regulate their activities via allostery - or action at a distance - in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins,…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
We theoretically study the transport properties of self-propelled particles on complex structures, such as motor proteins on filament networks. A general master equation formalism is developed to investigate the persistent motion 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…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
We derive exact solutions of simplified models for the temporal evolution of the protein concentration within a cell population arbitrarily far from the stationary state. We show that monitoring the dynamics can assist in modeling and…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
We study the basepairing dynamics of DNA with repetitive sequences where local strand slippage can create, annihilate, and move bulge loops. Using an explicit theoretical model, we find a rich dynamical behavior as a function of an applied…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…