27,129 research outputs found
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
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The influence of direct -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 -meson in DIS may make substantial influence to the
measurement of nucleon strange distributions. The direct -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 -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
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 and 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
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