ODEbase: A Repository of ODE Systems for Systems Biology

Recently, symbolic computation and computer algebra systems have beensuccessfully applied in systems biology, especially in chemical reactionnetwork theory. One advantage of symbolic computation is its potential forqualitative answers to biological questions. Qualitative methods analyzedynamical input systems as formal objects, in contrast to investigating onlypart of the state space, as is the case with numerical simulation. However,symbolic computation tools and libraries have a different set of requirementsfor their input data than their numerical counterparts. A common format used inmathematical modeling of biological processes is SBML. We illustrate that theuse of SBML data in symbolic computation requires significant pre-processing,incorporating external biological and mathematical expertise. ODEbase provideshigh quality symbolic computation input data derived from established existingbiomodels, covering in particular the BioModels database.<br

Algorithmic Reduction of Biological Networks With Multiple Time Scales

We present a symbolic algorithmic approach that allows to compute invariant manifolds and corresponding reduced systems for differential equations modeling biological networks which comprise chemical reaction networks for cellular biochemistry, and compartmental models for pharmacology, epidemiology and ecology. Multiple time scales of a given network are obtained by scaling, based on tropical geometry. Our reduction is mathematically justified within a singular perturbation setting using a recent result by Cardin and Teixeira. The existence of invariant manifolds is subject to hyperbolicity conditions, which we test algorithmically using Hurwitz criteria. We finally obtain a sequence of nested invariant manifolds and respective reduced systems on those manifolds. Our theoretical results are generally accompanied by rigorous algorithmic descriptions suitable for direct implementation based on existing off-the-shelf software systems, specifically symbolic computation libraries and Satisfiability Modulo Theories solvers. We present computational examples taken from the well-known BioModels database using our own prototypical implementations

Strong Correlations in Electron Doped Phthalocyanine Conductors Near Half Filling

We propose that electron doped nontransition metal-phthalocyanines (MPc) like ZnPc and MgPc, similar to those very recently reported, should constitute novel strongly correlated metals. Due to orbital degeneracy, Jahn-Teller coupling and Hund's rule exchange, and with a large on-site Coulomb repulsion, these molecular conductors should display, particularly near half filling at two electrons/molecule, very unconventional properties, including Mott insulators, strongly correlated superconductivity, and other intriguing phases.Comment: 4 pages, 1 figure, submited to PR

Analysis of Public Bus Transportation of a Brazilian City Based on the Theory of Complex Networks Using the P-Space

The city of Curitiba, located at Southern Brazil, is recognized by its urban planning structured on three pillars: land use, collective transportation, and traffic. With 3.8 million people in its metropolitan area, the public transport system deals with approximately 2.5 million passengers daily. The structure and properties of such a transportation system have substantial implications for the urban planning and public politics for sustainable development of Curitiba. Therefore, this paper analyzes the structure of the public transportation system of Curitiba through the theory of complex networks in a static approach of network topology and presents a comparative analysis of the results from Curitiba, three cities from China (Shanghai, Beijing, and Guangzhou), and three cities from Poland (GOP, Warszawa, and Łódź). The transportation network was modeled as a complex network with exact geographical coordinates of its bus stops. In all bus lines, the method used was the P-Space. The results show that this bus network has characteristics of both small-world and scale-free networks

Pressure Induced Charge Disproportionation in LaMnO3_{3}

We present a total energy study as a function of volume in the cubic phase of LaMnO$_{3}$. A charge disproportionated state into planes of Mn$^{3+}$O$_{2}$/Mn$^{4+}$O$_{2}$ was found. It is argued that the pressure driven localisation/delocalisation transition might go smoothly through a region of Mn$^{3+}$ and Mn$^{4+}$ coexistence.Comment: 3 pages, 1 figure, Conference Proceedings: Nanospintronics: Design and Realization (Kyoto, Japan 24-28 May, 2004

Measured quantum probability distribution functions for Brownian motion

The quantum analog of the joint probability distributions describing a classical stochastic process is introduced. A prescription is given for constructing the quantum distribution associated with a sequence of measurements. For the case of quantum Brownian motion this prescription is illustrated with a number of explicit examples. In particular it is shown how the prescription can be extended in the form of a general formula for the Wigner function of a Brownian particle entangled with a heat bath.Comment: Phys. Rev. A, in pres

Language assessment in Wada test: Comparison of methohexital and amobarbital

AbstractIntroductionMethohexital has replaced amobarbital during Wada testing at many centers. The objective of our study was to compare the use of methohexital and amobarbital during Wada testing regarding language and memory lateralization quotients as well as speech arrest times.MethodsA chart review of 582 consecutive patients undergoing 1041 Wada-procedures was performed (left=60, right=63, bilateral=459). Language lateralization was calculated based on duration of speech arrest using a laterality index, defined as (L−R)/(L+R). Memory lateralization was expressed as percentage of retained objects and laterality quotient.ResultsLanguage and memory lateralization revealed a similar distribution with amobarbital and methohexital. Speech arrest after left and right-sided injection was significantly longer in the amobarbital group as compared to the methohexital group. Language lateralization did not differ in the two groups. Percentage of retained memory items was higher in the methohexital group and there were fewer presented test items in the methohexital group.DiscussionLanguage and memory testing during the Wada test can successfully be performed with methohexital instead of amobarbital. The shorter half-life of methohexital allows repeated injections and shorter interhemispheric testing intervals, but also shortens the testing window

CPT Violation, Strings, and Neutral-Meson Systems

This talk provides a short overview of recent results on possible CPT violation and some associated experimental signatures.Comment: Presented at Orbis Scientiae, January 199

Cosmological horizons and reconstruction of quantum field theories

As a starting point, we state some relevant geometrical properties enjoyed by the cosmological horizon of a certain class of Friedmann-Robertson-Walker backgrounds. Those properties are generalised to a larger class of expanding spacetimes $M$ admitting a geodesically complete cosmological horizon \scrim common to all co-moving observers. This structure is later exploited in order to recast, in a cosmological background, some recent results for a linear scalar quantum field theory in spacetimes asymptotically flat at null infinity. Under suitable hypotheses on $M$, encompassing both the cosmological de Sitter background and a large class of other FRW spacetimes, the algebra of observables for a Klein-Gordon field is mapped into a subalgebra of the algebra of observables \cW(\scrim) constructed on the cosmological horizon. There is exactly one pure quasifree state $\lambda$ on \cW(\scrim) which fulfils a suitable energy-positivity condition with respect to a generator related with the cosmological time displacements. Furthermore $\lambda$ induces a preferred physically meaningful quantum state $\lambda_M$ for the quantum theory in the bulk. If $M$ admits a timelike Killing generator preserving \scrim, then the associated self-adjoint generator in the GNS representation of $\lambda_M$ has positive spectrum (i.e. energy). Moreover $\lambda_M$ turns out to be invariant under every symmetry of the bulk metric which preserves the cosmological horizon. In the case of an expanding de Sitter spacetime, $\lambda_M$ coincides with the Euclidean (Bunch-Davies) vacuum state, hence being Hadamard in this case. Remarks on the validity of the Hadamard property for $\lambda_M$ in more general spacetimes are presented.Comment: 32 pages, 1 figure, to appear on Comm. Math. Phys., dedicated to Professor Klaus Fredenhagen on the occasion of his 60th birthda