On the orientational ordering of long rods on a lattice

We argue that a system of straight rigid rods of length k on square lattice with only hard-core interactions shows two phase transitions as a function of density, rho, for k >= 7. The system undergoes a phase transition from the low-density disordered phase to a nematic phase as rho is increased from 0, at rho = rho_c1, and then again undergoes a reentrant phase transition from the nematic phase to a disordered phase at rho = rho_c2 < 1.Comment: epl.cl

Two-State Migration of DNA in a structured Microchannel

DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In particular, the experimentally observed migration order of Lambda- and T2-DNA molecules is reproduced by the simulations. The simulation data indicate that the mobility may depend on the chain length in a nonmonotonic way at high electric fields. This is found to be the signature of a nonequilibrium phase transition between two different migration states, a slow one and a fast one, which can also be observed experimentally under appropriate conditions.Comment: Revised edition corresponding to the comments by the referees, submitted to Physical Review

Phase Transitions of Single Semi-stiff Polymer Chains

We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth Method" (PERM). It is very efficient both for relatively open configurations at high temperatures and for compact and frozen-in low-T states. This allows us to study in detail the phase diagram as a function of nn-attraction epsilon and stiffness x. It shows a theta-collapse line with a transition from open coils to molten compact globules (large epsilon) and a freezing transition toward a state with orientational global order (large stiffness x). Qualitatively this is similar to a recently studied mean field theory (Doniach et al. (1996), J. Chem. Phys. 105, 1601), but there are important differences. In contrast to the mean field theory, the theta-temperature increases with stiffness x. The freezing temperature increases even faster, and reaches the theta-line at a finite value of x. For even stiffer chains, the freezing transition takes place directly without the formation of an intermediate globule state. Although being in contrast with mean filed theory, the latter has been conjectured already by Doniach et al. on the basis of low statistics Monte Carlo simulations. Finally, we discuss the relevance of the present model as a very crude model for protein folding.Comment: 11 pages, Latex, 8 figure

Structure Function of Polymer Nematic Liquid Crystals: A Monte Carlo Simulation

We present a Monte Carlo simulation of a polymer nematic for varying volume fractions, concentrating on the structure function of the sample. We achieve nematic ordering with stiff polymers made of spherical monomers that would otherwise not form a nematic state. Our results are in good qualitative agreement with theoretical and experimental predictions, most notably the bowtie pattern in the static structure function.Comment: 10 pages, plain TeX, macros included, 3 figures available from archive. Published versio

Interacting Crumpled Manifolds: Exact Results to all Orders of Perturbation Theory

In this letter, we report progress on the field theory of polymerized tethered membranes. For the toy-model of a manifold repelled by a single point, we are able to sum the perturbation expansion in the strength g of the interaction exactly in the limit of internal dimension D -> 2. This exact solution is the starting point for an expansion in 2-D, which aims at connecting to the well studied case of polymers (D=1). We here give results to order (2-D)^4, where again all orders in g are resummed. This is a first step towards a more complete solution of the self-avoiding manifold problem, which might also prove valuable for polymers.Comment: 8 page

Anomalous Dynamics of Translocation

We study the dynamics of the passage of a polymer through a membrane pore (translocation), focusing on the scaling properties with the number of monomers $N$. The natural coordinate for translocation is the number of monomers on one side of the hole at a given time. Commonly used models which assume Brownian dynamics for this variable predict a mean (unforced) passage time $\tau$ that scales as $N^2$, even in the presence of an entropic barrier. However, the time it takes for a free polymer to diffuse a distance of the order of its radius by Rouse dynamics scales with an exponent larger than 2, and this should provide a lower bound to the translocation time. To resolve this discrepancy, we perform numerical simulations with Rouse dynamics for both phantom (in space dimensions $d=1$ and 2), and self-avoiding (in $d=2$) chains. The results indicate that for large $N$, translocation times scale in the same manner as diffusion times, but with a larger prefactor that depends on the size of the hole. Such scaling implies anomalous dynamics for the translocation process. In particular, the fluctuations in the monomer number at the hole are predicted to be non-diffusive at short times, while the average pulling velocity of the polymer in the presence of a chemical potential difference is predicted to depend on $N$.Comment: 9 pages, 9 figures. Submitted to Physical Review

P-Band Induced Self-Organization and Dynamics with Repulsively Driven Ultracold Atoms in an Optical Cavity.

We investigate a Bose-Einstein condensate strongly coupled to an optical cavity via a repulsive optical lattice. We detect a stable self-ordered phase in this regime, and show that the atoms order through an antisymmetric coupling to the P band of the lattice, limiting the extent of the phase and changing the geometry of the emergent density modulation. Furthermore, we find a nonequilibrium phase with repeated intense bursts of the intracavity photon number, indicating nontrivial driven-dissipative dynamics

Assembly of viral genomes from metagenomes

Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.This work was partially funded by the Virgo Consortium, funded by the Dutch government project number FES0908, by Netherlands Genomics Initiative (NGI) project number 050-060-452 and ZonMW TOP project 91213058. A. Ruiz-Gonzalez holds a Post doc fellowship awarded by the Department of Education, Universities and Research of the Basque Government (Ref. DKR-2012-64) and was partially supported by the Research group on "Systematics, Biogeography and Population Dynamics" (Basque Government; Ref. IT317-10; GIC10/76)