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

A Test of CPT Symmetry in K^0 vs \bar{K}^0 to \pi^+\pi^-\pi^0 Decays

I show that the CP-violating asymmetry in K^0 vs \bar{K}^0 \to \pi^+\pi^-\pi^0 decays differs from that in K_L \to \pi^+\pi^-, K_L \to \pi^0\pi^0 or the semileptonic K_L transitions, if there exists CPT violation in K^0-\bar{K}^0 mixing. A delicate measurement of this difference at a super flavor factory (e.g., the \phi factory) will provide us with a robust test of CPT symmetry in the neutral kaon system.Comment: 4 pages, 1 figure. To appear in the Proceedings of the International PHIPSI09 Workshop, October 2009, Beijing, Chin

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

Microbial methane formation in deep aquifers of a coal-bearing sedimentary basin, Germany

Published version. Also available at http://dx.doi.org/10.3389/fmicb.2015.00200Coal-bearing sediments are major reservoirs of organic matter potentially available for methanogenic subsurface microbial communities. In this study the specific microbial community inside lignite-bearing sedimentary basin in Germany and its contribution to methanogenic hydrocarbon degradation processes was investigated. The stable isotope signature of methane measured in groundwater and coal-rich sediment samples indicated methanogenic activity. Analysis of 16S rRNA gene sequences showed the presence of methanogenic Archaea, predominantly belonging to the orders Methanosarcinales and Methanomicrobiales, capable of acetoclastic or hydrogenotrophic methanogenesis. Furthermore, we identified fermenting, sulfate-, nitrate-, and metal-reducing, or acetogenic Bacteria clustering within the phyla Proteobacteria, complemented by members of the classes Actinobacteria, and Clostridia. The indigenous microbial communities found in the groundwater as well as in the coal-rich sediments are able to degrade coal-derived organic components and to produce methane as the final product. Lignite-bearing sediments may be an important nutrient and energy source influencing larger compartments via groundwater transport

Hadamard States and Adiabatic Vacua

Reversing a slight detrimental effect of the mailer related to TeXabilityComment: 10pages, LaTeX (RevTeX-preprint style

Does threat trigger prosociality? The relation between basic individual values, threat appraisals, and prosocial helping intentions during the COVID-19 pandemic

Prosociality is often considered as quintessential in coping with the threats of health emergencies. As previous research has suggested, prosocial behaviors are shaped by both dispositional factors and situational cues about the helping situation. In the present research, we investigated whether “bonding” types of prosociality, helping directed towards close others within one’s social network, and “bridging” types of prosociality, helping directed towards vulnerable people across group boundaries, are predicted by basic individual values and threat appraisals concerning COVID-19. During the pandemic, we conducted a cross-sectional study in the US and India (Ntotal = 954), using the Schwartz value inventory and a multifaceted measure of threat assessment to predict prosocial helping intentions. After controlling for other value and threat facets, self-transcendence values and threat for vulnerable groups uniquely predicted both bonding and bridging types of prosociality. Furthermore, threat for vulnerable groups partially mediated the effect of self-transcendence on prosocial helping intentions: People who endorsed self-transcendent values were particularly concerned by the effect of the pandemic on vulnerable groups, and thus willing to engage in prosocial behaviours to help those in need. Our findings support the idea that prosociality is stimulated by empathic concerns towards others in need and underline the importance for future research to consider the broad spectrum of threats appraised by people during health emergencies

Electric field effects on magnetotransport properties of multiferroic Py/YMnO3/Pt heterostructures

We report on the exchange bias between antiferromagnetic and ferroelectric hexagonal YMnO3 epitaxial thin films sandwiched between a metallic electrode (Pt) and a soft ferromagnetic layer (Py). Anisotropic magnetoresistance measurements are performed to monitor the presence of an exchange bias field. When the heteroestructure is biased by an electric field, it turns out that the exchange bias field is suppressed. We discuss the dependence of the observed effect on the amplitude and polarity of the electric field. Particular attention is devoted to the role of current leakage across the ferroelectric layer.Comment: Accepted for publication in Philosophical Magazine Letters (Special issue on multiferroics