Effective interactions between star polymers

We study numerically the effective pair potential between star polymers with equal arm lengths and equal number $f$ of arms. The simulations were done for the soft core Domb-Joyce model on the simple cubic lattice, to minimize corrections to scaling and to allow for an unlimited number of arms. For the sampling, we used the pruned-enriched Rosenbluth method (PERM). We find that the potential is much less soft than claimed in previous papers, in particular for $f\gg 1$. While we verify the logarithmic divergence of $V(r)$, with $r$ being the distance between the two cores, predicted by Witten and Pincus, we find for $f>20$ that the Mayer function is hardly distinguishable from that for a Gaussian potential.Comment: 5 pages, 5 figure

Dragging a polymer chain into a nanotube and subsequent release

We present a scaling theory and Monte Carlo (MC) simulation results for a flexible polymer chain slowly dragged by one end into a nanotube. We also describe the situation when the completely confined chain is released and gradually leaves the tube. MC simulations were performed for a self-avoiding lattice model with a biased chain growth algorithm, the pruned-enriched Rosenbluth method. The nanotube is a long channel opened at one end and its diameter $D$ is much smaller than the size of the polymer coil in solution. We analyze the following characteristics as functions of the chain end position $x$ inside the tube: the free energy of confinement, the average end-to-end distance, the average number of imprisoned monomers, and the average stretching of the confined part of the chain for various values of $D$ and for the number of monomers in the chain, $N$. We show that when the chain end is dragged by a certain critical distance $x^*$ into the tube, the polymer undergoes a first-order phase transition whereby the remaining free tail is abruptly sucked into the tube. This is accompanied by jumps in the average size, the number of imprisoned segments, and in the average stretching parameter. The critical distance scales as $x^*\sim ND^{1-1/\nu}$. The transition takes place when approximately 3/4 of the chain units are dragged into the tube. The theory presented is based on constructing the Landau free energy as a function of an order parameter that provides a complete description of equilibrium and metastable states. We argue that if the trapped chain is released with all monomers allowed to fluctuate, the reverse process in which the chain leaves the confinement occurs smoothly without any jumps. Finally, we apply the theory to estimate the lifetime of confined DNA in metastable states in nanotubes.Comment: 13pages, 14figure

A review of Monte Carlo simulations of polymers with PERM

In this review, we describe applications of the pruned-enriched Rosenbluth method (PERM), a sequential Monte Carlo algorithm with resampling, to various problems in polymer physics. PERM produces samples according to any given prescribed weight distribution, by growing configurations step by step with controlled bias, and correcting "bad" configurations by "population control". The latter is implemented, in contrast to other population based algorithms like e.g. genetic algorithms, by depth-first recursion which avoids storing all members of the population at the same time in computer memory. The problems we discuss all concern single polymers (with one exception), but under various conditions: Homopolymers in good solvents and at the $\Theta$ point, semi-stiff polymers, polymers in confining geometries, stretched polymers undergoing a forced globule-linear transition, star polymers, bottle brushes, lattice animals as a model for randomly branched polymers, DNA melting, and finally -- as the only system at low temperatures, lattice heteropolymers as simple models for protein folding. PERM is for some of these problems the method of choice, but it can also fail. We discuss how to recognize when a result is reliable, and we discuss also some types of bias that can be crucial in guiding the growth into the right directions.Comment: 29 pages, 26 figures, to be published in J. Stat. Phys. (2011

Sagnac Interferometer Enhanced Particle Tracking in Optical Tweezers

A setup is proposed to enhance tracking of very small particles, by using optical tweezers embedded within a Sagnac interferometer. The achievable signal-to-noise ratio is shown to be enhanced over that for a standard optical tweezers setup. The enhancement factor increases asymptotically as the interferometer visibility approaches 100%, but is capped at a maximum given by the ratio of the trapping field intensity to the detector saturation threshold. For an achievable visibility of 99%, the signal-to-noise ratio is enhanced by a factor of 200, and the minimum trackable particle size is 2.4 times smaller than without the interferometer

Reversible Embedding to Covers Full of Boundaries

In reversible data embedding, to avoid overflow and underflow problem, before data embedding, boundary pixels are recorded as side information, which may be losslessly compressed. The existing algorithms often assume that a natural image has little boundary pixels so that the size of side information is small. Accordingly, a relatively high pure payload could be achieved. However, there actually may exist a lot of boundary pixels in a natural image, implying that, the size of side information could be very large. Therefore, when to directly use the existing algorithms, the pure embedding capacity may be not sufficient. In order to address this problem, in this paper, we present a new and efficient framework to reversible data embedding in images that have lots of boundary pixels. The core idea is to losslessly preprocess boundary pixels so that it can significantly reduce the side information. Experimental results have shown the superiority and applicability of our work

Rational Approximate Symmetries of KdV Equation

We construct one-parameter deformation of the Dorfman Hamiltonian operator for the Riemann hierarchy using the quasi-Miura transformation from topological field theory. In this way, one can get the approximately rational symmetries of KdV equation and then investigate its bi-Hamiltonian structure.Comment: 14 pages, no figure

Spectral Properties of Statistical Mechanics Models

The full spectrum of transfer matrices of the general eight-vertex model on a square lattice is obtained by numerical diagonalization. The eigenvalue spacing distribution and the spectral rigidity are analyzed. In non-integrable regimes we have found eigenvalue repulsion as for the Gaussian orthogonal ensemble in random matrix theory. By contrast, in integrable regimes we have found eigenvalue independence leading to a Poissonian behavior, and, for some points, level clustering. These first examples from classical statistical mechanics suggest that the conjecture of integrability successfully applied to quantum spin systems also holds for classical systems.Comment: 4 pages, 1 Revtex file and 4 postscript figures tarred, gzipped and uuencode

Biostratigraphic and magnetostratigraphic synthesis of the Celebes and Sulu Seas, Leg 124

During ODP Leg 124, late middle Eocene to Quaternary sediment sequences were recovered from 13 holes drilled at five sites in the Celebes and Sulu basins. Paleomagnetic measurements and biostratigraphic studies using calcareous nannofossils, planktonic and benthic foraminifers, radiolarians, and diatoms were completed and summarized here. Two Neogene sediment sections recovered in the Sulu Basin yielded excellent core recoveries and magnetic reversal records, allowing direct magnetobiostratigraphic correlations for the Pliocene and Quaternary at Site 768 and for the middle Miocene to Quaternary at Site 769. The interpolated ages of biohorizons are not consistent between sites and only a few of them are in good agreement with previous calibrations. The differences may be the results of redeposition by turbidity currents and selective dissolution of key fossils

Collapsing lattice animals and lattice trees in two dimensions

We present high statistics simulations of weighted lattice bond animals and lattice trees on the square lattice, with fugacities for each non-bonded contact and for each bond between two neighbouring monomers. The simulations are performed using a newly developed sequential sampling method with resampling, very similar to the pruned-enriched Rosenbluth method (PERM) used for linear chain polymers. We determine with high precision the line of second order transitions from an extended to a collapsed phase in the resulting 2-dimensional phase diagram. This line includes critical bond percolation as a multicritical point, and we verify that this point divides the line into two different universality classes. One of them corresponds to the collapse driven by contacts and includes the collapse of (weakly embeddable) trees, but the other is {\it not yet} bond driven and does not contain the Derrida-Herrmann model as special point. Instead it ends at a multicritical point $P^*$ where a transition line between two collapsed phases (one bond-driven and the other contact-driven) sparks off. The Derrida-Herrmann model is representative for the bond driven collapse, which then forms the fourth universality class on the transition line (collapsing trees, critical percolation, intermediate regime, and Derrida-Herrmann). We obtain very precise estimates for all critical exponents for collapsing trees. It is already harder to estimate the critical exponents for the intermediate regime. Finally, it is very difficult to obtain with our method good estimates of the critical parameters of the Derrida-Herrmann universality class. As regards the bond-driven to contact-driven transition in the collapsed phase, we have some evidence for its existence and rough location, but no precise estimates of critical exponents.Comment: 11 pages, 16 figures, 1 tabl

Quantum limited particle sensing in optical tweezers

Particle sensing in optical tweezers systems provides information on the position, velocity and force of the specimen particles. The conventional quadrant detection scheme is applied ubiquitously in optical tweezers experiments to quantify these parameters. In this paper we show that quadrant detection is non-optimal for particle sensing in optical tweezers and propose an alternative optimal particle sensing scheme based on spatial homodyne detection. A formalism for particle sensing in terms of transverse spatial modes is developed and numerical simulations of the efficacy of both quadrant and spatial homodyne detection are shown. We demonstrate that an order of magnitude improvement in particle sensing sensitivity can be achieved using spatial homodyne over quadrant detection.Comment: Submitted to Biophys