@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} }