Items where Year is 2015

A

Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606

Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 1367-2630

Aiche, S. and Sachsenberg, T. and Kenar, E. and Walzer, M. and Wiswedel, B. and Kristl, T. and Boyles, M. and Duschl, A. and Huber, C. G. and Berthold, M. R. and Reinert, K. and Kohlbacher, O. (2015) Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. PROTEOMICS, 15 (8). pp. 1443-1447. ISSN 16159853

Akyuz, N. and Georgieva, E. R. and Zhou, Z. and Stolzenberg, S. and Cuendet, M. A. and Khelashvili, G. and Altman, R. B. and Terry, D. S. and Freed, J. H. and Weinstein, H. and Boudker, O. and Blanchard, S. (2015) Transport domain unlocking sets the uptake rate of an aspartate transporter. Nature, 518 (7537). p. 68. ISSN 0028-0836

Andreotti, Sandro (2015) Linear Programming and Integer Linear Programming in Bioinformatics. PhD thesis, Freie Universität Berlin.

B

Babushkina, E. S. and Bessonov, N. M. and Ataullakhanov, F. I. and Panteleev, M. A. (2015) Continuous modeling of arterial platelet thrombus formation using a spatial adsorption equation. PLoS ONE, 10 (10). ISSN 1932-6203

Banisch, Ralf and Djurdjevac, N. (2015) Cycle-flow–based module detection in directed recurrence networks. EPL (Europhysics Letters) , 108 (6). ISSN 0295-5075

Banisch, Ralf and Djurdjevac, N. and Schütte, Ch. (2015) Reactive flows and unproductive cycles in irreversible Markov chains. The European Physical Journal Special Topics, 224 (12). pp. 2369-2387. ISSN 1951-6355

Becker, N. and Ulbrich, U. and Klein, R. (2015) Systematic large-scale secondary circulations in a regional climate model. Geophysical Research Letters, 42 (10). 4142-4149 .

Benacchio, T. and Klein, R. and Dubos, T. and Voitus, F. (2015) Comments on “A Semihydrostatic Theory of Gravity-Dominated Compressible Flow”. Journal of the Atmospheric Sciences , 72 (7). pp. 2850-2851. ISSN Online: 1520-0469 Print: 0022-4928

Berninger, H. and Kornhuber, R. and Sander, O. (2015) A multidomain discretization of the Richards equation in layered soil. Computational Geosciences, 19 (1). pp. 213-232. ISSN 1420-0597

Biedermann, J. and Ullrich, A. and Schöneberg, J. and Noé, F. (2015) ReaDDyMM: fast interacting-particle reaction-diffusion simulations using graphical processing units. Biophys. J., 108 . pp. 457-461. ISSN 00063495

Billesbølle, C. B. and Krüger, M. B. and Shi, L. and Quick, M. and Li, Z. and Stolzenberg, S. and Kniazeff, J. and Gotfryd, K. and Mortensen, J. S. and Javitch, J. A. and Weinstein, H. and Loland, C.J. and Gether, U. (2015) Substrate-induced Unlocking of the Inner Gate Determines the Catalytic Efficiency of a Neurotransmitter:Sodium Symporter. Journal of Biological Chemistry, 290 (44). p. 26725. ISSN 0021-9258

Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter (2015) Pseudo generators for under-resolved molecular dynamics. The European Physical Journal Special Topics, 224 (12). pp. 2463-2490. ISSN 1951-6355

Bittracher, Andreas and Koltai, Péter and Junge, Oliver (2015) Pseudogenerators of spatial transfer operators. SIAM Journal on Applied Dynamical Systems, 14 (3). pp. 1478-1517. ISSN 1536-0040

Bobusch, B. and Berndt, P. and Paschereit, O. C. and Klein, R. (2015) Investigation of fluid devices for mixing enhancemet for the shockless explosion combustion process. In: Active Flow and Combustion Control. Springer International Publishing. ISBN 978-3-319-11966-3 (Print) 978-3-319-11967-0 (Online)

Boger, M. and Jägle, F. and Munz , C.-D. and Klein, R. (2015) Coupling of compressible and incompressible flow regions using the multiple pressure variables approach. Mathematical Methods in the Applied Sciences, 38 (3). pp. 458-477.

Boninsegna, L. and Gobbo, G. and Noé, F. and Clementi, C. (2015) Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps. J. Chem. Theory Comput., 11 . pp. 5947-5960.

D

Delle Site, L. (2015) Levy-Lieb principle: The bridge between the electron density of Density Functional Theory and the wavefunction of Quantum Monte Carlo. Chemical Physics Letters, 619 . pp. 148-151. ISSN 0009-2614

Delle Site, L. (2015) Shannon entropy and many-electron correlations: Theoretical concepts, numerical results, and Collins conjecture. International Journal of Quantum Chemistry, 115 (19). pp. 1396-1404. ISSN 1097-461X

Deuflhard, P. and Röblitz, S. (2015) A Guide to Numerical Modelling in Systems Biology. Texts in Computational Science and Engineering, 12 . Springer International Publishing, Basel. ISBN 978-3-319-20058-3 (print) / 978-3-319-20059-0 (online)

Di Giuseppe, E. and Corbi, F. and Funiciello, F. and Massmeyer, A. and Santimano, T.N. and Rosenau, M. and Davaille, A. (2015) Characterization of Carbopol hydrogel rheology for experimental tectonics and geodynamics, , 642, 29-45, doi:10.1016/j.tecto.2014.12.005. Tectonophysics . pp. 29-45.

Djurdjevac, N. and Banisch, Ralf and Schütte, Ch. (2015) Modularity of Directed Networks: Cycle Decomposition Approach. Journal of Computational Dynamics, 2 (1). pp. 1-24. ISSN 2158-2491

Duwal, S. and Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2015) Optimal treatment strategies in the context of 'treatment for prevention' against HIV-1 in resource-poor settings. PLOS Computational Biology, 11 . e1004200.

E

Ehrig, R. and Dierkes, T. and Schäfer, S. and Röblitz, S. and Tronci, E. and Mancini, T. and Salvo, I. and Alimguzhin, V. and Mari, F. and Melatti, I. and Massini, A. and Krüger, T. H. C. and Egli, M. and Ille, F. and Leeners, B. (2015) An integrative approach for model driven computation of treatments in reproductive medicine. In: BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, 07.11.2015 - 11.11.2015, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India - USA.

Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606

Erbar, M. and Maas, J. and Renger, M. (2015) From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability, 20 (89).

F

Fröhner, Christoph (2015) Reversible integrators for particle based reaction-diffusion simulations. Masters thesis, FU Berlin.

G

Grohs, P. and Hardering, H. and Sander, O. (2015) Optimal a priori discretization error bounds for geodesic finite elements. Foundations of Computational Mathematics, 15 (6). pp. 1357-1411. ISSN 1615-3375

Gräser, C. (2015) A note on Poincaré- and Friedrichs-type inequalities. arXiv:1512.02842 . (Submitted)

Gräser, C. and Kornhuber, R. and Sack, U. (2015) Nonsmooth Schur-Newton methods for multicomponent Cahn-Hilliard systems. IMA Journal of Numerical Analysis, 35 (2). pp. 652-679. ISSN 0272-4979

Gul, Rahim and Bernhard, S. (2015) Parametric uncertainty and global sensitivity analysis in a model of the carotid bifurcation: Identification and ranking of most sensitive model parameters. Mathematical Biosciences, 269 . pp. 104-116. ISSN 0025-5564

Gunkel, M. and Schöneberg, J. and Alkhaldi, W. and Irsen, S. and Noé, F. and Kaupp, U. B. and Al-Amoudi, A. (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure, 23 . pp. 628-638.

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Harlander, U. and von Larcher, T. and Wright, G.B. and Hoff, M. and Alexandrov, K. and Egbers, C. (2015) Orthogonal decomposition methods to analyze PIV, LDA and thermography data of a thermally driven rotating annulus laboratory experiment. American Geophysical Union. ISBN 978-1-118-85593-5

Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355

Holtgrewe, M. and Kuchenbecker, L. and Reinert, K. (2015) Methods for the Detection and Assembly of Novel Sequence in High-Throughput Sequencing Data. Bioinformatics, 31 (12). pp. 1904-1912. ISSN 1367-4803

Holtgrewe, Manuel (2015) Engineering Algorithms for Personal Genome Pipelines. PhD thesis, Freie Universität Berlin.

Horenko, I. and Gerber, S. (2015) Improving clustering by imposing network information. Science Advances, 1 (7). ISSN 2375-2548

Hu, J. and Reinert, K. (2015) LocalAli: An Evolutionary-based Local Alignment Approach to Identify Functionally Conserved Modules in Multiple Networks. Bioinformatics, 30 (1). pp. 363-372. ISSN 1367-4803

Hu, Jialu (2015) Algorithms to Identify Functional Orthologs And Functional Modules from High- Throughput Data. PhD thesis, Freie Universität Berlin.

K

Kappler, J. and Netz, R.R. (2015) Multiple surface wave solutions on linear viscoelastic media. EPL, 112 (1). p. 19002.

Karsch, K. and Obermeier, P. and Seeber, L. and Chen, X. and Tief, F. and Muehlhans, S. and Hoppe, Ch. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2015) Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children. The Pediatric Infectious Disease Journal, 34 (10).

Kim, W.K. and Netz, R.R. (2015) The mean shape of transition and first-passage paths. J. Chem. Phys., 143 (224108).

Klein, R. (2015) Comments on "Adaptive Resolution Simulation in Equilibrium and Beyond" by H. Wang and A. Agarwal. The European Physical Journal, 224 (12). pp. 2497-2499.

Klein, R. (2015) Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer R. Potestio. The European Physical Journal, 224 (12). pp. 2503-2504. ISSN Online: 1951-6401 Print: 1951-6355

Klein, R. (2015) Comments on "Open Boundary Molecular Dynamics " by R. Delgado-Buscalioni, J. Sablic, and M. Praprotnik. The European Physical Journal, 224 (12). pp. 2509-2510. ISSN Online: 1951-6401 Print: 1951-6355

Kryven, I. and Röblitz, S. and Schütte, Ch. (2015) Solution of the chemical master equation by radial basis functions approximation with interface tracking. BMC Systems Biology, 9 (67). ISSN 1752-0509

Kuchenbecker, L. and Nienen, M. and Hecht, J. and Neumann, A. U. and Babel, N. and Reinert, K. and Robinson, P. N. (2015) IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinformatics, 31 (18). pp. 2963-2971. ISSN 1367-4803

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Langfeld, B. and Mischau, A. (2015) MathematikerInnen und PhysikerInnen an Hochschulen: Repairing or Redesigning the Leaky Pipeline? In: Akademische Wissenskulturen und soziale Praxis. Geschlechterforschung zu natur-, technik- und geisteswissenschaftlichen Fächern im Vergleich. Sektionsreihe Forum Frauen- und Geschlechterforschung (42). Westfälisches Dampfboot, pp. 37-59. ISBN 978-3-89691-242-8

Langfeldt, B. and Mischau, A. (2015) Die akademische Laufbahn in der Mathematik und Physik. Eine Analyse fach- und geschlechterbezogener Unterschiede bei der Umsetzung von Karrierewissen. Beiträge zur Hochschulforschung, 37 . pp. 80-99. ISSN 0171-645X

Li, S. and Moreno, M. and Bedford, J. and Rosenau, M. and Oncken, O. (2015) Revisiting viscoelastic effects on interseismic deformation and locking degree: A case study of the Peru-North Chile subduction zone. Journal of Geophysical Research-Solid Earth, 120 (6). pp. 4522-4538.

Li, Shujuan and Schmidt, B. (2015) Molecular Dynamics Simulations of Proton-Ordered Water Confined in Low-Diameter Carbon Nanotubes. Phys. Chem. Chem. Phys., 17 (11). pp. 7303-7316.

M

Matera, S. and Blomberg, S. and Hoffmann, M. J. and Zetterberg, J. and Gustafson, J. and Lundgren, E. and Reuter, K. (2015) Evidence for the Active Phase of Heterogeneous Catalysts through In Situ Reaction Product Imaging and Multiscale Modeling. ACS Catalysis, 5 (8). pp. 4514-4518.

Metzner, Ph. and Waidmann, M. and Igdalov, D. and von Larcher, T. and Horenko, I. and Klein, R. and Beck, A. and Gassner, G. (2015) A stochastic closure approach for LES with application to turbulent channel flow. In: Direct and Large-Eddy Simulation IX. ERCOFTAC Series, 20 . Springer. ISBN 978-3-319-14448-1

Mireles, Victor and Conrad, T. O. F. (2015) Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrices. Procedia Computer Science, 51 . pp. 2967-2971. ISSN 1877-0509

Moualeu-Ngangue, D. P. and Röblitz, S. and Ehrig, R. and Deuflhard, P. (2015) Parameter Identification in a Tuberculosis Model for Cameroon. PLoS ONE, 10 (4). e0120607. ISSN 1932-6203

Münch, M. (2015) Absicherung von CFD-Simulationen im Brandschutz. Bauphysik-Kalender 2015 : Schwerpunkt: Simulations- und Berechnungsverfahren . Ernst, Wilhelm & Sohn, Berlin. ISBN 978-3-433-03105-6

Münch, M. (2015) Brandereignisse in Flüchtlingsunterkünften. BRANDSchutz / Deutsche Feuerwehr-Zeitung .

Münch, M. (2015) Vertrauenswürdige Brandsimulationen - Können kleinskalige Brandexperimente helfen? In: 29. Fachtagung Brandschutz bei Sonderbauten, 15.-16. September 2015, Institut für Baustoffe, Massivbau und Brandschutz (iBMB), Braunschweig.

Münch, M. (2015) Zwischen Glaskugel und Wissenschaft. Wann sind Brandsimulationen vertrauenswürdig? In: 4. Magdeburger Brand- und Explosionsschutztage, 26./27. März 2015, Otto-von-Guericke Universität Magdeburg, Hochschule Magdeburg. (Unpublished)

Münch, M. and Belaschk, H.C. and Klein, R. (2015) Grundlagen der Brandsimulation - Einführung in die übergeordneten Zusammenhänge. Bauphysik-Kalender 2015 : Schwerpunkt: Simulations- und Berechnungsverfahren . Ernst, Wilhelm & Sohn, Berlin. ISBN 978-3-433-03105-6

N

Noé, F. (2015) Beating the Millisecond Barrier in Molecular Dynamics Simulations. Biophys J., 108 . pp. 228-229.

Noé, F. (2015) Statistical inefficiency of Markov model count matrices. preprint . (Unpublished)

Noé, F. and Clementi, C. (2015) Kinetic distance and kinetic maps from molecular dynamics simulation. J. Chem. Theory Comput., 11 . pp. 5002-5011.

O

Ozdoba, Christopher (2015) Ensemble Machine Learning Techniques for Analyzing Large Biological Datasets Using the SAP In-Memory Database HANA. Masters thesis, Freie Universität Berlin.

O’Kane, T.J. and Risbey, J.S. and Monselesan, D.P. and Horenko, I. and Franzke, Ch.L.E. (2015) On the dynamics of persistent states and their secular trends in the waveguides of the Southern Hemisphere troposphere. Climate Dynamics . ISSN Print: 0930-7575, Online: 1432-0894

P

Pipping, E. and Sander, O. and Kornhuber, R. (2015) Variational formulation of rate- and state-dependent friction problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 95 (4). pp. 377-395. ISSN 0044-2267

Plagge, M. and Münch, M. (2015) Bug oder Feature? Über numerische Lichtschutzfaktoren im fvDOM-Strahlungsmodell. In: 3. vfdb-Workshop Brandschutzforschung, 26./27. März 2015, Otto-von-Guericke Universität Magdeburg, Hochschule Magdeburg. (Unpublished)

Plattner, N. and Noé, F. (2015) Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat. Commun., 6 . p. 7653.

Plöntzke, J. and Berg, M. and Stötzel, C. and Röblitz, S. (2015) A systems biology approach to bovine fertility and metabolism: Introduction of a glucose insulin model. In: BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, 07.11.2015 - 11.11.2015, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India - USA.

R

Ransiek, A. and Rosenthal, G. and Völter, B. (2015) Diskursanalyse. In: Interpretative Sozialforschung. Eine Einführung. Beltz Juventa, Weinheim:, pp. 247-258.

Reinert, K. and Langmead, B. and Weese, D. and Evers, D.J. (2015) Alignment of Next-Generation Sequencing Reads. Annual Review of Genomics and Human Genetics, 16 (1). pp. 133-151. ISSN 1527-8204

Reubold, T. F. and Faelber, K. and Plattner, N. and Posor, Y. and Branz, K. and Curth, U. and Schlegel, J. and Anand, R. and Manstein, D. and Noé, F. and Haucke, V. and Daumke, O. and Eschenburg, S. (2015) Crystal structure of the dynamin tetramer. Nature, 525 . pp. 404-408.

Riechelmann, T. and Wacker, U. and Beheng, K.D. and Etling, D. and Raasch, S. (2015) Influence of turbulence on the drop growth in warm clouds, Part II: sensitivity studies with a spectral bin microphysics and a Lagrangian cloud model. Meteorologische Zeitschrift .

Rinne, K.F. and Schulz, J.C.F. and Netz, R.R. (2015) Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water. J. Chem. Phys., 142 (215104).

S

Santimano, T.N. and Rosenau, M. and Oncken, O. (2015) Intrinsic versus extrinsic variability of analogue sand-box experiments - Insights from statistical analysis of repeated accretionary sand wedge experiments. Journal of Structural Geology, 75 . pp. 80-100.

Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F. (2015) PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. J. Chem. Theory Comput., 11 (11). pp. 5525-5542.

Schillings, Claudia and Sunnåker, Mikael and Stelling, Jörg and Schwab, Christoph (2015) Efficient characterization of parametric uncertainty of complex (bio) chemical networks. PLOS Computational Biology .

Schlegel, F. and Stiller, J. and Bienert, A. and Maas, H.-G and Queck, R. and Bernhofer, C. (2015) Large-Eddy Simulation Study of the Effects on Flow of a Heterogeneous Forest at Sub-tree Resolution. Boundary-Layer Meteorology, 154 . pp. 27-56.

Schmidt, B. and Friedrich, B. (2015) Supersymmetry and eigensurface topology of the spherical quantum pendulum. Phys. Rev. A, 91 (02). 022111.

Schmidt, B. and Lorenz, U. (2015) WavePacket 5.1: A Matlab program package for quantum-mechanical wavepacket propagation and time-dependent spectroscopy. Freely available at SourceForge.net.

Schror, M. and Mey, A.S.J.S. and Noé, F. and MacPhee, C. (2015) Shedding Light on the Dock-Lock Mechanism in Amyloid Fibril Growth Using Markov State Models. J. Chem. Phys. Lett., 6 . pp. 1076-1081.

Schultz, L. and Zurich, M.-G. and Culot, M. and da Costa, A. and Landry, C. and Bellwon, P. and Kristl, T. and Hörmann, K. and Ruzek, S. and Aiche, S. and Reinert, K. and Bielow, C. and Gosselet, F. and Cecchelli, R. and Huber, C. G. and Schroeder, O. H.-U. and Gramowski-Voss, A. and Weiss, D. G. and Bal-Price, A. (2015) Evaluation of drug-induced neurotoxicity based on metabolomics, proteomics and electrical activity measurements in complementary CNS in vitro models. Toxicology in Vitro, 30 (1). pp. 138-165. ISSN 08872333

Schulz, J.C.F. and Miettinen, M.S. and Netz, R.R. (2015) Unfolding and Folding Internal Friction of β‑Hairpins Is Smaller than That of α‑Helices. Journal of Physical Chemistry B, 119 (13). pp. 4565-4574.

Schuster, I. and Strathmann, H. and Paige, B. and Sejdinovic, Dino (2015) Kernel Sequential Monte Carlo. SFB 1114 Preprint in arXiv:1510.03105 . (Submitted)

Schütte, Ch. and Nielsen, A. and Weber, M. (2015) Markov state models and molecular alchemy. Molecular Physics, 113 (1). pp. 69-78. ISSN 0026-8976

Schütte, Ch. and Sarich, M. (2015) A Critical Appraisal of Markov State Models. SFB 1114 Preprint, 15-18 . ISSN 1438-0064

Schütte, Ch. and Sarich, M. (2015) A critical appraisal of Markov state models. The European Physical Journal Special Topics, 224 (12). pp. 2445-2462. ISSN 1951-6355

Schütte, Ch. and Wang, H. (2015) Building Markov State Models for Periodically Driven Non-Equilibrium Systems. Journal of Chemical Theory and Computation, 11 (4). pp. 1819-1831. ISSN 1549-9618

Shao, Borong and Conrad, T. O. F. (2015) Are NoSQL data stores useful for bioinformatics researchers? "International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), 3 (3). pp. 1704-1708. ISSN 2321-8169

Siragusa, Enrico (2015) Approximate string matching for high-throughput sequencing. PhD thesis, Freie Universität Berlin.

Smyth, R.P. and Despons, L. and Huili, G. and Bernacchi, S. and Hijnen, M. and Mak, J. and Jossinet, F. and Weixi, L. and Paillart, J.-C. and von Kleist, M. and Marquet, R. (2015) Mutational Interference Mapping Experiment (MIME) for studying the relationship between RNA structure and function. Nature Methods, 12 . pp. 866-872. ISSN 1548-7091

Stolzenberg, S. and Quick, M. and Zhao, C. and Gotfryd, K. and Khelashvili, G. and Gether, U. and Loland, C. J. and Javitch, J. A. and Noskov, S. and Weinstein, H. and Shi, L. (2015) Mechanism of the Association between Na+Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters. Journal of Biological Chemistry, 290 (22). p. 13992. ISSN 0021-9258

Stötzel, C. and Ehrig, R. and Boer, H.M.T. and Plöntzke, J. and Röblitz, S. (2015) Exploration of different wave patterns in a model of the bovine estrous cycle by Fourier analysis. In: BIOMAT - Proceedings of the 14th International Symposium on Mathematical and Computational Biology, 02.11.2014 - 08.11.2014, Bedlewo - Poland.

Stötzel, C. and Röblitz, S. and Siebert, H. (2015) Complementing ODE-Based System Analysis Using Boolean Networks Derived from an Euler-Like Transformation. PLoS ONE, 10 (10). e0140954. ISSN 1932-6203

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Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F. (2015) Estimation and uncertainty of reversible Markov models. J. Chem. Phys., 143 (17). p. 174101.

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Ullrich, A. and Böhme, M. A. and Schöneberg, J. and Depner, H. and Sigrist, S. J. and Noé, F. (2015) Dynamical organization of Syntaxin-1A at the presynaptic active zone. PLoS Comput. Biol., 11 . e1004407.

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Vater, S. and Beisiegel, N. and Behrens, J. (2015) A limiter-based well-balanced discontinuous Galerkin method for shallow-water flows with wetting and drying: One-dimensional case. Advances in Water Resources, 85 . pp. 1-13. ISSN 0309-1708

Vener, M. V. and Odinokov, A. V. and Wehmeyer, C. and Sebastiani, D. (2015) The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. The Journal of Chemical Physics, 142 (21). p. 215106. ISSN 0021-9606

Vercauteren, N. and Klein, R. (2015) A clustering method to characterize intermittent bursts of turbulence and interaction with submeso motions in the stable boundary layer. Journal of the Atmospheric Sciences, 72 (1). ISSN Online: 1520-0469 Print: 0022-4928

Vitalini, F. and Mey, A.S.J.S. and Noé, F. and Keller, B. (2015) Dynamic Properties of Force Fields. J. Chem. Phys., 142 . 084101.

Vitalini, F. and Noé, F. and Keller, B. (2015) A basis set for peptides for the variational approach to conformational kinetics. J. Chem. Theory Comput., 11 . pp. 3992-4004.

von Larcher, T. and Beck, A. and Klein, R. and Horenko, I. and Metzner, Ph. and Waidmann, M. and Igdalov, D. and Gassner, G. and Munz , C.-D. (2015) Towards a Framework for the Stochastic Modelling of Subgrid Scale Fluxes for Large Eddy Simulation. Meteorologische Zeitschrift, 24 (3). pp. 313-342.

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Wang, H. and Agarwal, A. (2015) Adaptive resolution simulation in equilibrium and beyond. The European Physical Journal Special Topics, 224 (12). pp. 2269-2287. ISSN 1951-6355

Wang, H. and Agarwal, A. (2015) Reply to comment by R. Klein on “Adaptive resolution simulation in equilibrium and beyond”. The European Physical Journal Special Topics, 224 (12). pp. 2501-2502. ISSN 1951-6355

Weber, Britta (2015) Reconstruction of Microtubule Centerlines from Electron Tomograms. PhD thesis, Freie Universität Berlin.

Wilmes, Anja and Bielow, Chris and Ranninger, Christina and Bellwon, Patricia and Aschauer, Lydia and Limonciel, Alice and Chassaigne, Hubert and Kristl, Theresa and Aiche, Stephan and Huber, Christian G. and Guillou, Claude and Hewitt, Philipp and Leonard, Martin O. and Dekant, Wolfgang and Bois, Frederic and Jennings, Paul (2015) Mechanism of cisplatin proximal tubule toxicity revealed by integrating transcriptomics, proteomics, metabolomics and biokinetics. Toxicology in Vitro, 30 (1, Part A). pp. 117-127. ISSN 08872333

Wolff, S. and Schäpel, J.S. and Berndt, P. and King, R. (2015) State estimation for homogeneous 1-D Euler Equation by Unscented Kalman Filtering. In: ASME 2015 Dynamic Systems and Control Conference 2., 28.-30. Oktober 2015, Columbus, Ohio. (Submitted)

Wu, H. (2015) Maximum Margin Clustering for State Decomposition of Metastable Systems. Neurocomputing, 164 . pp. 5-22. ISSN 0925-2312

Wu, H. and Prinz, J.-H. and Noé, F. (2015) Projected Metastable Markov Processes and Their Estimation with Observable Operator Models. J. Chem. Phys., 143 (14). p. 144101.

Wu, H. and Noé, F. (2015) Gaussian Markov transition models of molecular kinetics. J. Chem. Phys., 142 (8). 084104.

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You, Xintian Arthur (2015) Hastings: An R pipeline for large-scale RNA-Seq data analysis. Technical Report . (Unpublished)

You, Xintian Arthur (2015) Tailored Analysis in Studying Transcriptome Landscape. PhD thesis, Freie Universität Berlin.

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