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148 results on '"Johnson, Philip J. M."'

1. Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography

Author

Cellini, Andrea, Shankar, Madan Kumar, Nimmrich, Amke, Hunt, Leigh Anna, Monrroy, Leonardo, Mutisya, Jennifer, Furrer, Antonia, Beale, Emma V., Carrillo, Melissa, Malla, Tek Narsingh, Maj, Piotr, Vrhovac, Lidija, Dworkowski, Florian, Cirelli, Claudio, Johnson, Philip J. M., Ozerov, Dmitry, Stojković, Emina A., Hammarström, Leif, Bacellar, Camila, Standfuss, Jörg, Maj, Michał, Schmidt, Marius, Weinert, Tobias, Ihalainen, Janne A., Wahlgren, Weixiao Yuan, and Westenhoff, Sebastian

Published
2024
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2. Influence of pump laser fluence on ultrafast myoglobin structural dynamics

Author

Barends, Thomas R. M., Gorel, Alexander, Bhattacharyya, Swarnendu, Schirò, Giorgio, Bacellar, Camila, Cirelli, Claudio, Colletier, Jacques-Philippe, Foucar, Lutz, Grünbein, Marie Luise, Hartmann, Elisabeth, Hilpert, Mario, Holton, James M., Johnson, Philip J. M., Kloos, Marco, Knopp, Gregor, Marekha, Bogdan, Nass, Karol, Nass Kovacs, Gabriela, Ozerov, Dmitry, Stricker, Miriam, Weik, Martin, Doak, R. Bruce, Shoeman, Robert L., Milne, Christopher J., Huix-Rotllant, Miquel, Cammarata, Marco, and Schlichting, Ilme

Published
2024
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3. A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

Author

Wranik, Maximilian, Kepa, Michal W., Beale, Emma V., James, Daniel, Bertrand, Quentin, Weinert, Tobias, Furrer, Antonia, Glover, Hannah, Gashi, Dardan, Carrillo, Melissa, Kondo, Yasushi, Stipp, Robin T., Khusainov, Georgii, Nass, Karol, Ozerov, Dmitry, Cirelli, Claudio, Johnson, Philip J. M., Dworkowski, Florian, Beale, John H., Stubbs, Scott, Zamofing, Thierry, Schneider, Marco, Krauskopf, Kristina, Gao, Li, Thorn-Seshold, Oliver, Bostedt, Christoph, Bacellar, Camila, Steinmetz, Michel O., Milne, Christopher, and Standfuss, Jörg

Published
2023
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4. Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography

Author

Wranik, Maximilian, Weinert, Tobias, Slavov, Chavdar, Masini, Tiziana, Furrer, Antonia, Gaillard, Natacha, Gioia, Dario, Ferrarotti, Marco, James, Daniel, Glover, Hannah, Carrillo, Melissa, Kekilli, Demet, Stipp, Robin, Skopintsev, Petr, Brünle, Steffen, Mühlethaler, Tobias, Beale, John, Gashi, Dardan, Nass, Karol, Ozerov, Dmitry, Johnson, Philip J. M., Cirelli, Claudio, Bacellar, Camila, Braun, Markus, Wang, Meitian, Dworkowski, Florian, Milne, Chris, Cavalli, Andrea, Wachtveitl, Josef, Steinmetz, Michel O., and Standfuss, Jörg

Published
2023
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5. Hard X-ray Transient Grating Spectroscopy on Bismuth Germanate

Author

Rouxel, Jeremy R., Fainozzi, Danny, Mankowsky, Roman, Rosner, Benedikt, Seniutinas, Gediminas, Mincigrucci, Riccardo, Catalini, Sara, Foglia, Laura, Cucini, Riccardo, Doring, Florian, Kubec, Adam, Koch, Frieder, Bencivenga, Filippo, Haddad, Andre Al, Gessini, Alessandro, Maznev, Alexei A., Cirelli, Claudio, Gerber, Simon, Pedrini, Bill, Mancini, Giulia F., Razzoli, Elia, Burian, Max, Ueda, Hiroki, Pamfilidis, Georgios, Ferrari, Eugenio, Deng, Yunpei, Mozzanica, Aldo, Johnson, Philip J. M., Ozerov, Dmitry, Izzo, Maria G., Bottari, Cettina, Arrell, Christopher, Divall, Edwin J., Zerdane, Serhane, Sander, Mathias, Knopp, Gregor, Beaud, Paul, Lemke, Henrik T., Milne, Chris J., David, Christian, Torre, Renato, Chergui, Majed, Nelson, Keith A., Masciovecchio, Claudio, Staub, Urs, Patthey, Luc, and Svetina, Cristian

Subjects
Physics - Optics, Condensed Matter - Materials Science
Abstract

Optical-domain Transient Grating (TG) spectroscopy is a versatile background-free four-wave-mixing technique used to probe vibrational, magnetic and electronic degrees of freedom in the time domain. The newly developed coherent X-ray Free Electron Laser sources allow its extension to the X-ray regime. Xrays offer multiple advantages for TG: their large penetration depth allows probing the bulk properties of materials, their element-specificity can address core-excited states, and their short wavelengths create excitation gratings with unprecedented momentum transfer and spatial resolution. We demonstrate for the first time TG excitation in the hard X-ray range at 7.1 keV. In Bismuth Germanate (BGO), the nonresonant TG excitation generates coherent optical phonons detected as a function of time by diffraction of an optical probe pulse. This experiment demonstrates the ability to probe bulk properties of materials and paves the way for ultrafast coherent four-wave-mixing techniques using X-ray probes and involving nanoscale TG spatial periods., Comment: 11 pages, 4 figures

Published
2021
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6. The Speed of Allosteric Signaling Within a Single-Domain Protein

Author

Bozovic, Olga, Ruf, Jeannette, Zanobini, Claudio, Jankovic, Brankica, Buhrke, David, Johnson, Philip J. M., and Hamm, Peter

Subjects
Physics - Biological Physics
Abstract

While much is known about different allosteric regulation mechanisms, the nature of the "allosteric signal", and the timescale on which it propagates, remains elusive. The PDZ3 domain from postsynaptic density-95 protein is a small protein domain with a terminal third alpha helix -- the $\alpha$3-helix, which is known to be allosterically active. By cross-linking the allosteric helix with an azobenzene moiety, we obtained a photocontrollable PDZ3 variant. Photoswitching triggers its allosteric transition, resulting in a change in binding affnity of a peptide to the remote binding pocket. Using time-resolved infrared and UV/Vis spectroscopy, we follow the allosteric signal transduction and reconstruct the timeline in which the allosteric signal propagates through the protein within 200 ns.

Published
2021

7. Ultrafast structural changes direct the first molecular events of vision

Author

Gruhl, Thomas, Weinert, Tobias, Rodrigues, Matthew J., Milne, Christopher J., Ortolani, Giorgia, Nass, Karol, Nango, Eriko, Sen, Saumik, Johnson, Philip J. M., Cirelli, Claudio, Furrer, Antonia, Mous, Sandra, Skopintsev, Petr, James, Daniel, Dworkowski, Florian, Båth, Petra, Kekilli, Demet, Ozerov, Dmitry, Tanaka, Rie, Glover, Hannah, Bacellar, Camila, Brünle, Steffen, Casadei, Cecilia M., Diethelm, Azeglio D., Gashi, Dardan, Gotthard, Guillaume, Guixà-González, Ramon, Joti, Yasumasa, Kabanova, Victoria, Knopp, Gregor, Lesca, Elena, Ma, Pikyee, Martiel, Isabelle, Mühle, Jonas, Owada, Shigeki, Pamula, Filip, Sarabi, Daniel, Tejero, Oliver, Tsai, Ching-Ju, Varma, Niranjan, Wach, Anna, Boutet, Sébastien, Tono, Kensuke, Nogly, Przemyslaw, Deupi, Xavier, Iwata, So, Neutze, Richard, Standfuss, Jörg, Schertler, Gebhard, and Panneels, Valerie

Published
2023
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8. Doming and spin cascade in Ferric Haems: Femtosecond X-ray Absorption and X-ray Emission Studies

Author

Bacellar, Camila, Kinschel, Dominik, Mancini, Giulia F., Ingle, Rebecca A., Rouxel, Jérémy, Cannelli, Oliviero, Cirelli, Claudio, Knopp, Gregor, Szlachetko, Jakub, Lima, Frederico A., Menzi, Samuel, Pamfilidis, Georgios, Kubicek, Katharina, Khakhulin, Dmitry, Gawelda, Wojciech, Rodriguez-Fernandez, Angel, Biednov, Mykola, Bressler, Christian, Arrell, Christopher A., Johnson, Philip J. M., Milne, Christopher, and Chergui, Majed

Subjects
Physics - Chemical Physics
Abstract

The structure-function relationship is at the heart of biology and major protein deformations are correlated to specific functions. In the case of heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobin, while ruffling has been correlated with electron transfer processes, such as in the case of Cytochrome c (Cyt c). The latter has indeed evolved to become an important electron transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe K-edge X-ray absorption near-edge structure (XANES) studies and femtosecond Fe Kalpha and Kbeta X-ray emission spectroscopy (XES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the Iron ion, causing the ferric heme to undergo doming, which we identify for the first time. We also argue that this pattern is common to all ferric haems, raising the question of the biological relevance of doming in such proteins.

Published
2020

9. Enhancement and maximum in the isobaric specific-heat capacity measurements of deeply supercooled water using ultrafast calorimetry

Author

Pathak, Harshad, Späh, Alexander, Esmaeildoost, Niloofar, Sellberg, Jonas A., Kim, Kyung Hwan, Perakis, Fivos, Amann-Winkel, Katrin, Ladd-Parada, Marjorie, Koliyadu, Jayanath, Lane, Thomas J., Yang, Cheolhee, Lemke, Henrik Till, Oggenfuss, Alexander Roland, Johnson, Philip J. M., Deng, Yunpei, Zerdane, Serhane, Mankowsky, Roman, Beaud, Paul, and Nilsson, Anders

Published
2021

10. Transient X‐Ray Absorption Near Edge Structure Spectroscopy Using Broadband Free‐Electron Laser Pulses.

Author

Juranić, Pavle, Cirelli, Claudio, Mamyrbayev, Talgat, Uemura, Yohei, Vila‐Comamala, Joan, Lima, Frederico Alves, Bacellar, Camila, Johnson, Philip J. M., Prat, Eduard, Reiche, Sven, Wach, Anna, Bykova, Iuliia, Kahraman, Abdullah, Kabanova, Victoria, Milne, Christopher, and David, Christian

Subjects
OXALATES, X-ray absorption near edge structure, ACQUISITION of data, SPECTROMETRY, BANDWIDTHS, FREE electron lasers, ABSORPTION, LASER pulses
Abstract

A new method for time‐resolved X‐ray absorption near edge structure (XANES) spectroscopy that enables faster data acquisition and requires smaller sample quantities for high‐quality data, thus allowing the analysis of more samples in a shorter time is introduced. The method uses large bandwidth free electron laser pulses to measure laser‐excited XANES spectra in transmission mode. A beam‐splitting grating configuration allows simultaneous measurements of the spectra of the incoming X‐ray Free Electron Laser (XFEL) pulses and transmission XANES, which is crucial for compensating the pulse‐dependent intensity and spectrum fluctuations due to the self‐amplified spontaneous emission operation. The implementation of this new methodology is applied on a liquid solution of ammonium iron(III) oxalate jet and is compared to previous results, showing great improvements in the speed of acquisition and spectral resolution, and the ability to measure a large 2‐D spectral‐time map quickly. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Correlation of refractive index based and THz streaking arrival time tools for a hard X-ray free-electron laser

Author

Błachucki, Wojciech, primary, Johnson, Philip J. M., additional, Usov, Ivan, additional, Divall, Edwin, additional, Cirelli, Claudio, additional, Knopp, Gregor, additional, Juranić, Pavle, additional, Patthey, Luc, additional, Szlachetko, Jakub, additional, Lemke, Henrik, additional, Milne, Christopher, additional, and Arrell, Christopher, additional

Published
2024
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12. Accessing metal-specific orbital interactions in C–H activation with resonant inelastic X-ray scattering

Author

Banerjee, Ambar, primary, Jay, Raphael M., additional, Leitner, Torsten, additional, Wang, Ru-Pan, additional, Harich, Jessica, additional, Stefanuik, Robert, additional, Coates, Michael R., additional, Beale, Emma V., additional, Kabanova, Victoria, additional, Kahraman, Abdullah, additional, Wach, Anna, additional, Ozerov, Dmitry, additional, Arrell, Christopher, additional, Milne, Christopher, additional, Johnson, Philip J. M., additional, Cirelli, Claudio, additional, Bacellar, Camila, additional, Huse, Nils, additional, Odelius, Michael, additional, and Wernet, Philippe, additional

Published
2024
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13. Spin cascade and doming in ferric hemes : Femtosecond X-ray absorption and X-ray emission studies

Author

Bacellar, Camila, Kinschel, Dominik, Mancini, Giulia F., Ingle, Rebecca A., Rouxel, Jérémy, Cannelli, Oliviero, Cirelli, Claudio, Knopp, Gregor, Szlachetko, Jakub, Lima, Frederico A., Menzi, Samuel, Pamfilidis, Georgios, Kubicek, Katharina, Khakhulin, Dmitry, Gawelda, Wojciech, Rodriguez-Fernandez, Angel, Biednov, Mykola, Bressler, Christian, Arrell, Christopher A., Johnson, Philip J. M., Milne, Christopher J., and Chergui, Majed

Published
2020

14. Visualizing the DNA repair process by a photolyase at atomic resolution

Author

Maestre-Reyna, Manuel, primary, Wang, Po-Hsun, additional, Nango, Eriko, additional, Hosokawa, Yuhei, additional, Saft, Martin, additional, Furrer, Antonia, additional, Yang, Cheng-Han, additional, Gusti Ngurah Putu, Eka Putra, additional, Wu, Wen-Jin, additional, Emmerich, Hans-Joachim, additional, Caramello, Nicolas, additional, Franz-Badur, Sophie, additional, Yang, Chao, additional, Engilberge, Sylvain, additional, Wranik, Maximilian, additional, Glover, Hannah Louise, additional, Weinert, Tobias, additional, Wu, Hsiang-Yi, additional, Lee, Cheng-Chung, additional, Huang, Wei-Cheng, additional, Huang, Kai-Fa, additional, Chang, Yao-Kai, additional, Liao, Jiahn-Haur, additional, Weng, Jui-Hung, additional, Gad, Wael, additional, Chang, Chiung-Wen, additional, Pang, Allan H., additional, Yang, Kai-Chun, additional, Lin, Wei-Ting, additional, Chang, Yu-Chen, additional, Gashi, Dardan, additional, Beale, Emma, additional, Ozerov, Dmitry, additional, Nass, Karol, additional, Knopp, Gregor, additional, Johnson, Philip J. M., additional, Cirelli, Claudio, additional, Milne, Chris, additional, Bacellar, Camila, additional, Sugahara, Michihiro, additional, Owada, Shigeki, additional, Joti, Yasumasa, additional, Yamashita, Ayumi, additional, Tanaka, Rie, additional, Tanaka, Tomoyuki, additional, Luo, Fangjia, additional, Tono, Kensuke, additional, Zarzycka, Wiktoria, additional, Müller, Pavel, additional, Alahmad, Maisa Alkheder, additional, Bezold, Filipp, additional, Fuchs, Valerie, additional, Gnau, Petra, additional, Kiontke, Stephan, additional, Korf, Lukas, additional, Reithofer, Viktoria, additional, Rosner, Christian Joshua, additional, Seiler, Elisa Marie, additional, Watad, Mohamed, additional, Werel, Laura, additional, Spadaccini, Roberta, additional, Yamamoto, Junpei, additional, Iwata, So, additional, Zhong, Dongping, additional, Standfuss, Jörg, additional, Royant, Antoine, additional, Bessho, Yoshitaka, additional, Essen, Lars-Oliver, additional, and Tsai, Ming-Daw, additional

Published
2023
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15. A compact and cost-effective hard X-ray free-electron laser driven by a high-brightness and low-energy electron beam

Author

Prat, Eduard, Abela, Rafael, Aiba, Masamitsu, Alarcon, Arturo, Alex, Jürgen, Arbelo, Yunieski, Arrell, Christopher, Arsov, Vladimir, Bacellar, Camila, Beard, Carl, Beaud, Paul, Bettoni, Simona, Biffiger, Roger, Bopp, Markus, Braun, Hans-Heinrich, Calvi, Marco, Cassar, Ariana, Celcer, Tine, Chergui, Majed, Chevtsov, Pavel, Cirelli, Claudio, Citterio, Alessandro, Craievich, Paolo, Divall, Marta Csatari, Dax, Andreas, Dehler, Micha, Deng, Yunpei, Dietrich, Alexander, Dijkstal, Philipp, Dinapoli, Roberto, Dordevic, Sladana, Ebner, Simon, Engeler, Daniel, Erny, Christian, Esposito, Vincent, Ferrari, Eugenio, Flechsig, Uwe, Follath, Rolf, Frei, Franziska, Ganter, Romain, Garvey, Terence, Geng, Zheqiao, Gobbo, Alexandre, Gough, Christopher, Hauff, Andreas, Hauri, Christoph P., Hiller, Nicole, Hunziker, Stephan, Huppert, Martin, Ingold, Gerhard, Ischebeck, Rasmus, Janousch, Markus, Johnson, Philip J. M., Johnson, Steven L., Juranić, Pavle, Jurcevic, Mario, Kaiser, Maik, Kalt, Roger, Keil, Boris, Kiselev, Daniela, Kittel, Christoph, Knopp, Gregor, Koprek, Waldemar, Laznovsky, Michael, Lemke, Henrik T., Sancho, Daniel Llorente, Löhl, Florian, Malyzhenkov, Alexander, Mancini, Giulia Fulvia, Mankowsky, Roman, Marcellini, Fabio, Marinkovic, Goran, Martiel, Isabelle, Märki, Fabian, Milne, Christopher J., Mozzanica, Aldo, Nass, Karol, Orlandi, Gian Luca, Loch, Cigdem Ozkan, Paraliev, Martin, Patterson, Bruce, Patthey, Luc, Pedrini, Bill, Pedrozzi, Marco, Pradervand, Claude, Radi, Peter, Raguin, Jean-Yves, Redford, Sophie, Rehanek, Jens, Reiche, Sven, Rivkin, Leonid, Romann, Albert, Sala, Leonardo, Sander, Mathias, Schietinger, Thomas, Schilcher, Thomas, Schlott, Volker, Schmidt, Thomas, Seidel, Mike, Stadler, Markus, Stingelin, Lukas, Svetina, Cristian, Treyer, Daniel M., Trisorio, Alexandre, Vicario, Carlo, Voulot, Didier, Wrulich, Albin, Zerdane, Serhane, and Zimoch, Elke

Published
2020
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16. Femtosecond-to-millisecond structural changes in a light-driven sodium pump

Author

Skopintsev, Petr, Ehrenberg, David, Weinert, Tobias, James, Daniel, Kar, Rajiv K., Johnson, Philip J. M., Ozerov, Dmitry, Furrer, Antonia, Martiel, Isabelle, Dworkowski, Florian, Nass, Karol, Knopp, Gregor, Cirelli, Claudio, Arrell, Christopher, Gashi, Dardan, Mous, Sandra, Wranik, Maximilian, Gruhl, Thomas, Kekilli, Demet, Brünle, Steffen, Deupi, Xavier, Schertler, Gebhard F. X., Benoit, Roger M., Panneels, Valerie, Nogly, Przemyslaw, Schapiro, Igor, Milne, Christopher, Heberle, Joachim, and Standfuss, Jörg

Published
2020
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17. Accessing Metal-Specific Orbital Interactions in C-H Activation using Resonant Inelastic X-ray Scattering

Author

Banerjee, Ambar, primary, Jay, Raphael M., additional, Leitner, Torsten, additional, Wang, Ru-Pan, additional, Harich, Jessica, additional, Stefanuik, Robert, additional, Coates, Michael R., additional, Beale, Emma V., additional, Kabanova, Victoria, additional, Kahraman, Abdullah, additional, Wach, Anna, additional, Ozerov, Dmitry, additional, Arrell, Christopher, additional, Milne, Christopher, additional, Johnson, Philip J. M., additional, Cirelli, Claudio, additional, Bacellar, Camila, additional, Huse, Nils, additional, Odelius, Michael, additional, and Wernet, Philippe, additional

Published
2023
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18. Tracking C–H activation with orbital resolution

Author

Jay, Raphael M., primary, Banerjee, Ambar, additional, Leitner, Torsten, additional, Wang, Ru-Pan, additional, Harich, Jessica, additional, Stefanuik, Robert, additional, Wikmark, Hampus, additional, Coates, Michael R., additional, Beale, Emma V., additional, Kabanova, Victoria, additional, Kahraman, Abdullah, additional, Wach, Anna, additional, Ozerov, Dmitry, additional, Arrell, Christopher, additional, Johnson, Philip J. M., additional, Borca, Camelia N., additional, Cirelli, Claudio, additional, Bacellar, Camila, additional, Milne, Christopher, additional, Huse, Nils, additional, Smolentsev, Grigory, additional, Huthwelker, Thomas, additional, Odelius, Michael, additional, and Wernet, Philippe, additional

Published
2023
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19. Anomalous temperature dependence of the experimental x-ray structure factor of supercooled water.

Author

Esmaeildoost, Niloofar, Pathak, Harshad, Späh, Alexander, Lane, Thomas J., Kim, Kyung Hwan, Yang, Cheolhee, Amann-Winkel, Katrin, Ladd-Parada, Marjorie, Perakis, Fivos, Koliyadu, Jayanath, Oggenfuss, Alexander R., Johnson, Philip J. M., Deng, Yunpei, Zerdane, Serhane, Mankowsky, Roman, Beaud, Paul, Lemke, Henrik T., Nilsson, Anders, and Sellberg, Jonas A.

Subjects
FACTOR structure, MOMENTUM transfer, X-ray scattering, SUPERCOOLING, TEMPERATURE, X-rays, ICE
Abstract

The structural changes of water upon deep supercooling were studied through wide-angle x-ray scattering at SwissFEL. The experimental setup had a momentum transfer range of 4.5 Å−1, which covered the principal doublet of the x-ray structure factor of water. The oxygen–oxygen structure factor was obtained for temperatures down to 228.5 ± 0.6 K. Similar to previous studies, the second diffraction peak increased strongly in amplitude as the structural change accelerated toward a local tetrahedral structure upon deep supercooling. We also observed an anomalous trend for the second peak position of the oxygen–oxygen structure factor (q2). We found that q2 exhibits an unprecedented positive partial derivative with respect to temperature for temperatures below 236 K. Based on Fourier inversion of our experimental data combined with reference data, we propose that the anomalous q2 shift originates from that a repeat spacing in the tetrahedral network, associated with all peaks in the oxygen–oxygen pair-correlation function, gives rise to a less dense local ordering that resembles that of low-density amorphous ice. The findings are consistent with that liquid water consists of a pentamer-based hydrogen-bonded network with low density upon deep supercooling. [ABSTRACT FROM AUTHOR]

Published
2021
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20. Author Correction: Hard X-ray transient grating spectroscopy on bismuth germanate

Author

Rouxel, Jérémy R., Fainozzi, Danny, Mankowsky, Roman, Rösner, Benedikt, Seniutinas, Gediminas, Mincigrucci, Riccardo, Catalini, Sara, Foglia, Laura, Cucini, Riccardo, Döring, Florian, Kubec, Adam, Koch, Frieder, Bencivenga, Filippo, Al Haddad, Andre, Gessini, Alessandro, Maznev, Alexei A., Cirelli, Claudio, Gerber, Simon, Pedrini, Bill, Mancini, Giulia F., Razzoli, Elia, Burian, Max, Ueda, Hiroki, Pamfilidis, Georgios, Ferrari, Eugenio, Deng, Yunpei, Mozzanica, Aldo, Johnson, Philip J. M., Ozerov, Dmitry, Izzo, Maria Grazia, Bottari, Cettina, Arrell, Christopher, Divall, Edwin James, Zerdane, Serhane, Sander, Mathias, Knopp, Gregor, Beaud, Paul, Lemke, Henrik T., Milne, Chris J., David, Christian, Torre, Renato, Chergui, Majed, Nelson, Keith A., Masciovecchio, Claudio, Staub, Urs, Patthey, Luc, and Svetina, Cristian

Published
2021
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21. Ultrafast Energy Transfer from Photoexcited Tryptophan to the Haem in Cytochrome c

Author

Bacellar, Camila, primary, Rouxel, Jérémy R., additional, Ingle, Rebecca A., additional, Mancini, Giulia F., additional, Kinschel, Dominik, additional, Cannelli, Oliviero, additional, Zhao, Yang, additional, Cirelli, Claudio, additional, Knopp, Gregor, additional, Szlachetko, Jakub, additional, Lima, Frederico A., additional, Menzi, Samuel, additional, Ozerov, Dmitry, additional, Pamfilidis, Georgios, additional, Kubicek, Katharina, additional, Khakhulin, Dmitry, additional, Gawelda, Wojciech, additional, Rodriguez-Fernandez, Angel, additional, Biednov, Mykola, additional, Bressler, Christian, additional, Arrell, Christopher A., additional, Johnson, Philip J. M., additional, Milne, Christopher J., additional, and Chergui, Majed, additional

Published
2023
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22. ULTRAFAST STRUCTURAL CHANGES DIRECT THE FIRST MOLECULAR EVENTS OF VISION

Author

Gruhl, Thomas, primary, Weinert, Tobias, additional, Rodrigues, Matthew, additional, Milne, Christopher J, additional, Ortolani, Giorgia, additional, Nass, Karol, additional, Nango, Eriko, additional, Sen, Saumik, additional, Johnson, Philip J M, additional, Cirelli, Claudio, additional, Furrer, Antonia, additional, Mous, Sandra, additional, Skopintsev, Petr, additional, James, Daniel, additional, Dworkowski, Florian, additional, Båth, Petra, additional, Kekilli, Demet, additional, Ozerov, Dmitry, additional, Tanaka, Rie, additional, Glover, Hannah, additional, Bacellar, Camila, additional, Brünle, Steffen, additional, Casadei, Cecilia M, additional, Diethelm, Azeglio D, additional, Gashi, Dardan, additional, Gotthard, Guillaume, additional, Guixà-González, Ramon, additional, Joti, Yasumasa, additional, Kabanova, Victoria, additional, Knopp, Gregor, additional, Lesca, Elena, additional, Ma, Pikyee, additional, Martiel, Isabelle, additional, Mühle, Jonas, additional, Owada, Shigeki, additional, Pamula, Filip, additional, Sarabi, Daniel, additional, Tejero, Oliver, additional, Tsai, Ching-Ju, additional, Varma, Niranjan, additional, Wach, Anna, additional, Boutet, Sébastien, additional, Tono, Kensuke, additional, Nogly, Przemyslaw, additional, Deupi, Xavier, additional, Iwata, So, additional, Neutze, Richard, additional, Standfuss, Jörg, additional, Schertler, Gebhard FX, additional, and Panneels, Valerie, additional

Published
2022
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23. Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre

Author

Båth, Petra, primary, Banacore, Analia, additional, Börjesson, Per, additional, Bosman, Robert, additional, Wickstrand, Cecilia, additional, Safari, Cecilia, additional, Dods, Robert, additional, Ghosh, Swagatha, additional, Dahl, Peter, additional, Ortolani, Giorgia, additional, Björg Ulfarsdottir, Tinna, additional, Hammarin, Greger, additional, García Bonete, María-José, additional, Vallejos, Adams, additional, Ostojić, Lucija, additional, Edlund, Petra, additional, Linse, Johanna-Barbara, additional, Andersson, Rebecka, additional, Nango, Eriko, additional, Owada, Shigeki, additional, Tanaka, Rie, additional, Tono, Kensuke, additional, Joti, Yasumasa, additional, Nureki, Osamu, additional, Luo, Fangjia, additional, James, Daniel, additional, Nass, Karol, additional, Johnson, Philip J. M., additional, Knopp, Gregor, additional, Ozerov, Dmitry, additional, Cirelli, Claudio, additional, Milne, Christopher, additional, Iwata, So, additional, Brändén, Gisela, additional, and Neutze, Richard, additional

Published
2022
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24. Dynamics and mechanism of a light-driven chloride pump

Author

Mous, Sandra, primary, Gotthard, Guillaume, additional, Ehrenberg, David, additional, Sen, Saumik, additional, Weinert, Tobias, additional, Johnson, Philip J. M., additional, James, Daniel, additional, Nass, Karol, additional, Furrer, Antonia, additional, Kekilli, Demet, additional, Ma, Pikyee, additional, Brünle, Steffen, additional, Casadei, Cecilia Maria, additional, Martiel, Isabelle, additional, Dworkowski, Florian, additional, Gashi, Dardan, additional, Skopintsev, Petr, additional, Wranik, Maximilian, additional, Knopp, Gregor, additional, Panepucci, Ezequiel, additional, Panneels, Valerie, additional, Cirelli, Claudio, additional, Ozerov, Dmitry, additional, Schertler, Gebhard F. X., additional, Wang, Meitian, additional, Milne, Chris, additional, Standfuss, Joerg, additional, Schapiro, Igor, additional, Heberle, Joachim, additional, and Nogly, Przemyslaw, additional

Published
2022
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25. From Femtosecond Excited-State and Dissociation Dynamics to Nanosecond Reaction Kinetics: Following C-H Bond Activation with X-rays

Author

Jay, Raphael M., primary, Banerjee, Ambar, additional, Leitner, Torsten, additional, Stefanuik, Robert, additional, Wang, Ru-Pan, additional, Harich, Jessica, additional, Beale, Emma, additional, Kabanova, Victoria, additional, Kahraman, Abdullah, additional, Wach, Anna, additional, Ozerov, Dimitri, additional, Arrell, Christopher A., additional, Johnson, Philip J. M., additional, Smolentsev, Grigory, additional, Huthwelker, Thomas, additional, Borca, Camilia N., additional, Cirelli, Claudio, additional, Bacellar, Camila, additional, Milne, Christopher J., additional, Huse, Nils, additional, Odelius, Michael, additional, and Wernet, Philippe, additional

Published
2022
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26. Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser

Author

Nass, Karol, primary, Bacellar, Camila, additional, Cirelli, Claudio, additional, Dworkowski, Florian, additional, Gevorkov, Yaroslav, additional, James, Daniel, additional, Johnson, Philip J. M., additional, Kekilli, Demet, additional, Knopp, Gregor, additional, Martiel, Isabelle, additional, Ozerov, Dmitry, additional, Tolstikova, Alexandra, additional, Vera, Laura, additional, Weinert, Tobias, additional, Yefanov, Oleksandr, additional, Standfuss, Jörg, additional, Reiche, Sven, additional, and Milne, Christopher J., additional

Published
2021
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28. Hard X-ray transient grating spectroscopy on bismuth germanate

Author

Rouxel, Jérémy R., primary, Fainozzi, Danny, additional, Mankowsky, Roman, additional, Rösner, Benedikt, additional, Seniutinas, Gediminas, additional, Mincigrucci, Riccardo, additional, Catalini, Sara, additional, Foglia, Laura, additional, Cucini, Riccardo, additional, Döring, Florian, additional, Kubec, Adam, additional, Koch, Frieder, additional, Bencivenga, Filippo, additional, Haddad, Andre Al, additional, Gessini, Alessandro, additional, Maznev, Alexei A., additional, Cirelli, Claudio, additional, Gerber, Simon, additional, Pedrini, Bill, additional, Mancini, Giulia F., additional, Razzoli, Elia, additional, Burian, Max, additional, Ueda, Hiroki, additional, Pamfilidis, Georgios, additional, Ferrari, Eugenio, additional, Deng, Yunpei, additional, Mozzanica, Aldo, additional, Johnson, Philip J. M., additional, Ozerov, Dmitry, additional, Izzo, Maria Grazia, additional, Bottari, Cettina, additional, Arrell, Christopher, additional, Divall, Edwin James, additional, Zerdane, Serhane, additional, Sander, Mathias, additional, Knopp, Gregor, additional, Beaud, Paul, additional, Lemke, Henrik T., additional, Milne, Chris J., additional, David, Christian, additional, Torre, Renato, additional, Chergui, Majed, additional, Nelson, Keith A., additional, Masciovecchio, Claudio, additional, Staub, Urs, additional, Patthey, Luc, additional, and Svetina, Cristian, additional

Published
2021
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29. Femtosecond X-ray spectroscopy of haem proteins

Author

Bacellar, Camila, primary, Kinschel, Dominik, additional, Cannelli, Oliviero, additional, Sorokin, Boris, additional, Katayama, Tetsuo, additional, Mancini, Giulia F., additional, Rouxel, Jeremy R., additional, Obara, Yuki, additional, Nishitani, Junichi, additional, Ito, Hironori, additional, Ito, Terumasa, additional, Kurahashi, Naoya, additional, Higashimura, Chika, additional, Kudo, Shotaro, additional, Cirelli, Claudio, additional, Knopp, Gregor, additional, Nass, Karol, additional, Johnson, Philip J. M., additional, Wach, Anna, additional, Szlachetko, Jakub, additional, Lima, Frederico A., additional, Milne, Christopher J., additional, Yabashi, Makina, additional, Suzuki, Toshinori, additional, Misawa, Kazuhiko, additional, and Chergui, Majed, additional

Published
2021
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31. Optical second harmonic generation in LiB3O5 modulated by intense femtosecond X-ray pulses

Author

Deng, Yunpei, primary, Zerdane, Serhane, additional, Xie, Xinhua, additional, Divall, Edwin, additional, Johnson, Philip J. M., additional, Arrell, Christopher, additional, Lemke, Henrik Till, additional, Mankowsky, Roman, additional, Oggenfuss, Alex, additional, Svetina, Cristian, additional, Erny, Christian, additional, Cirelli, Claudio, additional, Milne, Christopher, additional, Knopp, Gregor, additional, Beaud, Paul, additional, and Johnson, Steven L., additional

Published
2020
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32. Heme Doming in Ferric Cytochrome c: Femtosecond X-ray Absorption and X-ray Emission Studies

Author

Bacellar, Camila, primary, Kinschel, Dominik, additional, Mancini, Giulia F., additional, Ingle, Rebecca A., additional, Rouxel, Jérémy, additional, Cannelli, Oliviero, additional, Cirelli, Claudio, additional, Knopp, Gregor, additional, Szlachetko, Jakub, additional, Lima, Frederico A., additional, Menzi, Samuel, additional, Pamfilidis, Georgios, additional, Kubicek, Katharina, additional, Khakhulin, Dmitry, additional, Gawelda, Wojciech, additional, Rodriguez-Fernandez, Angel, additional, Biednov, Mykola, additional, Bressler, Christian, additional, Arrell, Christopher A., additional, Johnson, Philip J. M., additional, Milne, Christopher, additional, and Chergui, Majed, additional

Published
2020
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33. Mixed Potential Energy Surfaces of the Ultrafast Isomerization of Retinal in Bacteriorhodopsin

Author

Prokhorenko Valentyn I., Morizumi Takefumi, Halpin Alexei, Johnson Philip J. M., Ernst Oliver P., and Dwayne Miller R. J.

Subjects
Physics, QC1-999
Abstract

We observe, using electronic two-dimensional photon echo spectroscopy, that the cis and trans potential energy surfaces of the ultrafast isomerization of retinal in bacteriorhodopsin are mixed via the hydrogen out of plane (HOOP) mode.

Published
2013
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34. 2D-IR Spectroscopy of an AHA Labeled Photoswitchable PDZ2 Domain

Author

Stucki-Buchli, Brigitte, Johnson, Philip J M, Bozovic, Olga, Zanobini, Claudio, Koziol, Klemens L, Hamm, Peter, Gulzar, Adnan, Wolf, Steffen, Buchenberg, Sebastian, Stock, Gerhard, University of Zurich, and Hamm, Peter

Subjects
10120 Department of Chemistry, 540 Chemistry, 1606 Physical and Theoretical Chemistry
Published
2017

36. 2D-IR Spectroscopy of an AHA Labeled Photoswitchable PDZ2 Domain

Author

Stucki-Buchli, Brigitte, Johnson, Philip J. M., Bozovic, Olga, Zanobini, Claudio, Koziol, Klemens L., Hamm, Peter, Gulzar, Adnan, Wolf, Steffen, Buchenberg, Sebastian, and Stock, Gerhard

Abstract

We explore the capability of the non-natural amino acid azidohomoalanine (AHA) as an IR label to sense relatively small structural changes in proteins with the help of 2D IR difference spectroscopy. To that end, we AHA-labeled an allosteric protein (the PDZ2 domain from human tyrosine-phosphatase 1E) and furthermore covalently linked it to an azobenzene-derived photoswitch as to mimic its conformational transition upon ligand binding. To determine the strengths and limitations of the AHA label, in total six mutants have been investigated with the label at sites with varying properties. Only one mutant revealed a measurable 2D IR difference signal. In contrast to the commonly observed frequency shifts that report on the degree of solvation, in this case we observe an intensitychange. To understand this spectral response, we performed classical MD simulations, evaluating local contacts of the AHA labels to water molecules and protein side chains and calculating the vibrational frequency on the basis of an electrostatic model. Although these simulations revealed in part significant and complex changes of the number of intraprotein and water contacts upon trans–cisphotoisomerization, they could not provide a clear explanation of why this one label would stick out. Subsequent quantum-chemistry calculations suggest that the response is the result of an electronic interaction involving charge transfer of the azido group with sulfonate groups from the photoswitch. To the best of our knowledge, such an effect has not been described before.

Published
2024
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37. Coherent control of the isomerization of retinal in bacteriorhodopsin in the high intensity regime.

Author

Prokhorenko, Valentyn I., Halpin, Alexei, Johnson, Philip J. M., Miller, R. J. Dwayne, and Brown, Leonid S.

Subjects
RETINAL (Visual pigment), BACTERIORHODOPSIN, QUANTUM interference, PHOTOISOMERIZATION, COHERENCE (Optics), BIOMOLECULES, CHEMICAL kinetics
Abstract

Coherent control protocols provide a direct experimental determination of the relative importance of quantum interference or phase relationships of coupled states along a selected pathway. These effects are most readily observed in the high intensity regime where the field amplitude is sufficient to overcome decoherence effects. The coherent response of retinal photoisomerization in bacteriorhodopsin to the phase of the photoexcitation pulses was examined at fluences of 1015 - 2.5 × 1016 photons per square centimeter, comparable to or higher than the saturation excitation level of the S0 - S1 retinal electronic transition. At moderate excitation levels of ∼6 × 1015 photons/cm2 (<100 GW/cm2), chirping the excitation pulses increases the all-trans to 13-cis isomerization yield by up to 16% relative to transform limited pulses. The reported results extend previous weak-field studies [Prokhorenko et al., Science 313, 1257 (2006)] and further illustrate that quantum coherence effects persist along the reaction coordinate in strong fields even for systems as complex as biological molecules. However, for higher excitation levels of ∼200 GW/cm2, there is a dramatic change in photophysics that leads to multiphoton generated photoproducts unrelated to the target isomerization reaction channel and drastically changes the observed isomerization kinetics that appears, in particular, as a red shift of the transient spectra. These results explain the apparent contradictions of the work by Florean et al. [Proc. Natl. Acad. Sci. U.S.A. 106, 10896 (2009)] in the high intensity regime. We are able to show that the difference in observations and interpretation is due to artifacts associated with additional multiphoton-induced photoproducts. At the proper monitoring wavelengths, coherent control in the high intensity regime is clearly observable. The present work highlights the importance of conducting coherent control experiments in the low intensity regime to access information on quantum interference effects along specific reaction coordinates. [ABSTRACT FROM AUTHOR]

Published
2011
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38. 2D-IR Spectroscopy of an AHA Labeled Photoswitchable PDZ2 Domain

Author

Stucki-Buchli, Brigitte, primary, Johnson, Philip J. M., additional, Bozovic, Olga, additional, Zanobini, Claudio, additional, Koziol, Klemens L., additional, Hamm, Peter, additional, Gulzar, Adnan, additional, Wolf, Steffen, additional, Buchenberg, Sebastian, additional, and Stock, Gerhard, additional

Published
2017
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42. Laser-Limited Signatures of Quantum Coherence

Author

Tempelaar, Roel, primary, Halpin, Alexei, additional, Johnson, Philip J. M., additional, Cai, Jianxin, additional, Murphy, R. Scott, additional, Knoester, Jasper, additional, Miller, R. J. Dwayne, additional, and Jansen, Thomas L. C., additional

Published
2015
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44. Toward single-molecule DNA uptake by Haemophilus influenzae

Author

Johnson, Philip J. M.

Abstract

Haemophilus influenzae is a Gram-negative, non-motile bacterium found in the respiratory tract of higher organisms which is naturally competent; that is, it naturally has the ability to internalise exogenous DNA. The DNA uptake machinery spans two membranes and has been shown to require an asymmetric nine basepair uptake signaling sequence to initiate DNA uptake, but the mechanism is still poorly understood. This thesis presents work toward single molecule DNA uptake experiments involving optical tweezers, including optical tweezer construction and characterization, DNA force-extension relations, plasmid design for single molecule uptake experiments, and efforts to immobilise H. influenzae cells to surfaces of polystyrene beads.

Published
2007

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