---
_id: '62981'
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. "
author:
- first_name: Sadaf
full_name: Ehtesabi, Sadaf
id: '116116'
last_name: Ehtesabi
- first_name: Manoar
full_name: Hossain, Manoar
id: '114619'
last_name: Hossain
orcid: https://orcid.org/0000-0002-0737-7981
- first_name: Tobias
full_name: Kenter, Tobias
id: '3145'
last_name: Kenter
- first_name: Andreas
full_name: Krawinkel, Andreas
id: '15275'
last_name: Krawinkel
- first_name: Lukas
full_name: Ostermann, Lukas
id: '69976'
last_name: Ostermann
- first_name: Christian
full_name: Plessl, Christian
id: '16153'
last_name: Plessl
orcid: 0000-0001-5728-9982
- first_name: Heinrich
full_name: Riebler, Heinrich
id: '8961'
last_name: Riebler
- first_name: Stefan
full_name: Rohde, Stefan
id: '34009'
last_name: Rohde
- first_name: Robert
full_name: Schade, Robert
id: '75963'
last_name: Schade
orcid: 0000-0002-6268-5397
- first_name: Michael
full_name: Schwarz, Michael
id: '5312'
last_name: Schwarz
- first_name: Jens
full_name: Simon, Jens
id: '15273'
last_name: Simon
- first_name: Nils
full_name: Winnwa, Nils
id: '61189'
last_name: Winnwa
- first_name: Alex
full_name: Wiens, Alex
id: '23522'
last_name: Wiens
orcid: 0000-0003-1764-9773
- first_name: Xin
full_name: Wu, Xin
id: '77439'
last_name: Wu
citation:
ama: Ehtesabi S, Hossain M, Kenter T, et al. Otus Supercomputer. Vol 1. Paderborn
Center for Parallel Computing (PC2); 2025. doi:10.48550/ARXIV.2512.07401
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., & Wu, X. (2025). Otus Supercomputer (Vol. 1). Paderborn Center
for Parallel Computing (PC2). https://doi.org/10.48550/ARXIV.2512.07401
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={10.48550/ARXIV.2512.07401},
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} }'
chicago: 'Ehtesabi, Sadaf, Manoar Hossain, Tobias Kenter, Andreas Krawinkel, Lukas
Ostermann, Christian Plessl, Heinrich Riebler, et al. Otus Supercomputer.
Vol. 1. PC2 Technical Report Series. Paderborn: Paderborn Center for Parallel
Computing (PC2), 2025. https://doi.org/10.48550/ARXIV.2512.07401.'
ieee: 'S. Ehtesabi et al., Otus Supercomputer, vol. 1. Paderborn:
Paderborn Center for Parallel Computing (PC2), 2025.'
mla: Ehtesabi, Sadaf, et al. Otus Supercomputer. Paderborn Center for Parallel
Computing (PC2), 2025, doi:10.48550/ARXIV.2512.07401.
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.
date_created: 2025-12-09T09:11:04Z
date_updated: 2026-03-25T11:50:31Z
ddc:
- '004'
department:
- _id: '27'
- _id: '518'
doi: 10.48550/ARXIV.2512.07401
file:
- access_level: open_access
content_type: application/pdf
creator: deffel
date_created: 2025-12-09T09:19:12Z
date_updated: 2026-03-25T11:50:30Z
file_id: '62982'
file_name: 2512.07401v1.pdf
file_size: 4535595
relation: main_file
file_date_updated: 2026-03-25T11:50:30Z
has_accepted_license: '1'
intvolume: ' 1'
keyword:
- Otus
- Supercomputer
- FPGA
- PC2
- Paderborn Center for Parallel Computing
- Noctua 2
- HPC
language:
- iso: eng
oa: '1'
page: '33'
place: Paderborn
publication_status: published
publisher: Paderborn Center for Parallel Computing (PC2)
report_number: PC2TR-2025-1
series_title: PC2 Technical Report Series
status: public
title: Otus Supercomputer
type: report
user_id: '23522'
volume: 1
year: '2025'
...
---
_id: '53663'
abstract:
- lang: eng
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.'
article_type: original
author:
- first_name: Carsten
full_name: Bauer, Carsten
id: '90082'
last_name: Bauer
- first_name: Tobias
full_name: Kenter, Tobias
id: '3145'
last_name: Kenter
- first_name: Michael
full_name: Lass, Michael
id: '24135'
last_name: Lass
orcid: 0000-0002-5708-7632
- first_name: Lukas
full_name: Mazur, Lukas
id: '90492'
last_name: Mazur
orcid: ' 0000-0001-6304-7082'
- first_name: Marius
full_name: Meyer, Marius
id: '40778'
last_name: Meyer
- first_name: Holger
full_name: Nitsche, Holger
id: '15272'
last_name: Nitsche
- first_name: Heinrich
full_name: Riebler, Heinrich
id: '8961'
last_name: Riebler
- first_name: Robert
full_name: Schade, Robert
id: '75963'
last_name: Schade
orcid: 0000-0002-6268-5397
- first_name: Michael
full_name: Schwarz, Michael
id: '5312'
last_name: Schwarz
- first_name: Nils
full_name: Winnwa, Nils
id: '61189'
last_name: Winnwa
- first_name: Alex
full_name: Wiens, Alex
id: '23522'
last_name: Wiens
orcid: 0000-0003-1764-9773
- first_name: Xin
full_name: Wu, Xin
id: '77439'
last_name: Wu
- first_name: Christian
full_name: Plessl, Christian
id: '16153'
last_name: Plessl
orcid: 0000-0001-5728-9982
- first_name: Jens
full_name: Simon, Jens
id: '15273'
last_name: Simon
citation:
ama: Bauer C, Kenter T, Lass M, et al. Noctua 2 Supercomputer. Journal of large-scale
research facilities. 2024;9. doi:10.17815/jlsrf-8-187
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., &
Simon, J. (2024). Noctua 2 Supercomputer. Journal of Large-Scale Research Facilities,
9. https://doi.org/10.17815/jlsrf-8-187
bibtex: '@article{Bauer_Kenter_Lass_Mazur_Meyer_Nitsche_Riebler_Schade_Schwarz_Winnwa_et
al._2024, title={Noctua 2 Supercomputer}, volume={9}, DOI={10.17815/jlsrf-8-187 }, 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} }'
chicago: Bauer, Carsten, Tobias Kenter, Michael Lass, Lukas Mazur, Marius Meyer,
Holger Nitsche, Heinrich Riebler, et al. “Noctua 2 Supercomputer.” Journal
of Large-Scale Research Facilities 9 (2024). https://doi.org/10.17815/jlsrf-8-187 .
ieee: 'C. Bauer et al., “Noctua 2 Supercomputer,” Journal of large-scale
research facilities, vol. 9, 2024, doi: 10.17815/jlsrf-8-187 .'
mla: Bauer, Carsten, et al. “Noctua 2 Supercomputer.” Journal of Large-Scale
Research Facilities, vol. 9, 2024, doi:10.17815/jlsrf-8-187 .
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).
date_created: 2024-04-26T07:39:41Z
date_updated: 2024-04-26T08:44:30Z
ddc:
- '004'
department:
- _id: '27'
- _id: '518'
doi: '10.17815/jlsrf-8-187 '
file:
- access_level: open_access
content_type: application/pdf
creator: deffel
date_created: 2024-04-26T07:30:20Z
date_updated: 2024-04-26T08:35:17Z
file_id: '53664'
file_name: Noctua2_Supercomputer.pdf
file_size: 3825480
relation: main_file
file_date_updated: 2024-04-26T08:35:17Z
has_accepted_license: '1'
intvolume: ' 9'
keyword:
- Noctua 2
- Supercomputer
- FPGA
- PC2
- Paderborn Center for Parallel Computing
language:
- iso: eng
oa: '1'
project:
- _id: '52'
name: 'PC2: Computing Resources Provided by the Paderborn Center for Parallel Computing'
publication: Journal of large-scale research facilities
publication_status: published
status: public
title: Noctua 2 Supercomputer
type: journal_article
user_id: '8961'
volume: 9
year: '2024'
...
---
_id: '46547'
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
full_name: Fritsch, Lorena
id: '44418'
last_name: Fritsch
- first_name: José D.
full_name: Ardisson, José D.
last_name: Ardisson
- first_name: Marcos A. R.
full_name: da Silva, Marcos A. R.
last_name: da Silva
- first_name: Gabriel Ali
full_name: Atta Diab, Gabriel Ali
last_name: Atta Diab
- first_name: Ingrid Fernandes
full_name: Silva, Ingrid Fernandes
last_name: Silva
- first_name: Carlos André Ferreira
full_name: Moraes, Carlos André Ferreira
last_name: Moraes
- first_name: Moacir Rossi
full_name: Forim, Moacir Rossi
last_name: Forim
- first_name: Matthias
full_name: Bauer, Matthias
id: '47241'
last_name: Bauer
orcid: 0000-0002-9294-6076
- first_name: Thomas D.
full_name: Kühne, Thomas D.
last_name: Kühne
- first_name: Markus
full_name: Antonietti, Markus
last_name: Antonietti
- first_name: Ivo F.
full_name: Teixeira, Ivo F.
last_name: Teixeira
citation:
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.
ACS Catalysis. 2023;13(13):8662-8669. doi:10.1021/acscatal.3c02092
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., & Teixeira, I. F. (2023). Direct Synthesis of
Acetone by Aerobic Propane Oxidation Promoted by Photoactive Iron(III) Chloride
under Mild Conditions. ACS Catalysis, 13(13), 8662–8669. https://doi.org/10.1021/acscatal.3c02092
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={10.1021/acscatal.3c02092},
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} }'
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.” ACS Catalysis 13, no. 13 (2023): 8662–69.
https://doi.org/10.1021/acscatal.3c02092.'
ieee: 'A. Rogolino et al., “Direct Synthesis of Acetone by Aerobic Propane
Oxidation Promoted by Photoactive Iron(III) Chloride under Mild Conditions,” ACS
Catalysis, vol. 13, no. 13, pp. 8662–8669, 2023, doi: 10.1021/acscatal.3c02092.'
mla: Rogolino, Andrea, et al. “Direct Synthesis of Acetone by Aerobic Propane Oxidation
Promoted by Photoactive Iron(III) Chloride under Mild Conditions.” ACS Catalysis,
vol. 13, no. 13, American Chemical Society (ACS), 2023, pp. 8662–69, doi:10.1021/acscatal.3c02092.
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.
date_created: 2023-08-16T14:44:11Z
date_updated: 2024-03-07T09:34:41Z
doi: 10.1021/acscatal.3c02092
intvolume: ' 13'
issue: '13'
keyword:
- Catalysis
- General Chemistry
- pc2-ressources
- Computing Resources Provided by the Paderborn Center for Parallel Computing
language:
- iso: eng
page: 8662-8669
publication: ACS Catalysis
publication_identifier:
issn:
- 2155-5435
- 2155-5435
publication_status: published
publisher: American Chemical Society (ACS)
status: public
title: Direct Synthesis of Acetone by Aerobic Propane Oxidation Promoted by Photoactive
Iron(III) Chloride under Mild Conditions
type: journal_article
user_id: '44418'
volume: 13
year: '2023'
...
---
_id: '21208'
abstract:
- lang: eng
text: 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).
article_number: '406'
author:
- first_name: Daniel
full_name: Granhão, Daniel
last_name: Granhão
- first_name: João Canas
full_name: Canas Ferreira, João Canas
last_name: Canas Ferreira
citation:
ama: Granhão D, Canas Ferreira JC. Transparent Control Flow Transfer between CPU
and Accelerators for HPC. Electronics. 2021. doi:10.3390/electronics10040406
apa: Granhão, D., & Canas Ferreira, J. C. (2021). Transparent Control Flow Transfer
between CPU and Accelerators for HPC. Electronics. https://doi.org/10.3390/electronics10040406
bibtex: '@article{Granhão_Canas Ferreira_2021, title={Transparent Control Flow Transfer
between CPU and Accelerators for HPC}, DOI={10.3390/electronics10040406},
number={406}, journal={Electronics}, author={Granhão, Daniel and Canas Ferreira,
João Canas}, year={2021} }'
chicago: Granhão, Daniel, and João Canas Canas Ferreira. “Transparent Control Flow
Transfer between CPU and Accelerators for HPC.” Electronics, 2021. https://doi.org/10.3390/electronics10040406.
ieee: D. Granhão and J. C. Canas Ferreira, “Transparent Control Flow Transfer between
CPU and Accelerators for HPC,” Electronics, 2021.
mla: Granhão, Daniel, and João Canas Canas Ferreira. “Transparent Control Flow Transfer
between CPU and Accelerators for HPC.” Electronics, 406, 2021, doi:10.3390/electronics10040406.
short: D. Granhão, J.C. Canas Ferreira, Electronics (2021).
date_created: 2021-02-12T07:22:03Z
date_updated: 2022-01-06T06:54:49Z
doi: 10.3390/electronics10040406
keyword:
- pc2-harp-ressources
language:
- iso: eng
publication: Electronics
publication_identifier:
issn:
- 2079-9292
publication_status: published
status: public
title: Transparent Control Flow Transfer between CPU and Accelerators for HPC
type: journal_article
user_id: '61189'
year: '2021'
...
---
_id: '35131'
abstract:
- lang: eng
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.
author:
- first_name: David
full_name: Castells-Rufas, David
last_name: Castells-Rufas
- first_name: Santiago
full_name: Marco-Sola, Santiago
last_name: Marco-Sola
- first_name: Quim
full_name: Aguado-Puig, Quim
last_name: Aguado-Puig
- first_name: Antonio
full_name: Espinosa-Morales, Antonio
last_name: Espinosa-Morales
- first_name: Juan Carlos
full_name: Moure, Juan Carlos
last_name: Moure
- first_name: Lluc
full_name: Alvarez, Lluc
last_name: Alvarez
- first_name: Miquel
full_name: Moreto, Miquel
last_name: Moreto
citation:
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: 2021
31st International Conference on Field-Programmable Logic and Applications (FPL).
IEEE; 2021. doi:10.1109/fpl53798.2021.00036'
apa: Castells-Rufas, D., Marco-Sola, S., Aguado-Puig, Q., Espinosa-Morales, A.,
Moure, J. C., Alvarez, L., & Moreto, M. (2021). OpenCL-based FPGA Accelerator
for Semi-Global Approximate String Matching Using Diagonal Bit-Vectors. 2021
31st International Conference on Field-Programmable Logic and Applications (FPL).
https://doi.org/10.1109/fpl53798.2021.00036
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={10.1109/fpl53798.2021.00036},
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} }'
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 2021
31st International Conference on Field-Programmable Logic and Applications (FPL).
IEEE, 2021. https://doi.org/10.1109/fpl53798.2021.00036.
ieee: 'D. Castells-Rufas et al., “OpenCL-based FPGA Accelerator for Semi-Global
Approximate String Matching Using Diagonal Bit-Vectors,” 2021, doi: 10.1109/fpl53798.2021.00036.'
mla: Castells-Rufas, David, et al. “OpenCL-Based FPGA Accelerator for Semi-Global
Approximate String Matching Using Diagonal Bit-Vectors.” 2021 31st International
Conference on Field-Programmable Logic and Applications (FPL), IEEE, 2021,
doi:10.1109/fpl53798.2021.00036.
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.'
date_created: 2023-01-03T10:05:13Z
date_updated: 2024-01-22T09:56:25Z
doi: 10.1109/fpl53798.2021.00036
keyword:
- pc2-harp-ressources
language:
- iso: eng
project:
- _id: '52'
name: 'PC2: Computing Resources Provided by the Paderborn Center for Parallel Computing'
publication: 2021 31st International Conference on Field-Programmable Logic and Applications
(FPL)
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: OpenCL-based FPGA Accelerator for Semi-Global Approximate String Matching Using
Diagonal Bit-Vectors
type: conference
user_id: '3145'
year: '2021'
...
---
_id: '19501'
article_number: '231102'
author:
- first_name: Bin
full_name: Zhao, Bin
last_name: Zhao
- first_name: Uwe
full_name: Manthe, Uwe
last_name: Manthe
citation:
ama: Zhao B, Manthe U. Non-adiabatic transitions in the reaction of fluorine with
methane. The Journal of Chemical Physics. 2020. doi:10.1063/5.0013852
apa: Zhao, B., & Manthe, U. (2020). Non-adiabatic transitions in the reaction
of fluorine with methane. The Journal of Chemical Physics. https://doi.org/10.1063/5.0013852
bibtex: '@article{Zhao_Manthe_2020, title={Non-adiabatic transitions in the reaction
of fluorine with methane}, DOI={10.1063/5.0013852},
number={231102}, journal={The Journal of Chemical Physics}, author={Zhao, Bin
and Manthe, Uwe}, year={2020} }'
chicago: Zhao, Bin, and Uwe Manthe. “Non-Adiabatic Transitions in the Reaction of
Fluorine with Methane.” The Journal of Chemical Physics, 2020. https://doi.org/10.1063/5.0013852.
ieee: B. Zhao and U. Manthe, “Non-adiabatic transitions in the reaction of fluorine
with methane,” The Journal of Chemical Physics, 2020.
mla: Zhao, Bin, and Uwe Manthe. “Non-Adiabatic Transitions in the Reaction of Fluorine
with Methane.” The Journal of Chemical Physics, 231102, 2020, doi:10.1063/5.0013852.
short: B. Zhao, U. Manthe, The Journal of Chemical Physics (2020).
date_created: 2020-09-17T07:35:18Z
date_updated: 2022-01-06T06:54:06Z
doi: 10.1063/5.0013852
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: The Journal of Chemical Physics
publication_identifier:
issn:
- 0021-9606
- 1089-7690
publication_status: published
status: public
title: Non-adiabatic transitions in the reaction of fluorine with methane
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '19503'
author:
- first_name: Marco
full_name: Eckhoff, Marco
last_name: Eckhoff
- first_name: Peter E.
full_name: Blöchl, Peter E.
last_name: Blöchl
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
citation:
ama: Eckhoff M, Blöchl PE, Behler J. Hybrid density functional theory benchmark
study on lithium manganese oxides. Physical Review B. 2020. doi:10.1103/physrevb.101.205113
apa: Eckhoff, M., Blöchl, P. E., & Behler, J. (2020). Hybrid density functional
theory benchmark study on lithium manganese oxides. Physical Review B.
https://doi.org/10.1103/physrevb.101.205113
bibtex: '@article{Eckhoff_Blöchl_Behler_2020, title={Hybrid density functional theory
benchmark study on lithium manganese oxides}, DOI={10.1103/physrevb.101.205113},
journal={Physical Review B}, author={Eckhoff, Marco and Blöchl, Peter E. and Behler,
Jörg}, year={2020} }'
chicago: Eckhoff, Marco, Peter E. Blöchl, and Jörg Behler. “Hybrid Density Functional
Theory Benchmark Study on Lithium Manganese Oxides.” Physical Review B,
2020. https://doi.org/10.1103/physrevb.101.205113.
ieee: M. Eckhoff, P. E. Blöchl, and J. Behler, “Hybrid density functional theory
benchmark study on lithium manganese oxides,” Physical Review B, 2020.
mla: Eckhoff, Marco, et al. “Hybrid Density Functional Theory Benchmark Study on
Lithium Manganese Oxides.” Physical Review B, 2020, doi:10.1103/physrevb.101.205113.
short: M. Eckhoff, P.E. Blöchl, J. Behler, Physical Review B (2020).
date_created: 2020-09-17T07:39:26Z
date_updated: 2022-01-06T06:54:06Z
doi: 10.1103/physrevb.101.205113
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: Physical Review B
publication_identifier:
issn:
- 2469-9950
- 2469-9969
publication_status: published
status: public
title: Hybrid density functional theory benchmark study on lithium manganese oxides
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '19507'
article_number: '1192'
author:
- first_name: Franziska
full_name: Barkhausen, Franziska
last_name: Barkhausen
- first_name: Stefan
full_name: Schumacher, Stefan
last_name: Schumacher
- first_name: Xuekai
full_name: Ma, Xuekai
last_name: Ma
citation:
ama: Barkhausen F, Schumacher S, Ma X. Multistable circular currents of polariton
condensates trapped in ring potentials. Optics Letters. 2020. doi:10.1364/ol.386250
apa: Barkhausen, F., Schumacher, S., & Ma, X. (2020). Multistable circular currents
of polariton condensates trapped in ring potentials. Optics Letters. https://doi.org/10.1364/ol.386250
bibtex: '@article{Barkhausen_Schumacher_Ma_2020, title={Multistable circular currents
of polariton condensates trapped in ring potentials}, DOI={10.1364/ol.386250},
number={1192}, journal={Optics Letters}, author={Barkhausen, Franziska and Schumacher,
Stefan and Ma, Xuekai}, year={2020} }'
chicago: Barkhausen, Franziska, Stefan Schumacher, and Xuekai Ma. “Multistable Circular
Currents of Polariton Condensates Trapped in Ring Potentials.” Optics Letters,
2020. https://doi.org/10.1364/ol.386250.
ieee: F. Barkhausen, S. Schumacher, and X. Ma, “Multistable circular currents of
polariton condensates trapped in ring potentials,” Optics Letters, 2020.
mla: Barkhausen, Franziska, et al. “Multistable Circular Currents of Polariton Condensates
Trapped in Ring Potentials.” Optics Letters, 1192, 2020, doi:10.1364/ol.386250.
short: F. Barkhausen, S. Schumacher, X. Ma, Optics Letters (2020).
date_created: 2020-09-17T07:50:19Z
date_updated: 2022-01-06T06:54:06Z
doi: 10.1364/ol.386250
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: Optics Letters
publication_identifier:
issn:
- 0146-9592
- 1539-4794
publication_status: published
status: public
title: Multistable circular currents of polariton condensates trapped in ring potentials
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '19511'
author:
- first_name: Matthias
full_name: Pukrop, Matthias
last_name: Pukrop
- first_name: Stefan
full_name: Schumacher, Stefan
last_name: Schumacher
citation:
ama: Pukrop M, Schumacher S. Externally controlled Lotka-Volterra dynamics in a
linearly polarized polariton fluid. Physical Review E. 2020. doi:10.1103/physreve.101.012207
apa: Pukrop, M., & Schumacher, S. (2020). Externally controlled Lotka-Volterra
dynamics in a linearly polarized polariton fluid. Physical Review E. https://doi.org/10.1103/physreve.101.012207
bibtex: '@article{Pukrop_Schumacher_2020, title={Externally controlled Lotka-Volterra
dynamics in a linearly polarized polariton fluid}, DOI={10.1103/physreve.101.012207},
journal={Physical Review E}, author={Pukrop, Matthias and Schumacher, Stefan},
year={2020} }'
chicago: Pukrop, Matthias, and Stefan Schumacher. “Externally Controlled Lotka-Volterra
Dynamics in a Linearly Polarized Polariton Fluid.” Physical Review E, 2020.
https://doi.org/10.1103/physreve.101.012207.
ieee: M. Pukrop and S. Schumacher, “Externally controlled Lotka-Volterra dynamics
in a linearly polarized polariton fluid,” Physical Review E, 2020.
mla: Pukrop, Matthias, and Stefan Schumacher. “Externally Controlled Lotka-Volterra
Dynamics in a Linearly Polarized Polariton Fluid.” Physical Review E, 2020,
doi:10.1103/physreve.101.012207.
short: M. Pukrop, S. Schumacher, Physical Review E (2020).
date_created: 2020-09-17T07:56:54Z
date_updated: 2022-01-06T06:54:06Z
doi: 10.1103/physreve.101.012207
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: Physical Review E
publication_identifier:
issn:
- 2470-0045
- 2470-0053
publication_status: published
status: public
title: Externally controlled Lotka-Volterra dynamics in a linearly polarized polariton
fluid
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '19560'
article_number: '101917'
author:
- first_name: Consuelo
full_name: Parreño-Torres, Consuelo
last_name: Parreño-Torres
- first_name: Ramon
full_name: Alvarez-Valdes, Ramon
last_name: Alvarez-Valdes
- first_name: Rubén
full_name: Ruiz, Rubén
last_name: Ruiz
- first_name: Kevin
full_name: Tierney, Kevin
last_name: Tierney
citation:
ama: 'Parreño-Torres C, Alvarez-Valdes R, Ruiz R, Tierney K. Minimizing crane times
in pre-marshalling problems. Transportation Research Part E: Logistics and
Transportation Review. 2020. doi:10.1016/j.tre.2020.101917'
apa: 'Parreño-Torres, C., Alvarez-Valdes, R., Ruiz, R., & Tierney, K. (2020).
Minimizing crane times in pre-marshalling problems. Transportation Research
Part E: Logistics and Transportation Review. https://doi.org/10.1016/j.tre.2020.101917'
bibtex: '@article{Parreño-Torres_Alvarez-Valdes_Ruiz_Tierney_2020, title={Minimizing
crane times in pre-marshalling problems}, DOI={10.1016/j.tre.2020.101917},
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} }'
chicago: 'Parreño-Torres, Consuelo, Ramon Alvarez-Valdes, Rubén Ruiz, and Kevin
Tierney. “Minimizing Crane Times in Pre-Marshalling Problems.” Transportation
Research Part E: Logistics and Transportation Review, 2020. https://doi.org/10.1016/j.tre.2020.101917.'
ieee: 'C. Parreño-Torres, R. Alvarez-Valdes, R. Ruiz, and K. Tierney, “Minimizing
crane times in pre-marshalling problems,” Transportation Research Part E: Logistics
and Transportation Review, 2020.'
mla: 'Parreño-Torres, Consuelo, et al. “Minimizing Crane Times in Pre-Marshalling
Problems.” Transportation Research Part E: Logistics and Transportation Review,
101917, 2020, doi:10.1016/j.tre.2020.101917.'
short: 'C. Parreño-Torres, R. Alvarez-Valdes, R. Ruiz, K. Tierney, Transportation
Research Part E: Logistics and Transportation Review (2020).'
date_created: 2020-09-18T07:52:23Z
date_updated: 2022-01-06T06:54:07Z
doi: 10.1016/j.tre.2020.101917
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: 'Transportation Research Part E: Logistics and Transportation Review'
publication_identifier:
issn:
- 1366-5545
publication_status: published
status: public
title: Minimizing crane times in pre-marshalling problems
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '19561'
author:
- first_name: Meinolf
full_name: Sellmann, Meinolf
last_name: Sellmann
- first_name: Kevin
full_name: Tierney, Kevin
last_name: Tierney
citation:
ama: 'Sellmann M, Tierney K. Hyper-parameterized Dialectic Search for Non-linear
Box-Constrained Optimization with Heterogenous Variable Types. In: Lecture
Notes in Computer Science. Cham; 2020. doi:10.1007/978-3-030-53552-0_12'
apa: Sellmann, M., & Tierney, K. (2020). Hyper-parameterized Dialectic Search
for Non-linear Box-Constrained Optimization with Heterogenous Variable Types.
In Lecture Notes in Computer Science. Cham. https://doi.org/10.1007/978-3-030-53552-0_12
bibtex: '@inbook{Sellmann_Tierney_2020, place={Cham}, title={Hyper-parameterized
Dialectic Search for Non-linear Box-Constrained Optimization with Heterogenous
Variable Types}, DOI={10.1007/978-3-030-53552-0_12},
booktitle={Lecture Notes in Computer Science}, author={Sellmann, Meinolf and Tierney,
Kevin}, year={2020} }'
chicago: Sellmann, Meinolf, and Kevin Tierney. “Hyper-Parameterized Dialectic Search
for Non-Linear Box-Constrained Optimization with Heterogenous Variable Types.”
In Lecture Notes in Computer Science. Cham, 2020. https://doi.org/10.1007/978-3-030-53552-0_12.
ieee: M. Sellmann and K. Tierney, “Hyper-parameterized Dialectic Search for Non-linear
Box-Constrained Optimization with Heterogenous Variable Types,” in Lecture
Notes in Computer Science, Cham, 2020.
mla: Sellmann, Meinolf, and Kevin Tierney. “Hyper-Parameterized Dialectic Search
for Non-Linear Box-Constrained Optimization with Heterogenous Variable Types.”
Lecture Notes in Computer Science, 2020, doi:10.1007/978-3-030-53552-0_12.
short: 'M. Sellmann, K. Tierney, in: Lecture Notes in Computer Science, Cham, 2020.'
date_created: 2020-09-18T07:54:06Z
date_updated: 2022-01-06T06:54:07Z
doi: 10.1007/978-3-030-53552-0_12
keyword:
- pc2-ressources
language:
- iso: eng
place: Cham
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: Lecture Notes in Computer Science
publication_identifier:
isbn:
- '9783030535513'
- '9783030535520'
issn:
- 0302-9743
- 1611-3349
publication_status: published
status: public
title: Hyper-parameterized Dialectic Search for Non-linear Box-Constrained Optimization
with Heterogenous Variable Types
type: book_chapter
user_id: '61189'
year: '2020'
...
---
_id: '19562'
author:
- first_name: Stefan
full_name: Kuhlemann, Stefan
last_name: Kuhlemann
- first_name: Kevin
full_name: Tierney, Kevin
last_name: Tierney
citation:
ama: Kuhlemann S, Tierney K. A genetic algorithm for finding realistic sea routes
considering the weather. Journal of Heuristics. 2020. doi:10.1007/s10732-020-09449-7
apa: Kuhlemann, S., & Tierney, K. (2020). A genetic algorithm for finding realistic
sea routes considering the weather. Journal of Heuristics. https://doi.org/10.1007/s10732-020-09449-7
bibtex: '@article{Kuhlemann_Tierney_2020, title={A genetic algorithm for finding
realistic sea routes considering the weather}, DOI={10.1007/s10732-020-09449-7},
journal={Journal of Heuristics}, author={Kuhlemann, Stefan and Tierney, Kevin},
year={2020} }'
chicago: Kuhlemann, Stefan, and Kevin Tierney. “A Genetic Algorithm for Finding
Realistic Sea Routes Considering the Weather.” Journal of Heuristics, 2020.
https://doi.org/10.1007/s10732-020-09449-7.
ieee: S. Kuhlemann and K. Tierney, “A genetic algorithm for finding realistic sea
routes considering the weather,” Journal of Heuristics, 2020.
mla: Kuhlemann, Stefan, and Kevin Tierney. “A Genetic Algorithm for Finding Realistic
Sea Routes Considering the Weather.” Journal of Heuristics, 2020, doi:10.1007/s10732-020-09449-7.
short: S. Kuhlemann, K. Tierney, Journal of Heuristics (2020).
date_created: 2020-09-18T07:56:45Z
date_updated: 2022-01-06T06:54:07Z
doi: 10.1007/s10732-020-09449-7
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: Journal of Heuristics
publication_identifier:
issn:
- 1381-1231
- 1572-9397
publication_status: published
status: public
title: A genetic algorithm for finding realistic sea routes considering the weather
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '17359'
abstract:
- lang: eng
text: 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.
article_number: '843'
author:
- first_name: Carlos
full_name: Alberto Oliveira de Souza Junior, Carlos
last_name: Alberto Oliveira de Souza Junior
- first_name: João
full_name: Bispo, João
last_name: Bispo
- first_name: João M. P.
full_name: Cardoso, João M. P.
last_name: Cardoso
- first_name: Pedro C.
full_name: Diniz, Pedro C.
last_name: Diniz
- first_name: Eduardo
full_name: Marques, Eduardo
last_name: Marques
citation:
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. Electronics.
2020. doi:10.3390/electronics9050843
apa: Alberto Oliveira de Souza Junior, C., Bispo, J., Cardoso, J. M. P., Diniz,
P. C., & Marques, E. (2020). Exploration of FPGA-Based Hardware Designs for
QR Decomposition for Solving Stiff ODE Numerical Methods Using the HARP Hybrid
Architecture. Electronics. https://doi.org/10.3390/electronics9050843
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={10.3390/electronics9050843},
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} }'
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.” Electronics, 2020. https://doi.org/10.3390/electronics9050843.
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,” 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.” Electronics, 843, 2020, doi:10.3390/electronics9050843.
short: C. Alberto Oliveira de Souza Junior, J. Bispo, J.M.P. Cardoso, P.C. Diniz,
E. Marques, Electronics (2020).
date_created: 2020-07-08T08:18:59Z
date_updated: 2022-01-06T06:53:09Z
doi: 10.3390/electronics9050843
keyword:
- pc2-harp-ressources
language:
- iso: eng
publication: Electronics
publication_identifier:
issn:
- 2079-9292
publication_status: published
status: public
title: Exploration of FPGA-Based Hardware Designs for QR Decomposition for Solving
Stiff ODE Numerical Methods Using the HARP Hybrid Architecture
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '20496'
author:
- first_name: Martin
full_name: Streiter, Martin
last_name: Streiter
- first_name: Tillmann G.
full_name: Fischer, Tillmann G.
last_name: Fischer
- first_name: Christian
full_name: Wiebeler, Christian
last_name: Wiebeler
- first_name: Sebastian
full_name: Reichert, Sebastian
last_name: Reichert
- first_name: Jörn
full_name: Langenickel, Jörn
last_name: Langenickel
- first_name: Kirsten
full_name: Zeitler, Kirsten
last_name: Zeitler
- first_name: Carsten
full_name: Deibel, Carsten
last_name: Deibel
citation:
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. The Journal of Physical Chemistry C. 2020:15007-15014.
doi:10.1021/acs.jpcc.0c03341
apa: Streiter, M., Fischer, T. G., Wiebeler, C., Reichert, S., Langenickel, J.,
Zeitler, K., & Deibel, C. (2020). Impact of Chlorine on the Internal Transition
Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule
3CzClIPN. The Journal of Physical Chemistry C, 15007–15014. https://doi.org/10.1021/acs.jpcc.0c03341
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={10.1021/acs.jpcc.0c03341},
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} }'
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.” The Journal of Physical Chemistry C, 2020,
15007–14. https://doi.org/10.1021/acs.jpcc.0c03341.
ieee: M. Streiter et al., “Impact of Chlorine on the Internal Transition
Rates and Excited States of the Thermally Delayed Activated Fluorescence Molecule
3CzClIPN,” The Journal of Physical Chemistry C, pp. 15007–15014, 2020.
mla: Streiter, Martin, et al. “Impact of Chlorine on the Internal Transition Rates
and Excited States of the Thermally Delayed Activated Fluorescence Molecule 3CzClIPN.”
The Journal of Physical Chemistry C, 2020, pp. 15007–14, doi:10.1021/acs.jpcc.0c03341.
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.
date_created: 2020-11-25T07:19:15Z
date_updated: 2022-01-06T06:54:27Z
doi: 10.1021/acs.jpcc.0c03341
keyword:
- pc2-ressources
language:
- iso: eng
page: 15007-15014
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: The Journal of Physical Chemistry C
publication_identifier:
issn:
- 1932-7447
- 1932-7455
publication_status: published
status: public
title: Impact of Chlorine on the Internal Transition Rates and Excited States of the
Thermally Delayed Activated Fluorescence Molecule 3CzClIPN
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '16953'
abstract:
- lang: eng
text: 'AbstractThe 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 Ca2+ 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 Ca2+-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 Ca2+-coordinating aspartic acid. This destabilizes Ca2+
in the binding pocket, which we probed by steered molecular dynamics. After Ca2+-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
Ca2+-rebinding.'
author:
- first_name: Jan-O.
full_name: Joswig, Jan-O.
last_name: Joswig
- first_name: Jennifer
full_name: Anders, Jennifer
last_name: Anders
- first_name: Hengxi
full_name: Zhang, Hengxi
last_name: Zhang
- first_name: Christoph
full_name: Rademacher, Christoph
last_name: Rademacher
- first_name: Bettina G.
full_name: Keller, Bettina G.
last_name: Keller
citation:
ama: Joswig J-O, Anders J, Zhang H, Rademacher C, Keller BG. Molecular Mechanism
of the pH-Dependent Calcium Affinity in Langerin. bioRxiv. 2020.
apa: Joswig, J.-O., Anders, J., Zhang, H., Rademacher, C., & Keller, B. G. (2020).
Molecular Mechanism of the pH-Dependent Calcium Affinity in Langerin. BioRxiv.
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} }'
chicago: Joswig, Jan-O., Jennifer Anders, Hengxi Zhang, Christoph Rademacher, and
Bettina G. Keller. “Molecular Mechanism of the PH-Dependent Calcium Affinity in
Langerin.” BioRxiv, 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,” bioRxiv. 2020.
mla: Joswig, Jan-O., et al. “Molecular Mechanism of the PH-Dependent Calcium Affinity
in Langerin.” BioRxiv, 2020.
short: J.-O. Joswig, J. Anders, H. Zhang, C. Rademacher, B.G. Keller, BioRxiv (2020).
date_created: 2020-05-15T07:08:54Z
date_updated: 2022-01-06T06:53:00Z
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: bioRxiv
publication_status: published
status: public
title: Molecular Mechanism of the pH-Dependent Calcium Affinity in Langerin
type: preprint
user_id: '61189'
year: '2020'
...
---
_id: '16956'
article_number: '094503'
author:
- first_name: René Spencer
full_name: Chatwell, René Spencer
last_name: Chatwell
- first_name: Jadran
full_name: Vrabec, Jadran
last_name: Vrabec
citation:
ama: Chatwell RS, Vrabec J. Bulk viscosity of liquid noble gases. The Journal
of Chemical Physics. 2020. doi:10.1063/1.5142364
apa: Chatwell, R. S., & Vrabec, J. (2020). Bulk viscosity of liquid noble gases.
The Journal of Chemical Physics. https://doi.org/10.1063/1.5142364
bibtex: '@article{Chatwell_Vrabec_2020, title={Bulk viscosity of liquid noble gases},
DOI={10.1063/1.5142364}, number={094503},
journal={The Journal of Chemical Physics}, author={Chatwell, René Spencer and
Vrabec, Jadran}, year={2020} }'
chicago: Chatwell, René Spencer, and Jadran Vrabec. “Bulk Viscosity of Liquid Noble
Gases.” The Journal of Chemical Physics, 2020. https://doi.org/10.1063/1.5142364.
ieee: R. S. Chatwell and J. Vrabec, “Bulk viscosity of liquid noble gases,” The
Journal of Chemical Physics, 2020.
mla: Chatwell, René Spencer, and Jadran Vrabec. “Bulk Viscosity of Liquid Noble
Gases.” The Journal of Chemical Physics, 094503, 2020, doi:10.1063/1.5142364.
short: R.S. Chatwell, J. Vrabec, The Journal of Chemical Physics (2020).
date_created: 2020-05-15T07:25:13Z
date_updated: 2022-01-06T06:53:00Z
doi: 10.1063/1.5142364
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: The Journal of Chemical Physics
publication_identifier:
issn:
- 0021-9606
- 1089-7690
publication_status: published
status: public
title: Bulk viscosity of liquid noble gases
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '16957'
article_number: '119497'
author:
- first_name: Melinda A.
full_name: Fodor, Melinda A.
last_name: Fodor
- first_name: Zoltán
full_name: Ható, Zoltán
last_name: Ható
- first_name: Tamás
full_name: Kristóf, Tamás
last_name: Kristóf
- first_name: Mihály
full_name: Pósfai, Mihály
last_name: Pósfai
citation:
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. Chemical Geology. 2020. doi:10.1016/j.chemgeo.2020.119497'
apa: 'Fodor, M. A., Ható, Z., Kristóf, T., & Pósfai, M. (2020). The role of
clay surfaces in the heterogeneous nucleation of calcite: Molecular dynamics simulations
of cluster formation and attachment. Chemical Geology. https://doi.org/10.1016/j.chemgeo.2020.119497'
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={10.1016/j.chemgeo.2020.119497},
number={119497}, journal={Chemical Geology}, author={Fodor, Melinda A. and Ható,
Zoltán and Kristóf, Tamás and Pósfai, Mihály}, year={2020} }'
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.” Chemical Geology, 2020.
https://doi.org/10.1016/j.chemgeo.2020.119497.'
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,” Chemical Geology, 2020.'
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.” Chemical Geology, 119497, 2020, doi:10.1016/j.chemgeo.2020.119497.'
short: M.A. Fodor, Z. Ható, T. Kristóf, M. Pósfai, Chemical Geology (2020).
date_created: 2020-05-15T07:25:23Z
date_updated: 2022-01-06T06:53:00Z
doi: 10.1016/j.chemgeo.2020.119497
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: Chemical Geology
publication_identifier:
issn:
- 0009-2541
publication_status: published
status: public
title: 'The role of clay surfaces in the heterogeneous nucleation of calcite: Molecular
dynamics simulations of cluster formation and attachment'
type: journal_article
user_id: '61189'
year: '2020'
...
---
_id: '19504'
author:
- first_name: Chuan-Ding
full_name: Dong, Chuan-Ding
last_name: Dong
- first_name: Stefan
full_name: Schumacher, Stefan
last_name: Schumacher
citation:
ama: 'Dong C-D, Schumacher S. Molecular Doping of PCPDT–BT Copolymers: Comparison
of Molecular Complexes with and without Integer Charge Transfer. The Journal
of Physical Chemistry C. 2019:30863-30870. doi:10.1021/acs.jpcc.9b09970'
apa: 'Dong, C.-D., & Schumacher, S. (2019). Molecular Doping of PCPDT–BT Copolymers:
Comparison of Molecular Complexes with and without Integer Charge Transfer. The
Journal of Physical Chemistry C, 30863–30870. https://doi.org/10.1021/acs.jpcc.9b09970'
bibtex: '@article{Dong_Schumacher_2019, title={Molecular Doping of PCPDT–BT Copolymers:
Comparison of Molecular Complexes with and without Integer Charge Transfer}, DOI={10.1021/acs.jpcc.9b09970},
journal={The Journal of Physical Chemistry C}, author={Dong, Chuan-Ding and Schumacher,
Stefan}, year={2019}, pages={30863–30870} }'
chicago: 'Dong, Chuan-Ding, and Stefan Schumacher. “Molecular Doping of PCPDT–BT
Copolymers: Comparison of Molecular Complexes with and without Integer Charge
Transfer.” The Journal of Physical Chemistry C, 2019, 30863–70. https://doi.org/10.1021/acs.jpcc.9b09970.'
ieee: 'C.-D. Dong and S. Schumacher, “Molecular Doping of PCPDT–BT Copolymers: Comparison
of Molecular Complexes with and without Integer Charge Transfer,” The Journal
of Physical Chemistry C, pp. 30863–30870, 2019.'
mla: 'Dong, Chuan-Ding, and Stefan Schumacher. “Molecular Doping of PCPDT–BT Copolymers:
Comparison of Molecular Complexes with and without Integer Charge Transfer.” The
Journal of Physical Chemistry C, 2019, pp. 30863–70, doi:10.1021/acs.jpcc.9b09970.'
short: C.-D. Dong, S. Schumacher, The Journal of Physical Chemistry C (2019) 30863–30870.
date_created: 2020-09-17T07:43:24Z
date_updated: 2022-01-06T06:54:06Z
doi: 10.1021/acs.jpcc.9b09970
keyword:
- pc2-ressources
language:
- iso: eng
page: 30863-30870
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: The Journal of Physical Chemistry C
publication_identifier:
issn:
- 1932-7447
- 1932-7455
publication_status: published
status: public
title: 'Molecular Doping of PCPDT–BT Copolymers: Comparison of Molecular Complexes
with and without Integer Charge Transfer'
type: journal_article
user_id: '61189'
year: '2019'
...
---
_id: '19513'
article_number: '123008'
author:
- first_name: Xuekai
full_name: Ma, Xuekai
last_name: Ma
- first_name: Yaroslav Y
full_name: Kartashov, Yaroslav Y
last_name: Kartashov
- first_name: Tingge
full_name: Gao, Tingge
last_name: Gao
- first_name: Stefan
full_name: Schumacher, Stefan
last_name: Schumacher
citation:
ama: Ma X, Kartashov YY, Gao T, Schumacher S. Controllable high-speed polariton
waves in a PT-symmetric lattice. New Journal of Physics. 2019. doi:10.1088/1367-2630/ab5a9b
apa: Ma, X., Kartashov, Y. Y., Gao, T., & Schumacher, S. (2019). Controllable
high-speed polariton waves in a PT-symmetric lattice. New Journal of Physics.
https://doi.org/10.1088/1367-2630/ab5a9b
bibtex: '@article{Ma_Kartashov_Gao_Schumacher_2019, title={Controllable high-speed
polariton waves in a PT-symmetric lattice}, DOI={10.1088/1367-2630/ab5a9b},
number={123008}, journal={New Journal of Physics}, author={Ma, Xuekai and Kartashov,
Yaroslav Y and Gao, Tingge and Schumacher, Stefan}, year={2019} }'
chicago: Ma, Xuekai, Yaroslav Y Kartashov, Tingge Gao, and Stefan Schumacher. “Controllable
High-Speed Polariton Waves in a PT-Symmetric Lattice.” New Journal of Physics,
2019. https://doi.org/10.1088/1367-2630/ab5a9b.
ieee: X. Ma, Y. Y. Kartashov, T. Gao, and S. Schumacher, “Controllable high-speed
polariton waves in a PT-symmetric lattice,” New Journal of Physics, 2019.
mla: Ma, Xuekai, et al. “Controllable High-Speed Polariton Waves in a PT-Symmetric
Lattice.” New Journal of Physics, 123008, 2019, doi:10.1088/1367-2630/ab5a9b.
short: X. Ma, Y.Y. Kartashov, T. Gao, S. Schumacher, New Journal of Physics (2019).
date_created: 2020-09-17T07:57:45Z
date_updated: 2022-01-06T06:54:06Z
doi: 10.1088/1367-2630/ab5a9b
keyword:
- pc2-ressources
language:
- iso: eng
project:
- _id: '52'
name: Computing Resources Provided by the Paderborn Center for Parallel Computing
publication: New Journal of Physics
publication_identifier:
issn:
- 1367-2630
publication_status: published
status: public
title: Controllable high-speed polariton waves in a PT-symmetric lattice
type: journal_article
user_id: '61189'
year: '2019'
...
---
_id: '16411'
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.
author:
- first_name: Matheus A.
full_name: Souza, Matheus A.
last_name: Souza
- first_name: Lucas A.
full_name: Maciel, Lucas A.
last_name: Maciel
- first_name: Pedro Henrique
full_name: Penna, Pedro Henrique
last_name: Penna
- first_name: Henrique C.
full_name: Freitas, Henrique C.
last_name: Freitas
citation:
ama: 'Souza MA, Maciel LA, Penna PH, Freitas HC. Energy Efficient Parallel K-Means
Clustering for an Intel® Hybrid Multi-Chip Package. In: 2018 30th International
Symposium on Computer Architecture and High Performance Computing (SBAC-PAD).
; 2019. doi:10.1109/cahpc.2018.8645850'
apa: Souza, M. A., Maciel, L. A., Penna, P. H., & Freitas, H. C. (2019). Energy
Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package.
In 2018 30th International Symposium on Computer Architecture and High Performance
Computing (SBAC-PAD). https://doi.org/10.1109/cahpc.2018.8645850
bibtex: '@inproceedings{Souza_Maciel_Penna_Freitas_2019, title={Energy Efficient
Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip Package}, DOI={10.1109/cahpc.2018.8645850},
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} }'
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 2018 30th International Symposium on Computer Architecture
and High Performance Computing (SBAC-PAD), 2019. https://doi.org/10.1109/cahpc.2018.8645850.
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 2018
30th International Symposium on Computer Architecture and High Performance Computing
(SBAC-PAD), 2019.
mla: Souza, Matheus A., et al. “Energy Efficient Parallel K-Means Clustering for
an Intel® Hybrid Multi-Chip Package.” 2018 30th International Symposium on
Computer Architecture and High Performance Computing (SBAC-PAD), 2019, doi:10.1109/cahpc.2018.8645850.
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.'
date_created: 2020-04-06T09:41:41Z
date_updated: 2022-01-06T06:52:50Z
doi: 10.1109/cahpc.2018.8645850
keyword:
- pc2-harp-ressources
language:
- iso: eng
publication: 2018 30th International Symposium on Computer Architecture and High Performance
Computing (SBAC-PAD)
publication_identifier:
isbn:
- '9781538677698'
publication_status: published
status: public
title: Energy Efficient Parallel K-Means Clustering for an Intel® Hybrid Multi-Chip
Package
type: conference
user_id: '61189'
year: '2019'
...