Repository: Freie Universität Berlin, Math Department

Items where Year is 2016

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Number of items: 78.


Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H. (2016) Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J. Cell Biol., 215 . pp. 37-46.


Babushkina, E. and Kornhuber, R. (2016) Adaptive multilevel Monte Carlo methods for stochastic variational inequalities. arXiv:1611.06012 . (Submitted)

Banisch, Ralf and Hartmann, C. (2016) A sparse Markov chain approximation of LQ-type stochastic control problems. Math. Control Relat. F., 6 (3). pp. 363-389. ISSN 1064-8275

Bennett, W.P. and Nikiforakis, N. and Klein, R. (2016) A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting. Journal of Computational Physics . (Submitted)

Berndt, P. and Klein, R. and Paschereit, O. C. (2016) A Kinetics Model For The Shockless Explosion Combustion.

Bienefeld, Kaspar and Zautke, F. and Gupta, Pooja (2016) A novel method for undisturbed long-term observation of honey bee (Apis mellifera) behavior – illustrated by hygienic behavior towards varroa infestation. Journal of Apicultural Research, 54 (5). 541-547 . ISSN 0021-8839 (print) 2078-6913 (online)

Blatt, M. and Burchardt, A. and Dedner, A. and Engwer, C. and Fahlke, J. and Flemisch, B. and Gersbacher, C. and Gräser, C. and Gruber, F. and Grüninger, C. and Kempf, D. and Klöfkorn, R. and Malkmus, T. and Müthing, S. and Nolte, M. and Piatkowski, M. and Sander, O. (2016) The Distributed and Unified Numerics Environment, Version 2.4. Archive of Numerical Software, 4 (100). pp. 13-29. ISSN 2197-8263


Canzar, S. and Andreotti, S. and Weese, D. and Reinert, K. and Klau, G. W. (2016) CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biology, 17 (1). ISSN 1474-760X

Chustagulprom, N. and Reich, S. and Reinhardt, M. (2016) A HYBRID ENSEMBLE TRANSFORM FILTER FOR HIGH DIMENSIONAL DYNAMICAL SYSTEMS. SIAM/ASA Journal on Uncertainty Quantification, 4 (1). pp. 592-608. ISSN 2166-2525


Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130).

Delle Site, L. and Agarwal, A. (2016) Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application. Computer Physics Communications (206). pp. 26-34.

Delle Site, L. and Agarwal, A. and Junghans, C. and Wang, H. (2016) Adaptive Resolution Simulation as a Grand Canonical Molecular Dynamics Scheme: Principles, Applications and Perspectives. In: Multiscale Methods in Molecular Biophysics. Series in Computational Biophysics . CRC Press. ISBN 1482225700 (In Press)

Dellnitz, M. and Klus, S. (2016) Sensing and control in symmetric networks. Dynamical Systems. An International Journal . pp. 1-19. (Submitted)

Dewar, W. and Schoonover, J. and McDougall, T. and Klein, R. (2016) Semicrompressible Ocean Thermodynamics and Boussinesq Energy Conservation. Fluids, 1 (9).

Djurdjevac, N. and Weber, M. and Schütte, Ch. (2016) Finding dominant structures of nonreversible Markov processes. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 14 (4). pp. 1319-1340. ISSN 1540-3459

Doerr, S. and Harvey, M. J. and Noé, F. and De Fabritiis, G. (2016) HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. J. Chem. Theory Comput., 12 . pp. 1845-1852.

Dolaptchiev, S. and Klein, R. (2016) A multi-scale model for the planetary and synoptic motions in the atmosphere. In: Annual Meeting of the European Geophysical Union, 2016, Frankfurt. (Unpublished)

Duwal, S. and Sunkara, V. and von Kleist, M. (2016) Multiscale Systems-Pharmacology Pipeline to Assess the Prophylactic Efficacy of NRTIs Against HIV-1. CPT: Pharmacometrics & Systems Pharmacology, 5 (7). pp. 377-387. ISSN 2163-8306

Duwal, S. and von Kleist, M. (2016) Top-down and bottom-up modelling in system pharmacology to understand clinical efficacy : An example with NRTIs of HIV-1. European Journal of Pharmaceutical Sciences . ISSN 0928-0987 (In Press)


Elliott, C.M. and Gräser, C. and Hobbs, G. and Kornhuber, R. and Wolf, M.W. (2016) A Variational Approach to Particles in Lipid Membranes. Archive for Rational Mechanics and Analysis, 222 (2). pp. 1011-1075. ISSN Print: 0003-9527; Online:1432-0673


Feireisl, E. and Klein, R. and Novotný, A. and Zatorska, E. (2016) On singular limits arising in the scale analysis of stratified fluid flows. Mathematical Models and Methods in Applied Sciences, World Scientific, 26 (3). pp. 419-443. ISSN Print: 0218-2025 Online: 1793-6314


Gelß, P. and Matera, S. and Schütte, Ch. (2016) Solving the master equation without kinetic Monte Carlo: tensor train approximations for a CO oxidation model. Journal of Computational Physics, 314 . pp. 489-502. ISSN 0021-9991

Gray, J. and Vinkeloe, J. and Berndt, P. and Moeck, J. and Paschereit, O. C. and Klein, R. and Stathopoulos, P. (2016) Thermodynamic Evaluation of Pulse Detonation Combustion for Gas Turbine Power Cycles. In: Turbo Expo Turbomachinery Technical Conference & Exposition, June 13 – 17, 2016, COEX Convention Center, SEOUL SOUTH KOREA.

Gräser, C. and Kahnt, M. and Kornhuber, R. (2016) Numerical approximation of multi-phase Penrose-Fife systems. Computational Methods in Applied Mathematics, 16 (4). pp. 523-542. ISSN Online: 1609-9389, Print: 1609-4840


Hallier, M. and Hartmann, C. (2016) Constructing Markov State Models of Reduced Complexity from Agent-Based Simulation Data. Social Simulation Conference 2016 . (Submitted)

Hallier, M. and Hartmann, C. (2016) A Markov state modelling approach to characterizing the punctuated equilibrium dynamics of stochastic evolutionary games. Games 2016, 5th World Conference of the Game Theory Society, . (Submitted)

Hartmann, C. and Schütte, Ch. and Zhang, W. (2016) Model reduction algorithms for optimal control and importance sampling of diffusions. Nonlinearity, 29 (8). pp. 2298-2326. ISSN 0951-7715

Hoppe, C. and Obermeier, P. and Muehlhans, S. and Alchikh, M. and Seeber, L. and Tief, F. and Karsch, K. and Chen, X. and Boettcher, S. and Diedrich, S. and Conrad, T. O. F. and Kisler, B. and Rath , B. (2016) Article: Innovative Digital Tools and Surveillance Systems for the Timely Detection of Adverse Events at the Point of Care: A Proof-of-Concept Study. Drug Safety, 39 (10). pp. 977-988. ISSN 1179-1942


Jäger, Marten and Schubach, Max and Zemojtel, Tomasz and Reinert, Knut and Church, Deanna M. and Robinson, Peter N. (2016) Alternate-locus aware variant calling in whole genome sequencing. Genome Medicine, 8 (1). ISSN 1756-994X


Klein, R. and Benacchio, T. (2016) A doubly blended model for multiscale atmospheric dynamics. Journal of the Atmospheric Sciences, 73 . pp. 1179-1186. ISSN Online: 1520-0469 Print: 0022-4928

Klinkmüller, M. and Schreurs, G. and Rosenau, M. and Kemnitz, H. (2016) Properties of granular analogue materials: A community wide survey. Tectonophysics, 666 . pp. 23-38.

Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2016) Tensor-based dynamic mode decomposition. SIAM Journal on Scientific Computing . ISSN ISSN 1064-8275 (print); 1095-7197 (electronic) (Submitted)

Klus, S. and Koltai, Péter and Schütte, Ch. (2016) On the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics, 3 (1). pp. 51-79. ISSN 2158-2491

Klus, S. and Schütte, Ch. (2016) Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics . ISSN 2158-2491

Kornhuber, R. and Peterseim, D. and Yserentant, H. (2016) An analysis of a class of variational multiscale methods based on subspace decomposition. Mathematics of Computation . ISSN 0025-5718 (In Press)

Kornhuber, R. and Yserentant, H. (2016) Numerical Homogenization of Elliptic Multiscale Problems by Subspace Decomposition. Multiscale Model. Simul., 14 (3). pp. 1017-1036. ISSN print: 1540-3459; online: 1540-3467


Lei, Shulai and Paulus, B. and Li, Shujuan and Schmidt, B. (2016) Curvature-dependent adsorption of water inside and outside armchair carbon nanotubes. J. Comp. Chem., 37 (14). pp. 1313-1320.

Lemke, O. and Keller, B.G. (2016) Density-based cluster algorithms for the identification of core sets. Journal of Chemical Physics, 145 (164104).

Lorenzi, J. M. and Matera, S. and Reuter, K. (2016) Synergistic Inhibition of Oxide Formation in Oxidation Catalysis: A First-Principles Kinetic Monte Carlo Study of NO + CO Oxidation at Pd(100). ACS Catalysis, 6 (8). pp. 5191-5197. ISSN 2155-5435


Marschall, T. and Reinert, K. and others, (59 authors in total) (2016) Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics . ISSN 1477-4054 (Online)

Mielke, A. and Roubícek, T. (2016) Rate-Independent elastoplasticity at finite strain and its numerical approximation. Mathematical Models and Methods in Applied Sciences, 26 (12). pp. 2203-2236. ISSN 1793-6314

Mireles, Victor and Conrad, T. O. F. (2016) Decomposing biological systems into reusable modules reveals characteristic module size distributions. n/a . (Submitted)


Nielsen, A. (2016) The Monte Carlo computation error of transition probabilities. Statistics & Probability Letters, 118 . pp. 163-170. ISSN 0167-7152

Noé, F. and Banisch, Ralf and Clementi, C. (2016) Commute maps: separating slowly-mixing molecular configurations for kinetic modeling. J. Chem. Theory Comput., 12 . pp. 5620-5630.

Nüske, F. and Schneider, R. and Vitalini, F. and Noé, F. (2016) Variational Tensor Approach for Approximating the Rare-Event Kinetics of Macromolecular Systems. J. Chem. Phys., 144 (5). 054105.


Obermeier, P. and Muehlhans, S. and Hoppe, Ch. and Karsch, K. and Tief, F. and Seeber, L. and Chen, X. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2016) Enabling Precision Medicine With Digital Case Classification at the Point-of-Care. EBioMedicine, 4 . pp. 191-196.


Patterson, R. I. A (2016) Properties of the solutions of delocalised coagulation and inception problems with outflow boundaries. Journal of Evolution Equations . (Submitted)

Paul, F. and Weikl, T. (2016) How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates. PLOS Computational Biology .

Peters, J.H. and Klein, R. and Delle Site, L. (2016) Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique /PhysRevE.94.023309. Phys. Rev. E, 94 (2).

Pipping, E. and Kornhuber, R. and Rosenau, M. and Oncken, O. (2016) On the efficient and reliable numerical solution of rate-and-state friction problems. Geophysical Journal International, 204 (3). pp. 1858-1866. ISSN Online: 1365-246X Print: 0956-540X

Pérez-Hernández, G. and Noé, F. (2016) Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems. J. Chem. Theory Comput., 12 . pp. 6118-6129.


Rams, Mona (2016) A new approach for biomarker detection using fusion networks. Masters thesis, Freie Universität Berlin.

Reichel , T. and Schäpel, J.S. and Bobusch, B. and Klein, R. and King, R. and Paschereit, C. O. (2016) Shockless Explosion Combustion: Experimental Investigation of a New Approximate Constant Volume Combustion Process. Journal of Engineering for Gas Turbines and Power, 139 (2). 021504 -021511. ISSN 0742-4795

Ritter, M. and Leever, K. and Rosenau, M. and Oncken, O. (2016) Scaling the Sand Box - Mechanical (Dis-) Similarities of Granular Materials and Brittle Rock. Journal of Geophysical Research: Solid Earth . (In Press)

Rosenau, M. and Leever, K. and Oncken, O. (2016) Experimental tectonics: Convergent plate margins. Earth Sys. Env. Sci. SFB 1114 Preprint . (Submitted)

Rudolf, M. and Boutelier, D. and Rosenau, M. and Schreurs, G. and Oncken, O. (2016) Rheological benchmark of silicone oils used for analog modeling of short- and long-term lithospheric deformation. Tectonophysics, 666 . pp. 12-20.


Schmidt, B. and Lorenz, U. (2016) WavePacket 5.2: A Matlab program package for quantum-mechanical wavepacket propagation and time-dependent spectroscopy. Freely available at

Schreurs, G. and et al, . (2016) Benchmarking analogue models of brittle thrust wedges. J. Struct. Geol. . (In Press)

Shao, Borong and Conrad, T. O. F. (2016) Epithelial Mesenchymal Transition Regulatory Network-based Feature Selection in Lung Cancer Prognosis Prediction. Lecture Notes in Computer Science (LNCS): Proceeding of IWBBIO 2016, 9656 .

Smith, M. and Smyth, R.P. and Marquet, R. and von Kleist, M. (2016) MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments. Bioinformatics . ISSN 1367-4803 (Submitted)

Spötter, Andreas and Gupta, Pooja and Mayer, Manfred and Reinsch , Norbert and Bienefeld, Kaspar (2016) Genome-Wide Association Study of a Varroa-Specific Defense Behavior in Honeybees (Apis mellifera). Journal of Heredity, 107 (3). pp. 220-227. ISSN 0022-1503 (Print) 1465-7333 (online)

Stolzenberg, S. and Michino, M. and LeVine, M. and Weinstein, H. and Shi, L. (2016) Computational approaches to detect allosteric pathways in transmembrane molecular machines. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858 (7). p. 1652. ISSN 00052736


Tief, F. and Hoppe, Ch. and Seeber, L. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Adamou, E. and Conrad, T. O. F. and Schweiger, B. and Adam, T. and Rath , B. (2016) An inception cohort study assessing the role of bacterial co-infections in children with influenza and ILI and a clinical decision model for stringent antibiotic use. Antiviral Therapy, 21 (5). pp. 413-424. ISSN 1359-6535 (print); 2040-2058 (online)

Trendelkamp-Schroer, B. and Noé, F. (2016) Efficient estimation of rare-event kinetics. Phys. Rev. X, 6 . 011009.

Trendelkamp-Schroer, B. and Wu, H. and Noé, F. (2016) Reversible Markov chain estimation using convex-concave programming. arXiv . 1603.01640.


Vega del Valle, I. and Schütte, Ch. and Conrad, T. O. F. (2016) Finding metastable states in real-world time series with recurrence networks. Physica A, 445 .

Vercauteren, N. and Mahrt, L. and Klein, R. (2016) Investigation of interactions between scales of motion in the stable boundary layer. Quarterly Journal of the Royal Meteorological Society .

Vitalini, F. and Noé, F. and Keller, B. (2016) Molecular dynamics simulations data of the twenty encoded amino acids in different force fields. Data in Brief, 7 . pp. 582-590.


Wieczorek, M. and Sticht, J. and Stolzenberg, S. and Günther, S. and Wehmeyer, C. and El Habre, Z. and Àlvaro-Benito, M. and Noé, F. and Freund, C. (2016) MHC class II complexes sample intermediate states along the peptide exchange pathway. Nature Communications, 7 . p. 13224.

Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107. (In Press)

Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F. (2016) Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 113 (23). E3221-E3230 . ISSN 0027-8424

Wu, H. and Noé, F. (2016) Spectral learning of dynamic systems from nonequilibrium data. NIPS, 29 . pp. 4179-4187.


Yapp, E.K.Y. and Patterson, R. I. A and Akroyd, J. and Mosbach, S. and Adkins, E.M. and Miller, J.H. and Kraft, M. (2016) Simulation and parametric sensitivity study of optical band gap in a laminar co-flow ethylene diffusion flame. Combustion and Flame . (Submitted)

You, Xintian Arthur and Conrad, T. O. F. (2016) Acfs: accurate circRNA identification and quantification from NGS data. Nature Scientific Reports, 6 . ISSN 2045-2322

Youett, J. and Sander, O. and Kornhuber, R. (2016) A globally convergent filter-trust-region method for large deformation contact problems. Preprint 1116, Matheon Berlin . (Submitted)

Yousef, K. P. and Meixenberger, K. and Smith, M. and Jansen, K. and Bartmeyer, B. and Hamouda, O. and Kücherer, C. and von Kleist, M. (2016) Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses. Journal of Acquired Immunodeficiency Virus, 73 (3). pp. 356-363. ISSN 1525-4135


Zhang, W. and Hartmann, C. and Schütte, Ch. (2016) Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday discussions . ISSN 1359-6640 (In Press)

Zhu, J. and Klein, R. and Delle Site, L. (2016) Adaptive Molecular Resolution Approach in Hamiltonian Form: An Asymptotic Analysis. Physical Review E, 94 (043321).

This list was generated on Sat Sep 23 19:45:43 2017 CEST.