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103. Digital MEMS microphones for remote monitoring system based on sound analysis

Author

Budanov, Dmitry, Morozov, Dmitry, and Pilipko, Mikhail

Subjects
MEMS, sound analysis, анализ звука, Bluetooth, пьезоэлектрический микрофон, Bluetooth Low Energy, piezoelectric microphone, capacitive microphone, емкостной микрофон, digital microphone, МЭМС, цифровой микрофон
Abstract

Sounds emitted by mechanisms and organisms contain information that can be used to diagnose the current state of an object and make predictions. There are known examples of the use of sound for diagnostics of pipelines, composite materials, industrial equipment. In most cases, devices with one sensor and limited functionality are used for this purpose, requiring a specialist to be in close proximity to the object under analysis. The system includes a set of digital microelectromechanical (MEMS) microphones, information from which is transmitted via Bluetooth to the mobile device. The system in a round-the-clock mode quickly registers changes in the spectrum of the sound signaland indicates possible malfunctions, damage to equipment and materials, etc. This allows preventing irreversible consequences. In this system, it is expedient to use digital MEMS microphones due to their low power consumption and low sensitivity to environmental influences, which is an important factor when deploying a remote monitoring system of industrial equipment., Звуки, издаваемые механизмами и организмами, содержат информацию, которую можно использовать для диагностики текущего состояния объекта и прогноза на будущее. Известны примеры использования звука для диагностики трубопроводов, композитных материалов, промышленного оборудования. В большинстве случаев для этой цели применяются устройства с одним датчиком и ограниченным функционалом, требующие нахождения специалиста в непосредственной близости к исследуемому объекту. Предлагается система для дистанционного мониторинга, включающая в себя набор датчиков-микрофонов, информация с которых передается посредством Bluetooth на мобильное устройство. Система в круглосуточном режиме оперативно регистрирует изменения в спектре звукового сигнала, свидетельствующие о возможных неисправностях, повреждении оборудования и материалов и т. д., что позволяет предупредить необратимые последствия. В данной системе целесообразно применять цифровые МЭМС-микрофоны вследствие их низкого энергопотребления и низкой чувствительности к воздействию окружающей среды, что является важным фактором при развертывании системы дистанционного мониторинга промышленного оборудования.

Published
2021
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104. 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

105. 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

109. 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
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111. Mid-infrared two-photon interference and polarization entanglement

Author

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

Published
2021
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112. 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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113. BioExcel Webinar #51: Multiscale QM/MM simulations: exploring chemical reactions using novel GROMACS/CP2K interface (2020-12-08)

Author

Morozov, Dmitry

Subjects
Webinar
Abstract

Nowadays, computer simulations play an important role in modern chemistry and biophysics. Simulations of chemical reaction pathways could provide an atomistic insight into many natural and technological processes. To perform such kind of modelling in complex systems that include solvent and/or proteins, Multi-scale Quantum Mechanics / Molecular Mechanics (QM/MM) approaches are often used. In this webinar, I will present the newly developed fully integrated QM/MM interface between the GROMACS molecular dynamics program and the CP2K quantum chemistry package. The new interface enables users to smoothly set up QM/MM models of their system and use all simulation techniques available in GROMACS to study the chemistry.

Published
2020
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114. Linux Privilege Increase Threat Analysis

Author

Ponomareva Elena and Morozov Dmitry

Subjects
Software_OPERATINGSYSTEMS, Automatic control, Computer science, Law enforcement, Confidentiality, Linux kernel, Privilege (computing), Information security, Computer security, computer.software_genre, Mobile device, computer, Vulnerability (computing)
Abstract

Today, Linux is one of the main operating systems (OS) used both on desktop computers and various mobile devices. This OS is also widely applied in state and municipal structures, including law enforcement agencies and automated control systems used in the Armed Forces of the Russian Federation. It’s worth noting that the process of replacing the Linux OS with domestic protected OSs that use the Linux kernel has now begun. In this regard, the analysis of threats to information security of the Linux OS is highly relevant. In this article, the authors discuss the security problems of Linux OS associated with unauthorized user privileges increase, as a result of which an attacker can gain full control over the OS. The approaches to differentiating user privileges in Linux are analyzed and their advantages and disadvantages are considered. As an example, the causes of the vulnerability CVE-2018-14665 were identified and measures to eliminate it were proposed.

Published
2020
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115. Photon-pair source at 2090 nm for long-distance quantum communication

Author

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

Subjects
Physics::Optics, Quantum Physics
Abstract

We report the generation of entangled photon pairs at 2090 nm, as a basis for free-space quantum communication in an atmospheric window with low solar background. The source is based on spontaneous parametric down-conversion in periodically poled lithium niobate crystal delivering high coincidence-to-accidental ratio. We demonstrate the two-photon Hong-Ou-Mandel quantum interference and polarization entanglement.

Published
2020

116. Predictive First-principles Modeling of a Photosynthetic Antenna Protein : The Fenna-Matthews-Olson Complex

Author

Kim, Yongbin, Morozov, Dmitry, Stadnytskyi, Valentyn, Savikhin, Sergei, and Slipchenko, Lyudmila

Subjects
polarizable embedding, mallintaminen, pigment-protein complex, QM/EFP, effective fragment potential, spektroskopia, Fenna-Matthews-Olson protein, proteiinit, QM/MM, pigmentit (värijauheet)
Abstract

High efficiency of light harvesting in photosynthetic pigment-protein complexes is governed by evolutionary-perfected protein-assisted tuning of individual pigment properties and inter-pigment interactions. Due to the large number of spectrally overlapping pigments in a typical photosynthetic complex, experimental methods often fail to unambiguously identify individual chromophore properties. Here we report a first principles-based modeling protocol capable of predicting properties of pigments in protein environment to a high precision. The technique was applied to successfully uncover electronic properties of the Fenna-Matthews-Olson (FMO) pigment-protein complex. Each of the three subunits of the FMO complex contains eight strongly coupled bacteriochlorophyll a (BChl a) pigments. The excitonic structure of FMO can be described by an electronic Hamiltonian containing excitation (site) energies of BChl a pigments and electronic couplings between them. Several such Hamiltonians have been developed in the past based on the information from various spectroscopic measurements of FMO; however, fine details of the excitonic structure and energy transfer in FMO, especially assignments of short-lived high-energy sites, remain elusive. Utilizing polarizable embedding QM/MM with the effective fragment potentials (EFP) we were able to compute the electronic Hamiltonian of FMO that is in general agreement with previously reported empirical Hamiltonians and quantitatively reproduces experimental absorption and circular dichroism (CD) spectra of the FMO protein. The developed computational protocol is sufficiently simple and can be utilized for predictive modeling of other wild type and mutated photosynthetic pigment-protein complexes. peerReviewed

Published
2020

117. Observe while it happens : catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations

Author

Groenhof, Gerrit, Modi, Vaibhav, and Morozov, Dmitry

Subjects
photoactive proteins, molecular biology, sense organs, proteiinit, molekyylibiologia
Abstract

Organisms use photo-receptors to react to light. The first step is usually the absorption of a photon by a prosthetic group embedded inside the photo-receptor, often a conjugated chromophore. The electronic changes in the chromophore induced by photo-absorption can trigger a cascade of structural or chemical transformations that culminate into a response to light. Understanding how these proteins have evolved to mediate their activation process has remained challenging because the required time and spacial resolutions are notoriously difficult to achieve experimentally. Therefore, mechanistic insights into photoreceptor activation have been predominantly obtained with computer simulations. Here we briefly outline the challenges associated with such computations and review the progress made in this field. peerReviewed

Published
2020

118. Two-photon quantum interference and entanglement at 2.1 µm

Author

Prabhakar, Shashi, Shields, Taylor, Dada, Adetunmise C., 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
lithium niobate crystals, optical system, nanowire single-photon detectors, Physics::Optics, photons, ddc:500, Dewey Decimal Classification::500 | Naturwissenschaften
Abstract

Quantum-enhanced optical systems operating within the 2- to 2.5-μm 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-μm 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. Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

Published
2020

119. Mechanical properties of cells probed by atomic force microscopy

Author

Morozov, Dmitry

Subjects
Cells, technology, industry, and agriculture, Force Spectroscopy, Atomic Force Microscopy, Stiffness
Abstract

Atomic force microscopy (AFM) is widely used to study various biologicalobjects, among others also mammalian cells in physiologically adequate conditions. Force-distance curves provide information about mechanical characteristics of the cell, such as contact stiffness, deformation, Young's modulus etc. Such properties have been linked to various states of disease. AFM studies of the morphology and mechanical properties of native cells can be used in biomedical applications, such as determining the physiological and pathological states of cells. In this work, AFM was applied to examine the mechanical properties of the human umbilical vein endothelial cells (HUVEC) and their dependence on different measurement settings. The influence of the loading rate, maximum load and indenter geometry on the measurement of mechanical properties of such cells has been studied. By applying a linear fitting to a Force-Distance-Curves obtained during nanoindentation experiments the stiffness and the Young’s modulus were calculated. Relation of the mechanical properties of the cells and the experiment condition was demonstrated. Obtained results can be used in a further studies to compare viscoelastic properties of the approach and the retracting curve.

Published
2020
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120. Investigation of the linear and mode-coupled flow harmonics in Au+Au collisions at √sNN = 200 GeV

Author

Adam, Jaroslav, Adamczyk, Leszek, Adams, Joseph R., Adkins, J. Kevin, Agakishiev, Geydar, Aggarwal, Madan Mohan, Ahammed, Zubayer, Alekseev, Igor G., Anderson, Derek M., Aparin, Alexey, Aschenauer, Elke Caroline, Ashraf, Muhammad Usman, Atetalla, Fareha, Attri, Anjali, Averichev, Georgy S., Bairathi, Vipul, Barish, Kenneth, Behera, Arabinda, Bellwied, Rene, Bhasin, Anju, Bielčík, Jaroslav, Bielčíková, Jana, Bland, Leslie C., Bordyuzhin, Igor G., Brandenburg, James D., Brandin, Andrei V., Butterworth, Joseph, Caines, Helen Louise, Calderón de la Barca Sánchez, Manuel, Cebra, Daniel A., Chakaberia, Irakli, Chaloupka, Petr, Chan, B.K., Chang, F.-H., Chang, Z., Chankova-Bunzarova, N., Chatterjee, A., Chen, D., Chen, J.H., Chen, X., Chen, Z., Cheng, J., Cherney, Michael Gerard, Chevalier, M., Choudhury, Subikash, Christie, William, Chu, X., Crawford, Henry J., Csanád, Máté, Daugherity, M., Dedovič, Tatiana G., Deppner, Ingo Martin, Derevschikov, Anatoly A., Didenko, Lidia, Dong, X., Drachenberg, James Lucus, Dunlop, James C., Edmonds, Terrence, Elsey, Nicholas, Engelage, Jon M., Eppley, Geary Wareham, Esha, Roli, Esumi, ShinIchi, Evdokimov, Olga Y., Ewigleben, A., Eyser, Kjeld Oleg, Fatemi, Renee H., Fazio, Salvatore, Federič, Pavol, Fedorišin, Jan, Feng, C.J., Feng, Y., Filip, Peter, Finch, Evan, Fisyak, Yuri V., Francisco, Audrey, Fulek, Łukasz, Gagliardi, Carl A., Galatyuk, Tetyana, Geurts, Frank, Gibson, Adam, Gopal, Krishan, Grosnick, David P., Guryn, Włodzimierz, Hamad, Ayman, Hamed, Ahmed M., Harabasz, Szymon, Harris, John W., He, S., He, W., He, X.H., Heppelmann, Steven Francis, Herrmann, Norbert, Hoffman, E., Holub, Lukáš, Hong, Y., Horvat, S., Hu, Y., Huang, H.Z., Huang, Shengli, Huang, T., Huang, X., Humanic, Thomas J., Huo, P., Igo, George J., Isenhower, D., Jacobs, William W., Jena, Chitrasen, Jentsch, Alexander, Ji, Y., Jia, J., Jiang, K., Jowzaee, S., 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., Kim, C., Kimelman, B., Kincses, D., Kinghorn, Todd Adler, Kisel, Ivan, Kiselev, A., Kocan, Michal, Kočenda, L. M., Kosarzewski, Leszek Krzysztof, Kramárik, Lukáš, Kravtsov, Peter, Krueger, Keith William, Kulathunga Mudiyanselage, Nalinda, Kumar, Lokesh, 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., Li, C., Li, W., Li, Xiaomei, Li, Y., 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., Lukow, N.S., Luo, S., Luo, X., Ma, G.L., Ma, L., Ma, R., Ma, Yu-Gang, Magdy Abdelwahab Abdelrahman, Niseem, Majka, Richard Daniel, Mallick, Dukhishyam, Margetis, Spyridon, Markert, Christina, Matis, Howard S., Mazer, Joel Anthony, Minaev, Nikolai G., Mioduszewski, Saskia, Mohanty, Bedangadas, Mondal, Mriganka Mouli, Mooney, Isaac A., Moravcova, Zuzana, Morozov, Dmitry A., Nagy, M., Nam, J.D., Nasim, Md., Nayak, Kishora, Neff, D., Nelson, John M., Nemes, Daniel B., Nie, Maowu, Nigmatkulov, Grigory A., Niida, Takafumi, Nogach, Larisa V., Nonaka, Toshihiro, Nunes, A.S., Odyniec, Grazyna Janina, Ogawa, Akio, Oh, S., Okorokov, Vitaly A., Page, Brian S., Pak, Robert, Pandav, A., Panebratsev, Yuri, Pawlik, Bogdan, Pawłowska, Diana, Pei, Hua, Perkins, Chris, Pinsky, Lawrence, Pintér, Roland Laszlo, Pluta, Jan Marian, Porter, Jeffrey Brent, Posik, Matthew, Pruthi, Navneet Kumar, Przybycien, Mariusz, Putschke, Jörn H., Qiu, H., Quintero, Amilkar, Radhakrishnan, Sooraj Krishnan, Ramachandran, Suvarna, Ray, Robert L., Reed, Rosi Jan, Ritter, Hans Georg, Roberts, Jabus B., Rogačevskij, Oleg V., Romero, Juan L., Ruan, Lijuan, Rusnak, Jan, Sahoo, Nihar Ranjan, Sako, H., Salur, Sevil, Sandweiss, Jack H., Sato, S., Schmidke, William B., Schmitz, Norbert, Schweid, Benjamin R., Seck, Florian, Seger, Janet Elizabeth, Sergeeva, Maria, Seto, Richard, Seyboth, Peter, Shah, N., Shahaliev, Ehtiram, Shanmuganathan, Prashanth V., Shao, M., Shen, F., Shen, W.Q., Shi, S.S., Shou, Q.Y., Sichtermann, Ernst P., Sikora, Rafał, Šimko, Miroslav, Singh, Jagbir, Singha, Subhash, Smirnov, Nikolai, Solyst, William, Sorensen, Paul Richard, 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., Szymański, Paweł, Tang, Aihong, Tang, Zebo, Taranenko, Arkadiy, Tarnowsky, Terence J., Thomas, James H., Timmins, Anthony Robert, Tlusty, David, Tokarev, Mikhail V., Tomkiel, Catherine A., Trentalange, Stephen, Tribble, Robert E., Tribedy, Prithwish, Tripathy, Srikanta Kumar, Tsai, Oleg D., Tu, Z., Ullrich, Thomas, Underwood, David G., Upsal, Isaac, Van Buren, Gene, Vanek, Jan, Vasiliev, Alexander Nikolaevich, Vassiliev, Iouri, Videbæk, Flemming, Vokal, Stanislav, Voloshin, Sergei, Wang, F., Wang, G., Wang, J.S., Wang, P., Wang, Y., Wang, Z., Webb, Jason C., Weidenkaff, P.C., Wen, L., Westfall, Gary D., Wieman, Howard, Wissink, Scott W., Witt, Richard, Wu, Y., Xiao, Z.G., Xie, G., Xie, W., Xu, H., Xu, N., Xu, Q.H., Xu, Y.F., Xu, Y., Xu, Z., Yang, C., Yang, Q., Yang, S., Yang, Y., Yang, Z., Ye, Z., Yi, L., Yip, K., Zbroszczyk, Hanna Paulina, Zha, W., Zhang, C., Zhang, D., Zhang, S., Zhang, X.P., Zhang, Y., Zhang, Z.J., Zhang, Zuman, Zhao, J., Zhong, C., Zhou, C., Zhu, X., Zhu, Z., Zurek, Marian, Zyzak, Maksym, Adam, Jaroslav, Adamczyk, Leszek, Adams, Joseph R., Adkins, J. Kevin, Agakishiev, Geydar, Aggarwal, Madan Mohan, Ahammed, Zubayer, Alekseev, Igor G., Anderson, Derek M., Aparin, Alexey, Aschenauer, Elke Caroline, Ashraf, Muhammad Usman, Atetalla, Fareha, Attri, Anjali, Averichev, Georgy S., Bairathi, Vipul, Barish, Kenneth, Behera, Arabinda, Bellwied, Rene, Bhasin, Anju, Bielčík, Jaroslav, Bielčíková, Jana, Bland, Leslie C., Bordyuzhin, Igor G., Brandenburg, James D., Brandin, Andrei V., Butterworth, Joseph, Caines, Helen Louise, Calderón de la Barca Sánchez, Manuel, Cebra, Daniel A., Chakaberia, Irakli, Chaloupka, Petr, Chan, B.K., Chang, F.-H., Chang, Z., Chankova-Bunzarova, N., Chatterjee, A., Chen, D., Chen, J.H., Chen, X., Chen, Z., Cheng, J., Cherney, Michael Gerard, Chevalier, M., Choudhury, Subikash, Christie, William, Chu, X., Crawford, Henry J., Csanád, Máté, Daugherity, M., Dedovič, Tatiana G., Deppner, Ingo Martin, Derevschikov, Anatoly A., Didenko, Lidia, Dong, X., Drachenberg, James Lucus, Dunlop, James C., Edmonds, Terrence, Elsey, Nicholas, Engelage, Jon M., Eppley, Geary Wareham, Esha, Roli, Esumi, ShinIchi, Evdokimov, Olga Y., Ewigleben, A., Eyser, Kjeld Oleg, Fatemi, Renee H., Fazio, Salvatore, Federič, Pavol, Fedorišin, Jan, Feng, C.J., Feng, Y., Filip, Peter, Finch, Evan, Fisyak, Yuri V., Francisco, Audrey, Fulek, Łukasz, Gagliardi, Carl A., Galatyuk, Tetyana, Geurts, Frank, Gibson, Adam, Gopal, Krishan, Grosnick, David P., Guryn, Włodzimierz, Hamad, Ayman, Hamed, Ahmed M., Harabasz, Szymon, Harris, John W., He, S., He, W., He, X.H., Heppelmann, Steven Francis, Herrmann, Norbert, Hoffman, E., Holub, Lukáš, Hong, Y., Horvat, S., Hu, Y., Huang, H.Z., Huang, Shengli, Huang, T., Huang, X., Humanic, Thomas J., Huo, P., Igo, George J., Isenhower, D., Jacobs, William W., Jena, Chitrasen, Jentsch, Alexander, Ji, Y., Jia, J., Jiang, K., Jowzaee, S., 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., Kim, C., Kimelman, B., Kincses, D., Kinghorn, Todd Adler, Kisel, Ivan, Kiselev, A., Kocan, Michal, Kočenda, L. M., Kosarzewski, Leszek Krzysztof, Kramárik, Lukáš, Kravtsov, Peter, Krueger, Keith William, Kulathunga Mudiyanselage, Nalinda, Kumar, Lokesh, 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., Li, C., Li, W., Li, Xiaomei, Li, Y., 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., Lukow, N.S., Luo, S., Luo, X., Ma, G.L., Ma, L., Ma, R., Ma, Yu-Gang, Magdy Abdelwahab Abdelrahman, Niseem, Majka, Richard Daniel, Mallick, Dukhishyam, Margetis, Spyridon, Markert, Christina, Matis, Howard S., Mazer, Joel Anthony, Minaev, Nikolai G., Mioduszewski, Saskia, Mohanty, Bedangadas, Mondal, Mriganka Mouli, Mooney, Isaac A., Moravcova, Zuzana, Morozov, Dmitry A., Nagy, M., Nam, J.D., Nasim, Md., Nayak, Kishora, Neff, D., Nelson, John M., Nemes, Daniel B., Nie, Maowu, Nigmatkulov, Grigory A., Niida, Takafumi, Nogach, Larisa V., Nonaka, Toshihiro, Nunes, A.S., Odyniec, Grazyna Janina, Ogawa, Akio, Oh, S., Okorokov, Vitaly A., Page, Brian S., Pak, Robert, Pandav, A., Panebratsev, Yuri, Pawlik, Bogdan, Pawłowska, Diana, Pei, Hua, Perkins, Chris, Pinsky, Lawrence, Pintér, Roland Laszlo, Pluta, Jan Marian, Porter, Jeffrey Brent, Posik, Matthew, Pruthi, Navneet Kumar, Przybycien, Mariusz, Putschke, Jörn H., Qiu, H., Quintero, Amilkar, Radhakrishnan, Sooraj Krishnan, Ramachandran, Suvarna, Ray, Robert L., Reed, Rosi Jan, Ritter, Hans Georg, Roberts, Jabus B., Rogačevskij, Oleg V., Romero, Juan L., Ruan, Lijuan, Rusnak, Jan, Sahoo, Nihar Ranjan, Sako, H., Salur, Sevil, Sandweiss, Jack H., Sato, S., Schmidke, William B., Schmitz, Norbert, Schweid, Benjamin R., Seck, Florian, Seger, Janet Elizabeth, Sergeeva, Maria, Seto, Richard, Seyboth, Peter, Shah, N., Shahaliev, Ehtiram, Shanmuganathan, Prashanth V., Shao, M., Shen, F., Shen, W.Q., Shi, S.S., Shou, Q.Y., Sichtermann, Ernst P., Sikora, Rafał, Šimko, Miroslav, Singh, Jagbir, Singha, Subhash, Smirnov, Nikolai, Solyst, William, Sorensen, Paul Richard, 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., Szymański, Paweł, Tang, Aihong, Tang, Zebo, Taranenko, Arkadiy, Tarnowsky, Terence J., Thomas, James H., Timmins, Anthony Robert, Tlusty, David, Tokarev, Mikhail V., Tomkiel, Catherine A., Trentalange, Stephen, Tribble, Robert E., Tribedy, Prithwish, Tripathy, Srikanta Kumar, Tsai, Oleg D., Tu, Z., Ullrich, Thomas, Underwood, David G., Upsal, Isaac, Van Buren, Gene, Vanek, Jan, Vasiliev, Alexander Nikolaevich, Vassiliev, Iouri, Videbæk, Flemming, Vokal, Stanislav, Voloshin, Sergei, Wang, F., Wang, G., Wang, J.S., Wang, P., Wang, Y., Wang, Z., Webb, Jason C., Weidenkaff, P.C., Wen, L., Westfall, Gary D., Wieman, Howard, Wissink, Scott W., Witt, Richard, Wu, Y., Xiao, Z.G., Xie, G., Xie, W., Xu, H., Xu, N., Xu, Q.H., Xu, Y.F., Xu, Y., Xu, Z., Yang, C., Yang, Q., Yang, S., Yang, Y., Yang, Z., Ye, Z., Yi, L., Yip, K., Zbroszczyk, Hanna Paulina, Zha, W., Zhang, C., Zhang, D., Zhang, S., Zhang, X.P., Zhang, Y., Zhang, Z.J., Zhang, Zuman, Zhao, J., Zhong, C., Zhou, C., Zhu, X., Zhu, Z., Zurek, Marian, and Zyzak, Maksym

Abstract

Flow harmonics (vn) of the Fourier expansion for the azimuthal distributions of hadrons are commonly employed to quantify the azimuthal anisotropy of particle production relative to the collision symmetry planes. While lower order Fourier coefficients (v2 and v3) are more directly related to the corresponding eccentricities of the initial state, the higher-order flow harmonics (vn>3) can be induced by a modecoupled response to the lower-order anisotropies, in addition to a linear response to the same-order anisotropies. These higher-order flow harmonics and their linear and mode-coupled contributions can be used to more precisely constrain the initial conditions and the transport properties of the medium in theoretical models. The multiparticle azimuthal cumulant method is used to measure the linear and mode-coupled contributions in the higher-order anisotropic flow, the mode-coupled response coefficients, and the correlations of the event plane angles for charged particles as functions of centrality and transverse momentum in Au+Au collisions at nucleon-nucleon center-of-mass energy √sN N= 200 GeV. The results are compared to similar LHC measurements as well as to several viscous hydrodynamic calculations with varying initial conditions.

Published
2020

121. Measurement of groomed jet substructure observables in p+p collisions at √s = 200 GeV with STAR

Author

Adam, Jaroslav, Adamczyk, Leszek, Adams, Joseph R., Adkins, J. Kevin, Agakishiev, Geydar, Aggarwal, Madan Mohan, Ahammed, Zubayer, Alekseev, Igor G., Anderson, Derek M., Aparin, Alexey, Aschenauer, Elke Caroline, Ashraf, Muhammad Usman, Atetalla, Fareha, Attri, Anjali, Averichev, Georgy S., Bairathi, Vipul, Barish, Kenneth, Behera, Arabinda, Bellwied, Rene, Bhasin, Anju, Bielčík, Jaroslav, Bielčíková, Jana, Bland, Leslie C., Bordyuzhin, Igor G., Brandenburg, James D., Brandin, Andrei V., Butterworth, Joseph, Caines, Helen Louise, Calderón de la Barca Sánchez, Manuel, Cebra, Daniel A., Chakaberia, Irakli, Chaloupka, Petr, Chan, B.K., Chang, F.-H., Chang, Z., Chankova-Bunzarova, N., Chatterjee, A., Chen, D., Chen, J.H., Chen, X., Chen, Z., Cheng, J., Cherney, Michael Gerard, Chevalier, M., Choudhury, Subikash, Christie, William, Chu, X., Crawford, Henry J., Csanád, Máté, Daugherity, M., Dedovič, Tatiana G., Deppner, Ingo Martin, Derevschikov, Anatoly A., Didenko, Lidia, Dong, X., Drachenberg, James Lucus, Dunlop, James C., Edmonds, Terrence, Elsey, Nicholas, Engelage, Jon M., Eppley, Geary Wareham, Esha, Roli, Esumi, ShinIchi, Evdokimov, Olga Y., Ewigleben, A., Eyser, Kjeld Oleg, Fatemi, Renee H., Fazio, Salvatore, Federič, Pavol, Fedorišin, Jan, Feng, C.J., Feng, Y., Filip, Peter, Finch, Evan, Fisyak, Yuri V., Francisco, Audrey, Fulek, Łukasz, Gagliardi, Carl A., Galatyuk, Tetyana, Geurts, Frank, Gibson, Adam, Gopal, Krishan, Grosnick, David P., Guryn, Włodzimierz, Hamad, Ayman, Hamed, Ahmed M., Harabasz, Szymon, Harris, John W., He, S., He, W., He, X.H., Heppelmann, Steven Francis, Herrmann, Norbert, Hoffman, E., Holub, Lukáš, Hong, Y., Horvat, S., Hu, Y., Huang, H.Z., Huang, Shengli, Huang, T., Huang, X., Humanic, Thomas J., Huo, P., Igo, George J., Isenhower, D., Jacobs, William W., Jena, Chitrasen, Jentsch, Alexander, Ji, Y., Jia, J., Jiang, K., Jowzaee, S., 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., Kim, C., Kimelman, B., Kincses, D., Kinghorn, Todd Adler, Kisel, Ivan, Kiselev, A., Kocan, Michal, Kočenda, L. M., Kosarzewski, Leszek Krzysztof, Kramárik, Lukáš, Kravtsov, Peter, Krueger, Keith William, Kulathunga Mudiyanselage, Nalinda, Kumar, Lokesh, 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., Li, C., Li, W., Li, Xiaomei, Li, Y., 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., Lukow, N.S., Luo, S., Luo, X., Ma, G.L., Ma, L., Ma, R., Ma, Yu-Gang, Magdy Abdelwahab Abdelrahman, Niseem, Majka, Richard Daniel, Mallick, Dukhishyam, Margetis, Spyridon, Markert, Christina, Matis, Howard S., Mazer, Joel Anthony, Minaev, Nikolai G., Mioduszewski, Saskia, Mohanty, Bedangadas, Mondal, Mriganka Mouli, Mooney, Isaac A., Moravcova, Zuzana, Morozov, Dmitry A., Nagy, M., Nam, J.D., Nasim, Md., Nayak, Kishora, Neff, D., Nelson, John M., Nemes, Daniel B., Nie, Maowu, Nigmatkulov, Grigory A., Niida, Takafumi, Nogach, Larisa V., Nonaka, Toshihiro, Nunes, A.S., Odyniec, Grazyna Janina, Ogawa, Akio, Oh, S., Okorokov, Vitaly A., Page, Brian S., Pak, Robert, Pandav, A., Panebratsev, Yuri, Pawlik, Bogdan, Pawłowska, Diana, Pei, Hua, Perkins, Chris, Pinsky, Lawrence, Pintér, Roland Laszlo, Pluta, Jan Marian, Porter, Jeffrey Brent, Posik, Matthew, Pruthi, Navneet Kumar, Przybycien, Mariusz, Putschke, Jörn H., Qiu, H., Quintero, Amilkar, Radhakrishnan, Sooraj Krishnan, Ramachandran, Suvarna, Ray, Robert L., Reed, Rosi Jan, Ritter, Hans Georg, Roberts, Jabus B., Rogačevskij, Oleg V., Romero, Juan L., Ruan, Lijuan, Rusnak, Jan, Sahoo, Nihar Ranjan, Sako, H., Salur, Sevil, Sandweiss, Jack H., Sato, S., Schmidke, William B., Schmitz, Norbert, Schweid, Benjamin R., Seck, Florian, Seger, Janet Elizabeth, Sergeeva, Maria, Seto, Richard, Seyboth, Peter, Shah, N., Shahaliev, Ehtiram, Shanmuganathan, Prashanth V., Shao, M., Shen, F., Shen, W.Q., Shi, S.S., Shou, Q.Y., Sichtermann, Ernst P., Sikora, Rafał, Šimko, Miroslav, Singh, Jagbir, Singha, Subhash, Smirnov, Nikolai, Solyst, William, Sorensen, Paul Richard, 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., Szymański, Paweł, Tang, Aihong, Tang, Zebo, Taranenko, Arkadiy, Tarnowsky, Terence J., Thomas, James H., Timmins, Anthony Robert, Tlusty, David, Tokarev, Mikhail V., Tomkiel, Catherine A., Trentalange, Stephen, Tribble, Robert E., Tribedy, Prithwish, Tripathy, Srikanta Kumar, Tsai, Oleg D., Tu, Z., Ullrich, Thomas, Underwood, David G., Upsal, Isaac, Van Buren, Gene, Vanek, Jan, Vasiliev, Alexander Nikolaevich, Vassiliev, Iouri, Videbæk, Flemming, Vokal, Stanislav, Voloshin, Sergei, Wang, F., Wang, G., Wang, J.S., Wang, P., Wang, Y., Wang, Z., Webb, Jason C., Weidenkaff, P.C., Wen, L., Westfall, Gary D., Wieman, Howard, Wissink, Scott W., Witt, Richard, Wu, Y., Xiao, Z.G., Xie, G., Xie, W., Xu, H., Xu, N., Xu, Q.H., Xu, Y.F., Xu, Y., Xu, Z., Yang, C., Yang, Q., Yang, S., Yang, Y., Yang, Z., Ye, Z., Yi, L., Yip, K., Zbroszczyk, Hanna Paulina, Zha, W., Zhang, C., Zhang, D., Zhang, S., Zhang, X.P., Zhang, Y., Zhang, Z.J., Zhang, Zuman, Zhao, J., Zhong, C., Zhou, C., Zhu, X., Zhu, Z., Zurek, Marian, Zyzak, Maksym, Adam, Jaroslav, Adamczyk, Leszek, Adams, Joseph R., Adkins, J. Kevin, Agakishiev, Geydar, Aggarwal, Madan Mohan, Ahammed, Zubayer, Alekseev, Igor G., Anderson, Derek M., Aparin, Alexey, Aschenauer, Elke Caroline, Ashraf, Muhammad Usman, Atetalla, Fareha, Attri, Anjali, Averichev, Georgy S., Bairathi, Vipul, Barish, Kenneth, Behera, Arabinda, Bellwied, Rene, Bhasin, Anju, Bielčík, Jaroslav, Bielčíková, Jana, Bland, Leslie C., Bordyuzhin, Igor G., Brandenburg, James D., Brandin, Andrei V., Butterworth, Joseph, Caines, Helen Louise, Calderón de la Barca Sánchez, Manuel, Cebra, Daniel A., Chakaberia, Irakli, Chaloupka, Petr, Chan, B.K., Chang, F.-H., Chang, Z., Chankova-Bunzarova, N., Chatterjee, A., Chen, D., Chen, J.H., Chen, X., Chen, Z., Cheng, J., Cherney, Michael Gerard, Chevalier, M., Choudhury, Subikash, Christie, William, Chu, X., Crawford, Henry J., Csanád, Máté, Daugherity, M., Dedovič, Tatiana G., Deppner, Ingo Martin, Derevschikov, Anatoly A., Didenko, Lidia, Dong, X., Drachenberg, James Lucus, Dunlop, James C., Edmonds, Terrence, Elsey, Nicholas, Engelage, Jon M., Eppley, Geary Wareham, Esha, Roli, Esumi, ShinIchi, Evdokimov, Olga Y., Ewigleben, A., Eyser, Kjeld Oleg, Fatemi, Renee H., Fazio, Salvatore, Federič, Pavol, Fedorišin, Jan, Feng, C.J., Feng, Y., Filip, Peter, Finch, Evan, Fisyak, Yuri V., Francisco, Audrey, Fulek, Łukasz, Gagliardi, Carl A., Galatyuk, Tetyana, Geurts, Frank, Gibson, Adam, Gopal, Krishan, Grosnick, David P., Guryn, Włodzimierz, Hamad, Ayman, Hamed, Ahmed M., Harabasz, Szymon, Harris, John W., He, S., He, W., He, X.H., Heppelmann, Steven Francis, Herrmann, Norbert, Hoffman, E., Holub, Lukáš, Hong, Y., Horvat, S., Hu, Y., Huang, H.Z., Huang, Shengli, Huang, T., Huang, X., Humanic, Thomas J., Huo, P., Igo, George J., Isenhower, D., Jacobs, William W., Jena, Chitrasen, Jentsch, Alexander, Ji, Y., Jia, J., Jiang, K., Jowzaee, S., 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., Kim, C., Kimelman, B., Kincses, D., Kinghorn, Todd Adler, Kisel, Ivan, Kiselev, A., Kocan, Michal, Kočenda, L. M., Kosarzewski, Leszek Krzysztof, Kramárik, Lukáš, Kravtsov, Peter, Krueger, Keith William, Kulathunga Mudiyanselage, Nalinda, Kumar, Lokesh, 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., Li, C., Li, W., Li, Xiaomei, Li, Y., 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., Lukow, N.S., Luo, S., Luo, X., Ma, G.L., Ma, L., Ma, R., Ma, Yu-Gang, Magdy Abdelwahab Abdelrahman, Niseem, Majka, Richard Daniel, Mallick, Dukhishyam, Margetis, Spyridon, Markert, Christina, Matis, Howard S., Mazer, Joel Anthony, Minaev, Nikolai G., Mioduszewski, Saskia, Mohanty, Bedangadas, Mondal, Mriganka Mouli, Mooney, Isaac A., Moravcova, Zuzana, Morozov, Dmitry A., Nagy, M., Nam, J.D., Nasim, Md., Nayak, Kishora, Neff, D., Nelson, John M., Nemes, Daniel B., Nie, Maowu, Nigmatkulov, Grigory A., Niida, Takafumi, Nogach, Larisa V., Nonaka, Toshihiro, Nunes, A.S., Odyniec, Grazyna Janina, Ogawa, Akio, Oh, S., Okorokov, Vitaly A., Page, Brian S., Pak, Robert, Pandav, A., Panebratsev, Yuri, Pawlik, Bogdan, Pawłowska, Diana, Pei, Hua, Perkins, Chris, Pinsky, Lawrence, Pintér, Roland Laszlo, Pluta, Jan Marian, Porter, Jeffrey Brent, Posik, Matthew, Pruthi, Navneet Kumar, Przybycien, Mariusz, Putschke, Jörn H., Qiu, H., Quintero, Amilkar, Radhakrishnan, Sooraj Krishnan, Ramachandran, Suvarna, Ray, Robert L., Reed, Rosi Jan, Ritter, Hans Georg, Roberts, Jabus B., Rogačevskij, Oleg V., Romero, Juan L., Ruan, Lijuan, Rusnak, Jan, Sahoo, Nihar Ranjan, Sako, H., Salur, Sevil, Sandweiss, Jack H., Sato, S., Schmidke, William B., Schmitz, Norbert, Schweid, Benjamin R., Seck, Florian, Seger, Janet Elizabeth, Sergeeva, Maria, Seto, Richard, Seyboth, Peter, Shah, N., Shahaliev, Ehtiram, Shanmuganathan, Prashanth V., Shao, M., Shen, F., Shen, W.Q., Shi, S.S., Shou, Q.Y., Sichtermann, Ernst P., Sikora, Rafał, Šimko, Miroslav, Singh, Jagbir, Singha, Subhash, Smirnov, Nikolai, Solyst, William, Sorensen, Paul Richard, 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., Szymański, Paweł, Tang, Aihong, Tang, Zebo, Taranenko, Arkadiy, Tarnowsky, Terence J., Thomas, James H., Timmins, Anthony Robert, Tlusty, David, Tokarev, Mikhail V., Tomkiel, Catherine A., Trentalange, Stephen, Tribble, Robert E., Tribedy, Prithwish, Tripathy, Srikanta Kumar, Tsai, Oleg D., Tu, Z., Ullrich, Thomas, Underwood, David G., Upsal, Isaac, Van Buren, Gene, Vanek, Jan, Vasiliev, Alexander Nikolaevich, Vassiliev, Iouri, Videbæk, Flemming, Vokal, Stanislav, Voloshin, Sergei, Wang, F., Wang, G., Wang, J.S., Wang, P., Wang, Y., Wang, Z., Webb, Jason C., Weidenkaff, P.C., Wen, L., Westfall, Gary D., Wieman, Howard, Wissink, Scott W., Witt, Richard, Wu, Y., Xiao, Z.G., Xie, G., Xie, W., Xu, H., Xu, N., Xu, Q.H., Xu, Y.F., Xu, Y., Xu, Z., Yang, C., Yang, Q., Yang, S., Yang, Y., Yang, Z., Ye, Z., Yi, L., Yip, K., Zbroszczyk, Hanna Paulina, Zha, W., Zhang, C., Zhang, D., Zhang, S., Zhang, X.P., Zhang, Y., Zhang, Z.J., Zhang, Zuman, Zhao, J., Zhong, C., Zhou, C., Zhu, X., Zhu, Z., Zurek, Marian, and Zyzak, Maksym

Abstract

In this letter, measurements of the shared momentum fraction (zg) and the groomed jet radius (Rg), as defined in the SoftDrop algorithm, are reported in p+p collisions at √s = 200 GeV collected by the STAR experiment. These substructure observables are differentially measured for jets of varying resolution parameters from R = 0.2 − 0.6 in the transverse momentum range 15 < pT,jet < 60 GeV/c. These studies show that, in the pT,jet range accessible at √s = 200 GeV and with increasing jet resolution parameter and jet transverse momentum, the zg distribution asymptotically converges to the DGLAP splitting kernel for a quark radiating a gluon. The groomed jet radius measurements reflect a momentum-dependent narrowing of the jet structure for jets of a given resolution parameter, i.e., the larger the pT,jet, the narrower the first splitting. For the first time, these fully corrected measurements are compared to Monte Carlo generators with leading order QCD matrix elements and leading log in the parton shower, and to state-of-the-art theoretical calculations at next-to-leading-log accuracy. We observe that PYTHIA 6 with parameters tuned to reproduce RHIC measurements is able to quantitatively describe data, whereas PYTHIA 8 and HERWIG 7, tuned to reproduce LHC data, are unable to provide a simultaneous description of both zg and Rg, resulting in opportunities for fine parameter tuning of these models for p+p collisions at RHIC energies. We also find that the theoretical calculations without non-perturbative corrections are able to qualitatively describe the trend in data for jets of large resolution parameters at high pT,jet, but fail at small jet resolution parameters and low jet transverse momenta.

Published
2020

130. Transconductance amplifier with low-power consumption

Author

Morozov, Dmitry V. and Korotkov, Alexander S.

Subjects
Circuit components -- Design and construction, Amplifiers (Electronics) -- Design and construction, Feedback (Electronics) -- Analysis, Semiconductor device, Business, Computers and office automation industries, Electronics, Electronics and electrical industries
Abstract

A modified transconductance amplifier with low harmonic distortion and high current efficiency is proposed. It can be used in high-frequency applications up to 10 MHz. Each half of the transconductor differential input stage consists of a pair of transistors in saturation and linear regimes with a voltage feedback loop. Results of theoretical analysis are confirmed by SPICE simulations. Index Terms--Feedback, harmonic distortion, noise, transconductance amplifier, transconductor.

Published
2005

131. Ultrafast structural changes within a photosynthetic reaction centre

Author

Dods, Robert, primary, Båth, Petra, additional, Morozov, Dmitry, additional, Gagnér, Viktor Ahlberg, additional, Arnlund, David, additional, Luk, Hoi Ling, additional, Kübel, Joachim, additional, Maj, Michał, additional, Vallejos, Adams, additional, Wickstrand, Cecilia, additional, Bosman, Robert, additional, Beyerlein, Kenneth R., additional, Nelson, Garrett, additional, Liang, Mengning, additional, Milathianaki, Despina, additional, Robinson, Joseph, additional, Harimoorthy, Rajiv, additional, Berntsen, Peter, additional, Malmerberg, Erik, additional, Johansson, Linda, additional, Andersson, Rebecka, additional, Carbajo, Sergio, additional, Claesson, Elin, additional, Conrad, Chelsie E., additional, Dahl, Peter, additional, Hammarin, Greger, additional, Hunter, Mark S., additional, Li, Chufeng, additional, Lisova, Stella, additional, Royant, Antoine, additional, Safari, Cecilia, additional, Sharma, Amit, additional, Williams, Garth J., additional, Yefanov, Oleksandr, additional, Westenhoff, Sebastian, additional, Davidsson, Jan, additional, DePonte, Daniel P., additional, Boutet, Sébastien, additional, Barty, Anton, additional, Katona, Gergely, additional, Groenhof, Gerrit, additional, Brändén, Gisela, additional, and Neutze, Richard, additional

Published
2020
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135. Illuminating a Phytochrome Paradigm – a Light-Activated Phosphatase in Two-Component Signaling Uncovered

Author

Multamäki, Elina, primary, Nanekar, Rahul, additional, Morozov, Dmitry, additional, Lievonen, Topias, additional, Golonka, David, additional, Yuan Wahlgren, Weixiao, additional, Stucki-Buchli, Brigitte, additional, Rossi, Jari, additional, Hytönen, Vesa P., additional, Westenhoff, Sebastian, additional, Ihalainen, Janne A., additional, Möglich, Andreas, additional, and Takala, Heikki, additional

Published
2020
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138. The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Author

Claesson, Elin, primary, Wahlgren, Weixiao Yuan, additional, Takala, Heikki, additional, Pandey, Suraj, additional, Castillon, Leticia, additional, Kuznetsova, Valentyna, additional, Henry, Léocadie, additional, Panman, Matthijs, additional, Carrillo, Melissa, additional, Kübel, Joachim, additional, Nanekar, Rahul, additional, Isaksson, Linnéa, additional, Nimmrich, Amke, additional, Cellini, Andrea, additional, Morozov, Dmitry, additional, Maj, Michał, additional, Kurttila, Moona, additional, Bosman, Robert, additional, Nango, Eriko, additional, Tanaka, Rie, additional, Tanaka, Tomoyuki, additional, Fangjia, Luo, additional, Iwata, So, additional, Owada, Shigeki, additional, Moffat, Keith, additional, Groenhof, Gerrit, additional, Stojković, Emina A, additional, Ihalainen, Janne A, additional, Schmidt, Marius, additional, and Westenhoff, Sebastian, additional

Published
2020
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139. Two-photon quantum interference and entanglement at 2.1 μm

Author

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

Published
2020
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141. Author response: The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

Author

Claesson, Elin, primary, Wahlgren, Weixiao Yuan, additional, Takala, Heikki, additional, Pandey, Suraj, additional, Castillon, Leticia, additional, Kuznetsova, Valentyna, additional, Henry, Léocadie, additional, Panman, Matthijs, additional, Carrillo, Melissa, additional, Kübel, Joachim, additional, Nanekar, Rahul, additional, Isaksson, Linnéa, additional, Nimmrich, Amke, additional, Cellini, Andrea, additional, Morozov, Dmitry, additional, Maj, Michał, additional, Kurttila, Moona, additional, Bosman, Robert, additional, Nango, Eriko, additional, Tanaka, Rie, additional, Tanaka, Tomoyuki, additional, Fangjia, Luo, additional, Iwata, So, additional, Owada, Shigeki, additional, Moffat, Keith, additional, Groenhof, Gerrit, additional, Stojković, Emina A, additional, Ihalainen, Janne A, additional, Schmidt, Marius, additional, and Westenhoff, Sebastian, additional

Published
2020
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145. Mid-infrared Quantum Interference and Polarization Entanglement

Author

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

Published
2020
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148. Photon counting LIDAR at 2.3μm wavelength with superconducting nanowires

Author

Taylor, Gregor G., Morozov, Dmitry, Gemmell, Nathan, Erotokritou, Kleanthis, Miki, Shigehito, Terai, Hirotaka, and Hadfield, Robert

Subjects
TK, Physics::Optics, QC
Abstract

In this work, we show a proof-of-principle benchtop single-photon light detection\ud and ranging (LIDAR) depth imager at 2.3μm, utilizing superconducting nanowire single-photon detectors (SNSPDs). We fabricate and fiber-couple SNSPDs to exhibit enhanced photon counting performance in the mid-infrared. We present characterization results using an optical parametric oscillator source and deploy these detectors in a scanning LIDAR setup at 2.3μm wavelength. This demonstrates the viability of these detectors for future free-space photon counting applications in the mid-infrared where atmospheric absorption and background solar flux are low.

Published
2019

149. Two-photon Quantum Interference and Entanglement at 2 ��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
Physics::Optics, FOS: Physical sciences, Quantum Physics (quant-ph), Optics (physics.optics)
Abstract

Quantum-enhanced optical systems operating within the 2- to 2.5-$��$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-$��$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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150. Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of Bacteriophytochrome

Author

Modi, Vaibhav, Donnini, Serena, Groenhof, Gerrit, and Morozov, Dmitry

Subjects
phytochrome, kvanttikemia, molekyylidynamiikka, valokemia, proteiinit, excited states
Abstract

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra. peerReviewed

Published
2019

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