Items where Year is 2007

Article

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2007) A generic grid interface for parallel and adaptive scientific computing. I: Abstract framework. Computing, 82 (2-3). pp. 103-119.

Bauer, M. and Klau, G. W. and Reinert, K. (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, 8 (1). p. 271.

Bodirsky, M. and Gröpl, C. and Johannsen, D. and Kang, M. (2007) A direct decomposition of 3-connected planar graphs. Séminaire Lotharingien de Combinatoire, B54Ak . 15 pages.

Bodirsky, M. and Gröpl, C. and Kang, M. (2007) Generating labeled planar graphs uniformly at random. Theoretical Computer Science, 379 (3). pp. 377-386.

Christen, M. and Keller, B. and van Gunsteren, W. F. (2007) Local elevation on the dihedral angles to improve the J-values. Journal of Biomolecular NMR, 39 . pp. 265-273.

Debrabant, K. and Lang, J. (2007) On Global Error Estimation and Control for Parabolic Equations, Report No. 2512. Appl. Num. Math. . (Submitted)

Fischer, A. and Waldhausen, S. and Horenko, I. and Meerbach, E. and Schütte, Ch. (2007) Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models. J. Comp. Chem., 28 (15). pp. 2453-2464.

Gu, W. and Frigato, T. and Straatsma, T. P. and Helms, V. (2007) Dynamic Protonation Equilibrium of Solvated Acetic Acid. Angew. Chem. Int. Ed., 46 (16). pp. 2939-2943.

Hartmann, C. and Schütte, Ch. (2007) Comment on Two Distinct Notions of Free Energy. Physica D, 228 (1). pp. 59-63.

Horenko, I. and Hartmann, C. and Schütte, Ch. and Noé, F. (2007) Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes. Phys. Rev. E, 76 (01). 016706.

Jahnke, T. and Huisinga, W. (2007) Solving the Chemical Master Equation for Monomolecular Reaction Systems Analytically. J. Math. Biol., 54 (1). pp. 1-26.

Keller, B. and Christen, M. and Oostenbrink, C. and van Gunsteren, W. F. (2007) On using oscillating time-dependent restraints in MD simulation. Journal Of Biomolecular NMR, 37 . pp. 1-14.

Klau, G. W. and Rahmann, S. and Schliep, A. and Vingron, M. and Reinert, K. (2007) Integer Linear Programming Approaches for Non-unique Probe Selection. Discrete Applied Mathematics, 155 . pp. 840-856.

Lang, J. and Verwer, J. (2007) On Global Error Estimation and Control for Initial Value Problems. SIAM J. Sci. Comp., 29 (4). pp. 1460-1475. ISSN 1064-8275 (print) 1095-7197 (online)

Lange, E. and Gröpl, C. and Schulz-Trieglaff, O. and Leinenbach, A. and Huber, Ch. and Reinert, K. (2007) A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data. Oxford Journals, 23 (13). i273-i281. ISSN 1460-2059 (online), 1367-4803 (print)

Lasser, C. and Swart, T. and Teufel, St. (2007) Construction and validation of a rigorous surface hopping algorithm for conical crossings. Comm. Math. Sci., 5 (4). pp. 789-814.

Lorenz, S. and Diederichs, E. and Telgmann, R. and Schütte, Ch. (2007) Discrimination of Dynamical System Models for Biological and Chemical Processes. J. Comp. Chem., 28 (8). pp. 1384-1399.

Lörcher, F. and Gassner, G. and Munz , C.-D. (2007) A Discontinuous Galerkin Scheme Based on a Space–Time Expansion. I. Inviscid Compressible Flow in One Space Dimension. Journal of Scientific Computing, 32 (2). pp. 175-199. ISSN 0885-7474 (Print) 1573-7691 (Online)

Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2007) Buoyancy-reversal in cloud-top mixing layers. Quarterly journal of the royal meteorological society . pp. 1-21.

Metzner, Ph. and Dittmer, E. and Jahnke, T. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes. J. Comp. Phys., 227 (1). pp. 353-375.

Metzner, Ph. and Horenko, I. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time. Phys. Rev. E, 76 (06). 066702.

Noé, F. and Oswald, M. and Reinelt, G. (2007) Optimization in Graphs with Limited Information on the Edge Weights. Operations Research Proceedings 2007. Editors: J. Kalcsics and S. Nickel . pp. 435-440.

Noé, F. and Smith, J. C. (2007) Transition Networks: a unifying theme for molecular simulation and computer science. Mathematical Modeling of Biological Systems I, A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (Eds) . pp. 125-144.

Noé, F. and Horenko, I. and Schütte, Ch. and Smith, J. C. (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J. Chem. Phys., 126 (15). p. 155102.

Noé, F. and Smith, J. C. and Schütte, Ch. (2007) A network-based approach to biomolecular dynamics. From Computational Biophysics to Systems Biology (CBSB07). Editors: U. H. E. Hansmann, J. Meinke, S. Mohanty and O. Zimmermann, NIC Se .

Pingen, G. and Waidmann, M. and Evgrafov, A. and Maute, K. (2007) Application of a Parametric Level-Set Approach to Topology Optimization of Fluids with the Navier–Stokes and Lattice Boltzmann Equations. 7th World Congress on Structural and Multidisciplinary Optimization .

von Kleist, M. and Huisinga, W. (2007) Physiologically Based Pharmacokinetic Modelling: A Sub-Compartmentalized Model of Tissue Distribution. J. Pharmacokin. Pharmacodyn., 34 (6). pp. 789-806.

Book Section

Berninger, H. and Kornhuber, R. and Sander, O. (2007) On nonlinear Dirichlet-Neumann Algorithms for jumping nonlinearities. In: Domain Decomposition Methods in Science and Engineering XVI. In: Domain Decomposition Methods in Science and Engineering XVI. LNCSE, 55 . Springer, pp. 489-496. ISBN 978-3-540-34469-8

Futterer, B. and Koch, S. and Dahley, N. and von Larcher, T. and Scurtu, N. and Jehring, L. and Egbers, C. (2007) Das GeoFlow-Experiment auf der ISS: Interferogrammauswertung für die thermische Konvektion im Kugelspalt. In: Lasermethoden in der Strömungsmesstechnik. Proceedings zur 15. GALA-Fachtagung . Universität Rostock, Rostock. ISBN 978-3-86009-007-7

Gräser, C. and Kornhuber, R. (2007) On preconditioned Uzawa-type iterations for a saddle point problem with inequality constraints. In: Domain Decomposition Methods in Science and Engineering XVI. Lecture Notes in Computational Science and Engineering, 55 . Springer Berlin Heidelberg, pp. 91-102. ISBN 978-3-540-34468-1

Kiljunen, T. and Schmidt, B. (2007) Alignment and Orientation of Molecules in Matrices. In: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics, 87 . Springer, Berlin, pp. 337-352.

Kornhuber, R. and Gräser, C. (2007) On preconditioned Uzawa-type iterations for a saddle point problem with inequality constraints. In: Decomposition Methods in Science and Engineering XVI. LNCSE (55). Springer, pp. 91-102. ISBN 978-3-540-34469-8

Meerbach, E. and Schütte, Ch. and Horenko, I. and Schmidt, B. (2007) Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution. In: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics, 87 . Springer, Berlin, pp. 796-806.

Reinert, K. and Huson, D. H. (2007) Sequence Assembly. In: UNSPECIFIED Bioinformatics - From Genomes to Therapies, 1 . Wiley-VCH, Weinheim, pp. 25-55.

Ting, L. and Klein, R. and Knio, O.M. (2007) Vortex Dominated Flows: Analysis and Computation for Multiple Scales. In: Series in Applied Mathematical Sciences. Springer Verlag. ISBN 978-3-540-68581-4

von Larcher, T. (2007) Zur Stabilität barokliner Wellen im starr rotierenden Zylinderspalt. In: VDI-Fortschrittsberichte. VDI, Strömungstechnik, Reihe 7. ISBN 978-3-18-348607-6

Monograph

Ruprecht, D. and Schaedle, A. and Schmidt, F. and Zschiedrich, L. (2007) Transparent Boundary Conditions for Time-Dependent Problems. Technical Report. Konrad Zuse Zentrum Berlin.

Vater, S. and Klein, R. (2007) Stability of a Cartesian grid projection method for zero Froude number shallow water flows. Technical Report. Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB).

Conference or Workshop Item

Dolaptchiev, S. and Klein, R. (2007) Model Equations For Atmospheric Motions on Planetary Scales. In: European Geosciences Union, Vienna.

Fasulo, D. and Emde, A.-K. and Wang, L.-Y. and Edwards, N. J. (2007) Alignment of Mass Spectrometry Data by Clique Finding and Optimization. In: Systems Biology and Computational Proteomics.

Futterer, B. and von Larcher, T. and Egbers, C. (2007) GeoFlow: The ISS experiment and 3D numerical simulation on thermal convection in spherical shell. In: Biennial Symposium and General Assembly, 4-7 September, 2007, European Low Gravity Research Association (ELGRA), Florence Italy.

González, L. and Rozgonyi, T. and Ambrosek, D. and Pérez-Hernández, G. and Maroulis, G. and Simos, T. E. (2007) Laser Control of Wavepacket Photodissociation and Photoisomerization Dynamics in Isolated Molecules. In: ICCMSE 2007, 25–30 September 2007 , Corfu (Greece).

Held, M. and Meerbach, E. and Hinderlich, S. and Reutter, W. and Schütte, Ch. (2007) Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity. In: From Computational Biophysics to Systems Biology.

Klein, R. (2007) A Unified Approach to Meteorological Modelling based on Multiple Scales Asymptotics. In: European Geosciences Union, Vienna.

May, P. and Klau, G. W. and Bauer, M. and Steinke, T. (2007) Accelerated microRNA Precursor Detection Using the Smith-Waterman Algorithm on FPGAs. In: Proc. of GCCB 2006.

Moeck, J. and Schmidt, H. and Oevermann, M. and Paschereit, O. C. and Klein, R. (2007) An asymptotically motivated hyrodynamic-acoustic two-way coupling for modeling thermoacoustic instabilities in a Rijke tube. In: Fourteenth Intl. Congress on Sound and Vibration (ICSV14), , 9-12 July 2007, Cairns, Australia, (2007).

Reinert, K. and Bauer, M. and Döring, A. and Halpern, A. L. (2007) A general paradigm for fast and adaptive clustering of biological sequences. In: German Conference on Bioinformatics (GCB 2007).

Ruprecht, D. and Majda, A. J. and Klein, R. (2007) A multiscale model for the interaction of bulk microscale hot towers with convective scale motions. In: European Geosciences Union, General Assembly 2007, 15 – 20 April 2007, Vienna.

Schaedle, A. and Ruprecht, D. and Schmidt, F. (2007) Transparent boundary conditions - the pole condition approach. In: The 8th International Conference on Mathematical and Numerical Aspects of Waves, 23rd - 27th July 2007, Reading UK.

Schmidt, H. and Veynante, D. and Klein, R. (2007) A Modular Two Scale Capturing/Tracking Scheme for Turbulent Premixed Flames. In: 21th Intl. Colloquium on the Dynamics of Explosions and Reactive Systems, 2007, Poitiers.

Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and Hildebrandt, A. and Reinert, K. (2007) A Fast and Accurate Algorithm for the Quantification of Peptides from Mass Spectrometry data. In: Proceedings of the Eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007).

von Kleist, M. and Kloft, Ch. and Huisinga, W. (2007) Combining Systems Biology with Physiologically Based Pharmacokinetics to Support the Understanding of Drug Effects. In: Proceedings of the 2nd Foundations of Systems Biology in Engineering Conference, FOSBE 2007, 09.-12.09.2007, Stuttgart, Germany.

Thesis

Hartmann, C. (2007) Model Reduction in Classical Molecular Dynamics. PhD thesis, Freie Universität Berlin.

Held, M. (2007) Conformational Studies of UDP-N-Acetyl-Glucosamine in Environments of Increasing Complexity. Masters thesis, FU Berlin.

Metzner, Ph. (2007) Transition Path Theory for Markov Processes. PhD thesis, Free University of Berlin.

Mikusky, E. (2007) On the structure of concentrated atmospheric vortices in a gradient wind regime and its motion on synoptic scales. PhD thesis, Universität Hamburg.

Rungsarityotin, Wasinee (2007) Algorithm to identify protein complexes from high-throughput data. PhD thesis, Freie Universität Berlin.

Tomm, S. (2007) Fehlererfassung für die Large Eddy Simulation auf gestreckten Gittern. Masters thesis, Universität Karlsruhe.

Wolski, Witold Eryk (2007) Analysis of sets and collections of Peptide Mass Fingerprint data. PhD thesis, Freie Universität Berlin.

Other

Meier, Ch. (2007) Bioinformatik: Aktuelle Proteinausstattung erlaubt Aussagen über den Gesundheitszustand. Software hilft Ärzten künftig bei der Diagnose. UNSPECIFIED.