Items where Year is 2012

Article

Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203

Andreotti, S. and Klau, G. W. and Reinert, K. (2012) Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) , 9 (2). pp. 385-394.

Assêncio, D.C. and Teran, J.M. (2012) A Second Order Virtual Node Algorithm for Stokes Flow Problems with Interfacial Forces and Discontinuous Material Properties. Journal of Computational Physics . (Submitted)

Bordás, R. and John, V. and Schmeyer, E. and Thévenin, D. (2012) Measurement and Simulation of a Droplet Population in a Turbulent Flow Field. Computers and Fluids . (Submitted)

Braack, M. and Lang, J. and Taschenberger, N. (2012) Hierarchical a posteriori residual based error estimators for bilinear finite elements. Comput. Meth. Appl. Mech. Eng. . (Submitted)

Brdar, S. and Baldauf, M. and Dedner, A. and Klöfkorn, R. (2012) Comparison of dynamical cores for NWP models. Theoretical and Computational Fluid Dynamics . ISSN 0935-4964 (In Press)

Brdar, S. and Dedner, A. and Klöfkorn, R. (2012) Compact and stable Discontinuous Galerkin methods for convection-diffusion problems. SIAM Journal of Scientific Computation, 34 (1). 263-282 . ISSN Print: 1064-8275 Online: 1095-7197

Bruckner, S. and Hüffner, F. and Komusiewicz, Ch. and Niedermeier, R. and Thiel, S. and Uhlmann, J. (2012) Partitioning into colorful components by minimum edge deletions. Lecture Notes in Computer Science, 7354 . pp. 56-69.

Buchholz, M. and Goletz, Ch.-M. and Grossmann, F. and Schmidt, B. and Heyda, J. and Jungwirth, P. (2012) Semiclassical Hybrid Approach to Condensed Phase Molecular Dynamics: Application to the I2Kr17 Cluster. J. Phys. Chem. A, 116 (46). pp. 11199-11210.

Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2012) Random Walks on Complex Modular Networks. Journal of Numerical Analysis, Industrial and Applied Mathematics, 6 (1-2). pp. 29-50. ISSN 1790–8140

Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2012) Estimating the eigenvalue error of Markov State Models. Multiscale Modeling & Simulation, 10 (1). pp. 61-81.

Doll, J. D. and Plattner, N. and Freeman, D. L. and Liu, Y. and Dupuis, P. (2012) Rare-event sampling: Occupation-based performance measures for parallel tempering and infinite swapping Monte Carlo methods. The Journal of Chemical Physics, 137 (20). p. 204112. ISSN 00219606

Dommert, F. and Wendler, K. and Berger, R. and Delle Site, L. and Holm, C. (2012) Force fields for studying structure and dynamics of imidazolium based ionic liquids - a critical review of recent developments. ChemPhysChem, 13 . p. 1625.

Donadio, D. and Ghiringhelli, L. M. and Delle Site, L. (2012) Autocatalytic and cooperatively-stabilized dissociation of water on a stepped platinum surface. Journal of the American Chemical Society, 134 . pp. 19217-19222.

Dupuis, P. and Yufei, L. and Plattner, N. and Doll, J. D. (2012) On the infinite swapping limit for parallel tempering. Multiscale Modeling & Simulation, 10 (3). pp. 986-1022.

Duwal, S. and Schütte, Ch. and von Kleist, M. (2012) Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. PLoS One, 7 (7). e40382.

Emde, A.-K. and Schulz, M. H. and Weese, D. and Sun, R. and Vingron, M. and Kalscheuer, V. M. and Haas, S. A. and Reinert, K. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28 (5). pp. 619-627.

Faelber, K. and Held, M. and Gao, S. and Posor, Y. and Haucke, V. and Noé, F. and Daumke, O. (2012) Structural insights into dynamin-mediated membrane fission. Structure, 20 . 1621-1628.

Fritsch, S. and Poblete, S. and Junghans, C. and Ciccotti, G. and Delle Site, L. and Kremer, K. (2012) Adaptive Resolution Molecular Dynamics Simulation Through Coupling to an Internal Particle Reservoir. Physical Review Letters, 108 . p. 170602.

Gupta, Pooja and Conrad, T. O. F. and Spötter, Andreas and Reinsch, Norbert and Bienefeld, Kaspar (2012) Simulating a base population in honey bee for molecular genetic studies. Genetics Selection Evolution, 44 . p. 14.

Hartmann, C. and Schütte, Ch. (2012) Efficient rare event simulation by optimal nonequilibrium forcing. J. Stat. Mech. Theor. Exp., 2012 . P11004.

Held, M. and Imhof, P. and Keller, B. and Noé, F. (2012) Modulation of a ligand’s energy landscape and kinetics by the chemical environment. J. Phys. Chem. B, 116 . pp. 13597-13607.

Held, M. and Noé, F. (2012) Calculating kinetics and pathways of protein–ligand association. Eur. J. Cell Biol., 91 . pp. 357-364.

Higgins, C. W. and Froidevaux, M. and Simeonov, V. and Vercauteren, N. and Barry, C. and Parlange, M. B. (2012) The Effect of Scale on the Applicability of Taylor's Frozen Turbulence Hypothesis in the Atmospheric Boundary Layer. Boundary-Layer Meteorology, 143 (2). 379 -391. ISSN Print: 0006-8314 Online: 1573-1472

John, V. and Thein, F. (2012) On the efficiency and robustness of the core routine of the quadrature method of moments (QMOM). Chemical Engineering Science, 75 . pp. 327-333.

Jouvet, G. and Bueler, E. (2012) Steady, shallow ice sheets as obstacle problems: Well-posedness and finite element approximation. SIAM J. Appl. Math., 72 (4). pp. 1292-1314. ISSN 0036-1399

Junker, J. and Bielow, C. and Bertsch, A. and Sturm, M. and Reinert, K. and Kohlbacher, O. (2012) TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J. Proteome Res., 11 (7). pp. 3914-3920. ISSN 1535-3893

Keller, B. and Prinz, J.-H. and Noé, F. (2012) Markov models and dynamical fingerprints: unraveling the complexity of molecular kinetics. Chem. Phys., 396 . pp. 92-107.

Keller, B. and Prinz, J.-H. and Noé, F. (2012) Resolving the apparent gap in complexity between simulated and measured kinetics of biomolecules. From Computational Biophysics to Systems Biology (CBSB11) Proceedings, IAS Series, 8 . pp. 61-64.

Klein, R. and Pauluis, O. (2012) Thermodynamic Consistency of a Pseudo-Incompressible Approximation for General Equations of State. Journal of the Atmospheric Sciences, 69 (3 ). pp. 961-968. ISSN Online: 1520-0469; Print : 0022-4928

Kumar, B. and Janetzko , F. and Schumacher, J. and Shaw, R.A. (2012) Extreme responses of a coupled scalar–particle system during turbulent mixing. New Journal of Physics, 14 115020 .

Kupfer, S. and Pérez-Hernández, G. and González, L. (2012) Singlet oxygen generation versus O–O homolysis in phenyl-substituted anthracene endoperoxides investigated by RASPT2, CASPT2, CC2, and TD-DFT methods. Theoretical Chemistry Accounts, 131 (12). ISSN 1432-881X

Kühnlein, C. and Smolarkiewicz, P. and Dörnbrack, A. (2012) Modelling atmospheric flows with adaptive moving meshes. Journal of Computational Physics, 231 (7). pp. 2741-2763. ISSN 0021-9991

Lee, M. W. and Plattner, N. and Meuwly, M. (2012) Structure, spectroscopy and dynamics of layered H2O and CO2 ices. Physical Chemistry Chemical Physics, 14 (44). pp. 15464-15474. ISSN 1463-9076

Leichtle, A. and Nuoffer, J.-M. and Ceglarek, U. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2012) Serum amino acid profiles and their alterations in colorectal cancer. Metabolomics . ISSN 1573-3890

Letzel, M.O. and Helmke, C. and Ng, E. and An, X. and Lai, A. and Raasch, S. (2012) LES case study on pedestrian level ventilation in two neighbourhoods in Hong Kong. Meteorologische Zeitschrift, 21 (6). pp. 575-589.

Leyendecker, S. and Hartmann, C. and Koch, M. (2012) Variational collision integrator for polymer chains. J. Comput. Phys, 231 (10). pp. 3896-3911.

Leyendecker, S. and Hartmann, C. and Koch, M. and Johnson, G. and Ortiz, M. (2012) Variational collision integrators in forward dynamics and optimal control. Proceedings of the 7th International Conference Croatian Society of Mechanics (7ICCSM2012) .

Matera, S. and Reuter, K. (2012) When atomic-scale resolution is not enough: Spatial effects on in situ model catalyst studies. Journal of Catalysis, 295 . pp. 261-268.

Meerbach, E. and Latorre, J.C. and Schütte, Ch. (2012) Sequential Change Point Detection in Molecular Dynamics Trajectories. Multicale Model. Sim., 10 (4). pp. 1263-1291.

Menz, S. and Latorre, J.C. and Schütte, Ch. and Huisinga, W. (2012) Hybrid Stochastic–Deterministic Solution of the Chemical Master Equation. SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS), 10 (4). pp. 1232-1262.

Metzner, Ph. and Putzig, L. and Horenko, I. (2012) Analysis of persistent non-stationary time series and applications. Communications in Applied Mathematics and Computational Science, 7 (2). pp. 175-229.

Mischau, A. (2012) Genderkompetenz in der Lehramtsausbildung Mathematik: Möglichkeiten der Integration und Vermittlung. Wissenschaftlerinnen-Rundbrief, 1 . pp. 19-22. ISSN ISBN: 978-3-929968-42-2

Mischau, A. and Grabarz, K. and Langfeldt, B. and Reith, F. (2012) Geschlechterdisparitäten in Berufs- und Karriereverläufen von MathematikerInnen und PhysikerInnen. IFFOnZeit, Onlinezeitschrift des Interdisziplinären Zentrums für Frauen- und Geschlechterforschung (IFF), 2 . pp. 67-75. ISSN 1868-7156

Mukherjee, B. and Delle Site, L. and Kremer, K. and Peter, C. (2012) Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions. Journal of Physical Chemistry B, 116 . 8474.

Mukherji, D. and van der Vegt, N.F.A. and Kremer, K. and Delle Site, L. (2012) Kirkwood-Buff analysis of liquid mixtures in an open boundary simulation. Journal of Chemical Theory and Computation, 8 . pp. 375-379.

Mukhopadhyay, A. and Jasor, G. and Polifke, W. (2012) Simulation of Pure Sedimentation of Raindrops using Quadrature Method of Moments. J. Atmospheric Research, 106 . pp. 61-70.

Münch, M. (2012) Brände mit Beteiligung von Wärmedämmverbundsystemen. AIZ - Das Immobilienmagazin . pp. 52-55.

Münch, M. and Kaiser, G. (2012) Kinderwagen und andere Brandlasten in Treppenhäusern. Der feine Unterschied zwischen richtig und rechtmäßig. Das Grundeigentum, Recht und Praxis, 17 . pp. 1144-1148.

Paeschke, E. and Marschalik, P. and Owinoh, A.Z. and Klein, R. (2012) Motion and structure of atmospheric mesoscale baroclinic vortices: dry air and weak environmental shear. Journal of Fluid Mechanics, 701 . pp. 137-170.

Park, S.B. and Baik, J.J. and Raasch, S. and Letzel, M.O. (2012) A large-eddy simulation study of thermal effects on turbulent flow and dispersion in and above a street canyon. J. Appl. Meteor. Climatol., 51 (5). pp. 829-841. ISSN Online: 1558-8432 Print: 1558-8424

Plattner, N. and Meuwly, M. (2012) Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin. Biophysical Journal, 102 (2). pp. 333-341. ISSN 00063495

Pluharova, E. and Marsalek, O. and Schmidt, B. and Jungwirth, P. (2012) Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations. J. Chem. Phys., 137 (18). p. 185101.

Potestio, R. and Delle Site, L. (2012) Quantum Locality and Equilibrium Properties in Low-temperature Parahydrogen: A Multiscale Simulation Study. Journal of Chemical Physics, 136 . 054101.

Pérez-Hernández, G. and González-Vázquez, J. and González, L. (2012) IR Spectrum of FHF–and FDF–Revisited Using a Spectral Method in Four Dimensions. The Journal of Physical Chemistry A, 116 (46). pp. 11361-11369. ISSN 1089-5639

Rath, B. and von Kleist, M. and Tief, F. and Karsch, K. and Tuerk, E. and Muehlhans, S. and Louis, F. and Skopnik, H. and Schweiger, B. and Duwe, S. (2012) Virus Load Kinetics and Resistance Development during Oseltamivir Treatment in Infants and Children Infected with Influenza A(H1N1)2009 and Influenza B Viruses. Pediatr. Infect. Dis. J., 31 (9). pp. 899-905.

Remmler, S. and Hickel, S. (2012) Direct and large-eddy simulation of stratified turbulence. International Journal of Heat and Fluid Flow, 35 . pp. 13-24. ISSN 0142-727X

Riechelmann, T. and Noh, Y . and Raasch, S. (2012) A new method for large-eddy simulations of clouds with Lagrangian droplets including the effects of turbulent collision. New Journal of Physics, 14 (065008).

Rieper, F. and Achatz, U. and Klein, R. (2012) Validation of an extended non-linear WKB theory: 1D and 2D case. Journal of Fluid Mechanics . (Submitted)

Sadiq, S. K. and Noé, F. and de Fabritiis, G. (2012) Kinetic characterization of the critical step in HIV-1 protease maturation. Proc. Natl. Acad. Sci. USA, 109 . pp. 20449-20454.

Sander, O. (2012) Geodesic finite elements on simplicial grids. International Journal for Numerical Methods in Engeneering, 92 (12). pp. 999-1025. ISSN Online: 1097-0207

Sander, O. and Schiela, A. (2012) Energy minimizers of the coupling of a Cosserat rod to an elastic continuum. Mathematical Modelling, 7 (1). pp. 1118-1123.

Sarich, M. and Schütte, Ch. (2012) Approximating Selected Non-dominant Timescales by Markov State Models. Comm. Math. Sci., 10 (3). pp. 1001-1013.

Schillings, Claudia and Schulz, Volker (2012) Problem Formulations and Treatment of Uncertainties in Aerodynamic Design. AIAA Journal, 47 (3).

Schlegel, F. and Stiller, J. and Bienert, A. and Maas, H.-G and Queck, R. and Bernhofer, C. (2012) Large-Eddy Simulation of inhomogeneous canopy flows using high resolution terrestrial laser scanning data. Boundary-Layer Meteorology, 142 . pp. 223-243. ISSN 0006-8314 (Print) 1573-1472 (Online)

Schwab, Christoph and Schillings, Claudia (2012) Sparse, adaptive Smolyak algorithms for Bayesian inverse problems. Research Report No. 2012-37 .

Schütte, Ch. and Winkelmann, S. and Hartmann, C. (2012) Optimal control of molecular dynamics using Markov state models. Math. Program. (Series B), 134 (1). pp. 259-282.

Senne, M. and Trendelkamp-Schroer, B. and Mey, A.S.J.S. and Schütte, Ch. and Noé, F. (2012) EMMA - A software package for Markov model building and analysis. Journal of Chemical Theory and Computation, 8 . pp. 2223-2238.

Spötter, Andreas and Gupta, Pooja and Nürnberg, G. and Reinsch , Norbert and Bienefeld, Kaspar (2012) Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica). Molecular Ecology Resources, 12 . pp. 323-332.

Stolzenberg, S. and Khelashvili, G. and Weinstein, H. (2012) Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh. The Journal of Physical Chemistry B, 116 (18). p. 5372. ISSN 1520-6106

Vetter, A. and Witt, F. and Sander, O. and Duda, G. and Weinkamer, E. (2012) The spatio-temporal arrangement of different tissues during bone healing as a result of simple mechanobiological rules. Biomechanics and Modeling in Mechanobiology, 11 (1-2). pp. 147-160. ISSN 1617-7959

Wang, H. and Schütte, Ch. and Delle Site, L. (2012) Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. J. Chem. Theo. Comp., 8 (8). pp. 2878-2887.

Wang, H. and Schütte, Ch. and Zhang, P. (2012) Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems. Phys. Rev. E, 86 (02). 026704.

Wang, H. and Zhang, P. and Schütte, Ch. (2012) On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems. J. Chem. Theo. Comp., 8 (9). pp. 3243-3256.

Weese, D. and Holtgrewe, M. and Reinert, K. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20). pp. 2592-2599.

Wehmeyer, C. and Falk von Rudorff, G. and Wolf, S. and Kabbe, G. and Schärf, D. and Kühne, T. D. and Sebastiani, D. (2012) Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry. The Journal of Chemical Physics, 137 (19). p. 194110. ISSN 00219606

Weiss, M. E. R. and Paulus, F. and Steinhilber, D. and Nikitin, A. and Haag, R. and Schütte, Ch. (2012) Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures. MACROMOLECULAR THEORY and SIMULATIONS, 21 (7). pp. 470-481.

Wendler, K. and Brehm, M. and Malberg, F. and Kirchner, B. and Delle Site, L. (2012) Short time dynamics of ionic liquids in AIMD based power spectra. Journal of Chemical Theory and Computation, 8 . p. 1570.

Wendler, K. and Dommert, F. and Zhao, Y.Y. and Berger, R. and Holm, C. and Delle Site, L. (2012) Ionic Liquids studied across different Scales: A Computational Perspective. Faraday Discussions, 154 . pp. 111-132.

Youett, J. and Sander, O. (2012) A dissipative discretization for large deformation frictionless dynamic contact problems. MATHEON Preprint #1184 .

Ziemer, C. and Wacker, U. (2012) Parameterisation of the Sedimentation of Raindrops with Finite Maximum Diameter. Monthly Weather Review, 140 (5). 1589 -1602. ISSN Online: 1520-0493 Print : 0027-0644

Ziemer, C. and Wacker, U. (2012) Parameterization of the Sedimentation of Raindrops with Finite Maximum Diameter. Monthly Weather Review , 140 (5). 1589 -1602. ISSN Online: 1520-0493 Print: 0027-0644

von Kleist, M. and Metzner, Ph. and Marquet, R. and Schütte, Ch. (2012) Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection. Plos Computational Biology, 8 (1). e1002359.

Book Section

Bastian, P. and Berninger, H. and Dedner, A. and Engwer, C. and Henning, P. and Kornhuber, R. and Kröner, D. and Ohlberger, M. and Sander, O. and Schiffler, G. and Shokina, N. and Smetana, K. (2012) Adaptive modelling of coupled hydrological processes with application in water management. In: Progress in Industrial Mathematics at ECMI 2010. Mathematics in Industry: The European Consortium for Mathematics in Industry (17). Springer Berlin Heidelberg, pp. 561-567. ISBN 978-3-642-25100-9

Brdar, S. and Dedner, A. and Klöfkorn, R. (2012) CDG Method for Navier-Stokes Equations. In: Hyperbolic Problems - Theory, Numerics and Applications. World Scientific Publishing Co Pte Ltd, pp. 320-327. ISBN 9789814417068

Kehr, B. and Reinert, K. and Darling, A. E. (2012) Hidden Breakpoints in Genome Alignments. In: Lecture Notes in Computer Science: Algorithms in Bioinformatics. Springer-Verlag, Berlin, pp. 391-403. ISBN 978-3-642-33121-3

Langfeldt, B. and Mischau, A. and Michel, J. (2012) Make Engineering and Technology more appealing to women via gender competence as an innovative element of teacher-training in Mathematics. In: GIEE 2011: Gender and Interdisciplinary Education for Engineers. SensePublishers, Rotterdam, pp. 327-339. ISBN 978-94-6091-982-4_24

Münch, M. and Klein, R. (2012) CFD at its Limits: Scaling Issues, Uncertain Data, and the User's Role. In: Process and Plant Safety, Applying Computational Fluid Dynamics. Wiley-VCH Verlag GmbH & Co.KGaA, pp. 189-212. ISBN 978-3-527-33027-0

Plattner, N. and Kunikeev, S. and Freeman, D. L. and Doll, J. D. (2012) Numerical Investigation of the Cumulant Expansion for Fourier Path Integrals. In: Applied Parallel and Scientific Computing. Lecture Notes in Computer Science , 7134 (7134). Springer, pp. 13-22. ISBN 978-3-642-28144-0

Conference or Workshop Item

Mukhopadhyay, A. and Carneiro, J. and Jasor, G. and Polifke, W. (2012) A Comparative Assessment of Presumed Function Method of Moments and Quadrature Method of Moments for Simulation of Polydisperse Flows. In: Theoretical and Applied Mechanics, August 19--24, Beijing, China.

Münch, M. (2012) On the application of CFD in fire safety - Between theory and practice or the user’s role. In: Computational methods in modern railway design, September 10-14, Vienna, Austria.

Thesis

Bielow, C. (2012) Quantification and Simulation of Liquid Chromatography-Mass Spectrometry Data. PhD thesis, Freie Universität Berlin.

Bielow, Chris (2012) Quantification and simulation of liquid chromatography-mass spectrometry data. PhD thesis, Freie Universität Berlin.

Nüske, F. (2012) A variational approach for conformation dynamics. Masters thesis, FU Berlin.

Prinz, J.-H. (2012) Advanced estimation methods for Markov models of dynamical systems. PhD thesis, FU Berlin.

Other

Schmidt, B. and Lorenz, U. (2012) WavePacket 4.8: A Matlab program package for quantum-mechanical wavepacket propagation and time-dependent spectroscopy. Freely available at SourceForge.net.