Enzyme kinetics for a two-step enzymic reaction with comparable initial enzyme-substrate ratios

We extend the validity of the quasi-steady state assumption for a model double intermediate enzyme-substrate reaction to include the case where the ratio of initial enzyme to substrate concentration is not necessarily small. Simple analytical solutions are obtained when the reaction rates and the initial substrate concentration satisfy a certain condition. These analytical solutions compare favourably with numerical solutions of the full system of differential equations describing the reaction. Experimental methods are suggested which might permit the application of the quasi-steady state assumption to reactions where it may not have been obviously applicable before

Nonlinear dynamics of coupled transverse-rotational waves in granular chains

The nonlinear dynamics of coupled waves in one-dimensional granular chains with and without a substrate is theoretically studied accounting for quadratic nonlinearity. The multiple time scale method is used to derive the nonlinear dispersion relations for infinite granular chains and to obtain the wave solutions for semiinfinite systems. It is shown that the sum-frequency and difference-frequency components of the coupled transverse-rotational waves are generated due to their nonlinear interactions with the longitudinal wave. Nonlinear resonances are not present in the chain with no substrate where these frequency components have low amplitudes and exhibit beating oscillations. In the chain positioned on a substrate two types of nonlinear resonances are predicted. At resonance, the fundamental frequency wave amplitudes decrease and the generated frequency component amplitudes increase along the chain, accompanied by the oscillations due to the wave numbers asynchronism. The results confirm the possibility of a highly efficient energy transfer between the waves of different frequencies, which could find applications in the design of acoustic devices for energy transfer and energy rectification

Theory for a dissipative droplet soliton excited by a spin torque nanocontact

A novel type of solitary wave is predicted to form in spin torque oscillators when the free layer has a sufficiently large perpendicular anisotropy. In this structure, which is a dissipative version of the conservative droplet soliton originally studied in 1977 by Ivanov and Kosevich, spin torque counteracts the damping that would otherwise destroy the mode. Asymptotic methods are used to derive conditions on perpendicular anisotropy strength and applied current under which a dissipative droplet can be nucleated and sustained. Numerical methods are used to confirm the stability of the droplet against various perturbations that are likely in experiments, including tilting of the applied field, non-zero spin torque asymmetry, and non-trivial Oersted fields. Under certain conditions, the droplet experiences a drift instability in which it propagates away from the nanocontact and is then destroyed by damping.Comment: 15 pages, 12 figure

Chapman-Enskog method and synchronization of globally coupled oscillators

The Chapman-Enskog method of kinetic theory is applied to two problems of synchronization of globally coupled phase oscillators. First, a modified Kuramoto model is obtained in the limit of small inertia from a more general model which includes ``inertial'' effects. Second, a modified Chapman-Enskog method is used to derive the amplitude equation for an O(2) Takens-Bogdanov bifurcation corresponding to the tricritical point of the Kuramoto model with a bimodal distribution of oscillator natural frequencies. This latter calculation shows that the Chapman-Enskog method is a convenient alternative to normal form calculations.Comment: 7 pages, 2-column Revtex, no figures, minor change

Linearizability of the Perturbed Burgers Equation

We show in this letter that the perturbed Burgers equation $u_t = 2uu_x + u_{xx} + \epsilon ( 3 \alpha_1 u^2 u_x + 3\alpha_2 uu_{xx} + 3\alpha_3 u_x^2 + \alpha_4 u_{xxx} )$ is equivalent, through a near-identity transformation and up to order \epsilon, to a linearizable equation if the condition $3\alpha_1 - 3\alpha_3 - 3/2 \alpha_2 + 3/2 \alpha_4 = 0$ is satisfied. In the case this condition is not fulfilled, a normal form for the equation under consideration is given. Then, to illustrate our results, we make a linearizability analysis of the equations governing the dynamics of a one-dimensional gas.Comment: 10 pages, RevTeX, no figure

Dislocation-induced superfluidity in a model supersolid

Motivated by recent experiments on the supersolid behavior of $^4$He, we study the effect of an edge dislocation in promoting superfluidity in a Bose crystal. Using Landau theory, we couple the elastic strain field of the dislocation to the superfluid density, and use a linear analysis to show that superfluidity nucleates on the dislocation before occurring in the bulk of the solid. Moving beyond the linear analysis, we develop a systematic perturbation theory in the weakly nonlinear regime, and use this method to integrate out transverse degrees of freedom and derive a one-dimensional Landau equation for the superfluid order parameter. We then extend our analysis to a network of dislocation lines, and derive an XY model for the dislocation network by integrating over fluctuations in the order parameter. Our results show that the ordering temperature for the network has a sensitive dependence on the dislocation density, consistent with numerous experiments that find a clear connection between the sample quality and the supersolid response.Comment: 10 pages, 6 figure

A Complete Expression Profile of Matrix-Degrading Metalloproteinases in Dupuytren’s Disease

Dupuytren’s disease (DD) is a common fibrotic condition of the palmar fascia, leading to deposition of collagen-rich cords and finger contractions. The metzincin superfamily contains key enzymes in the turnover of collagen and other extracellular matrix macromolecules. A number of broad-spectrum matrix metalloproteinase inhibitors, used in cancer clinical trials, caused side effects of DD-like contractures. We tested the hypothesis that changes in the expression of specific metalloproteinases underlie or contribute to the fibrosis and contracture seen in DD. We collected tissue from patients with DD and used normal palmar fascia as a control. We profiled the expression of the entire matrix metalloproteinase (MMP), tissue inhibitor of metalloproteinases (TIMP), and a disintegrin and metalloproteinase domain with thrombospondin motif (ADAMTS) gene families in these tissues using real-time reverse-transcription polymerase chain reaction. A number of metalloproteinases and inhibitors are regulated in DD. The expression of 3 key collagenases, MMP1, MMP13, and MMP14 is increased significantly in the DD nodule, as is the expression of the collagen biosynthetic enzyme ADAMTS14. The expression of MMP7, an enzyme with broad substrate specificity, is increased in the DD nodule and remains equally expressed in the DD cord. TIMP1 expression is increased significantly in DD nodule compared with normal palmar fascia. This study measured the expression of all MMP, ADAMTS, and TIMP genes in DD. Contraction and fibrosis may result from: (1) increased collagen biosynthesis mediated by increased ADAMTS-14; (2) an increased level of TIMP-1 blocking MMP-1– and MMP-13–mediated collagenolysis; and (3) contraction enabled by MMP-14–mediated pericellular collagenolysis (and potentially MMP-7), which may escape inhibition by TIMP-1. The complete expression profile will provide a knowledge-based approach to novel therapeutics targeting these genes

Strong curvature singularities in quasispherical asymptotically de Sitter dust collapse

We study the occurrence, visibility, and curvature strength of singularities in dust-containing Szekeres spacetimes (which possess no Killing vectors) with a positive cosmological constant. We find that such singularities can be locally naked, Tipler strong, and develop from a non-zero-measure set of regular initial data. When examined along timelike geodesics, the singularity's curvature strength is found to be independent of the initial data.Comment: 16 pages, LaTeX, uses IOP package, 2 eps figures; accepted for publication in Class. Quantum Gra

Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study

The last decade has seen an explosion in models that describe phenomena in systems medicine. Such models are especially useful for studying signaling pathways, such as the Wnt pathway. In this chapter we use the Wnt pathway to showcase current mathematical and statistical techniques that enable modelers to gain insight into (models of) gene regulation, and generate testable predictions. We introduce a range of modeling frameworks, but focus on ordinary differential equation (ODE) models since they remain the most widely used approach in systems biology and medicine and continue to offer great potential. We present methods for the analysis of a single model, comprising applications of standard dynamical systems approaches such as nondimensionalization, steady state, asymptotic and sensitivity analysis, and more recent statistical and algebraic approaches to compare models with data. We present parameter estimation and model comparison techniques, focusing on Bayesian analysis and coplanarity via algebraic geometry. Our intention is that this (non exhaustive) review may serve as a useful starting point for the analysis of models in systems medicine.Comment: Submitted to 'Systems Medicine' as a book chapte

Geographies of landscape: Representation, power and meaning

Green criminology has sought to blur the nature-culture binary and this article seeks to extend recent work by geographers writing on landscape to further our understanding of the shifting contours of the divide. The article begins by setting out these different approaches, before addressing how dynamics of surveillance and conquest are embedded in landscape photography. It then describes how the ways we visualize the Earth were reconfigured with the emergence of photography in the 19th century and how the world itself has been transformed into a target in our global media culture