Nonlinear denoising of transient signals with application to event related potentials

We present a new wavelet based method for the denoising of {\it event related potentials} ERPs), employing techniques recently developed for the paradigm of deterministic chaotic systems. The denoising scheme has been constructed to be appropriate for short and transient time sequences using circular state space embedding. Its effectiveness was successfully tested on simulated signals as well as on ERPs recorded from within a human brain. The method enables the study of individual ERPs against strong ongoing brain electrical activity.Comment: 16 pages, Postscript, 6 figures, Physica D in pres

Impact of Sodium Layer variations on the performance of the E-ELT MCAO module

Multi-Conjugate Adaptive Optics systems based on sodium Laser Guide Stars may exploit Natural Guide Stars to solve intrinsic limitations of artificial beacons (tip-tilt indetermination and anisoplanatism) and to mitigate the impact of the sodium layer structure and variability. The sodium layer may also have transverse structures leading to differential effects among Laser Guide Stars. Starting from the analysis of the input perturbations related to the Sodium Layer variability, modeled directly on measured sodium layer profiles, we analyze, through a simplified end-to-end simulation code, the impact of the low/medium orders induced on global performance of the European Extremely Large Telescope Multi-Conjugate Adaptive Optics module MAORY.Comment: 7 pages, 5 figures, SPIE conference Proceedin

Divergence Measure Between Chaotic Attractors

We propose a measure of divergence of probability distributions for quantifying the dissimilarity of two chaotic attractors. This measure is defined in terms of a generalized entropy. We illustrate our procedure by considering the effect of additive noise in the well known H\'enon attractor. Comparison of two H\'enon attractors for slighly different parameter values, has shown that the divergence has complex scaling structure. Finally, we show how our approach allows to detect non-stationary events in a time series.Comment: 9 pages, 6 figure

Editing, validating and translating of SBGN maps

Motivation: The recently proposed Systems Biology Graphical Notation (SBGN) provides a standard for the visual representation of biochemical and cellular processes. It aims to support more efficient and accurate communication of biological knowledge between different research communities in the life sciences. However, to increase the use of SBGN, tools for editing, validating and translating SBGN maps are desirable

Coherent laser control of the current through molecular junctions

The electron tunneling through a molecular junction modeled by a single site weakly coupled to two leads is studied in the presence of a time-dependent external field using a master equation approach. In the case of small bias voltages and high carrier frequencies of the external field, we observe the phenomenon of coherent destruction of tunneling, i.e. the current through the molecular junction vanishes completely for certain parameters of the external field. In previous studies the tunneling within isolated and open multi-site systems was suppressed; it is shown here that the tunneling between a single site and electronic reservoirs, i.e. the leads, can be suppressed as well. For larger bias voltages the current does not vanish any more since further tunneling channels participate in the electron conduction and we also observe photon-assisted tunneling which leads to steps in the current-voltage characteristics. The described phenomena are demonstrated not only for monochromatic fields but also for laser pulses and therefore could be used for ultrafast optical switching of the current through molecular junctions.Comment: 6 pages and 4 figure

Spatially explicit analysis of gastropod biodiversity in ancient Lake Ohrid

The quality of spatial analyses of biodiversity is improved by (i) utilizing study areas with well defined physiogeographical boundaries, (ii) limiting the impact of widespread species, and (iii) using taxa with heterogeneous distributions. These conditions are typically met by ecosystems such as oceanic islands or ancient lakes and their biota. While research on ancient lakes has contributed significantly to our understanding of evolutionary processes, statistically sound studies of spatial variation of extant biodiversity have been hampered by the frequently vast size of ancient lakes, their limited accessibility, and the lack of scientific infrastructure. The European ancient Lake Ohrid provides a rare opportunity for such a reliable spatial study. The comprehensive horizontal and vertical sampling of a species-rich taxon, the Gastropoda, presented here, revealed interesting patterns of biodiversity, which, in part, have not been shown before for other ancient lakes. <br><br> In a total of 284 samples from 224 different locations throughout the Ohrid Basin, 68 gastropod species, with 50 of them (= 73.5%) being endemic, could be reported. The spatial distribution of these species shows the following characteristics: (i) within Lake Ohrid, the most frequent species are endemic taxa with a wide depth range, (ii) widespread species (i.e. those occurring throughout the Balkans or beyond) are rare and mainly occur in the upper layer of the lake, (iii) while the total number of species decreases with water depth, the proportion of endemics increases, and (iv) the deeper layers of Lake Ohrid appear to have a higher spatial homogeneity of biodiversity. Moreover, gastropod communities of Lake Ohrid and its feeder springs are both distinct from each other and from the surrounding waters. The analysis also shows that community similarity of Lake Ohrid is mainly driven by niche processes (e.g. environmental factors), but also by neutral processes (e.g. dispersal limitation and evolutionary histories of species). For niche-based mechanisms it is shown that large scale effects such as type of water body or water depth are mainly responsible for the similarity of gastropod communities, whereas small scale effects like environmental gradients affect gastropod compositions only marginally. In fact, neutral processes appear to be more important than the small scale environmental factors, thus emphasizing the importance of dispersal capacities and evolutionary histories of species

Invasive compute balancing for applications with shared and hybrid parallelization

This is the author manuscript. The final version is available from the publisher via the DOI in this record.Achieving high scalability with dynamically adaptive algorithms in high-performance computing (HPC) is a non-trivial task. The invasive paradigm using compute migration represents an efficient alternative to classical data migration approaches for such algorithms in HPC. We present a core-distribution scheduler which realizes the migration of computational power by distributing the cores depending on the requirements specified by one or more parallel program instances. We validate our approach with different benchmark suites for simulations with artificial workload as well as applications based on dynamically adaptive shallow water simulations, and investigate concurrently executed adaptivity parameter studies on realistic Tsunami simulations. The invasive approach results in significantly faster overall execution times and higher hardware utilization than alternative approaches. A dynamic resource management is therefore mandatory for a more efficient execution of scenarios similar to our simulations, e.g. several Tsunami simulations in urgent computing, to overcome strong scalability challenges in the area of HPC. The optimizations obtained by invasive migration of cores can be generalized to similar classes of algorithms with dynamic resource requirements.This work was supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Centre ”Invasive Computing” (SFB/TR 89)

Test your surrogate data before you test for nonlinearity

The schemes for the generation of surrogate data in order to test the null hypothesis of linear stochastic process undergoing nonlinear static transform are investigated as to their consistency in representing the null hypothesis. In particular, we pinpoint some important caveats of the prominent algorithm of amplitude adjusted Fourier transform surrogates (AAFT) and compare it to the iterated AAFT (IAAFT), which is more consistent in representing the null hypothesis. It turns out that in many applications with real data the inferences of nonlinearity after marginal rejection of the null hypothesis were premature and have to be re-investigated taken into account the inaccuracies in the AAFT algorithm, mainly concerning the mismatching of the linear correlations. In order to deal with such inaccuracies we propose the use of linear together with nonlinear polynomials as discriminating statistics. The application of this setup to some well-known real data sets cautions against the use of the AAFT algorithm.Comment: 14 pages, 15 figures, submitted to Physical Review