Related papers: Excluded Volume Effects in Gene Stretching
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…
We study thin films with residual strain by analyzing the $\Gamma-$limit of non-Euclidean elastic energy functionals as the material's thickness tends to $0.$ We begin by extending prior results \cite{bhattacharya2016plates}…
Linear viscoelastic properties for a dilute polymer solution are predicted by modeling the solution as a suspension of non-interacting bead-spring chains. The present model, unlike the Rouse model, can describe the solution's rheological…
We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force…
We discuss the quantitative consequences of the resummation of the small-x contributions to the anomalous dimensions beyond next-to-leading order in alpha_s and up to next order in ln(1/x) (NLx) in a framework based on the renormalization…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
To investigate the structural dynamics of the homology pairing of polymers, we mod- eled the scenario of homologous chromosome pairings during meiosis in Schizosaccharomyces pombe, one of the simplest model organisms of eukaryotes. We…
We use nonequilibrium molecular dynamics simulations to verify recent tube-model predictions that associative polymer networks exhibit broad stretch fluctuations during elongational flow. Simulations further show that these fluctuating…
We discuss how compactified extra dimensions may have potentially observable effects which grow as the compactification scale decreases. This arises because of lightcone fluctuations in the uncompactified dimensions which can result in the…
Motivated by recent single molecule studies of proteins sliding on a DNA molecule, we explore the targeting dynamics of N particles ("proteins") sliding diffusively along a line ("DNA") in search of their target site (specific target…
It has been shown in [1] that a class of restricted spin foam models can feature a reduced spectral dimension of space-time. However, it is still an open question how curvature affects the flow of the spectral dimension. To answer this…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
The effects of extra dimensions on gauge coupling unification is studied. We start with a comparison between power law running of the gauge couplings in models with extra dimensions and logarithmic running that happens in many realistic…
We propose a new geometry and/or topology of a single extra dimension whose Kaluza-Klein excitations do appear at much higher scale than the inverse of the length/volume. For a single extra dimenion with volume $N\pi\rho$ which is made of N…
Gene expression via transcription-translation is the most fundamental reaction to sustain biological systems, and complex reactions such as this one occur in a small compartment of living cells. There is increasing evidence that t physical…
In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand,…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
A dilute polymer solution is modeled as a suspension of non-interacting Hookean dumbbells and the effect of excluded volume is taken into account by incorporating a narrow Gaussian repulsive potential between the beads of each dumbbell. The…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed…