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

Circulation signature of vortical structures in turbulent boundary layers

The strength of vortical structures in a turbulent boundary layer is of interest in determining the generation and development of hairpin vortices. The dual-plane Particle Image Velocimetry (PIV) data at z+ = 110 (z/ = 0.09) and z/ = 0.53 (z+ = 575) in a turbulent boundary layer at Re = 1160 obtained by Ganapathisubramani et al. [7] were used to characterize the strength of the vortical structures by their circulation. The 3Dswirl was used to identify the vortex cores. The average number of swirl cores per field identified at z+ = 110 was approximately twice the average number at z/ = 0.53. The mean radius of the cores was found to decrease with increasing wall-normal distance. The main eigenvector of the velocity gradient tensor was used to determine the orientation of each vortex core. Circulation of the vortical structures was then calculated using the vorticity vector projected onto the main eigenvector direction. At z/ = 0.53, the mean circulation calculated using the eigenvector was almost the same as that using the full vorticity vector, but for z+ = 110 the mean circulation calculated using the eigenvector was 12% less than the mean circulation calculated using the vorticity vector

A Simultaneous Quantum Secure Direct Communication Scheme between the Central Party and Other M Parties

We propose a simultaneous quantum secure direct communication scheme between one party and other three parties via four-particle GHZ states and swapping quantum entanglement. In the scheme, three spatially separated senders, Alice, Bob and Charlie, transmit their secret messages to a remote receiver Diana by performing a series local operations on their respective particles according to the quadripartite stipulation. From Alice, Bob, Charlie and Diana's Bell measurement results, Diana can infer the secret messages. If a perfect quantum channel is used, the secret messages are faithfully transmitted from Alice, Bob and Charlie to Diana via initially shared pairs of four-particle GHZ states without revealing any information to a potential eavesdropper. As there is no transmission of the qubits carrying the secret message in the public channel, it is completely secure for the direct secret communication. This scheme can be considered as a network of communication parties where each party wants to communicate secretly with a central party or server.Comment: 4 pages, no figur

The CP-violating asymmetry in \eta\to\pi^+ \pi^- e^+e^-

We study the CP-violating asymmetry {\cal A}_{\rm CP}, which arises, in \eta\to\pi^+\pi^- e^+e^-, from the angular correlation of the e^+ e^- and \pi^+\pi^- planes due to the interference between the magnetic and electric decay amplitudes. With the phenomenologically determined magnetic amplitude and branching ratio as input, the asymmetry, induced by the electric bremsstrahlung amplitude through the CP-violating decay \eta\to\pi^+\pi^-, and by an unconventional tensor type operator, has been estimated respectively. The upper bound of {\cal A}_{\rm CP} from the former is about 10^{-3}, and the asymmetry from the latter might be up to O(10^{-2}). One can therefore expect that this CP asymmetry would be an interesting CP-violating observable for the future precise measurements in the \eta factories.Comment: LaTeX, 6 pages. One reference corrected, and some new references adde

The influence of direct DD-meson production to the determination on the nucleon strangeness asymmetry via dimuon events in neutrino experiments

Experimentally, the production of oppositely charged dimuon events by neutrino and anti-neutrino deep inelastic scattering (DIS) is used to determine the strangeness asymmetry inside a nucleon. Here we point out that the direct production of $D$-meson in DIS may make substantial influence to the measurement of nucleon strange distributions. The direct $D$-meson production is via the heavy quark recombination (HQR) and via the light quark fragmentation from perturbative QCD (LQF-P). To see the influence precisely, we compute the direct $D$-meson productions via HQR and LQF-P quantitatively and estimate their corrections to the analysis of the strangeness asymmetry. The results show that HQR has stronger effect than LQF-P does, and the former may influence the experimental determination of the nucleon strangeness asymmetry.Comment: 9 latex pages, 7 figure

Trans-phonon effects in ultrafast nano-devices

We report a novel phenomenon in carbon nanotube (CNT) based devices, the transphonon effects, which resemble the transonic effects in aerodynamics. It is caused by dissipative resonance of nanotube phonons similar to the radial breathing mode, and subsequent drastic surge of the dragging force on the sliding tube, and multiple phonon barriers are encountered as the intertube sliding velocity reaches critical values. It is found that the transphonon effects can be tuned by applying geometric constraints or varying chirality combinations of the nanotubes

New decoupling zmethod for spiral phase array HTS coil

published_or_final_versio

The trispectrum in ghost inflation

We calculate the trispectrum in ghost inflation where both the contact diagram and scale-exchange diagram are taken into account. The shape of trispectrum is discussed carefully and we find that the local form is absent in ghost inflation. In general, for the non-local shape trispectrum there are not analogous parameters to $\tau_{NL}^{loc.}$ and $g_{NL}^{loc.}$ which can completely characterize the size of local form trispectrum.Comment: 19 pages, 8 figures; clarifications and corrections added, version accepted for publication in JCA