TY - GEN A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Höfling, Felix T1 - Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles N2 - 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. T3 - ZIB-Report - 22-21 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88179 SN - 1438-0064 ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - The near nucleus gas and dust environment around comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - 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. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-281 SP - EPSC2022-281 ER - TY - CHAP A1 - Bürger, Johanna A1 - Gundlach, Bastian A1 - Blum, Jürgen A1 - Hayne, Paul A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Lunar regolith properties derived from LRO/Diviner data and thermophysical modelling T2 - Europlanet Science Congress N2 - 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. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-92 SP - EPSC2022-92 ER - TY - JOUR A1 - Lößer, Angar A1 - Witzke, Joel A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis JF - arXiv Y1 - 2022 U6 - https://doi.org/10.48550/arXiv.2209.05358 SP - 1 EP - 20 ER - TY - CHAP A1 - Bader, Jonathan A1 - Witzke, Joel A1 - Becker, Soeren A1 - Lößer, Ansgar A1 - Lehmann, Fabian A1 - Doehler, Leon A1 - Vu, Anh Duc A1 - Kao, Odej T1 - Towards Advanced Monitoring for Scientific Workflows T2 - 2022 IEEE International Conference on Big Data, 11th Workshop on Scalable Cloud Data Management Y1 - 2022 ER - TY - CHAP A1 - Lößer, Angar A1 - Witzke, Joel A1 - Schintke, Florian A1 - Scheuermann, Björn T1 - BottleMod: Modeling Data Flows and Tasks for Fast Bottleneck Analysis T2 - 2022 IEEE International Conference on Big Data, Posters Y1 - 2022 ER - TY - JOUR A1 - Schintke, Florian A1 - Belhajjame, Khalid A1 - De Mecquenem, Ninon A1 - Frantz, David A1 - Guarino, Vanessa Emanuela A1 - Hilbrich, Marcus A1 - Lehmann, Fabian A1 - Missier, Paolo A1 - Sattler, Rebecca A1 - Sparka, Jan Arne A1 - Speckhard, Daniel T. A1 - Stolte, Hermann A1 - Vu, Anh Duc A1 - Leser, Ulf T1 - Validity constraints for data analysis workflows JF - Future Generation Computer Systems Y1 - 2024 U6 - https://doi.org/10.1016/j.future.2024.03.037 VL - 157 SP - 82 EP - 97 ER - TY - CHAP A1 - Witzke, Joel A1 - Schintke, Florian A1 - Lößer, Ansgar A1 - Scheuermann, Björn T1 - Proactive Resource Management to Optimize Distributed Workflow Executions T2 - IEEE International Conference on Big Data, BigData 2023, Sorrento, Italy, December 15-18, 2023 Y1 - 2023 U6 - https://doi.org/10.1109/BigData59044.2023.10386493 SP - 6305 EP - 6307 PB - IEEE ER - TY - JOUR A1 - Bürger, Johanna A1 - Hayne, Paul A1 - Gundlach, Bastian A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Blum, Jürgen T1 - A Microphysical Thermal Model for the Lunar Regolith: Investigating the Latitudinal Dependence of Regolith Properties JF - Journal of Geophysical Research: Planets N2 - 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. Y1 - 2024 U6 - https://doi.org/10.1029/2023JE008152 VL - 129 IS - 3 ER - TY - JOUR A1 - Lambo, Ricardo Lewis A1 - Koyanagi, Gregory K. A1 - Ragyanszki, Anita A1 - Horbatsch, Marko A1 - Fournier, Rene A1 - Hessels, Eric A. T1 - 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 JF - Molecular Physics Y1 - 2023 U6 - https://doi.org/10.1080/00268976.2023.2198044 VL - 121 IS - 6 ER - TY - JOUR A1 - Koyanagi, Gregory K. A1 - Lambo, Ricardo Lewis A1 - Ragyanszki, Anita A1 - Fournier, Rene A. A1 - Horbatsch, Marko W. A1 - Hessels, Eric A. T1 - 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 JF - Journal of Molecular Spectroscopy Y1 - 2023 U6 - https://doi.org/10.1016/j.jms.2023.111736 VL - 391 SP - 111736 ER - TY - JOUR A1 - Krämer, Andreas A1 - Durumeric, Aleksander A1 - Charron, Nicholas A1 - Chen, Yaoyi A1 - Clementi, Cecilia A1 - Noé, Frank T1 - Statistically optimal force aggregation for coarse-graining molecular dynamics JF - The Journal of Physical Chemistry Letters N2 - 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. Y1 - 2023 U6 - https://doi.org/10.1021/acs.jpclett.3c00444 VL - 14 IS - 17 SP - 3970 EP - 3979 ER - TY - JOUR A1 - Durumeric, Aleksander A1 - Charron, Nicholas A1 - Templeton, Clark A1 - Musil, Félix A1 - Bonneau, Klara A1 - Pasos-Trejo, Aldo A1 - Chen, Yaoyi A1 - Kelkar, Atharva A1 - Noé, Frank A1 - Clementi, Cecilia T1 - Machine learned coarse-grained protein force-fields: Are we there yet? JF - Current Opinion in Structural Biology N2 - 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. Y1 - 2023 U6 - https://doi.org/10.1016/j.sbi.2023.102533 VL - 79 ER -