J-factors of short DNA molecules

The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair fluctuations with respect to the helix diameter are treated as path trajectories in the imaginary time path integral formalism. The partition function for the sub-ensemble of closed molecules is computed by imposing chain ends boundary conditions both on the radial fluctuations and on the angular degrees of freedom. The cyclization probability, the J-factor, proves to be highly sensitive to the stacking potential, mostly to its nonlinear parameters. We find that the J-factor generally decreases by reducing the sequence length ( N ) and, more significantly, below N = 100 base pairs. However, even for very small molecules, the J-factors remain sizeable in line with recent experimental indications. Large bending angles between adjacent base pairs and anharmonic stacking appear as the causes of the helix flexibility at short length scales.Comment: The Journal of Chemical Physics - May 2016 ; 9 page

Validation of a model of regulation in the tryptophan operon against multiple experiment data using global optimisation

This paper is concerned with validating a mathematical model of regulation in the tryptophan operon using global optimization. Although a number of models for this biochemical network are proposed, in many cases only qualitative agreement between the model output and experimental data was demonstrated, since very little information is currently available to guide the selection of parameter values for the models. This paper presents a model validating method using both multiple experimental data and global optimization

On the spectral properties of L_{+-} in three dimensions

This paper is part of the radial asymptotic stability analysis of the ground state soliton for either the cubic nonlinear Schrodinger or Klein-Gordon equations in three dimensions. We demonstrate by a rigorous method that the linearized scalar operators which arise in this setting, traditionally denoted by L_{+-}, satisfy the gap property, at least over the radial functions. This means that the interval (0,1] does not contain any eigenvalues of L_{+-} and that the threshold 1 is neither an eigenvalue nor a resonance. The gap property is required in order to prove scattering to the ground states for solutions starting on the center-stable manifold associated with these states. This paper therefore provides the final installment in the proof of this scattering property for the cubic Klein-Gordon and Schrodinger equations in the radial case, see the recent theory of Nakanishi and the third author, as well as the earlier work of the third author and Beceanu on NLS. The method developed here is quite general, and applicable to other spectral problems which arise in the theory of nonlinear equations

Longtime behavior of nonlocal Cahn-Hilliard equations

Here we consider the nonlocal Cahn-Hilliard equation with constant mobility in a bounded domain. We prove that the associated dynamical system has an exponential attractor, provided that the potential is regular. In order to do that a crucial step is showing the eventual boundedness of the order parameter uniformly with respect to the initial datum. This is obtained through an Alikakos-Moser type argument. We establish a similar result for the viscous nonlocal Cahn-Hilliard equation with singular (e.g., logarithmic) potential. In this case the validity of the so-called separation property is crucial. We also discuss the convergence of a solution to a single stationary state. The separation property in the nonviscous case is known to hold when the mobility degenerates at the pure phases in a proper way and the potential is of logarithmic type. Thus, the existence of an exponential attractor can be proven in this case as well

Using airborne laser altimetry to improve river flood extents delineated from SAR data

Flood extent maps derived from SAR images are a useful source of data for validating hydraulic models of river flood flow. The accuracy of such maps is reduced by a number of factors, including changes in returns from the water surface caused by different meteorological conditions and the presence of emergent vegetation. The paper describes how improved accuracy can be achieved by modifying an existing flood extent delineation algorithm to use airborne laser altimetry (LiDAR) as well as SAR data. The LiDAR data provide an additional constraint that waterline (land-water boundary) heights should vary smoothly along the flooded reach. The method was tested on a SAR image of a flood for which contemporaneous aerial photography existed, together with LiDAR data of the un-flooded reach. Waterline heights of the SAR flood extent conditioned on both SAR and LiDAR data matched the corresponding heights from the aerial photo waterline significantly more closely than those from the SAR flood extent conditioned only on SAR data

Nonholonomic systems with symmetry allowing a conformally symplectic reduction

Non-holonomic mechanical systems can be described by a degenerate almost-Poisson structure (dropping the Jacobi identity) in the constrained space. If enough symmetries transversal to the constraints are present, the system reduces to a nondegenerate almost-Poisson structure on a ``compressed'' space. Here we show, in the simplest non-holonomic systems, that in favorable circumnstances the compressed system is conformally symplectic, although the ``non-compressed'' constrained system never admits a Jacobi structure (in the sense of Marle et al.).Comment: 8 pages. A slight edition of the version to appear in Proceedings of HAMSYS 200

Goals, Strategies and First Discoveries of AO327, the Arecibo All-Sky 327 MHz Drift Pulsar Survey

We report initial results from AO327, a drift survey for pulsars with the Arecibo telescope at 327 MHz. The first phase of AO327 will cover the sky at declinations of -1 to 28 degrees, excluding the region within 5 degrees of the Galactic plane, where high scattering and dispersion make low-frequency surveys sub-optimal. We record data from a 57 MHz bandwidth with 1024 channels and 125 us sampling time. The 60 s transit time through the AO327 beam means that the survey is sensitive to very tight relativistic binaries even with no acceleration searches. To date we have detected 44 known pulsars with periods ranging from 3 ms to 2.21 s and discovered 24 new pulsars. The new discoveries include three millisecond pulsars, three objects with periods of a few tens of milliseconds typical of young as well as mildly recycled pulsars, a nuller, and a rotating radio transient. Five of the new discoveries are in binary systems. The second phase of AO327 will cover the sky at declinations of 28 to 38 degrees. We compare the sensitivity and search volume of AO327 to the Green Bank North Celestial Cap survey and the GBT350 drift survey, both of which operate at 350 MHz.Comment: Accepted for publication in Ap

Giving Miss Marple a makeover : graduate recruitment, systems failure and the Scottish voluntary sector

The voluntary sector in Scotland, as across the globe, is becoming increasingly business like. Resultantly, there is an increasing demand for graduates to work in business and support functions. In Scotland, however, despite an oversupply of graduates in the labor market, the voluntary sector reports skills shortages for graduate-level positions; a leadership deficit was also reported in countries such as the United States. Through exploratory, mainly qualitative, case study and stakeholder research, this article proposes that one reason for this mismatch between the supply of and demand for graduates is a systems failure within the sector. Many graduates and university students remain unaware of potentially suitable paid job opportunities, in part because of the sector's voluntary label. To rectify this systems failure, thought needs to be given to the sector's nomenclature and the manner in which voluntary sector organizations attract graduate recruits, for example, through levering value congruence in potential recruits

Gender, foundation degrees and the knowledge economy

This article questions the concept of ‘education for employment’, which constructs a discourse of individual and societal benefit in a knowledge‐driven economy. Recent policy emphasis in the European Union promotes the expansion of higher education and short‐cycle vocational awards such as the intermediate two‐year Foundation Degree recently introduced into England and Wales. Studies of vocational education and training (VET) and the knowledge economy have focused largely on the governance of education and on the development and drift of policy. Many VET programmes have also been considered for their classed, raced and gendered take‐up and subsequent effect on employment. This article builds on both fields of study to engage with the finer cross‐analyses of gender, social class, poverty, race and citizenship. In its analysis of policy texts the article argues that in spite of a discourse of inclusivity, an expanded higher education system has generated new inequalities, deepening social stratification. Drawing on early analyses of national quantitative data sets, it identifies emerging gendered, classed and raced patterns and considers these in relation to occupationally and hierarchically stratified labour markets, both within and without the knowledge economy