Numerical equilibrium analysis for structured consumer resource models

In this paper, we present methods for a numerical equilibrium and stability analysis for models of a size structured population competing for an unstructured resource. We concentrate on cases where two model parameters are free, and thus existence boundaries for equilibria and stability boundaries can be defined in the (two-parameter) plane. We numerically trace these implicitly defined curves using alternatingly tangent prediction and Newton correction. Evaluation of the maps defining the curves involves integration over individual size and individual survival probability (and their derivatives) as functions of individual age. Such ingredients are often defined as solutions of ODE, i.e., in general only implicitly. In our case, the right-hand sides of these ODE feature discontinuities that are caused by an abrupt change of behavior at the size where juveniles are assumed to turn adult. So, we combine the numerical solution of these ODE with curve tracing methods. We have implemented the algorithms for “Daphnia consuming algae” models in C-code. The results obtained by way of this implementation are shown in the form of graphs

Decreased myocardial injury and improved contractility after administration of a peptide derived against the alpha-interacting domain of the L-type calcium channel.

BackgroundMyocardial infarction remains the leading cause of morbidity and mortality associated with coronary artery disease. The L-type calcium channel (IC a-L) is critical to excitation and contraction. Activation of the channel also alters mitochondrial function. Here, we investigated whether application of a alpha-interacting domain/transactivator of transcription (AID-TAT) peptide, which immobilizes the auxiliary β2 subunit of the channel and decreases metabolic demand, could alter mitochondrial function and myocardial injury.Methods and resultsTreatment with AID-TAT peptide decreased ischemia-reperfusion injury in guinea-pig hearts ex vivo (n=11) and in rats in vivo (n=9) assessed with uptake of nitroblue tetrazolium, release of creatine kinase, and lactate dehydrogenase. Contractility (assessed with catheterization of the left ventricle) was improved after application of AID-TAT peptide in hearts ex vivo (n=6) and in vivo (n=8) up to 12 weeks before sacrifice. In search of the mechanism for the effect, we found that intracellular calcium ([Ca(2+)]i, Fura-2), superoxide production (dihydroethidium fluorescence), mitochondrial membrane potential (Ψm, JC-1 fluorescence), reduced nicotinamide adenine dinucleotide production, and flavoprotein oxidation (autofluorescence) are decreased after application of AID-TAT peptide.ConclusionsApplication of AID-TAT peptide significantly decreased infarct size and supported contractility up to 12 weeks postcoronary artery occlusion as a result of a decrease in metabolic demand during reperfusion

Deterministic entanglement of ions in thermal states of motion

We give a detailed description of the implementation of a Molmer-Sorensen gate entangling two Ca+ ions using a bichromatic laser beam near-resonant with a quadrupole transition. By amplitude pulse shaping and compensation of AC-Stark shifts we achieve a fast gate operation without compromising the error rate. Subjecting different input states to concatenations of up to 21 individual gate operations reveals Bell state fidelities above 0.80. In principle, the entangling gate does not require ground state cooling of the ions as long as the Lamb-Dicke criterion is fulfilled. We present the first experimental evidence for this claim and create Bell states with a fidelity of 0.974(1) for ions in a thermal state of motion with a mean phonon number of =20(2) in the mode coupling to the ions' internal states.Comment: 18 pages, 9 figures (author name spelling corrected

Irreversible nucleation in molecular beam epitaxy: From theory to experiments

Recently, the nucleation rate on top of a terrace during the irreversible growth of a crystal surface by MBE has been determined exactly. In this paper we go beyond the standard model usually employed to study the nucleation process, and we analyze the qualitative and quantitative consequences of two important additional physical ingredients: the nonuniformity of the Ehrlich-Schwoebel barrier at the step-edge, because of the existence of kinks, and the steering effects, due to the interaction between the atoms of the flux and the substrate. We apply our results to typical experiments of second layer nucleation.Comment: 11 pages. Table I corrected and one appendix added. To be published in Phys. Rev. B (scheduled issue: 15 February 2003

EIT ground-state cooling of long ion strings

Electromagnetically-induced-transparency (EIT) cooling is a ground-state cooling technique for trapped particles. EIT offers a broader cooling range in frequency space compared to more established methods. In this work, we experimentally investigate EIT cooling in strings of trapped atomic ions. In strings of up to 18 ions, we demonstrate simultaneous ground state cooling of all radial modes in under 1 ms. This is a particularly important capability in view of emerging quantum simulation experiments with large numbers of trapped ions. Our analysis of the EIT cooling dynamics is based on a novel technique enabling single-shot measurements of phonon numbers, by rapid adiabatic passage on a vibrational sideband of a narrow transition

A Linked Data Approach to Sharing Workflows and Workflow Results

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users