CONTENTS -- Workshop photographs -- Organizing Committees -- Preface -- Memory of Livio Scarsi -- Part A - Astrophysics, Cosmology and Earth Physics -- Simulations for UHE Cosmic Ray Experiments J. Knapp -- 1. Cosmic Rays and Air Showers -- 2. The Pierre Auger Observatory -- 3. Simulations versus Models -- 4. Air Shower Simulations and the CORSIKA Program -- 5. Some Selected Details -- 6. Outlook -- Acknowledgement -- References -- Detector Modeling in Astroparticle Physics S. Petrera -- 1. Introduction -- 2. MACRO as a ν detector -- 2.1. Atmospheric neutrinos and their oscillation -- 2.2. Physics and detector simulation -- 2.3. Data interpretation -- 3. Cosmic Rays studies with the Pierre Auger experiment -- 3.1. The detector simulation -- 3.2. The Surface Detector -- 3.3. The Fluorescence Detector -- 3.4. Hybrid events -- References -- Simulating a Large Cosmic Ray Experiment: The Pierre Auger Observatory T. Paul -- 1. Introduction -- 2. The Pierre Auger Observatory -- 3. Software Framework -- 4. Detector Simulation -- 4.1. Surface array -- 4.1.1. Water tank simulation -- 4.2. Fluorescence telescopes -- 5. Conclusions -- 6. Acknowledgments -- References -- Testing of Cosmic Ray Interaction Models at LHC Collider P. Neˇcesal, J. ˇR ídký -- 1. Introduction -- 2. Comparison of Models -- 3. Conclusions -- References -- Observations, Simulations, and Modeling of Space Plasma Waves: A Perspective on Space Weather V. S. Sonwalkar -- 1. Introduction -- 2. Atmosphere-Ionosphere-Magnetosphere System and its Solar Drivers -- 3. Plasma Waves -- 3.1. Observations of plasma waves -- 3.2. Generation and propagation of plasma waves -- 3.3. Modeling and simulations of plasma waves -- 3.4. Contribution of plasma waves to space weather: wave-particle interactions -- 3.5. Monitoring space weather using plasma waves -- 4. Concluding Remarks -- Acknowledgments.

References -- Electron Flux Maps of Solar Flares: A Regularization Approach to Rhessi Imaging Spectroscopy A. M. Massone, M. Piana, M. Prato, A. G. Emslie, G. J. Hurford, E. P. Kontar, R. A. Scwartz -- 1. Introduction -- 2. Visibilities -- 3. Electron Flux Spectrum Images -- 4. Application to RHESSI Data -- 5. Conclusions -- References -- Problems and Solutions in Climate Modeling A. Sutera -- 1. Introduction -- 2. The Equations of Motion -- 3. Parameter Settings and Numerical Solutions -- 4. An Heuristic Model -- 5. Conclusions -- Acknowledgments -- References -- Numerical Simulations and Diagnostics in Astrophysics: A few Magnetohydrodynamics Examples G. Peres, R. Bonito, S. Orlando, F. Reale -- 1. Introduction -- 2. Supernovae Remnants -- 3. Protostellar Jets -- 4. Conclusions -- 5. Acknowledgements -- References -- Numerical Simulations of Multi-Scale Astrophysical Problems: The example of Type Ia Supernovae F. K. Röpke -- 1. Introduction -- 2. Astrophysical Model -- 3. Challenges -- 4. Governing Equations -- 5. Modeling Approaches -- 6. Numerical Methods -- 7. Three-dimensional Type Ia Supernova Simulations -- References -- Numerical Simulations in Astropysics: From the Stellar Jets to the White Dwarfs F. Rubini, L. Delzanna, J. A. Biello, J. W. Truran -- 1. The Origin of the Optical Knots in Stellar Jets -- 1.1. Observations, physical model and numerical simulations -- 1.2. Results and comments -- 2. Numerical Simulations of pre-runaway CO White Dwarfs -- 2.1. Physical models, numerical tools and FAQ -- 2.2. Results -- 2.3. The small Rayleigh number case -- 2.4. The large Rayleigh number case -- 3. Conclusions -- Acknowledgments -- References -- Statistical Analysis of Quasar Data and Validity of the Hubble Law S. Roy, J. Ghosh, M. Roy, M. Kafatos -- 1. Introduction.

2. Statistical Analysis of Data from the V-C(2006) and SDSS Quasar Catalogues -- 2.1. Truncation relationship -- 2.2. Permutation tests of independence -- 3. Possible Implications and Discussion -- References -- Non-Parametric Tests for Quasar Data and Hubble Diagram S. Roy, D. Datta, J. Ghosh, M. Roy, M. Kafatos -- 1. Introduction -- 2. Statistical Analysis of Quasar Data from Véron-Cetty Catalogues -- 2.1. Truncation Relationship -- 2.2. Permutation Tests of Independence -- 3. Regression analysis of Data and Hubble Law -- 4. Possible Cosmological Implications -- References -- Doping: A New Non-Parametric Deprojection Scheme D. Chakrabarty, L. Ferrarese -- 1. Introduction -- 2. Method -- 3. Tests -- 4. Applications -- 5. 3-D Morphology of Galaxy Clusters -- 6. Summary -- References -- Quantum Astronomy and Information C. Barbieri -- 1. Introduction -- 2. Properties of Light in Astronomical Observations -- 3. The Intensity Interferometer -- 4. Intensity-Correlation Spectroscopy -- 5. Approaching the Heisenberg Limit: High Time Resolution Astrophysics -- 6. Ultimate Data Rates -- 7. Conclusions -- Acknowledgments -- References -- Mining the Structure of the Nearby Universe R. D'Abrusco, G. Longo, M. Brescia, E. De Filippis, M. Paolillo, A. Staiano, R. Tagliaferri -- 1. Introduction -- 2. Supervised and Unsupervised Methods -- 3. Photometric Redshifts for the SDSS Galaxies -- 3.1. Dataset and base of knowledge -- 3.2. Features selection -- 4. Steps Towards a Photometric Classi.cation of Galaxies -- Acknowledgments -- References -- Numerical Characterization of the Observed Point Spread Function of the VST Wide-Field Telescope G. Sedmak, S. Carrozza, G. Marra -- 1. Introduction -- 2. Simulation of the Atmospheric Seeing -- 3. Simulation of the Observed Point Spread Function -- 4. Mapping the Point Spread Function over the Field of View -- 5. Results.

6. Conclusions -- Acknowledgments -- References -- Part B - Biology, Biochemistry and Bioinformatics -- From Genomes to Protein Models and Back A. Tramontano, A. Giorgetti, M. Orsini, D. Raimondo -- 1. Introduction -- 1.1. The ENCODE project -- 1.2. The BioSapiens consortium -- 1.3. Protein structure prediction -- 1.4. The prediction of the structures of the GENCODE gene products -- 2. Results -- 3. Discussion -- Acknowledgments -- References -- Exploring Biomolecular Recognition by Modeling and Simulation R. Wade -- Acknowledgments -- References -- From Allergen Back to Antigen: A Rational Approach to New Forms of Immunotherapy P. Colombo, A. Trapani, D. Geraci, M. Golino, F. Gianguzza, A. Bonura -- 1. Introduction -- 2. Experimental Results -- 3. Conclusions -- References -- Sulfonylureas and Glinidies as New PPARγ Agonists: Virtual Screening and Biological Assays M. Scarsi, M. Podvinec, A. Roth, H. Hug, S. Kersten, H. Albrecht, T. Schwede, U. A. Meyer, C. Rücker -- 1. Introduction -- 2. Materials and Methods -- 3. Results -- 4. Discussion -- References -- A Multi-Layer Model to Study Genome-Scale Positions of Nucleosomes V. Di Gesú, G. Lo Bosco, L. Pinello, D. Corona, M. Collesano, G.-C. Yuan -- 1. Introduction -- 2. Multi-Layers Model -- 3. MLM validation -- 3.1. Synthetic data generation -- 3.2. Experimental results -- 4. Final remarks -- References -- BioInfogrid: BioInformatics Simulation and Modeling Based on Grid L. Milanesi -- 1. The GRID Bioinformatics Platform -- 1.1. Introduction -- 1.2. BioinfoGRID project -- 2. Methodology -- 2.1. Technology description -- 2.2. GRID database applications example -- 2.3. GRID large scale in silico docking application on avian .u -- 2.4. GRID based microarray expression pro.ling analysis -- 2.5. GRID based system biology model simulator -- 3. Conclusion -- Acknowledgments -- References.

Geometrical and Topological Modelling of Supercoiling in Supramolecular Structures L. Boi -- 1. The topological compaction of the double-helix molecule into the chromatin and the role of supercoiling -- 2. A mathematical model for explaining the interphase folding of chromatin .ber -- 3. Biological justi.cations for the model above -- 4. Conclusions and prospects -- References -- Part C - Methods and Techniques -- Optimisation Strategies for Modelling and Simulation J. Louchet -- 1. Exploring Parameter Spaces using Evolutionary Programming -- 2. Retrieving Patterns: following the Hough Transform -- 3. From Phenomena to Processes: Identifying Internal Parameters -- 4. Parisian Evolution or How To Split Optimisation: The Fly Algorithm -- 5. Conclusion -- References -- Modeling Complexity using Hierarchical Multi-Agent Systems J.-C. Heudin -- 1. Introduction -- 2. The Approach -- 3. Hierarchical Multi-agent Systems -- 4. Virtual Ecosystem Example -- 4.1. Overview -- 4.2. The hierarchical model -- 4.2.1. level 1 -- 4.2.2. level 2 -- 4.2.3. level 3 -- 4.3. Experimental results -- 4.4. Discussion -- 5. Cosmological Example -- 5.1. Overview -- 5.2. The hierarchical model -- 5.2.1. Level 1 -- 5.2.2. Level 2 -- 5.2.3. Level 3 -- 5.2.4. Level 4 -- 5.3. Experimental results -- 6. Discussion -- 7. Conclusion -- References -- Topological Approaches to Search and Matching in Massive Data Sets F. Murtagh -- 1. Introduction -- 2. Quantifying Degree of Ultrametricity -- 3. Ultrametricity and Dimensionality -- 3.1. Distance properties in very sparse spaces -- 3.2. No "curse of dimensionality" in very high dimensions -- 4. Increasing Ultrametricity Through Data Recoding: Ultrametricity of Time Series -- 5. Fast Clustering through Baire Space Embedding -- 6. Conclusions -- References.

Data Mining: Computational Theory of Perceptions and Rough-Fuzzy Granular Computing S. K. Pal.