arXiv subjects

EJ Janse van Rensburg

Publications and source records attributed to EJ Janse van Rensburg.

32 records · Page 2Linked to original sources

arXiv2019

Adsorbed self-avoiding walks pulled at an interior vertex

We consider self-avoiding walks terminally attached to a surface at which they can adsorb. A force is applied, normal to the surface, to desorb the walk and we investigate how the behaviour depends on the vertex of the walk at which the force is applied. We use rigorous arguments to map out some features of the phase diagram, including bounds on the locations of some phase boundaries, and we use Monte Carlo methods to make quantitative predictions about the locations of these boundaries and the nature of the various phase transitions.

cond-mat.stat-mech↗

arXiv2019

The free energy of compressed lattice knots

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.

cond-mat.stat-mech↗

arXiv2019

Osmotic pressure of compressed lattice knots

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.

cond-mat.soft↗

arXiv2018

Force-induced desorption of uniform branched polymers

We analyze the phase diagrams of self-avoiding walk models of uniform branched polymers adsorbed at a surface and subject to an externally applied vertical pulling force which, at critical values, desorbs the polymer. In particular, models of adsorbed branched polymers with homeomorphism types stars, tadpoles, dumbbells and combs are examined. These models generalize earlier results on linear, ring and $3$-star polymers. In the case of star polymers we confirm a phase diagram with four phases (a free, an adsorbed, a ballistic, and a mixed phase) first seen in the paper by Janse van Rensburg EJ and Whittington SG 2018 J. Phys. A: Math. Theor. 51 204001 for $3$-star polymers. The phase diagram of tadpoles may include four phases (including a mixed phase) if the tadpole is pulled from the adsorbing surface by the end vertex of its tail. If it is instead pulled from the middle vertex of its head, then there are only three phases (the mixed phase is absent). For a dumbbell pulled from the middle vertex of a ring, there are only three phases. For combs with $t$ teeth there are four phases, independent of the value of $t$ for all $t \ge 1$.

cond-mat.stat-mech↗

arXiv2018

Osmotic Pressure of Confined Square Lattice Self-Avoiding Walks

Flory-Huggins theory is a mean field theory for modelling the free energy of dense polymer solutions and polymer melts. In this paper we use Flory-Huggins theory as a model of a dense two dimensional self-avoiding walk confined to a square in the square lattice. The theory describes the free energy of the walk well, and we estimate the Flory interaction parameter of the walk to be $χ_{saw} = 0.32(1)$.

cond-mat.stat-mech↗

arXiv2018

Force-induced desorption of $3$-star polymers: a self-avoiding walk model

We consider a simple cubic lattice self-avoiding walk model of 3-star polymers adsorbed at a surface and then desorbed by pulling with an externally applied force. We determine rigorously the free energy of the model in terms of properties of a self-avoiding walk, and show that the phase diagram includes 4 phases, namely a ballistic phase where the extension normal to the surface is linear in the length, an adsorbed phase and a mixed phase, in addition to the free phase where the model is neither adsorbed nor ballistic. In the adsorbed phase all three branches or arms of the star are adsorbed at the surface. In the ballistic phase two arms of the star are pulled into a ballistic phase, while the remaining arm is in a free phase. In the mixed phase two arms in the star are adsorbed while the third arm is ballistic. The phase boundaries separating the ballistic and mixed phases, and the adsorbed and mixed phases, are both first order phase transitions. The presence of the mixed phase is interesting because it doesn't occur for pulled, adsorbed self-avoiding walks. In an atomic force microscopy experiment it would appear as an additional phase transition as a function of force.

cond-mat.stat-mech↗

arXiv2018

Partition function zeros of adsorbing Dyck paths

The zeros of the size-$n$ partition functions for a statistical mechanical model can be used to help understand the critical behaviour of the model as $n\to\infty$. Here we use weighted Dyck paths as a simple model of two-dimensional polymer adsorption, and study the behaviour of the partition function zeros, particularly in the thermodynamic limit. The exact solvability of the model allows for a precise calculation of the locus of the zeros and the way in which an edge-singularity on the positive real axis is formed. We also show that in the limit $n\to\infty$ the zeros converge on a limaçon in the complex plane.

math-ph↗

arXiv2017

Polygons pulled from an adsorbing surface

We consider self-avoiding lattice polygons, in the hypercubic lattice, as a model of a ring polymer adsorbed at a surface and either being desorbed by the action of a force, or pushed towards the surface. We show that, when there is no interaction with the surface, then the response of the polygon to the applied force is identical (in the thermodynamic limit) for two ways in which we apply the force. When the polygon is attracted to the surface then, when the dimension is at least 3, we have a complete characterization of the critical force--temperature curve in terms of the behaviour, (a) when there is no force, and, (b) when there is no surface interaction. For the 2-dimensional case we have upper and lower bounds on the free energy. We use both Monte Carlo and exact enumeration and series analysis methods to investigate the form of the phase diagram in two dimensions. We find evidence for the existence of a \emph{mixed phase} where the free energy depends on the strength of the interaction with the adsorbing line and on the applied force.

cond-mat.stat-mech↗

arXiv2017

Mean Field Analysis of Algorithms for Scale-free Networks in Molecular Biology

The sampling of scale-free networks in Molecular Biology is usually achieved by growing networks from a seed using recursive algorithms with elementary moves which include the addition and deletion of nodes and bonds. These algorithms include the Barabasi-Albert algorithm. Later algorithms, such as the Duplication-Divergence algorithm, the Solé algorithm and the iSite algorithm, were inspired by biological processes underlying the evolution of protein networks, and the networks they produce differ essentially from networks grown by the Barabasi-Albert algorithm. In this paper the mean field analysis of these algorithms is reconsidered, and extended to variant and modified implementations of the algorithms. The degree sequences of scale-free networks decay according to a powerlaw distribution, namely $P(k) \sim k^{-γ}$, where $γ$ is a scaling exponent. We derive mean field expressions for $γ$, and test these by numerical simulations. Generally, good agreement is obtained. We also found that some algorithms do not produce scale-free networks (for example some variant Barabasi-Albert and Solé networks).

physics.soc-ph↗

arXiv2017

Partition and generating function zeros in adsorbing self-avoiding walks

The Lee-Yang theory of adsorbing self-avoiding walks is presented. It is shown that Lee-Yang zeros of the generating function of this model asymptotically accumulate uniformly on a circle in the complex plane, and that Fisher zeros of the partition function distribute in the complex plane such that a positive fraction are located in annular regions centered at the origin. These results are examined in a numerical study of adsorbing self-avoiding walks in the square and cubic lattices. The numerical data are consistent with the rigorous results; for example, Lee-Yang zeros are found to accumulate on a circle in the complex plane and a positive fraction of partition function zeros appear to accumulate on a critical circle. The radial and angular distribution of partition function zeros are also examined and it is found to be consistent with the rigorous results on the Fisher zeros of interacting lattice clusters.

cond-mat.stat-mech↗

arXiv2016

Self-avoiding walks adsorbed at a surface and pulled at their mid-point

We consider a self-avoiding walk on the $d$-dimensional hypercubic lattice, terminally attached to an impenetrable hyperplane at which it can adsorb. When a force is applied the walk can be pulled off the surface and we consider the situation where the force is applied at the middle vertex of the walk. We show that the temperature dependence of the critical force required for desorption differs from the corresponding value when the force is applied at the end-point of the walk. This is of interest in single molecule pulling experiments since it shows that the required force can depend on where the force is applied. We also briefly consider the situation when the force is applied at other interior vertices of the walk.

cond-mat.stat-mech↗

arXiv2016

Self-avoiding walks adsorbed at a surface and subject to a force

We consider self-avoiding walks terminally attached to an impenetrable surface at which they can adsorb. We call the vertices farthest away from this plane the top vertices and we consider applying a force at the plane containing the top vertices. This force can be directed away from the adsorbing surface or towards it. In both cases we prove that the free energy (in the thermodynamic limit) is identical to the free energy when the force is applied at the last vertex. This means that the criterion determining the critical force - temperature curve is identical for the two ways in which the force is applied and the response to pushing the walk is also the same in the two cases.

cond-mat.stat-mech↗

arXiv2015

Self-avoiding walks subject to a force

We prove some theorems about self-avoiding walks attached to an impenetrable surface (i.e. positive walks) and subject to a force. Specifically we show the force dependence of the free energy is identical when the force is applied at the last vertex or at the top (confining) plane. We discuss the relevance of this result to numerical results and to a recent result about convergence rates when the walk is being pushed towards the surface.

cond-mat.stat-mech↗

arXiv2014

The entropic pressure of lattice knots

The entropic pressure in the vicinity of a cubic lattice knot is examined as a model of the entropic pressure near a knotted ring polymer in a good solvent. A model for the scaling of the pressure is developed and this is tested numerically by sampling lattice knots using a Monte Carlo algorithm. Good agreement is found between scaling predictions and numerical experiments.

cond-mat.stat-mech↗