Simulation of a semiflexible polymer in a narrow cylindrical pore

The probability that a randomly accelerated particle in two dimensions has not yet left a simply connected domain ${\cal A}$ after a time $t$ decays as $e^{-E_0t}$ for long times. The same quantity $E_0$ also determines the confinement free energy per unit length $\Delta f=k_BT\thinspace E_0$ of a semiflexible polymer in a narrow cylindrical pore with cross section ${\cal A}$. From simulations of a randomly accelerated particle we estimate the universal amplitude of $\Delta f$ for both circular and rectangular cross sections.Comment: 10 pages, 2 eps figure

A closed form for the electrostatic interaction between two rod-like charged objects

We have calculated the electrostatic interaction between two rod-like charged objects with arbitrary orientations in three dimensions. we obtained a closed form formula expressing the interaction energy in terms of the separation distance between the centers of the two rod-like objects, $r$, their lengths (denoted by $2l_1$ and $2l_2$), and their relative orientations (indicated by $\theta$ and $\phi$). When the objects have the same length ($2l_1=2l_2=l$), for particular values of separations, i.e for $r\leq0.8 l$, two types of minimum are appeared in the interaction energy with respect to $\theta$. By employing the closed form formula and introducing a scaled temperature $t$, we have also studied the thermodynamic properties of a one dimensional system of rod-like charged objects. For different separation distances, the dependence of the specific heat of the system to the scaled temperature has been studied. It is found that for $r<0.8 l$, the specific heat has a maximum.Comment: 10 pages, 9 figures, 1 table, Accepted by J. Phys.: Condens. Matte

Forces During Bacteriophage DNA Packaging and Ejection

The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a beneficiary of these experimental techniques is the study of viruses. In this paper we describe how the insights obtained from such experiments can be utilized to construct physical models of processes in the viral life cycle. We focus on dsDNA bacteriophages and show that the bending elasticity of DNA and its electrostatics in solution can be combined to determine the forces experienced during packaging and ejection of the viral genome. Furthermore, we quantitatively analyze the effect of fluid viscosity and capsid expansion on the forces experienced during packaging. Finally, we present a model for DNA ejection from bacteriophages based on the hypothesis that the energy stored in the tightly packed genome within the capsid leads to its forceful ejection. The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure

Controlled DNA compaction within chromatin: the tail-bridging effect

We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation can be controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte