Pub Date : 2018-11-29DOI: 10.1007/978-3-319-94743-3_16
M. Paz, Young Hoon Kim
{"title":"Time History Response of Multi-Degree-of-Freedom Systems","authors":"M. Paz, Young Hoon Kim","doi":"10.1007/978-3-319-94743-3_16","DOIUrl":"https://doi.org/10.1007/978-3-319-94743-3_16","url":null,"abstract":"","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2018-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-319-94743-3_16","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44147068","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}
It is with a heavy heart that we learned of the passing of Judith on March 31, 2018. Her role with our journal, Structural Dynamics, was integral and valued in a way that words cannot express. She was the key person in the foundation of the relationship between AIP Publishing and the American Crystallographic Association, one of AIP’s member societies. A long-time member of the ACA and the crystallography community, Judith spent 35 years as a small molecule crystallographer at the Naval Research Laboratory in Washington, D.C., and later worked for Rutgers University in New Jersey on a project for the Protein Data Bank. She was co-editor of the magazine ACA RefleXions and a former editor of the International Union of Crystallography (IUCr) Newsletter. She was a past chair of the U.S. National Committee for Crystallography, served as ACA president in 1991, and was named to its inaugural class of Fellows in 2011. Judith served as ACA’s representative on the AIP Publishing Board of Managers since its inception in 2013 and was AIP’s corporate secretary. In this respect, she was the driving force behind the creation of ACA’s first journal, Structural Dynamics—an open access title launched jointly with AIP Publishing in 2014. It was during this time where I got to know Judith, as she was the person who interviewed me for the position of Editor-in-Chief on behalf of the ACA. From this first meeting, it was immediately clear that there was accord in our vision for the journal. We understood each other very well, and I was very pleased by how much our views echoed each other. Judith was very supportive of my vision for the journal and accepted the suggestion to name the journal Structural Dynamics. Most of all, I remember her constant support and encouragement of strategic initiatives. I was extremely pleased to be accompanied by such a constructive partner in the challenging but fascinating adventure of launching a new journal. The evolution of the journal was closely followed by Judith, as she was an active member of the team participating in conference calls, attending conferences, and commissioning prominent authors to publish in the journal. In addition, Judith’s commitment to promoting the journal was repeatedly showcased in ACA’s quarterly newsletter, ACA RefleXions, where featured articles of Structural Dynamics were displayed for ACA members. Judith was wonderful in the way she took the destiny of the journal to heart. I recall how excited and happy she was when the journal achieved its first Impact Factor of 3.667 in 2015 and how thrilled she would have been to know the latest Impact Factor of 3.969. The journal and our team owe Judith a debt of gratitude. May she rest in peace.
{"title":"Editorial: In Memoriam – Judith Flippen-Anderson (1941–2018)","authors":"M. Chergui","doi":"10.1063/1.5049131","DOIUrl":"https://doi.org/10.1063/1.5049131","url":null,"abstract":"It is with a heavy heart that we learned of the passing of Judith on March 31, 2018. Her role with our journal, Structural Dynamics, was integral and valued in a way that words cannot express. She was the key person in the foundation of the relationship between AIP Publishing and the American Crystallographic Association, one of AIP’s member societies. A long-time member of the ACA and the crystallography community, Judith spent 35 years as a small molecule crystallographer at the Naval Research Laboratory in Washington, D.C., and later worked for Rutgers University in New Jersey on a project for the Protein Data Bank. She was co-editor of the magazine ACA RefleXions and a former editor of the International Union of Crystallography (IUCr) Newsletter. She was a past chair of the U.S. National Committee for Crystallography, served as ACA president in 1991, and was named to its inaugural class of Fellows in 2011. Judith served as ACA’s representative on the AIP Publishing Board of Managers since its inception in 2013 and was AIP’s corporate secretary. In this respect, she was the driving force behind the creation of ACA’s first journal, Structural Dynamics—an open access title launched jointly with AIP Publishing in 2014. It was during this time where I got to know Judith, as she was the person who interviewed me for the position of Editor-in-Chief on behalf of the ACA. From this first meeting, it was immediately clear that there was accord in our vision for the journal. We understood each other very well, and I was very pleased by how much our views echoed each other. Judith was very supportive of my vision for the journal and accepted the suggestion to name the journal Structural Dynamics. Most of all, I remember her constant support and encouragement of strategic initiatives. I was extremely pleased to be accompanied by such a constructive partner in the challenging but fascinating adventure of launching a new journal. The evolution of the journal was closely followed by Judith, as she was an active member of the team participating in conference calls, attending conferences, and commissioning prominent authors to publish in the journal. In addition, Judith’s commitment to promoting the journal was repeatedly showcased in ACA’s quarterly newsletter, ACA RefleXions, where featured articles of Structural Dynamics were displayed for ACA members. Judith was wonderful in the way she took the destiny of the journal to heart. I recall how excited and happy she was when the journal achieved its first Impact Factor of 3.667 in 2015 and how thrilled she would have been to know the latest Impact Factor of 3.969. The journal and our team owe Judith a debt of gratitude. May she rest in peace.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2018-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5049131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42186389","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}
Runze Li, K. Sundqvist, Jie Chen, H. Elsayed-Ali, Jie Zhang, P. Rentzepis
Ultrafast lattice deformation of tens to hundreds of nanometer thick metallic crystals, after femtosecond laser excitation, was measured directly using 8.04 keV subpicosecond x-ray and 59 keV femtosecond electron pulses. Coherent phonons were generated in both single crystal and polycrystalline films. Lattice compression was observed within the first few picoseconds after laser irradiation in single crystal aluminum, which was attributed to the generation of a blast force and the propagation of elastic waves. The different time scales of lattice heating for tens and hundreds nanometer thick films are clearly distinguished by electron and x-ray pulse diffraction. The electron and lattice heating due to ultrafast deposition of photon energy was simulated using the two-temperature model and the results agreed with experimental observations. This study demonstrates that the combination of two complementary ultrafast time-resolved methods, ultrafast x-ray, and electron diffraction will provide a panoramic picture of the transient structural changes in crystals.Ultrafast lattice deformation of tens to hundreds of nanometer thick metallic crystals, after femtosecond laser excitation, was measured directly using 8.04 keV subpicosecond x-ray and 59 keV femtosecond electron pulses. Coherent phonons were generated in both single crystal and polycrystalline films. Lattice compression was observed within the first few picoseconds after laser irradiation in single crystal aluminum, which was attributed to the generation of a blast force and the propagation of elastic waves. The different time scales of lattice heating for tens and hundreds nanometer thick films are clearly distinguished by electron and x-ray pulse diffraction. The electron and lattice heating due to ultrafast deposition of photon energy was simulated using the two-temperature model and the results agreed with experimental observations. This study demonstrates that the combination of two complementary ultrafast time-resolved methods, ultrafast x-ray, and electron diffraction will provide a panoramic pict...
{"title":"Transient lattice deformations of crystals studied by means of ultrafast time-resolved x-ray and electron diffraction","authors":"Runze Li, K. Sundqvist, Jie Chen, H. Elsayed-Ali, Jie Zhang, P. Rentzepis","doi":"10.1063/1.5029970","DOIUrl":"https://doi.org/10.1063/1.5029970","url":null,"abstract":"Ultrafast lattice deformation of tens to hundreds of nanometer thick metallic crystals, after femtosecond laser excitation, was measured directly using 8.04 keV subpicosecond x-ray and 59 keV femtosecond electron pulses. Coherent phonons were generated in both single crystal and polycrystalline films. Lattice compression was observed within the first few picoseconds after laser irradiation in single crystal aluminum, which was attributed to the generation of a blast force and the propagation of elastic waves. The different time scales of lattice heating for tens and hundreds nanometer thick films are clearly distinguished by electron and x-ray pulse diffraction. The electron and lattice heating due to ultrafast deposition of photon energy was simulated using the two-temperature model and the results agreed with experimental observations. This study demonstrates that the combination of two complementary ultrafast time-resolved methods, ultrafast x-ray, and electron diffraction will provide a panoramic picture of the transient structural changes in crystals.Ultrafast lattice deformation of tens to hundreds of nanometer thick metallic crystals, after femtosecond laser excitation, was measured directly using 8.04 keV subpicosecond x-ray and 59 keV femtosecond electron pulses. Coherent phonons were generated in both single crystal and polycrystalline films. Lattice compression was observed within the first few picoseconds after laser irradiation in single crystal aluminum, which was attributed to the generation of a blast force and the propagation of elastic waves. The different time scales of lattice heating for tens and hundreds nanometer thick films are clearly distinguished by electron and x-ray pulse diffraction. The electron and lattice heating due to ultrafast deposition of photon energy was simulated using the two-temperature model and the results agreed with experimental observations. This study demonstrates that the combination of two complementary ultrafast time-resolved methods, ultrafast x-ray, and electron diffraction will provide a panoramic pict...","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2018-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.5029970","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48937896","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}
Capturing protein structural dynamics in real-time has tremendous potential in elucidating biological functions and providing information for structure-based drug design. While time-resolved structure determination has long been considered inaccessible for a vast majority of protein targets, serial methods for crystallography have remarkable potential in facilitating such analyses. Here, we review the impact of microfluidic technologies on protein crystal growth and X-ray diffraction analysis. In particular, we focus on applications of microfluidics for use in serial crystallography experiments for the time-resolved determination of protein structural dynamics.
{"title":"Microfluidics: From crystallization to serial time-resolved crystallography","authors":"Shuo Sui, S. Perry","doi":"10.1063/1.4979640","DOIUrl":"https://doi.org/10.1063/1.4979640","url":null,"abstract":"Capturing protein structural dynamics in real-time has tremendous potential in elucidating biological functions and providing information for structure-based drug design. While time-resolved structure determination has long been considered inaccessible for a vast majority of protein targets, serial methods for crystallography have remarkable potential in facilitating such analyses. Here, we review the impact of microfluidic technologies on protein crystal growth and X-ray diffraction analysis. In particular, we focus on applications of microfluidics for use in serial crystallography experiments for the time-resolved determination of protein structural dynamics.","PeriodicalId":48683,"journal":{"name":"Structural Dynamics-Us","volume":"4 1","pages":"032202"},"PeriodicalIF":2.8,"publicationDate":"2017-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1063/1.4979640","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46341970","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}
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.
{"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}
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.
{"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
[This corrects the article DOI: 10.1063/1.4964892.].
[此更正文章DOI: 10.1063/1.4964892.]。
{"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}
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.
{"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}
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