Gender violence in schools: taking the ‘girls-as-victims’ discourse forward

This paper draws attention to the gendered nature of violence in schools. Recent recognition that schools can be violent places has tended to ignore the fact that many such acts originate in unequal and antagonistic gender relations, which are tolerated and ‘normalised’ by everyday school structures and processes. After examining some key concepts and definitions, we provide a brief overview of the scope and various manifestations of gender violence in schools, noting that most research to date has focused on girls as victims of gender violence within a heterosexual context and ignores other forms such as homophobic and girl violence. We then move on to look at a few interventions designed to address gender violence in schools in the developing world and end by highlighting the need for more research and improved understanding of the problem and how it can be addressed

Quantum Charge Transport and Conformational Dynamics of Macromolecules

We study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion which simultaneously describe the molecular and quantum transport dynamics, and obey the fluctuation/dissipation relationship. We also introduce an algorithm which yields the most probable molecular and quantum transport pathways in rare, thermally-activated reactions. In the second part of the paper, we apply this formalism to simulate the propagation of a charge during the collapse of a polymer from an initial stretched conformation to a final globular state. We find that the charge dynamics is quenched when the chain reaches a molten globule state. Using random matrix theory we show that this transition is due to an increase of quantum localization driven by dynamical disorder.Comment: 11 pages, 2 figure

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignment

Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous recombination, the mechanism of homology recognition is still an unsolved puzzle. While specific proteins are known to play a role at later stages of recombination, an initial coarse grained recognition step has been proposed. This relies on the sequence dependence of the DNA structural parameters, such as twist and rise, mediated by intermolecular interactions, in particular electrostatic ones. In this proposed mechanism, sequences having the same base pair text, or are homologous, have lower interaction energy than those sequences with uncorrelated base pair texts; the difference termed the recognition energy. Here, we probe how the recognition energy changes when one DNA fragment slides past another, and consider, for the first time, homologous sequences in antiparallel alignment. This dependence on sliding was termed the recognition well. We find that there is recognition well for anti-parallel, homologous DNA tracts, but only a very shallow one, so that their interaction will differ little from the interaction between two nonhomologous tracts. This fact may be utilized in single molecule experiments specially targeted to test the theory. As well as this, we test previous theoretical approximations in calculating the recognition well for parallel molecules against MC simulations, and consider more rigorously the optimization of the orientations of the fragments about their long axes. The more rigorous treatment affects the recognition energy a little, when the molecules are considered rigid. However when torsional flexibility of the DNA molecules is introduced, we find excellent agreement between analytical approximation and simulation.Comment: Paper with supplemental material attached. 41 pages in all, 4 figures in main text, 3 figures in supplmental. To be submitted to Journa

Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained level of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, the other containing only one particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The coarse-grained and the atomistically resolved systems have the same statistical properties at the same physical conditions.Comment: 17 pages, 11 figures, 5 table

Frobenius theorem and invariants for Hamiltonian systems

We apply Frobenius integrability theorem in the search of invariants for one-dimensional Hamiltonian systems with a time-dependent potential. We obtain several classes of potential functions for which Frobenius theorem assures the existence of a two-dimensional foliation to which the motion is constrained. In particular, we derive a new infinite class of potentials for which the motion is assurately restricted to a two-dimensional foliation. In some cases, Frobenius theorem allows the explicit construction of an associated invariant. It is proven the inverse result that, if an invariant is known, then it always can be furnished by Frobenius theorem

The Fallacy of Year-Round Breeding in Polyphagous Tropical Fruit Flies (Diptera: Tephritidae): Evidence for a Seasonal Reproductive Arrestment in Bactrocera Species

Bactrocera fruit flies are major pests of horticulture in tropical parts of the world and are highly invasive. Able to breed in many different fruit types, and living in hot to warm climates where temperature is not limiting, it is assumed that these flies breed continuously in their native environment. However, Bactrocera are native to monsoonal rainforests, where the mature fruit needed for breeding is largely absent for four to five months a year during the dry season. Reviewing literature and published population graphs of these flies, we argue that there is evidence to suggest that these flies undergo a reproductive arrest during the dry season when breeding hosts are scarce. We believe females stop or limit reproduction through a diapause or quiescence mechanism, so extending their life-span during the unfavourable breeding period. Once through that period they then switch their life-history strategy to focus on reproduction. Evidence is that this behaviour continues in invaded and agricultural systems and is not just restricted to rainforests. We cannot confirm this hypothesis with the information available, but because of its potential significance in managing these pests we urge that targeted research be carried out to confirm or deny the hypothesis

Quasi-Lie schemes and Emden--Fowler equations

The recently developed theory of quasi-Lie schemes is studied and applied to investigate several equations of Emden type and a scheme to deal with them and some of their generalisations is given. As a first result we obtain t-dependent constants of the motion for particular instances of Emden equations by means of some of their particular solutions. Previously known results are recovered from this new perspective. Finally some t-dependent constants of the motion for equations of Emden type satisfying certain conditions are recovered

Analytic Behaviour of Competition among Three Species

We analyse the classical model of competition between three species studied by May and Leonard ({\it SIAM J Appl Math} \textbf{29} (1975) 243-256) with the approaches of singularity analysis and symmetry analysis to identify values of the parameters for which the system is integrable. We observe some striking relations between critical values arising from the approach of dynamical systems and the singularity and symmetry analyses.Comment: 14 pages, to appear in Journal of Nonlinear Mathematical Physic

The roles of bacterial DNA double-strand break repair proteins in chromosomal DNA replication

It is well established that DNA double-strand break (DSB) repair is required to underpin chromosomal DNA replication. Because DNA replication forks are prone to breakage, faithful DSB repair and correct replication fork restart are critically important. Cells, where the proteins required for DSB repair are absent or altered, display characteristic disturbances to genome replication. In this review, we analyze how bacterial DNA replication is perturbed in DSB repair mutant strains and explore the consequences of these perturbations for bacterial chromosome segregation and cell viability. Importantly, we look at how DNA replication and DSB repair processes are implicated in the striking recent observations of DNA amplification and DNA loss in the chromosome terminus of various mutant Escherichia coli strains. We also address the mutant conditions required for the remarkable ability to copy the entire E. coli genome, and to maintain cell viability, even in the absence of replication initiation from oriC, the unique origin of DNA replication in wild type cells. Furthermore, we discuss the models that have been proposed to explain these phenomena and assess how these models fit with the observed data, provide new insights, and enhance our understanding of chromosomal replication and termination in bacteria

Novel Roles for Selected Genes in Meiotic DNA Processing

High-throughput studies of the 6,200 genes of Saccharomyces cerevisiae have provided valuable data resources. However, these resources require a return to experimental analysis to test predictions. An in-silico screen, mining existing interaction, expression, localization, and phenotype datasets was developed with the aim of selecting minimally characterized genes involved in meiotic DNA processing. Based on our selection procedure, 81 deletion mutants were constructed and tested for phenotypic abnormalities. Eleven (13.6%) genes were identified to have novel roles in meiotic DNA processes including DNA replication, recombination, and chromosome segregation. In particular, this analysis showed that Def1, a protein that facilitates ubiquitination of RNA polymerase II as a response to DNA damage, is required for efficient synapsis between homologues and normal levels of crossover recombination during meiosis. These characteristics are shared by a group of proteins required for Zip1 loading (ZMM proteins). Additionally, Soh1/Med31, a subunit of the RNA pol II mediator complex, Bre5, a ubiquitin protease cofactor and an uncharacterized protein, Rmr1/Ygl250w, are required for normal levels of gene conversion events during meiosis. We show how existing datasets may be used to define gene sets enriched for specific roles and how these can be evaluated by experimental analysis