Repository: Freie Universität Berlin, Math Department

Items where Year is 2011

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Number of items: 74.

A

Assêncio, D.C. and Teran, J.M. (2011) A Second Order Virtual Node Algorithm for Stokes Flow Problems with Interfacial Forces and Irregular Domains. Journal of Computational Physics . (Submitted)

Audusse, E. and Klein, R. and Nguyen, D.D. and Vater, S. (2011) Preservation of the discrete geostrophic equilibrium in shallow water flows. In: Finite Volumes for Complex Applications VI - Problems& Perspectives, 6.6.-10.6. 2011, Prague, Czech Republic.

B

Benacchio, T. and Bonaventura, L. (2011) A spectral collocation method for the one dimensional shallow water equations on semi-infinite domain. MOX–Report, 34 .

Bernhard, S. and Al Zoukra, K. and Schütte, Ch. (2011) Statistical parameter estimation and signal classification in cardiovascular diagnosis. In: Modelling in Medicine and Biology. WIT Transactions on Biomedicine and Health, IX (15). WIT Press, Southampton & Boston. ISBN 978-1-84564-546-5

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Convergence behaviour of Dirichlet-Neumann and Robin methods for a nonlinear transmission problem. In: Domain Decomposition Methods in Science and Engineering XIX. Lecture Notes in Computational Science and Engineering, 78 . Springer Berlin Heidelberg, pp. 87-98. ISBN 978-3-642-11303-1

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Fast and robust numerical solution of the Richards equation in homogeneous soil. SIAM Journal on Numerical Analysis, 49 (6). pp. 2576-2597. ISSN 0036-1429

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Heterogeneous domain decomposition of surface and porous media flow. AIP Conference Proceedings, 1389 . pp. 2025-2028. ISSN 0094-243X

Bielow, C. and Gröpl, C. and Kohlbacher, O. and Reinert, K. (2011) Bioinformatics for qualitative and quantitative proteomics. In: Bioinformatics for Omics Data Methods and Protocols. Humana Press, pp. 331-49.

Bielow, C. and Aiche, S. and Andreotti, S. and Reinert, K. (2011) MSSimulator: Simulation of Mass Spectrometry Data. Journal of Proteome Research, 10 (7). pp. 2922-2929.

Bienert, A. and Pech, K. and Maas, H.-G (2011) Verfahren zur Registrierung von Laserscannerdaten in Waldbeständen. Schweizerische Zeitschrift für Forstwesen, 162 (6). pp. 178-185.

Bordás, R. and Hagemeier, T. and Wunderlich, B. and Thévenin, D. (2011) Droplet Collisions and Interaction with the Turbulent Flow within a Two-Phase Wind Tunnel. Physics of Fluids, 23 (8). ISSN 1070-6631 (print) 1089-7666 (online)

Braack, M. and Burman, E. and Taschenberger, N. (2011) Duality based a posteriori error estimation for quasi periodic solutions using time averages. SIAM J. Scientific Computing, 33 (10.1137/100809519). pp. 2199-2216. ISSN print: 1064-8275; online: 1095-7197

Brdar, S. and Dedner, A. and Klöfkorn, R. (2011) Compact and Stable Discontinuous Galerkin Methods with Application to Atmospheric Flows. In: Computational Methods in Science and Engineering. KIT Scientific Publishing., pp. 109-116. ISBN 978-3-86644-693-9

Bresch, D. and Klein, R. and Lucas, C. (2011) Multiscale analyses for the Shallow Water equations. Computational Science and High Performance Computing IV, 115/20 . pp. 149-164. ISSN 1612-2909 (Print) 1060-0824 (Online)

Böcker, S. and Kehr, B. and Rasche, F. (2011) Determination of Glycan Structure from Tandem Mass Spectra. IEEE/ACM Transactions on Computational Biology and Bioinformatics , 8 (4). pp. 976-986. ISSN 1545-4963

C

Chodera, J. D. and Swope, W. D. and Noé, F. and Prinz, J.-H. and Shirts, M. R. and Pande, V. S. (2011) Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures. J. Chem. Phys., 134 (24). p. 244107.

D

Dedner, A. and Klöfkorn, R. (2011) A Generic Stabilization Approach for Higher Order Discontinuous Galerkin Methods for Convection Dominated Problems. J. Sci. Comput. . (Submitted)

Dziuk, G. and Elliott, C.M. and Huisken, G. and Kornhuber, R. (2011) Geometric partial differential equations: Theory, numerics and applications. Oberwolfach Reports, 8 (4). European Mathematical Society.

F

Faelber, Katja and Posor, York and Held, M. and Roske, Yvette and Schulze, Dennis and Haucke, Volker and Noé, F. and Daumke, Oliver (2011) Crystal structure of nucleotide-free dynamin. Nature, 477 . pp. 556-560.

Fischer, M. and Lorenz, U. and Schmidt, B. and Schmidt, R. (2011) Fragmentation due to centrifugal forces in the photodissociation of H2+ in intense laser fields. Phys. Rev. A, 84 (3). 033422.

Frank, M. and von Kleist, M. and Kunz, A. and Harms, G. and Schütte, Ch. and Kloft, Ch. (2011) Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1: A combined pharmacokinetic, pharmaco- and viral dynamic analysis to predict clinical outcomes. Antimicrob. Agents Chemother., 55 (12). pp. 5529-5540.

H

Han, D. S. and Golebiewska, U. and Stolzenberg, S. and Scarlata, S. F. and Weinstein, H. (2011) A Dynamic Model of Membrane-Bound Phospholipase C 2 Activation by G Subunits. Molecular Pharmacology, 80 (3). p. 434. ISSN 0026-895X

Harlander, U. and Wentzel, J. and Alexandrov, K. and Wang, Y. and Egbers, C. (2011) PIV- and LDV-measurements of baroclinic wave interactions in a thermally driven rotating annulus. Experiments in Fluids . (Submitted)

Harlander, U. and von Larcher, T. and Wang, Y. and Egbers, C. (2011) PIV- and LDV-measurements of baroclinic wave interactions in a thermally driven rotating annulus. Experiments in Fluids, 51 (1). pp. 37-49.

Hartmann, C. (2011) Balanced model reduction of partially-observed Langevin processes: an averaging principle. Math. Comput. Model. Dyn. Syst., 17 (5). pp. 463-490.

Hartmann, C. and Latorre, J.C. (2011) Computing free energy differences using conditioned diffusions. AIP Conf. Proc., 1332 (1). pp. 218-220.

Hartmann, C. and Latorre, J.C. and Ciccotti, G. (2011) On two possible definitions of the free energy for collective variables. Eur. Phys. J. Special Topics, 200 (1). pp. 73-89.

Held, M. and Metzner, Ph. and Prinz, J.-H. and Noé, F. (2011) Mechanisms of Protein-Ligand association and its modulation by protein mutations. Biophys. J., 100 (3). pp. 701-710.

Hertwig, D. and Leitl, B. and Schatzmann, M. (2011) Organized turbulent structures –- Link between experimental data and LES. Journal of Wind Engineering and Industrial Aerodynamics, 99 (4). pp. 296-307. ISSN 01676105

Holtgrewe, M. and Emde, A.-K. and Weese, D. and Reinert, K. (2011) A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinformatics, 12 (120). ISSN 1471-2105

I

Ihrig, A C and Schiffmann, C and Sebastiani, D (2011) Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups. The Journal of Chemical Physics, 135 (21). p. 214107. ISSN 00219606

J

Jasor, G. and Wacker, U. and Beheng, K.D. and Polifke, W. (2011) Application of Quadrature Method of Moments for Sedimentation and Coagulation of Raindrops. In: International Metstroem Conference, Juni 2011, Berlin.

Jebens, .S. and Knoth, O. and Weiner, R. (2011) Partially Implicit PeerMethods for the Compressible Euler Equations. Journal of Computational Physics . (Submitted)

Jouvet, G. and Huss, M. and Funk, M. and Blatter, H. (2011) Modelling the retreat of Grosser Aletschgletscher, Switzerland, in a changing climate. Journal of Glaciology, 57 (206). pp. 1033-1045. ISSN 0022-1430

Jouvet, G. and Rappaz, J. (2011) Analysis and finite element approximation of a nonlinear stationary stokes problem arising in glaciology. Advances in Numerical Analysis, 2011 (Articl). ISSN 1687-9562

K

Kehr, B. and Weese, D. and Reinert, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12 (S9). S15. ISSN 1471-2105

Keller, B. and Hünenberger, Philippe and van Gunsteren, Wilfred (2011) An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles. J. Chem. Theo. Comput., 7 . pp. 1032-1044.

Klein, R. and Vater, S. and Paeschke, E. and Ruprecht, D. (2011) Multiple scales methods in meteorology. In: Asymptotic Methods in Fluid Mechanics: Survey and Recent Advances. CISM International Centre for Mechanical Sciences, 523 . Springer Verlag, pp. 127-196. ISBN 978-3-7091-0407-1

Kornhuber, R. and Zou, Q. (2011) Efficient and reliable hierarchical error estimates for the discretization error of elliptic obstacle problems. Mathematics of Computation, 80 . pp. 69-88. ISSN 0025-5718

L

Latorre, J.C. and Metzner, Ph. and Hartmann, C. and Schütte, Ch. (2011) A Structure-preserving numerical discretization of reversible diffusions. Commun. Math. Sci., 9 (4). pp. 1051-1072.

M

Matera, S. and Meskine, H. and Reuter, K. (2011) Adlayer inhomogeneity without lateral interactions: Rationalizing correlation effects in CO oxidation at RuO2(110) with first-principles kinetic Monte Carlo. The Journal of Chemical Physics, 134 (6). 064713.

Münch, M. and Belaschk, H.C. and Klein, R. (2011) Numerische Simulation im Brandschutz - Zwischen Theorie und Praxis. In: Bauphysik-Kalender 2011. Ernst & Sohn Verlag für Architektur und technische Wissenschaften GmbH & Co. KG, Berlin, pp. 159-197. ISBN ISBN 978-3-433-02965-7

N

Noé, F. and Doose, S. and Daidone, I. and Löllmann, M. and Chodera, J. D. and Sauer, M. and Smith, J. C. (2011) Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc. Natl. Acad. Sci. USA, 108 . pp. 4822-4827.

O

Owinoh, A.Z. and Stevens, B. and Klein, R. (2011) Multiscale Asymptotics Analysis for the Mesoscale Dynamics of Cloud-Topped Boundary Layers. Journal of the Atmospheric Sciences, 68 (2). pp. 379-402. ISSN Online 1520-0469, Print 0022-4928

Owschimikow, N. and Schmidt, B. and Schwentner, N. (2011) Laser-induced alignment and anti-alignment of rotationally excited molecules. Phys. Chem. Chem. Phys., 13 (19). pp. 8671-8680.

P

Plattner, N. and Doll, J. D. and Dupuis, P. and Wang, H. and Liu, Y. and Gubernatis, J. E. (2011) An infinite swapping approach to the rare-event sampling problem. The Journal of Chemical Physics, 135 (13). p. 134111. ISSN 00219606

Prinz, J.-H. and Chodera, J. D. and Pande, V. S. and Swope, W. D. and Smith, J. C. and Noé, F. (2011) Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J. Chem. Phys., 134 (24). p. 244108.

Prinz, J.-H. and Held, M. and Smith, J. C. and Noé, F. (2011) Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes. Multiscale Model. Simul., 9 . pp. 545-567.

Prinz, J.-H. and Keller, B. and Noé, F. (2011) Probing molecular kinetics with Markov models: Metastable states, transition pathways and spectroscopic observables. Phys. Chem. Chem. Phys., 13 . pp. 16912-16927.

Prinz, J.-H. and Wu, H. and Sarich, M. and Keller, B. and Senne, M. and Held, M. and Chodera, J. D. and Schütte, Ch. and Noé, F. (2011) Markov models of molecular kinetics: Generation and Validation. J. Chem. Phys., 134 . p. 174105.

Q

Queck, R. and Bienert, A. and Maas, H.-G and Hermansa, S. and Goldberg, V. and Bernhofer, C. (2011) Wind fields in heterogeneous conifer canopies: parameterisation of momentum absorption using high-resolution 3D vegetation scans. European Journal of Forest Research, 130 . ISSN 1612-4669 (Print) 1612-4677 (Online)

R

Rausch, T. and Reinert, K. (2011) Practical multiple Sequence alignment. In: Problem Solving Handbook in Computational Biology and Bioinformatics. Springer Science+Business Media, pp. 21-43. ISBN 978-0-387-09759-6

Ruprecht, D. and Klein, R. (2011) A Model for Nonlinear Interactions of Internal Gravity Waves with Saturated Regions. Meteorologische Zeitschrift, 20 (2). pp. 243-252.

S

Sander, O. (2011) The PSurface library. Computing and Visualization in Science, 14 (8). pp. 353-370. ISSN 1432-9360

Schiffmann, C and Sebastiani, D (2011) Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations. Journal of Chemical Theory and Computation, 7 (5). p. 1307. ISSN 1549-9618

Schiffmann, C and Sebastiani, D (2011) Hydrogen bond networks: Structure and dynamics via first-principles spectroscopy. physica status solidi (b), 249 (2). p. 368. ISSN 03701972

Schäfer-Bung, B. and Hartmann, C. and Schmidt, B. and Schütte, Ch. (2011) Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems. J. Chem. Phys., 135 (1). 014112.

Schütte, Ch. and Noé, F. and Lu, Jianfeng and Sarich, M. and Vanden-Eijnden, E. (2011) Markov State Models Based on Milestoning. J. Chem. Phys., 134 (20). p. 204105.

Splettstößer, T. and Holmes, K. C. and Noé, F. and Smith, J. C. (2011) Structural modeling and molecular dynamics simulation of the actin filament. Proteins, 79 . pp. 2033-2043.

U

Ullrich, Alexander (2011) Computational Studies on the Evolution of Metabolism. PhD thesis, Universität Leipzig.

Ullrich, Alexander and Flamm, Christoph (2011) A Sequence-to-Function Map for Ribozyme-catalyzed Metabolisms. Advances in Artificial Life, 5778 . p. 481. ISSN 978-3-642-21313-7

Ullrich, Alexander and Rohrschneider, Markus and Scheuermann, Gerik and Stadler, Peter F. and Flamm, Christoph (2011) In Silico Evolution of Early Metabolism. Artificial Life, 17 (2). pp. 87-108. ISSN 1064-5462

V

Vater, S. and Klein, R. and Knio, O.M. (2011) A Scale-selective Multilevel Method for Long-Wave Linear Acoustics. Acta Geophysica, 59 (6). pp. 1076-1108.

Vater, S. and Klein, R. and Knio, O.M. (2011) Scale-selective time integration for Long-Wave Linear Acoustics. In: Finite Volumes for Complex Applications VI - Problems & Perspectives, 6.6.-10.6. 2011, Prague, Czech Republic.

Vercauteren, N. (2011) Water Vapor and Heat Exchanges over Lakes. PhD thesis, École polytechnique fédérale de Lausanne EPFL.

Vercauteren, N. and Huwald, H. and Bou-Zeid, E. and Selker, J. S. and Lemmin, U. and Parlange, M. B. and Lunati, I. (2011) Evolution of Superficial Lake Water Temperature Profile Under Diurnal Radiative Forcing. Water Resources Research, 47 (9).

Vetter, A. and Liu, Y. and Witt, F. and Manjubala, I. and Sander, O. and Rao Epari, D. and Fratzl, P. and Duda, G. and Weinkamer, R. (2011) The mechanical heterogeneity of the hard callus influences local tissue strains during bone healing. Journal of Biomechanics, 44 (3). pp. 517-523. ISSN 0021-9290

Vitalini, Francesca (2011) Effect of a point mutation on the conformational ensemble of an intrisecally disordered peptide: a molecular dynamics study on Amyloid-β. Masters thesis, Università degli Studi Roma Tre, Thesis developed at UC Berkeley.

von Kleist, M. and Menz, S. and Stocker, H. and Arasteh, K. and Huisinga, W. and Schütte, Ch. (2011) HIV Quasispecies Dynamics during Pro-active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs. Plos One, 6 (3). e18204.

W

Walter, J. and Hartmann, C. and Maddocks, J. (2011) Ambient space formulations and statistical mechanics of holonomically constrained Langevin systems. Eur. Phys. J. Special Topics, 200 (1). pp. 153-181.

Wandel, M. and Thormann, L and Münch, M. (2011) Anwendung von Simulationsrechnungen in der Brandschutzaufklärung. In: vfdb Jahresfachtagung 2011, 30. Mai bis 1. Juni 2011, Berlin.

Wu, H. and Noé, F. (2011) Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations. Phys. Rev. E, 83 (3). 036705.

Wu, H. and Noé, F. (2011) A flat Dirichlet process switching model for Bayesian estimation of hybrid systems. Procedia Computer Science, 4 . pp. 1393-1402.

Z

Zou, Q. and Veeser, A. and Kornhuber, R. and Gräser, C. (2011) Hierarchical error estimates for the energy functional in obstacle problems. Numerische Mathematik, 117 (4). pp. 653-677. ISSN 0029-599X

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