{"title":"A short history of structure based research on the photocycle of photoactive yellow protein","authors":"Marius Schmidt","doi":"10.1063/1.4974172","DOIUrl":"https://doi.org/10.1063/1.4974172","url":null,"abstract":"The goals of time-resolved macromolecular crystallography are to extract the molecular structures of the reaction intermediates and the reaction dynamics from time-resolved X-ray data alone. To develop the techniques of time-resolved crystallography, biomolecules with special properties are required. The Photoactive Yellow Protein is the most sparkling of these.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2017-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4974172","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42243135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Shaped cathodes for the production of ultra-short multi-electron pulses","authors":"A. Petruk, K. Pichugin, G. Sciaini","doi":"10.1063/1.4974779","DOIUrl":"https://doi.org/10.1063/1.4974779","url":null,"abstract":"An electrostatic electron source design capable of producing sub-20 femtoseconds (rms) multi-electron pulses is presented. The photoelectron gun concept builds upon geometrical electric field enhancement at the cathode surface. Particle tracer simulations indicate the generation of extremely short bunches even beyond 40 cm of propagation. Comparisons with compact electron sources commonly used for femtosecond electron diffraction are made.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2017-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4974779","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43733444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. Salvatella, R. Gort, K. Bühlmann, S. Däster, A. Vaterlaus, Y. Acremann
{"title":"Erratum: “Ultrafast demagnetization by hot electrons: Diffusion or super-diffusion?” [Struct. Dyn. 3, 055101 (2016)]","authors":"G. Salvatella, R. Gort, K. Bühlmann, S. Däster, A. Vaterlaus, Y. Acremann","doi":"10.1063/1.4975037","DOIUrl":"https://doi.org/10.1063/1.4975037","url":null,"abstract":"[This corrects the article DOI: 10.1063/1.4964892.].","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4975037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48684584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Photoinduced molecular chirality probed by ultrafast resonant X-ray spectroscopy","authors":"J. Rouxel, M. Kowalewski, S. Mukamel","doi":"10.1063/1.4974260","DOIUrl":"https://doi.org/10.1063/1.4974260","url":null,"abstract":"Recently developed circularly polarized X-ray light sources can probe the ultrafast chiral electronic and nuclear dynamics through spatially localized resonant core transitions. We present simulations of time-resolved circular dichroism signals given by the difference of left and right circularly polarized X-ray probe transmission following an excitation by a circularly polarized optical pump with the variable time delay. Application is made to formamide which is achiral in the ground state and assumes two chiral geometries upon optical excitation to the first valence excited state. Probes resonant with various K-edges (C, N, and O) provide different local windows onto the parity breaking geometry change thus revealing the enantiomer asymmetry.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"4 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2016-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4974260","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58774186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A general method for baseline-removal in ultrafast electron powder diffraction data using the dual-tree complex wavelet transform","authors":"L. P. René de Cotret, B. Siwick","doi":"10.1063/1.4972518","DOIUrl":"https://doi.org/10.1063/1.4972518","url":null,"abstract":"The general problem of background subtraction in ultrafast electron powder diffraction (UEPD) is presented with a focus on the diffraction patterns obtained from materials of moderately complex structure which contain many overlapping peaks and effectively no scattering vector regions that can be considered exclusively background. We compare the performance of background subtraction algorithms based on discrete and dual-tree complex (DTCWT) wavelet transforms when applied to simulated UEPD data on the M1–R phase transition in VO2 with a time-varying background. We find that the DTCWT approach is capable of extracting intensities that are accurate to better than 2% across the whole range of scattering vector simulated, effectively independent of delay time. A Python package is available.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"4 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2016-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4972518","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58761220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christopher Kupitz, J. L. Olmos, M. Holl, L. Tremblay, K. Pande, S. Pandey, D. Oberthür, M. Hunter, M. Liang, A. Aquila, J. Tenboer, George D. Calvey, Andrea M. Katz, Yujie Chen, M. Wiedorn, J. Knoška, A. Meents, Valerio Majriani, Tyler Norwood, I. Poudyal, T. Grant, Mitchell D. Miller, Weijun Xu, A. Tolstikova, A. Morgan, M. Metz, J. Martin-Garcia, James D. Zook, Shatabdi Roy-Chowdhury, J. Coe, Nirupa Nagaratnam, Domingo Meza, R. Fromme, S. Basu, M. Frank, T. White, A. Barty, S. Bajt, O. Yefanov, H. Chapman, N. Zatsepin, G. Nelson, U. Weierstall, J. Spence, P. Schwander, L. Pollack, P. Fromme, A. Ourmazd, G. Phillips, Marius Schmidt
{"title":"Structural enzymology using X-ray free electron lasers","authors":"Christopher Kupitz, J. L. Olmos, M. Holl, L. Tremblay, K. Pande, S. Pandey, D. Oberthür, M. Hunter, M. Liang, A. Aquila, J. Tenboer, George D. Calvey, Andrea M. Katz, Yujie Chen, M. Wiedorn, J. Knoška, A. Meents, Valerio Majriani, Tyler Norwood, I. Poudyal, T. Grant, Mitchell D. Miller, Weijun Xu, A. Tolstikova, A. Morgan, M. Metz, J. Martin-Garcia, James D. Zook, Shatabdi Roy-Chowdhury, J. Coe, Nirupa Nagaratnam, Domingo Meza, R. Fromme, S. Basu, M. Frank, T. White, A. Barty, S. Bajt, O. Yefanov, H. Chapman, N. Zatsepin, G. Nelson, U. Weierstall, J. Spence, P. Schwander, L. Pollack, P. Fromme, A. Ourmazd, G. Phillips, Marius Schmidt","doi":"10.1063/1.4972069","DOIUrl":"https://doi.org/10.1063/1.4972069","url":null,"abstract":"Mix-and-inject serial crystallography (MISC) is a technique designed to image enzyme catalyzed reactions in which small protein crystals are mixed with a substrate just prior to being probed by an X-ray pulse. This approach offers several advantages over flow cell studies. It provides (i) room temperature structures at near atomic resolution, (ii) time resolution ranging from microseconds to seconds, and (iii) convenient reaction initiation. It outruns radiation damage by using femtosecond X-ray pulses allowing damage and chemistry to be separated. Here, we demonstrate that MISC is feasible at an X-ray free electron laser by studying the reaction of M. tuberculosis ß-lactamase microcrystals with ceftriaxone antibiotic solution. Electron density maps of the apo-ß-lactamase and of the ceftriaxone bound form were obtained at 2.8 Å and 2.4 Å resolution, respectively. These results pave the way to study cyclic and non-cyclic reactions and represent a new field of time-resolved structural dynamics for numerous substrate-triggered biological reactions.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"4 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2016-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4972069","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58752263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Johnson, L. Miseikis, D. Wood, D. Austin, C. Brahms, S. Jarosch, C. Strüber, P. Ye, J. Marangos
{"title":"Measurement of sulfur L2,3 and carbon K edge XANES in a polythiophene film using a high harmonic supercontinuum","authors":"A. Johnson, L. Miseikis, D. Wood, D. Austin, C. Brahms, S. Jarosch, C. Strüber, P. Ye, J. Marangos","doi":"10.1063/1.4964821","DOIUrl":"https://doi.org/10.1063/1.4964821","url":null,"abstract":"We use a high harmonic generated supercontinuum in the soft X-ray region to measure X-ray absorption near edge structure (XANES) spectra in polythiophene (poly(3-hexylthiophene)) films at multiple absorption edges. A few-cycle carrier-envelope phase-stable laser pulse centered at 1800 nm was used to generate a stable soft X-ray supercontinuum, with amplitude gating limiting the generated pulse duration to a single optical half-cycle. We report a quantitative transmission measurement of the sulfur L2,3 edge over the range 160–200 eV and the carbon K edge from 280 to 330 eV. These spectra show all the features previously reported in the XANES spectra of polythiophene, but for the first time they are measured with a source that has an approximately 1 fs pulse duration. This study opens the door to measurements that can fully time-resolve the photoexcited electronic dynamics in these systems.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"3 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2016-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4964821","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58677519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Single-order laser high harmonics in XUV for ultrafast photoelectron spectroscopy of molecular wavepacket dynamics","authors":"M. Fushitani, A. Hishikawa","doi":"10.1063/1.4964775","DOIUrl":"https://doi.org/10.1063/1.4964775","url":null,"abstract":"We present applications of extreme ultraviolet (XUV) single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N2 molecules.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"3 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2016-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4964775","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58675275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
F. Santomauro, J. Grilj, L. Mewes, G. Nedelcu, S. Yakunin, T. Rossi, G. Capano, A. Al Haddad, J. Budarz, D. Kinschel, D. Ferreira, G. Rossi, Mario Gutiérrez Tovar, D. Grolimund, V. Samson, M. Nachtegaal, G. Smolentsev, M. Kovalenko, M. Chergui
{"title":"Localized holes and delocalized electrons in photoexcited inorganic perovskites: Watching each atomic actor by picosecond X-ray absorption spectroscopy","authors":"F. Santomauro, J. Grilj, L. Mewes, G. Nedelcu, S. Yakunin, T. Rossi, G. Capano, A. Al Haddad, J. Budarz, D. Kinschel, D. Ferreira, G. Rossi, Mario Gutiérrez Tovar, D. Grolimund, V. Samson, M. Nachtegaal, G. Smolentsev, M. Kovalenko, M. Chergui","doi":"10.1063/1.4971999","DOIUrl":"https://doi.org/10.1063/1.4971999","url":null,"abstract":"We report on an element-selective study of the fate of charge carriers in photoexcited inorganic CsPbBr3 and CsPb(ClBr)3 perovskite nanocrystals in toluene solutions using time-resolved X-ray absorption spectroscopy with 80 ps time resolution. Probing the Br K-edge, the Pb L3-edge, and the Cs L2-edge, we find that holes in the valence band are localized at Br atoms, forming small polarons, while electrons appear as delocalized in the conduction band. No signature of either electronic or structural changes is observed at the Cs L2-edge. The results at the Br and Pb edges suggest the existence of a weakly localized exciton, while the absence of signatures at the Cs edge indicates that the Cs+ cation plays no role in the charge transport, at least beyond 80 ps. This first, time-resolved element-specific study of perovskites helps understand the rather modest charge carrier mobilities in these materials.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"4 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2016-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4971999","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58751367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. V. Reppert, J. Pudell, A. Koç, M. Reinhardt, W. Leitenberger, K. Dumesnil, F. Zamponi, M. Bargheer
{"title":"Persistent nonequilibrium dynamics of the thermal energies in the spin and phonon systems of an antiferromagnet","authors":"A. V. Reppert, J. Pudell, A. Koç, M. Reinhardt, W. Leitenberger, K. Dumesnil, F. Zamponi, M. Bargheer","doi":"10.1063/1.4961253","DOIUrl":"https://doi.org/10.1063/1.4961253","url":null,"abstract":"We present a temperature and fluence dependent Ultrafast X-Ray Diffraction study of a laser-heated antiferromagnetic dysprosium thin film. The loss of antiferromagnetic order is evidenced by a pronounced lattice contraction. We devise a method to determine the energy flow between the phonon and spin system from calibrated Bragg peak positions in thermal equilibrium. Reestablishing the magnetic order is much slower than the cooling of the lattice, especially around the Néel temperature. Despite the pronounced magnetostriction, the transfer of energy from the spin system to the phonons in Dy is slow after the spin-order is lost.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"3 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4961253","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"58597298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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