'BioNessie(G) - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

BioNessie - a grid enabled biochemical networks simulation environment

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations

Magnetization reversal through synchronization with a microwave

Based on the Landau-Lifshitz-Gilbert equation, it can be shown that a circularly-polarized microwave can reverse the magnetization of a Stoner particle through synchronization. In comparison with magnetization reversal induced by a static magnetic field, it can be shown that when a proper microwave frequency is used the minimal switching field is much smaller than that of precessional magnetization reversal. A microwave needs only to overcome the energy dissipation of a Stoner particle in order to reverse magnetization unlike the conventional method with a static magnetic field where the switching field must be of the order of magnetic anisotropy.Comment: 4 pages, 5 figure

Critical layer and radiative instabilities in shallow-water shear flows

In this study a linear stability analysis of shallow-water flows is undertaken for a representative Froude number $\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}F=3.5$F=3.5 . The focus is on monotonic base flow profiles $U$U without an inflection point, in order to study critical layer instability (CLI) and its interaction with radiative instability (RI). First the dispersion relation is presented for the piecewise linear profile studied numerically by Satomura (J. Meterol. Soc. Japan, vol. 59, 1981, pp. 148–167) and using WKBJ analysis an interpretation given of mode branches, resonances and radiative instability. In particular surface gravity (SG) waves can resonate with a limit mode (LM) (or Rayleigh wave), localised near the discontinuity in shear in the flow; in this piecewise profile there is no critical layer. The piecewise linear profile is then continuously modified in a family of nonlinear profiles, to show the effect of the vorticity gradient $Q^{\prime } = - U^{\prime \prime }$Q ′ =−U ′′ on the nature of the modes. Some modes remain as modes and others turn into quasi-modes (QM), linked to Landau damping of disturbances to the flow, depending on the sign of the vorticity gradient at the critical point. Thus an interpretation of critical layer instability for continuous profiles is given, as the remnant of the resonance with the LM. Numerical results and WKBJ analysis of critical layer instability and radiative instability for more general smooth profiles are provided. A link is made between growth rate formulae obtained by considering wave momentum and those found via the WKBJ approximation. Finally the competition between the stabilising effect of vorticity gradients in a critical layer and the destabilising effect of radiation (radiative instability) is studied

Grid-enabled SIMAP utility: Motivation, integration technology and performance results

A biological system comprises large numbers of functionally diverse and frequently multifunctional sets of elements that interact selectively and nonlinearly to produce coherent behaviours. Such a system can be anything from an intracellular biological process (such as a biochemical reaction cycle, gene regulatory network or signal transduction pathway) to a cell, tissue, entire organism, or even an ecological web. Biochemical systems are responsible for processing environmental signals, inducing the appropriate cellular responses and sequence of internal events. However, such systems are not fully or even poorly understood. Systems biology is a scientific field that is concerned with the systematic study of biological and biochemical systems in terms of complex interactions rather than their individual molecular components. At the core of systems biology is computational modelling (also called mathematical modelling), which is the process of constructing and simulating an abstract model of a biological system for subsequent analysis. This methodology can be used to test hypotheses via insilico experiments, providing predictions that can be tested by in-vitro and in-vivo studies. For example, the ERbB1-4 receptor tyrosine kinases (RTKs) and the signalling pathways they activate, govern most core cellular processes such as cell division, motility and survival (Citri and Yarden, 2006) and are strongly linked to cancer when they malfunction due to mutations etc. An ODE (ordinary differential equation)-based mass action ErbB model has been constructed and analysed by Chen et al. (2009) in order to depict what roles of each protein plays and ascertain to how sets of proteins coordinate with each other to perform distinct physiological functions. The model comprises 499 species (molecules), 201 parameters and 828 reactions. These in silico experiments can often be computationally very expensive, e.g. when multiple biochemical factors are being considered or a variety of complex networks are being simulated simultaneously. Due to the size and complexity of the models and the requirement to perform comprehensive experiments it is often necessary to use high-performance computing (HPC) to keep the experimental time within tractable bounds. Based on this as part of an EC funded cancer research project, we have developed the SIMAP Utility that allows the SImulation modeling of the MAP kinase pathway (http://www.simap-project.org). In this paper we present experiences with Grid-enabling SIMAP using Condor

Detection of spin reversal and nutations through current measurements

The dynamics of a single spin embedded in a the tunnel junction between ferromagnetic contacts is strongly affected by the exchange coupling to the tunneling electrons. Moment reversal of the local spin induced by the bias voltage across the junction is shown to have a measurable effect on the tunneling current. Furthermore, the frequency of a harmonic bias voltage is picked up by the local spin dynamics and transferred back to the current generating a double frequency component.Comment: 5 pages, 5 figures; published version (with minor corrections

A Python script for adaptive layout optimization of trusses

Numerical layout optimization employing an adaptive ‘member adding’ solution scheme provides a computationally efficient means of generating (near-)optimum trusses for problems involving single or multiple load cases. To encourage usage of the method, a Python script is presented, allowing medium to large-scale problems to be solved efficiently. As well as handling multiple load cases, the short (98 line) script presented can tackle truss optimization problems involving unequal limiting tensile and compressive stresses, joint costs, and non-convex polygonal domains, with or without holes. Various numerical examples are used to demonstrate the efficacy of the script presented

On the form of the viscous term for two dimensional Navier-Stokes flows

This is a pre-copyedited, author-produced PDF of an article accepted for publication in Quarterly Journal of Mechanics and Applied Mathematics following peer review. The version of record, Andrew D. Gilbert, Xavier Riedinger, and John Thuburn, On the form of the viscous term for two dimensional Navier–Stokes flows, Q J Mechanics Appl Math (2014) 67 (2): 205-228 first published online February 27, 2014 is available online at: http://qjmam.oxfordjournals.org/content/67/2/205The form of the viscous term is discussed for incompressible flow on a two-dimensional curved surface S and for the shallow water equations. In the case of flow on a surface three versions are considered. These correspond to taking curl twice, to applying the Laplacian defined in terms of a metric, and to taking the divergence of a symmetric stress tensor. These differ on a curved surface, for example a sphere. The three terms are related and their properties discussed, in particular energy and angular momentum conservation. In the case of the shallow water equations again three forms of dissipation are considered, the last of which involves the divergence of a stress tensor. Their properties are discussed, including energy conservation and whether the rotating bucket solution of the three-dimensional Navier–Stokes equation is reproduced. A derivation of the viscous term is also given based on shallow water equations as a truncation of the Navier–Stokes equation, with forces on a column determined by integration over the vertical. For both incompressible flow on a surface and for the shallow water equations, it is argued that a viscous term based on a symmetric stress tensor should be used as this leads to correct treatment of angular momentum

Microscopic mechanisms of magnetization reversal

Two principal scenarios of magnetization reversal are considered. In the first scenario all spins perform coherent motion and an excess of magnetic energy directly goes to a nonmagnetic thermal bath. A general dynamic equation is derived which includes a tensor damping term similar to the Bloch-Bloembergen form but the magnetization magnitude remains constant for any deviation from equilibrium. In the second reversal scenario, the absolute value of the averaged sample magnetization is decreased by a rapid excitation of nonlinear spin-wave resonances by uniform magnetization precession. We have developed an analytic k-space micromagnetic approach that describes this entire reversal process in an ultra-thin soft ferromagnetic film for up to 90^{o} deviation from equilibrium. Conditions for the occurrence of the two scenarios are discussed