Related papers: Excluded Volume Effects in Gene Stretching
The large momentum expansion for the inverse propagator of the auxiliary field $\lambda(x)$ in the conformally invariant O(N) vector model is calculated to leading order in 1/N, in a strip-like geometry with one finite dimension of length…
This study systematically investigates the effect of stretching boundary conditions, ranging from conservation of cross-sectional area to conservation of volume, on the rupture behavior of phantom star polymer networks using…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
Recent proofs of the convergence of the linear delta expansion in zero and in one dimensions have been limited to the analogue of the vacuum generating functional in field theory. In zero dimensions it was shown that with an appropriate,…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
We explore semi-dilute and concentrated oligomers and polymers in a broad range of polymerization indices N ranging from 1 to a 100 and in a range of monomer number densities $\phi$ from 0.1 to 0.8 via molecular dynamics simulations and…
We study the conformations of polymer chains in a poor solvent, with and without bending rigidity, by means of a simple statistical mechanics model. This model can be exactly solved for chains of length up to N=55 using exact enumeration…
The preceding theory of excluded volume effects is applied to the Daud and coworkers' observations. Based on various researchers' experimental data, it is suggested that the Daud and coworkers' value in the bulk state may be revised from 82…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
Much recent attention has focused on theories with large extra compactified dimensions. However, while the phenomenological implications of the volume moduli associated with such compactifications are well understood, relatively little…
The classical bond-fluctuation model (BFM) is an efficient lattice Monte Carlo algorithm for coarse-grained polymer chains where each monomer occupies exclusively a certain number of lattice sites. In this paper we propose a generalization…
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…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
We show that the simple analytical model proposed by Zhang and Marko (Phys. Rev. E 77, 031916 (2008)) to illustrate Maxwell relations for single-DNA experiments can be improved by including the zero-force entropy of a Gaussian chain. The…
An experimental investigation of the impact of sample inhomogeneity on measurements of the linear elongational viscosity of two low-density polyethelenes is presented. A novel method of in-situ measurements of the diameter of samples under…
The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Large extra dimensions lower the Planck scale to values soon accessible. Motivated by string theory, the models of large extra dimensions predict a vast number of new effects in the energy range of the lowered Planck scale, among them the…