Asymptotic analysis of multiscale approximations to reaction networks

A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as possible transitions of the chain. In many cases of biological interest some of the chemical species in the network are present in much greater abundance than others and reaction rate constants can vary over several orders of magnitude. We consider approaches to approximation of such models that take the multiscale nature of the system into account. Our primary example is a model of a cell's viral infection for which we apply a combination of averaging and law of large number arguments to show that the ``slow'' component of the model can be approximated by a deterministic equation and to characterize the asymptotic distribution of the ``fast'' components. The main goal is to illustrate techniques that can be used to reduce the dimensionality of much more complex models.Comment: Published at http://dx.doi.org/10.1214/105051606000000420 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Exploiting Behavioral Hierarchy for Efficient Model Checking

Inspired by the success of model checking in hardware and protocol verification, model checking techniques for software have been the focus of a lot of research in the last few years [5,3,2,6]. Model checking can be applied only to relatively small models due to its inherently high computational requirements, and there are two complementary trends to address scalability. The model extraction approach, exemplified by projects such as Bandera [6] and SLAM [3], involves constructing inputs to model checkers by abstracting programs written in languages such as C and Java. The model-based design approach, exemplified by modeling notations such as Statecharts [7], promotes design using high-level models that are compiled into code. Our research agenda is to develop model checking techniques for model-based design of software. Modern software design languages promote hierarchy as one of the key constructs for structuring complex specifications. The input language to our model checker is based on hierarchic reactive modules [1]. This choice was motivated by the fact that, unlike STATECHARTS and other languages, in hierarchic reactive modules, the notion of hierarchy is semantic with an observational trace-based semantics and a notion of refinement with assume-guarantee rules. The first contribution of this paper is the Hermes toolkit that implements hierarchic reactive modules. Our implementation has a visual front-end and XML-based back-end, consistent with modern software design tools, and is in Java. There are two basic techniques for reachability analysis. Enumerative model checkers such as SPIN [8] perform an on-the-fly exploration of the state-space using a depth-first search, while symbolic model checkers such as SMV [9] perform a breadth-first search by manipulating sets of states, rather than individual states, encoded typically by ordered binary (or multi-valued) decision diagrams. Since the two approaches are incomparable, and have been shown to be successful, Hermes supports both enumerative and symbolic reachability analysis. In this paper, we report progress on exploiting the structuring information in the behavioral hierarchy of the input model to speed up the exploration of reachable state-space of the model for both the approaches. More information about the tool is available at http://www.cis.upenn.edu/sdrl/hermes

Trauma systems in Norway: implementation of national recommendations three years down the line

publishedVersio

Policy, Performativity and Partnership: an Ethical Leadership Perspective

This article identifies the need to think differently about educational partnerships in a changing and turbulent post compulsory policy environment in England. The policy and institutional contexts in which universities and colleges currently operate seem to be fuelling performativity at the expense of educational values. There appears to be a sharp interruption in the steady increase in educational partnerships as a vehicle for increasing and widening participation in higher education. We are witnessing a marked change in university / college relationships that appears to be a consequence of government calling a halt to increased participation in higher education, creating an increasingly competitive market for a more limited pool of student places. The implication that educational policy at the national level determines a particular pattern or mode of leadership decision making throughout an institution should however be resisted. Policy developments that challenge the moral precepts of education should not be allowed to determine how a leader acts, rather they should prompt actions that are truly educational, rooted in morality, and atached to identifiable educational values. Educational leaders have agency to resist restricted discourses in favour of ethical and principled change strategies that are a precondition for sustainable transformative partnerships in post compulsory education. University leaders in particular are called upon to use their considerable influence to resist narrow policy or managerial instrumentalism or performativity and embrace alternatives that are both educationally worthwhile and can enhance institutional resilience

Diffusion-limited aggregation as branched growth

I present a first-principles theory of diffusion-limited aggregation in two dimensions. A renormalized mean-field approximation gives the form of the unstable manifold for branch competition, following the method of Halsey and Leibig [Phys. Rev. A {\bf 46}, 7793 (1992)]. This leads to a result for the cluster dimensionality, D \approx 1.66, which is close to numerically obtained values. In addition, the multifractal exponent \tau(3) = D in this theory, in agreement with a proposed `electrostatic' scaling law.Comment: 13 pages, one figure not included (available by request, by ordinary mail), Plain Te

On the Determination of ∣Vub∣|V_{ub}| from Inclusive Semileptonic Decay Spectra

We propose a model independent method to determine $|V_{ub}|$ from the energy spectrum of the charged lepton in inclusive semileptonic $B$ decays. The method includes perturbative QCD corrections as well as nonperturbative ones.Comment: LaTeX, 19 pages, 8 figures appended after \end{document} as uu-encoded and compressed .eps files, uses epsf, Technion-PH-94/9, CERN-TH.7308/9

Metamorphosis of plasma turbulence-shear flow dynamics through a transcritical bifurcation

The structural properties of an economical model for a confined plasma turbulence governor are investigated through bifurcation and stability analyses. A close relationship is demonstrated between the underlying bifurcation framework of the model and typical behavior associated with low- to high-confinement transitions such as shear flow stabilization of turbulence and oscillatory collective action. In particular, the analysis evinces two types of discontinuous transition that are qualitatively distinct. One involves classical hysteresis, governed by viscous dissipation. The other is intrinsically oscillatory and non-hysteretic, and thus provides a model for the so-called dithering transitions that are frequently observed. This metamorphosis, or transformation, of the system dynamics is an important late side-effect of symmetry-breaking, which manifests as an unusual non-symmetric transcritical bifurcation induced by a significant shear flow drive.Comment: 17 pages, revtex text, 9 figures comprised of 16 postscript files. Submitted to Phys. Rev.

Elasticity of entangled polymer loops: Olympic gels

In this note we present a scaling theory for the elasticity of olympic gels, i.e., gels where the elasticity is a consequence of topology only. It is shown that two deformation regimes exist. The first is the non affine deformation regime where the free energy scales linear with the deformation. In the large (affine) deformation regime the free energy is shown to scale as $F \propto \lambda^{5/2}$ where $\lambda$ is the deformation ratio. Thus a highly non Hookian stress - strain relation is predicted.Comment: latex, no figures, accepted in PRE Rapid Communicatio

Anomalous diffusion in polymers: long-time behaviour

We study the Dirichlet boundary value problem for viscoelastic diffusion in polymers. We show that its weak solutions generate a dissipative semiflow. We construct the minimal trajectory attractor and the global attractor for this problem.Comment: 13 page