Compositionality, stochasticity and cooperativity in dynamic models of gene regulation

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ode-description. While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first-level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07

Enhanced flight performance by genetic manipulation of wing shape in Drosophila

Insect wing shapes are remarkably diverse and the combination of shape and kinematics determines both aerial capabilities and power requirements. However, the contribution of any specific morphological feature to performance is not known. Using targeted RNA interference to modify wing shape far beyond the natural variation found within the population of a single species, we show a direct effect on flight performance that can be explained by physical modelling of the novel wing geometry. Our data show that altering the expression of a single gene can significantly enhance aerial agility and that the Drosophila wing shape is not, therefore, optimized for certain flight performance characteristics that are known to be important. Our technique points in a new direction for experiments on the evolution of performance specialities in animals

Convergence of chiral effective field theory

We formulate the expansion for the mass of the nucleon as a function of pion mass within chiral perturbation theory using a number of different ultra-violet regularisation schemes; including dimensional regularisation and various finite-ranged regulators. Leading and next-to-leading order non-analytic contributions are included through the standard one-loop Feynman graphs. In addition to the physical nucleon mass, the expansion is constrained by recent, extremely accurate, lattice QCD data obtained with two flavors of dynamical quarks. The extent to which different regulators can describe the chiral expansion is examined, while varying the range of quark mass over which the expansions are matched. Renormalised chiral expansion parameters are recovered from each regularisation prescription and compared. We find that the finite-range regulators produce consistent, model-independent results over a wide range of quark mass sufficient to solve the chiral extrapolation problem in lattice QCD.Comment: 13 pages, 13 figures; To appear in Progress in Particle and Nuclear Physics; presented at Erice School on Quarks in Hadrons and Nuclei, September 200

(Anti-)Brane backreaction beyond perturbation theory

We improve on the understanding of the backreaction of anti-D6-branes in a flux background that is mutually BPS with D6-branes. This setup is analogous to the study of the backreaction of anti-D3-branes inserted in the KS throat, but does not require us to smear the anti-branes or do a perturbative analysis around the BPS background. We solve the full equations of motion near the anti-D6-branes and show that only two boundary conditions are consistent with the equations of motion. Upon invoking a topological argument we eliminate the boundary condition with regular H flux since it cannot lead to a solution that approaches the right kind of flux away from the anti-D6-brane. This leaves us with a boundary condition which has singular, but integrable, H flux energy density.Comment: 12 pages + appendices, 1 figure; v2: minor changes, version published in JHE

MRI-based visual and haptic catheter feedback: simulating a novel system's contribution to efficient and safe MRI-guided cardiac electrophysiology procedures

Oral Presentationpublished_or_final_versio

Efficiency of Lift Production in Flapping and Gliding Flight of Swifts

Many flying animals use both flapping and gliding flight as part of their routine behaviour. These two kinematic patterns impose conflicting requirements on wing design for aerodynamic efficiency and, in the absence of extreme morphing, wings cannot be optimised for both flight modes. In gliding flight, the wing experiences uniform incident flow and the optimal shape is a high aspect ratio wing with an elliptical planform. In flapping flight, on the other hand, the wing tip travels faster than the root, creating a spanwise velocity gradient. To compensate, the optimal wing shape should taper towards the tip (reducing the local chord) and/or twist from root to tip (reducing local angle of attack). We hypothesised that, if a bird is limited in its ability to morph its wings and adapt its wing shape to suit both flight modes, then a preference towards flapping flight optimization will be expected since this is the most energetically demanding flight mode. We tested this by studying a well-known flap-gliding species, the common swift, by measuring the wakes generated by two birds, one in gliding and one in flapping flight in a wind tunnel. We calculated span efficiency, the efficiency of lift production, and found that the flapping swift had consistently higher span efficiency than the gliding swift. This supports our hypothesis and suggests that even though swifts have been shown previously to increase their lift-to-drag ratio substantially when gliding, the wing morphology is tuned to be more aerodynamically efficient in generating lift during flapping. Since body drag can be assumed to be similar for both flapping and gliding, it follows that the higher total drag in flapping flight compared with gliding flight is primarily a consequence of an increase in wing profile drag due to the flapping motion, exceeding the reduction in induced drag

The problematic backreaction of SUSY-breaking branes

In this paper we investigate the localisation of SUSY-breaking branes which, in the smeared approximation, support specific non-BPS vacua. We show, for a wide class of boundary conditions, that there is no flux vacuum when the branes are described by a genuine delta-function. Even more, we find that the smeared solution is the unique solution with a regular brane profile. Our setup consists of a non-BPS AdS_7 solution in massive IIA supergravity with smeared anti-D6-branes and fluxes T-dual to ISD fluxes in IIB supergravity.Comment: 27 pages, Latex2e, 5 figure

Cooper pairing near charged black holes

We show that a quartic contact interaction between charged fermions can lead to Cooper pairing and a superconducting instability in the background of a charged asymptotically Anti-de Sitter black hole. For a massless fermion we obtain the zero mode analytically and compute the dependence of the critical temperature T_c on the charge of the fermion. The instability we find occurs at charges above a critical value, where the fermion dispersion relation near the Fermi surface is linear. The critical temperature goes to zero as the marginal Fermi liquid is approached, together with the density of states at the Fermi surface. Besides the charge, the critical temperature is controlled by a four point function of a fermionic operator in the dual strongly coupled field theory.Comment: 1+33 pages, 4 figure

Rapid planetesimal formation in turbulent circumstellar discs

The initial stages of planet formation in circumstellar gas discs proceed via dust grains that collide and build up larger and larger bodies (Safronov 1969). How this process continues from metre-sized boulders to kilometre-scale planetesimals is a major unsolved problem (Dominik et al. 2007): boulders stick together poorly (Benz 2000), and spiral into the protostar in a few hundred orbits due to a head wind from the slower rotating gas (Weidenschilling 1977). Gravitational collapse of the solid component has been suggested to overcome this barrier (Safronov 1969, Goldreich & Ward 1973, Youdin & Shu 2002). Even low levels of turbulence, however, inhibit sedimentation of solids to a sufficiently dense midplane layer (Weidenschilling & Cuzzi 1993, Dominik et al. 2007), but turbulence must be present to explain observed gas accretion in protostellar discs (Hartmann 1998). Here we report the discovery of efficient gravitational collapse of boulders in locally overdense regions in the midplane. The boulders concentrate initially in transient high pressures in the turbulent gas (Johansen, Klahr, & Henning 2006), and these concentrations are augmented a further order of magnitude by a streaming instability (Youdin & Goodman 2005, Johansen, Henning, & Klahr 2006, Johansen & Youdin 2007) driven by the relative flow of gas and solids. We find that gravitationally bound clusters form with masses comparable to dwarf planets and containing a distribution of boulder sizes. Gravitational collapse happens much faster than radial drift, offering a possible path to planetesimal formation in accreting circumstellar discs.Comment: To appear in Nature (30 August 2007 issue). 18 pages (in referee mode), 3 figures. Supplementary Information can be found at 0708.389

Factors associated with self-care activities among adults in the United Kingdom: a systematic review

Background: The Government has promoted self-care. Our aim was to review evidence about who uses self-tests and other self-care activities (over-the-counter medicine, private sector,complementary and alternative medicine (CAM), home blood pressure monitors). Methods: During April 2007, relevant bibliographic databases (Medline, Embase, Cumulative Index to Nursing and Allied Health Literature, Applied Social Sciences Index and Abstracts, PsycINFO,British Nursing Index, Allied and Complementary Medicine Database, Sociological Abstracts, International Bibliography of the Social Sciences, Arthritis and Complementary Medicine Database, Complementary and Alternative Medicine and Pain Database) were searched, and potentially relevant studies were reviewed against eligibility criteria. Studies were included if they were published during the last 15 years and identified factors, reasons or characteristics associated with a relevant activity among UK adults. Two independent reviewers used proformas to assess the quality of eligible studies. Results: 206 potentially relevant papers were identified, 157 were excluded, and 49 papers related to 46 studies were included: 37 studies were, or used data from questionnaire surveys, 36 had quality scores of five or more out of 10, and 27 were about CAM. Available evidence suggests that users of CAM and over-the-counter medicine are female, middle-aged, affluent and/or educated with some measure of poor health, and that people who use the private sector are affluent and/or educated. Conclusion: People who engage in these activities are likely to be affluent. Targeted promotion may, therefore, be needed to ensure that use is equitable. People who use some activities also appear to have poorer measures of health than non-users or people attending conventional services. It is, therefore, also important to ensure that self-care is not used as a second choice for people who have not had their needs met by conventional service