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

Artificial Neural Network Methods in Quantum Mechanics

In a previous article we have shown how one can employ Artificial Neural Networks (ANNs) in order to solve non-homogeneous ordinary and partial differential equations. In the present work we consider the solution of eigenvalue problems for differential and integrodifferential operators, using ANNs. We start by considering the Schr\"odinger equation for the Morse potential that has an analytically known solution, to test the accuracy of the method. We then proceed with the Schr\"odinger and the Dirac equations for a muonic atom, as well as with a non-local Schr\"odinger integrodifferential equation that models the $n+\alpha$ system in the framework of the resonating group method. In two dimensions we consider the well studied Henon-Heiles Hamiltonian and in three dimensions the model problem of three coupled anharmonic oscillators. The method in all of the treated cases proved to be highly accurate, robust and efficient. Hence it is a promising tool for tackling problems of higher complexity and dimensionality.Comment: Latex file, 29pages, 11 psfigs, submitted in CP

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

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

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

Treatment-Induced Changes in Plasma Adiponectin Do Not Reduce Urinary Albumin Excretion in the Diabetes Prevention Program Cohort.

BACKGROUND AND OBJECTIVES: Molecular data suggests that adiponectin may directly regulate urinary albumin excretion. In the Diabetes Prevention Program (DPP) we measured adiponectin and albuminuria before and after intervention, and we previously reported increases in adiponectin with interventions. Here we have used the DPP dataset to test the hypothesis that treatment-related increases in adiponectin may reduce albuminuria in obesity. DESIGN, SETTING, PARTICIPANTS AND METHODS: We evaluated cross-sectional correlations between plasma adiponectin and urinary albumin excretion at baseline, and the relationship of treatment-related changes in adiponectin and albuminuria. Baseline and follow-up urine albumin to creatinine ratios (ACR (albumin to creatinine ratio)) and plasma adiponectin concentration were available in 2553 subjects. RESULTS: Adjusting for age, sex and race/ethnicity, we observed a statistically significant but weak inverse relationship between adiponectin and ACR at baseline (conditional Spearman\u27s rho = (-) 0.04, p = 0.04). Although DPP treatments significantly increased plasma adiponectin, there were no treatment effects on ACR and no differences in ACR across treatment groups. There was a weak direct (not inverse) association between change in adiponectin and change in albuminuria (adjusted Spearman\u27s rho = (+) 0.04, p = 0.03). CONCLUSIONS: In a large, well-characterized cohort of obese dysglycemic subjects we observed a weak inverse association between circulating adiponectin concentrations and urinary albumin excretion at baseline. Contrary to the hypothesized effect, treatment-related increases in plasma adiponectin were not associated with a reduction in ACR. The association of change in adiponectin with change in ACR should be assessed in populations with overt albuminuria before excluding a beneficial effect of increasing adiponectin to reduce ACR in obesity

Measurement of parity-nonconserving rotation of neutron spin in the 0.734-eV p-wave resonance of 139La^{139}La

The parity nonconserving spin rotation of neutrons in the 0.734-eV p-wave resonance of $^{139}La$ was measured with the neutron transmission method. Two optically polarized $^3He$ cells were used before and behind a a 5-cm long $^{139}La$ target as a polarizer and an analyzer of neutron spin. The rotation angle was carefully measured by flipping the direction of $^3He$ polarization in the polarizer in sequence. The peak-to-peak value of the spin rotation was found to be $(7.4 \pm 1.1) \times 10^{-3}$ rad/cm which was consistent with the previous experiments. But the result was statisticallly improved. The s-p mixing model gives the weak matrix element as $xW = (1.71 \pm 0.25)$ meV. The value agrees well with the one deduced from the parity-nonconserving longitudinal asymmetry in the same resonance

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