[{"intvolume":"         1","page":"33","citation":{"mla":"Ehtesabi, Sadaf, et al. <i>Otus Supercomputer</i>. Paderborn Center for Parallel Computing (PC2), 2025, doi:<a href=\"https://doi.org/10.48550/ARXIV.2512.07401\">10.48550/ARXIV.2512.07401</a>.","short":"S. Ehtesabi, M. Hossain, T. Kenter, A. Krawinkel, L. Ostermann, C. Plessl, H. Riebler, S. Rohde, R. Schade, M. Schwarz, J. Simon, N. Winnwa, A. Wiens, X. Wu, Otus Supercomputer, Paderborn Center for Parallel Computing (PC2), Paderborn, 2025.","bibtex":"@book{Ehtesabi_Hossain_Kenter_Krawinkel_Ostermann_Plessl_Riebler_Rohde_Schade_Schwarz_et al._2025, place={Paderborn}, series={PC2 Tech­nic­al Re­port Series}, title={Otus Supercomputer}, volume={1}, DOI={<a href=\"https://doi.org/10.48550/ARXIV.2512.07401\">10.48550/ARXIV.2512.07401</a>}, publisher={Paderborn Center for Parallel Computing (PC2)}, author={Ehtesabi, Sadaf and Hossain, Manoar and Kenter, Tobias and Krawinkel, Andreas and Ostermann, Lukas and Plessl, Christian and Riebler, Heinrich and Rohde, Stefan and Schade, Robert and Schwarz, Michael and et al.}, year={2025}, collection={PC2 Tech­nic­al Re­port Series} }","apa":"Ehtesabi, S., Hossain, M., Kenter, T., Krawinkel, A., Ostermann, L., Plessl, C., Riebler, H., Rohde, S., Schade, R., Schwarz, M., Simon, J., Winnwa, N., Wiens, A., &#38; Wu, X. (2025). <i>Otus Supercomputer</i> (Vol. 1). Paderborn Center for Parallel Computing (PC2). <a href=\"https://doi.org/10.48550/ARXIV.2512.07401\">https://doi.org/10.48550/ARXIV.2512.07401</a>","chicago":"Ehtesabi, Sadaf, Manoar Hossain, Tobias Kenter, Andreas Krawinkel, Lukas Ostermann, Christian Plessl, Heinrich Riebler, et al. <i>Otus Supercomputer</i>. Vol. 1. PC2 Tech­nic­al Re­port Series. Paderborn: Paderborn Center for Parallel Computing (PC2), 2025. <a href=\"https://doi.org/10.48550/ARXIV.2512.07401\">https://doi.org/10.48550/ARXIV.2512.07401</a>.","ieee":"S. Ehtesabi <i>et al.</i>, <i>Otus Supercomputer</i>, vol. 1. Paderborn: Paderborn Center for Parallel Computing (PC2), 2025.","ama":"Ehtesabi S, Hossain M, Kenter T, et al. <i>Otus Supercomputer</i>. Vol 1. Paderborn Center for Parallel Computing (PC2); 2025. doi:<a href=\"https://doi.org/10.48550/ARXIV.2512.07401\">10.48550/ARXIV.2512.07401</a>"},"place":"Paderborn","has_accepted_license":"1","publication_status":"published","doi":"10.48550/ARXIV.2512.07401","volume":1,"author":[{"first_name":"Sadaf","last_name":"Ehtesabi","full_name":"Ehtesabi, Sadaf","id":"116116"},{"first_name":"Manoar","orcid":"https://orcid.org/0000-0002-0737-7981","last_name":"Hossain","full_name":"Hossain, Manoar","id":"114619"},{"first_name":"Tobias","last_name":"Kenter","id":"3145","full_name":"Kenter, Tobias"},{"full_name":"Krawinkel, Andreas","id":"15275","last_name":"Krawinkel","first_name":"Andreas"},{"last_name":"Ostermann","full_name":"Ostermann, Lukas","id":"69976","first_name":"Lukas"},{"full_name":"Plessl, Christian","id":"16153","last_name":"Plessl","orcid":"0000-0001-5728-9982","first_name":"Christian"},{"id":"8961","full_name":"Riebler, Heinrich","last_name":"Riebler","first_name":"Heinrich"},{"first_name":"Stefan","last_name":"Rohde","id":"34009","full_name":"Rohde, Stefan"},{"full_name":"Schade, Robert","id":"75963","last_name":"Schade","orcid":"0000-0002-6268-5397","first_name":"Robert"},{"first_name":"Michael","full_name":"Schwarz, Michael","id":"5312","last_name":"Schwarz"},{"last_name":"Simon","full_name":"Simon, Jens","id":"15273","first_name":"Jens"},{"first_name":"Nils","full_name":"Winnwa, Nils","id":"61189","last_name":"Winnwa"},{"first_name":"Alex","last_name":"Wiens","orcid":"0000-0003-1764-9773","full_name":"Wiens, Alex","id":"23522"},{"last_name":"Wu","full_name":"Wu, Xin","id":"77439","first_name":"Xin"}],"oa":"1","date_updated":"2026-03-25T11:50:31Z","status":"public","type":"report","file_date_updated":"2026-03-25T11:50:30Z","department":[{"_id":"27"},{"_id":"518"}],"user_id":"23522","series_title":"PC2 Tech­nic­al Re­port Series","_id":"62981","year":"2025","title":"Otus Supercomputer","date_created":"2025-12-09T09:11:04Z","publisher":"Paderborn Center for Parallel Computing (PC2)","file":[{"content_type":"application/pdf","relation":"main_file","creator":"deffel","date_created":"2025-12-09T09:19:12Z","date_updated":"2026-03-25T11:50:30Z","file_name":"2512.07401v1.pdf","file_id":"62982","access_level":"open_access","file_size":4535595}],"abstract":[{"lang":"eng","text":"Otus is a high-performance computing cluster that was launched in 2025 and is operated by the Paderborn Center for Parallel Computing (PC2) at Paderborn University in Germany. The system is part of the National High Performance Computing (NHR) initiative. Otus complements the previous supercomputer Noctua 2, offering approximately twice the computing power while retaining the three node types that were characteristic of Noctua 2: 1) CPU compute nodes with different memory capacities, 2) high-end GPU nodes, and 3) HPC-grade FPGA nodes. On the Top500 list, which ranks the 500 most powerful supercomputers in the world, Otus is in position 164 with the CPU partition and in position 255 with the GPU partition (June 2025). On the Green500 list, ranking the 500 most energy-efficient supercomputers in the world, Otus is in position 5 with the GPU partition (June 2025).\r\n\r\n\r\nThis article provides a comprehensive overview of the system in terms of its hardware, software, system integration, and its overall integration into the data center building to ensure energy-efficient operation. The article aims to provide unique insights for scientists using the system and for other centers operating HPC clusters. The article will be continuously updated to reflect the latest system setup and measurements. "}],"report_number":"PC2TR-2025-1","language":[{"iso":"eng"}],"keyword":["Otus","Supercomputer","FPGA","PC2","Paderborn Center for Parallel Computing","Noctua 2","HPC"],"ddc":["004"]},{"type":"journal_article","status":"public","project":[{"_id":"52","name":"PC2: Computing Resources Provided by the Paderborn Center for Parallel Computing"}],"_id":"53663","user_id":"8961","department":[{"_id":"27"},{"_id":"518"}],"article_type":"original","file_date_updated":"2024-04-26T08:35:17Z","publication_status":"published","has_accepted_license":"1","citation":{"ieee":"C. Bauer <i>et al.</i>, “Noctua 2 Supercomputer,” <i>Journal of large-scale research facilities</i>, vol. 9, 2024, doi: <a href=\"https://doi.org/10.17815/jlsrf-8-187 \">10.17815/jlsrf-8-187 </a>.","chicago":"Bauer, Carsten, Tobias Kenter, Michael Lass, Lukas Mazur, Marius Meyer, Holger Nitsche, Heinrich Riebler, et al. “Noctua 2 Supercomputer.” <i>Journal of Large-Scale Research Facilities</i> 9 (2024). <a href=\"https://doi.org/10.17815/jlsrf-8-187 \">https://doi.org/10.17815/jlsrf-8-187 </a>.","ama":"Bauer C, Kenter T, Lass M, et al. Noctua 2 Supercomputer. <i>Journal of large-scale research facilities</i>. 2024;9. doi:<a href=\"https://doi.org/10.17815/jlsrf-8-187 \">10.17815/jlsrf-8-187 </a>","mla":"Bauer, Carsten, et al. “Noctua 2 Supercomputer.” <i>Journal of Large-Scale Research Facilities</i>, vol. 9, 2024, doi:<a href=\"https://doi.org/10.17815/jlsrf-8-187 \">10.17815/jlsrf-8-187 </a>.","short":"C. Bauer, T. Kenter, M. Lass, L. Mazur, M. Meyer, H. Nitsche, H. Riebler, R. Schade, M. Schwarz, N. Winnwa, A. Wiens, X. Wu, C. Plessl, J. Simon, Journal of Large-Scale Research Facilities 9 (2024).","bibtex":"@article{Bauer_Kenter_Lass_Mazur_Meyer_Nitsche_Riebler_Schade_Schwarz_Winnwa_et al._2024, title={Noctua 2 Supercomputer}, volume={9}, DOI={<a href=\"https://doi.org/10.17815/jlsrf-8-187 \">10.17815/jlsrf-8-187 </a>}, journal={Journal of large-scale research facilities}, author={Bauer, Carsten and Kenter, Tobias and Lass, Michael and Mazur, Lukas and Meyer, Marius and Nitsche, Holger and Riebler, Heinrich and Schade, Robert and Schwarz, Michael and Winnwa, Nils and et al.}, year={2024} }","apa":"Bauer, C., Kenter, T., Lass, M., Mazur, L., Meyer, M., Nitsche, H., Riebler, H., Schade, R., Schwarz, M., Winnwa, N., Wiens, A., Wu, X., Plessl, C., &#38; Simon, J. (2024). Noctua 2 Supercomputer. <i>Journal of Large-Scale Research Facilities</i>, <i>9</i>. <a href=\"https://doi.org/10.17815/jlsrf-8-187 \">https://doi.org/10.17815/jlsrf-8-187 </a>"},"intvolume":"         9","date_updated":"2024-04-26T08:44:30Z","oa":"1","author":[{"full_name":"Bauer, Carsten","id":"90082","last_name":"Bauer","first_name":"Carsten"},{"full_name":"Kenter, Tobias","id":"3145","last_name":"Kenter","first_name":"Tobias"},{"last_name":"Lass","orcid":"0000-0002-5708-7632","id":"24135","full_name":"Lass, Michael","first_name":"Michael"},{"first_name":"Lukas","orcid":" 0000-0001-6304-7082","last_name":"Mazur","id":"90492","full_name":"Mazur, Lukas"},{"first_name":"Marius","full_name":"Meyer, Marius","id":"40778","last_name":"Meyer"},{"last_name":"Nitsche","full_name":"Nitsche, Holger","id":"15272","first_name":"Holger"},{"id":"8961","full_name":"Riebler, Heinrich","last_name":"Riebler","first_name":"Heinrich"},{"first_name":"Robert","last_name":"Schade","orcid":"0000-0002-6268-5397","full_name":"Schade, Robert","id":"75963"},{"first_name":"Michael","last_name":"Schwarz","id":"5312","full_name":"Schwarz, Michael"},{"first_name":"Nils","id":"61189","full_name":"Winnwa, Nils","last_name":"Winnwa"},{"first_name":"Alex","full_name":"Wiens, Alex","id":"23522","last_name":"Wiens","orcid":"0000-0003-1764-9773"},{"first_name":"Xin","id":"77439","full_name":"Wu, Xin","last_name":"Wu"},{"first_name":"Christian","id":"16153","full_name":"Plessl, Christian","last_name":"Plessl","orcid":"0000-0001-5728-9982"},{"id":"15273","full_name":"Simon, Jens","last_name":"Simon","first_name":"Jens"}],"volume":9,"doi":"10.17815/jlsrf-8-187 ","publication":"Journal of large-scale research facilities","abstract":[{"text":"Noctua 2 is a supercomputer operated at the Paderborn Center for Parallel Computing (PC2) at Paderborn University in Germany. Noctua 2 was inaugurated in 2022 and is an Atos BullSequana XH2000 system. It consists mainly of three node types: 1) CPU Compute nodes with AMD EPYC processors in different main memory configurations, 2) GPU nodes with NVIDIA A100 GPUs, and 3) FPGA nodes with Xilinx Alveo U280 and Intel Stratix 10 FPGA cards. While CPUs and GPUs are known off-the-shelf components in HPC systems, the operation of a large number of FPGA cards from different vendors and a dedicated FPGA-to-FPGA network are unique characteristics of Noctua 2. This paper describes in detail the overall setup of Noctua 2 and gives insights into the operation of the cluster from a hardware, software and facility perspective.","lang":"eng"}],"file":[{"file_size":3825480,"file_id":"53664","file_name":"Noctua2_Supercomputer.pdf","access_level":"open_access","date_updated":"2024-04-26T08:35:17Z","creator":"deffel","date_created":"2024-04-26T07:30:20Z","relation":"main_file","content_type":"application/pdf"}],"ddc":["004"],"keyword":["Noctua 2","Supercomputer","FPGA","PC2","Paderborn Center for Parallel Computing"],"language":[{"iso":"eng"}],"year":"2024","date_created":"2024-04-26T07:39:41Z","title":"Noctua 2 Supercomputer"},{"language":[{"iso":"eng"}],"keyword":["Catalysis","General Chemistry","pc2-ressources","Computing Resources Provided by the Paderborn Center for Parallel Computing"],"user_id":"44418","_id":"46547","status":"public","publication":"ACS Catalysis","type":"journal_article","doi":"10.1021/acscatal.3c02092","title":"Direct Synthesis of Acetone by Aerobic Propane Oxidation Promoted by Photoactive Iron(III) Chloride under Mild Conditions","volume":13,"author":[{"first_name":"Andrea","full_name":"Rogolino, Andrea","last_name":"Rogolino"},{"first_name":"José B. G.","full_name":"Filho, José B. G.","last_name":"Filho"},{"first_name":"Lorena","id":"44418","full_name":"Fritsch, Lorena","last_name":"Fritsch"},{"full_name":"Ardisson, José D.","last_name":"Ardisson","first_name":"José D."},{"first_name":"Marcos A. R.","full_name":"da Silva, Marcos A. R.","last_name":"da Silva"},{"first_name":"Gabriel Ali","last_name":"Atta Diab","full_name":"Atta Diab, Gabriel Ali"},{"first_name":"Ingrid Fernandes","last_name":"Silva","full_name":"Silva, Ingrid Fernandes"},{"first_name":"Carlos André Ferreira","full_name":"Moraes, Carlos André Ferreira","last_name":"Moraes"},{"full_name":"Forim, Moacir Rossi","last_name":"Forim","first_name":"Moacir Rossi"},{"first_name":"Matthias","last_name":"Bauer","orcid":"0000-0002-9294-6076","full_name":"Bauer, Matthias","id":"47241"},{"full_name":"Kühne, Thomas D.","last_name":"Kühne","first_name":"Thomas D."},{"last_name":"Antonietti","full_name":"Antonietti, Markus","first_name":"Markus"},{"first_name":"Ivo F.","full_name":"Teixeira, Ivo F.","last_name":"Teixeira"}],"date_created":"2023-08-16T14:44:11Z","date_updated":"2024-03-07T09:34:41Z","publisher":"American Chemical Society (ACS)","page":"8662-8669","intvolume":"        13","citation":{"ieee":"A. Rogolino <i>et al.</i>, “Direct Synthesis of Acetone by Aerobic Propane Oxidation Promoted by Photoactive Iron(III) Chloride under Mild Conditions,” <i>ACS Catalysis</i>, vol. 13, no. 13, pp. 8662–8669, 2023, doi: <a href=\"https://doi.org/10.1021/acscatal.3c02092\">10.1021/acscatal.3c02092</a>.","chicago":"Rogolino, Andrea, José B. G. Filho, Lorena Fritsch, José D. Ardisson, Marcos A. R. da Silva, Gabriel Ali Atta Diab, Ingrid Fernandes Silva, et al. “Direct Synthesis of Acetone by Aerobic Propane Oxidation Promoted by Photoactive Iron(III) Chloride under Mild Conditions.” <i>ACS Catalysis</i> 13, no. 13 (2023): 8662–69. <a href=\"https://doi.org/10.1021/acscatal.3c02092\">https://doi.org/10.1021/acscatal.3c02092</a>.","ama":"Rogolino A, Filho JBG, Fritsch L, et al. Direct Synthesis of Acetone by Aerobic Propane Oxidation Promoted by Photoactive Iron(III) Chloride under Mild Conditions. <i>ACS Catalysis</i>. 2023;13(13):8662-8669. doi:<a href=\"https://doi.org/10.1021/acscatal.3c02092\">10.1021/acscatal.3c02092</a>","mla":"Rogolino, Andrea, et al. “Direct Synthesis of Acetone by Aerobic Propane Oxidation Promoted by Photoactive Iron(III) Chloride under Mild Conditions.” <i>ACS Catalysis</i>, vol. 13, no. 13, American Chemical Society (ACS), 2023, pp. 8662–69, doi:<a href=\"https://doi.org/10.1021/acscatal.3c02092\">10.1021/acscatal.3c02092</a>.","bibtex":"@article{Rogolino_Filho_Fritsch_Ardisson_da Silva_Atta Diab_Silva_Moraes_Forim_Bauer_et al._2023, title={Direct Synthesis of Acetone by Aerobic Propane Oxidation Promoted by Photoactive Iron(III) Chloride under Mild Conditions}, volume={13}, DOI={<a href=\"https://doi.org/10.1021/acscatal.3c02092\">10.1021/acscatal.3c02092</a>}, number={13}, journal={ACS Catalysis}, publisher={American Chemical Society (ACS)}, author={Rogolino, Andrea and Filho, José B. G. and Fritsch, Lorena and Ardisson, José D. and da Silva, Marcos A. R. and Atta Diab, Gabriel Ali and Silva, Ingrid Fernandes and Moraes, Carlos André Ferreira and Forim, Moacir Rossi and Bauer, Matthias and et al.}, year={2023}, pages={8662–8669} }","short":"A. Rogolino, J.B.G. Filho, L. Fritsch, J.D. Ardisson, M.A.R. da Silva, G.A. Atta Diab, I.F. Silva, C.A.F. Moraes, M.R. Forim, M. Bauer, T.D. Kühne, M. Antonietti, I.F. Teixeira, ACS Catalysis 13 (2023) 8662–8669.","apa":"Rogolino, A., Filho, J. B. G., Fritsch, L., Ardisson, J. D., da Silva, M. A. R., Atta Diab, G. A., Silva, I. F., Moraes, C. A. F., Forim, M. R., Bauer, M., Kühne, T. D., Antonietti, M., &#38; Teixeira, I. F. (2023). Direct Synthesis of Acetone by Aerobic Propane Oxidation Promoted by Photoactive Iron(III) Chloride under Mild Conditions. <i>ACS Catalysis</i>, <i>13</i>(13), 8662–8669. <a href=\"https://doi.org/10.1021/acscatal.3c02092\">https://doi.org/10.1021/acscatal.3c02092</a>"},"year":"2023","issue":"13","publication_identifier":{"issn":["2155-5435","2155-5435"]},"publication_status":"published"},{"publication_status":"published","publication_identifier":{"issn":["2079-9292"]},"year":"2021","citation":{"chicago":"Granhão, Daniel, and João Canas Canas Ferreira. “Transparent Control Flow Transfer between CPU and Accelerators for HPC.” <i>Electronics</i>, 2021. <a href=\"https://doi.org/10.3390/electronics10040406\">https://doi.org/10.3390/electronics10040406</a>.","ieee":"D. Granhão and J. C. Canas Ferreira, “Transparent Control Flow Transfer between CPU and Accelerators for HPC,” <i>Electronics</i>, 2021.","ama":"Granhão D, Canas Ferreira JC. Transparent Control Flow Transfer between CPU and Accelerators for HPC. <i>Electronics</i>. 2021. doi:<a href=\"https://doi.org/10.3390/electronics10040406\">10.3390/electronics10040406</a>","bibtex":"@article{Granhão_Canas Ferreira_2021, title={Transparent Control Flow Transfer between CPU and Accelerators for HPC}, DOI={<a href=\"https://doi.org/10.3390/electronics10040406\">10.3390/electronics10040406</a>}, number={406}, journal={Electronics}, author={Granhão, Daniel and Canas Ferreira, João Canas}, year={2021} }","short":"D. Granhão, J.C. Canas Ferreira, Electronics (2021).","mla":"Granhão, Daniel, and João Canas Canas Ferreira. “Transparent Control Flow Transfer between CPU and Accelerators for HPC.” <i>Electronics</i>, 406, 2021, doi:<a href=\"https://doi.org/10.3390/electronics10040406\">10.3390/electronics10040406</a>.","apa":"Granhão, D., &#38; Canas Ferreira, J. C. (2021). Transparent Control Flow Transfer between CPU and Accelerators for HPC. <i>Electronics</i>. <a href=\"https://doi.org/10.3390/electronics10040406\">https://doi.org/10.3390/electronics10040406</a>"},"date_updated":"2022-01-06T06:54:49Z","date_created":"2021-02-12T07:22:03Z","author":[{"first_name":"Daniel","last_name":"Granhão","full_name":"Granhão, Daniel"},{"last_name":"Canas Ferreira","full_name":"Canas Ferreira, João Canas","first_name":"João Canas"}],"title":"Transparent Control Flow Transfer between CPU and Accelerators for HPC","doi":"10.3390/electronics10040406","type":"journal_article","publication":"Electronics","abstract":[{"text":"<jats:p>Heterogeneous platforms with FPGAs have started to be employed in the High-Performance Computing (HPC) field to improve performance and overall efficiency. These platforms allow the use of specialized hardware to accelerate software applications, but require the software to be adapted in what can be a prolonged and complex process. The main goal of this work is to describe and evaluate mechanisms that can transparently transfer the control flow between CPU and FPGA within the scope of HPC. Combining such a mechanism with transparent software profiling and accelerator configuration could lead to an automatic way of accelerating regular applications. In this work, a mechanism based on the ptrace system call is proposed, and its performance on the Intel Xeon+FPGA platform is evaluated. The feasibility of the proposed approach is demonstrated by a working prototype that performs the transparent control flow transfer of any function call to a matching hardware accelerator. This approach is more general than shared library interposition at the cost of a small time overhead in each accelerator use (about 1.3ms in the prototype implementation).</jats:p>","lang":"eng"}],"status":"public","_id":"21208","user_id":"61189","article_number":"406","keyword":["pc2-harp-ressources"],"language":[{"iso":"eng"}]},{"user_id":"3145","project":[{"name":"PC2: Computing Resources Provided by the Paderborn Center for Parallel Computing","_id":"52"}],"_id":"35131","language":[{"iso":"eng"}],"keyword":["pc2-harp-ressources"],"type":"conference","publication":"2021 31st International Conference on Field-Programmable Logic and Applications (FPL)","status":"public","abstract":[{"text":"An FPGA accelerator for the computation of the semi-global Levenshtein distance between a pattern and a reference text is presented. The accelerator provides an important benefit to reduce the execution time of read-mappers used in short-read genomic sequencing. Previous attempts to solve the same problem in FPGA use the Myers algorithm following a column approach to compute the dynamic programming table. We use an approach based on diagonals that allows for some resource savings while maintaining a very high throughput of 1 alignment per clock cycle. The design is implemented in OpenCL and tested on two FPGA accelerators. The maximum performance obtained is 91.5 MPairs/s for 100 × 120 sequences and 47 MPairs/s for 300 × 360 sequences, the highest ever reported for this problem.","lang":"eng"}],"author":[{"full_name":"Castells-Rufas, David","last_name":"Castells-Rufas","first_name":"David"},{"first_name":"Santiago","full_name":"Marco-Sola, Santiago","last_name":"Marco-Sola"},{"first_name":"Quim","last_name":"Aguado-Puig","full_name":"Aguado-Puig, Quim"},{"last_name":"Espinosa-Morales","full_name":"Espinosa-Morales, Antonio","first_name":"Antonio"},{"last_name":"Moure","full_name":"Moure, Juan Carlos","first_name":"Juan Carlos"},{"last_name":"Alvarez","full_name":"Alvarez, Lluc","first_name":"Lluc"},{"full_name":"Moreto, Miquel","last_name":"Moreto","first_name":"Miquel"}],"date_created":"2023-01-03T10:05:13Z","publisher":"IEEE","date_updated":"2024-01-22T09:56:25Z","doi":"10.1109/fpl53798.2021.00036","title":"OpenCL-based FPGA Accelerator for Semi-Global Approximate String Matching Using Diagonal Bit-Vectors","publication_status":"published","quality_controlled":"1","citation":{"apa":"Castells-Rufas, D., Marco-Sola, S., Aguado-Puig, Q., Espinosa-Morales, A., Moure, J. C., Alvarez, L., &#38; Moreto, M. (2021). OpenCL-based FPGA Accelerator for Semi-Global Approximate String Matching Using Diagonal Bit-Vectors. <i>2021 31st International Conference on Field-Programmable Logic and Applications (FPL)</i>. <a href=\"https://doi.org/10.1109/fpl53798.2021.00036\">https://doi.org/10.1109/fpl53798.2021.00036</a>","short":"D. Castells-Rufas, S. Marco-Sola, Q. Aguado-Puig, A. Espinosa-Morales, J.C. Moure, L. Alvarez, M. Moreto, in: 2021 31st International Conference on Field-Programmable Logic and Applications (FPL), IEEE, 2021.","mla":"Castells-Rufas, David, et al. “OpenCL-Based FPGA Accelerator for Semi-Global Approximate String Matching Using Diagonal Bit-Vectors.” <i>2021 31st International Conference on Field-Programmable Logic and Applications (FPL)</i>, IEEE, 2021, doi:<a href=\"https://doi.org/10.1109/fpl53798.2021.00036\">10.1109/fpl53798.2021.00036</a>.","bibtex":"@inproceedings{Castells-Rufas_Marco-Sola_Aguado-Puig_Espinosa-Morales_Moure_Alvarez_Moreto_2021, title={OpenCL-based FPGA Accelerator for Semi-Global Approximate String Matching Using Diagonal Bit-Vectors}, DOI={<a href=\"https://doi.org/10.1109/fpl53798.2021.00036\">10.1109/fpl53798.2021.00036</a>}, booktitle={2021 31st International Conference on Field-Programmable Logic and Applications (FPL)}, publisher={IEEE}, author={Castells-Rufas, David and Marco-Sola, Santiago and Aguado-Puig, Quim and Espinosa-Morales, Antonio and Moure, Juan Carlos and Alvarez, Lluc and Moreto, Miquel}, year={2021} }","ieee":"D. Castells-Rufas <i>et al.</i>, “OpenCL-based FPGA Accelerator for Semi-Global Approximate String Matching Using Diagonal Bit-Vectors,” 2021, doi: <a href=\"https://doi.org/10.1109/fpl53798.2021.00036\">10.1109/fpl53798.2021.00036</a>.","chicago":"Castells-Rufas, David, Santiago Marco-Sola, Quim Aguado-Puig, Antonio Espinosa-Morales, Juan Carlos Moure, Lluc Alvarez, and Miquel Moreto. “OpenCL-Based FPGA Accelerator for Semi-Global Approximate String Matching Using Diagonal Bit-Vectors.” In <i>2021 31st International Conference on Field-Programmable Logic and Applications (FPL)</i>. IEEE, 2021. <a href=\"https://doi.org/10.1109/fpl53798.2021.00036\">https://doi.org/10.1109/fpl53798.2021.00036</a>.","ama":"Castells-Rufas D, Marco-Sola S, Aguado-Puig Q, et al. OpenCL-based FPGA Accelerator for Semi-Global Approximate String Matching Using Diagonal Bit-Vectors. In: <i>2021 31st International Conference on Field-Programmable Logic and Applications (FPL)</i>. IEEE; 2021. doi:<a href=\"https://doi.org/10.1109/fpl53798.2021.00036\">10.1109/fpl53798.2021.00036</a>"},"year":"2021"},{"title":"Non-adiabatic transitions in the reaction of fluorine with methane","doi":"10.1063/5.0013852","date_updated":"2022-01-06T06:54:06Z","date_created":"2020-09-17T07:35:18Z","author":[{"last_name":"Zhao","full_name":"Zhao, Bin","first_name":"Bin"},{"last_name":"Manthe","full_name":"Manthe, Uwe","first_name":"Uwe"}],"year":"2020","citation":{"short":"B. Zhao, U. Manthe, The Journal of Chemical Physics (2020).","bibtex":"@article{Zhao_Manthe_2020, title={Non-adiabatic transitions in the reaction of fluorine with methane}, DOI={<a href=\"https://doi.org/10.1063/5.0013852\">10.1063/5.0013852</a>}, number={231102}, journal={The Journal of Chemical Physics}, author={Zhao, Bin and Manthe, Uwe}, year={2020} }","mla":"Zhao, Bin, and Uwe Manthe. “Non-Adiabatic Transitions in the Reaction of Fluorine with Methane.” <i>The Journal of Chemical Physics</i>, 231102, 2020, doi:<a href=\"https://doi.org/10.1063/5.0013852\">10.1063/5.0013852</a>.","apa":"Zhao, B., &#38; Manthe, U. (2020). Non-adiabatic transitions in the reaction of fluorine with methane. <i>The Journal of Chemical Physics</i>. <a href=\"https://doi.org/10.1063/5.0013852\">https://doi.org/10.1063/5.0013852</a>","ieee":"B. Zhao and U. Manthe, “Non-adiabatic transitions in the reaction of fluorine with methane,” <i>The Journal of Chemical Physics</i>, 2020.","chicago":"Zhao, Bin, and Uwe Manthe. “Non-Adiabatic Transitions in the Reaction of Fluorine with Methane.” <i>The Journal of Chemical Physics</i>, 2020. <a href=\"https://doi.org/10.1063/5.0013852\">https://doi.org/10.1063/5.0013852</a>.","ama":"Zhao B, Manthe U. 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Behler, Physical Review B (2020).","mla":"Eckhoff, Marco, et al. “Hybrid Density Functional Theory Benchmark Study on Lithium Manganese Oxides.” <i>Physical Review B</i>, 2020, doi:<a href=\"https://doi.org/10.1103/physrevb.101.205113\">10.1103/physrevb.101.205113</a>.","bibtex":"@article{Eckhoff_Blöchl_Behler_2020, title={Hybrid density functional theory benchmark study on lithium manganese oxides}, DOI={<a href=\"https://doi.org/10.1103/physrevb.101.205113\">10.1103/physrevb.101.205113</a>}, journal={Physical Review B}, author={Eckhoff, Marco and Blöchl, Peter E. and Behler, Jörg}, year={2020} }"},"_id":"19503","project":[{"name":"Computing Resources Provided by the Paderborn Center for Parallel Computing","_id":"52"}],"user_id":"61189","keyword":["pc2-ressources"],"language":[{"iso":"eng"}],"publication":"Physical Review B","type":"journal_article","status":"public"},{"date_created":"2020-09-17T07:50:19Z","author":[{"last_name":"Barkhausen","full_name":"Barkhausen, Franziska","first_name":"Franziska"},{"first_name":"Stefan","full_name":"Schumacher, Stefan","last_name":"Schumacher"},{"last_name":"Ma","full_name":"Ma, Xuekai","first_name":"Xuekai"}],"date_updated":"2022-01-06T06:54:06Z","doi":"10.1364/ol.386250","title":"Multistable circular currents of polariton condensates trapped in ring potentials","publication_identifier":{"issn":["0146-9592","1539-4794"]},"publication_status":"published","citation":{"ama":"Barkhausen F, Schumacher S, Ma X. 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Ma, Optics Letters (2020).","bibtex":"@article{Barkhausen_Schumacher_Ma_2020, title={Multistable circular currents of polariton condensates trapped in ring potentials}, DOI={<a href=\"https://doi.org/10.1364/ol.386250\">10.1364/ol.386250</a>}, number={1192}, journal={Optics Letters}, author={Barkhausen, Franziska and Schumacher, Stefan and Ma, Xuekai}, year={2020} }","mla":"Barkhausen, Franziska, et al. “Multistable Circular Currents of Polariton Condensates Trapped in Ring Potentials.” <i>Optics Letters</i>, 1192, 2020, doi:<a href=\"https://doi.org/10.1364/ol.386250\">10.1364/ol.386250</a>."},"year":"2020","user_id":"61189","_id":"19507","project":[{"name":"Computing Resources Provided by the Paderborn Center for Parallel Computing","_id":"52"}],"language":[{"iso":"eng"}],"keyword":["pc2-ressources"],"article_number":"1192","publication":"Optics Letters","type":"journal_article","status":"public"},{"author":[{"first_name":"Matthias","full_name":"Pukrop, Matthias","last_name":"Pukrop"},{"first_name":"Stefan","last_name":"Schumacher","full_name":"Schumacher, Stefan"}],"date_created":"2020-09-17T07:56:54Z","date_updated":"2022-01-06T06:54:06Z","doi":"10.1103/physreve.101.012207","title":"Externally controlled Lotka-Volterra dynamics in a linearly polarized polariton fluid","publication_status":"published","publication_identifier":{"issn":["2470-0045","2470-0053"]},"citation":{"ama":"Pukrop M, Schumacher S. Externally controlled Lotka-Volterra dynamics in a linearly polarized polariton fluid. <i>Physical Review E</i>. 2020. doi:<a href=\"https://doi.org/10.1103/physreve.101.012207\">10.1103/physreve.101.012207</a>","ieee":"M. Pukrop and S. Schumacher, “Externally controlled Lotka-Volterra dynamics in a linearly polarized polariton fluid,” <i>Physical Review E</i>, 2020.","chicago":"Pukrop, Matthias, and Stefan Schumacher. “Externally Controlled Lotka-Volterra Dynamics in a Linearly Polarized Polariton Fluid.” <i>Physical Review E</i>, 2020. <a href=\"https://doi.org/10.1103/physreve.101.012207\">https://doi.org/10.1103/physreve.101.012207</a>.","apa":"Pukrop, M., &#38; Schumacher, S. (2020). Externally controlled Lotka-Volterra dynamics in a linearly polarized polariton fluid. <i>Physical Review E</i>. <a href=\"https://doi.org/10.1103/physreve.101.012207\">https://doi.org/10.1103/physreve.101.012207</a>","short":"M. Pukrop, S. Schumacher, Physical Review E (2020).","bibtex":"@article{Pukrop_Schumacher_2020, title={Externally controlled Lotka-Volterra dynamics in a linearly polarized polariton fluid}, DOI={<a href=\"https://doi.org/10.1103/physreve.101.012207\">10.1103/physreve.101.012207</a>}, journal={Physical Review E}, author={Pukrop, Matthias and Schumacher, Stefan}, year={2020} }","mla":"Pukrop, Matthias, and Stefan Schumacher. “Externally Controlled Lotka-Volterra Dynamics in a Linearly Polarized Polariton Fluid.” <i>Physical Review E</i>, 2020, doi:<a href=\"https://doi.org/10.1103/physreve.101.012207\">10.1103/physreve.101.012207</a>."},"year":"2020","user_id":"61189","project":[{"_id":"52","name":"Computing Resources Provided by the Paderborn Center for Parallel Computing"}],"_id":"19511","language":[{"iso":"eng"}],"keyword":["pc2-ressources"],"type":"journal_article","publication":"Physical Review E","status":"public"},{"publication_status":"published","publication_identifier":{"issn":["1366-5545"]},"year":"2020","citation":{"ieee":"C. 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Minimizing crane times in pre-marshalling problems. <i>Transportation Research Part E: Logistics and Transportation Review</i>. <a href=\"https://doi.org/10.1016/j.tre.2020.101917\">https://doi.org/10.1016/j.tre.2020.101917</a>","mla":"Parreño-Torres, Consuelo, et al. “Minimizing Crane Times in Pre-Marshalling Problems.” <i>Transportation Research Part E: Logistics and Transportation Review</i>, 101917, 2020, doi:<a href=\"https://doi.org/10.1016/j.tre.2020.101917\">10.1016/j.tre.2020.101917</a>.","bibtex":"@article{Parreño-Torres_Alvarez-Valdes_Ruiz_Tierney_2020, title={Minimizing crane times in pre-marshalling problems}, DOI={<a href=\"https://doi.org/10.1016/j.tre.2020.101917\">10.1016/j.tre.2020.101917</a>}, number={101917}, journal={Transportation Research Part E: Logistics and Transportation Review}, author={Parreño-Torres, Consuelo and Alvarez-Valdes, Ramon and Ruiz, Rubén and Tierney, Kevin}, year={2020} }","short":"C. Parreño-Torres, R. Alvarez-Valdes, R. Ruiz, K. Tierney, Transportation Research Part E: Logistics and Transportation Review (2020)."},"date_updated":"2022-01-06T06:54:07Z","author":[{"first_name":"Consuelo","last_name":"Parreño-Torres","full_name":"Parreño-Torres, Consuelo"},{"first_name":"Ramon","full_name":"Alvarez-Valdes, Ramon","last_name":"Alvarez-Valdes"},{"last_name":"Ruiz","full_name":"Ruiz, Rubén","first_name":"Rubén"},{"first_name":"Kevin","full_name":"Tierney, Kevin","last_name":"Tierney"}],"date_created":"2020-09-18T07:52:23Z","title":"Minimizing crane times in pre-marshalling problems","doi":"10.1016/j.tre.2020.101917","type":"journal_article","publication":"Transportation Research Part E: Logistics and Transportation Review","status":"public","project":[{"name":"Computing Resources Provided by the Paderborn Center for Parallel Computing","_id":"52"}],"_id":"19560","user_id":"61189","article_number":"101917","keyword":["pc2-ressources"],"language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["9783030535513","9783030535520"]},"publication_status":"published","year":"2020","place":"Cham","citation":{"mla":"Sellmann, Meinolf, and Kevin Tierney. “Hyper-Parameterized Dialectic Search for Non-Linear Box-Constrained Optimization with Heterogenous Variable Types.” <i>Lecture Notes in Computer Science</i>, 2020, doi:<a href=\"https://doi.org/10.1007/978-3-030-53552-0_12\">10.1007/978-3-030-53552-0_12</a>.","bibtex":"@inbook{Sellmann_Tierney_2020, place={Cham}, title={Hyper-parameterized Dialectic Search for Non-linear Box-Constrained Optimization with Heterogenous Variable Types}, DOI={<a href=\"https://doi.org/10.1007/978-3-030-53552-0_12\">10.1007/978-3-030-53552-0_12</a>}, booktitle={Lecture Notes in Computer Science}, author={Sellmann, Meinolf and Tierney, Kevin}, year={2020} }","short":"M. 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Hyper-parameterized Dialectic Search for Non-linear Box-Constrained Optimization with Heterogenous Variable Types. In: <i>Lecture Notes in Computer Science</i>. Cham; 2020. doi:<a href=\"https://doi.org/10.1007/978-3-030-53552-0_12\">10.1007/978-3-030-53552-0_12</a>"},"date_updated":"2022-01-06T06:54:07Z","date_created":"2020-09-18T07:54:06Z","author":[{"full_name":"Sellmann, Meinolf","last_name":"Sellmann","first_name":"Meinolf"},{"first_name":"Kevin","full_name":"Tierney, Kevin","last_name":"Tierney"}],"title":"Hyper-parameterized Dialectic Search for Non-linear Box-Constrained Optimization with Heterogenous Variable Types","doi":"10.1007/978-3-030-53552-0_12","publication":"Lecture Notes in Computer Science","type":"book_chapter","status":"public","_id":"19561","project":[{"_id":"52","name":"Computing Resources Provided by the Paderborn Center for Parallel Computing"}],"user_id":"61189","keyword":["pc2-ressources"],"language":[{"iso":"eng"}]},{"status":"public","publication":"Journal of Heuristics","type":"journal_article","language":[{"iso":"eng"}],"keyword":["pc2-ressources"],"user_id":"61189","_id":"19562","project":[{"_id":"52","name":"Computing Resources Provided by the Paderborn Center for Parallel Computing"}],"citation":{"short":"S. Kuhlemann, K. Tierney, Journal of Heuristics (2020).","bibtex":"@article{Kuhlemann_Tierney_2020, title={A genetic algorithm for finding realistic sea routes considering the weather}, DOI={<a href=\"https://doi.org/10.1007/s10732-020-09449-7\">10.1007/s10732-020-09449-7</a>}, journal={Journal of Heuristics}, author={Kuhlemann, Stefan and Tierney, Kevin}, year={2020} }","mla":"Kuhlemann, Stefan, and Kevin Tierney. “A Genetic Algorithm for Finding Realistic Sea Routes Considering the Weather.” <i>Journal of Heuristics</i>, 2020, doi:<a href=\"https://doi.org/10.1007/s10732-020-09449-7\">10.1007/s10732-020-09449-7</a>.","apa":"Kuhlemann, S., &#38; Tierney, K. (2020). A genetic algorithm for finding realistic sea routes considering the weather. <i>Journal of Heuristics</i>. <a href=\"https://doi.org/10.1007/s10732-020-09449-7\">https://doi.org/10.1007/s10732-020-09449-7</a>","chicago":"Kuhlemann, Stefan, and Kevin Tierney. “A Genetic Algorithm for Finding Realistic Sea Routes Considering the Weather.” <i>Journal of Heuristics</i>, 2020. <a href=\"https://doi.org/10.1007/s10732-020-09449-7\">https://doi.org/10.1007/s10732-020-09449-7</a>.","ieee":"S. Kuhlemann and K. Tierney, “A genetic algorithm for finding realistic sea routes considering the weather,” <i>Journal of Heuristics</i>, 2020.","ama":"Kuhlemann S, Tierney K. A genetic algorithm for finding realistic sea routes considering the weather. <i>Journal of Heuristics</i>. 2020. doi:<a href=\"https://doi.org/10.1007/s10732-020-09449-7\">10.1007/s10732-020-09449-7</a>"},"year":"2020","publication_identifier":{"issn":["1381-1231","1572-9397"]},"publication_status":"published","doi":"10.1007/s10732-020-09449-7","title":"A genetic algorithm for finding realistic sea routes considering the weather","date_created":"2020-09-18T07:56:45Z","author":[{"first_name":"Stefan","last_name":"Kuhlemann","full_name":"Kuhlemann, Stefan"},{"first_name":"Kevin","last_name":"Tierney","full_name":"Tierney, Kevin"}],"date_updated":"2022-01-06T06:54:07Z"},{"title":"Exploration of FPGA-Based Hardware Designs for QR Decomposition for Solving Stiff ODE Numerical Methods Using the HARP Hybrid Architecture","doi":"10.3390/electronics9050843","date_updated":"2022-01-06T06:53:09Z","author":[{"first_name":"Carlos","last_name":"Alberto Oliveira de Souza Junior","full_name":"Alberto Oliveira de Souza Junior, Carlos"},{"full_name":"Bispo, João","last_name":"Bispo","first_name":"João"},{"first_name":"João M. P.","full_name":"Cardoso, João M. P.","last_name":"Cardoso"},{"full_name":"Diniz, Pedro C.","last_name":"Diniz","first_name":"Pedro C."},{"full_name":"Marques, Eduardo","last_name":"Marques","first_name":"Eduardo"}],"date_created":"2020-07-08T08:18:59Z","year":"2020","citation":{"ieee":"C. Alberto Oliveira de Souza Junior, J. Bispo, J. M. P. Cardoso, P. C. Diniz, and E. Marques, “Exploration of FPGA-Based Hardware Designs for QR Decomposition for Solving Stiff ODE Numerical Methods Using the HARP Hybrid Architecture,” <i>Electronics</i>, 2020.","chicago":"Alberto Oliveira de Souza Junior, Carlos, João Bispo, João M. P. Cardoso, Pedro C. Diniz, and Eduardo Marques. “Exploration of FPGA-Based Hardware Designs for QR Decomposition for Solving Stiff ODE Numerical Methods Using the HARP Hybrid Architecture.” <i>Electronics</i>, 2020. <a href=\"https://doi.org/10.3390/electronics9050843\">https://doi.org/10.3390/electronics9050843</a>.","ama":"Alberto Oliveira de Souza Junior C, Bispo J, Cardoso JMP, Diniz PC, Marques E. Exploration of FPGA-Based Hardware Designs for QR Decomposition for Solving Stiff ODE Numerical Methods Using the HARP Hybrid Architecture. <i>Electronics</i>. 2020. doi:<a href=\"https://doi.org/10.3390/electronics9050843\">10.3390/electronics9050843</a>","bibtex":"@article{Alberto Oliveira de Souza Junior_Bispo_Cardoso_Diniz_Marques_2020, title={Exploration of FPGA-Based Hardware Designs for QR Decomposition for Solving Stiff ODE Numerical Methods Using the HARP Hybrid Architecture}, DOI={<a href=\"https://doi.org/10.3390/electronics9050843\">10.3390/electronics9050843</a>}, number={843}, journal={Electronics}, author={Alberto Oliveira de Souza Junior, Carlos and Bispo, João and Cardoso, João M. P. and Diniz, Pedro C. and Marques, Eduardo}, year={2020} }","short":"C. Alberto Oliveira de Souza Junior, J. Bispo, J.M.P. Cardoso, P.C. Diniz, E. Marques, Electronics (2020).","mla":"Alberto Oliveira de Souza Junior, Carlos, et al. “Exploration of FPGA-Based Hardware Designs for QR Decomposition for Solving Stiff ODE Numerical Methods Using the HARP Hybrid Architecture.” <i>Electronics</i>, 843, 2020, doi:<a href=\"https://doi.org/10.3390/electronics9050843\">10.3390/electronics9050843</a>.","apa":"Alberto Oliveira de Souza Junior, C., Bispo, J., Cardoso, J. M. P., Diniz, P. C., &#38; Marques, E. (2020). Exploration of FPGA-Based Hardware Designs for QR Decomposition for Solving Stiff ODE Numerical Methods Using the HARP Hybrid Architecture. <i>Electronics</i>. <a href=\"https://doi.org/10.3390/electronics9050843\">https://doi.org/10.3390/electronics9050843</a>"},"publication_status":"published","publication_identifier":{"issn":["2079-9292"]},"article_number":"843","keyword":["pc2-harp-ressources"],"language":[{"iso":"eng"}],"_id":"17359","user_id":"61189","abstract":[{"text":"<jats:p>In this article, we focus on the acceleration of a chemical reaction simulation that relies on a system of stiff ordinary differential equation (ODEs) targeting heterogeneous computing systems with CPUs and field-programmable gate arrays (FPGAs). Specifically, we target an essential kernel of the coupled chemistry aerosol-tracer transport model to the Brazilian developments on the regional atmospheric modeling system (CCATT-BRAMS). We focus on a linear solve step using the QR factorization based on the modified Gram-Schmidt method as the basis of the ODE solver in this application. We target Intel hardware accelerator research program (HARP) architecture with the OpenCL programming environment for these early experiments. Our design exploration reveals a hardware design that is up to 4 times faster than the original iterative Jacobi method used in this solver. Still, even with hardware support, the overall performance of our QR-based hardware is lower than its original software version.</jats:p>","lang":"eng"}],"status":"public","type":"journal_article","publication":"Electronics"},{"publication":"The Journal of Physical Chemistry C","type":"journal_article","status":"public","user_id":"61189","_id":"20496","project":[{"name":"Computing Resources Provided by the Paderborn Center for Parallel Computing","_id":"52"}],"language":[{"iso":"eng"}],"keyword":["pc2-ressources"],"publication_identifier":{"issn":["1932-7447","1932-7455"]},"publication_status":"published","page":"15007-15014","citation":{"chicago":"Streiter, Martin, Tillmann G. Fischer, Christian Wiebeler, Sebastian Reichert, Jörn Langenickel, Kirsten Zeitler, and Carsten Deibel. “Impact of Chlorine on the Internal Transition Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule 3CzClIPN.” <i>The Journal of Physical Chemistry C</i>, 2020, 15007–14. <a href=\"https://doi.org/10.1021/acs.jpcc.0c03341\">https://doi.org/10.1021/acs.jpcc.0c03341</a>.","ieee":"M. Streiter <i>et al.</i>, “Impact of Chlorine on the Internal Transition Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule 3CzClIPN,” <i>The Journal of Physical Chemistry C</i>, pp. 15007–15014, 2020.","ama":"Streiter M, Fischer TG, Wiebeler C, et al. Impact of Chlorine on the Internal Transition Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule 3CzClIPN. <i>The Journal of Physical Chemistry C</i>. 2020:15007-15014. doi:<a href=\"https://doi.org/10.1021/acs.jpcc.0c03341\">10.1021/acs.jpcc.0c03341</a>","short":"M. Streiter, T.G. Fischer, C. Wiebeler, S. Reichert, J. Langenickel, K. Zeitler, C. Deibel, The Journal of Physical Chemistry C (2020) 15007–15014.","mla":"Streiter, Martin, et al. “Impact of Chlorine on the Internal Transition Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule 3CzClIPN.” <i>The Journal of Physical Chemistry C</i>, 2020, pp. 15007–14, doi:<a href=\"https://doi.org/10.1021/acs.jpcc.0c03341\">10.1021/acs.jpcc.0c03341</a>.","bibtex":"@article{Streiter_Fischer_Wiebeler_Reichert_Langenickel_Zeitler_Deibel_2020, title={Impact of Chlorine on the Internal Transition Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule 3CzClIPN}, DOI={<a href=\"https://doi.org/10.1021/acs.jpcc.0c03341\">10.1021/acs.jpcc.0c03341</a>}, journal={The Journal of Physical Chemistry C}, author={Streiter, Martin and Fischer, Tillmann G. and Wiebeler, Christian and Reichert, Sebastian and Langenickel, Jörn and Zeitler, Kirsten and Deibel, Carsten}, year={2020}, pages={15007–15014} }","apa":"Streiter, M., Fischer, T. G., Wiebeler, C., Reichert, S., Langenickel, J., Zeitler, K., &#38; Deibel, C. (2020). Impact of Chlorine on the Internal Transition Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule 3CzClIPN. <i>The Journal of Physical Chemistry C</i>, 15007–15014. <a href=\"https://doi.org/10.1021/acs.jpcc.0c03341\">https://doi.org/10.1021/acs.jpcc.0c03341</a>"},"year":"2020","author":[{"last_name":"Streiter","full_name":"Streiter, Martin","first_name":"Martin"},{"first_name":"Tillmann G.","full_name":"Fischer, Tillmann G.","last_name":"Fischer"},{"full_name":"Wiebeler, Christian","last_name":"Wiebeler","first_name":"Christian"},{"last_name":"Reichert","full_name":"Reichert, Sebastian","first_name":"Sebastian"},{"first_name":"Jörn","last_name":"Langenickel","full_name":"Langenickel, Jörn"},{"first_name":"Kirsten","last_name":"Zeitler","full_name":"Zeitler, Kirsten"},{"first_name":"Carsten","last_name":"Deibel","full_name":"Deibel, Carsten"}],"date_created":"2020-11-25T07:19:15Z","date_updated":"2022-01-06T06:54:27Z","doi":"10.1021/acs.jpcc.0c03341","title":"Impact of Chlorine on the Internal Transition Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule 3CzClIPN"},{"language":[{"iso":"eng"}],"keyword":["pc2-ressources"],"user_id":"61189","_id":"16953","project":[{"name":"Computing Resources Provided by the Paderborn Center for Parallel Computing","_id":"52"}],"status":"public","abstract":[{"lang":"eng","text":"<jats:title>Abstract</jats:title><jats:p>The C-type lectin receptor langerin plays a vital role in the mammalian defense against invading pathogens. Its function hinges on the affinity to its co-factor Ca<jats:sup>2+</jats:sup> which in turn is regulated by the pH. We studied the structural consequences of pro-tonating the allosteric pH-sensor histidine H294 by molecular dynamics simulations (total simulation time: about 120 μs) and Markov models. We discovered a mechanism in which the signal that the pH has dropped is transferred to the Ca<jats:sup>2+</jats:sup>-binding site without transferring the initial proton. Instead, protonation of H294 unlocks a conformation in which a protonated lysine side-chain forms a hydrogen bond with a Ca<jats:sup>2+</jats:sup>-coordinating aspartic acid. This destabilizes Ca<jats:sup>2+</jats:sup> in the binding pocket, which we probed by steered molecular dynamics. After Ca<jats:sup>2+</jats:sup>-release, the proton is likely transferred to the aspartic acid and stabilized by a dyad with a nearby glutamic acid, triggering a conformational transition and thus preventing Ca<jats:sup>2+</jats:sup>-rebinding.</jats:p>"}],"publication":"bioRxiv","type":"preprint","title":"Molecular Mechanism of the pH-Dependent Calcium Affinity in Langerin","author":[{"first_name":"Jan-O.","last_name":"Joswig","full_name":"Joswig, Jan-O."},{"last_name":"Anders","full_name":"Anders, Jennifer","first_name":"Jennifer"},{"last_name":"Zhang","full_name":"Zhang, Hengxi","first_name":"Hengxi"},{"first_name":"Christoph","full_name":"Rademacher, Christoph","last_name":"Rademacher"},{"full_name":"Keller, Bettina G.","last_name":"Keller","first_name":"Bettina G."}],"date_created":"2020-05-15T07:08:54Z","date_updated":"2022-01-06T06:53:00Z","citation":{"mla":"Joswig, Jan-O., et al. “Molecular Mechanism of the PH-Dependent Calcium Affinity in Langerin.” <i>BioRxiv</i>, 2020.","short":"J.-O. Joswig, J. Anders, H. Zhang, C. Rademacher, B.G. Keller, BioRxiv (2020).","bibtex":"@article{Joswig_Anders_Zhang_Rademacher_Keller_2020, title={Molecular Mechanism of the pH-Dependent Calcium Affinity in Langerin}, journal={bioRxiv}, author={Joswig, Jan-O. and Anders, Jennifer and Zhang, Hengxi and Rademacher, Christoph and Keller, Bettina G.}, year={2020} }","apa":"Joswig, J.-O., Anders, J., Zhang, H., Rademacher, C., &#38; Keller, B. G. (2020). Molecular Mechanism of the pH-Dependent Calcium Affinity in Langerin. <i>BioRxiv</i>.","ama":"Joswig J-O, Anders J, Zhang H, Rademacher C, Keller BG. Molecular Mechanism of the pH-Dependent Calcium Affinity in Langerin. <i>bioRxiv</i>. 2020.","ieee":"J.-O. Joswig, J. Anders, H. Zhang, C. Rademacher, and B. G. Keller, “Molecular Mechanism of the pH-Dependent Calcium Affinity in Langerin,” <i>bioRxiv</i>. 2020.","chicago":"Joswig, Jan-O., Jennifer Anders, Hengxi Zhang, Christoph Rademacher, and Bettina G. Keller. “Molecular Mechanism of the PH-Dependent Calcium Affinity in Langerin.” <i>BioRxiv</i>, 2020."},"year":"2020","publication_status":"published"},{"date_updated":"2022-01-06T06:53:00Z","date_created":"2020-05-15T07:25:13Z","author":[{"first_name":"René Spencer","last_name":"Chatwell","full_name":"Chatwell, René Spencer"},{"first_name":"Jadran","last_name":"Vrabec","full_name":"Vrabec, Jadran"}],"title":"Bulk viscosity of liquid noble gases","doi":"10.1063/1.5142364","publication_identifier":{"issn":["0021-9606","1089-7690"]},"publication_status":"published","year":"2020","citation":{"apa":"Chatwell, R. S., &#38; Vrabec, J. (2020). Bulk viscosity of liquid noble gases. <i>The Journal of Chemical Physics</i>. <a href=\"https://doi.org/10.1063/1.5142364\">https://doi.org/10.1063/1.5142364</a>","mla":"Chatwell, René Spencer, and Jadran Vrabec. “Bulk Viscosity of Liquid Noble Gases.” <i>The Journal of Chemical Physics</i>, 094503, 2020, doi:<a href=\"https://doi.org/10.1063/1.5142364\">10.1063/1.5142364</a>.","bibtex":"@article{Chatwell_Vrabec_2020, title={Bulk viscosity of liquid noble gases}, DOI={<a href=\"https://doi.org/10.1063/1.5142364\">10.1063/1.5142364</a>}, number={094503}, journal={The Journal of Chemical Physics}, author={Chatwell, René Spencer and Vrabec, Jadran}, year={2020} }","short":"R.S. Chatwell, J. Vrabec, The Journal of Chemical Physics (2020).","ama":"Chatwell RS, Vrabec J. Bulk viscosity of liquid noble gases. <i>The Journal of Chemical Physics</i>. 2020. doi:<a href=\"https://doi.org/10.1063/1.5142364\">10.1063/1.5142364</a>","chicago":"Chatwell, René Spencer, and Jadran Vrabec. “Bulk Viscosity of Liquid Noble Gases.” <i>The Journal of Chemical Physics</i>, 2020. <a href=\"https://doi.org/10.1063/1.5142364\">https://doi.org/10.1063/1.5142364</a>.","ieee":"R. S. Chatwell and J. Vrabec, “Bulk viscosity of liquid noble gases,” <i>The Journal of Chemical Physics</i>, 2020."},"_id":"16956","project":[{"_id":"52","name":"Computing Resources Provided by the Paderborn Center for Parallel Computing"}],"user_id":"61189","keyword":["pc2-ressources"],"article_number":"094503","language":[{"iso":"eng"}],"publication":"The Journal of Chemical Physics","type":"journal_article","status":"public"},{"publication_status":"published","publication_identifier":{"issn":["0009-2541"]},"year":"2020","citation":{"apa":"Fodor, M. A., Ható, Z., Kristóf, T., &#38; Pósfai, M. (2020). The role of clay surfaces in the heterogeneous nucleation of calcite: Molecular dynamics simulations of cluster formation and attachment. <i>Chemical Geology</i>. <a href=\"https://doi.org/10.1016/j.chemgeo.2020.119497\">https://doi.org/10.1016/j.chemgeo.2020.119497</a>","mla":"Fodor, Melinda A., et al. “The Role of Clay Surfaces in the Heterogeneous Nucleation of Calcite: Molecular Dynamics Simulations of Cluster Formation and Attachment.” <i>Chemical Geology</i>, 119497, 2020, doi:<a href=\"https://doi.org/10.1016/j.chemgeo.2020.119497\">10.1016/j.chemgeo.2020.119497</a>.","bibtex":"@article{Fodor_Ható_Kristóf_Pósfai_2020, title={The role of clay surfaces in the heterogeneous nucleation of calcite: Molecular dynamics simulations of cluster formation and attachment}, DOI={<a href=\"https://doi.org/10.1016/j.chemgeo.2020.119497\">10.1016/j.chemgeo.2020.119497</a>}, number={119497}, journal={Chemical Geology}, author={Fodor, Melinda A. and Ható, Zoltán and Kristóf, Tamás and Pósfai, Mihály}, year={2020} }","short":"M.A. Fodor, Z. Ható, T. Kristóf, M. Pósfai, Chemical Geology (2020).","ama":"Fodor MA, Ható Z, Kristóf T, Pósfai M. The role of clay surfaces in the heterogeneous nucleation of calcite: Molecular dynamics simulations of cluster formation and attachment. <i>Chemical Geology</i>. 2020. doi:<a href=\"https://doi.org/10.1016/j.chemgeo.2020.119497\">10.1016/j.chemgeo.2020.119497</a>","chicago":"Fodor, Melinda A., Zoltán Ható, Tamás Kristóf, and Mihály Pósfai. “The Role of Clay Surfaces in the Heterogeneous Nucleation of Calcite: Molecular Dynamics Simulations of Cluster Formation and Attachment.” <i>Chemical Geology</i>, 2020. <a href=\"https://doi.org/10.1016/j.chemgeo.2020.119497\">https://doi.org/10.1016/j.chemgeo.2020.119497</a>.","ieee":"M. A. Fodor, Z. Ható, T. Kristóf, and M. Pósfai, “The role of clay surfaces in the heterogeneous nucleation of calcite: Molecular dynamics simulations of cluster formation and attachment,” <i>Chemical Geology</i>, 2020."},"date_updated":"2022-01-06T06:53:00Z","date_created":"2020-05-15T07:25:23Z","author":[{"full_name":"Fodor, Melinda A.","last_name":"Fodor","first_name":"Melinda A."},{"first_name":"Zoltán","full_name":"Ható, Zoltán","last_name":"Ható"},{"first_name":"Tamás","last_name":"Kristóf","full_name":"Kristóf, Tamás"},{"first_name":"Mihály","full_name":"Pósfai, Mihály","last_name":"Pósfai"}],"title":"The role of clay surfaces in the heterogeneous nucleation of calcite: Molecular dynamics simulations of cluster formation and attachment","doi":"10.1016/j.chemgeo.2020.119497","type":"journal_article","publication":"Chemical Geology","status":"public","project":[{"_id":"52","name":"Computing Resources Provided by the Paderborn Center for Parallel Computing"}],"_id":"16957","user_id":"61189","article_number":"119497","keyword":["pc2-ressources"],"language":[{"iso":"eng"}]},{"status":"public","publication":"The Journal of Physical Chemistry C","type":"journal_article","keyword":["pc2-ressources"],"language":[{"iso":"eng"}],"_id":"19504","project":[{"name":"Computing Resources Provided by the Paderborn Center for Parallel Computing","_id":"52"}],"user_id":"61189","year":"2019","page":"30863-30870","citation":{"chicago":"Dong, Chuan-Ding, and Stefan Schumacher. “Molecular Doping of PCPDT–BT Copolymers: Comparison of Molecular Complexes with and without Integer Charge Transfer.” <i>The Journal of Physical Chemistry C</i>, 2019, 30863–70. <a href=\"https://doi.org/10.1021/acs.jpcc.9b09970\">https://doi.org/10.1021/acs.jpcc.9b09970</a>.","ieee":"C.-D. Dong and S. Schumacher, “Molecular Doping of PCPDT–BT Copolymers: Comparison of Molecular Complexes with and without Integer Charge Transfer,” <i>The Journal of Physical Chemistry C</i>, pp. 30863–30870, 2019.","ama":"Dong C-D, Schumacher S. Molecular Doping of PCPDT–BT Copolymers: Comparison of Molecular Complexes with and without Integer Charge Transfer. <i>The Journal of Physical Chemistry C</i>. 2019:30863-30870. doi:<a href=\"https://doi.org/10.1021/acs.jpcc.9b09970\">10.1021/acs.jpcc.9b09970</a>","apa":"Dong, C.-D., &#38; Schumacher, S. (2019). Molecular Doping of PCPDT–BT Copolymers: Comparison of Molecular Complexes with and without Integer Charge Transfer. <i>The Journal of Physical Chemistry C</i>, 30863–30870. <a href=\"https://doi.org/10.1021/acs.jpcc.9b09970\">https://doi.org/10.1021/acs.jpcc.9b09970</a>","short":"C.-D. Dong, S. Schumacher, The Journal of Physical Chemistry C (2019) 30863–30870.","bibtex":"@article{Dong_Schumacher_2019, title={Molecular Doping of PCPDT–BT Copolymers: Comparison of Molecular Complexes with and without Integer Charge Transfer}, DOI={<a href=\"https://doi.org/10.1021/acs.jpcc.9b09970\">10.1021/acs.jpcc.9b09970</a>}, journal={The Journal of Physical Chemistry C}, author={Dong, Chuan-Ding and Schumacher, Stefan}, year={2019}, pages={30863–30870} }","mla":"Dong, Chuan-Ding, and Stefan Schumacher. “Molecular Doping of PCPDT–BT Copolymers: Comparison of Molecular Complexes with and without Integer Charge Transfer.” <i>The Journal of Physical Chemistry C</i>, 2019, pp. 30863–70, doi:<a href=\"https://doi.org/10.1021/acs.jpcc.9b09970\">10.1021/acs.jpcc.9b09970</a>."},"publication_identifier":{"issn":["1932-7447","1932-7455"]},"publication_status":"published","title":"Molecular Doping of PCPDT–BT Copolymers: Comparison of Molecular Complexes with and without Integer Charge Transfer","doi":"10.1021/acs.jpcc.9b09970","date_updated":"2022-01-06T06:54:06Z","author":[{"full_name":"Dong, Chuan-Ding","last_name":"Dong","first_name":"Chuan-Ding"},{"last_name":"Schumacher","full_name":"Schumacher, Stefan","first_name":"Stefan"}],"date_created":"2020-09-17T07:43:24Z"},{"publication_identifier":{"issn":["1367-2630"]},"publication_status":"published","citation":{"apa":"Ma, X., Kartashov, Y. Y., Gao, T., &#38; Schumacher, S. (2019). Controllable high-speed polariton waves in a PT-symmetric lattice. <i>New Journal of Physics</i>. <a href=\"https://doi.org/10.1088/1367-2630/ab5a9b\">https://doi.org/10.1088/1367-2630/ab5a9b</a>","mla":"Ma, Xuekai, et al. “Controllable High-Speed Polariton Waves in a PT-Symmetric Lattice.” <i>New Journal of Physics</i>, 123008, 2019, doi:<a href=\"https://doi.org/10.1088/1367-2630/ab5a9b\">10.1088/1367-2630/ab5a9b</a>.","bibtex":"@article{Ma_Kartashov_Gao_Schumacher_2019, title={Controllable high-speed polariton waves in a PT-symmetric lattice}, DOI={<a href=\"https://doi.org/10.1088/1367-2630/ab5a9b\">10.1088/1367-2630/ab5a9b</a>}, number={123008}, journal={New Journal of Physics}, author={Ma, Xuekai and Kartashov, Yaroslav Y and Gao, Tingge and Schumacher, Stefan}, year={2019} }","short":"X. Ma, Y.Y. Kartashov, T. Gao, S. Schumacher, New Journal of Physics (2019).","ieee":"X. Ma, Y. Y. Kartashov, T. Gao, and S. Schumacher, “Controllable high-speed polariton waves in a PT-symmetric lattice,” <i>New Journal of Physics</i>, 2019.","chicago":"Ma, Xuekai, Yaroslav Y Kartashov, Tingge Gao, and Stefan Schumacher. “Controllable High-Speed Polariton Waves in a PT-Symmetric Lattice.” <i>New Journal of Physics</i>, 2019. <a href=\"https://doi.org/10.1088/1367-2630/ab5a9b\">https://doi.org/10.1088/1367-2630/ab5a9b</a>.","ama":"Ma X, Kartashov YY, Gao T, Schumacher S. Controllable high-speed polariton waves in a PT-symmetric lattice. <i>New Journal of Physics</i>. 2019. doi:<a href=\"https://doi.org/10.1088/1367-2630/ab5a9b\">10.1088/1367-2630/ab5a9b</a>"},"year":"2019","date_created":"2020-09-17T07:57:45Z","author":[{"full_name":"Ma, Xuekai","last_name":"Ma","first_name":"Xuekai"},{"full_name":"Kartashov, Yaroslav Y","last_name":"Kartashov","first_name":"Yaroslav Y"},{"first_name":"Tingge","last_name":"Gao","full_name":"Gao, Tingge"},{"last_name":"Schumacher","full_name":"Schumacher, Stefan","first_name":"Stefan"}],"date_updated":"2022-01-06T06:54:06Z","doi":"10.1088/1367-2630/ab5a9b","title":"Controllable high-speed polariton waves in a PT-symmetric lattice","publication":"New Journal of Physics","type":"journal_article","status":"public","user_id":"61189","_id":"19513","project":[{"name":"Computing Resources Provided by the Paderborn Center for Parallel Computing","_id":"52"}],"language":[{"iso":"eng"}],"keyword":["pc2-ressources"],"article_number":"123008"},{"publication_identifier":{"isbn":["9781538677698"]},"publication_status":"published","year":"2019","citation":{"ama":"Souza MA, Maciel LA, Penna PH, Freitas HC. Energy Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package. In: <i>2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD)</i>. ; 2019. doi:<a href=\"https://doi.org/10.1109/cahpc.2018.8645850\">10.1109/cahpc.2018.8645850</a>","chicago":"Souza, Matheus A., Lucas A. Maciel, Pedro Henrique Penna, and Henrique C. Freitas. “Energy Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package.” In <i>2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD)</i>, 2019. <a href=\"https://doi.org/10.1109/cahpc.2018.8645850\">https://doi.org/10.1109/cahpc.2018.8645850</a>.","ieee":"M. A. Souza, L. A. Maciel, P. H. Penna, and H. C. Freitas, “Energy Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package,” in <i>2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD)</i>, 2019.","short":"M.A. Souza, L.A. Maciel, P.H. Penna, H.C. Freitas, in: 2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), 2019.","bibtex":"@inproceedings{Souza_Maciel_Penna_Freitas_2019, title={Energy Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package}, DOI={<a href=\"https://doi.org/10.1109/cahpc.2018.8645850\">10.1109/cahpc.2018.8645850</a>}, booktitle={2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD)}, author={Souza, Matheus A. and Maciel, Lucas A. and Penna, Pedro Henrique and Freitas, Henrique C.}, year={2019} }","mla":"Souza, Matheus A., et al. “Energy Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package.” <i>2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD)</i>, 2019, doi:<a href=\"https://doi.org/10.1109/cahpc.2018.8645850\">10.1109/cahpc.2018.8645850</a>.","apa":"Souza, M. A., Maciel, L. A., Penna, P. H., &#38; Freitas, H. C. (2019). Energy Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package. In <i>2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD)</i>. <a href=\"https://doi.org/10.1109/cahpc.2018.8645850\">https://doi.org/10.1109/cahpc.2018.8645850</a>"},"date_updated":"2022-01-06T06:52:50Z","author":[{"first_name":"Matheus A.","last_name":"Souza","full_name":"Souza, Matheus A."},{"first_name":"Lucas A.","full_name":"Maciel, Lucas A.","last_name":"Maciel"},{"first_name":"Pedro Henrique","full_name":"Penna, Pedro Henrique","last_name":"Penna"},{"full_name":"Freitas, Henrique C.","last_name":"Freitas","first_name":"Henrique C."}],"date_created":"2020-04-06T09:41:41Z","title":"Energy Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package","doi":"10.1109/cahpc.2018.8645850","publication":"2018 30th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD)","type":"conference","abstract":[{"lang":"eng","text":"FPGA devices have been proving to be good candidates to accelerate applications from different research topics. For instance, machine learning applications such as K-Means clustering usually relies on large amount of data to be processed, and, despite the performance offered by other architectures, FPGAs can offer better energy efficiency. With that in mind, Intel has launched a platform that integrates a multicore and an FPGA in the same package, enabling low latency and coherent fine-grained data offload. In this paper, we present a parallel implementation of the K-Means clustering algorithm, for this novel platform, using OpenCL language, and compared it against other platforms. We found that the CPU+FPGA platform was more energy efficient than the CPU-only approach from 70.71% to 85.92%, with Standard and Tiny input sizes respectively, and up to 68.21% of performance improvement was obtained with Tiny input size. Furthermore, it was up to 7.2×more energy efficient than an Intel® Xeon Phi ™, 21.5×than a cluster of Raspberry Pi boards, and 3.8×than the low-power MPPA-256 architecture, when the Standard input size was used."}],"status":"public","_id":"16411","user_id":"61189","keyword":["pc2-harp-ressources"],"language":[{"iso":"eng"}]}]