@article{HoeflingDietrich2020, author = {H{\"o}fling, Felix and Dietrich, Siegfried}, title = {Finite-size corrections for the static structure factor of a liquid slab with open boundaries}, volume = {153}, journal = {The Journal of Chemical Physics}, doi = {10.1063/5.0017923}, pages = {054119}, year = {2020}, abstract = {The presence of a confining boundary can modify the local structure of a liquid markedly. In addition, small samples of finite size are known to exhibit systematic deviations of thermodynamic quantities relative to their bulk values. Here, we consider the static structure factor of a liquid sample in slab geometry with open boundaries at the surfaces, which can be thought of as virtually cutting out the sample from a macroscopically large, homogeneous fluid. This situation is a relevant limit for the interpretation of grazing-incidence diffraction experiments at liquid interfaces and films. We derive an exact, closed expression for the slab structure factor, with the bulk structure factor as the only input. This shows that such free boundary conditions cause significant differences between the two structure factors, in particular, at small wavenumbers. An asymptotic analysis of this result yields the scaling exponent and an accurate, useful approximation of these finite-size corrections. Furthermore, the open boundaries permit the interpretation of the slab as an open system, supporting particle exchange with a reservoir. We relate the slab structure factor to the particle number fluctuations and discuss conditions under which the subvolume of the slab represents a grand canonical ensemble with chemical potential μ and temperature T. Thus, the open slab serves as a test-bed for the small-system thermodynamics in a μT reservoir. We provide a microscopically justified and exact result for the size dependence of the isothermal compressibility. Our findings are corroborated by simulation data for Lennard-Jones liquids at two representative temperatures.}, language = {en} } @article{EbrahimiViandHoeflingKleinetal.2020, author = {Ebrahimi Viand, Roya and H{\"o}fling, Felix and Klein, Rupert and Delle Site, Luigi}, title = {Theory and simulation of open systems out of equilibrium}, volume = {153}, journal = {The Journal of Chemical Physics}, doi = {10.1063/5.0014065}, pages = {101102}, year = {2020}, abstract = {We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations.}, language = {en} } @article{delRazoDibakSchuetteetal.2021, author = {del Razo, Mauricio J. and Dibak, Manuel and Sch{\"u}tte, Christof and No{\´e}, Frank}, title = {Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics}, volume = {155}, journal = {The Journal of Chemical Physics}, number = {12}, doi = {10.1063/5.0060314}, year = {2021}, language = {en} } @article{SunkaraHeinzHeinrichetal.2021, author = {Sunkara, Vikram and Heinz, Gitta A. and Heinrich, Frederik F. and Durek, Pawel and Mobasheri, Ali and Mashreghi, Mir-Farzin and Lang, Annemarie}, title = {Combining segmental bulk- and single-cell RNA-sequencing to define the chondrocyte gene expression signature in the murine knee joint}, volume = {29}, journal = {Osteoarthritis and Cartilage}, number = {6}, doi = {10.1016/j.joca.2021.03.007}, pages = {905 -- 914}, year = {2021}, language = {en} } @article{LueckeLuQuevedo2022, author = {L{\"u}cke, Marvin and Lu, Jingyi and Quevedo, Daniel E.}, title = {Coding for secrecy in remote state estimation with an adversary}, volume = {67}, journal = {IEEE Transactions on Automatic Control}, number = {9}, doi = {10.1109/TAC.2022.3169839}, pages = {4955 -- 4962}, year = {2022}, abstract = {We study the problem of remote state estimation in the presence of an eavesdropper. A sensor transmits state information over a packet-dropping link to a legitimate user. This information is randomly overheard by an eavesdropper. To reduce information leakage to the eavesdropper, previous studies have shown that by encoding the estimate with the acknowledgments (Acks), perfect secrecy can be achieved. However, this strategy greatly relies on the accuracy of the Acks and may easily fail if the Acks are compromised by cyberattacks. In this article, we tackle this issue by proposing to switch between sending an encoded state and sending the plain state to stay resilient against fake Acks. Specifically, we assume the Acks to be randomly attacked and derive recursive expressions for the minimum-mean-squared error estimates and error covariance matrices at the legitimate user and at the eavesdropper. Based upon this, we propose a transmission policy that depends on the probability of synchronization. We formulate a partially observable Markov decision process to model the evolution of the synchronization status and derive associated optimal transmission policies. Numerical examples are provided to verify the theoretical results.}, language = {en} } @article{FroehlerElberfeldMoelleretal.2020, author = {Fr{\"o}hler, Bernhard and Elberfeld, Tim and M{\"o}ller, Torsten and Hege, Hans-Christian and De Beenhouwer, Jan and Sijbers, Jan and Kastner, Johann and Heinzl, Christoph}, title = {Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres}, volume = {35}, journal = {Nondestructive Testing and Evaluation}, number = {3}, doi = {10.1080/10589759.2020.1774583}, pages = {328 -- 341}, year = {2020}, abstract = {We present visual methods for the analysis and comparison of the results of curved fibre reconstruction algorithms, i.e., of algorithms extracting characteristics of curved fibres from X-ray computed tomography scans. In this work, we extend previous methods for the analysis and comparison of results of different fibre reconstruction algorithms or parametrisations to the analysis of curved fibres. We propose fibre dissimilarity measures for such curved fibres and apply these to compare multiple results to a specified reference. We further propose visualisation methods to analyse differences between multiple results quantitatively and qualitatively. In two case studies, we show that the presented methods provide valuable insights for advancing and parametrising fibre reconstruction algorithms, and support in improving their results in characterising curved fibres.}, language = {en} } @phdthesis{Eshtewy2020, author = {Eshtewy, Neveen Ali Salem}, title = {Mathematical Modeling of Metabolic-Genetic Networks}, year = {2020}, language = {en} } @article{LangHelfmeierStefanowskietal.2020, author = {Lang, Annemarie and Helfmeier, Sarah and Stefanowski, Jonathan and Kuppe, Aditi and Sunkara, Vikram and Pfeiffenberger, Moritz and Wolter, Angelique and Damerau, Alexandra and Hemmati-Sadeghi, Shabnam and Ringe, Jochen and Haag, Rainer and Hauser, Anja E. and L{\"o}hning, Max and Perka, Carsten and Duda, Georg and Hoff, Paula and Schmidt-Bleek, Katharina and Gaber, Timo and Buttgereit, Frank}, title = {HIF-stabilization prevents delayed fracture healing}, journal = {bioarxiv}, doi = {10.1101/2020.07.02.182832}, year = {2020}, language = {en} } @inproceedings{ShinanoTateiwaNakamuraetal.2020, author = {Shinano, Yuji and Tateiwa, N. and Nakamura, S. and Yoshida, A. and Yasuda, M. and Kaji, S. and Fujisawa, K.}, title = {Massive Parallelization for Finding Shortest Lattice Vectors Based on Ubiquity Generator Framework}, booktitle = {2020 SC20: International Conference for High Performance Computing, Networking, Storage and Analysis (SC)}, doi = {10.1109/SC41405.2020.00064}, pages = {834 -- 848}, year = {2020}, abstract = {Lattice-based cryptography has received attention as a next-generation encryption technique, because it is believed to be secure against attacks by classical and quantum computers. Its essential security depends on the hardness of solving the shortest vector problem (SVP). In the cryptography, to determine security levels, it is becoming significantly more important to estimate the hardness of the SVP by high-performance computing. In this study, we develop the world's first distributed and asynchronous parallel SVP solver, the MAssively Parallel solver for SVP (MAP-SVP). It can parallelize algorithms for solving the SVP by applying the Ubiquity Generator framework, which is a generic framework for branch-and-bound algorithms. The MAP-SVP is suitable for massive-scale parallelization, owing to its small memory footprint, low communication overhead, and rapid checkpoint and restart mechanisms. We demonstrate its performance and scalability of the MAP-SVP by using up to 100,032 cores to solve instances of the Darmstadt SVP Challenge.}, language = {en} } @inproceedings{PfetschPokutta2020, author = {Pfetsch, Marc and Pokutta, Sebastian}, title = {IPBoost - Non-Convex Boosting via Integer Programming}, booktitle = {Proceedings of ICML}, arxiv = {http://arxiv.org/abs/2002.04679}, year = {2020}, language = {en} } @inproceedings{PokuttaSinghTorrico2020, author = {Pokutta, Sebastian and Singh, M. and Torrico, A.}, title = {On the Unreasonable Effectiveness of the Greedy Algorithm: Greedy Adapts to Sharpness}, booktitle = {Proceedings of ICML}, arxiv = {http://arxiv.org/abs/2002.04063}, year = {2020}, language = {en} }