Items where Year is 2022

Article

Ague, Jay J. and Tassara, Santiago and Holycross, Megan E. and Li, Jei-Li and Cottrell, Elizabeth and Schwarzenbach, Esther M. and Fassoulas, Charalampos and John, Timm (2022) Slab-derived devolatilization fluids oxidized by subducted metasedimentary rocks. Nature Geoscience, 15 . pp. 320-326.

Ayaz, Cihan and Dalton, Benjamin and Netz, Roland R. (2022) Generalized Langevin Equation with a Non-Linear Potential of Mean Force and Non-Linear Friction From a Hybrid Projection Scheme. Preprint . (Unpublished)

Ayaz, Cihan and Scalfi, Laura and Dalton, Benjamin and Netz, Roland R. (2022) Generalized Langevin equation with a nonlinear potential of mean force and nonlinear memory friction from a hybrid projection scheme. PHYSICAL REVIEW E, 105 . pp. 1-19.

Ayaz, Cihan and Tepper, Lucas and Netz, Roland R. (2022) Markovian embedding of generalized Langevin equations with a nonlinear friction kernel and configuration-dependent mass. Turkish Journal of Physics, 46 (6). pp. 194-205.

Basaric, Danica and Bella, Peter and Feireisl, Eduard and Oschmann, Florian and Titi, Edriss (2022) On the incompressible limit of a strongly stratified heat conducting fluid. On the incompressible limit of a strongly stratified heat conducting fluid . pp. 1-20. (Unpublished)

Becker, Simon and Hartmann, Carsten and Redmann, Martin and Richter, Lorenz (2022) Error bounds for model reduction of feedback-controlled linear stochastic dynamics on Hilbert spaces. Stochastic Processes and their Applications, 149 . pp. 107-141.

Blömker, Dirk and Schillings, Claudia and Wacker, Philipp and Weissmann, Simon (2022) Continuous time limit of the stochastic ensemble Kalman inversion: Strong convergence analysis. SIAM Journal on Numerical Analysis, 60 (6). pp. 3181-3215.

Boltz, Horst-Holger and Sirbu, Alexei and Stelzer, Nina and de Lanerolle, Primal and Winkelmann, Stefanie and Annibale, Paolo (2022) The impact of membrane protein diffusion on GPCR signaling. Cells, 11 (10).

Bresch, D. and Klein, R. and Liu, X. (2022) The Soundproof Model of an Acoustic–internal Waves System with Low Stratification. Journal of Mathematical Fluid Mechanics, 24 (149). ISSN 1422-6928 (Print) 1422-6952 (Online)

Bresch, D. and Klein, R. and Liu, X. (2022) The soundproof model of an acoustic-internal waves system with low stratification. Journal of Mathematical Fluid Mechanics, 25 (2). ISSN Electronic 1422-6952; Print 1422-6928

Brösigke, G. and Jens-Uwe Repke, J.U. and Schomäcker, R. and Matera, S. (2022) The closer the better? Theoretical assessment of the impact of catalytic site separation for bifunctional core–shell catalyst particles. Chemical Engineering Journal, 446 (1).

Brünig, Florian N. and Daldrop, Jan O. and Netz, Roland R. (2022) Pair-Reaction Dynamics in Water: Competition of Memory, Potential Shape, and Inertial Effects. J. Phys. Chem. B, 126 . pp. 1-10.

Brünig, Florian N. and Geburtig, Otto and von Canal, Alexander and Kappler, Julian and Netz, Roland R. (2022) Time-dependent friction effects on vibrational infrared frequencies and line shapes of liquid water. J. Phys. Chem. B, 126 . pp. 1579-1589.

Chada, Neil and Schillings, Claudia and Tong, Xin and Weissmann, Simon (2022) Consistency analysis of bilevel data-driven learning in inverse problems. Communications in Mathematical Sciences, 20 (1). pp. 123-164.

Chew, R. and Benacchio, T. and Hastermann, G. and Klein, R. (2022) A one-step blended soundproof-compressible model with balanced data assimilation: theory and idealised tests. Monthly Weather Review, 150 (9). pp. 2231-2254. ISSN 0027-0644; elSSN: 1520-0493

Chew, R. and Schlutow, M. and Klein, R. (2022) Instability of the isothermal, hydrostatic equatorial atmosphere at rest under the full Coriolis acceleration. J. Atmos. Sci. . (Submitted)

Darvish, Mitra and Seiler, Enrico and Mehringer, Svenja and Rahn, René and Reinert, Knut and Ponty, Yann (2022) Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinformatics, 38 (17). pp. 4100-4108. ISSN 1367-4803

Delle Site, L. and Klein, R. (2022) Derivation of Liouville-like equation for the n-state probability density of an open system with thermalized particle reservoirs and its link to molecular simulation. J. Physics A:Math. Theor., 55 (15).

Dibak, Manuel and Klein, Leon and Krämer, Andreas and Noé, Frank (2022) Temperature steerable flows and Boltzmann generators. Physical Review Research, 4 (4).

Djurdjevac, Ana and Kremp, Helena and Perkowski, Nicolas (2022) Weak error analysis for a nonlinear SPDE approximation of the Dean-Kawasaki equation. Unpublished . (Unpublished)

Djurdjevac Conrad, Nataša and Köppl, Jonas and Djurdjevac, Ana (2022) Feedback Loops in Opinion Dynamics of Agent-Based Models with Multiplicative Noise. Entropy, 24 (10). pp. 1-23.

Dolores-Tesillos, Edgar and Teubler, Franziska and Pfahl, Stephan (2022) Future changes in North Atlantic winter cyclones in CESM-LE – Part 1: Cyclone intensity, potential vorticity anomalies, and horizontal wind speed. Weather Clim. Dynam., 3 . pp. 429-448.

Donati, Luca and Weber, Marcus and Keller, Bettina (2022) A review of Girsanov reweighting and of square root approximation for building molecular Markov state models. J. Math. Phys., 63 (12). pp. 1-22.

Engel, Maximilian and Olicon-Mendez, Guillermo and Unger, Nathalie and Winkelmann, Stefanie (2022) Synchronization and random attractors for reaction jump processes. in Press . pp. 1-39. (In Press)

Ernst, Ariane and Schütte, Christof and Sigrist, Stephan J. and Winkelmann, Stefanie (2022) Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics. Mathematical Biosciences, 343 .

Gelß, P. and Klein, R. and Matera, S. and Schmidt, B. (2022) Solving the time-independent Schrödinger equation for chains of coupled excitons and phonons using tensor trains. J. Chem. Phys., 156 (02). 024109.

Gholami, A. and Klein, R. and Delle Site, L. (2022) Simulation of a particle domain in a continuum/fluctuating hydrodynamics reservoir. Phys. Rev. Lett., 129 (23).

Gholami, Abbas and Klein, R. and Delle Site, Luigi (2022) Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir. Physical Review Letters, 129 (23).

Gholami, Jafar and Kamankesh, Mohamad Reza and Mohammadi, Somayeh and Hosseinkhani, Elahe and Abdi, Somayeh (2022) Powerful enhanced Jaya algorithm for efficiently optimizing numerical and engineering problems. Soft Computing . ISSN 1432-7643

Guth, Philipp A. and Kaarnioja, Vesa and Kuo, Frances Y. and Sloan, Ian H. (2022) Parabolic PDE-constrained optimal control under uncertainty with entropic risk measure using quasi-Monte Carlo integration. arXiv preprint arXiv:2208.02767 . (Submitted)

Haghdoost, M.R. and Thethy, B.S. and Nadolski, M. and Klein, R. and Honnery, D. and Hennington- Mitchell, D. and Seo, B. and Paschereit, O. C. and Oberleithner, K. (2022) Numerical and Experimental Evaluation of Shock Dividers. Shock Waves, 32 . pp. 195-211.

Kiefer, Henrik and Dalton, Benjamin and Bruenig, Florian N. and Netz, Roland R. (2022) Connection between Macroscopic Hydrodynamics and Molecular Friction in Liquids. Preprint . pp. 1-26. (Unpublished)

Kieninger, Stefanie and Keller, Bettina (2022) GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms. J. Chem. Theory Comput., 18 (10).

Klein, R. and Delle Site, Luigi (2022) Derivation of Liouville-like equations for the n-state probability density of an open system with thermalized particle reservoirs and its link to molecular simulation. Journal of Physics A: Mathematical and Theoretical, 55 . pp. 1-18.

Klein, R. and Schielicke, L. and Pfahl, S. and Khouider, B. (2022) QG-DL-Ekman: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences, 79 (3). pp. 887-905.

Klimek, Anton and Netz, Roland R. (2022) Optimal non-Markovian composite search algorithms for spatially correlated targets. EPL A Letters Journal Exploring The Frontiers of Physics, 139 . pp. 1-8.

Kornhuber, R. and Podlesny, J. and Yserentant, H. (2022) Numerical homogenization of fractal interface problems. ESAIM: M2AN, 56 (4). 1451- 1481. ISSN 2822-7840 - eISSN: 2804-7214

Kosari, Ehsan and Rosenau, Matthias and Oncken, Onno (2022) Strain signals governed by frictional-elastoplastic interaction of the upper plate and shallow subduction megathrust interface over seismic cycles. Tectonics . pp. 1-41. ISSN 1944-9194

Kosari, Ehsan and Rosenau, Matthias and Ziegenhagen, Thomas and Oncken, Onno (2022) Upper plate dynamic response to a sequential elastic rebound and slab acceleration in laboratory-scale subduction megathrust. Earth and Space Science Open Archive .

Kosari, Ehsan and Rosenau, Matthias and Ziegenhagen, Thomas and Oncken, Onno (2022) Upper plate response to a sequential elastic rebound and slab acceleration during laboratory-scale subduction megathrust earthquakes. JGR Solid Earth, 127 (9). pp. 1-16.

Lavacchi, Laura and Daldrop, Jan O. and Netz, Roland R. (2022) Non-Arrhenius barrier crossing dynamics of non-equilibrium non-Markovian systems. Europhysics Letters, 139 (5). pp. 1-7.

Mardt, Andreas and Hempel, Tim and Clementi, Cecilia and Noé, Frank (2022) Deep learning to decompose macromolecules into independent Markovian domains. nature communications, 13 .

Mastella, G. and Corbi, Fabio and Bedford, Jonathan and Funiciello, Francesca and Rosenau, Matthias (2022) Forecasting Surface Velocity Fields Associated With Laboratory Seismic Cycles Using Deep Learning. AGU-Geophysical Research Letters, 49 (15). pp. 1-12.

Mastella, G. and Corbi, Fabio and Funiciello, Francesca and Rosenau, Matthias (2022) Foamquake: a novel analog model mimicking megathrust seismic cycles. JGR Solid Earth . pp. 1-32. (In Press)

Meyer, F. and Fritz, A. and Deng, Z.-L. and Koslicki, D. and Gurevich, A. and Robertson, G. and Alser, M. and Antipov, D. and Beghini, F. and Bertrand, D. and Brito, J. J. and Brown, C.T. and Buchmann, J. and Buluç, A. and Chen, B. and Chikhi, R. and Clausen, P. T. and Cristian, A. and Dabrowski, P. W. and Darling, A. E. and Egan, R. and Eskin, E. and Georganas, E. and Goltsman, E. and Gray, M. A. and Hansen, L. H. and Hofmeyr, S. and Huang, P. and Irber, L. and Jia, H. and Jørgensen, T. S. and Kieser, S. D. and Klemetsen, T. and Kola, A. and Kolmogorov, M. and Korobeynikov, A. and Kwan, J. and LaPierre, N. and Lemaitre, C. and Li, C. and Limasset, A. and Malcher-Miranda, F. and Mangul, S. and Marcelino, V. R. and Marchet, C. and Marijon, P. and Meleshko, D. and Mende, D. R. and Milanese, A. and Nagarajan, N. and Nissen, J. and Nurk, S. and Oliker, L. and Paoli, L. and Peterlongo, P. and Piro, V. C. and Porter, J. S. and Rasmussen, S. and Rees, E. R. and Reinert, K. and Renard, B. and Robertsen, E. M. and Rosen, G. L. and Ruscheweyh, H.-J. and Sarwal, V. and Segata, N. and Seiler, E. and Shi, L. and Sun, F. and Sunagawa, S. and Sørensen, S. J. and Thomas, A. and Tong, C. and Trajkovski, M. and Tremblay, J. and Uritskiy, G. and Vicedomini, R. and Wang, Zi. and Wang, Zhe. and Wang, Zho. and Warren, A. and Willassen, N. P. and Yelick, K. and You, R. and Zeller, G. and Zhao, Z. and Zhu, S. and Zhu, J. and Garrido-Oter, R. and Gastmeier, P. and Hacquard, S. and Häußler, S. and Khaledi, A. and Maechler, F. and Mesny, F. and Radutoiu, S. and Schulze-Lefert, P. and Smit, N. and Strowig, T. and Bremges, A. and Sczyrba, A. and McHardy, A. C. (2022) Critical Assessment of Metagenome Interpretation - the second round of challenges. Nature Methods, 19 (4). pp. 429-440. ISSN 1548-7091

Mikula, Natalia and Dörffel, Tom and Baum, Daniel and Hege, Hans-Christian (2022) An Interactive Approach for Identifying Structure Definitions. Computer Graphics Forum . pp. 1-29.

Mollenhauer, Mattes and Klus, Stefan and Schütte, Christof and Koltai, Péter (2022) Kernel autocovariance operators of stationary processes: Estimation and convergence. Journal of Machine Learning Research, 23 (327). pp. 1-34.

Mollenhauer, Mattes and Mücke, Nicole and Sullivan, T.J. (2022) Learning linear operators: Infinite-dimensional regression as a well-behaved non-compact inverse problem. arXiv . (Submitted)

Musil, Félix and Zaporozhets, Iryna and Noé, Frank and Clementi, Cecilia and Kapil, Venkat (2022) Quantum dynamics using path integral coarse-graining. The Journal of Chemical Physics, 157 (18).

Nowatzky, Yannek and Benner, Philipp and Reinert, Knut and Muth, Thilo (2022) Mistle: bringing spectral library predictions to metaproteomics with an efficient search index. bioRxiv .

Obermeier, P. and Heim, A. and Biere, B. and Hage, E. and Alchikh, M. and Conrad, T. O. F. and Schweiger, B. and Rath, B. (2022) Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations. iScience, 25 (5). ISSN 25890042

Panahian Jand, Sara and Nourbakhsh, Zahra and Delle Site, Luigi (2022) Nuclear Quantum Effects in Fullerene-Fullerene Aggregation in Water. Front. Chem., 10 . pp. 1-8.

Peschka, Dirk and Zafferi, Andrea and Heltai, Luca and Thomas, Marita (2022) Variational Approach to Fluid–Structure Interaction via GENERIC. Journal of Non-Equilibrium Thermodynamics . ISSN 1437-4358

Polzin, Robert and Müller, Annette and Rust, Henning W. and Névir, Peter and Koltai, Péter (2022) Direct Bayesian model reduction of smaller scale convective activity conditioned on large-scale dynamics. Nonlinear Processes in Geophysics, 29 (1). pp. 37-52.

Rams, Mona and Conrad, T. O. F. (2022) Sparse dictionary learning allows model-free pseudotime estimation of transcriptomics data. BMC Genomics, 23 (56). ISSN 1471-2105

Reible, Benedikt and Hartmann, Carsten and Delle Site, Luigi (2022) Two-sided Bogoliubov inequality to estimate finite size effects in quantum molecular simulations. Letters in Mathematical Physics, 112 (97).

Sadeghi, Mohsen (2022) Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins. Soft Matter (18). pp. 3917-3927.

Thethy, Bhavraj S. and Haghdoost, M.R. and Kirby, R. and Seo, B. and Nadolski, M. and Zenker, C. and Oevermann, M. and Klein, R. and Oberleithner, K. and Edgington-Mitchell, D. (2022) Diffraction of shock waves through a non-quiescent medium. Journal of Fluid Mechanics, 944 .

Trung, Minh Nguyen and Kieninger, Stefanie and Fandi, Zeinab and Qiu, Danye and Liu, Guizhen and Mehendale, Neelay K. and Saiardi, Adolfo and Jessen, Henning and Keller, Bettina and Fiedler, Dorothea (2022) Stable Isotopomers of myo-Inositol Uncover a Complex MINPP1-Dependent Inositol Phosphate Network. ACS Cent. Sci., 8 (12). pp. 1683-1694.

Tuncay, E. G. and Erdur, R. C. and Conrad, T. O. F. (2022) Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA. IEEE Transactions on Computational Biology and Bioinformatics . ISSN 1557-9964 (In Press)

Viennet, Akim and Vercauteren, Nikki and Engel, Maximilian and Faranda, Davide (2022) Guidelines for data-driven approaches to study transitions in multiscale systems: The case of Lyapunov vectors. Chaos, 32 . pp. 1-15.

Weimann, K. and Conrad, T. O. F. (2022) Forget Embedding Layers: Representation Learning for Recommender Systems. IEEE Transactions on Pattern Analysis and Machine Intelligence . ISSN 1939-3539 (Submitted)

Weissmann, Simon and Chada, Neil and Schillings, Claudia and Tong, Xin (2022) Adaptive Tikhonov strategies for stochastic ensemble Kalman inversion. Inverse Problems, 38 (4).

Winkler, Jörg and Urgese, Gianvito and Ficarra, Elisa and Reinert, Knut (2022) LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences. BMC Bioinformatics, 23 (1). ISSN 1471-2105

Zendehroud, Sina and Loche, Philip and Kornhuber, Ralf and Netz, Roland R. (2022) Boundary Conditions on Conical Hydrophobic Inclusions in Lipid Membranes. Preprint . (Unpublished)

Zendehroud, Sina and Netz, Roland R. and Kappler, Julian (2022) Linear Waves at Viscoelastic Interfaces Between Viscoelastic Media. Physical Review Fluids, 7 . pp. 1-32.

Zertani, Sascha and John, Timm and Brachmann, Caroline and Vrijmoed, Johannes and Plümper, Oliver (2022) Reactive fluid flow guided by grain-scale equilibrium reactions during eclogitization of dry crustal rocks. Contributions to Mineralogy and Petrology, 177 (61).

Zwaan, Frank and Schreurs, Guido and Buiter, Susanne and Ferrer, Oriol and Reitano, Riccardo and Rudolf, Michael and Willingshofer, Ernst (2022) Analogue modelling of basin inversion: a review and future perspectives. Preprint se-2022-8 Solid Earth . (Submitted)

del Razo, Mauricio J. and Frömberg, Daniela and Straube, Arthur V. and Schütte, Christof and Höfling, Felix and Winkelmann, Stefanie (2022) A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations. Letters in Mathematical Physics, 112 (49).

von Lindheim, Johannes and Harikrishnan, A. P. and Dörffel, T. and Klein, R. and Koltai, Péter and Mikula, Natalia and Müller, Annette and Névir, Peter and Pacey, George and Polzin, Robert and Vercauteren, N. (2022) Definition, detection and trackingof persistent structures in atmospheric flows. J. Math. Phys . (Submitted)

Conference or Workshop Item

Knaust, Marius and Seiler, Enrico and Reinert, Knut and Steinke, Thomas (2022) Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA. In: The 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays (FPGA '22), 27 February - 1 March 2022, virtual.

Book

Schwieger, Robert and Siebert, Heike (2022) Structure and behavior in Boolean monotonic model pools. Elsevier, Biosystems.

Thesis

Krannich, Thomas (2022) Contributions to the detection of non-reference sequences in population-scale NGS data. PhD thesis, Freie Universität Berlin.

Niehus, Sebastian (2022) Multi-Sample Approaches and Applications for Structural Variant Detection. PhD thesis, Freie Universität Berlin.