Monte Carlo simulations of infinitely dilute solutions of amphiphilic diblock star copolymers

Single-chain Monte Carlo simulations of amphiphilic diblock star copolymers were carried out in continuous space using implicit solvents. Two distinct architectures were studied: stars with the hydrophobic blocks attached to the core, and stars with the polar blocks attached to the core, with all arms being of equal length. The ratio of the lengths of the hydrophobic block to the length of the polar block was varied from 0 to 1. Stars with 3, 6, 9 or 12 arms, each of length 10, 15, 25, 50, 75 and 100 Kuhn segments were analysed. Four distinct types of conformations were observed for these systems. These, apart from studying the snapshots from the simulations, have been quantitatively characterised in terms of the mean-squared radii of gyration, mean-squared distances of monomers from the centre-of-mass, asphericity indices, static scattering form factors in the Kratky representation as well as the intra-chain monomer-monomer radial distribution functions.Comment: 12 pages, 11 ps figures. Accepted for publication in J. Chem. Phy

A New Framework for Network Disruption

Traditional network disruption approaches focus on disconnecting or lengthening paths in the network. We present a new framework for network disruption that attempts to reroute flow through critical vertices via vertex deletion, under the assumption that this will render those vertices vulnerable to future attacks. We define the load on a critical vertex to be the number of paths in the network that must flow through the vertex. We present graph-theoretic and computational techniques to maximize this load, firstly by removing either a single vertex from the network, secondly by removing a subset of vertices.Comment: Submitted for peer review on September 13, 201

Neutral genomic microevolution of a recently emerged pathogen, salmonella enterica serovar agona

Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs), but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks