532 research outputs found
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 after a time decays as
for long times. The same quantity also determines the
confinement free energy per unit length of a
semiflexible polymer in a narrow cylindrical pore with cross section . From simulations of a randomly accelerated particle we estimate the
universal amplitude of 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, , their lengths
(denoted by and ), and their relative orientations (indicated by
and ). When the objects have the same length (),
for particular values of separations, i.e for , two types of
minimum are appeared in the interaction energy with respect to . By
employing the closed form formula and introducing a scaled temperature , 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 , 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
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