@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} } @inproceedings{GholamiSchintke2021, author = {Gholami, Masoud and Schintke, Florian}, title = {Combining XOR and Partner Checkpointing for Resilient Multilevel Checkpoint/Restart}, booktitle = {2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS)}, doi = {10.1109/IPDPS49936.2021.00036}, pages = {277 -- 288}, year = {2021}, language = {en} } @inproceedings{ThostrupSkrzypczakJasnyetal.2021, author = {Thostrup, Lasse and Skrzypczak, Jan and Jasny, Matthias and Ziegler, Tobias and Binnig, Carsten}, title = {DFI: The Data Flow Interface for High-Speed Networks}, booktitle = {SIGMOD '21: International Conference on Management of Data}, publisher = {ACM}, doi = {10.1145/3448016.3452816}, pages = {1825 -- 1837}, year = {2021}, language = {en} } @article{SteinStraubeWeinzierletal.2020, author = {Stein, Lewin and Straube, Florian and Weinzierl, Stefan and Lemke, Mathias}, title = {Directional sound source modeling using the adjoint Euler equations in a finite-difference time-domain approach}, volume = {148}, journal = {Acoustical Society of America}, number = {5}, publisher = {The Journal of the Acoustical Society of America}, doi = {https://doi.org/10.1121/10.0002425}, pages = {3075 -- 3085}, year = {2020}, abstract = {An adjoint-based approach for synthesizing complex sound sources by discrete, grid-based monopoles in finite-difference time-domain simulations is presented. Previously [Stein et al., 2019a, J. Acoust. Soc. Am. 146(3), 1774-1785] demonstrated that the approach allows to consider unsteady and non-uniform ambient conditions such as wind flow and thermal gradient in contrast to standard methods of numerical sound field simulation. In this work, it is proven that not only ideal monopoles but also realistic sound sources with complex directivity characteristics can be synthesized. In detail, an oscillating circular piston and a real 2-way near-field monitor are modeled. The required number of monopoles in terms of the SPL deviation between the directivity of the original and the synthesized source is analyzed. Since the computational effort is independent of the number of monopoles used for the synthesis, also more complex sources can be reproduced by increasing the number of monopoles utilized. In contrast to classical least-square problem solvers, this does not increase the computational effort, which makes the method attractive for predicting the effect of sound reinforcement systems with highly directional sources under difficult acoustic boundary conditions.}, language = {en} } @incollection{LemkeStein2020, author = {Lemke, Mathias and Stein, Lewin}, title = {Adjoint-Based Identification of Sound Sources for Sound Reinforcement and Source Localization}, volume = {145}, booktitle = {Notes on Numerical Fluid Mechanics and Multidisciplinary Design}, publisher = {Springer, Cham}, isbn = {978-3-030-52429-6}, doi = {https://doi.org/10.1007/978-3-030-52429-6_17}, pages = {263 -- 278}, year = {2020}, abstract = {The identification of sound sources is a common problem in acoustics. Different parameters are sought, among these are signal and position of the sources. We present an adjoint-based approach for sound source identification, which employs computational aeroacoustic techniques. Two different applications are presented as a proof-of-concept: optimization of a sound reinforcement setup and the localization of (moving) sound sources.}, language = {en} } @misc{LemkeSteinHoelteretal.2020, author = {Lemke, Mathias and Stein, Lewin and H{\"o}lter, Arne and Straube, Florian and Weinzierl, Stefan}, title = {Synthese komplexer Richtcharakteristiken f{\"u}r eine Schallfeldoptimierung im Zeitbereich}, editor = {Peissig, J{\"u}rgen}, publisher = {Deutsche Gesellschaft f{\"u}r Akustik e.V.}, isbn = {978-3939296171}, doi = {https://doi.org/10.14279/depositonce-9997}, year = {2020}, abstract = {Die Bestimmung optimaler Treiberfunktionen von Lautsprechern in beliebiger Anordnung ist ein schlecht gestelltes Optimierungsproblem, da die Anzahl der Quellen immer erheblich kleiner als die Anzahl der Empf{\"a}nger ist. Typischerweise werden frequenz-basierte L{\"o}ser eingesetzt. In einem vorangegangenen Beitrag haben die Autoren einen Adjungierten-basierten Ansatz vorgestellt, um optimale Treiberfunktionen im Zeitbereich zu bestimmen. Die Methode erlaubt es, inhomogene Windprofile und Temperaturschichtungen einzubeziehen, die typischerweise bei auf der Wellengleichung beruhenden L{\"o}sungen nicht ber{\"u}cksichtigt werden. Daru ̈ber hinaus k{\"o}nnen komplexe Geometrien und Randbedingungen ber{\"u}cksichtigt werden. Bisher war diese Methode auf Monopolquellen beschr{\"a}nkt. Hier stellen die Autoren eine Erweiterung des Ansatzes in Bezug auf eine Adjungierten-basierte Monopolsynthese vor, die es erm{\"o}glicht, auch Quellen mit komplexen Richtcharakteristiken zu betrachten. Das Verfahren wird f{\"u}r typische Quellsignale und ein repr{\"a}sentatives Lautsprechermodell mit komplexer Richtcharakteristik validiert.}, language = {de} } @inproceedings{ChristgauKnaustSteinke2022, author = {Christgau, Steffen and Knaust, Marius and Steinke, Thomas}, title = {A First Step towards Support for MPI Partitioned Communication on SYCL-programmed FPGAs}, booktitle = {IEEE/ACM International Workshop on Heterogeneous High-performance Reconfigurable Computing, H2RC@SC 2022, Dallas, TX, USA, November 13-18, 2022}, publisher = {IEEE}, doi = {10.1109/H2RC56700.2022.00007}, pages = {9 -- 17}, year = {2022}, abstract = {Version 4.0 of the Message Passing Interface standard introduced the concept of Partitioned Communication which adds support for multiple contributions to a communication buffer. Although initially targeted at multithreaded MPI applications, Partitioned Communication currently receives attraction in the context of accelerators, especially GPUs. In this publication it is demonstrated that this communication concept can also be implemented for SYCL-programmed FPGAs. This includes a discussion of the design space and the presentation of a prototypical implementation. Experimental results show that a lightweight implementation on top of an existing MPI library is possible. In addition, the presented approach also reveals issues in both the SYCL and the MPI standard which need to be addresses for improved support of the intended communication style.}, language = {en} } @inproceedings{LaeuterKramerRubinetal.2022, author = {L{\"a}uter, Matthias and Kramer, Tobias and Rubin, Martin and Altwegg, Kathrin}, title = {Determination of the ice composition near the surface of comet 67P/Churyumov-Gerasimenko}, booktitle = {Europlanet Science Congress}, doi = {10.5194/epsc2022-826}, pages = {EPSC2022-826}, year = {2022}, abstract = {During the apparition of comet 67P/Churyumov-Gerasimenko (67P/C-G) solar irradiation causes varying rates for sublimation of volatile species from the cometary nucleus. Because sublimation processes take place close to the cometary surface, the relative abundance of volatiles in the coma and the ice composition are related to each other. To quantify this relation we assume a model for the expansion of a collisionless gas from the surface into the surrounding space. We use an inverse model approach to relate the in situ measurements of gas densities from the two Rosetta instruments COPS (COmet Pressure Sensor) and DFMS (Double Focusing Mass Spectrometer) at the positions of the spacecraft to the locations of surface gas emissions during the Rosetta mission 2014-2016. We assume the temporally integrated gas emissions to be representative for the ice composition close to the surface. Our analysis shows characteristic differences in the ice compositions between both hemispheres of 67P/C-G. In particular CO2 ice has a reduced abundance on the northern hemisphere. In contrast to the hemispherical differences, the two lobes do not show significant differences in terms of their ice composition.}, language = {en} } @inproceedings{BrookFullerSwinburneetal.2022, author = {Brook, Glenn and Fuller, Douglas and Swinburne, John and Christgau, Steffen and L{\"a}uter, Matthias and Rodrigues Pel{\´a}, Ronaldo and Lewin, Stein and Christian, Tuma and Steinke, Thomas}, title = {An Early Scalability Study of Omni-Path Express}, address = {Hamburg}, organization = {ISC 2022 IXPUG}, doi = {10.13140/RG.2.2.21353.57442}, pages = {8}, year = {2022}, abstract = {This work provides a brief description of Omni-Path Express and the current status of its development, stability, and performance. Basic benchmarks that highlight the gains of OPX over PSM2 are provided, and the results of an initial performance and scalability study of several applications are presented.}, language = {en} } @misc{StraubeWinkelmannHoefling2022, author = {Straube, Arthur and Winkelmann, Stefanie and H{\"o}fling, Felix}, title = {Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles}, issn = {1438-0064}, doi = {10.12752/8817}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-88179}, year = {2022}, abstract = {Our theoretical study concerns an urea-urease-based pH oscillator confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the limit cycle, which controls the dynamics for giant vesicles and dominates the strongly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, amenable to analytic treatments, and show that the accuracy of predictions, including the period of oscillations, is highly sensitive to the choice of the reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The accurate description of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms.}, language = {en} } @inproceedings{KramerLaeuter2022, author = {Kramer, Tobias and L{\"a}uter, Matthias}, title = {The near nucleus gas and dust environment around comet 67P/Churyumov-Gerasimenko}, booktitle = {Europlanet Science Congress}, doi = {10.5194/epsc2022-281}, pages = {EPSC2022-281}, year = {2022}, abstract = {The Rosetta mission to comet 67P/C-G provided a detailed view of the near nucleus environment of an active Jupiter family comet. The continuous monitoring of the gas pressure with the ROSINA experiment at the location of the Rosetta spacecraft in combination with the images of the dust environment acquired by the OSIRIS cameras allows one to test different hypotheses about the origin of the dust and gas emissions. In addition the orbital elements and the rotation axis and spin rate of the nucleus are affected by the gas release.}, language = {en} } @inproceedings{BuergerGundlachBlumetal.2022, author = {B{\"u}rger, Johanna and Gundlach, Bastian and Blum, J{\"u}rgen and Hayne, Paul and L{\"a}uter, Matthias and Kramer, Tobias}, title = {Lunar regolith properties derived from LRO/Diviner data and thermophysical modelling}, booktitle = {Europlanet Science Congress}, doi = {10.5194/epsc2022-92}, pages = {EPSC2022-92}, year = {2022}, abstract = {The Moon as our nearest celestial object is one of the most important bodies for space resource exploration and planetary science. However, knowledge of the physical properties of the lunar regolith is required for the exploitation of lunar resources and for understanding the Moon's geologic history. This knowledge comes mainly from Apollo in-situ experiments and returned samples, but the global distribution of these properties is still poorly understood. Remote sensing measurements offer the opportunity to derive properties of unsampled areas with the help of models. In our study, a microphysical thermal model for the lunar regolith was developed and the simulated surface temperatures were compared with thermal emission measurements from the Diviner radiometer on board the Lunar Reconnaissance Orbiter (LRO) to derive regolith properties. This work expands upon previous investigations of lunar regolith properties using Diviner data, by more directly simulating physical properties such as particle size and porosity.}, language = {en} } @article{LoesserWitzkeSchintkeetal.2022, author = {L{\"o}ßer, Angar and Witzke, Joel and Schintke, Florian and Scheuermann, Bj{\"o}rn}, title = {BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis}, journal = {arXiv}, arxiv = {http://arxiv.org/abs/2209.05358}, doi = {10.48550/arXiv.2209.05358}, pages = {1 -- 20}, year = {2022}, language = {en} } @inproceedings{BaderWitzkeBeckeretal.2022, author = {Bader, Jonathan and Witzke, Joel and Becker, Soeren and L{\"o}ßer, Ansgar and Lehmann, Fabian and Doehler, Leon and Vu, Anh Duc and Kao, Odej}, title = {Towards Advanced Monitoring for Scientific Workflows}, booktitle = {2022 IEEE International Conference on Big Data, 11th Workshop on Scalable Cloud Data Management}, arxiv = {http://arxiv.org/abs/2211.12744}, year = {2022}, language = {en} } @inproceedings{LoesserWitzkeSchintkeetal.2022, author = {L{\"o}ßer, Angar and Witzke, Joel and Schintke, Florian and Scheuermann, Bj{\"o}rn}, title = {BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis}, booktitle = {2022 IEEE International Conference on Big Data, Posters}, year = {2022}, language = {en} } @article{SchintkeBelhajjameDeMecquenemetal.2024, author = {Schintke, Florian and Belhajjame, Khalid and De Mecquenem, Ninon and Frantz, David and Guarino, Vanessa Emanuela and Hilbrich, Marcus and Lehmann, Fabian and Missier, Paolo and Sattler, Rebecca and Sparka, Jan Arne and Speckhard, Daniel T. and Stolte, Hermann and Vu, Anh Duc and Leser, Ulf}, title = {Validity constraints for data analysis workflows}, volume = {157}, journal = {Future Generation Computer Systems}, doi = {10.1016/j.future.2024.03.037}, pages = {82 -- 97}, year = {2024}, language = {en} } @inproceedings{WitzkeSchintkeLoesseretal.2023, author = {Witzke, Joel and Schintke, Florian and L{\"o}ßer, Ansgar and Scheuermann, Bj{\"o}rn}, title = {Proactive Resource Management to Optimize Distributed Workflow Executions}, booktitle = {IEEE International Conference on Big Data, BigData 2023, Sorrento, Italy, December 15-18, 2023}, publisher = {IEEE}, doi = {10.1109/BigData59044.2023.10386493}, pages = {6305 -- 6307}, year = {2023}, language = {en} } @article{BuergerHayneGundlachetal.2024, author = {B{\"u}rger, Johanna and Hayne, Paul and Gundlach, Bastian and L{\"a}uter, Matthias and Kramer, Tobias and Blum, J{\"u}rgen}, title = {A Microphysical Thermal Model for the Lunar Regolith: Investigating the Latitudinal Dependence of Regolith Properties}, volume = {129}, journal = {Journal of Geophysical Research: Planets}, number = {3}, doi = {10.1029/2023JE008152}, year = {2024}, abstract = {The microphysical structure of the lunar regolith provides information on the geologic history of the Moon. We used remote sensing measurements of thermal emission and a thermophysical model to determine the microphysical properties of the lunar regolith. We expand upon previous investigations by developing a microphysical thermal model, which more directly simulates regolith properties, such as grain size and volume filling factor. The modeled temperatures are matched with surface temperatures measured by the Diviner Lunar Radiometer Experiment on board the Lunar Reconnaissance Orbiter. The maria and highlands are investigated separately and characterized in the model by a difference in albedo and grain density. We find similar regolith temperatures for both terrains, which can be well described by similar volume filling factor profiles and mean grain sizes obtained from returned Apollo samples. We also investigate a significantly lower thermal conductivity for highlands, which formally also gives a very good solution, but in a parameter range that is well outside the Apollo data. We then study the latitudinal dependence of regolith properties up to ±80° latitude. When assuming constant regolith properties, we find that a variation of the solar incidence-dependent albedo can reduce the initially observed latitudinal gradient between model and Diviner measurements significantly. A better match between measurements and model can be achieved by a variation in intrinsic regolith properties with a decrease in bulk density with increasing latitude. We find that a variation in grain size alone cannot explain the Diviner measurements at higher latitudes.}, language = {en} } @article{LamboKoyanagiRagyanszkietal.2023, author = {Lambo, Ricardo Lewis and Koyanagi, Gregory K. and Ragyanszki, Anita and Horbatsch, Marko and Fournier, Rene and Hessels, Eric A.}, title = {Calculation of the local environment of a barium monofluoride molecule in an argon matrix: a step towards using matrix-isolated BaF for determining the electron electric dipole moment}, volume = {121}, journal = {Molecular Physics}, number = {6}, doi = {10.1080/00268976.2023.2198044}, year = {2023}, language = {en} } @article{KoyanagiLamboRagyanszkietal.2023, author = {Koyanagi, Gregory K. and Lambo, Ricardo Lewis and Ragyanszki, Anita and Fournier, Rene A. and Horbatsch, Marko W. and Hessels, Eric A.}, title = {Accurate calculation of the interaction of a barium monofluoride molecule with an argon atom: A step towards using matrix isolation of BaF for determining the electron electric dipole moment}, volume = {391}, journal = {Journal of Molecular Spectroscopy}, doi = {10.1016/j.jms.2023.111736}, pages = {111736}, year = {2023}, language = {en} } @article{KraemerDurumericCharronetal.2023, author = {Kr{\"a}mer, Andreas and Durumeric, Aleksander and Charron, Nicholas and Chen, Yaoyi and Clementi, Cecilia and No{\´e}, Frank}, title = {Statistically optimal force aggregation for coarse-graining molecular dynamics}, volume = {14}, journal = {The Journal of Physical Chemistry Letters}, number = {17}, doi = {10.1021/acs.jpclett.3c00444}, pages = {3970 -- 3979}, year = {2023}, abstract = {Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used methodology for learning bottom-up CG force fields maps forces from all-atom molecular dynamics to the CG representation and matches them with a CG force field on average. We show that there is flexibility in how to map all-atom forces to the CG representation and that the most commonly used mapping methods are statistically inefficient and potentially even incorrect in the presence of constraints in the all-atom simulation. We define an optimization statement for force mappings and demonstrate that substantially improved CG force fields can be learned from the same simulation data when using optimized force maps. The method is demonstrated on the miniproteins chignolin and tryptophan cage and published as open-source code.}, language = {en} } @article{DurumericCharronTempletonetal.2023, author = {Durumeric, Aleksander and Charron, Nicholas and Templeton, Clark and Musil, F{\´e}lix and Bonneau, Klara and Pasos-Trejo, Aldo and Chen, Yaoyi and Kelkar, Atharva and No{\´e}, Frank and Clementi, Cecilia}, title = {Machine learned coarse-grained protein force-fields: Are we there yet?}, volume = {79}, journal = {Current Opinion in Structural Biology}, doi = {10.1016/j.sbi.2023.102533}, year = {2023}, abstract = {The successful recent application of machine learning methods to scientific problems includes the learning of flexible and accurate atomic-level force-fields for materials and biomolecules from quantum chemical data. In parallel, the machine learning of force-fields at coarser resolutions is rapidly gaining relevance as an efficient way to represent the higher-body interactions needed in coarse-grained force-fields to compensate for the omitted degrees of freedom. Coarse-grained models are important for the study of systems at time and length scales exceeding those of atomistic simulations. However, the development of transferable coarse-grained models via machine learning still presents significant challenges. Here, we discuss recent developments in this field and current efforts to address the remaining challenges.}, language = {en} } @article{MajewskiPerezThoelkeetal.2023, author = {Majewski, Maciej and P{\´e}rez, Adri{\`a} and Th{\"o}lke, Philipp and Doerr, Stefan and Charron, Nicholas and Giorgino, Toni and Husic, Brooke and Clementi, Cecilia and No{\´e}, Frank and De Fabritiis, Gianni}, title = {Machine learning coarse-grained potentials of protein thermodynamics}, volume = {14}, journal = {Nature Communications}, doi = {10.1038/s41467-023-41343-1}, year = {2023}, abstract = {A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics.}, language = {en} } @inproceedings{BuergerHayneGundlachetal.2023, author = {B{\"u}rger, Johanna and Hayne, Paul and Gundlach, Bastian and L{\"a}uter, Matthias and Kramer, Tobias and Blum, J{\"u}rgen}, title = {Investigating the Latitudinal Dependence of Lunar Regolith Properties Using LRO/Diviner Data and a Microphysical Thermal Model}, volume = {55}, booktitle = {Bulletin of the AAS}, number = {8}, year = {2023}, abstract = {Regolith is formed through weathering of the local rock by meteorite bombardment, space weathering (Pieters \& Noble, 2016) and thermal erosion (Delbo et al., 2014). In the case of the Moon, the space weathering effects and diurnal temperature variations are reduced towards the poles. The aim of this study is to investigate whether the lunar regolith properties derived from the comparison of regolith temperatures measured by the Diviner radiometer (Paige et al., 2010) on board the Lunar Reconnaissance Orbiter (LRO) with simulated temperatures derived from a microphysical thermal model show a latitudinal dependence. The developed microphysical thermal model expands upon previous models by more directly simulating regolith properties, such as grain radius and volume filling factor.}, language = {en} } @inproceedings{LaeuterKramer2023, author = {L{\"a}uter, Matthias and Kramer, Tobias}, title = {Non-gravitational acceleration and torque on comet 67P/Churyumov-Gerasimenko}, volume = {55}, booktitle = {Bulletin of the AAS}, number = {8}, year = {2023}, abstract = {From August 2014 to September 2016, the ESA operated the Rosetta spacecraft mission alongside with comet 67P/Churyumov-Gerasimenko (67P). The mission provided valuable long-term data on the comet's nucleus, including its volume, mass, tensor of inertia, spatial position of the orbital trajectory, and rotational state.}, language = {en} } @article{LaeuterKramerRubinetal.2022, author = {L{\"a}uter, Matthias and Kramer, Tobias and Rubin, Martin and Altwegg, Kathrin}, title = {The ice composition close to the surface of comet 67P/Churyumov-Gerasimenko}, volume = {6}, journal = {ACS Earth and Space Chemistry}, number = {5}, arxiv = {http://arxiv.org/abs/2305.16201}, doi = {10.1021/acsearthspacechem.1c00378}, pages = {1189 -- 1203}, year = {2022}, abstract = {The relation between ice composition in the nucleus of comet 67P/Churyumov-Gerasimenko on the one hand and relative abundances of volatiles in the coma on the other hand is important for the interpretation of density measurements in the environment of the cometary nucleus. For the 2015 apparition, in situ measurements from the two ROSINA (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) sensors COPS (COmet Pressure Sensor) and DFMS (Double Focusing Mass Spectrometer) determined gas densities at the spacecraft position for the 14 gas species H2O, CO2, CO, H2S, O2, C2H6, CH3OH, H2CO, CH4, NH3, HCN, C2H5OH, OCS, and CS2. We derive the spatial distribution of the gas emissions on the complex shape of the nucleus separately for 50 subintervals of the two-year mission time. The most active patches of gas emission are identified on the surface. We retrieve the relation between solar irradiation and observed emissions from these patches. The emission rates are compared to a minimal thermophysical model to infer the surface active fraction of H2O and CO2. We obtain characteristic differences in the ice composition close to the surface between the two hemispheres with a reduced abundance of CO2 ice on the northern hemisphere (locations with positive latitude). We do not see significant differences for the ice composition on the two lobes of 67P/C-G.}, 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{LaeuterKramerRubinetal.2018, author = {L{\"a}uter, Matthias and Kramer, Tobias and Rubin, Martin and Altwegg, Kathrin}, title = {Gas production of comet 67P/Churyumov-Gerasimenko reconstructed from DFMS/COPS data}, volume = {12}, booktitle = {Europlanet Science Congress}, publisher = {Europlanet Science Congress}, pages = {EPSC2018-515-1}, year = {2018}, abstract = {We reconstruct the temporal evolution of surface emissions for the four major gas species H2O, CO2, CO, and O2 emitted during the 2015 apparition of comet 67P/Churyumov-Gerasimenko (67P/C-G). Measurements from the Double Focusing Mass Spectrometer (DFMS) of the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) and the COmet Pressure Sensor (COPS) are used to determine the gas sources on the surface with an inverse gas model for the entire coma. For all species, peak production rates and integrated production rates per orbit are evaluated separately for the northern and the southern hemisphere. Complemented with the total mass production, this allows us to estimate the dust-to-gas ratio of the emitted material.}, language = {en} } @inproceedings{KramerLaeuter2018, author = {Kramer, Tobias and L{\"a}uter, Matthias}, title = {Modelling the inner coma of comet 67P/Churyumov-Gerasimenko}, volume = {12}, booktitle = {Europlanet Science Congress}, publisher = {Europlanet Science Congress}, pages = {EPSC2018-115-1}, year = {2018}, abstract = {Based on about 1 million of pressure measurements around comet 67P/Churyumov-Gerasimenko we reconstruct the gas emission across the entire nucleus. Dust particles are seeded in the gas model and the resulting dust distribution follows a daily pattern which agrees with observations if a uniform dust release across the entire sunlit surface is assumed.}, language = {en} } @article{RodriguesPelaDraxl2022, author = {Rodrigues Pel{\´a}, Ronaldo and Draxl, Claudia}, title = {Ehrenfest dynamics implemented in the all-electron package exciting}, volume = {4}, journal = {Electron. Struct.}, doi = {10.1088/2516-1075/ac7afc}, pages = {037001}, year = {2022}, abstract = {Ehrenfest dynamics combined with real-time time-dependent density functional theory has proven to be a reliable tool to study non-adiabatic molecular dynamics with a reasonable computational cost. Among other possibilities, it allows for assessing in real time electronic excitations generated by ultra-fast laser pulses, as e.g., in pump-probe spectroscopy, and their coupling to the nuclear vibrations even beyond the linear regime. In this work, we present its implementation in the all-electron full-potential package exciting. Three cases are presented as examples: diamond and cubic boron nitride (BN) relaxed after an initial lattice distortion, and cubic BN exposed to a laser pulse. Comparison with the Octopus code exhibits good agreement.}, language = {en} } @article{SalemSchintke2022, author = {Salem, Farouk and Schintke, Florian}, title = {Large-Scale Performance of the Data-Flow Scheduler (DFS) and FLESnet}, journal = {CBM Progress Report 2021}, doi = {10.15120/GSI-2022-00599}, pages = {170 -- 171}, year = {2022}, language = {en} } @inproceedings{KnaustSeilerReinertetal.2022, author = {Knaust, Marius and Seiler, Enrico and Reinert, Knut and Steinke, Thomas}, title = {Co-Design for Energy Efficient and Fast Genomic Search: Interleaved Bloom Filter on FPGA}, booktitle = {FPGA '22: Proceedings of the 2022 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays}, doi = {10.1145/3490422.3502366}, pages = {180 -- 189}, year = {2022}, abstract = {Next-Generation Sequencing technologies generate a vast and exponentially increasing amount of sequence data. The Interleaved Bloom Filter (IBF) is a novel indexing data structure which is state-of-the-art for distributing approximate queries with an in-memory data structure. With it, a main task of sequence analysis pipelines, (approximately) searching large reference data sets for sequencing reads or short sequence patterns like genes, can be significantly accelerated. To meet performance and energy-efficiency requirements, we chose a co-design approach of the IBF data structure on the FPGA platform. Further, our OpenCL-based implementation allows a seamless integration into the widely used SeqAn C++ library for biological sequence analysis. Our algorithmic design and optimization strategy takes advantage of FPGA-specific features like shift register and the parallelization potential of many bitwise operations. We designed a well-chosen schema to partition data across the different memory domains on the FPGA platform using the Shared Virtual Memory concept. We can demonstrate significant improvements in energy efficiency of up to 19x and in performance of up to 5.6x, respectively, compared to a well-tuned, multithreaded CPU reference.}, language = {en} } @article{GholamiSchintke2022, author = {Gholami, Masoud and Schintke, Florian}, title = {IOSIG: Declarative I/O-Stream Properties Using Pragmas}, volume = {22}, journal = {Datenbank-Spektrum}, number = {2}, publisher = {Springer Berlin Heidelberg}, doi = {10.1007/s13222-022-00419-w}, pages = {109 -- 119}, year = {2022}, language = {en} } @inproceedings{BaumannNoackSteinke2021, author = {Baumann, Tobias and Noack, Matthias and Steinke, Thomas}, title = {Performance Evaluation and Improvements of the PoCL Open-Source OpenCL Implementation on Intel CPUs}, booktitle = {IWOCL'21: International Workshop on OpenCL}, doi = {10.1145/3456669.3456698}, year = {2021}, abstract = {The Portable Computing Language (PoCL) is a vendor independent open-source OpenCL implementation that aims to support a variety of compute devices in a single platform. Evaluating PoCL versus the Intel OpenCL implementation reveals significant performance drawbacks of PoCL on Intel CPUs - which run 92 \% of the TOP500 list. Using a selection of benchmarks, we identify and analyse performance issues in PoCL with a focus on scheduling and vectorisation. We propose a new CPU device-driver based on Intel Threading Building Blocks (TBB), and evaluate LLVM with respect to automatic compiler vectorisation across work-items in PoCL. Using the TBB driver, it is possible to narrow the gap to Intel OpenCL and even outperform it by a factor of up to 1.3× in our proxy application benchmark with a manual vectorisation strategy.}, language = {en} } @inproceedings{ScheltenChristgauSchulteetal.2026, author = {Schelten, Niklas and Christgau, Steffen and Schulte, Anton and Schnor, Bettina and Signer, Hannes and Stabernack, Benno}, title = {A Flexible Open-Source Framework for FPGA-based Network-Attached Accelerators using SpinalHDL}, booktitle = {Architecture of Computing Systems - 39th International Conference, ARCS 2026, Mainz, Germany, March 24-26, 2026, Proceedings.}, year = {2026}, abstract = {Domain-specific accelerators are increasingly vital in heterogeneous computing systems, driven by the demand for higher computational capacity and especially energy efficiency. Network-attached FPGAs promise a scalable and flexible alternative to closely coupled FPGAs for integrating accelerators into computing environments. While the advantages of specialized hardware implementations are apparent, traditional hardware development and integration remain time-consuming and complex. We present an open-source framework which combines a hardware shell with supporting software libraries, which enables fast development and deployment of FPGA-based network-attached accelerators. In contrast to traditional approaches using VHDL or Verilog, we leverage generative programming with SpinalHDL, providing a flexible hardware description with multi-level abstractions. This work eases the integration of accelerators into existing network infrastructures and simplifies adaptation to different FPGAs, eliminating complex and lengthy top-level hardware descriptions.}, language = {en} } @article{JiAnitaFournier2025, author = {Ji, Hongchen and Anita, Ragyanszki and Fournier, Rene}, title = {Computational Study of the Reactions of CH2 with HCNO and HNCO}, volume = {103}, journal = {Canadian Journal of Chemistry}, number = {7}, doi = {10.1139/cjc-2024-0203}, pages = {386 -- 395}, year = {2025}, abstract = {We present a computational approach for screening reaction mechanisms with machine learning estimates of energy barriers. A comprehensive screening of thousands of reactions identified the CH2 reactions with HCNO and HNCO as possible sources of relatively complex organic molecules in space. We report detailed reaction mechanisms, including TS, intermediate, and product energies, calculated with density functional theory and coupled cluster theory. Singlet CH2, located 9 kcal/mol above the triplet ground state, reacts with HCNO or HNCO without a barrier, producing four prod11 ucts: CH2NCHO, N-methyleneformamide, the thermodynamically favored product; NHCHCHO, imine acetaldehyde; NHCHOCH; and (CH2OC)NH, oxiran-2-ylazanide. The lowest energy pathway for CH2 + HCNO, involving a triplet-to-singlet crossing, has a barrier of 8 kcal/mol and leads to N -methyleneformamide, imine acetaldehyde, and NHCHOCH. The reaction of triplet CH2 with HNCO has a lowest energy pathway with a barrier of 11 kcal/mol, yielding CH2(CO)NH.}, language = {en} } @article{RayaMorenoDaschFarahanietal.2026, author = {Raya-Moreno, Mart{\´i} and Dasch, Noah Alexy and Farahani, Nasrin and Gonzalez Oliva, Ignacio and Gulans, Andris and Hossain, Manoar and Kleine, Hannah and Kuban, Martin and Lubeck, Sven and Maurer, Benedikt and Pavone, Pasquale and Peschel, Fabian and Popova-Gorelova, Daria and Qiao, Lu and Richter, Elias and Rigamonti, Santiago and Rodrigues Pel{\´a}, Ronaldo and Sinha, Kshitij and Speckhard, Daniel T. and Tillack, Sebastian and Tumakov, Dmitry and Hong, Seokhyun and Uzulis, Janis and Voiculescu, Mara and Vona, Cecilia and Yang, Mao and Draxl, Claudia}, title = {An exciting approach to theoretical spectroscopy}, arxiv = {http://arxiv.org/abs/2601.11388}, year = {2026}, language = {en} } @article{QiaoRodriguesPelaDraxl2026, author = {Qiao, Lu and Rodrigues Pel{\´a}, Ronaldo and Draxl, Claudia}, title = {First-principles approach to ultrafast pump-probe spectroscopy in solids}, arxiv = {http://arxiv.org/abs/2509.07612}, year = {2026}, language = {en} } @inproceedings{ScheltenChristgauHutzleretal.2026, author = {Schelten, Niklas and Christgau, Steffen and Hutzler, Merit and Kreowsky, Philipp and De Lucia, Marco and Schnor, Bettina and Signer, Hannes and Spazier, Johannes and Stabernack, Benno and Yahdzhyiev, Serhii}, title = {Using FPGA-based Network-Attached Accelerators for Energy-Efficient AI Training in HPC Datacenters}, booktitle = {2026 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)}, year = {2026}, abstract = {FPGA-based Network-Attached Accelerators offer a disaggregated alternative to closely-coupled FPGAs or GPUs, but their adoption is very limited due to missing hardware/software frameworks. However, the usability and energy-efficiency of FPGAs for HPC use-cases has been demonstrated previously. Yet, the support by HPC infrastructure for those devices is lacking behind other accelerators. This paper addresses this shortcoming and demonstrates a full-stack approach that seamlessly integrates Network-Attached Accelerators in HPC datacenters and allows flexible and scalable usage of FPGAs. The presented work includes the according framework, integration steps and a show-case application from the geoscience domain. We evaluate our approach by comparing the training of a Physics-Informed Neural Network on the NAA against two GPU implementations. The NAA reduces total energy consumption by about 50\% and 17\% compared to the Keras and CUDA implementation, respectively. These results demonstrate that FPGA-based NAAs can be successfully integrated into HPC environments and are a viable path toward more energy-efficient AI training.}, language = {en} } @misc{RamakiSchintke2025, author = {Ramaki, Niaz Mohammad and Schintke, Florian}, title = {Ensuring Reproducibility in Stream Processing with Blockchain Technologies}, journal = {2025 11th International Conference on Computer and Communications (ICCC)}, publisher = {IEEE}, doi = {10.1109/ICCC68654.2025.11437772}, pages = {1383 -- 1391}, year = {2025}, language = {en} } @misc{KharmaWiesSchintke2026, author = {Kharma, Sami and Wies, Tobias and Schintke, Florian}, title = {Comprehensive Plugin-Based Monitoring of Nexflow Workflow Executions}, journal = {SCA/HPC Asia 2026}, arxiv = {http://arxiv.org/abs/2603.28783}, year = {2026}, language = {en} }