376 research outputs found
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
. 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 that
scales as , 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
and 2), and self-avoiding (in ) chains. The results indicate that
for large , 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
.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)
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