Exchange Gate on the Qudit Space and Fock Space

We construct the exchange gate with small elementary gates on the space of qudits, which consist of three controlled shift gates and three "reverse" gates. This is a natural extension of the qubit case. We also consider a similar subject on the Fock space, but in this case we meet with some different situation. However we can construct the exchange gate by making use of generalized coherent operator based on the Lie algebra su(2) which is a well--known method in Quantum Optics. We moreover make a brief comment on "imperfect clone".Comment: Latex File, 12 pages. I could solve the problems in Sec. 3 in the preceding manuscript, so many corrections including the title were mad

SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Temperature dependence of the charge carrier mobility in gated quasi-one-dimensional systems

The many-body Monte Carlo method is used to evaluate the frequency dependent conductivity and the average mobility of a system of hopping charges, electronic or ionic on a one-dimensional chain or channel of finite length. Two cases are considered: the chain is connected to electrodes and in the other case the chain is confined giving zero dc conduction. The concentration of charge is varied using a gate electrode. At low temperatures and with the presence of an injection barrier, the mobility is an oscillatory function of density. This is due to the phenomenon of charge density pinning. Mobility changes occur due to the co-operative pinning and unpinning of the distribution. At high temperatures, we find that the electron-electron interaction reduces the mobility monotonically with density, but perhaps not as much as one might intuitively expect because the path summation favour the in-phase contributions to the mobility, i.e. the sequential paths in which the carriers have to wait for the one in front to exit and so on. The carrier interactions produce a frequency dependent mobility which is of the same order as the change in the dc mobility with density, i.e. it is a comparably weak effect. However, when combined with an injection barrier or intrinsic disorder, the interactions reduce the free volume and amplify disorder by making it non-local and this can explain the too early onset of frequency dependence in the conductivity of some high mobility quasi-one-dimensional organic materials.Comment: 9 pages, 8 figures, to be published in Physical Review

Thermoelectric properties of the layered Pd oxide R_2PdO_4 (R = La, Nd, Sm and Gd)

We prepared polycrystalline samples of R$_2$PdO$_4$ (R = La, Nd, Sm and Gd) using a NaCl-flux technique. The measured resistivity is of the order of 10$^3-10^4$ $\Omega$cm at room temperature, which is two orders of magnitude smaller than the values reported so far. We further studied the substitution effects of Ce for Nd in Nd$_{1.9}$Ce$_{0.1}$PdO$_4$, where the substituted Ce decreases the resistivity and the magnitude of the thermopower. The activation energy gap of 70-80 meV and the effective mass of 15 evaluated from the measured data are suitable for thermoelectric materials, but the mobility of 10$^{-6}$ cm$^2$/Vs is much lower than a typical value of 1-10 cm$^2$/Vs for other thermoelectric oxides.Comment: 5 pages, 5 figures, to appear in J. Phys. Soc. Jp

Splay states in finite pulse-coupled networks of excitable neurons

The emergence and stability of splay states is studied in fully coupled finite networks of N excitable quadratic integrate-and-fire neurons, connected via synapses modeled as pulses of finite amplitude and duration. For such synapses, by introducing two distinct types of synaptic events (pulse emission and termination), we were able to write down an exact event-driven map for the system and to evaluate the splay state solutions. For M overlapping post synaptic potentials the linear stability analysis of the splay state should take in account, besides the actual values of the membrane potentials, also the firing times associated to the M previous pulse emissions. As a matter of fact, it was possible, by introducing M complementary variables, to rephrase the evolution of the network as an event-driven map and to derive an analytic expression for the Floquet spectrum. We find that, independently of M, the splay state is marginally stable with N-2 neutral directions. Furthermore, we have identified a family of periodic solutions surrounding the splay state and sharing the same neutral stability directions. In the limit of $\delta$-pulses, it is still possible to derive an event-driven formulation for the dynamics, however the number of neutrally stable directions, associated to the splay state, becomes N. Finally, we prove a link between the results for our system and a previous theory [Watanabe and Strogatz, Physica D, 74 (1994), pp. 197- 253] developed for networks of phase oscillators with sinusoidal coupling.Comment: 27 pages, 12 Figures, submitted to SIAM Journal on Applied Dynamical Systems (SIADS

Notch modulates VEGF action in endothelial cells by inducing Matrix Metalloprotease activity

In the vasculature, Notch signaling functions as a downstream effecter of Vascular Endothelial Growth Factor (VEGF) signaling. VEGF regulates sprouting angiogenesis in part by inducing and activating matrix metalloproteases (MMPs). This study sought to determine if VEGF regulation of MMPs was mediated via Notch signaling and to determine how Notch regulation of MMPs influenced endothelial cell morphogenesis. We assessed the relationship between VEGF and Notch signaling in cultured human umbilical vein endothelial cells. Overexpression of VEGF-induced Notch4 and the Notch ligand, Dll4, activated Notch signaling, and altered endothelial cell morphology in a fashion similar to that induced by Notch activation. Expression of a secreted Notch antagonist (Notch1 decoy) suppressed VEGF-mediated activation of endothelial Notch signaling and endothelial morphogenesis. We demonstrate that Notch mediates VEGF-induced matrix metalloprotease activity via induction of MMP9 and MT1-MMP expression and activation of MMP2. Introduction of a MMP inhibitor blocked Notch-mediated endothelial morphogenesis. In mice, analysis of VEGF-induced dermal angiogenesis demonstrated that the Notch1 decoy reduced perivascular MMP9 expression. Taken together, our data demonstrate that Notch signaling can act downstream of VEGF signaling to regulate endothelial cell morphogenesis via induction and activation of specific MMPs. In a murine model of VEGF-induced dermal angiogenesis, Notch inhibition led to reduced MMP9 expression

Software that goes with the flow in systems biology

A recent article in BMC Bioinformatics describes new advances in workflow systems for computational modeling in systems biology. Such systems can accelerate, and improve the consistency of, modeling through automation not only at the simulation and results-production stages, but also at the model-generation stage. Their work is a harbinger of the next generation of more powerful software for systems biologists

The Nondeterministic Waiting Time Algorithm: A Review

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells