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

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

Representations and Properties of Generalized ArA_r Statistics, Coherent States and Robertson Uncertainty Relations

The generalization of $A_r$ statistics, including bosonic and fermionic sectors, is performed by means of the so-called Jacobson generators. The corresponding Fock spaces are constructed. The Bargmann representations are also considered. For the bosonic $A_r$ statistics, two inequivalent Bargmann realizations are developed. The first (resp. second) realization induces, in a natural way, coherent states recognized as Gazeau-Klauder (resp. Klauder-Perelomov) ones. In the fermionic case, the Bargamnn realization leads to the Klauder-Perelomov coherent states. For each considered realization, the inner product of two analytic functions is defined in respect to a measure explicitly computed. The Jacobson generators are realized as differential operators. It is shown that the obtained coherent states minimize the Robertson-Schr\"odinger uncertainty relation.Comment: 16 pages, published in JP

Impurity-induced transition and impurity-enhanced thermopower in the thermoelectric oxide NaCo_{2-x}Cu_x$O_4

Various physical quantities are measured and analysed for the Cu-substituted thermoelectric oxide NaCo_{2-x}Cu_xO_4. As was previously known, the substituted Cu enhances the thermoelectric power, while it does not increase the resistivity significantly. The susceptibility and the electron specific-heat are substantially decreased with increasing x, which implies that the substituted Cu decreases the effective-mass enhancement. Through a quantitative comparison with the heavy fermion compounds and the valence fluctuation systems, we have found that the Cu substitution effectively increases the coupling between the conduction electron and the magnetic fluctuation. The Cu substitution induces a phase transition at 22 K that is very similar to a spin-density-wave transition.Comment: 8 pages, 7 figures, submitted to Phys. Rev.

Photon generation by laser-Compton scattering at the KEK-ATF

We performed a photon generation experiment by laser-Compton scattering at the KEK-ATF, aiming to develop a Compton based polarized positron source for linear colliders. In the experiment, laser pulses with a 357 MHz repetition rate were accumulated and their power was enhanced by up to 250 times in the Fabry-Perot optical resonant cavity. We succeeded in synchronizing the laser pulses and colliding them with the 1.3 GeV electron beam in the ATF ring while maintaining the laser pulse accumulation in the cavity. As a result, we observed 26.0 +/- 0.1 photons per electron-laser pulse crossing, which corresponds to a yield of 10^8 photons in a second.Comment: 3 pages, 5 figures, Preprint submitted to TIPP09 Proceedings in NIM