37 research outputs found
Knots in Charged Polymers
The interplay of topological constraints and Coulomb interactions in static
and dynamic properties of charged polymers is investigated by numerical
simulations and scaling arguments. In the absence of screening, the long-range
interaction localizes irreducible topological constraints into tight molecular
knots, while composite constraints are factored and separated. Even when the
forces are screened, tight knots may survive as local (or even global)
equilibria, as long as the overall rigidity of the polymer is dominated by the
Coulomb interactions. As entanglements involving tight knots are not easy to
eliminate, their presence greatly influences the relaxation times of the
system. In particular, we find that tight knots in open polymers are removed by
diffusion along the chain, rather than by opening up. The knot diffusion
coefficient actually decreases with its charge density, and for highly charged
polymers the knot's position appears frozen.Comment: Revtex4, 9 pages, 9 eps figure
Effective interaction between helical bio-molecules
The effective interaction between two parallel strands of helical
bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using
computer simulations of the "primitive" model of electrolytes. In particular we
study a simple model for B-DNA incorporating explicitly its charge pattern as a
double-helix structure. The effective force and the effective torque exerted
onto the molecules depend on the central distance and on the relative
orientation. The contributions of nonlinear screening by monovalent counterions
to these forces and torques are analyzed and calculated for different salt
concentrations. As a result, we find that the sign of the force depends
sensitively on the relative orientation. For intermolecular distances smaller
than it can be both attractive and repulsive. Furthermore we report a
nonmonotonic behaviour of the effective force for increasing salt
concentration. Both features cannot be described within linear screening
theories. For large distances, on the other hand, the results agree with linear
screening theories provided the charge of the bio-molecules is suitably
renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog