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- TRENTOOL: an open source toolbox to estimate neural directed interactions with transfer entropy (2011)
- Poster presentation from Twentieth Annual Computational Neuroscience Meeting: CNS*2011 Stockholm, Sweden. 23-28 July 2011. Poster presentation To investigate directed interactions in neural networks we often use Norbert Wiener's famous definition of observational causality. Wiener’s definition states that an improvement of the prediction of the future of a time series X from its own past by the incorporation of information from the past of a second time series Y is seen as an indication of a causal interaction from Y to X. Early implementations of Wiener's principle – such as Granger causality – modelled interacting systems by linear autoregressive processes and the interactions themselves were also assumed to be linear. However, in complex systems – such as the brain – nonlinear behaviour of its parts and nonlinear interactions between them have to be expected. In fact nonlinear power-to-power or phase-to-power interactions between frequencies are reported frequently. To cover all types of non-linear interactions in the brain, and thereby to fully chart the neural networks of interest, it is useful to implement Wiener's principle in a way that is free of a model of the interaction [1]. Indeed, it is possible to reformulate Wiener's principle based on information theoretic quantities to obtain the desired model-freeness. The resulting measure was originally formulated by Schreiber [2] and termed transfer entropy (TE). Shortly after its publication transfer entropy found applications to neurophysiological data. With the introduction of new, data efficient estimators (e.g. [3]) TE has experienced a rapid surge of interest (e.g. [4]). Applications of TE in neuroscience range from recordings in cultured neuronal populations to functional magnetic resonanace imaging (fMRI) signals. Despite widespread interest in TE, no publicly available toolbox exists that guides the user through the difficulties of this powerful technique. TRENTOOL (the TRansfer ENtropy TOOLbox) fills this gap for the neurosciences by bundling data efficient estimation algorithms with the necessary parameter estimation routines and nonparametric statistical testing procedures for comparison to surrogate data or between experimental conditions. TRENTOOL is an open source MATLAB toolbox based on the Fieldtrip data format. We evaluated the performance of the toolbox on simulation data and also a neuronal dataset that provides connections that are truly unidirectional to circumvent the following generic problem: typically, for any result of an analysis of directed interactions in the brain there will be a plausible explanation because of the combination of feedforward and feedback connectivity between any two measurement sites. Therefore, we estimated TE between the electroretinogram (ERG) and the LFP response in the tectum of the turtle (Chrysemys scripta elegans) under visual stimulation by random light pulses. In addition, we also investigated transfer entropy between the input to the light source (TTL pulse) and the ERG, to test the ability of TE to detect directed interactions between signals with vastly different properties. We found significant (p<0.0005) causal interactions from the TTL pulse to the ERG and from the ERG to the tectum – as expected. No significant TE was detected in the reverse direction. CONCLUSION: TRENTOOL is an easy to use implementation of transfer entropy estimation combined with statistical testing routines suitable for the analysis of directed interactions in neuronal data.

- The new p-process database of KADoNiS (2010)
- The KADoNiS (Karlsruhe Astrophysical Database of Nucleosynthesis in Stars) project is an online database (www.kadonis.org) for cross sections relevant to the s-process and the p-process. The first version was an updated sequel to the previous Bao et al. [1] compilations from 1987 and 2000 for (n; g) cross sections relevant to Big Bang and s-process nucleosynthesis. The first update, KADoNiS v0.2, was published in 2006 [2]. It contained mainly Maxwellian averaged (n; g) cross sections relevant to the s-process, and some experimental charged particle induced reaction relevant to the p-process. After that a second update was presented in 2009 [3]. Recently, we started to collect and review all existing experimental data relevant for p-process nucleosynthesis and to provide a user-friendly database based on the KADoNiS framework. The p-process part of the KADoNiS database is currently being extended and will include all available experimental data from (p; g), (p;n), (p;a), (a,g), (a;n) and (a; p) reactions in or close to the respective Gamow window.

- Fluctuations in statistical models (2007)
- Proceedings of 4th International Workshop "Critical Point and Onset of Deconfinement", July 9-13, 2007, Darmstadt, Germany: The multiplicity fluctuations of hadrons are studied within the statistical hadron-resonance gas model in the large volume limit. The role of quantum statistics and resonance decay effects are discussed. The microscopic correlator method is used to enforce conservation of three charges - baryon number, electric charge, and strangeness - in the canonical ensemble. In addition, in the micro-canonical ensemble energy conservation is included. An analytical method is used to account for resonance decays. The multiplicity distributions and the scaled variances for negatively and positively charged hadrons are calculated for the sets of thermodynamical parameters along the chemical freeze-out line of central Pb+Pb (Au+Au) collisions from SIS to LHC energies. Predictions obtained within different statistical ensembles are compared with the preliminary NA49 experimental results on central Pb+Pb collisions in the SPS energy range. The measured fluctuations are significantly narrower than the Poisson ones and clearly favor expectations for the micro-canonical ensemble. Thus, this is a first observation of the recently predicted suppression of the multiplicity fluctuations in relativistic gases in the thermodynamical limit due to conservation laws.

- Molecular dynamics simulations and docking of non-nucleoside reverse transcriptase inhibitors (NNRTIs): a possible approach to personalized HIV treatment : from 7th German Conference on Chemoinformatics: 25 CIC-Workshop Goslar, Germany, 6 - 8 November 2011 (2012)
- The human immunodeficiency virus (HIV) is currently ranked sixth in the worldwide causes of death [1]. One treatment approach is to inhibit reverse transcriptase (RT), an enzyme essential for reverse transcription of viral RNA into DNA before integration into the host genome [2]. By using non-nucleoside RT inhibitors (NNRTIs) [3], which target an allosteric binding site, major side effects can be evaded. Unfortunately, high genetic variability of HIV in combination with selection pressure introduced by drug treatment enables the virus to develop resistance against this drug class by developing point mutations. This situation necessitates treatment with alternative NNRTIs that target the particular RT mutants encountered in a patient. Previously, proteochemometric approaches have demonstrated some success in predicting binding of particular NNRTIs to individual mutants; however a structurebased approach may help to further improve the predictive success of such models. Hence, our aim is to rationalize the experimental activity of known NNRTIs against a variety of RT mutants by combining molecular modeling, long-timescale atomistic molecular dynamics (MD) simulation sampling and ensemble docking. Initial control experiments on known inhibitor-RT mutant complexes using this protocol were successful, and the predictivity for further complexes is currently being evaluated. In addition to predictive power, MD simulations of multiple RT mutants are providing fundamental insight into the dynamics of the allosteric NNRTI binding site which is useful for the design of future inhibitors. Overall, work of this type is hoped to contribute to the development of predictive efficacy models for individual patients, and hence towards personalized HIV treatment options.

- A demonstrator for the Micro-Vertex-Detector of the CBM experiment (2010)
- CMOS sensors are the most promising candidates for the Micro-Vertex-Detector (MVD) of the CBM experiment at GSI, as they provide an unprecedented compromise between spatial resolution, low material budget, adequate radiation tolerance and readout speed. To study the integration of these sensors into a detector module, a so-called MVD-demonstrator has been developed. The demonstrator and its in-beam performance will be presented and discussed in this work.

- Status of the Micro Vertex Detector of the Compressed Baryonic Matter Experiment (2010)
- The CBM experiment will investigate heavy-ion collisions at beam energies from 8 to 45 AGeV at the future accelerator facility FAIR. The goal of the experiment is to study the QCD phase diagram in the vincinity of the QCD critical point. To do so, CBM aims at measuring rare probes among them open charm. In order to identify those rare and short lived particles despite the rich combinatorial background generated in heavy ion collisions, a micro vertex detector (MVD) providing an unprecedented combination of high rate capability and radiation hardness, very light material budget and excellent granularity is required. In this work, we will discuss the concept of this detector and summarize the status of the R&D.

- The QCD phase diagram at zero and small baryon density (2005)
- I review recent developments in determining the QCD phase diagram by means of lattice simulations. Since the invention of methods to side-step the sign problem a few years ago, a number of additional variants have been proposed, and progress has been made towards understanding some of the systematics involved. All available techniques agree on the transition temperature as a function of density in the regime mq/T <~1. There are by now four calculations with signals for a critical point, two of them at similar parameter values and with consistent results. However, it also emerges that the location of the critical point is exceedingly quark mass sensitive. At the same time sizeable finite volume, cut-off and step size effects have been uncovered, demanding additional investigations with exact algorithms on larger and finer lattices before quantitative conclusions can be drawn. Depending on the sign of these corrections, there is ample room for the eventual phase diagram to look as expected or also quite different, with no critical point at all.

- QCD equation of state and dark matter (2006)
- The QCD equation of state is not often discussed in cosmology. However, the relic density of weakly interacting massive particles (WIMPs) depends on the entropy and the expansion rate of the Universe when they freeze out, at a temperature in the range 400 MeV – 40GeV, where QCD corrections are still important. We use recent analytic and lattice calculations of the QCD pressure to produce a new equation of state suitable for use in relic density calculations. As an example, we show that relic densities calculated by the dark matter package DarkSUSY receive corrections of several per cent, within the observational accuracy of the Planck CMB mission, due for launch in 2007.

- Strong coupling expansion for Yang-Mills theory at finite temperature (2007)
- Euclidean strong coupling expansion of the partition function is applied to lattice Yang-Mills theory at finite temperature, i.e. for lattices with a compactified temporal direction. The expansions have a finite radius of convergence and thus are valid only for b <bc, where bc denotes the nearest singularity of the free energy on the real axis. The accessible temperature range is thus the confined regime up to the deconfinement transition. We have calculated the first few orders of these expansions of the free energy density as well as the screening masses for the gauge groups SU(2) and SU(3). The resulting free energy series can be summed up and corresponds to a glueball gas of the lowest mass glueballs up to the calculated order. Our result can be used to fix the lower integration constant for Monte Carlo calculations of the thermodynamic pressure via the integral method, and shows from first principles that in the confined phase this constant is indeed exponentially small. Similarly, our results also explain the weak temperature dependence of glueball screening masses below Tc, as observed in Monte Carlo simulations. Possibilities and difficulties in extracting bc from the series are discussed.