Repository: Freie Universität Berlin, Math Department

Items where Year is 2017

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Number of items: 75.

A

Abramyan, A. and Stolzenberg, S. and Li, Z. and Loland, C. J. and Noé, F. and Shi, L. (2017) The isomeric preference of an atypical dopamine transporter inhibitor contributes to its selection of the transporter conformation. ACS Chem. Neurosc., 8 . pp. 1735-1746.

Acevedo, W. and de Wiljes, J. and Reich, S. (2017) Second-order accurate ensemble transform particle filters. SFB 1114 Preprint . (Submitted)

Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics, 19 . pp. 13030-13037. ISSN 1463-9084

Audain, Enrique and Uszkoreit, Julian and Sachsenberg, Timo and Pfeuffer, Julianus and Liang, Xiao and Hermjakob, Henning and Sanchez, Aniel and Eisenacher, Martin and Reinert, Knut and Tabb, David L. and Kohlbacher, Oliver and Perez-Riverol, Yasset (2017) In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of Proteomics, 150 . pp. 170-182. ISSN 18743919

B

Banisch, Ralf and Koltai, Péter (2017) Understanding the geometry of transport: diffusion maps for Lagrangian trajectory data unravel coherent sets. Chaos: An Interdisciplinary Journal of Nonlinear Science, 23 (23). ISSN 1054-1500 (print); 1089-7682 (online) (Submitted)

Becker, S. and Mirahmadi, M. and Schmidt, B. and Schatz, K. and Friedrich, B. (2017) Conditional Quasi-Exact Solvability of the Quantum Planar Pendulum and its Anti-Isospectral Hyperbolic Counterpart. Eur. J. Phys. D, 71 (6). p. 149.

Benner, P. and Breiten, T. and Hartmann, C. and Schmidt, B. (2017) Model reduction of controlled Fokker-Planck and Liouville-von Neumann equations. SIAM J. Appl. Dyn. Syst. . (Submitted)

Berndt, P. and Klein, R. (2017) Modeling the kinetics of the Shockless Explosion Combustion. Combustion and Flame, 175 . pp. 16-26.

C

Conrad, T. O. F. and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Vybiral, Jan and Kutyniok, Gitta and Schütte, Ch. (2017) Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. BMC Bioinformatics, 18 (160). ISSN 1471-2105 (In Press)

D

Dadi, Temesgen Hailemariam and Renard, Bernhard Y. and Wieler, Lothar H. and Semmler, Torsten and Reinert, Knut (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ, 5 . e3138. ISSN 2167-8359

Dellnitz, M. and Klus, S. and Ziessler, A. (2017) A Set-Oriented Numerical Approach for Dynamical Systems with Parameter Uncertainty. SIAM Journal on Applied Dynamical Systems, 16 (1). pp. 120-138. ISSN 1536-0040

Djordjevic, N. and Hanraths, N. and Gray, J. and Berndt, P. and Moeck, J. (2017) Numerical study on the abatement of NOx emissions from pulse detonation combustion. In: ASME GT2017. (Submitted)

Djurdjevac, A. and Elliott, C.M. and Kornhuber, R. and Ranner, Th. (2017) Evolving surface finite element methods for random advection-diffusion equations. arXiv.org . pp. 1-25. (Submitted)

Donati, L. and Hartmann, C. and Keller, B.G. (2017) Girsanov reweighting for path ensembles and Markov state models. SFB 1114 Preprint . (Submitted)

Dörffel, T. and Papke, A. and Klein, R. and Smolarkiewicz, P. (2017) Intensification of tilted atmospheric vortices by asymmetric diabatic heating. SFB 1114 Preprint in arXiv:1708.07674 . pp. 1-22. (Unpublished)

E

Engwer, C. and Gräser, C. and Müthing, S. and Sander, O. (2017) The interface for functions in the dune-functions module. Archive of Numerical Software, 5 (1). pp. 95-110. ISSN 2197-8263

G

Gelß, P. and Klus, S. and Matera, S. and Schütte, Ch. (2017) Nearest-neighbor interaction systems in the tensor-train format. Journal of Computational Physics, 341 . pp. 140-162. ISSN 0021-9991

Gerber, S. and Horenko, I. (2017) Toward a direct and scalable identification of reduced models for categorical processes. Proceedings of the National Academy of Sciences, 114 (19). pp. 4863-4868.

Gerber, S. and Münch, M. and Plagge, M. and Kermas, P. and Klein, R. (2017) Konvergenzverhalten von fvDOM-Strahlungsmodellen. In: 5. Magdeburger Brand- und Explosionsschutztage, 23.-24.3.17.

Gerber, S. and Olsson, S. and Noé, F. and Horenko, I. (2017) A scalable approach to the computation of invariant measures for high-dimensional Markovian systems. SFB 1114 Preprint . pp. 1-22. (Unpublished)

Gokhale, N. and Nikiforakis, N. and Klein, R. (2017) A dimensionally split Cartesian cut cell method for hyperbolic conservation laws. Journal of Computational Physics . (Submitted)

Gräser, C. and Kies, T. (2017) Discretization Error Estimates for Penalty Formulations of a Linearized Canham-Helfrich Type Energy. arXiv.com .

H

Hittmeir, S. and Klein, R. (2017) Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts. Theoretical and Computational Fluid Dynamics . pp. 1-28. ISSN 0935-4964 (Print) 1432-2250 (Online)

Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2017) GLOBAL WELL-POSEDNESS FOR PASSIVELY TRANSPORTED NONLINEAR MOISTURE DYNAMICS WITH PHASE CHANGES. Nonlinearity, 30 (10). pp. 3676-3718. ISSN 0951-7715

Hittmeir, S. and Klein, R. and Müller, A. and Névir, P. (2017) The Dynamic State Index with Moisture and Phase Changes. SFB 1114 Preprint . pp. 1-12. (Unpublished)

Hoffmann, M. J. and Engelmann, F. and Matera, S. (2017) A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis. The Journal of Chemical Physics, 146 (044118). ISSN 00219606

Horenko, I. and Gerber, S. and O'Kane, T.J. and Risbey, J.S. and Monselesan, D.P. (2017) On inference and validation of causality relations in climate teleconnections. In: Nonlinear and Stochastic Climate Dynamics. Cambridge University Press, pp. 184-208. ISBN 9781107118140

Huttary, R. and Goubergrits, L. and Schütte, Ch. and Bernhard, S. (2017) Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling. Computers in Biology and Medicine . ISSN 0010-4825 (In Press)

J

Jayrannejad, Fahrnaz and Conrad, T. O. F. (2017) Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining. Springer Lecture Notes in Artificial Intelligence . (In Press)

Junghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655

K

Klus, S. and Nüske, F. and Koltai, Péter and Wu, H. and Kevrekidis, Ioannis and Schütte, Ch. and Noé, F. (2017) Data-driven model reduction and transfer operator approximation. J. Nonlin. Sci. . (Submitted)

Kornhuber, R. and Podlesny, J. and Yserentant, H. (2017) Direct and Iterative Methods for Numerical Homogenization. In: Domain Decomposition Methods in Science and Engineering. Lecture Notes in Computational Science and Engineering, XXIII (116). SpringerLink, pp. 217-225. ISBN 978-3-319-52389-7

Krekeler, C. and Delle Site, L. (2017) Towards open boundary molecular dynamics simulation of ionic liquids. Physical Chemistry Chemical Physics, 6 (19). pp. 4701-4709. ISSN 1463-9076

M

Mardt, A. and Pasquali, L. and Wu, H. and Noé, F. (2017) VAMPnets: Deep learning of molecular kinetics. arXiv:1710.06012 . (Submitted)

Mazza, E. and Ulbrich, U. and Klein, R. (2017) The Tropical Transition of the October 1996 Medicane in the Western Mediterranean Sea: A Warm Seclusion Event. Monthly Weather Review, 145 . pp. 2575-2595. ISSN Online: 1520-0493 Print: 0027-0644

Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2017) Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics. SIAM Journal on Applied Mathematics, 77 (4). pp. 1562-1585. ISSN 1095-712X (online)

Müller, A. and Névir, P. and Klein, R. (2017) Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the Quasi-Geostrophic Theory. Journal of Atmospheric Sciences . pp. 1-38. (Submitted)

N

Nevo, G. and Vercauteren, N. and Kaiser, A. and Dubrulle, B. and Faranda, D. (2017) A statistical-mechanical approach to study the hydrodynamic stability of stably stratified atmospheric boundary layer. Physical Review Fluids . (Submitted)

Noé, F. and Clementi, C. (2017) Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods. Curr. Opin. Struct. Biol., 43 . pp. 141-147.

Nüske, F. and Wu, H. and Wehmeyer, C. and Clementi, C. and Noé, F. (2017) Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias. J. Chem. Phys., 146 . 094104.

O

O'Kane, T.J. and Monselesan, D.P. and Risbey, J.S. and Horenko, I. and Franzke, Ch.L.E. (2017) On memory, dimension, and atmospheric teleconnection patterns. Math. Clim. Weather Forecast, 3 (1). pp. 1-27.

Olsson, Simon and Noé, F. (2017) Mechanistic models of chemical exchange induced relaxation in protein NMR. J. Am. Chem. Soc., 139 . pp. 200-210.

Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 8265-8270.

P

Papke, A. (2017) Atmospheric vortex stability under vertical shear. PhD thesis, FU Berlin, FB Mathematik & Informatik.

Pfeuffer, Julianus and Sachsenberg, Timo and Alka, Oliver and Walzer, Mathias and Fillbrunn, Alexander and Nilse, Lars and Schilling, Oliver and Reinert, Knut and Kohlbacher, Oliver (2017) OpenMS – A platform for reproducible analysis of mass spectrometry data. Journal of Biotechnology, 261 . pp. 142-148. ISSN 01681656

Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Comp. Theory Comput. , 13 . pp. 926-934.

Pipping, E. (2017) Existence of long-time solutions to dynamic problems of viscoelasticity with rate-and-state friction. SFB 1114 Preprint . (Submitted)

Plattner, N. and Doerr, S. and De Fabritiis, G. and Noé, F. (2017) Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nat. Chem., 9 . pp. 1005-1011.

Pockrandt, Christopher and Ehrhardt, Marcel and Reinert, Knut (2017) EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices. In: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science (LNCS), 10229 . Springer, Cham, pp. 190-206. ISBN 978-3-319-56970-3 (elektronisch)

Q

Quer, J. and Donati, L. and Keller, B.G. and Weber, M. (2017) An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates. SIAM J. Sci. Comput. . pp. 1-19. ISSN 1064-8275 (print) (Submitted)

Quer, J. and Lie, H. (2017) Some connections between importance sampling and enhanced sampling methods in molecular dynamics. Journal of Chemical Physics . pp. 1-19. ISSN 0021-9606 (Submitted)

R

Rath , B. and Conrad, T. O. F. and Myles, P. and Alchikh, M. and Ma, X. and Hoppe, Ch. and Tief, F. and Obermeier, P. and Reiche, J. and Kisler, B. and Schweiger, B. (2017) Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials. Expert Review of Anti-infective Therapy (IERZ), 15 (6). pp. 545-568.

Reinert, Knut and Dadi, Temesgen Hailemariam and Ehrhardt, Marcel and Hauswedell, Hannes and Mehringer, Svenja and Rahn, René and Kim, Jongkyu and Pockrandt, Christopher and Winkler, Jörg and Siragusa, Enrico and Urgese, Gianvito and Weese, David (2017) The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology, 261 . pp. 157-168. ISSN 01681656

Roehr, Johannes T. and Dieterich, Christoph and Reinert, Knut (2017) Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics, 33 (18). pp. 2941-2942. ISSN 1367-4803

Rüderich, Stefan and Sarich, M. and Schütte, Ch. (2017) Utilizing hitting times for finding metastable sets in non-reversible Markov chains. Journal of Comp. Dynamics . (In Press)

S

Sadeghi, M. and Weikl, T. and Noé, F. (2017) Particle-based membrane model for mesoscopic simulation of cellular dynamics. arXiv:1710.06907 . (Submitted)

Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106.

Schlutow, M. and Klein, R. and Achatz, U. (2017) Finite-amplitude pseudo-incompressible gravity wave trains. Journal of Fluid Mechanics, 826 . pp. 1034-1065.

Schmidt, B. and Lorenz, U. (2017) WavePacket: A Matlab package for numerical quantum dynamics. I: Closed quantum systems and discrete variable representations. Comp. Phys. Comm., 213 . pp. 223-234.

Schmidt, B. and Hartmann, C. (2017) WavePacket: A Matlab package for numerical quantum dynamics. II: Open quantum systems, optimal control, and model reduction. Comp. Phys. Comm. . (Submitted)

Schäpel, J.S. and Wolff, S. and Schulze, P. and Berndt, P. and Klein, R. and Mehrmann, V. and King, R. (2017) State estimation for reactive Euler equation by Kalman Filtering. CEAS Aeronautical Journal, 1 (10).

Schöneberg, J. and Lehmann, M. and Ullrich, A. and Posor, Y. and Lo, W.-T. and Lichtner, G. and Schmoranzer, J. and Haucke, V. and Noé, F. (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Comm., 8 . p. 15873.

Seeber, L. and Conrad, T. O. F. and Hoppe, Ch. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Tief, F. and Boettcher, S. and Diedrich, S. and Schweiger, B. and Rath , B. (2017) Educating parents about the vaccination status of their children: A user-centered mobile application. Preventive Medicine Reports, 5 . pp. 241-250.

Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197

Shao, Borong and Carlo, Cannistraci and Conrad, T. O. F. (2017) Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data. Genomics and Computational Biology, 3 (3). ISSN 2365-7154

V

Vatansever, B. and Muñoz, A. and Klein, C. L. and Reinert, K. (2017) Development and optimisation of a generic micro LC-ESI-MS method for the qualitative and quantitative determination of 30-mer toxic gliadin peptides in wheat flour for food analysis. Analytical and Bioanalytical Chemistry, 409 (4). pp. 989-997. ISSN 1618-2642

von Larcher, T. and Klein, R. (2017) On identification of self-similar characteristics using the Tensor Train decomposition method with application to channel turbulence flow. Theoretical and Computational Fluid Dynamics . pp. 1-22. ISSN 0935-4964 (Print) 1432-2250 (Online) (Submitted)

W

Waidmann, M. (2017) Towards a Strictly Conservative Hybrid Level-Set Volume-of-Fluid Finite Volume Method for Zero Mach Number Two-Phase Flow. In: UNSPECIFIED UNSPECIFIED.

Waidmann, M. and Gerber, S. and Oevermann, M. and Klein, R. (2017) Building Blocks for a Strictly Conservative Generalized Finite Volume Projection Method for Zero Mach Number Two-Phase Flows. In: Transport Processes at Fluidic Interfaces. Springer International Publishing AG, pp. 93-119.

Wieczorek, M. and Abualrous, E. T. and Sticht, J. and Alvaro-Benito, M. and Stolzenberg, S. and Noé, F. and Freund, C. (2017) Title: Major Histocompatibility Complex (MHC) class I and MHC class II proteins: Conformational Plasticity in Antigen Presentation. Frontiers Immunology, 8 . p. 292.

Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 1-34. ISSN 1024-2953

Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18.

Wu, H. and Noé, F. (2017) Variational approach for learning Markov processes from time series data. https://arxiv.org/abs/1707.04659 .

Wu, H. and Nüske, F. and Paul, F. and Klus, S. and Koltai, Péter and Noé, F. (2017) Variational Koopman models: slow collective variables and molecular kinetics from short off-equilibrium simulations. J. Chem. Phys., 146 . p. 154104.

Y

Yang, J. and Wang, Z.-H. and Li, Q. and Vercauteren, N. and Bou-Zeid, E. and Parlange, M. B. (2017) A novel approach for unraveling the energy balance of water surfaces with a single depth temperature measurement. Limnology and Oceanography, 62 (1). pp. 89-103. ISSN 00243590

This list was generated on Mon Nov 20 12:59:49 2017 CET.