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1. Key Algorithms for Keyphrase Generation: Instruction-Based LLMs for Russian Scientific Keyphrases

Author

Glazkova, Anna, Morozov, Dmitry, and Garipov, Timur

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, 68T50, I.2.7, I.7.m, H.3.3
Abstract

Keyphrase selection is a challenging task in natural language processing that has a wide range of applications. Adapting existing supervised and unsupervised solutions for the Russian language faces several limitations due to the rich morphology of Russian and the limited number of training datasets available. Recent studies conducted on English texts show that large language models (LLMs) successfully address the task of generating keyphrases. LLMs allow achieving impressive results without task-specific fine-tuning, using text prompts instead. In this work, we access the performance of prompt-based methods for generating keyphrases for Russian scientific abstracts. First, we compare the performance of zero-shot and few-shot prompt-based methods, fine-tuned models, and unsupervised methods. Then we assess strategies for selecting keyphrase examples in a few-shot setting. We present the outcomes of human evaluation of the generated keyphrases and analyze the strengths and weaknesses of the models through expert assessment. Our results suggest that prompt-based methods can outperform common baselines even using simple text prompts., Comment: The 12th International Conference on Analysis of Images, Social Networks and Texts (AIST'2024)

Published
2024

2. Exploring Fine-tuned Generative Models for Keyphrase Selection: A Case Study for Russian

Author

Glazkova, Anna and Morozov, Dmitry

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, Computer Science - Machine Learning, 68T50, I.2.7, I.7.m, H.3.3
Abstract

Keyphrase selection plays a pivotal role within the domain of scholarly texts, facilitating efficient information retrieval, summarization, and indexing. In this work, we explored how to apply fine-tuned generative transformer-based models to the specific task of keyphrase selection within Russian scientific texts. We experimented with four distinct generative models, such as ruT5, ruGPT, mT5, and mBART, and evaluated their performance in both in-domain and cross-domain settings. The experiments were conducted on the texts of Russian scientific abstracts from four domains: mathematics & computer science, history, medicine, and linguistics. The use of generative models, namely mBART, led to gains in in-domain performance (up to 4.9% in BERTScore, 9.0% in ROUGE-1, and 12.2% in F1-score) over three keyphrase extraction baselines for the Russian language. Although the results for cross-domain usage were significantly lower, they still demonstrated the capability to surpass baseline performances in several cases, underscoring the promising potential for further exploration and refinement in this research field., Comment: DAMDID-2024

Published
2024

3. Mid-infrared characterization of NbTiN superconducting nanowire single-photon detectors on silicon-on-insulator

Author

Azem, Adan, Morozov, Dmitry V., Kuznesof, Daniel, Bruscino, Ciro, Hadfield, Robert H., Chrostowski, Lukas, and Young, Jeff F.

Subjects
Quantum Physics, Condensed Matter - Superconductivity, Physics - Instrumentation and Detectors
Abstract

Superconducting nanowire single-photon detectors are widely used for detecting individual photons across various wavelengths from ultraviolet to near-infrared range. Recently, there has been increasing interest in enhancing their sensitivity to single photons in the mid-infrared spectrum, driven by applications in quantum communication, spectroscopy and astrophysics. Here, we present our efforts to expand the spectral detection capabilities of U-shaped NbTiN-based superconducting nanowire single-photon detectors, fabricated in a 2-wire configuration on a silicon-on-insulator substrate, into the mid-infrared range. We demonstrate saturated internal detection efficiency extending up to a wavelength of 3.5 {\mu}m for a 5 nm thick and 50 nm wide NbTiN nanowire with a dark count rate less than 10 counts per second at 0.9 K and a rapid recovery time of 4.3 ns. The detectors are engineered for integration on waveguides in a silicon-on-insulator platform for compact, multi-channel device applications., Comment: 5 figures, 7 pages

Published
2024

4. Alternant Hydrocarbon Diradicals as Optically Addressable Molecular Qubits

Author

Poh, Yong Rui, Morozov, Dmitry, Kazmierczak, Nathanael P., Hadt, Ryan G., Groenhof, Gerrit, and Yuen-Zhou, Joel

Subjects
Physics - Chemical Physics, Condensed Matter - Materials Science, Quantum Physics
Abstract

High-spin molecules allow for bottom-up qubit design and are promising platforms for magnetic sensing and quantum information science. Optical addressability of molecular electron spins has also been proposed in first-row transition metal complexes via optically-detected magnetic resonance (ODMR) mechanisms analogous to the diamond-NV colour centre. However, significantly less progress has been made on the front of metal-free molecules, which can deliver lower costs and milder environmental impacts. At present, most luminescent open-shell organic molecules are $\pi$-diradicals, but such systems often suffer from poor ground-state open-shell characters necessary to realise a stable ground-state molecular qubit. In this work, we use alternancy symmetry to selectively minimise radical-radical interactions in the ground state, generating $\pi$-systems with high diradical characters. We call them m-dimers, referencing the need to covalently link two benzylic radicals at their meta carbon atoms for the desired symmetry. Through a detailed electronic structure analysis, we find that the excited states of alternant hydrocarbon m-diradicals contain important symmetries that can be used to construct ODMR mechanisms leading to ground-state spin polarisation. The molecular parameters are set in the context of a tris(2,4,6-trichlorophenyl)methyl (TTM) radical dimer covalently tethered at the meta position, demonstrating the feasibility of alternant m-diradicals as molecular colour centres., Comment: 12 pages, 5 figures, 1 table. Minor edits made to the manuscript text

Published
2024
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5. Cross-Domain Robustness of Transformer-based Keyphrase Generation

Author

Glazkova, Anna and Morozov, Dmitry

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, Computer Science - Machine Learning, 68T50, I.2.7, I.7.m, H.3.3
Abstract

Modern models for text generation show state-of-the-art results in many natural language processing tasks. In this work, we explore the effectiveness of abstractive text summarization models for keyphrase selection. A list of keyphrases is an important element of a text in databases and repositories of electronic documents. In our experiments, abstractive text summarization models fine-tuned for keyphrase generation show quite high results for a target text corpus. However, in most cases, the zero-shot performance on other corpora and domains is significantly lower. We investigate cross-domain limitations of abstractive text summarization models for keyphrase generation. We present an evaluation of the fine-tuned BART models for the keyphrase selection task across six benchmark corpora for keyphrase extraction including scientific texts from two domains and news texts. We explore the role of transfer learning between different domains to improve the BART model performance on small text corpora. Our experiments show that preliminary fine-tuning on out-of-domain corpora can be effective under conditions of a limited number of samples., Comment: Presented at the XXV International Conference "Data Analytics and Management in Data Intensive Domains" (DAMDID/RCDL), October 2023

Published
2023
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7. Optical control of ultrafast structural dynamics in a fluorescent protein.

Author

Hutchison, Christopher, Baxter, James, Fitzpatrick, Ann, Dorlhiac, Gabriel, Fadini, Alisia, Perrett, Samuel, Maghlaoui, Karim, Lefèvre, Salomé, Cordon-Preciado, Violeta, Ferreira, Josie, Chukhutsina, Volha, Garratt, Douglas, Barnard, Jonathan, Galinis, Gediminas, Glencross, Flo, Morgan, Rhodri, Stockton, Sian, Taylor, Ben, Yuan, Letong, Romei, Matthew, Lin, Chi-Yun, Marangos, Jon, Schmidt, Marius, Chatrchyan, Viktoria, Buckup, Tiago, Morozov, Dmitry, Park, Jaehyun, Park, Sehan, Eom, Intae, Kim, Minseok, Jang, Dogeun, Choi, Hyeongi, Hyun, HyoJung, Park, Gisu, Nango, Eriko, Tanaka, Rie, Owada, Shigeki, Tono, Kensuke, DePonte, Daniel, Carbajo, Sergio, Seaberg, Matt, Aquila, Andrew, Boutet, Sebastien, Barty, Anton, Iwata, So, Boxer, Steven, Groenhof, Gerrit, and van Thor, Jasper

Subjects
Motion, Vibration, Rhodopsin, Hydrogen Bonding
Abstract

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Published
2023

8. Protein-protein docking using a tensor train black-box optimization method

Author

Morozov, Dmitry, Melnikov, Artem, Shete, Vishal, and Perelshtein, Michael

Subjects
Quantitative Biology - Biomolecules, Physics - Biological Physics, J.2, J.3, I.6.3
Abstract

Black-box optimization methods play an important role in many fields of computational simulation. In particular, such methods are often used in the design and modelling of biological systems, including proteins and their complexes with various ligands. This work is mainly focused on the protein-protein docking that plays a key role in modern drug-design workflows. We develop a black-box approach for such docking problems using a novel technique based on the tensor-train decomposition of high-dimensional interaction functions. Our method shows an advantage in terms of the discovered global minima and has a high potential for further implementation on a wide range of devices, including graphical processing units and quantum processing units., Comment: 6 pages, 3 figures, 1 table

Published
2023

9. Enhanced Excitation Energy Transfer under Strong Light-Matter Coupling: Insights from Multi-Scale Molecular Dynamics Simulations

Author

Sokolovskii, Ilia, Tichauer, Ruth H., Morozov, Dmitry, Feist, Johannes, and Groenhof, Gerrit

Subjects
Physics - Chemical Physics
Abstract

Exciton transport can be enhanced in the strong coupling regime where excitons hybridise with confined light modes to form polaritons. Because polaritons have group velocity, their propagation should be ballistic and long-ranged. However, experiments indicate that organic polaritons propagate in a diffusive manner and more slowly than their group velocity. Here, we resolve this controversy by means of molecular dynamics simulations of Rhodamine molecules in a Fabry-P\'{e}rot cavity. Our results suggest that polariton propagation is limited by the cavity lifetime and appears diffusive due to reversible population transfers between polaritonic states that propagate ballistically at their group velocity, and dark states that are stationary. Furthermore, because long-lived dark states transiently trap the excitation, propagation is observed on timescales beyond the intrinsic polariton lifetime. These insights not only help to better understand and interpret experimental observations, but also pave the way towards rational design of molecule-cavity systems for coherent exciton transport.

Published
2022
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10. Applying Transformer-based Text Summarization for Keyphrase Generation

Author

Glazkova, Anna and Morozov, Dmitry

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, Computer Science - Machine Learning, 68T50, I.2.7, I.7.m, H.3.3
Abstract

Keyphrases are crucial for searching and systematizing scholarly documents. Most current methods for keyphrase extraction are aimed at the extraction of the most significant words in the text. But in practice, the list of keyphrases often includes words that do not appear in the text explicitly. In this case, the list of keyphrases represents an abstractive summary of the source text. In this paper, we experiment with popular transformer-based models for abstractive text summarization using four benchmark datasets for keyphrase extraction. We compare the results obtained with the results of common unsupervised and supervised methods for keyphrase extraction. Our evaluation shows that summarization models are quite effective in generating keyphrases in the terms of the full-match F1-score and BERTScore. However, they produce a lot of words that are absent in the author's list of keyphrases, which makes summarization models ineffective in terms of ROUGE-1. We also investigate several ordering strategies to concatenate target keyphrases. The results showed that the choice of strategy affects the performance of keyphrase generation., Comment: 15 pages, 4 figures. DAMDID-2022

Published
2022
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11. MIPT-NSU-UTMN at SemEval-2021 Task 5: Ensembling Learning with Pre-trained Language Models for Toxic Spans Detection

Author

Kotyushev, Mikhail, Glazkova, Anna, and Morozov, Dmitry

Subjects
Computer Science - Computation and Language, Computer Science - Artificial Intelligence, Computer Science - Information Retrieval, Computer Science - Machine Learning, 68T50, I.2.7, I.7.m, H.3.3
Abstract

This paper describes our system for SemEval-2021 Task 5 on Toxic Spans Detection. We developed ensemble models using BERT-based neural architectures and post-processing to combine tokens into spans. We evaluated several pre-trained language models using various ensemble techniques for toxic span identification and achieved sizable improvements over our baseline fine-tuned BERT models. Finally, our system obtained a F1-score of 67.55% on test data., Comment: Accepted at SemEval-2021 Workshop, ACL-IJCNLP 2021

Published
2021
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13. Two-photon Quantum Interference and Entanglement at 2 {\mu}m

Author

Prabhakar, Shashi, Shields, Taylor, Dada, Adetunmise, Ebrahim, Mehdi, Taylor, Gregor G., Morozov, Dmitry, Erotokritou, Kleanthis, Miki, Shigehito, Yabuno, Masahiro, Terai, Hirotaka, Gawith, Corin, Kues, Michael, Caspani, Lucia, Hadfield, Robert H., and Clerici, Matteo

Subjects
Quantum Physics, Physics - Optics
Abstract

Quantum-enhanced optical systems operating within the 2- to 2.5-$\mu$m spectral region have the potential to revolutionize emerging applications in communications, sensing, and metrology. However, to date, sources of entangled photons have been realized mainly in the near-infrared 700- to 1550-nm spectral window. Here, using custom-designed lithium niobate crystals for spontaneous parametric down-conversion and tailored superconducting nanowire single-photon detectors, we demonstrate two-photon interference and polarization-entangled photon pairs at 2090 nm. These results open the 2- to 2.5-$\mu$m mid-infrared window for the development of optical quantum technologies such as quantum key distribution in next-generation mid-infrared fiber communication systems and future Earth-to-satellite communications.

Published
2019
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14. Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells

Author

Kichkailo, Anna S., Narodov, Andrey A., Komarova, Maria A., Zamay, Tatiana N., Zamay, Galina S., Kolovskaya, Olga S., Erakhtin, Evgeniy E., Glazyrin, Yury E., Veprintsev, Dmitry V., Moryachkov, Roman V., Zabluda, Vladimir V., Shchugoreva, Irina, Artyushenko, Polina, Mironov, Vladimir A., Morozov, Dmitry I., Khorzhevskii, Vladimir A., Gorbushin, Anton V., Koshmanova, Anastasia A., Nikolaeva, Elena D., Grinev, Igor P., Voronkovskii, Ivan I., Grek, Daniil S., Belugin, Kirill V., Volzhentsev, Alexander A., Badmaev, Oleg N., Luzan, Natalia A., Lukyanenko, Kirill A., Peters, Georgy, Lapin, Ivan N., Kirichenko, Andrey K., Konarev, Petr V., Morozov, Evgeny V., Mironov, Gleb G., Gargaun, Ana, Muharemagic, Darija, Zamay, Sergey S., Kochkina, Elena V., Dymova, Maya A., Smolyarova, Tatiana E., Sokolov, Alexey E., Modestov, Andrey A., Tokarev, Nikolay A., Shepelevich, Nikolay V., Ozerskaya, Anastasia V., Chanchikova, Natalia G., Krat, Alexey V., Zukov, Ruslan A., Bakhtina, Varvara I., Shnyakin, Pavel G., Shesternya, Pavel A., Svetlichnyi, Valery A., Petrova, Marina M., Artyukhov, Ivan P., Tomilin, Felix N., and Berezovski, Maxim V.

Published
2023
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15. Knowledge extraction, modeling and formalization: EEG case study

Author

Morozov, Dmitry, Lezoche, Mario, and Panetto, Hervé

Subjects
Computer Science - Information Retrieval, Electrical Engineering and Systems Science - Signal Processing
Abstract

Formal Concept Analysis (FCA) is a well-established method for data analysis which finds many applications in data mining. Its extension on complex data representation formats brought a wave of new applications to the problems such as gene expression mining, prediction of toxicity of chemical compounds or clustering of sequences in process event logs. Insipired from this work our research inherits their model and designs an experiment for mining electroencephalographic recordings for patterns of sleep spindles. The contribution of this paper lies in the specification of desritizition procedure and the architecture of FCA experiment. We also provide some reflection on the related research papers., Comment: arXiv admin note: text overlap with arXiv:1506.05018 by other authors

Published
2018

16. Optical performance of an ultra-sensitive horn-coupled transition-edge-sensor bolometer with hemispherical backshort in the far infrared

Author

Audley, Michael D., de Lange, Gert, Gao, Jian-Rong, Khosropanah, Pourya, Hijmering, Richard, Ridder, Marcel, Mauskopf, Philip D., Morozov, Dmitry, Trappe, Neil A., and Doherty, Stephen

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Instrumentation and Detectors
Abstract

The next generation of far infrared space observatories will require extremely sensitive detectors that can be realized only by combining extremely low intrinsic noise with high optical efficiency. We have measured the broad-band optical response of ultra-sensitive TES bolometers (NEP$\approx2\rm\ aW/\sqrt Hz$) in the 30--60-$\mu\rm m$ band where radiation is coupled to the detectors with a few-moded conical feedhorn and a hemispherical backshort. We show that these detectors have an optical efficiency of 60% (the ratio of the power detected by the TES bolometer to the total power propagating through the feedhorn). We find that the measured optical efficiency can be understood in terms of the modes propagating through the feedhorn with the aid of a spatial mode-filtering technique., Comment: 22 pages, 11 figures. The following article has been accepted by Review of Scientific Instruments. After it is published, it will be found at http://scitation.aip.org/content/aip/journal/rsi

Published
2016
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18. Ultrafast structural changes within a photosynthetic reaction centre

Author

Dods, Robert, Båth, Petra, Morozov, Dmitry, Gagnér, Viktor Ahlberg, Arnlund, David, Luk, Hoi Ling, and Kübel, Joachim

Subjects
Crystallography -- Methods, Blastochloris viridis -- Structure -- Observations -- Natural history -- Optical properties, Photosynthetic reaction centers -- Observations -- Structure, Electron transport -- Speed, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography.sup.1 using an X-ray free-electron laser.sup.2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions. Time-resolved serial femtosecond crystallography is used to reveal the structural changes that stabilize the charge-separation steps of electron-transfer reactions in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds., Author(s): Robert Dods [sup.1] , Petra Båth [sup.1] , Dmitry Morozov [sup.2] , Viktor Ahlberg Gagnér [sup.1] , David Arnlund [sup.1] , Hoi Ling Luk [sup.2] , Joachim Kübel [sup.1] [...]

Published
2021
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19. Corrigendum: Examination of critical factors influencing ruminant disease dynamics in the Black Sea Basin

Author

Arede, Margarida, primary, Beltrán-Alcrudo, Daniel, additional, Aliyev, Jeyhun, additional, Chaligava, Tengiz, additional, Keskin, Ipek, additional, Markosyan, Tigran, additional, Morozov, Dmitry, additional, Oste, Sarah, additional, Pavlenko, Andrii, additional, Ponea, Mihai, additional, Starciuc, Nicolae, additional, Zdravkova, Anna, additional, Raizman, Eran, additional, Casal, Jordi, additional, and Allepuz, Alberto, additional

Published
2024
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20. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein

Author

Pande, Kanupriya, Hutchison, Christopher DM, Groenhof, Gerrit, Aquila, Andy, Robinson, Josef S, Tenboer, Jason, Basu, Shibom, Boutet, Sébastien, DePonte, Daniel P, Liang, Mengning, White, Thomas A, Zatsepin, Nadia A, Yefanov, Oleksandr, Morozov, Dmitry, Oberthuer, Dominik, Gati, Cornelius, Subramanian, Ganesh, James, Daniel, Zhao, Yun, Koralek, Jake, Brayshaw, Jennifer, Kupitz, Christopher, Conrad, Chelsie, Roy-Chowdhury, Shatabdi, Coe, Jesse D, Metz, Markus, Xavier, Paulraj Lourdu, Grant, Thomas D, Koglin, Jason E, Ketawala, Gihan, Fromme, Raimund, Šrajer, Vukica, Henning, Robert, Spence, John CH, Ourmazd, Abbas, Schwander, Peter, Weierstall, Uwe, Frank, Matthias, Fromme, Petra, Barty, Anton, Chapman, Henry N, Moffat, Keith, van Thor, Jasper J, and Schmidt, Marius

Subjects
Biological Sciences, Chemical Sciences, Theoretical and Computational Chemistry, Bacterial Proteins, Crystallography, Isomerism, Light, Photochemical Processes, Photons, Photoreceptors, Microbial, Protein Conformation, Time Factors, General Science & Technology
Abstract

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.

Published
2016

25. Examination of critical factors influencing ruminant disease dynamics in the Black Sea Basin

Author

Arede, Margarida, primary, Beltrán-Alcrudo, Daniel, additional, Aliyev, Jeyhun, additional, Chaligava, Tengiz, additional, Keskin, Ipek, additional, Markosyan, Tigran, additional, Morozov, Dmitry, additional, Oste, Sarah, additional, Pavlenko, Andrii, additional, Ponea, Mihai, additional, Starciuc, Nicolae, additional, Zdravkova, Anna, additional, Raizman, Eran, additional, Casal, Jordi, additional, and Allepuz, Alberto, additional

Published
2023
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27. Examination of critical factors influencing ruminant disease dynamics in the Black Sea Basin.

Author

Arede, Margarida, Beltrán-Alcrudo, Daniel, Aliyev, Jeyhun, Chaligava, Tengiz, Keskin, Ipek, Markosyan, Tigran, Morozov, Dmitry, Oste, Sarah, Pavlenko, Andrii, Ponea, Mihai, Starciuc, Nicolae, Zdravkova, Anna, Raizman, Eran, Casal, Jordi, and Allepuz, Alberto

Subjects
LUMPY skin disease, BRUCELLA, PESTE des petits ruminants, RUMINANTS, ANIMAL diseases, FOOT & mouth disease, HEMORRHAGIC fever
Abstract

Introduction: Ruminant production in the Black Sea basin (BSB) is critical for national economies and the subsistence of rural populations. Yet, zoonoses and transboundary animal diseases (TADs) are limiting and threatening the sector. To gain a more comprehensive understanding, this study characterizes key aspects of the ruminant sector in nine countries of the BSB, including Armenia, Azerbaijan, Belarus, Bulgaria, Georgia, Moldova, Romania, Türkiye, and Ukraine. Methods: We selected six priority ruminant diseases (anthrax, brucellosis, Crimean Congo haemorrhagic fever (CCHF), foot-and-mouth disease (FMD), lumpy skin disease (LSD), and peste des petits ruminants (PPR)) that are present or threaten to emerge in the region. Standardized questionnaires were completed by a network of focal points and supplemented with external sources. We examined country and ruminant-specific data such as demographics, economic importance, and value chains in each country. For disease-specific data, we analysed the sanitary status, management strategies, and temporal trends of the selected diseases. Results and discussion: The shift from a centrally planned to a market economy, following the collapse of the Soviet Union, restructured the ruminant sector. This sector played a critical role in rural livelihoods within the BSB. Yet, it faced significant challenges such as the low sustainability of pastoralism, technological limitations, and unregistered farms. Additionally, ruminant health was hindered by informal animal trade as a result of economic factors, insufficient support for the development of formal trade, and socio-cultural drivers. In the Caucasus and Türkiye, where diseases were present, improvements to ruminant health were driven by access to trading opportunities. Conversely, European countries, mostly disease-free, prioritized preventing disease incursion to avoid a high economic burden. While international initiatives for disease management are underway in the BSB, there is still a need for more effective local resource allocation and international partnerships to strengthen veterinary health capacity, protect animal health and improve ruminant production. [ABSTRACT FROM AUTHOR]

Published
2024
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28. GROMACS 2023.2 Manual

Author

Abraham, Mark, Alekseenko, Andrey, Bergh, Cathrine, Blau, Christian, Briand, Eliane, Doijade, Mahesh, Fleischmann, Stefan, Gapsys, Vytautas, Gaurav Garg, Gorelov, Sergey, Gouaillardet, Gilles, Gray, Alan, M. Eric Irrgang, Jalalypour, Farzaneh, Jordan, Joe, Junghans, Christoph, Prashanth Kanduri, Keller, Sebastian, Kutzner, Carsten, Lemkul, Justin A., Lundborg, Magnus, Merz, Pascal, Miletić, Vedran, Morozov, Dmitry, Páll, Szilárd, Schulz, Roland, Shirts, Michael, Shvetsov, Alexey, Soproni, Bálint, Van Der Spoel, David, Turner, Philip, Uphoff, Carsten, Villa, Alessandra, Wingbermühle, Sebastian, Zhmurov, Artem, Bauer, Paul, Hess, Berk, and Lindahl, Erik

Subjects
Software MD Documentation
Abstract

Full documentation for the GROMACS 2023.2 release version.

Published
2023
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29. Serial femtosecond crystallography reveals that photoactivation in a fluorescent protein proceeds via the hula twist mechanism

Author

Fadini, Alisia, Hutchison, Christopher D. M., Morozov, Dmitry, Chang, Jeffrey, Maghlaoui, Karim, Perrett, Samuel, Luo, Fangjia, Kho, Jeslyn C. X., Romei, Matthew G., Morgan, R. Marc L., Orr, Christian M., Cordon-Preciado, Violeta, Fujiwara, Takaaki, Nuemket, Nipawan, Tosha, Takehiko, Tanaka, Rie, Owada, Shigeki, Tono, Kensuke, Iwata, So, Boxer, Steven G., Groenhof, Gerrit, Nango, Eriko, van Thor, Jasper J., and Biotechnology and Biological Sciences Research Council (BBSRC)

Subjects
fluoresenssi, proteiinit, valokemia, General Chemistry, 03 Chemical Sciences
Abstract

Chromophore cis/trans photoisomerization is a fundamental process in chemistry and in the activation of many photosensitive proteins. A major task is understanding the effect of the protein environment on the efficiency and direction of this reaction compared to what is observed in the gas and solution phases. In this study, we set out to visualize the hula twist (HT) mechanism in a fluorescent protein, which is hypothesized to be the preferred mechanism in a spatially constrained binding pocket. We use a chlorine substituent to break the twofold symmetry of the embedded phenolic group of the chromophore and unambiguously identify the HT primary photoproduct. Through serial femtosecond crystallography, we then track the photoreaction from femtoseconds to the microsecond regime. We observe signals for the photoisomerization of the chromophore as early as 300 fs, obtaining the first experimental structural evidence of the HT mechanism in a protein on its femtosecond-to-picosecond timescale. We are then able to follow how chromophore isomerization and twisting lead to secondary structure rearrangements of the protein β-barrel across the time window of our measurements. peerReviewed

Published
2023

30. Hyperon signatures in the PANDA experiment at FAIR

Author

Abazov, Viktor, Abramov, Victor, Achenbach, Patrick, Afedulidis, Orestis, Ahrens, Lennart, Akram, Adeel, Al-Turany, Mohammad, Albrecht, Malte, Alexeev, Gennady, Ali, Ahmed, Alicke, Anna, Amsler, Claude, Antokhin, Evgeny, Appagere, Gandharva, Augustin, Ingo, Azizi, Kazem, Balanutsa, Pavel, Balashoff, Alexander, Barnyakov, Alexander Yu., Barucca, Gianni, Belias, Anastasios, Beloborodov, Konstantin, Bergert, Roman, Bianconi, Andrea, Bleser, Sebastian, Blinov, Alexander E., Blinov, Vladimir E., Bloms, Johannes, Boca, Gianluigi, Bodenschatz, Simon, Boelger, Niels, Böhm, Merlin, Böhm, Ralph, Bökelmann, Stephan, Bölting, Michael, Bonaventura, Daniel, Boukharov, Alexander, Bracco, Gianangelo, Bragadireanu, Mario, Brand, Philipp, Brinkmann, Kai-Thomas, Brück, Lisa, Bukharova, Marina, Bukreeva, Sofia, Bumrungkoh, Denchay, Bussa, Maria Pia, Calen, Hans, Calvo, Daniela, Capozza, Luigi, Caselle, Michele, Cederwall, Bo, Chauhan, Vinee, Chernetsky, Viacheslav, Chilingaryan, Suren, Coen, Sebastian, Corell, Oliver, Crede, Volker, Dav`ı, Fabrizio, de Boer, Remco, De Remigis, Paolo, Demekhin, Alexey, Denig, Achim, Denizli, Haluk, Deppe, Harald, Derichs, Artur, Diehl, Stefan, Dippel, Lara, Dobbs, Sean, Dodokhov, Valery Kh., Dolgolenko, Anatoly, Domagala, Mariusz, Monasterio, Maria Doncel, Dormenev, Valery, Dosdall, Rene, Dritschler, Timo, Duda, Daniel, Düren, Michael, Dzhygadlo, Roman, Efremov, Alexander, Eick, Hanna, Er, Nuray, Erlen, Thorsten, Erokhin, Alexandr, Esmail, Waleed, Eugenio, Paul, Eyrich, Wolfgang, Falk, Aniko, Fedorets, Pavel, Fedotov, Gleb, Feldbauer, Florian, Ferapontov, Valeri, Filippi, Alessandra, Filo, Grzegorz, Finger Jr, Michael, Finger, Miroslav, Fink, Mario, Firlej, Miroslaw, Fiutowski, Tomasz, Flemming, Holger, Frech, Jens, Frenkel, Celina Marie, Fritsch, Miriam, Galoyan, Aida, Gandhi, Keval, Gerasimov, Alexander, Gerhardt, Andreas, Giebenhain, Kim Tabea, Glaab, Daniel, Glazier, Derek, Glennemeier-Marke, Simon, Goldenbaum, Frank, Golovanov, Georgy, Golubev, Alexander, Goncharenko, Yury, Götzen, Klaus, Gou, Boxing, Gumbert, Katja, Hagdorn, Rene, Hahn, Christopher, Hammann, Christian, Hartmann, Jan, Heine, Greta, Heinsius, Fritz-Herbert, Heinz, Andreas, Held, Thomas, Herold, Christoph, Hetz, Benjamin, Himmelreich, Mathilde, Hoek, Matthias, Hofmann, Jan, Holtmann, Tobias, Hölzken, Fabian, Huang, Guang Shun, Idzik, Marek, Ireland, David, Jary, Vladimir, Jiang, Peiyong, Jiang, Zhu, Johansson, Tord, Kalita, Kushal, Kalugin, Nikita, Kannika, Jakapat, Kantsyrev, Alexey, Karabowicz, Radoslaw, Käser, Alexander, Kazlou, Dzmitry, Kegel, Sophie, Keshk, Iman, Kesik, Grazina, Keskin, Umut, Ketzer, Bernhard, Khalid, Faiza, Khoukaz, Alfons, Klasen, Roman, Kliemt, Ralf, Kobdaj, Chinorat, Koch, Helmut, Koch, Stefan, Kohlen, Jonas, Kononov, Sergey, Kopf, Bertram, Kopmann, Andreas, Korchak, Oleksandr, Korcyl, Grzegorz, Korcyl, Krzysztof, Korzhik, Mikhail, Kosinski, Tymoteusz, Kozak, Natalia, Krauss, Steffen, Kravchenko, Evgeniy A., Kripko, Aron, Kristi, Nikolai, Kunze, Marcel, Kupsc, Andrzej, Kurilla, Udo, Küßner, Meike, Kutuzov, Sergey, Kuyanov, Ivan A., Kveton, Antonin, Ladygina, Elena, Lalik, Rafal, Lancioni, Giovanni, Lattery, Mark, Lauth, Werner, Lebiedowicz, Piotr, Lehmann, Albert, Lehmann, Dorothee, Lehmann, Inti, Leithoff, Hans Heinrich, Levin, Andrei, Li, Jinxin, Liang, Yutie, Limphirat, Ayut, Linzen, Lukas, Lisowski, Edward, Liu, Beijiang, Liu, Chunxiu, Liu, Dong, Liu, Zhenan, Loehner, Herbert, Lucherini, Vincenzo, Lühning, Jost, Luschevskaya, Elena, Lynen, Uli, Maas, Frank, Maldaner, Stephan, Malige, Akshay, Malyshev, Oleg, Manaenkov, Sergey, Manasatitpong, Keerati, Mannweiler, Christian, Marciniewski, Pawel, Marcisovsky, Michal, Marton, Johann, Maslova, Eseniya, Matusiak, Michal, Matveev, Vladimir A., Mazza, Giovanni, Melnychuk, Dmytro, Mengucci, Paolo, Merkel, Harald, Messchendorp, Johan, Micha lek, Mateusz, Miehling, Daniel, Miklukho, Oleg, Minaev, Nikolay, Missevitch, Oleg, Mochalov, Vasiliy V., Moiseev, Vyacheslav, Molenda, Aleksandra, Montalto, Luigi, Moron, Jakub, Morozov, Dmitry, Motzko, Christof, Müller, Ulrich, Müllers, Johannes, Nasawad, Thanachot, Natali, Pier Paolo, Nerling, Frank, Nogach, Larisa, Noll, Oliver, Novikov, Konstantin, Novy, Josef, Nowakowski, Krzysztof, Olgun, Asiye Tugba, Orfanitski, Sergey, Orsich, Pavel, Orth, Herbert, Panjushkin, Vsevolod, Pankonin, Sven, Panyuschkina, Alena, Paone, Nicola, Papenbrock, Michael, Pelizäus, Marc, Peng, Hai Ping, Perez-Andrade, Gabriela, Peter, Marvin, Peters, Klaus, Petersen, Jannik, Piskun, Alexey A., Pivovarov, Sergey, Pochodzalla, Josef, Pongampai, Surachai, Poznanski, Piotr, Prasuhn, Dieter, Prochazka, Ivan, Przygoda, Witold, Pyata, Evgeniy, Pysz, Krzysztof, lazek, Joanna P., Qi, Hang, Quin, Jiajia, Rai, Ajay Kumar, Rathod, Narendra, Reeh, Andreas, Regina, Jenny, Reher, Jan, Reicherz, Gerhard, Rieger, Jana, Rigato, Valentino, Rinaldi, Daniele, Ritman, James, Rocco, Elena, Piñeiro, David Rodríguez, Rosner, Christoph, Ryazantsev, Andrey, Ryzhikov, Sergey, Sachs, Matthias, Salisbury, Ben, Samartsev, Alexander, Scalise, Lorenzo, Schadmand, Susan, Schäfer, Wolfgang, Schepers, Georg, Schlimme, Soeren, Schmidt, Christian Joachim, Schmidt, Christoph, Schmidt, Mustafa, Schmitt, Lars, Schnier, Claudius, Schönning, Karin, Schubert, René, Schupp, Falk, Schwarz, Carsten, Schwiening, Joachim, Sefzick, Thomas, Seifen, Tobias, Seitz, Bjoern, Semenov, Pavel A., Seth, Kam, Sfienti, Concettina, Shein, Igor, Shen, Xiaoyan, Shimanski, Stepan, Simantathammakul, Tawanchat, Skachkova, Anna N., Slunecka, Miloslav, Smyrski, Jerzy, Snoeyink, Mark, Sobol, Bartosz, Spataro, Stefano, Stavinskiy, Alexey Valentinovich, Steinacher, Michael, Steinen, Marcell, Stepanov, Vladimir, Stockmanns, Tobias, Straube, Marcel, Strickert, Marc, Strokovsky, Evgeny A., Sun, Shengsen, Sun, Yan Kun, Suzuki, Ken, Swientek, Krzysztof, Szczurek, Antoni, Takatsch, Chris N., Tarasiuk, Jerzy, Täschner, Alexander, Tavukoglu, Zeynep, Tegner, Per-Erik, Terlecki, Przemyslaw, Thoma, Ulrike, Tikhonov, Yury, Tokmenin, Valery, Tomasek, Lukas, Tomasi-Gustafsson, Egle, Traxler, Michael, Triffterer, Tobias, Tröll, Nils, Uzhinsky, Vladimir, Varentsov, Victor, Vasiliev, Alexander N., Veretennikov, Denis, Verkheev, Alexander, Vestrick, Sophia, Virius, Miroslav, Vishnevsky, Evgeny, Vodopianov, Alexander, Volf, Michal, Voss, Bernd, Wang, Fei, Wasem, Thomas, Watts, Daniel, Weidner, Frederik, Welde, Leonard, Wendlandt, Katharina, Wenzel, Christopher, Wettig, Vincent, Wieczorek, Peter, Wiedner, Ulrich, Wintz, Peter, Wolf, Yannic, Wolff, Sahra, Wolke, Magnus, Wongprachanukul, Narupon, Wronka, Slawomir, Xiao, Ting, Xu, Huagen, Yakutin, Alexander, Yerlikaya, Seda, Yilmaz, Ali, Yu, Chunxu, Zakrzewski, Tomasz, Zaunick, Hans-Georg, Zhang, Xiao, Zhao, Guang, Zhao, Jingzhou, Zhdanov, Andrey, Zheng, Bo, Zhou, Xiao Rong, Zhu, Wenjing, Zhuravlev, Nikolai I., Zimmermann, Iris, Ziyu, Zhang, and Zwieglinski, Boguslaw

Subjects
High Energy Physics - Experiment (hep-ex), hep-ex, FOS: Physical sciences, Nuclear Physics - Experiment, Nuclear Experiment (nucl-ex), nucl-ex, Nuclear Experiment, Particle Physics - Experiment, High Energy Physics - Experiment
Abstract

We present a detailed simulation study of the signatures from the sequential decays of the triple-strange pbar p -> {\Omega}+{\Omega}- -> K+{\Lambda}barK- {\Lambda} -> K+pbar{\pi}+K-p{\pi}- process in the PANDA central tracking system with focus on hit patterns and precise time measurement. We present a systematic approach for studying physics channels at the detector level and develop input criteria for tracking algorithms and trigger lines. Finally, we study the beam momentum dependence on the reconstruction efficiency for the PANDA detector.

Published
2023
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32. Natural Products/Bioactive Compounds as a Source of Anticancer Drugs

Author

Asma, Syeda Tasmia, primary, Acaroz, Ulas, additional, Imre, Kálmán, additional, Morar, Adriana, additional, Shah, Syed Rizwan Ali, additional, Hussain, Syed Zajif, additional, Arslan-Acaroz, Damla, additional, Demirbas, Hayri, additional, Hajrulai-Musliu, Zehra, additional, Istanbullugil, Fatih Ramazan, additional, Soleimanzadeh, Ali, additional, Morozov, Dmitry, additional, Zhu, Kui, additional, Herman, Viorel, additional, Ayad, Abdelhanine, additional, Athanassiou, Christos, additional, and Ince, Sinan, additional

Published
2022
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33. Superconducting photon detectors

Author

Morozov, Dmitry V., Casaburi, Alessandro, and Hadfield, Robert H.

Subjects
General Physics and Astronomy
Abstract

The ability to detect individual light quanta – single photons – is prized across many fields of physics from astronomy to quantum optics. Superconducting photon detectors offer exceptional performance in terms of sensitivity, spectral range and timing resolution. In this review, we introduce the underlying physics of photon absorption in superconducting devices. We then present detailed case studies of contemporary superconducting detector technologies for photon counting at visible and infrared wavelengths. We conclude with a perspective on future developments in this exciting area.

Published
2021
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34. Renovation of former industrial areas by BREEAM in city of London

Author

Telichenko Valery, Benuzh Andrey, and Morozov Dmitry

Subjects
Environmental sciences, GE1-350
Abstract

The main focus at this article on BREEAM Community scheme which planning of large-scale developments taking into account the use of former industrial areas. Construction on such lands of new modern areas is beneficial for both the developer and the city. In this case, it is ideally possible to show the use of “green” technologies and standards with aim of increasing the environmental situation of the areas, the creation of reactionary zones. The article describes three steps involved in the assessment of sustainability at the masterplanning level and five assessment categories which are considered through appropriate criteria. Was made a diagram of division into types of reconstructed objects and their inherent functions after reconstruction. Considered an example of Renovation of former industrial areas by BREEAM at King’s Cross in London.

Published
2019
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36. BioExcel-2 D3.7 – User Community Support and Engagement Report (final)

Author

Proeme, Arno, Norman, Richard, Villa, Alessandra, Morozov, Dmitry, Hospital, Adam, Gapsys, Vytautas, Bonvin, Alexandre, Aristarc Suriñach, and Martí Municoy

Abstract

This document is a final update to deliverables D3.4 - User Community Support and Engagement Report (halftime update) (PM18) and D3.5 - Best Practice Guides (PM24). It describes BioExcel’s community support and engagement activities from PM19 (July 2020) up until and including PM42 (June 2022). It includes a summary for this period of the community events BioExcel (co-)organised or participated in, the in-depth support we have offered to users, our work on standards and best practice, including updates to our Best Practice Guides, and how we have analysed user & community needs to drive our activities. During this reporting period BioExcel has: (Co-)organised and/or participated in 136 community events, attended by around 10 000 community members, at which we shared scientific results from the BioExcel Use Cases and/or the capabilities of BioExcel software, at external workshops and conferences and at training courses run together with PRACE, the EuroHPC National Competence Centres, and other HPC CoEs. We organised a workshop - “Best Practices in QM/MM Simulation of Biomolecular Systems”, which was attended by around 1000 people. Through our support and engagement work we have started seeing increased uptake of the new GROMACS-CP2K interface we developed, and we deem to have successfully seeded a new user community. Hosted 23 BioExcel Webinars, attended live by over 1700 people. Seen our YouTube channel gain significant momentum, with ~4x greater content consumption rate and ~3x faster growth in subscribers than during the previous reporting period. Provided direct in-depth support to over 1900 community members, including by answering around 1500 questions on the AskBioExcel and GROMACS forums combined. Created, improved, and made available 16 tutorials for users of BioExcel core software. Engaged in existing and new pilot projects with industry and pursued our planned strategy regarding what BioExcel will deliver for industrial users, namely: Prepare and establish BioExcel Enterprises Consolidate existing and establish new business opportunities Further define and validate the BioExcel value proposition Supported the National Centre for Supercomputing Applications in Bulgaria, which hosts the EuroHPC Discoverer system by providing lectures and hands-on training in BioExcel software functionality, methodologies and performance on two separate courses. Continued to participate in community development of standards such as the Common Workflow Language, FAIR computational workflows, FAIR Digital Objects, BioCompute Objects and Research Object Crate Expanded the Best Practice Guides (BPGs) first published at PM24 as part of deliverable D3.5 - Best Practice Guides as we described and planned in that deliverable. We have: Updated the CP2K biomolecular QM/MM BPG to include usage of GROMACS together with CP2K for QM/MM simulation of biomolecular systems Captured the outcomes of our workshop on Best Practices in QM/MM Simulation of Biomolecular Systems in a new software-agnostic Best Practice Guide on general QM/MM modelling & simulation methodology. Added guidance to the GROMACS BPG detailing how to obtain good performance on two additional European HPC systems - JUWELS BOOSTER (PRACE) and Discoverer (EuroHPC) - and on using GROMACS postprocessing tools. Adapted activities on an ongoing basis, including after gathering input, including feedback, from over 1700 community members and analysing user needs. Interviewed 8 Key Opinion Leaders (KOLs) in a range of biomolecular modelling & simulation research areas to help us assess what we have achieved in BioExcel-2 and, crucially, to help us look ahead and calibrate our vision towards the exascale future. Designed and begun to prototype an Ambassador programme in order to strengthen links with local computational biomolecular research communities across the EU, starting with EU13 member states. &nbsp

Published
2022
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37. BioExcel-2 Deliverable D1.6 – Final project release

Author

Hess, Berk, Proeme, Arno, Morozov, Dmitry, Bonvin, Alexandre, Vargas Honorato, Rodrigo, Gapsys, Vytautas, and de Groot, Bert

Abstract

This document describes the contents of the fourth project release (second in BioExcel-2), of software developed for the core applications in BioExcel. In addition to describing the final releases in BioExcel-2 for the core applications, this document also presents what has been achieved in terms of features and performance for the codes over the entire project timeframe. To provide reference versions of all codes used in the project (e.g. to integrate them in BioExcel workflows and use by other BioExcel teams), the Work Package also makes these formal code releases. This also comes with records describing the current status of the software that results from the planning, development, documentation, and testing processes. The release itself takes the form of a package of Open Source licensed source code with accompanying documentation, tests, benchmarks, and benchmark reports and can be downloaded from https://doi.org/10.5281/zenodo.6761700 or from the BioExcel webpage at http://bioexcel.eu/software/code-repositories. All codes (apart from CP2K whose core development team is external to BioExcel) have now timed the BioExcel release to be in sync with the individual product releases, so there is less confusion for the users, as well as less maintenance and documentation overhead for the developers.

Published
2022
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38. Light nuclei collectivity from √sNN = 3 GeV Au+Au collisions at RHIC

Author

Abdallah, Mohamed Samy, Aboona, Bassam, Adam, Jaroslav, Adamczyk, Leszek, Adams, Joseph R., Adkins, J. Kevin, Agakishiev, Geydar, Aggarwal, I., Aggarwal, Madan Mohan, Ahammed, Zubayer, Aitbaev, A., Alekseev, Igor G., Anderson, Derek M., Aparin, Alexey, Aschenauer, Elke Caroline, Ashraf, Muhammad Usman, Atetalla, Fareha, Averichev, Georgy S., Bairathi, Vipul, Baker, W., Ball Cap, Jonathan Gonzalo, Barish, Kenneth, Behera, Arabinda, Bellwied, Rene, Bhagat, P., Bhasin, Anju, Bielčík, Jaroslav, Bielčíková, Jana, Bordyuzhin, Igor G., Brandenburg, James D., Brandin, Andrei V., Cai, X.Z., Caines, Helen Louise, Calderón de la Barca Sánchez, Manuel, Cebra, Daniel A., Chakaberia, Irakli, Chaloupka, Petr, Chan, B.K., Chang, F.-H., Chang, Z., Chatterjee, A., Chattopadhyay, S., Chen, D., Chen, J., Chen, J.H., Chen, X., Chen, Z., Cheng, J., Choudhury, Subikash, Christie, William, Chu, X., Crawford, Henry J., Csanád, Máté, Daugherity, M., Dedovič, Tatiana G., Deppner, Ingo Martin, Derevschikov, Anatoly A., Dhamija, A., Di Carlo, L., Didenko, Lidia, Dixit, P., Dong, X., Drachenberg, James Lucus, Duckworth, E., Dunlop, James C., Engelage, Jon M., Eppley, Geary Wareham, Esumi, ShinIchi, Evdokimov, Olga Y., Ewigleben, A., Eyser, Kjeld Oleg, Fatemi, Renee H., Fawzi, F.M., Fazio, Salvatore, Feng, C.J., Feng, Y., Finch, Evan, Fisyak, Yuri V., Francisco, Audrey, Fu, C., Gagliardi, Carl A., Galatyuk, Tetyana, Geurts, Frank, Ghimire, N., Gibson, Adam, Gopal, Krishan, Gou, X., Grosnick, David P., Gupta, Anik, Guryn, Włodzimierz, Hamed, Ahmed M., Han, Y., Harabasz, Szymon, Harasty, M.D., Harris, John W., Harrison, H., He, S., He, W., He, X.H., He, Y., Heppelmann, Steven Francis, Herrmann, Norbert, Hoffman, E., Holub, Lukáš, Hu, C., Hu, Q., Hu, Y., Huang, H., Huang, H.Z., Huang, Shengli, Huang, T., Huang, X., Huang, Y., Humanic, Thomas J., Isenhower, D., Isshiki, M., Jacobs, William W., Jena, Chitrasen, Jentsch, Alexander, Ji, Y., Jia, J., Jiang, K., Ju, X., Judd, Eleanor G., Kabana, Sonia, Kabir, M.L., Kagamaster, Skipper, Kalinkin, Dmitry, Kang, K., Kapukchyan, David, Kauder, Kolja, Ke, Hongwei, Keane, Declan, Kechechyan, Armen, Kelsey, Matthew, Khyzhniak, Yevheniia V., Kikoła, Daniel P., Kimelman, B., Kincses, D., Kisel, Ivan, Kiselev, A., Knospe, Anders Garritt, Ko, H.S., Kočenda, L. M., Korobitsin, A., Kosarzewski, Leszek Krzysztof, Kramárik, Lukáš, Kravtsov, Peter, Kumar, Lokesh, Kumar, Shyam, Kunnawalkam Elayavalli, Raghav, Kwasizur, Joseph H., Lacey, Roy Alphanso, Lan, S., Landgraf, Jeffery M., Lauret, Jerome, Lebedev, Alexei, Lednicky, Richard, Lee, J.H., Leung, Y.H., Lewis, N., Li, C., Li, W., Li, Xiaomei, Li, Y., Liang, X., Liang, Y., Licenik, Robert, Lin, T., Lin, Y., Lisa, Michael A., Liu, F., Liu, H., Liu, P., Liu, T., Liu, X., Liu, Y., Liu, Z., Ljubicic, Tonko A., Llope, William Joseph, Longacre, Ronald S., Loyd, E., Lu, T., Lukow, N.S., Luo, X.F., Ma, L., Ma, R., Ma, Yu-Gang, Magdy Abdelwahab Abdelrahman, Niseem, Mallick, Dukhishyam, Manukhov, S.L., Margetis, Spyridon, Markert, Christina, Matis, Howard S., Mazer, Joel Anthony, Minaev, Nikolai G., Mioduszewski, Saskia, Mohanty, Bedangadas, Mondal, Mriganka Mouli, Mooney, Isaac A., Morozov, Dmitry A., Mukherjee, Ayon, Nagy, M., Nam, J.D., Nasim, Md., Nayak, Kishora, Neff, D., Nelson, John M., Nemes, Daniel B., Nie, Maowu, Nigmatkulov, Grigory A., Niida, Takafumi, Nishitani, R., Nogach, Larisa V., Nonaka, Toshihiro, Nunes, A.S., Odyniec, Grazyna Janina, Ogawa, Akio, Oh, S., Okorokov, Vitaly A., Okubo, K., Page, Brian S., Pak, Robert, Pan, Jinjin, Pandav, A., Pandey, Ashutosh Kumar, Panebratsev, Yuri, Parfenov, P., Paul, A., Pawlik, Bogdan, Pawłowska, Diana, Perkins, Chris, Pinsky, Lawrence, Pluta, Jan Marian, Pokhrel, B.R., Porter, Jeffrey Brent, Posik, Matthew, Prozorova, V., Pruthi, Navneet Kumar, Przybycien, Mariusz, Putschke, Jörn H., Qiu, H., Quintero, Amilkar, Racz, C., Radhakrishnan, Sooraj Krishnan, Raha, N., Ray, Robert L., Reed, Rosi Jan, Ritter, Hans Georg, Robotkova, M., Rogačevskij, Oleg V., Romero, Juan L., Roy, D., Ruan, Lijuan, Sahoo, A.K., Sahoo, Nihar Ranjan, Sako, H., Salur, Sevil, Samigullin, Eduard, Sandweiss, Jack H., Sato, S., Schmidke, William B., Schmitz, Norbert, Schweid, Benjamin R., Seck, Florian, Seger, Janet Elizabeth, Seto, Richard, Seyboth, Peter, Shah, N., Shahaliev, Ehtiram, Shanmuganathan, Prashanth V., Shao, M., Shao, T., Sharma, R., Sheikh, Ashik Ikbal, Shen, D.Y., Shi, S.S., Shi, Y., Shou, Q.Y., Sichtermann, Ernst P., Sikora, Rafał, Singh, Jagbir, Singha, Subhash, Sinha, P., Skoby, M.J., Smirnov, Nikolai, Söhngen, Y., Solyst, William, Song, Y., Spinka, Harold. M., Srivastava, Brijesh Kumar, Stanislaus, T. D. Shirvel, Stefaniak, Maria, Stewart, David J., Strichanov, Michail Nikolaevič, Stringfellow, Blair, Suaide, Alexandre Alarcon do Passo, Šumbera, Michal, Summa, Branden, Sun, X.M., Sun, X., Sun, Y., Surrow, Bernd, Svirida, Dmitry N., Sweger, Z.W., Szymański, Paweł, Tang, Aihong, Tang, Zebo, Taranenko, Arkadiy, Tarnowsky, Terence J., Thomas, James H., Timmins, Anthony Robert, Tlusty, David, Todoroki, Takahito, Tokarev, Mikhail V., Tomkiel, Catherine A., Trentalange, Stephen, Tribble, Robert E., Tribedy, Prithwish, Tripathy, Srikanta Kumar, Truhlar, T., Trzeciak, Barbara Antonina, Tsai, Oleg D., Tu, Z., Ullrich, Thomas, Underwood, David G., Upsal, Isaac, Van Buren, Gene, Vanek, Jan, Vasiliev, Alexander Nikolaevich, Vassiliev, Iouri, Verkest, V., Videbæk, Flemming, Vokal, Stanislav, Voloshin, Sergei, Wang, F., Wang, G., Wang, J.S., Wang, P., Wang, X., Wang, Y., Wang, Z., Webb, Jason C., Weidenkaff, P.C., Westfall, Gary D., Wieman, Howard, Wissink, Scott W., Witt, Richard, Wu, J., Wu, Y., Xi, B., Xiao, Z.G., Xie, G., Xie, W., Xu, H., Xu, N., Xu, Q.H., Xu, Y., Xu, Z., Yan, G., Yang, C., Yang, Q., Yang, S., Yang, Y., Ye, Z., Yi, L., Yip, K., Yu, Y., Zbroszczyk, Hanna Paulina, Zha, W., Zhang, C., Zhang, D., Zhang, J., Zhang, S., Zhang, Y., Zhang, Z.J., Zhang, Zuman, Zhao, F., Zhao, J., Zhao, M., Zhou, C., Zhou, You, Zhu, X., Zurek, Marian, Zyzak, Maksym, Abdallah, Mohamed Samy, Aboona, Bassam, Adam, Jaroslav, Adamczyk, Leszek, Adams, Joseph R., Adkins, J. Kevin, Agakishiev, Geydar, Aggarwal, I., Aggarwal, Madan Mohan, Ahammed, Zubayer, Aitbaev, A., Alekseev, Igor G., Anderson, Derek M., Aparin, Alexey, Aschenauer, Elke Caroline, Ashraf, Muhammad Usman, Atetalla, Fareha, Averichev, Georgy S., Bairathi, Vipul, Baker, W., Ball Cap, Jonathan Gonzalo, Barish, Kenneth, Behera, Arabinda, Bellwied, Rene, Bhagat, P., Bhasin, Anju, Bielčík, Jaroslav, Bielčíková, Jana, Bordyuzhin, Igor G., Brandenburg, James D., Brandin, Andrei V., Cai, X.Z., Caines, Helen Louise, Calderón de la Barca Sánchez, Manuel, Cebra, Daniel A., Chakaberia, Irakli, Chaloupka, Petr, Chan, B.K., Chang, F.-H., Chang, Z., Chatterjee, A., Chattopadhyay, S., Chen, D., Chen, J., Chen, J.H., Chen, X., Chen, Z., Cheng, J., Choudhury, Subikash, Christie, William, Chu, X., Crawford, Henry J., Csanád, Máté, Daugherity, M., Dedovič, Tatiana G., Deppner, Ingo Martin, Derevschikov, Anatoly A., Dhamija, A., Di Carlo, L., Didenko, Lidia, Dixit, P., Dong, X., Drachenberg, James Lucus, Duckworth, E., Dunlop, James C., Engelage, Jon M., Eppley, Geary Wareham, Esumi, ShinIchi, Evdokimov, Olga Y., Ewigleben, A., Eyser, Kjeld Oleg, Fatemi, Renee H., Fawzi, F.M., Fazio, Salvatore, Feng, C.J., Feng, Y., Finch, Evan, Fisyak, Yuri V., Francisco, Audrey, Fu, C., Gagliardi, Carl A., Galatyuk, Tetyana, Geurts, Frank, Ghimire, N., Gibson, Adam, Gopal, Krishan, Gou, X., Grosnick, David P., Gupta, Anik, Guryn, Włodzimierz, Hamed, Ahmed M., Han, Y., Harabasz, Szymon, Harasty, M.D., Harris, John W., Harrison, H., He, S., He, W., He, X.H., He, Y., Heppelmann, Steven Francis, Herrmann, Norbert, Hoffman, E., Holub, Lukáš, Hu, C., Hu, Q., Hu, Y., Huang, H., Huang, H.Z., Huang, Shengli, Huang, T., Huang, X., Huang, Y., Humanic, Thomas J., Isenhower, D., Isshiki, M., Jacobs, William W., Jena, Chitrasen, Jentsch, Alexander, Ji, Y., Jia, J., Jiang, K., Ju, X., Judd, Eleanor G., Kabana, Sonia, Kabir, M.L., Kagamaster, Skipper, Kalinkin, Dmitry, Kang, K., Kapukchyan, David, Kauder, Kolja, Ke, Hongwei, Keane, Declan, Kechechyan, Armen, Kelsey, Matthew, Khyzhniak, Yevheniia V., Kikoła, Daniel P., Kimelman, B., Kincses, D., Kisel, Ivan, Kiselev, A., Knospe, Anders Garritt, Ko, H.S., Kočenda, L. M., Korobitsin, A., Kosarzewski, Leszek Krzysztof, Kramárik, Lukáš, Kravtsov, Peter, Kumar, Lokesh, Kumar, Shyam, Kunnawalkam Elayavalli, Raghav, Kwasizur, Joseph H., Lacey, Roy Alphanso, Lan, S., Landgraf, Jeffery M., Lauret, Jerome, Lebedev, Alexei, Lednicky, Richard, Lee, J.H., Leung, Y.H., Lewis, N., Li, C., Li, W., Li, Xiaomei, Li, Y., Liang, X., Liang, Y., Licenik, Robert, Lin, T., Lin, Y., Lisa, Michael A., Liu, F., Liu, H., Liu, P., Liu, T., Liu, X., Liu, Y., Liu, Z., Ljubicic, Tonko A., Llope, William Joseph, Longacre, Ronald S., Loyd, E., Lu, T., Lukow, N.S., Luo, X.F., Ma, L., Ma, R., Ma, Yu-Gang, Magdy Abdelwahab Abdelrahman, Niseem, Mallick, Dukhishyam, Manukhov, S.L., Margetis, Spyridon, Markert, Christina, Matis, Howard S., Mazer, Joel Anthony, Minaev, Nikolai G., Mioduszewski, Saskia, Mohanty, Bedangadas, Mondal, Mriganka Mouli, Mooney, Isaac A., Morozov, Dmitry A., Mukherjee, Ayon, Nagy, M., Nam, J.D., Nasim, Md., Nayak, Kishora, Neff, D., Nelson, John M., Nemes, Daniel B., Nie, Maowu, Nigmatkulov, Grigory A., Niida, Takafumi, Nishitani, R., Nogach, Larisa V., Nonaka, Toshihiro, Nunes, A.S., Odyniec, Grazyna Janina, Ogawa, Akio, Oh, S., Okorokov, Vitaly A., Okubo, K., Page, Brian S., Pak, Robert, Pan, Jinjin, Pandav, A., Pandey, Ashutosh Kumar, Panebratsev, Yuri, Parfenov, P., Paul, A., Pawlik, Bogdan, Pawłowska, Diana, Perkins, Chris, Pinsky, Lawrence, Pluta, Jan Marian, Pokhrel, B.R., Porter, Jeffrey Brent, Posik, Matthew, Prozorova, V., Pruthi, Navneet Kumar, Przybycien, Mariusz, Putschke, Jörn H., Qiu, H., Quintero, Amilkar, Racz, C., Radhakrishnan, Sooraj Krishnan, Raha, N., Ray, Robert L., Reed, Rosi Jan, Ritter, Hans Georg, Robotkova, M., Rogačevskij, Oleg V., Romero, Juan L., Roy, D., Ruan, Lijuan, Sahoo, A.K., Sahoo, Nihar Ranjan, Sako, H., Salur, Sevil, Samigullin, Eduard, Sandweiss, Jack H., Sato, S., Schmidke, William B., Schmitz, Norbert, Schweid, Benjamin R., Seck, Florian, Seger, Janet Elizabeth, Seto, Richard, Seyboth, Peter, Shah, N., Shahaliev, Ehtiram, Shanmuganathan, Prashanth V., Shao, M., Shao, T., Sharma, R., Sheikh, Ashik Ikbal, Shen, D.Y., Shi, S.S., Shi, Y., Shou, Q.Y., Sichtermann, Ernst P., Sikora, Rafał, Singh, Jagbir, Singha, Subhash, Sinha, P., Skoby, M.J., Smirnov, Nikolai, Söhngen, Y., Solyst, William, Song, Y., Spinka, Harold. M., Srivastava, Brijesh Kumar, Stanislaus, T. D. Shirvel, Stefaniak, Maria, Stewart, David J., Strichanov, Michail Nikolaevič, Stringfellow, Blair, Suaide, Alexandre Alarcon do Passo, Šumbera, Michal, Summa, Branden, Sun, X.M., Sun, X., Sun, Y., Surrow, Bernd, Svirida, Dmitry N., Sweger, Z.W., Szymański, Paweł, Tang, Aihong, Tang, Zebo, Taranenko, Arkadiy, Tarnowsky, Terence J., Thomas, James H., Timmins, Anthony Robert, Tlusty, David, Todoroki, Takahito, Tokarev, Mikhail V., Tomkiel, Catherine A., Trentalange, Stephen, Tribble, Robert E., Tribedy, Prithwish, Tripathy, Srikanta Kumar, Truhlar, T., Trzeciak, Barbara Antonina, Tsai, Oleg D., Tu, Z., Ullrich, Thomas, Underwood, David G., Upsal, Isaac, Van Buren, Gene, Vanek, Jan, Vasiliev, Alexander Nikolaevich, Vassiliev, Iouri, Verkest, V., Videbæk, Flemming, Vokal, Stanislav, Voloshin, Sergei, Wang, F., Wang, G., Wang, J.S., Wang, P., Wang, X., Wang, Y., Wang, Z., Webb, Jason C., Weidenkaff, P.C., Westfall, Gary D., Wieman, Howard, Wissink, Scott W., Witt, Richard, Wu, J., Wu, Y., Xi, B., Xiao, Z.G., Xie, G., Xie, W., Xu, H., Xu, N., Xu, Q.H., Xu, Y., Xu, Z., Yan, G., Yang, C., Yang, Q., Yang, S., Yang, Y., Ye, Z., Yi, L., Yip, K., Yu, Y., Zbroszczyk, Hanna Paulina, Zha, W., Zhang, C., Zhang, D., Zhang, J., Zhang, S., Zhang, Y., Zhang, Z.J., Zhang, Zuman, Zhao, F., Zhao, J., Zhao, M., Zhou, C., Zhou, You, Zhu, X., Zurek, Marian, and Zyzak, Maksym

Abstract

In high-energy heavy-ion collisions, partonic collectivity is evidenced by the constituent quark number scaling of elliptic flow anisotropy for identified hadrons. A breaking of this scaling and dominance of baryonic interactions is found for identified hadron collective flow measurements in √sNN = 3 GeV Au+Au collisions. In this paper, we report measurements of the first- and second-order azimuthal anisotropic parameters, v1 and v2, of light nuclei (d, t, 3He, 4He) produced in √sNN = 3 GeV Au+Au collisions at the STAR experiment. An atomic mass number scaling is found in the measured v1 slopes of light nuclei at mid-rapidity. For the measured v2 magnitude, a strong rapidity dependence is observed. Unlike v2 at higher collision energies, the v2 values at mid-rapidity for all light nuclei are negative and no scaling is observed with the atomic mass number. Calculations by the Jet AA Microscopic Transport Model (JAM), with baryonic mean-field plus nucleon coalescence, are in good agreement with our observations, implying baryonic interactions dominate the collective dynamics in 3 GeV Au+Au collisions at RHIC.

Published
2022

40. Fitness Check 2021 – BioExcel CoE Scalability Report of Flagship codes

Author

Hess, Berk, Gapsys, Vytautas, de Groot, Bert, Bonvin, Alexandre, Vargas Honorato, Rodrigo, Proeme, Arno, Judge, Holly, Morozov, Dmitry, Groenhof, Gerrit, Hospital Adam, Badia, Rosa, and Lezzi, Daniele

Abstract

Report describing the scalability of core BioExcel applications in response to a call in 2021 by the European Commission for a "fitness check" of the Centres of Excellence for HPC Applications.

Published
2022
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42. BioExcel-2 Deliverable 6.3 – High Performance Computing in support of COVID-19 Research

Author

Apostolov, Rossen, Bonvin, Alexandre, Morozov, Dmitry, Soiland-Reyes, Stian, Hospital, Adam, and De Groot, Bert

Abstract

The unexpected emergence and spread of the SARS-CoV-2 virus and COVID-19 disease had a dramatic impact on societies across the world. Very soon it became clear that concerted efforts are needed in the fight against the pandemic. As a focal point for the computational biomolecular research communities in Europe, BioExcel restructured its efforts in support of addressing the crisis. We developed and launched a number of portals for COVID-19 related data management and analysis. High-priority access to compute resources was provided by partner HPC centers. We started numerous collaborative research projects including close partnerships with pharma industry. Community support was extended. We participated in dedicated webinars and presentations to cover methodologies, experience and results from our work. We added a dedicated section to our website under category Research (https://bioexcel.eu/covid-19-research/) to present the various services and activities related to the disease. In this document we summarize the aforementioned activities., Deliverable will be published after it is accepted by the funding agency.

Published
2021
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43. BioExcel-2 D1.5 – Long-term hardware and application roadmap

Author

Hess, Berk, Honorato, Rodrigo Vargas, Teixeira, Jo��o, Bonvin, Alexandre, Proeme, Arno, Morozov, Dmitry, Gapsys, Vytautas, and Soiland-Reyes, Stian

Abstract

This deliverable reports updates on the BioExcel-2 core application roadmaps as presented in deliverable D1.3. The roadmaps have been updated for work performed, as well as for changes in needs driven by both developments on the hardware side and requests of users. In addition, there have been changes in prioritization and new tasks added due to the outbreak of Covid-19, which has spurred a massive amount of research in life sciences. This, in combination with the no-cost extension of the BioExcel-2 project duration, has led to some development tasks being moved to the extension period. The GROMACS development has focused on a number of key user-requested features, in particular adding multiple time stepping, driving simulations with external data, facilitating generation of input data, and better free energy tools. Some of this is still ongoing and a few new user requests have been identified that are worth implementing. The development of performance optimization has prioritized porting of the GPU acceleration of GROMACS to SYCL, targeting AMD GPUs for the new LUMI pre-exascale machine. Also multi-GPU PME is nearly ready through co-design with NVIDIA. Focus on these urgent tasks has meant work on other tasks started later. For the medium term, future effort is planned on performant and flexible APIs to enable more flexible ensemble parallelism for the Exascale. The development of the PMX package followed two main directions. Firstly, the core code was updated with the changes necessary for the successful future usability of the software. In particular, considering the depreciation of Python2, pmx was rewritten in Python3. The continuous support of the main pmx functionalities was ensured. The second major development direction comprises the incorporation of features frequently requested by users, the addition of new mutation libraries and creation of workflows for free energy calculation setup and analysis. HADDOCK’s development focuses on the continuous improvement of the web server, which functions as the main user’s interface, the implementation of relevant features and the design of the new version HADDOCK3. The web server is being co-developed alongside the local HADDOCK version, so that new features (coarse-grained and shape docking, etc.) are readily available in an intuitive and responsive user-friendly interface. A major rework of the current code is in place for what will become HADDOCK3, with a modular design we aim to provide flexibility for workflow creation and a straightforward framework to integrate new tools. This new modular architecture will also enable more efficient execution on HPC resources. To provide users with access to chemical reactivity in biomolecular simulations, we will develop an interface between GROMACS and CP2K, a highly parallelized density functional theory (DFT) computer program. With the new interface, users can perform multi-scale simulations, in which one part of the system is modelled with DFT, while the remainder is described with a molecular mechanics force field (i.e. QM/MM). Our developments focus on providing the community with an accurate, scalable and user-friendly QM/MM solution. Compared to the previous BioExcel software roadmap, which focused on CPMD for DFT functionality in QM/MM simulations, this updated roadmap reflects the project’s transition to CP2K, which has more wide-spread availability and uptake in the community

Published
2021
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44. Probing the Gluonic Structure of the Deuteron with J/ψ Photoproduction in d+Au Ultraperipheral Collisions

Author

Abdallah, Mohamed, Aboona, Bassam, Adam, Jaroslav, Adamczyk, Leszek, Adams, Joseph, Adkins, Kevin, Agakishiev, Geydar, Aggarwal, Ishu, Aggarwal, Madan, Ahammed, Zubayer, Aitbaev, A., Alekseev, Igor, Anderson, Derek, Aparin, Alexey, Aschenauer, Elke-Caroline, Ashraf, Muhammad Usman, Atetalla, Fareha, Attri, Anjali, Averichev, Georgy, Bairathi, Vipul, Baker, William, Ball Cap, Jonathan Gonzalo, Barish, Kenneth, Behera, Arabinda, Bellwied, Rene, Bhagat, Pratibha, Bhasin, Anju, Bielcik, Jaroslav, Bielcikova, Jana, Bordyuzhin, Igor, Brandenburg, James, Brandin, Andrei, Bunzarov, Ivan, Cai, Xiang-Zhou, Caines, Helen, Calderon de la Barca Sanchez, Manuel, Cebra, Daniel, Chakaberia, Irakli, Chaloupka, Petr, Chan, Brian, Chang, Feng-Han, Chang, Zilong, Chankova-Bunzarova, Nedialka, Chatterjee, Arghya, Chattopadhyay, Subhasis, Chen, Ding, Chen, Jia, Chen, Jinhui, Chen, Xiaolong, Chen, Zhenyu, Cheng, Jianping, Chevalier, Malia, Choudhury, Subikash, Christie, W., Christie, Bill, Chu, Xiaoxuan, Crawford, Hank, Csanad, Mate, Daugherity, Michael, Dedovich, Tatiana, Deppner, Ingo, Derevschikov, Anatoly, Dhamija, Arushi, Di Carlo, Launa, Didenko, Lidia, Dixit, Prabhupada, Dong, Xin, Drachenberg, James, Duckworth, Eddie, Dunlop, James, Elsey, Nicholas, Engelage, Jack, Eppley, Geary, Esumi, ShinIchi, Evdokimov, Olga, Ewigleben, Annika, Eyser, Oleg, Fatemi, Renee, Fawzi, Fares, Fazio, Salvatore, Federic, Pavol, Fedorisin, Jan, Feng, Chan-Jui, Feng, Yicheng, Filip, Peter, Finch, Evan, Fisyak, Yuri, Francisco, Audrey, Fu, Chuan, Fulek, Lukasz, Gagliardi, Carl, Galatyuk, Tatyana, Geurts, Frank, Ghimire, Navagyan, Gibson, Adam, Gopal, Krishan, Gou, Xingrui, Grosnick, David, Gupta, Anik, Guryn, Wlodek, Hamad, Ayman, Hamed, Ahmed, Han, Yiding, Harabasz, Szymon, Harasty, Matthew, Harris, John, Harrison, Hannah, He, Shu, He, Wanbing, He, Xionghong, He, Yang, Heppelmann, Samuel, Heppelmann, Steven, Herrmann, Norbert, Hoffman, Eric, Holub, Lukas, Hu, C., Hu, Q., Hu, Yu, Huang, Hao, Huang, Huan, Huang, Shengli, Huang, Te-Chuan, Huang, Xinjie, Huang, Yan, Humanic, T.J., Igo, George, Isenhower, Donald, Isshiki, M., Jacobs, William, Jena, Chitrasen, Jentsch, Alexander, Ji, Yuanjing, Jia, Jiangyong, Jiang, Kun, Ju, Xinyue, Judd, Eleanor, Kabana, Sonia, Kabir, Md Latiful, Kagamaster, Skipper, Kalinkin, Dmitry, Kang, Kejun, Kapukchyan, David, Kauder, Kolja, Ke, Hongwei, Keane, Declan, Kechechyan, Armen, Kelsey, Matthew, Khyzhniak, Yevheniia, Kikola, Daniel, Kim, Chong, Kimelman, Benjamin, Kincses, Daniel, Kisel, Ivan, Kiselev, Alexander, Knospe, Anders, Ko, Ho San, Kochenda, Leonid, Korobitsin, A., Kosarzewski, Leszek, Kramarik, Lukas, Kravtsov, Petr, Kumar, Lokesh, Kumar, Shyam, Kunnawalkam Elayavalli, Raghav, Kwasizur, Joseph, Lacey, Roy, Lan, Shaowei, Landgraf, Jeffery, Lauret, Jerome, Lebedev, Alexei, Lednicky, Richard, Lee, Jeong-Hun, Leung, Yue-Hang, Lewis, Nicole, Li, Changfeng, Li, Cheng, Li, Wei, Li, Xin, Li, Yuanjing, Liang, Xilin, Liang, Yue, Licenik, Robert, Lin, Ting, Lin, Yufu, Lisa, Mike, Liu, Feng, Liu, Huanzhao, Liu, Hui, Liu, Peifeng, Liu, Tong, Liu, Xiaoyu, Liu, Yanfang, Liu, Zhen, Ljubicic, Tonko, Llope, W.J., Longacre, R.S., Loyd, Erik, Lu, T., Lukow, Nicholas, Luo, Xiaofeng, Ma, Long, Ma, Rongrong, Ma, Yu-Gang, Magdy Abdelwahab Abdelrahman, Niseem, Mallick, Debasish, Manukhov, S.L., Margetis, Spiros, Markert, Christina, Matis, Howard, Mazer, Joel, Minaev, Nikolai, Mioduszewski, Saskia, Mohanty, Bedanga, Mondal, Mriganka, Mooney, Isaac, Morozov, Dmitry, Mukherjee, Ayon, Nagy, Marton, Nam, J.D., Nasim, Md., Nayak, Kishora, Neff, Dylan, Nelson, John, Nemes, Daniel, Nie, Maowu, Nigmatkulov, Grigory, Niida, Takafumi, Nishitani, Risa, Nogach, Larisa, Nonaka, Toshihiro, Nunes, Ana Sofia, Odyniec, Grazyna, Ogawa, Akio, Oh, Saehanseul, Okorokov, Vitalii, Okubo, K., Page, Brian, Pak, Robert, Pan, Jinjin, Pandav, Ashish, Pandey, Ashutosh, Panebratsev, Yuri, Parfenov, Petr, Pinsky, Lawrence, Paul, A., Pawlik, Bogdan, Pawlowska, Diana, Perkins, Chris, Pluta, Jan, Pokhrel, Babu, Ponimatkin, Georgij, Porter, Jeff, Posik, Matthew, Prozorova, Veronika, Pruthi, Navneet Kumar, Przybycien, Mariusz, Putschke, Joern, Qiu, Hao, Quintero, Amilkar, Racz, Cameron, Radhakrishnan, Sooraj, Raha, Nandita, Ray, Lanny, Reed, Rosi, Ritter, Hans Georg, Robotkova, Monika, Rogachevskiy, Oleg, Romero, Juan, Roy, Diptanil, Ruan, Lijuan, Rusnak, Jan, Sahoo, Aswini, Sahoo, Nihar, Sako, Hiroyuki, Salur, Sevil, Samigullin, E., Sandweiss, Jack, Sato, Susumu, Schmidke, Bill, Schmitz, Norbert, Schweid, Benjamin, Seck, Florian, Seger, Janet, Sergeeva, Maria, Seto, Richard, Seyboth, Peter, Shah, Neha, Shahaliev, Ehtiram, Shanmuganathan, Prashanth, Shao, Ming, Shao, Tianhao, Sharma, R., Sheikh, Ashik Ikbal, Shen, Diyu, Shi, Shusu, Shi, Yingying, Shou, Qi-Ye, Sichtermann, Ernst, Sikora, Rafal, Simko, Miroslav, Singh, Jagbir, Singha, Subhash, Sorensen, Paul, Sinha, P., Skoby, Michael, Smirnov, Nikolai, Soehngen, Yannick, Solyst, William, Song, Youqi, Spinka, H.M., Srivastava, Brijesh, Stanislaus, Shirvel, Stefaniak, Maria, Stewart, David, Strikhanov, Mikhail, Stringfellow, Blair, Suaide, Alexandre Alarcon, Sumbera, Michal, Summa, Branden, Sun, Xiangming, Sun, Xu, Sun, Yongjie, Sun, Yuliang, Surrow, Bernd, Svirida, Dmitry, Sweger, Zachary, Szymanski, Pawel, Tang, Aihong, Tang, Zebo, Taranenko, Arkadiy, Tarnowsky, Terry, Thomas, J.H., Timmins, Anthony, Tlusty, David, Todoroki, Takahito, Tokarev, Michael, Tomkiel, Catherine, Trentalange, Steven, Tribble, Robert, Tribedy, Prithwish, Tripathy, Srikanta Kumar, Truhlar, Tomas, Trzeciak, Barbara, Tsai, Oleg, Tu, Zhoudunming (Kong), Ullrich, Thomas, Underwood, Dave, Upsal, Isaac, Van Buren, Gene, Vanek, Jan, Vasiliev, Alexander, Vassiliev, Iouri, Verkest, Veronica, Videbaek, Flemming, Vokal, Stanislav, Voloshin, Sergei, Wang, Fuqiang, Wang, Gang, Wang, Jiansong, Wang, Pengfei, Wang, Xiaofeng, Wang, Yaping, Wang, Yi, Wang, Zhen, Webb, Jason, Weidenkaff, Philipp, Wen, Liwen, Westfall, Gary, Wieman, Howard, Wissink, Scott, Witt, Richard, Wu, Jin, Wu, Junlin, Wu, Yang, Xi, Baoshan, Xiao, Zhigang, Xie, Guannan, Xie, Wei, Xu, Haojie, Xu, Nu, Xu, Qinghua, Xu, Yike, Xu, Zhangbu, Xu, Zhiwan, Yan, Gaoguo, Yang, Chi, Yang, Qian, Yang, Shuai, Yang, Yi, Ye, Zaochen, Ye, Zhenyu, Yi, Li, Yip, Kin, Yu, Yi, Zbroszczyk, Hanna, Zha, Wangmei, Zhang, ChunJian, Zhang, Dingwei, Zhang, Jinlong, Zhang, Xiaoping, Zhao, F., Zhang, Shenghui, Zhang, Song, Zhang, Yapeng, Zhang, Yifei, Zhang, Yu, Zhang, Zhe-Jia, Zhang, Zhengqiao, Zhang, Ziyue, Zhao, Jie, Zhao, M., Zhou, Chensheng, Zhou, Yingjie, Zhu, Xianglei, Zurek, Maria, and Zyzak, Maksym

Subjects
Nuclear Theory, nucl-th, hep-ex, FOS: Physical sciences, nucl-ex, High Energy Physics - Experiment, Nuclear Theory (nucl-th), High Energy Physics - Experiment (hep-ex), Nuclear Physics - Theory, High Energy Physics::Experiment, Nuclear Physics - Experiment, Nuclear Experiment (nucl-ex), Nuclear Experiment, Particle Physics - Experiment
Abstract

Understanding gluon density distributions and how they are modified in nuclei are among the most important goals in nuclear physics. In recent years, diffractive vector meson production measured in ultra-peripheral collisions (UPCs) at heavy-ion colliders has provided a new tool for probing the gluon density. In this Letter, we report the first measurement of $J/\psi$ photoproduction off the deuteron in UPCs at the center-of-mass energy $\sqrt{s_{_{\rm NN}}}=200~\rm GeV$ in d$+$Au collisions. The differential cross section as a function of momentum transfer $-t$ is measured. In addition, data with a neutron tagged in the deuteron-going Zero-Degree Calorimeter is investigated for the first time, which is found to be consistent with the expectation of incoherent diffractive scattering at low momentum transfer. Theoretical predictions based on the Color Glass Condensate saturation model and the gluon shadowing model are compared with the data quantitatively. A better agreement with the saturation model has been observed. With the current measurement, the results are found to be directly sensitive to the gluon density distribution of the deuteron and the deuteron breakup, which provides insights into the nuclear gluonic structure., Comment: Final published version Phys. Rev. Lett. 128, 122303

Published
2021

45. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Author

Morozov, Dmitry, primary, Mironov, Vladimir, additional, Moryachkov, Roman V., additional, Shchugoreva, Irina A., additional, Artyushenko, Polina V., additional, Zamay, Galina S., additional, Kolovskaya, Olga S., additional, Zamay, Tatiana N., additional, Krat, Alexey V., additional, Molodenskiy, Dmitry S., additional, Zabluda, Vladimir N., additional, Veprintsev, Dmitry V., additional, Sokolov, Alexey E., additional, Zukov, Ruslan A., additional, Berezovski, Maxim V., additional, Tomilin, Felix N., additional, Fedorov, Dmitri G., additional, Alexeev, Yuri, additional, and Kichkailo, Anna S., additional

Published
2021
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47. The Role of Small-Angle X-Ray Scattering and Molecular Simulations in 3D Structure Elucidation of a DNA Aptamer Against Lung Cancer

Author

Morozov, Dmitry, Mironov, Vladimir, Moryachkov, Roman V., Shchugoreva, Irina A., Artyushenko, Polina V., Zamay, Galina S., Kolovskaya, Olga S., Zamay, Tatiana N., Krat, Alexey V., Molodenskiy, Dmitry S., Zabluda, Vladimir N., Veprintsev, Dmitry V., Sokolov, Alexey E., Zukov, Ruslan A., Berezovski, Maxim V., Tomilin, Felix N., Fedorov, Dmitri G., Alexeev, Yuri, and Kichkailo, Anna S.

Subjects
syöpäsolut, oligonukleotidit, immuunivaste, nukleotidit, vasta-aineet, molekyylidynamiikka, simulointi
Abstract

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here we present a general optimization procedure for finding most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated aptamer LC-18t was developed. A three-dimensional shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The truncated aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes. peerReviewed

Published
2021

48. Erratum: Azimuthal anisotropy at the relativistic heavy ion collider: the first and fourth harmonics [Phys. Rev. Lett. 92, 062301 (2004)]

Author

Adams, Joseph R., Adler, Clemens, Aggarwal, Madan Mohan, Ahammed, Zubayer, Amonett, John, Anderson, Bryon D., Anderson, Mike, Arkhipkin, Dmitry A., Averichev, Georgy S., Badyal, S. K., Balewski, Jan, Barannikova, Olga, Barnby, Lee Stuart, Baudot, Jérome, Bekele, Selemon, Belaga, Victoria Vladimirovna, Bellwied, Rene, Berger, Jens, Bezverkhny, B. I., Bhardwaj, S., Bhaskar, P., Bhati, Ashok Kumar, Bichsel, Hans, Billmeier, Anja, Bland, Leslie C., Blyth, Charles O., Bonner, Billy E., Botje, Michiel, Boucham, Abdelkrim, Brandin, Andrei V., Bravar, Alessandro, Cadman, R. V., Cai, Xiang-Zhou, Caines, Helen Louise, Calderón de la Barca Sánchez, Manuel, Carroll, J., Castillo Castellanos, Javier Ernesto, Castro, M., Cebra, Daniel A., Chaloupka, Petr, Chattopadhyay, S., Chen, H. F., Chen, Y., Chernenko, Sergey P., Cherney, Michael Gerard, Chikanian, Alexei, Choi, B., Christie, William, Coffin, Jean Pierre, Cormier, Thomas Michael, Cramer, John G., Crawford, Henry J., Csanád, Máté, Das, Debasish, Das, Supriya, Derevschikov, Anatoly A., Didenko, Lidia, Dietel, Thomas, Dong, W. J., Dong, X., Draper, James E., Du, F., Dubey, Anand Kumar, Dunin, V. B., Dunlop, James C., Dutta Majumdar, Mihir Ranjan, Eckardt, Volker, Efimov, Leonid G., Emelianov, V., Engelage, Jon M., Eppley, Geary Wareham, Erazmus, Barbara Ewa, Estienne, Magali Danielle, Fachini, Patricia, Faine, V., Faivre, Julien, Fatemi, Renee H., Filimonov, Kirill, Filip, Peter, Finch, Evan, Fisyak, Yuri V., Flierl, Dominik Bernhard, Foley, Kenneth John, Fu, J., Gagliardi, Carl A., Gagunashvili, N., Gans, J., Ganti, Murthy S., Gaudichet, L., Germain, Marie, Geurts, Frank, Ghazikhanian, Vahe, Ghosh, Premomoy, Gonzalez, Johan Enmanuel, Grachov, Oleg A., Grigoriev, Vladislav A., Gronstal, S., Grosnick, David P., Guedon, M., Guertin, Steven M., Gupta, Anik, Gushin, E., Gutierrez, Thomas Dominic, Hallman, Timothy J., Hardtke, David H., Harris, John W., Heinz, Mark Thomas, Henry, Thomas W., Heppelmann, Steven Francis, Herston, T., Hippolyte, Boris, Hirsch, Andrew S., Hjort, Eric, Hoffmann, Gerald W., Horsley, M., Huang, Huan Zhong, Huang, Shengli, Humanic, Thomas J., Igo, George J., Ishihara, A., Jacobs, Peter Martin, Jacobs, William W., Janik, Michał, Jiang, H., Johnson, I., Jones, Peter Graham, Judd, Eleanor G., Kabana, Sonia, Kaneta, Kaneta, Kaplan, Morton, Keane, Declan, Khodyrev, V. Yu., Kiryluk, Joanna, Kisiel, Adam Ryszard, Klay, Jennifer Lynn, Klein, Spencer Robert, Klyachko, A., Koetke, Donald D., Kollegger, Thorsten, Kopytine, M., Kotchenda, L., Kovalenko, A. D., Kramer, M., Kravtsov, Peter, Kravtsov, Vladimir I., Krueger, Keith William, Kuhn, Christian Claude, Kulikov, Anatoly I., Kumar, Ajay, Kunde, Gerd J., Kunz, Christopher Lee, Kutuev, R. Kh., Kuznetsov, A. A., Lamont, Matthew A. C., Landgraf, Jeffery M., Lange, S., Lansdell, Curtis Patrick Leon, Lasiuk, Brian, Laue, Frank, Lauret, Jerome, Lebedev, Alexei, Lednický, Richard, LeVine, Micheal J., Li, C., Li, Q., Lindenbaum, Sam J., Lisa, Michael A., Liu, F., Liu, L., Liu, Z., Liu, Q. J., Ljubicic, Tonko A., Llope, William Joseph, Long, H., Longacre, Ronald S., Lopez-Noriega, M., Love, William A., Ludlam, Thomas, Lynn, David, Ma, Jing-guo, Ma, R., Ma, Yu-Gang, Magestro, Daniel, Mahajan, Sanjay, Mangotra, Lalit K., Mahapatra, D. P., Majka, Richard Daniel, Manweiler, Robert W., Margetis, Spyridon, Markert, Christina, Martin, L., Marx, Jay N., Matis, Howard S., Matulenko, Yuri A., McShane, Tom S., Meissner, F., Melnick, Yu., Meščanin, Aleksei P., Messer, Matthias, Miller, M. L., Milosevich, Z., Minaev, Nikolai G., Mironov, Camelia, Mishra, Debadeepti, Mitchell, J., Mohanty, Bedangadas, Molnar, Levente, Moore, C. F., Mora-Corral, M. J., Morozov, Dmitry A., Morozov, V., de Moura, M. M., Munhoz, Marcelo Gameiro, Nandi, Basanta Kumar, Nayak, S. K., Nayak, Tapan Kumar, Nelson, John M., Nevski, P., Niida, Takafumi, Nikitin, Vladimir A., Nogach, Larisa V., Norman, B., Nurušev, Sandibek B., Odyniec, Grazyna Janina, Ogawa, Akio, Okorokov, Vitaly A., Oldenburg, Markus D., Olson, Douglas L., Paic, Guy, Pandey, S. U., Pal, Susanta Kumar, Panebratsev, Yuri, Panitkin, Sergei Yurievich, Pavlinov, A. I., Pawlak, Tomasz Jan, Perevoztchikov, V., Perkins, Chris, Peryt, Wiktor Stanislaw, Petrov, V. A., Phatak, S. C., Picha, R., Planinic, Mirko, Pluta, Jan Marian, Porile, Norbert T., Porter, Jeffrey Brent, Poskanzer, Arthur M., Potekhin, Maxim, Potrebenikova, E., Potukuchi, B. V. K. S., Prindle, Duncan J., Pruneau, Claude A., Putschke, Jörn H., Rai, Gulshan, Rakness, Gregory L., Raniwala, Rashmi, Raniwala, Sudhir, Ravel, Olivier, Ray, Robert L., Razin, Sergej V., Reichhold, Dennis Michael, Reid, Jeffrey G., Renault, G., Retiere, Fabrice, Ridiger, Alexey, Ritter, Hans Georg, Roberts, Jabus B., Rogachevski, O. V., Romero, Juan L., Rose, A., Roy, Christelle Sophie, Ruan, Lijuan, Sahoo, Raghunath, Sakrejda, Iwona, Salur, Sevil, Sandweiss, Jack H., Savin, Igor A., Schambach, Joachim, Scharenberg, Rolf Paul, Schmitz, Norbert, Schroeder, Lee S., Schweda, Kai, Seger, Janet Elizabeth, Seliverstov, D., Seyboth, Peter, Shahaliev, Ehtiram, Shao, M., Sharma, M., Shestermanov, Konstantin E., Shimanskii, S. S., Singaraju, Rama Narayana, Simon, F., Skoro, Goran P., Smirnov, Nikolai, Snellings, Raimond, Sood, Gopika, Sorensen, Paul Richard, Sowinski, James, Spinka, Harold. M., Srivastava, Brijesh Kumar, Stanislaus, S., Stock, Reinhard, Stolpovsky, Alexander, Strichanov, Michail Nikolaevič, Stringfellow, Blair, Struck, Christof, Suaide, Alexandre Alarcon do Passo, Sugarbaker, Evan R., Suire, Christophe Pierre, Šumbera, Michal, Surrow, Bernd, Symons, Timothy James MacNeil, Toledo, Alejandro Szanto de, Szarwas, Piotr, Tai, An, Takahashi, Jun, Tang, Aihong, Thein, Dylan, Thomas, James H., Tikhomirov, V., Todoroki, Takahito, Tokarev, Mikhail V., Tonjes, Marguerite Belt, Trainor, Thomas A., Trentalange, Stephen, Tribble, Robert E., Trivedi, M. D., Trofimov, V., Tsai, Oleg D., Ullrich, Thomas, Underwood, David G., Van Buren, Gene, VanderMolen, A. M., Vasiliev, Alexander Nikolaevich, Vasiliev, M., Vigdor, Steven E., Viyogi, Yogendra P., Voloshin, Sergei, Waggoner, William T., Wang, F., Wang, G., Wang, X. L., Wang, Z. M., Ward, H., Watson, J. W., Wells, R., Westfall, Gary D., Whitten, Charles A., Wieman, Howard, Willson, Robert, Wissink, Scott W., Witt, Richard, Wood, J., Wu, J., Xu, N., Xu, Z., Xu, Z. Z., Yamamoto, E., Yepes, Pablo P., Yurevich, Vladimir Yurevich, Zanevski, Y. V., Zborovský, Imrich, Zhang, Haitao, Zhang, W. M., Zhang, Z. P., Żołnierczuk, Piotr Adam, Zoulkarneev, R., Zoulkarneeva, J., Zubarev, A. N., Adams, Joseph R., Adler, Clemens, Aggarwal, Madan Mohan, Ahammed, Zubayer, Amonett, John, Anderson, Bryon D., Anderson, Mike, Arkhipkin, Dmitry A., Averichev, Georgy S., Badyal, S. K., Balewski, Jan, Barannikova, Olga, Barnby, Lee Stuart, Baudot, Jérome, Bekele, Selemon, Belaga, Victoria Vladimirovna, Bellwied, Rene, Berger, Jens, Bezverkhny, B. I., Bhardwaj, S., Bhaskar, P., Bhati, Ashok Kumar, Bichsel, Hans, Billmeier, Anja, Bland, Leslie C., Blyth, Charles O., Bonner, Billy E., Botje, Michiel, Boucham, Abdelkrim, Brandin, Andrei V., Bravar, Alessandro, Cadman, R. V., Cai, Xiang-Zhou, Caines, Helen Louise, Calderón de la Barca Sánchez, Manuel, Carroll, J., Castillo Castellanos, Javier Ernesto, Castro, M., Cebra, Daniel A., Chaloupka, Petr, Chattopadhyay, S., Chen, H. F., Chen, Y., Chernenko, Sergey P., Cherney, Michael Gerard, Chikanian, Alexei, Choi, B., Christie, William, Coffin, Jean Pierre, Cormier, Thomas Michael, Cramer, John G., Crawford, Henry J., Csanád, Máté, Das, Debasish, Das, Supriya, Derevschikov, Anatoly A., Didenko, Lidia, Dietel, Thomas, Dong, W. J., Dong, X., Draper, James E., Du, F., Dubey, Anand Kumar, Dunin, V. B., Dunlop, James C., Dutta Majumdar, Mihir Ranjan, Eckardt, Volker, Efimov, Leonid G., Emelianov, V., Engelage, Jon M., Eppley, Geary Wareham, Erazmus, Barbara Ewa, Estienne, Magali Danielle, Fachini, Patricia, Faine, V., Faivre, Julien, Fatemi, Renee H., Filimonov, Kirill, Filip, Peter, Finch, Evan, Fisyak, Yuri V., Flierl, Dominik Bernhard, Foley, Kenneth John, Fu, J., Gagliardi, Carl A., Gagunashvili, N., Gans, J., Ganti, Murthy S., Gaudichet, L., Germain, Marie, Geurts, Frank, Ghazikhanian, Vahe, Ghosh, Premomoy, Gonzalez, Johan Enmanuel, Grachov, Oleg A., Grigoriev, Vladislav A., Gronstal, S., Grosnick, David P., Guedon, M., Guertin, Steven M., Gupta, Anik, Gushin, E., Gutierrez, Thomas Dominic, Hallman, Timothy J., Hardtke, David H., Harris, John W., Heinz, Mark Thomas, Henry, Thomas W., Heppelmann, Steven Francis, Herston, T., Hippolyte, Boris, Hirsch, Andrew S., Hjort, Eric, Hoffmann, Gerald W., Horsley, M., Huang, Huan Zhong, Huang, Shengli, Humanic, Thomas J., Igo, George J., Ishihara, A., Jacobs, Peter Martin, Jacobs, William W., Janik, Michał, Jiang, H., Johnson, I., Jones, Peter Graham, Judd, Eleanor G., Kabana, Sonia, Kaneta, Kaneta, Kaplan, Morton, Keane, Declan, Khodyrev, V. Yu., Kiryluk, Joanna, Kisiel, Adam Ryszard, Klay, Jennifer Lynn, Klein, Spencer Robert, Klyachko, A., Koetke, Donald D., Kollegger, Thorsten, Kopytine, M., Kotchenda, L., Kovalenko, A. D., Kramer, M., Kravtsov, Peter, Kravtsov, Vladimir I., Krueger, Keith William, Kuhn, Christian Claude, Kulikov, Anatoly I., Kumar, Ajay, Kunde, Gerd J., Kunz, Christopher Lee, Kutuev, R. Kh., Kuznetsov, A. A., Lamont, Matthew A. C., Landgraf, Jeffery M., Lange, S., Lansdell, Curtis Patrick Leon, Lasiuk, Brian, Laue, Frank, Lauret, Jerome, Lebedev, Alexei, Lednický, Richard, LeVine, Micheal J., Li, C., Li, Q., Lindenbaum, Sam J., Lisa, Michael A., Liu, F., Liu, L., Liu, Z., Liu, Q. J., Ljubicic, Tonko A., Llope, William Joseph, Long, H., Longacre, Ronald S., Lopez-Noriega, M., Love, William A., Ludlam, Thomas, Lynn, David, Ma, Jing-guo, Ma, R., Ma, Yu-Gang, Magestro, Daniel, Mahajan, Sanjay, Mangotra, Lalit K., Mahapatra, D. P., Majka, Richard Daniel, Manweiler, Robert W., Margetis, Spyridon, Markert, Christina, Martin, L., Marx, Jay N., Matis, Howard S., Matulenko, Yuri A., McShane, Tom S., Meissner, F., Melnick, Yu., Meščanin, Aleksei P., Messer, Matthias, Miller, M. L., Milosevich, Z., Minaev, Nikolai G., Mironov, Camelia, Mishra, Debadeepti, Mitchell, J., Mohanty, Bedangadas, Molnar, Levente, Moore, C. F., Mora-Corral, M. J., Morozov, Dmitry A., Morozov, V., de Moura, M. M., Munhoz, Marcelo Gameiro, Nandi, Basanta Kumar, Nayak, S. K., Nayak, Tapan Kumar, Nelson, John M., Nevski, P., Niida, Takafumi, Nikitin, Vladimir A., Nogach, Larisa V., Norman, B., Nurušev, Sandibek B., Odyniec, Grazyna Janina, Ogawa, Akio, Okorokov, Vitaly A., Oldenburg, Markus D., Olson, Douglas L., Paic, Guy, Pandey, S. U., Pal, Susanta Kumar, Panebratsev, Yuri, Panitkin, Sergei Yurievich, Pavlinov, A. I., Pawlak, Tomasz Jan, Perevoztchikov, V., Perkins, Chris, Peryt, Wiktor Stanislaw, Petrov, V. A., Phatak, S. C., Picha, R., Planinic, Mirko, Pluta, Jan Marian, Porile, Norbert T., Porter, Jeffrey Brent, Poskanzer, Arthur M., Potekhin, Maxim, Potrebenikova, E., Potukuchi, B. V. K. S., Prindle, Duncan J., Pruneau, Claude A., Putschke, Jörn H., Rai, Gulshan, Rakness, Gregory L., Raniwala, Rashmi, Raniwala, Sudhir, Ravel, Olivier, Ray, Robert L., Razin, Sergej V., Reichhold, Dennis Michael, Reid, Jeffrey G., Renault, G., Retiere, Fabrice, Ridiger, Alexey, Ritter, Hans Georg, Roberts, Jabus B., Rogachevski, O. V., Romero, Juan L., Rose, A., Roy, Christelle Sophie, Ruan, Lijuan, Sahoo, Raghunath, Sakrejda, Iwona, Salur, Sevil, Sandweiss, Jack H., Savin, Igor A., Schambach, Joachim, Scharenberg, Rolf Paul, Schmitz, Norbert, Schroeder, Lee S., Schweda, Kai, Seger, Janet Elizabeth, Seliverstov, D., Seyboth, Peter, Shahaliev, Ehtiram, Shao, M., Sharma, M., Shestermanov, Konstantin E., Shimanskii, S. S., Singaraju, Rama Narayana, Simon, F., Skoro, Goran P., Smirnov, Nikolai, Snellings, Raimond, Sood, Gopika, Sorensen, Paul Richard, Sowinski, James, Spinka, Harold. M., Srivastava, Brijesh Kumar, Stanislaus, S., Stock, Reinhard, Stolpovsky, Alexander, Strichanov, Michail Nikolaevič, Stringfellow, Blair, Struck, Christof, Suaide, Alexandre Alarcon do Passo, Sugarbaker, Evan R., Suire, Christophe Pierre, Šumbera, Michal, Surrow, Bernd, Symons, Timothy James MacNeil, Toledo, Alejandro Szanto de, Szarwas, Piotr, Tai, An, Takahashi, Jun, Tang, Aihong, Thein, Dylan, Thomas, James H., Tikhomirov, V., Todoroki, Takahito, Tokarev, Mikhail V., Tonjes, Marguerite Belt, Trainor, Thomas A., Trentalange, Stephen, Tribble, Robert E., Trivedi, M. D., Trofimov, V., Tsai, Oleg D., Ullrich, Thomas, Underwood, David G., Van Buren, Gene, VanderMolen, A. M., Vasiliev, Alexander Nikolaevich, Vasiliev, M., Vigdor, Steven E., Viyogi, Yogendra P., Voloshin, Sergei, Waggoner, William T., Wang, F., Wang, G., Wang, X. L., Wang, Z. M., Ward, H., Watson, J. W., Wells, R., Westfall, Gary D., Whitten, Charles A., Wieman, Howard, Willson, Robert, Wissink, Scott W., Witt, Richard, Wood, J., Wu, J., Xu, N., Xu, Z., Xu, Z. Z., Yamamoto, E., Yepes, Pablo P., Yurevich, Vladimir Yurevich, Zanevski, Y. V., Zborovský, Imrich, Zhang, Haitao, Zhang, W. M., Zhang, Z. P., Żołnierczuk, Piotr Adam, Zoulkarneev, R., Zoulkarneeva, J., and Zubarev, A. N.

Published
2021

49. Spectral-Luminescent Properties of ZrO 2 -Y 2 O 3 -Pr 2 O 3 Crystals.

Author

Borik, Mikhail, Kulebyakin, Alexey, Larina, Nataliya, Lomonova, Elena, Morozov, Dmitry, Myzina, Valentina, Ryabochkina, Polina, and Tabachkova, Nataliya

Subjects
LUMINESCENCE measurement, CRYSTALS, ABSORPTION spectra, MELT crystallization, SPECTRUM analysis
Abstract

We studied the spectral-luminescent properties of (ZrO2)0.805(Y2O3)0.188(Pr2O3)0.007 and (ZrO2)0.802(Y2O3)0.195(Pr2O3)0.003 crystals grown by directional melt crystallization in a cold skull. Analysis of the absorption spectra of the crystals suggested the presence of Pr3+ and Pr4+ ions. Measurement of the relative intensities of the luminescence bands corresponding to the 3P0 → 3H4,5, 3P0 → 3F2,3,4, 3P1 → 3H5 and 1D2 → 3H4 optical transitions of the Pr3+ ions, and analysis of luminescence extinction kinetics for the 3P0 and 1D2 levels of the Pr3+ ions, suggests the presence of cross-relaxation (1D2 → 1G4) → (3H4 → 3F4) of the Pr3+ ions in the ZrO2-Y2O3-Pr2O3 crystals. [ABSTRACT FROM AUTHOR]

Published
2022
Full Text
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50. BioExcel-2 D1.3 – Updated Software Roadmap

Author

Hess, Berk, Bauer, Paul, Lindahl, Erik, Honorato, Rodrigo, Bonvin, Alexandre, Jimenez-Garcia, Brian, Proeme, Arno, Morozov, Dmitry, Groenhof, Gerrit, De Groot, Bert L., and Gapsys, Vytautas

Subjects
Roadmap, exascale computing, modularization, Software development, workflows
Abstract

This deliverable reports on the present state of the BioExcel-2 core application roadmaps, how user and infrastructure needs have been prioritized, the specific tasks this corresponds to in the codes, and what the long-term directions of the codes are – even beyond the present BioExcel funding period. As part of BioExcel2, the software roadmaps have been updated to balance development driven by user requests for features as well as strategic efforts targeting EuroHPC and preparing for next-generation processor and accelerator hardware. The GROMACS development will focus on a number of key user-requested features, in particular adding multiple time stepping, driving simulations with external data, facilitating generation of input data, and better free energy tools. The development of performance optimization for additional new platforms will also continue together with efforts targeting significantly improved scaling by using ensemble parallelism, as well as co-design projects to port the code to new accelerator platforms. The development of the PMX package will follow two main directions. Firstly, the core code will be updated with the changes necessary for the successful future usability of the software. In particular, with the end of Python2 lifetime, pmx will be fully rewritten in Python3. The continuous support of the main pmx functionalities will be ensured. The second major development direction comprises the incorporation of features frequently requested by users, the addition of new mutation libraries and creation of workflows for free energy calculation setup and analysis. HADDOCK’s development focuses on the continuous improvement of the web server, which functions as the main user’s interface, the implementation of relevant features and the design of a new modular version, HADDOCK3. The web server is being co-developed alongside the local HADDOCK version, so that new features (coarse-grained and shape docking, etc.) are readily available in an intuitive and responsive user-friendly interface. A major rework of the current code is in place, for what will become HADDOCK3, with this modular design we aim to provide flexibility for workflow creation and a straightforward framework to integrate new tools. This new modular architecture will also enable more efficient execution on HPC resources. To provide users with access to chemical reactivity in biomolecular simulations, we will develop an interface between GROMACS and CP2K, a highly parallelized density functional theory (DFT) computer program. With the new interface, users can perform multi-scale simulations, in which one part of the system is modelled with DFT, while the remainder is described with a molecular mechanics force field (i.e. QM/MM). Our developments focus on providing the community with an accurate, scalable and user-friendly QM/MM solution. Compared to the previous BioExcel software roadmap, which focused on CPMD for DFT functionality in QM/MM simulations, this updated roadmap reflects the project’s transition to CP2K, which has more wide-spread availability and uptake in the community.

Published
2020
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