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Register a new userLattice Knots in a Slab
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Added by
Esaias J Janse van Rensburg
Publication date
2012
fields
Physics
and research's language is
English
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In this paper the number and lengths of minimal length lattice knots confined to slabs of width $L$, is determined. Our data on minimal length verify the results by Sharein et.al. (2011) for the similar problem, expect in a single case, where an improvement is found. From our data we construct two models of grafted knotted ring polymers squeezed between hard walls, or by an external force. In each model, we determine the entropic forces arising when the lattice polygon is squeezed by externally applied forces. The profile of forces and compressibility of several knot types are presented and compared, and in addition, the total work done on the lattice knots when it is squeezed to a minimal state is determined.
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A numerical simulation shows that the osmotic pressure of compressed lattice knots is a function of knot type, and so of entanglements. The osmotic pressure for the unknot goes through a negative minimum at low concentrations, but in the case of non-trivial knot types $3_1$ and $4_1$ it is negative for low concentrations. At high concentrations the osmotic pressure is divergent, as predicted by Flory-Huggins theory. The numerical results show that each knot type has an equilibrium length where the osmotic pressure for monomers to migrate into or our of the lattice knot is zero. Moreover, the lattice unknot is found to have two equilibria, one unstable, and one stable, whereas the lattice knots of type $3_1$ and $4_1$ have one stable equilibrium each.
An extensive study of single block copolymer knots containing two kinds of monomers $A$ and $B$ is presented. The knots are in a solution and their monomers are subjected to short range interactions that can be attractive or repulsive. In view of possible applications in medicine and the construction of intelligent materials, it is shown that several features of copolymer knots can be tuned by changing the monomer configuration. A very fast and abrupt swelling with increasing temperature is obtained in certain multiblock copolymers, while the size and the swelling behavior at high temperatures may be controlled in diblock copolymers. Interesting new effects appear in the thermal diagrams of copolymer knots when their length is increased.
Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible polymers has not been explored much. Here, via extensive replica exchange Monte Carlo simulation we investigate the same for a bead-stick and a bead-spring homopolymer model that covers the whole range from flexible to stiff. We establish the fact that the presence of stable knotted phases in the phase diagram is dependent on the ratio $r_b/r_{rm{min}}$ where $r_b$ is the equilibrium bond length and $r_{rm{min}}$ is the distance for the strongest nonbonded contacts. Our results provide evidence for both models that if the ratio $r_b/r_{rm{min}}$ is outside a small window around unity then depending on the bending stiffness one always encounters stable knotted phases along with the usual frozen and bent-like structures at low temperatures. These findings prompt us to conclude that knots are generic stable phases in semiflexible polymers.
A compressed knotted ring polymer in a confining cavity is modelled by a knotted lattice polygon confined in a cube in ${mathbb Z}^3$. The GAS algorithm [17] is used to sample lattice polygons of fixed knot type in a confining cube and to estimate the free energy of confined lattice knots. Lattice polygons of knot types the unknot, the trefoil knot, and the figure eight knot, are sampled and the free energies are estimated as functions of the concentration of monomers in the confining cube. The data show that the free energy is a function of knot type at low concentrations, and (mean-field) Flory-Huggins theory [12,15] is used to model the free energy as a function of monomer concentration. The Flory interaction parameter of knotted lattice polygons in ${mathbb Z}^3$ is also estimated.
In this study we consider an idealization of a typical optical tweezers experiment involving a semiflexible double-knotted polymer, with steric hindrance and persistence length matching those of dsDNA in high salt concentration, under strong stretching. Using exhaustive Molecular Dynamics simulations we show that not only does a double-knotted dsDNA filament under tension possess a free energy minimum when the two knots are intertwined, but also that the depth of this minimum depends on the relative chirality of the two knots. We rationalize this dependence of the effective interaction on the chirality in terms of a competition between chain entropy and bending energy.
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