@inproceedings{ClauseckerKaiser2021, author = {Clausecker, Robert and Kaiser, Benjamin}, title = {Sliding Tile Puzzles}, booktitle = {Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions}, pages = {57}, year = {2021}, language = {en} } @misc{SikorskiSechiHelfmann2021, author = {Sikorski, Alexander and Sechi, Renata and Helfmann, Luzie}, title = {cmdtools}, doi = {https://doi.org/10.5281/zenodo.4749331}, year = {2021}, abstract = {Python implementation of severals tools (PCCA, AJC, SQRA, P/Q estimation) for the analysis of dynamical systems from the transfer operator perspective.}, language = {en} } @article{DonatiWeberKeller2021, author = {Donati, Luca and Weber, Marcus and Keller, Bettina G.}, title = {Markov models from the square root approximation of the Fokker-Planck equation: calculating the grid-dependent flux}, volume = {33}, journal = {Journal of Physics: Condensed Matter}, number = {11}, doi = {10.1088/1361-648X/abd5f7}, pages = {115902}, year = {2021}, abstract = {Molecular dynamics (MD) are extremely complex, yet understanding the slow components of their dynamics is essential to understanding their macroscopic properties. To achieve this, one models the MD as a stochastic process and analyses the dominant eigenfunctions of the associated Fokker-Planck operator, or of closely related transfer operators. So far, the calculation of the discretized operators requires extensive MD simulations. The square-root approximation of the Fokker-Planck equation is a method to calculate transition rates as a ratio of the Boltzmann densities of neighboring grid cells times a flux, and can in principle be calculated without a simulation. In a previous work we still used MD simulations to determine the flux. Here, we propose several methods to calculate the exact or approximate flux for various grid types, and thus estimate the rate matrix without a simulation. Using model potentials we test computational efficiency of the methods, and the accuracy with which they reproduce the dominant eigenfunctions and eigenvalues. For these model potentials, rate matrices with up to \$\mathcal{O}\left(1{0}^{6}\right)\$ states can be obtained within seconds on a single high-performance compute server if regular grids are used.}, language = {en} } @article{YokoyamaShinanoWakui2021, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakui, Tetsuya}, title = {エネルギー供給システムの設計および運用の 階層的関係を考慮した最適化 (蓄エネルギー機器を有するシステムへの適用)}, journal = {第40回エネルギー・資源学会研究発表会講演論文集}, pages = {398 -- 403}, year = {2021}, abstract = {Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies has been extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of re- ducing model is extended by aggregating representative days and sampling times differently in consideration of the characteristics of storage units. A case study is conducted on the optimal design of a gas turbine cogeneration system with a thermal storage unit for district energy supply. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solution as compared with a conventional method. It also turns out that the model reduction with the special time aggregation is effective to shorten the computation time as compared with that without time aggregation in case that the number of candidates for equipment capacities is relatively small.}, language = {ja} } @inproceedings{BinkowskiBetzColometal.2021, author = {Binkowski, Felix and Betz, Fridtjof and Colom, Remi and Hammerschmidt, Martin and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Burger, Sven}, title = {Contour integral methods for resonance phenomena in nano-optics}, booktitle = {The 11th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2021)}, editor = {Zouhdi, S. and Pawlak, D. and Kudelski, A.}, issn = {2429-1390}, pages = {523}, year = {2021}, language = {en} } @inproceedings{KramerLaeuter2021, author = {Kramer, Tobias and L{\"a}uter, Matthias}, title = {Matching the activity of comet 67P/Churyumov-Gerasimenko with long-term ground-based astrometry}, volume = {15}, booktitle = {Europlanet Science Congress}, publisher = {Europlanet Science Congress}, doi = {10.5194/epsc2021-337}, pages = {EPSC2021-337}, year = {2021}, abstract = {50 years of astrometric data for comet 67P/C-G (orbital period about 6.45 years) provides a unique opportunity to benchmark non-gravitational acceleration models to the in situ measurements of the volatile release performed from the Rosetta rendezvous mission (2014-2016). Taken together, the Earth-bound and in-situ data yields lower fit errors and serves as a test-case for our ability to deduce thermophysical quantities of cometary nuclei from the Earth-bound observations.}, language = {en} } @inproceedings{ChmielaMunozSerrano2021, author = {Chmiela, Antonia and Mu{\~n}oz, Gonzalo and Serrano, Felipe}, title = {On the implementation and strengthening of intersection cuts for QCQPs}, volume = {22}, booktitle = {Integer Programming and Combinatorial Optimization: 22nd International Conference, IPCO 2021}, doi = {10.1007/978-3-030-73879-2_10}, pages = {134 -- 147}, year = {2021}, abstract = {The generation of strong linear inequalities for QCQPs has been recently tackled by a number of authors using the intersection cut paradigm - a highly studied tool in integer programming whose flexibility has triggered these renewed efforts in non-linear settings. In this work, we consider intersection cuts using the recently proposed construction of maximal quadratic-free sets. Using these sets, we derive closed-form formulas to compute intersection cuts which allow for quick cut-computations by simply plugging-in parameters associated to an arbitrary quadratic inequality being violated by a vertex of an LP relaxation. Additionally, we implement a cut-strengthening procedure that dates back to Glover and evaluate these techniques with extensive computational experiments.}, language = {en} } @misc{Francobaldi2021, type = {Master Thesis}, author = {Francobaldi, Matteo}, title = {Learning to Use Local Cuts}, year = {2021}, abstract = {We propose a machine learning approach to address a specific algorithmic question that arises during the solving process of a mixed-integer linear programming problem, namely, whether to use cutting planes only at the root node or also at internal nodes of the branch-and-bound search tree, or equivalently, whether to run a cut-and-branch or rather a branch-and-cut algorithm. Within a supervised regression framework, we develop three machine learning models, Linear Model, Random Forest and Neural Network, for predicting the relative performance between the two methods, local-cut and no-local-cut. Hence, through an extensive computational study conducted with FICO Xpress over a large test bed of problems, we evaluate the produced strategies, and we show that they are able to provide, upon the existing policies, a significant improvement to the performance of the solver. In fact, a variant of the random forest suggested in the present work has already been implemented by the development team of Xpress, and released with version 8.13 of the software.}, language = {en} } @article{DaiFuellgrabePfeufferetal.2021, author = {Dai, Chengxin and F{\"u}llgrabe, Anja and Pfeuffer, Julianus and Solovyeva, Elizaveta M. and Deng, Jingwen and Moreno, Pablo and Kamatchinathan, Selvakumar and Kundu, Deepti Jaiswal and George, Nancy and Fexovy, Silvie and Gr{\"u}ning, Bj{\"o}rn and F{\"o}ll, Melanie Christine and Griss, Johannes and Vaudel, Marc and Audain, Enrique and Locard-Paulet, Marie and Turewicz, Michael and Eisenacher, Martin and Uszkoreit, Julian and Van Den Bossche, Tim and Schw{\"a}mmle, Veit and Webel, Henry and Schulze, Stefan and Bouyssi{\´e}, David and Jayaram, Savita and Duggineni, Vinay Kumar and Samaras, Patroklos and Wilhelm, Mathias and Choi, Meena and Wang, Mingxun and Kohlbacher, Oliver and Brazma, Alvis and Papatheodorou, Irene and Bandeira, Nuno and Deutsch, Eric W. and Vizca{\´i}no, Juan Antonio and Bai, Mingze and Sachsenberg, Timo and Levitsky, Lev I. and Perez-Riverol, Yasset}, title = {A proteomics sample metadata representation for multiomics integration and big data analysis}, volume = {12}, journal = {Nature Communications}, number = {5854}, doi = {https://doi.org/10.1038/s41467-021-26111-3}, year = {2021}, abstract = {The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets.}, language = {en} } @article{UmerZhuPfeufferetal.2021, author = {Umer, Husen M. and Zhu, Yafeng and Pfeuffer, Julianus and Sachsenberg, Timo and Lehti{\"o}, Janne and Branca, Rui and Perez-Riverol, Yasset}, title = {Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides}, journal = {Bioinformatics}, number = {5}, edition = {38}, publisher = {Oxford Academic}, pages = {1470 -- 1472}, year = {2021}, abstract = {We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10\% of the total number of peptides identified (43,501 out of 402,512).}, language = {en} } @article{DjurdjevacGraeserHerbert2021, author = {Djurdjevac, Ana and Gr{\"a}ser, Carsten and Herbert, Philip J.}, title = {Non-stationary incompressible linear fluid equations in a moving domain}, journal = {arXiv}, arxiv = {http://arxiv.org/abs/2106.08312}, year = {2021}, abstract = {This article considers non-stationary incompressible linear fluid equations in a moving domain. We demonstrate the existence and uniqueness of an appropriate weak formulation of the problem by making use of the theory of time-dependent Bochner spaces. It is not possible to directly apply established evolving Hilbert space theory due to the incompressibility constraint. After we have established the well-posedness, we derive and analyse a time discretisation of the system.}, language = {en} } @article{Djurdjevac2021, author = {Djurdjevac, Ana}, title = {Linear Parabolic Problems in Random Moving Domains}, volume = {9}, number = {2}, doi = {https://doi.org/10.1137/19M1284889}, pages = {848 -- 879}, year = {2021}, abstract = {We consider linear parabolic equations on a random non-cylindrical domain. Utilizing the domain mapping method, we write the problem as a partial differential equation with random coefficients on a cylindrical deterministic domain. Exploiting the deterministic results concerning equations on non-cylindrical domains, we state the necessary assumptions about the velocity filed and in addition, about the flow transformation that this field generates. In this paper we consider both cases, the uniformly bounded with respect to the sample and log-normal type transformation. In addition, we give an explicit example of a log-normal type transformation and prove that it does not satisfy the uniformly bounded condition. We define a general framework for considering linear parabolic problems on random non-cylindrical domains. As the first example, we consider the heat equation on a random tube domain and prove its well-posedness. Moreover, as the other example we consider the parabolic Stokes equation which illustrates the case when it is not enough just to study the plain-back transformation of the function, but instead to consider for example the Piola type transformation, in order to keep the divergence free property.}, language = {en} } @article{BergPloentzkeSiebertetal.2021, author = {Berg, Mascha and Pl{\"o}ntzke, Julia and Siebert, Heike and R{\"o}blitz, Susanna}, title = {Modelling Oscillatory Patterns in the Bovine Estrous Cycle with Boolean Delay Equations}, volume = {83}, journal = {Bulletin of Mathematical Biology}, number = {121}, doi = {10.1007/s11538-021-00942-z}, pages = {1 -- 25}, year = {2021}, abstract = {Boolean delay equations (BDEs), with their relatively simple and intuitive mode of modelling, have been used in many research areas including, for example, climate dynamics and earthquake propagation. Their application to biological systems has been scarce and limited to the molecular level. Here, we derive and present two BDE models. One is directly derived from a previously published ordinary differential equation (ODE) model for the bovine estrous cycle, whereas the second model includes a modification of a particular biological mechanism. We not only compare the simulation results from the BDE models with the trajectories of the ODE model, but also validate the BDE models with two additional numerical experiments. One experiment induces a switch in the oscillatory pattern upon changes in the model parameters, and the other simulates the administration of a hormone that is known to shift the estrous cycle in time. The models presented here are the first BDE models for hormonal oscillators, and the first BDE models for drug administration. Even though automatic parameter estimation still remains challenging, our results support the role of BDEs as a framework for the systematic modelling of complex biological oscillators.}, language = {en} } @misc{Mathew2021, type = {Master Thesis}, author = {Mathew, Maria}, title = {Numerical treatment of radiative heat transfer on cooling process}, pages = {53}, year = {2021}, abstract = {This thesis examines how taking into account surface to surface radiation impacts the cooling process in general. We formulate the non local bound- ary condition after introducing the general setting for the cooling model. In section 3, the mathematical description of the radiative heat transfer is dis- cussed. We cover the implementation of the radiative matrix in section 4, which is followed by a brief explanation of the radiative matrix's structure and several techniques to dealing with the accompanying challenges. We investigate the importance of radiative heat transport by applying the given approach to a two-dimensional geometry and computing the ensuing cooling curves. We compare the findings of our computation to those ac- quired from experiment conducted and find that they are extremely similar. There is a considerable difference (of about 35\%) in the time of cooling of the surface where there is a possibility of influence of radiation from the second surface to that of the surface with no influence at all. Although it is possible to infer that heat convection plays a role in the total result, this has yet to be proved. However, one can clearly see the significance of the surface to surface radiative heat transfer on these parts confirming the research question posed at the begining. The effect of the surface to surface radiative heat transfer has an influence on the resulting cooling time and should be considered in the model.}, language = {en} } @article{BirkRaharinirinaFackeldeyetal.2021, author = {Birk, Ralph and Raharinirina, N. Alexia and Fackeldey, Konstantin and Richter, Tonio Sebastian and Weber, Marcus}, title = {Inferring cultural and social processes based on patterns of statistical relationships between Synodal texts}, year = {2021}, abstract = {In this paper, we explore the relationship patterns between Ancient Egyptian texts of the corpus ``Synodal decrees'', which are originating between 243 and 185 BCE, during the Ptolemaic period. Particularly, we are interested in analyzing the grammatical features of the different texts. Conventional data analysis methods such as correspondence Analysis are very useful to explore the patterns of statistical interdependence between categories of variables. However, it is based on a PCA-like dimension-reduction method and turned out to be unsuitable for our dataset due to the high dimensionality of our data representations. Additionally, the similarity between pairs of texts and pairs of grammatical features is observed through the distance between their representation, but the degree of association between a particular grammatical feature and a text is not. Here, we applied a qualitative Euclidean embedding method that provides a new Euclidean representation of the categories of variables. This new representation of the categories is constructed in such a way that all the patterns of statistical interdependence, similarity, and association, are seen through the Euclidean distance between them. Nevertheless, the PCA-like dimension-reduction method also performed poorly on our new representation. Therefore, we obtained a two-dimensional visualization using non-linear methods such UMAP or t-SNE. Although these dimension-reduction methods reduced the interpretability of interpoint distances, we were still able to identify important similarity patterns between the Synodal text as well as their association patterns with the grammatical features.}, language = {en} } @article{GholamiHoeflingKleinetal.2021, author = {Gholami, Abbas and H{\"o}fling, Felix and Klein, Rupert and Delle Site, Luigi}, title = {Thermodynamic relations at the coupling boundary in adaptive resolution simulations for open systems}, volume = {4}, journal = {Advances Theory and Simulation}, doi = {10.1002/adts.202000303}, pages = {2000303}, year = {2021}, language = {en} } @article{KleinEbrahimiViandHoeflingetal.2021, author = {Klein, Rupert and Ebrahimi Viand, Roya and H{\"o}fling, Felix and Delle Site, Luigi}, title = {Nonequilibrium induced by reservoirs: Physico-mathematical model and numerical tests}, volume = {4}, journal = {Advances Theory and Simulation}, doi = {10.1002/adts.202100071}, pages = {2100071}, year = {2021}, language = {en} } @article{PathaniaChakrabortyHoefling2021, author = {Pathania, Yogyata and Chakraborty, Dipanjan and H{\"o}fling, Felix}, title = {Continuous demixing transition of binary liquids: finite-size scaling from the analysis of sub-systems}, volume = {4}, journal = {Advances Theory and Simulation}, doi = {10.1002/adts.202000235}, pages = {2000235}, year = {2021}, language = {en} } @article{FroembergHoefling2021, author = {Fr{\"o}mberg, Daniela and H{\"o}fling, Felix}, title = {Generalized master equation for first-passage problems in partitioned spaces}, volume = {54}, journal = {Journal of Physics A: Mathematical and Theoretical}, doi = {10.1088/1751-8121/abf2ec}, pages = {215601}, year = {2021}, language = {en} } @article{HungenbergSchwedeWulkowetal.2021, author = {Hungenberg, Klaus-Dieter and Schwede, Christian and Wulkow, Michael and Wulkow, Niklas}, title = {Determination of reactivity ratios for acrylic acid and its dimer from classical parameter estimation and Bayesian approach}, journal = {Canadian Journal of Chemical Engineering}, doi = {https://doi.org/10.1002/cjce.24330}, pages = {1 -- 10}, year = {2021}, abstract = {The reactivity ratios of acrylic acid (AA, M1) and its dimer beta-acroyloxypropionic acid (diAA, M2) are determined from cumulative copolymerization data by two different methods: classical parameter estimation (PE) by minimizing the objective function and a Bayesian analysis. Classical PE gives r1 =0.74 and r2 = 1.23 at the minimum of the residual. From the Bayesian analysis, the probability distribution of the parameter sets is obtained, revealing the existence of parameter sets with rather the same probability. The influence of the number of data and the size of the measurement error are discussed.}, language = {en} }