Related papers: Excluded Volume Effects in Gene Stretching
We extend and develop our previous work on the evolution of a network of cosmic strings. The new treatment is based on an analysis of the probability distribution of the end-to-end distance of a randomly chosen segment of left-moving string…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…
We study a matrix model of RNA in which an external perturbation acts on n nucleotides of the polymer chain. The effect of the perturbation appears in the exponential generating function of the partition function as a factor…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
We investigate the finite-size origin of the emission linewidth of a spatially-extended, one-dimensional non-equilibrium condensate. We show that the well-known Schawlow-Townes scaling of laser theory, possibly including the Henry…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force $F_c(T)$ is found to depend on the potential parameters $k$, represents the…
Numerical simulations are important when assessing the many characteristics of field emission related phenomena. In small simulation domains, the electrostatic effect from the boundaries is known to influence the calculated apex field…
We study unzipping of a complementary RNA-DNA helix applied to an external force, focusing on the force-force correlations. While at the microscopic level these are given by the sequence, the experiment measures effective, macroscopic…
We have applied density-functional theory (DFT) based calculations to investigate the size and strain effects on the electronic properties, such as band structures, energy gaps, and effective masses of the electron and the hole, in Si…
The extensional rheology of polymeric liquids has been extensively examined through experiments and theoretical predictions. However, a systematic study of the extensional rheology of polymer solutions in the semidilute regime, in terms of…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
We investigate the time evolution of the heteropolymer model introduced by Iori, Marinari and Parisi to describe some of the features of protein folding mechanisms. We study how the (folded) shape of the chain evolves in time. We find that…
We develop a strong stretching approximation for a polymer brush made of self-avoiding polymer chains. The density profile of the brush and the distribution of the end monomer positions in stretching direction are computed and compared with…
Molecular weight dependence of excluded volume effects is examined. The swollen-to-unperturbed coil transition point shifts to lower concentration range with increasing molecular weight (Mw). It is shown that in the limit of the infinite…
The conformational and dynamical properties of active ring polymers are studied by numerical simulations. The two-dimensionally confined polymer is modeled as a closed bead-spring chain, driven by tangential forces, put in contact with a…
In general, cellular phenotypes, as measured by concentrations of cellular components, involve large degrees of freedom. However, recent measurement has demonstrated that phenotypic changes resulting from adaptation and evolution in…
We investigate asymptotic properties of long polymers grafted to convex cylindrical and spherical surfaces, and, in particular, distribution of chain free ends. The parabolic potential profile, predicted for flat and concave brushes, fails…
We discuss the scaling properties of free branched polymers. The scaling behaviour of the model is classified by the Hausdorff dimensions for the internal geometry: d_L and d_H, and for the external one: D_L and D_H. The dimensions d_H and…