Items where Year is 2008

Article

Abida, R. and Bocquet, M. and Vercauteren, N. and Isnard, O. (2008) Design of a monitoring network over France in case of a radiological accidental release. Atmospheric Environment, 42 (21). pp. 5205-5219. ISSN 1352-2310

Baldauf, M. (2008) Stability analysis for linear discretisations of the advection equation with Runge–Kutta time integration. Journal of Computational Physics, 227 (13). pp. 6638-6659.

Barth, I. and Manz, J. and Pérez-Hernández, G. and Sebald, P. (2008) Towards Toroidal Hydrogen Bonds. Zeitschrift für Physikalische Chemie, 222 (8-9). pp. 1311-1331. ISSN 0942-9352

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138.

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138. ISSN 0010-485X

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part I: Abstract framework. Computing, 82 (2-3). pp. 103-119. ISSN 0010-485X

Bauer, M. and Klau, G. W. and Reinert, K. (2008) An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Operations Research .

Bodirsky, M. and Gröpl, C. and Kang, M. (2008) Generating unlabeled connected cubic planar graphs uniformly at random. Random Structures and Algorithms, 32 (2). pp. 157-180.

Bou-Zeid, E. and Vercauteren, N. and Parlange, M. B. and Meneveau, C. (2008) Scale dependence of subgrid-scale model coefficients: An a priori study. Physics of Fluid, 20 (115106).

Carqué, G. and Schmidt, H. and Stevens, B. and Klein, R. (2008) Plausibility Check of an Asymptotic Column Model for Deep Convective Clouds. ZIB-Report, 08 (44).

Carqué, G. and Owinoh, A.Z. and Klein, R. and Majda, A. J. (2008) Asymptotic Scale Analysis of Precipitating Clouds. ZIB-Report, 08-03 . ISSN 1438-0064

Craig, G.C. and Dörnbrack, A. (2008) Entrainment in Cumulus Clouds: What resolution is cloud resolving? J. Atmos. Sci., 65 . pp. 3978-3988. ISSN Online 1520-0469 Print 0022-4928

Doyle, J.D. and Grubišić, V. and Brown, W.O.J. and De Wekker, S.F.J. and Dörnbrack, A. and Jiang, Q. and Mayor, S.D. and Weissman, M. (2008) Observations and Numerical Simulations of Subrotor Vortices during T-REX. J. Atmos. Sci., 66 (5). ISSN Online 1520-0469 Print 0022-4928

Döring, A. and Weese, D. and Rausch, T. and Reinert, K. (2008) SeqAn -- An efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9 (1). p. 11.

Fermanian Kammerer, C. and Lasser, C. (2008) Propagation through Generic Level Crossings: A Surface Hopping Semigroup. J. Math. Anal., 40 (1). pp. 103-133.

Fermanian Kammerer, C. and Lasser, C. (2008) Single switch surface hopping for molecular dynamics with transitions. J. Chem. Phys., 128 (14). p. 144102.

Frigato, T. and VandeVondele, J. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2008) Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion: From an Interior to a Surface Located Excess Electron via a Delocalized State. J. Phys. Chem. A, 112 (27). pp. 6125-6133.

Futterer, B. and Gellert, M. and von Larcher, T. and Egbers, C. (2008) Thermal convection in rotating spherical shells: An experimental and numerical approach within GeoFlow. Acta Astronautica, 62 (4). pp. 300-307.

Gassner, G. and Lörcher, F. and Munz , C.-D. (2008) A Discontinuous Galerkin Scheme based on a Space-Time Expansion II. Viscous Flow Equations in Multi Dimensions. Journal of Scientific Computing, 34 (3). pp. 260-286. ISSN 0885-7474 (Print) 1573-7691 (Online)

Hartmann, C. and Schütte, Ch. (2008) Balancing of partially-observed stochastic differential equations. 47th IEEE Conference on Decision and Control . pp. 4867-4872.

Hartmann, C. (2008) An Ergodic Sampling Scheme for Constrained Hamiltonian Systems with Applications to Molecular Dynamics. J. Stat. Phys., 130 (4). pp. 687-712.

Hartmann, C. (2008) Structure-preserving model reduction of partially observed differential equations: molecular dynamics and beyond. Oberwolfach Reports, 5 (2). pp. 1111-1115.

Horenko, I. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model Reduction for Time Series Analysis. Multiscale Modeling & Simulation, 6 (4). p. 1125. ISSN 15403467

Horenko, I. (2008) On Simultaneous Data-Based Dimension Reduction and Hidden Phase Identification. J. Atm. Sci, 65 (6). pp. 1941-1954.

Horenko, I. and Dolaptchiev, S. and Eliseev, A. and Mokhov, I. and Klein, R. (2008) Metastable Decomposition of High-Dimensional Meteorological Data with Gaps. Journal of the Atmospheric Sciences, 65 (11). pp. 3479-3496.

Horenko, I. and Klein, R. and Dolaptchiev, S. and Schütte, Ch. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model reduction for Time Series Analysis. Mult. Mod. Sim., 6 (4). pp. 1125-1145.

Horenko, I. (2008) On robust estimation of low-frequency variability trends in discrete Markovian sequences of atmospheric circulation patterns. J. Atm. Sci. . (In Press)

Horenko, I. and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Schütte, Ch. (2008) Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA. J. Appl. Dyn. Syst., 7 (2). pp. 532-560.

Horenko, I. and Schütte, Ch. (2008) Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications. Adv. Data Anal. Class., submitted . (Submitted)

Horenko, I. and Schütte, Ch. (2008) Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics. Mult. Mod. Sim., 7 (2). pp. 731-773.

John, V. and Schmeyer, E. (2008) Finite element methods for time-dependent convection-diffusion-reaction equations with small diffusion. Computer methods in applied mechanics and engineering, 198 (3). pp. 475-494. ISSN 0045-7825

Kadioglu, S.Y. and Minion, M.L. and Klein, R. (2008) A Fourth-Order Auxiliary Variable Projection Method for Zero-Mach Number Gas Dynamics. Journal of Computational Physics , 227 (3). 2012-2043 .

Klein, R. (2008) An Unified Approach to Meteorological Modelling Based on Multiple-Scales Asymptotics. Advances in Geosciences, 15 . pp. 23-33.

Kornhuber, R. and Krause, R. and Sander, O. and Deuflhard, P. and Ertel, S. (2008) A monotone multigrid solver for two body contact problems in biomechanics. Computing and Visualization in Science, 11 (1). pp. 3-15. ISSN 1432-9360

Kornhuber, R. and Yserentant, H. (2008) Multigrid methods for discrete elliptic problems on triangular surfaces. Computing and Visualization in Science, 11 (4-6). pp. 251-257. ISSN 1432-9360

Lange, E. and Tautenhahn, R. and Neumann, S. and Gröpl, C. (2008) Critical assessment of alignment procedures for LC-MS proteomics and metabolomic measurements. BMC Bioinformatics, 9 (375).

Lasser, C. and Swart, T. (2008) Single switch surface hopping for a model of pyrazine. J. Chem.Phys., 129 (03). 034302.

Letzel, O. and Krane, M. and Raasch, S. (2008) High resolution urban large-eddy simulation studies from street canyon to neighbourhood scale. Atmospheric Environment, 42 (38). 8770-8784 .

Matute, R. A. and Contreras, R. and Pérez-Hernández, G. and González, L. (2008) The Chromophore Structure of the Cyanobacterial Phytochrome Cph1 As Predicted by Time-Dependent Density Functional Theory. The Journal of Physical Chemistry B, 112 (51). pp. 16253-16256. ISSN 1520-6106

Meerbach, E. and Schütte, Ch. (2008) Sequential Change Point Detection in Molecular Dynamics Trajectories. Journal of Multivariate Analysis, submitted .

Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2008) Two-fluid formulation of the cloud-top mixing layer for direct numerical simulation. Theoretical and Computational Fluid Dynamics . (Submitted)

Münch, M. and Klein, R. (2008) Anforderungen an numerische Berechnungen der Brand- und Rauchausbreitung im Vorbeugenden Brandschutz. vfdb-Zeitschrift Forschung, Technik und Management im Brandschutz, Jg. 57 (3). pp. 145-151. ISSN 0042-1804

Münch, M. and Klein, R. (2008) Critical numerical aspects for field model applications. EUSAS Journal (4). pp. 41-54.

Münch, M. (2008) MOLOCH - Ein Strömungsverfahren für inkompressible Strömungen - Technische Referenz. PIK-Report (109).

Noé, F. (2008) Probability Distributions of Molecular Observables computed from Markov Models. J. Chem. Phys., 128 . p. 244103.

Noé, F. and Daidone, I. and Smith, J. C. and Di Nola, A. and Amadei, A. (2008) Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation. J. Phys. Chem. B, 112 . pp. 11155-11163.

Noé, F. and Fischer, S. (2008) Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules. Curr. Opin. Struct. Biol., 18 . pp. 154-162.

Oevermann, M. and Schmidt, H. and Kerstein, A.R. (2008) HCCI combustion modeling using detailed chemistry coupled to LEM-based advection. Combustion and Flame, 155 . pp. 370-379.

Oevermann, M. and Schmidt, H. and Kerstein, A.R. (2008) Investigation of autoignition under thermal stratification using linear eddy modeling. Combustion and Flame Volume, 155 (3). 370-379 .

Papke, A. (2008) Wie viele Zahlen müssen es sein? Die Junge Wissenschaft, 79 . pp. 46-51.

Petoukhov, V. and Eliseev, A. and Klein, R. and Oesterle, H. (2008) On the statistics of the free-troposphere synoptic component. Part I: An evaluation of skewnesses and estimation of the third-order moments contribution to the synoptic-scale dynamics and meridional fluxes of heat and humidity. Tellus, 60 (1). pp. 11-31.

Pincus, R. and Stevens, B. (2008) Monte Carlo spectral integration: A consistent approximation for radiative transfer in large eddy simulations. Journal of Advancesin Modeling Earth Systems, 1 . p. 9.

Plattner, N. and Bandi, T. and Doll, J. D. and Freeman, D. and Meuwly, M. (2008) MD simulations using distributed multipole electrostatics: Structural and spectroscopic properties of CO- and methane-containing clathrates. Molecular Physics, 106 (12). pp. 1675-1684. ISSN 0026-8976

Plattner, N. and Meuwly, M. (2008) Atomistic Simulations of CO Vibrations in Ices Relevant to Astrochemistry. ChemPhysChem, 9 (9). pp. 1271-1277. ISSN 14394235

Plattner, N. and Meuwly, M. (2008) The Role of Higher CO-Multipole Moments in Understanding the Dynamics of Photodissociated Carbonmonoxide in Myoglobin. Biophysical Journal, 94 (7). pp. 2505-2515. ISSN 00063495

Pérez-Hernández, G. and González, L. and Serrano-Andrés, L. (2008) Rydberg or Valence? The Long-Standing Question in the UV Absorption Spectrum of 1,1′-Bicyclohexylidene. ChemPhysChem, 9 (17). p. 2544. ISSN 14394235

Rausch, T. and Emde, A.-K. and Reinert, K. (2008) Robust consensus computation. BMC Bioinformatics, 9 (Suppl 10). P4.

Rausch, T. and Thomas, A. and Camp, N. J. and Facelli, L. A. (2008) A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease. Comput. Biol. Med., 38 . pp. 826-836.

Rausch, T. and Emde, A.-K. and Weese, D. and Notredame, C. and Reinert, K. (2008) Segment-based multiple sequence alignment. Bioinformatics, 24 (16). i187-192.

Ruprecht, D. and Schaedle, A. and Schmidt, F. and Zschiedrich, L. (2008) Transparent Boundary Conditions for Time-dependent Problems. SIAM J. Sci. Comput., 30 (5). pp. 2358-2385. ISSN 1064-8275

Schmidt, H. and Mellado, J.- P. and Peters, N. and Stevens, B. (2008) Towards modular front tracking for Stratocumulus clouds considering unsteady entrainment processes. Geophysical Research Abstracts, 10 .

Schmidt, H. and Oevermann, M. and Bastiaans, R.J.M. and Kerstein, A.R. (2008) Tabulation of turbulent burning rates via a combination of a stochastic mixing model and tabulated chemistry. ZIB Report, 08 (2).

Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and Hildebrandt, A. and Hildebrandt, A. and Huber, Ch. and Reinert, K. (2008) Computational Quantification of Peptides from LC-MS data. Journal of Computational Biology, 15 (7). pp. 685-704.

Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2008) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining . accepted for publication. (In Press)

Schulz-Trieglaff, O. and Pfeifer, N. and Gröpl, C. and Kohlbacher, O. and Reinert, K. (2008) LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics, 9 (423).

Schäfer-Bung, B. (2008) The interplay of wave packet dephasing, optimization efficiency, and target state population in optimally controlled isotope selective photoionization. Chem. Phys., 343 . pp. 340-346.

Schäfer-Bung, B. and Nest , M. (2008) Correlated Dynamics of Electrons with Reduced 2-Electron Density Matrices. Phys. Rev. A, 78 (1). 012512.

Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Lingnau, A. and Lein, M. and Miller, K. and Schrader, M. (2008) Serum proteomic profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry in testicular germ cell cancer patients. European Urology Supplements, 7 (3). p. 83.

Sturm, M. and Andreas, B. and Gröpl, C. and Hussong, R. and Lange, E. and Pfeifer, N. and Schulz-Trieglaff, O. and Zerck, A. and Reinert, K. and Kohlbacher, O. (2008) OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics, 9 (163).

Teleaga, , I. and Lang, J. (2008) Higher-order linearly implicit one-step methods for three-dimensional incompressible Navier-Strokes equations. Studia Babes-Bolyai Matematica, 53 . pp. 109-121.

Tomm, S. and von Terzi, D.A. and Fröhlich, J. (2008) Interaction of the filter and spatial discretisation operators for Large-Eddy Simulation using the Approximate Deconvolution Model. PAMM, 8 . pp. 10605-10606.

Ullrich, Alexander and Flamm, Christoph (2008) Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe. Computational Methods in Systems Biology, 5307 . pp. 28-43.

Vercauteren, N. and Bou-Zeid, E. and Parlange, M. B. and Lemmin, U. and Huwald, H. and Selker, J. S. and Meneveau, C. (2008) Subgrid-Scale Dynamics of Water Vapour, Heat, and Momentum over a Lake. Boundary-Layer Meteorology, 128 (2). pp. 205-228. ISSN Print: 0006-8314 Online: 1573-1472

Warren, R. and de la Nava Santos, S. and Arnell, N.W. and Bane, M. and Barker, T. and Barton, C. and Ford, R. and Füssel, H.-M. and Hankin, Robin K.S. and Klein, R. and Linstead, C. and Kohlera, J. and Mitchella, T.D. and Osborna, T.J. and Pan, H. and Raper, S.C.B. and Riley, G. and Schellnhuber, H.J. and Winne, S. and Anderson, D. (2008) Development and illustrative outputs of the Community Integrated Assessment System (CIAS), a multi-institutional modular integrated assessment approach for modelling climate change. Environmental Modelling & Software, 23 (5). 592-610 .

von Larcher, T. and Futterer, B. and Egbers, C. (2008) GeoFlow: On the status of experimental preparation of spherical gap flow experiments with central force field on International Space Station (ISS). Journal of Physics: Conference Series, 137 (012025). p. 6.

von Larcher, T. and Futterer, B. and Egbers, C. and Hollerbach, R. and Chossat, P. and Beltrame, P. and Tuckerman, L. and Feudel, F. (2008) GeoFlow - European Microgravity Experiments on Thermal Convection in Rotating Spherical Shells under influence of Central Force Field. Journal of The Japan Society of Microgravity Application, 25 (3).

Book Section

Conrad, T. O. F. and Reinert, K. and Kohlbacher, O. (2008) Bioinformatics Support for Mass Spectrometry Quality Control. In: Proteomics Sample Preparation. Wiley-Vch, p. 485.

Forster, R. and Kornhuber, R. and Mautner, K. and Sander, O. (2008) Fast and reliable pricing of American options with local volatility. In: Domain Decomposition Methods in Science and Engineering XVII. Lecture Notes in Computational Science and Engineering, 60 . Springer Berlin Heidelberg, pp. 383-390. ISBN 978-3-540-75198-4

Forster, R. and Kornhuber, R. and Mautner, R. and Sander, O. (2008) Fast and reliable pricing of American options with local volatility. In: Decomposition Methods in Science and Engineering XVII. Springer, pp. 383-390. ISBN 978-3-540-75198-4

Gräfe, Ch. and Schütte, Ch. and Nordmeier, V. (2008) Spielend lernen - ein Online-Computerspiel zur Moleküldynamik. In: Didaktik der Physik – Berlin 2008. Lehmanns Media, Berlin.

Gräser, C. (2008) Globalization of nonsmooth Newton methods for optimal control problems. In: Numerical Mathematics and Advanced Applications. Proceedings of ENUMATH 2007, the 7th European Conference on Numerical Mathematics and Advanced Applications, Graz, Austria, September 2007 . Springer Berlin Heidelberg, pp. 605-612. ISBN 978-3-540-69776-3

John, V. and Schmeyer, E. (2008) On finite element methods for 3D time-dependent convection-diffusion-reaction equations with small diffusion. In: BAIL 2008 - Boundary and Interior Layers. Lecture Notes in Computational Science and Engineering, 69 . Springer Verlag, ISSN:1439-7358, pp. 173-181. ISBN 978-3-642-00604-3 (Print) 978-3-642-00605-0 (Online)

Schatzmann, M. and Leitl, B. (2008) Properties of field and wind tunnel boundary layers within and above the urban canopy. In: Atmospheric boundary layer flows in air pollution modelling. Karman Institute for Fluid Dynamics. ISBN 13 978-2-930389-85-0

von Larcher, T. and Futterer, B. and Egbers, C. (2008) The GeoFlow-Experiment on International Space Station (ISS): Research on Thermal Convective Flows in a Spherical Gap under influence of a Central Force Field. In: Sitzungsberichte der Leibniz-Sozietät der Wissenschaften zu Berlin. 96, 96 . trafo Verlag, D. B. Herrmann (Hrsg.). ISBN 978-3-89626-756-6

Conference or Workshop Item

Harlander, U. and von Larcher, T. and Wang, Y. and Egbers, C. (2008) The heated rotating annulus: PIV- and LDV-measurements of multiple-scale interactions in quasi-turbulent flows. In: 14th International Symposium on Application of Laser Techniques to Fluid Mechanics, Lisbon, Portugal.

Kühnlein, C. (2008) Adaptive meshes for meteorological applications. In: Atmospheric Boundary Layers: Concepts, Observations, and Numerical Simulations, Les Houches, Frankreich. (Unpublished)

Kühnlein, C. and Dörnbrack, A. (2008) Scalar advection with adaptive moving meshes. In: 1st International Workshop of EULAG Users, 7. Oktober 2008, Bad Tölz.

Moeck, J. and Oevermann, M. and Paschereit, O. C. and Klein, R. and Schmidt, H. (2008) Experimental and Numerical investigation of thermoacoustical instabilities in a flat flame burner. In: 32nd International Symposium on Combustion, August 3-8, 2008, Montreal, Canada. (Submitted)

Münch, M. (2008) Modellierung der Rauchausbreitung bei Gebäudebränden. In: Meterologisches Kolloquium, 10. Juli 2008, Berlin, FU-Berlin, Institut für Meterologie. (Unpublished)

Münch, M. and Gebauer, J. and Klein, R. (2008) Verification and Validation of CFD Models for Smoke Spreading Predictions. In: 9th Int. IAFSS Symposium , 21 - 26. Sept. 2008, Karlsruhe.

Münch, M. and Klein, R. (2008) Critical numerical aspects for field model applications. In: EUSAS conference on "Fire Safety Engineering and Smoke Control in Buildings", January 22-23, 2007, Vienna, Austria.

Schmidt, H. and Mellado, J.- P. and Peters, N. and Stevens, B. (2008) Towards a modular superparameterization for Stratocumulus clouds considering unsteady entrainment. In: 4th PAN-GCSS Meeting on "Advances in Modeling and Observing Clouds and Convection", 2-6 June 2008, Toulouse, France.

Schulz, M. H. and Weese, D. and Rausch, T. and Döring, A. and Reinert, K. and Vingron, M. (2008) Fast and Adaptive Variable Order Markov Chain Construction. In: Proceedings of the 8th International Workshop in Algorithms in Bioinformatics (WABI'08).

Weese, D. and Schulz, M. H. (2008) Efficient String Mining under Constraints via the Deferred Frequency Index. In: Proceedings of the 8th Industrial Conference on Data Mining (ICDM'08).

Thesis

Bais, Abha Singh (2008) Annotated Alignments. PhD thesis, Freie Universität Berlin.

Bauer, Markus Johann (2008) A combinatorial approach to RNA sequence-structure alignments. PhD thesis, Freie Universität Berlin.

Conrad, T. O. F. (2008) New statistical algorithms for the analysis of mass spectrometry time-of- flight mass data with applications in clinical diagnostics. PhD thesis, Freie Universität Berlin.

Dolaptchiev, S. (2008) Asymptotic models for planetary scale atmospheric motions. PhD thesis, Freie Universität Berlin.

Fischbach, M. (2008) Methods for modeling metastable conformational dynamics from trajectory data. Masters thesis, FU Berlin.

Lange, Eva (2008) Analysis of mass spectrometric data - peak picking and map alignment. PhD thesis, Freie Universität Berlin.

Sakalli, I. (2008) Parallelization Strategies for a Brownian Dynamics Algorithm. Other thesis, FU Berlin.

Thöns, Ch. (2008) Parallelizing Multigrid Solvers for Contact Problems on IBM’s Cell Processor. Masters thesis, Freie Universität Berlin.