Divergent RNA transcription:A role in promoter unwinding?

New approaches using biotinylated-psoralen as a probe for investigating DNA structure have revealed new insights into the relationship between DNA supercoiling, transcription and chromatin compaction. We explore a hypothesis that divergent RNA transcription generates negative supercoiling at promoters facilitating initiation complex formation and subsequent promoter clearance

Interpolating gamma factors in families

textIn this thesis, we extend the results of Jacquet, Piatetski-Shapiro, and Shalika [JPSS83] to construct interpolated local zeta integrals and gamma factors attached to families of admissible generic representations of GL[subscript n](F) where F is a p-adic field. Our families are parametrized by the spectrum of an ℓ-adic coefficient ring where ℓǂp. To show the importance of gamma factors, we prove a converse theorem in families, which says that suitable collections of interpolated gamma factors of pairs uniquely determine a family of representations, up to supercuspidal support. To prove the converse theorem we re-prove a classical vanishing Lemma, originally due to Jacquet and Shalika, in the setting of families. This is done by extending the geometric methods of Bushnell and Henniart to families, via Helm's theory of the integral Bernstein center.Mathematic

The molecular basis of storage organs in Brassicas

The LEAFY COTYLEDON (LEC) family of genes are intrinsically linked to the formation of the Arabidopsis embryo in morphogenesis and maturation. They play several roles in this process including maintenance of embryonic identity and the formation of storage products in the seed. This is important for desiccation protection and as an energy store for germination and growth before photomorphogenesis occurs. Loss of function mutations have been shown to exhibit non-embryonic traits such as trichomes and anthocyanin sequestration. When LECs are expressed outside of embryonic tissues in Arabidopsis, accumulation of storage oils and immature cell identity is observed. They appear to exhibit large amounts of crosstalk with the hormones auxin and gibberellins. This thesis investigates the link between Leafy Cotyledon 1 (LEC1) expression in the Arabidopsis turnip (tnp), a gain-of-function mutant of LEC1, and hypocotyl development in selected Brassica sp. In particular; Are LECs ectopically expressed in the hypocotyl of the Brassicas post germination? To what extent are LEC1, LEC2 and FUSCA3 (FUS3) expressed in relation to one another? Is the timing of starch and lipid accumulation linked temporally to LEC expression? Fatty acid profiles of the tnp mutant were explored in relation to the wild type and further investigations and comparisons to profiles in the Brassica hypocotyl tissues were examined. Relatively high ectopic LEC expression was observed in the Brassica hypocotyl tissue. LEC1 was found to be associated with hypocotyl expansion and starch accumulation. LEC2 expression levels increase after LEC1 levels decrease. The same oils observed to increase in the tnp mutant of Arabidopsis are present in large amounts in the Brassica hypocotyl tissue, suggesting a potential link between LECs and the molecular basis of storage organ development in Brassicas

Dynamo action in the ABC flows using symmetries

This is an Accepted Manuscript of an article published by Taylor & Francis in Geophysical and Astrophysical Fluid Dynamics, Volume 108, Issue 1, 2014 available online 25 Sep 2013: http://wwww.tandfonline.com/10.1080/03091929.2013.832762.This paper concerns kinematic dynamo action by the 1:1:1 ABC flow, in the highly conducting limit of large magnetic Reynolds number Rm. The flow possesses 24 symmetries, with a symmetry group isomorphic to the group O24 of orientation preserving transformations of a cube. This can be exploited to break up the linear eigenvalue problem into five distinct symmetry classes, or irreducible representations, which we label I–V. The paper discusses how to reduce the scale of the numerical problem to a subset of Fourier modes for a magnetic field in each representation, which then may be solved independently to obtain distinct branches of eigenvalues and magnetic field eigenfunctions. Two numerical methods are employed: the first is to time step a magnetic field in a given symmetry class and obtain the growth rate and frequency by measuring the magnetic energy as a function of time. The second method involves a more direct determination of the eigenvalue using the eigenvalue solver ARPACK for sparse matrix systems, which employs an implicitly restarted Arnoldi method. The two methods are checked against each other, and compared for efficiency and reliability. Eigenvalue branches for each symmetry class are obtained for magnetic Reynolds numbers Rm up to 104 together with spectra and magnetic field visualisations. A sequence of branches emerges as Rm increases and the magnetic field structures in the different branches are discussed and compared. In a parallel development,results are presented for the corresponding fluid stability problem as a function of the Reynolds number Re.Leverhulme Trus

Charge scheduling for electric freight vehicles

We consider a fleet of electric freight vehicles (EFVs) that must deliver goods to a set of customers over the course of multiple days. In an urban environment, EFVs are typically charged at a central depot and rarely use public charging stations during delivery routes. Therefore, the charging schedule at the depot must be planned ahead of time so as to allow the vehicles to complete their routes at minimal cost. Vehicle fleet operators are subject to commercial electricity rate plans, which should be accounted for in order to provide an accurate estimation of the energy-related costs and restrictions. In addition, high vehicle utilization rates can accelerate battery aging, thereby requiring degradation mitigation considerations. We develop and solve a comprehensive mathematical model that incorporates a large variety of features associated with the use of EFVs. These include a realistic charging process, time-dependent energy costs, battery degradation, grid restrictions, and facility-related demand charges. Extensive numerical experiments are conducted in order to draw managerial insights regarding the impact of such features on the charging schedules of EFVs.</p

The electric vehicle routing problem with energy consumption uncertainty

Compared with conventional freight vehicles, electric freight vehicles create less local pollution and are thus generally perceived as a more sustainable means of goods distribution. In urban areas, such vehicles must often perform the entirety of their delivery routes without recharging. However, their energy consumption is subject to a fair amount of uncertainty, which is due to exogenous factors such as the weather and road conditions, endogenous factors such as driver behaviour, and several energy consumption parameters that are difficult to measure precisely. Hence we propose a robust optimization framework to take into account these energy consumption uncertainties in the context of an electric vehicle routing problem. The objective is to determine minimum cost delivery routes capable of providing strong guarantees that a given vehicle will not run out of charge during its route. We formulate the problem as a robust mixed integer linear program and solve small instances to optimality using robust optimization techniques. Furthermore, we develop a two-phase heuristic method based on large neighbourhood search to solve larger instances of the problem, and we conduct several numerical tests to assess the quality of the methodology. The computational experiments illustrate the trade-off between cost and risk, and demonstrate the influence of several parameters on best found solutions. Furthermore, our heuristic identifies 42 new best solutions when tested on instances of the closely related robust capacitated vehicle routing problem

Charge scheduling for electric freight vehicles

We consider a fleet of electric freight vehicles (EFVs) that must deliver goods to a set of customers over the course of multiple days. In an urban environment, EFVs are typically charged at a central depot and rarely use public charging stations during delivery routes. Therefore, the charging schedule at the depot must be planned ahead of time so as to allow the vehicles to complete their routes at minimal cost. Vehicle fleet operators are subject to commercial electricity rate plans, which should be accounted for in order to provide an accurate estimation of the energy-related costs and restrictions. In addition, high vehicle utilization rates can accelerate battery aging, thereby requiring degradation mitigation considerations. We develop and solve a comprehensive mathematical model that incorporates a large variety of features associated with the use of EFVs. These include a realistic charging process, time-dependent energy costs, battery degradation, grid restrictions, and facility-related demand charges. Extensive numerical experiments are conducted in order to draw managerial insights regarding the impact of such features on the charging schedules of EFVs