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Structural dynamics at surfaces by ultrafast reflection high-energy electron diffraction Struct. Dyn. (IF 3.67) Pub Date : 2024-03-12 Michael Horn-von Hoegen
Many fundamental processes of structural changes at surfaces occur on a pico- or femtosecond timescale. In order to study such ultrafast processes, we have combined modern surface science techniques with fs-laser pulses in a pump–probe scheme. Grazing incidence of the electrons ensures surface sensitivity in ultrafast reflection high-energy electron diffraction (URHEED). Utilizing the Debye–Waller
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Ultrafast electron diffuse scattering as a tool for studying phonon transport: Phonon hydrodynamics and second sound oscillations Struct. Dyn. (IF 3.67) Pub Date : 2024-03-12 Laurenz Kremeyer, Tristan L. Britt, Bradley J. Siwick, Samuel C. Huberman
Hydrodynamic phonon transport phenomena, like second sound, have been observed in liquid helium more than 50 years ago. More recently second sound has been observed in graphite at over 200 K using transient thermal grating (TG) techniques. In this work, we explore signatures of phonon hydrodynamic transport and second sound oscillations in ultrafast electron diffuse scattering patterns, which can provide
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Transient grating spectroscopy on a DyCo5 thin film with femtosecond extreme ultraviolet pulses Struct. Dyn. (IF 3.67) Pub Date : 2024-03-06 Victor Ukleev, Ludmila Leroy, Riccardo Mincigrucci, Dario Deangelis, Danny Fainozzi, Nupur Ninad Khatu, Ettore Paltanin, Laura Foglia, Filippo Bencivenga, Chen Luo, Florian Ruske, Florin Radu, Cristian Svetina, Urs Staub
Surface acoustic waves (SAWs) are excited by femtosecond extreme ultraviolet (EUV) transient gratings (TGs) in a room-temperature ferrimagnetic DyCo5 alloy. TGs are generated by crossing a pair of EUV pulses from a free electron laser with the wavelength of 20.8 nm matching the Co M-edge, resulting in a SAW wavelength of Λ = 44 nm. Using the pump-probe transient grating scheme in reflection geometry
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Resonant multiphoton processes and excitation limits to structural dynamics Struct. Dyn. (IF 3.67) Pub Date : 2024-03-01 William J. C. Francis, Harmanjot Grewal, Alexander A. C. Wainwright, Xuchun Yang, Massimo Olivucci, R. J. Dwayne Miller
Understanding the chemical reactions that give rise to functional biological systems is at the core of structural biology. As techniques are developed to study the chemical reactions that drive biological processes, it must be ensured that the reaction occurring is indeed a biologically relevant pathway. There is mounting evidence indicating that there has been a propagation of systematic error in
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High-harmonic spectroscopy of impulsively aligned 1,3-cyclohexadiene: Signatures of attosecond charge migration Struct. Dyn. (IF 3.67) Pub Date : 2024-02-29 Andres Tehlar, Jakob T. Casanova, Andrey Dnestryan, Frank Jensen, Lars Bojer Madsen, Oleg I. Tolstikhin, Hans Jakob Wörner
High-harmonic spectroscopy is an all-optical technique with inherent attosecond temporal resolution that has been successfully employed to reconstruct charge migration, electron-tunneling dynamics, and conical-intersection dynamics. Here, we demonstrate the extension of two key components of high-harmonic spectroscopy, i.e., impulsive alignment and measurements with multiple driving wavelengths to
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Microscopic nonlinear optical response: Analysis and calculations with the Floquet–Bloch formalism Struct. Dyn. (IF 3.67) Pub Date : 2024-02-23 Daria Popova-Gorelova, Robin Santra
We analyze microscopic nonlinear optical response of periodic structures within the Floquet–Bloch formalism. The analysis is focused on the real-space distributions of optically induced charge and electron current density within the unit cell of a crystal. We demonstrate that the time-reversal symmetry of a crystal determines the phases of the temporal oscillations of these distributions. We further
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Spatial–temporal characterization of photoemission in a streak-mode dynamic transmission electron microscope Struct. Dyn. (IF 3.67) Pub Date : 2024-02-23 Samik Roy Moulik, Yingming Lai, Aida Amini, Patrick Soucy, Kenneth R. Beyerlein, Jinyang Liang
A long-standing motivation driving high-speed electron microscopy development is to capture phase transformations and material dynamics in real time with high spatial and temporal resolution. Current dynamic transmission electron microscopes (DTEMs) are limited to nanosecond temporal resolution and the ability to capture only a few frames of a transient event. With the motivation to overcome these
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Advanced manufacturing provides tailor-made solutions for crystallography with x-ray free-electron lasers Struct. Dyn. (IF 3.67) Pub Date : 2024-02-21 Lars Paulson, Sankar Raju Narayanasamy, Megan L. Shelby, Matthias Frank, Martin Trebbin
Serial crystallography at large facilities, such as x-ray free-electron lasers and synchrotrons, evolved as a powerful method for the high-resolution structural investigation of proteins that are critical for human health, thus advancing drug discovery and novel therapies. However, a critical barrier to successful serial crystallography experiments lies in the efficient handling of the protein microcrystals
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Conformational dynamics of adenylate kinase in crystals Struct. Dyn. (IF 3.67) Pub Date : 2024-02-21 Junhyung Kim, Sojin Moon, Tod D. Romo, Yifei Yang, Euiyoung Bae, George N. Phillips
Adenylate kinase is a ubiquitous enzyme in living systems and undergoes dramatic conformational changes during its catalytic cycle. For these reasons, it is widely studied by genetic, biochemical, and biophysical methods, both experimental and theoretical. We have determined the basic crystal structures of three differently liganded states of adenylate kinase from Methanotorrus igneus, a hyperthermophilic
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Raw diffraction data and reproducibility Struct. Dyn. (IF 3.67) Pub Date : 2024-02-16 Loes M. J. Kroon-Batenburg, Matthew P. Lightfoot, Natalie T. Johnson, John R. Helliwell
In recent years, there has been a major expansion in digital storage capability for hosting raw diffraction datasets. Naturally, the question has now arisen as to the benefits and costs for the preservation of such raw, i.e., experimental diffraction datasets. We describe the consultations made of the global structural chemistry, i.e., chemical crystallography community from the points of view of the
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Coherent acoustic phonons in a coupled hexagonal boron nitride–graphite heterostructure Struct. Dyn. (IF 3.67) Pub Date : 2024-02-16 Arne Ungeheuer, Nora Bach, Mashood T. Mir, Ahmed S. Hassanien, Lukas Nöding, Thomas Baumert, Sascha Schäfer, Arne Senftleben
Femtosecond optically excited coherent acoustic phonon modes (CAPs) are investigated in a free-standing van der Waals heterostructure composed of a 20-nm transparent hexagonal boron nitride (hBN) and a 42-nm opaque graphite layer. Employing ultrafast electron diffraction, which allows for the independent evaluation of strain dynamics in the constituent material layers, three different CAP modes are
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Phase field crystal models with applications to laser deposition: A review Struct. Dyn. (IF 3.67) Pub Date : 2024-02-16 Duncan Burns, Nikolas Provatas, Martin Grant
In this article, we address the application of phase field crystal (PFC) theory, a hybrid atomistic-continuum approach, for modeling nanostructure kinetics encountered in laser deposition. We first provide an overview of the PFC methodology, highlighting recent advances to incorporate phononic and heat transport mechanisms. To simulate laser heating, energy is deposited onto a number of polycrystalline
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Blue and red in the protein world: Photoactive yellow protein and phytochromes as revealed by time-resolved crystallography Struct. Dyn. (IF 3.67) Pub Date : 2024-01-31 Marius Schmidt, Emina A. Stojković
Time-resolved crystallography (TRX) is a method designed to investigate functional motions of biological macromolecules on all time scales. Originally a synchrotron-based method, TRX is enabled by the development of TR Laue crystallography (TRLX). TR serial crystallography (TR-SX) is an extension of TRLX. As the foundations of TRLX were evolving from the late 1980s to the turn of the millennium, TR-SX
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Synthesis technique and electron beam damage study of nanometer-thin single-crystalline thymine Struct. Dyn. (IF 3.67) Pub Date : 2024-01-31 Hazem Daoud, Sreelaja Pulleri Vadhyar, Ehsan Nikbin, Cheng Lu, R. J. Dwayne Miller
Samples suitable for electron diffraction studies must satisfy certain characteristics such as having a thickness in the range of 10–100 nm. We report, to our knowledge, the first successful synthesis technique of nanometer-thin sheets of single-crystalline thymine suitable for electron diffraction and spectroscopy studies. This development provides a well-defined system to explore issues related to
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BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules Struct. Dyn. (IF 3.67) Pub Date : 2024-01-31 Robert W. Henning, Irina Kosheleva, Vukica Šrajer, In-Sik Kim, Eric Zoellner, Rama Ranganathan
A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural
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Toward ultrafast soft x-ray spectroscopy of organic photovoltaic devices Struct. Dyn. (IF 3.67) Pub Date : 2024-01-19 Douglas Garratt, Mary Matthews, Jon Marangos
Novel ultrafast x-ray sources based on high harmonic generation and at x-ray free electron lasers are opening up new opportunities to resolve complex ultrafast processes in condensed phase systems with exceptional temporal resolution and atomic site specificity. In this perspective, we present techniques for resolving charge localization, transfer, and separation processes in organic semiconductors
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Angle-resolved photoelectron spectroscopy in a low-energy electron microscope Struct. Dyn. (IF 3.67) Pub Date : 2023-12-29 Alexander Neuhaus, Pascal Dreher, Florian Schütz, Helder Marchetto, Torsten Franz, Frank Meyer zu Heringdorf
Spectroscopic photoemission microscopy is a well-established method to investigate the electronic structure of surfaces. In modern photoemission microscopes, the electron optics allow imaging of the image plane, momentum plane, or dispersive plane, depending on the lens setting. Furthermore, apertures allow filtering of energy-, real-, and momentum space. Here, we describe how a standard spectroscopic
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Observations on Laue diffraction within synchrotron radiation and neutron macromolecular crystallography research and developments Struct. Dyn. (IF 3.67) Pub Date : 2023-12-15 John R. Helliwell
A seminal contribution in the domain of physiologically relevant biological structure and function determination was by Keith Moffat, of Cornell and latterly of the University of Chicago proposing that synchrotrons should offer the option of a Laue method data collection mode. I enthusiastically joined in supporting this initiative. This proposal needed detailed methods development though; theoretical
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Theoretical study of time-resolved photoelectron circular dichroism in the photodissociation of a chiral molecule Struct. Dyn. (IF 3.67) Pub Date : 2023-12-15 Marit R. Fiechter, Vít Svoboda, Hans Jakob Wörner
Photoelectron circular dichroism (PECD), the forward–backward asymmetry of the photoelectron angular distribution when ionizing randomly oriented chiral molecules with circularly polarized light, is an established method to investigate chiral properties of molecules in their electronic ground state. Here, we develop a computational strategy for predicting time-resolved PECD (TRPECD) of chemical reactions
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Few-femtosecond electronic and structural rearrangements of CH4+ driven by the Jahn–Teller effect Struct. Dyn. (IF 3.67) Pub Date : 2023-12-15 Kristina S. Zinchenko, Fernando Ardana-Lamas, Valentina Utrio Lanfaloni, Nicholas Monahan, Issaka Seidu, Michael S. Schuurman, Simon P. Neville, Hans Jakob Wörner
The Jahn–Teller effect (JTE) is central to the understanding of the physical and chemical properties of a broad variety of molecules and materials. Whereas the manifestations of the JTE in stationary properties of matter are relatively well studied, the study of JTE-induced dynamics is still in its infancy, largely owing to its ultrafast and non-adiabatic nature. For example, the time scales reported
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Relativistic ultrafast electron diffraction at high repetition rates Struct. Dyn. (IF 3.67) Pub Date : 2023-12-04 K. M. Siddiqui, D. B. Durham, F. Cropp, F. Ji, S. Paiagua, C. Ophus, N. C. Andresen, L. Jin, J. Wu, S. Wang, X. Zhang, W. You, M. Murnane, M. Centurion, X. Wang, D. S. Slaughter, R. A. Kaindl, P. Musumeci, A. M. Minor, D. Filippetto
The ability to resolve the dynamics of matter on its native temporal and spatial scales constitutes a key challenge and convergent theme across chemistry, biology, and materials science. The last couple of decades have witnessed ultrafast electron diffraction (UED) emerge as one of the forefront techniques with the sensitivity to resolve atomic motions. Increasingly sophisticated UED instruments are
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Simulation of ultrafast electron diffraction intensity under coherent acoustic phonons Struct. Dyn. (IF 3.67) Pub Date : 2023-11-13 Yongzhao Zhang, Jun Li, Wentao Wang, Huanfang Tian, Wenli Gao, Jianqi Li, Shuaishuai Sun, Huaixin Yang
Ultrafast electron diffraction has been proven to be a powerful tool for the study of coherent acoustic phonons owing to its high sensitivity to crystal structures. However, this sensitivity leads to complicated behavior of the diffraction intensity, which complicates the analysis process of phonons, especially higher harmonics. Here, we theoretically analyze the effects of photoinduced coherent transverse
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A Δ-learning strategy for interpretation of spectroscopic observables Struct. Dyn. (IF 3.67) Pub Date : 2023-11-06 Luke Watson, Thomas Pope, Raphael M. Jay, Ambar Banerjee, Philippe Wernet, Thomas J. Penfold
Accurate computations of experimental observables are essential for interpreting the high information content held within x-ray spectra. However, for complicated systems this can be difficult, a challenge compounded when dynamics becomes important owing to the large number of calculations required to capture the time-evolving observable. While machine learning architectures have been shown to represent
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Photodiode-based time zero determination for ultrafast electron microscopy Struct. Dyn. (IF 3.67) Pub Date : 2023-11-06 S. T. Kempers, S. Borrelli, E. R. Kieft, H. A. van Doorn, P. H. A. Mutsaers, O. J. Luiten
Pump-probe experiments in ultrafast electron microscopy require temporal overlap between the pump and probe pulses. Accurate measurements of the time delay between them allows for the determination of the time zero, the moment in time where both pulses perfectly overlap. In this work, we present the use of a photodiode-based alignment method for these time zero measurements. The cheap and easy-to-use
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Disentangling the evolution of electrons and holes in photoexcited ZnO nanoparticles Struct. Dyn. (IF 3.67) Pub Date : 2023-11-03 Christopher J. Milne, Natalia Nagornova, Thomas Pope, Hui-Yuan Chen, Thomas Rossi, Jakub Szlachetko, Wojciech Gawelda, Alexander Britz, Tim B. van Driel, Leonardo Sala, Simon Ebner, Tetsuo Katayama, Stephen H. Southworth, Gilles Doumy, Anne Marie March, C. Stefan Lehmann, Melanie Mucke, Denys Iablonskyi, Yoshiaki Kumagai, Gregor Knopp, Koji Motomura, Tadashi Togashi, Shigeki Owada, Makina Yabashi,
The evolution of charge carriers in photoexcited room temperature ZnO nanoparticles in solution is investigated using ultrafast ultraviolet photoluminescence spectroscopy, ultrafast Zn K-edge absorption spectroscopy, and ab initio molecular dynamics (MD) simulations. The photoluminescence is excited at 4.66 eV, well above the band edge, and shows that electron cooling in the conduction band and exciton
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Solution phase high repetition rate laser pump x-ray probe picosecond hard x-ray spectroscopy at the Stanford Synchrotron Radiation Lightsource Struct. Dyn. (IF 3.67) Pub Date : 2023-10-27 Marco Reinhard, Dean Skoien, Jacob A. Spies, Angel T. Garcia-Esparza, Benjamin D. Matson, Jeff Corbett, Kai Tian, James Safranek, Eduardo Granados, Matthew Strader, Kelly J. Gaffney, Roberto Alonso-Mori, Thomas Kroll, Dimosthenis Sokaras
We present a dedicated end-station for solution phase high repetition rate (MHz) picosecond hard x-ray spectroscopy at beamline 15-2 of the Stanford Synchrotron Radiation Lightsource. A high-power ultrafast ytterbium-doped fiber laser is used to photoexcite the samples at a repetition rate of 640 kHz, while the data acquisition operates at the 1.28 MHz repetition rate of the storage ring recording
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Non-thermal structural transformation of diamond driven by x-rays Struct. Dyn. (IF 3.67) Pub Date : 2023-10-27 Philip Heimann, Nicholas J. Hartley, Ichiro Inoue, Victor Tkachenko, Andre Antoine, Fabien Dorchies, Roger Falcone, Jérôme Gaudin, Hauke Höppner, Yuichi Inubushi, Konrad J. Kapcia, Hae Ja Lee, Vladimir Lipp, Paloma Martinez, Nikita Medvedev, Franz Tavella, Sven Toleikis, Makina Yabashi, Toshinori Yabuuchi, Jumpei Yamada, Beata Ziaja
Intense x-ray pulses can cause the non-thermal structural transformation of diamond. At the SACLA XFEL facility, pump x-ray pulses triggered this phase transition, and probe x-ray pulses produced diffraction patterns. Time delays were observed from 0 to 250 fs, and the x-ray dose varied from 0.9 to 8.0 eV/atom. The intensity of the (111), (220), and (311) diffraction peaks decreased with time, indicating
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Electron population dynamics in resonant non-linear x-ray absorption in nickel at a free-electron laser Struct. Dyn. (IF 3.67) Pub Date : 2023-10-11 Robin Y. Engel, Oliver Alexander, Kaan Atak, Uwe Bovensiepen, Jens Buck, Robert Carley, Michele Cascella, Valentin Chardonnet, Gheorghe Sorin Chiuzbaian, Christian David, Florian Döring, Andrea Eschenlohr, Natalia Gerasimova, Frank de Groot, Loïc Le Guyader, Oliver S. Humphries, Manuel Izquierdo, Emmanuelle Jal, Adam Kubec, Tim Laarmann, Charles-Henri Lambert, Jan Lüning, Jonathan P. Marangos, Laurent
Free-electron lasers provide bright, ultrashort, and monochromatic x-ray pulses, enabling novel spectroscopic measurements not only with femtosecond temporal resolution: The high fluence of their x-ray pulses can also easily enter the regime of the non-linear x-ray–matter interaction. Entering this regime necessitates a rigorous analysis and reliable prediction of the relevant non-linear processes
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Isotope effects in dynamics of water isotopologues induced by core ionization at an x-ray free-electron laser Struct. Dyn. (IF 3.67) Pub Date : 2023-10-03 R. Guillemin, L. Inhester, M. Ilchen, T. Mazza, R. Boll, Th. Weber, S. Eckart, P. Grychtol, N. Rennhack, T. Marchenko, N. Velasquez, O. Travnikova, I. Ismail, J. Niskanen, E. Kukk, F. Trinter, M. Gisselbrecht, R. Feifel, G. Sansone, D. Rolles, M. Martins, M. Meyer, M. Simon, R. Santra, T. Pfeifer, T. Jahnke, M. N. Piancastelli
Dynamical response of water exposed to x-rays is of utmost importance in a wealth of science areas. We exposed isolated water isotopologues to short x-ray pulses from a free-electron laser and detected momenta of all produced ions in coincidence. By combining experimental results and theoretical modeling, we identify significant structural dynamics with characteristic isotope effects in H2O2+, D2O2+
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RF acceleration of ultracold electron bunches Struct. Dyn. (IF 3.67) Pub Date : 2023-10-03 D. F. J. Nijhof, T. C. H. de Raadt, J. V. Huijts, J. G. H. Franssen, P. H. A. Mutsaers, O. J. Luiten
The ultrafast and ultracold electron source, based on laser cooling and trapping of atomic gas and its subsequent near-threshold two-step photoionization, is capable of generating electron bunches with a high transverse brightness at energies of roughly 10 keV. This paper investigates the possibility of increasing the range of applications of this source by accelerating the bunch using radio frequency
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Nonequilibrium warm dense matter investigated with laser–plasma-based XANES down to the femtosecond Struct. Dyn. (IF 3.67) Pub Date : 2023-09-15 F. Dorchies, K. Ta Phuoc, L. Lecherbourg
The use of laser–plasma-based x-ray sources is discussed, with a view to carrying out time-resolved x-ray absorption spectroscopy measurements, down to the femtosecond timescale. A review of recent experiments performed by our team is presented. They concern the study of the nonequilibrium transition of metals from solid to the warm dense regime, which imposes specific constraints (the sample being
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High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability Struct. Dyn. (IF 3.67) Pub Date : 2023-08-23 Violetta Weinreb, Gabriel Weinreb, Charles W. Carter
Landscape descriptions provide a framework for identifying functionally significant dynamic linkages in proteins but cannot supply details. Rate measurements of combinatorial mutations can implicate dynamic linkages in catalysis. A major difficulty is filtering dynamic linkages from the vastly more numerous static interactions that stabilize domain folding. The Geobacillus stearothermophilus (TrpRS)
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Quasi-elastic neutron scattering reveals the relationship between the dynamical behavior of phospholipid headgroups and hydration water Struct. Dyn. (IF 3.67) Pub Date : 2023-08-21 Md. Khalidur Rahman, Takeshi Yamada, Norifumi L. Yamada, Mafumi Hishida, Yuji Higuchi, Hideki Seto
The dynamics of hydration water (HW) in 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE) was investigated by means of quasi-elastic neutron scattering (QENS) and compared with those observed in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). The headgroup dynamics of DMPE was investigated using a mixture of tail-deuterated DMPE and D2O, and the QENS profiles were interpreted as consisting
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Practical considerations for the analysis of time-resolved x-ray data Struct. Dyn. (IF 3.67) Pub Date : 2023-08-16 Marius Schmidt
The field of time-resolved macromolecular crystallography has been expanding rapidly after free electron lasers for hard x rays (XFELs) became available. Techniques to collect and process data from XFELs spread to synchrotron light sources. Although time-scales and data collection modalities can differ substantially between these types of light sources, the analysis of the resulting x-ray data proceeds
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Observing ice structure of micron-sized vapor-deposited ice with an x-ray free-electron laser Struct. Dyn. (IF 3.67) Pub Date : 2023-08-09 Seonmyeong Kim, Matlabjon Sattorov, Dongpyo Hong, Heon Kang, Jaehun Park, Jae Hyuk Lee, Rory Ma, Andrew V Martin, Carl Caleman, Jonas A Sellberg, Prasanta Kumar Datta, Sang Yoon Park, Gun-Sik Park
The direct observation of the structure of micrometer-sized vapor-deposited ice is performed at Pohang Accelerator Laboratory x-ray free electron laser (PAL-XFEL). The formation of micrometer-sized ice crystals and their structure is important in various fields, including atmospheric science, cryobiology, and astrophysics, but understanding the structure of micrometer-sized ice crystals remains challenging
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Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase Struct. Dyn. (IF 3.67) Pub Date : 2023-07-18 Srinivas Niranj Chandrasekaran, Jhuma Das, Nikolay V. Dokholyan, Charles W. Carter
Mechanistic studies of Geobacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford an unusually detailed description—the escapement mechanism—for the distinct steps coupling catalysis to domain motion, efficiently converting the free energy of ATP hydrolysis into biologically useful alternative forms of information and work. Further elucidation of the escapement mechanism requires understanding
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Synergism between x-ray crystallography and NMR residual dipolar couplings in characterizing protein dynamics Struct. Dyn. (IF 3.67) Pub Date : 2023-07-11 Yang Shen, Ad Bax
The important role of structural dynamics in protein function is widely recognized. Thermal or B-factors and their anisotropy, seen in x-ray analysis of protein structures, report on the presence of atomic coordinate heterogeneity that can be attributed to motion. However, their quantitative evaluation in terms of protein dynamics by x-ray ensemble refinement remains challenging. NMR spectroscopy provides
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Imaging temperature and thickness of thin planar liquid water jets in vacuum Struct. Dyn. (IF 3.67) Pub Date : 2023-06-28 Tillmann Buttersack, Henrik Haak, Hendrik Bluhm, Uwe Hergenhahn, Gerard Meijer, Bernd Winter
We present spatially resolved measurements of the temperature of a flat liquid water microjet for varying ambient pressures, from vacuum to 100% relative humidity. The entire jet surface is probed in a single shot by a high-resolution infrared camera. Obtained 2D images are substantially influenced by the temperature of the apparatus on the opposite side of the infrared camera; a protocol to correct
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Projection to extract the perpendicular component (PEPC) method for extracting kinetics from time-resolved data Struct. Dyn. (IF 3.67) Pub Date : 2023-06-28 H. Ki, J. Gu, Y. Cha, K. W. Lee, H. Ihee
Time-resolved x-ray liquidography (TRXL) is a potent method for investigating the structural dynamics of chemical and biological reactions in the liquid phase. It has enabled the extraction of detailed structural aspects of various dynamic processes, the molecular structures of intermediates, and kinetics of reactions across a wide range of systems, from small molecules to proteins and nanoparticles
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Structural biology and public health response to biomedical threats Struct. Dyn. (IF 3.67) Pub Date : 2023-06-20 Joanna Lenkiewicz, Vanessa Bijak, Shrisha Poonuganti, Michal Szczygiel, Michal Gucwa, Krzysztof Murzyn, Wladek Minor
Over the course of the pandemic caused by SARS-CoV-2, structural biologists have worked hand in hand with groups developing vaccines and treatments. However, relying solely on in vitro and clinical studies may be insufficient to guide vaccination and treatment developments, and other healthcare policies during virus mutations or peaks in infections and fatalities. Therefore, it is crucial to track
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And now some updates for SDY readers from the Editor…. Struct. Dyn. (IF 3.67) Pub Date : 2023-06-15 George N Phillips
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In crystallo observation of active site dynamics and transient metal ion binding within DNA polymerases Struct. Dyn. (IF 3.67) Pub Date : 2023-06-15 Caleb Chang, Grace Zhou, Yang Gao
DNA polymerases are the enzymatic catalysts that synthesize DNA during DNA replication and repair. Kinetic studies and x-ray crystallography have uncovered the overall kinetic pathway and led to a two-metal-ion dependent catalytic mechanism. Diffusion-based time-resolved crystallography has permitted the visualization of the catalytic reaction at atomic resolution and made it possible to capture transient
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A theoretical study of the time-resolved x-ray absorption spectrum of the photoionized BT-1T cation Struct. Dyn. (IF 3.67) Pub Date : 2023-05-26 Anna Kristina Schnack-Petersen, Mátyás Pápai, Sonia Coriani, Klaus Braagaard Møller
The time-resolved x-ray absorption spectrum of the BT-1T cation (BT-1T+) is theoretically simulated in order to investigate the charge transfer reaction of the system. We employ both trajectory surface hopping and quantum dynamics to simulate the structural evolution over time and the changes in the state populations. To compute the static x-ray absorption spectra (XAS) of the ground and excited states
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Low-pass spectral analysis of time-resolved serial femtosecond crystallography data Struct. Dyn. (IF 3.67) Pub Date : 2023-05-26 Cecilia M. Casadei, Ahmad Hosseinizadeh, Spencer Bliven, Tobias Weinert, Jörg Standfuss, Russell Fung, Gebhard F. X. Schertler, Robin Santra
Low-pass spectral analysis (LPSA) is a recently developed dynamics retrieval algorithm showing excellent retrieval properties when applied to model data affected by extreme incompleteness and stochastic weighting. In this work, we apply LPSA to an experimental time-resolved serial femtosecond crystallography (TR-SFX) dataset from the membrane protein bacteriorhodopsin (bR) and analyze its parametric
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Deep mining of the protein energy landscape Struct. Dyn. (IF 3.67) Pub Date : 2023-04-27 A. Joshua Wand
For over half a century, it has been known that protein molecules naturally undergo extensive structural fluctuations, and that these internal motions are intimately related to their functional properties. The energy landscape view has provided a powerful framework for describing the various physical states that proteins visit during their lifetimes. This Perspective focuses on the commonly neglected
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Pump–probe x-ray microscopy of photo-induced magnetization dynamics at MHz repetition rates Struct. Dyn. (IF 3.67) Pub Date : 2023-03-21 Kathinka Gerlinger, Bastian Pfau, Martin Hennecke, Lisa-Marie Kern, Ingo Will, Tino Noll, Markus Weigand, Joachim Gräfe, Nick Träger, Michael Schneider, Christian M. Günther, Dieter Engel, Gisela Schütz, Stefan Eisebitt
We present time-resolved scanning x-ray microscopy measurements with picosecond photo-excitation via a tailored infrared pump laser at a scanning transmission x-ray microscope. Specifically, we image the laser-induced demagnetization and remagnetization of thin ferrimagnetic GdFe films proceeding on a few nanoseconds timescale. Controlling the heat load on the sample via additional reflector and heatsink
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Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction Struct. Dyn. (IF 3.67) Pub Date : 2023-03-17 Miki Nakano, Osamu Miyashita, Florence Tama
Single-particle analysis using x-ray free-electron lasers (XFELs) is a novel method for obtaining structural information of samples in a state close to nature. In particular, it is suitable for observing the inner structure of large biomolecules by taking advantage of the high transmittance of x-rays. However, systematic studies on the resolution achievable for large molecules are lacking. In this
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Protein dynamics: The future is bright and complicated! Struct. Dyn. (IF 3.67) Pub Date : 2023-02-27 Kwangho Nam, Magnus Wolf-Watz
Biological life depends on motion, and this manifests itself in proteins that display motion over a formidable range of time scales spanning from femtoseconds vibrations of atoms at enzymatic transition states, all the way to slow domain motions occurring on micro to milliseconds. An outstanding challenge in contemporary biophysics and structural biology is a quantitative understanding of the linkages
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Biological function investigated by time-resolved structure determination Struct. Dyn. (IF 3.67) Pub Date : 2023-02-21 Marius Schmidt
Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life. This is illustrated by examples where chemical and physical stimuli spawn biological responses on various length
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Solution characterization of the dynamic conjugative entry exclusion protein TraG Struct. Dyn. (IF 3.67) Pub Date : 2022-12-27 Nicholas Bragagnolo, Gerald F. Audette
The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain
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Accurate quantification of lattice temperature dynamics from ultrafast electron diffraction of single-crystal films using dynamical scattering simulations Struct. Dyn. (IF 3.67) Pub Date : 2022-12-05 Daniel B. Durham, Colin Ophus, Khalid M. Siddiqui, Andrew M. Minor, Daniele Filippetto
In ultrafast electron diffraction (UED) experiments, accurate retrieval of time-resolved structural parameters, such as atomic coordinates and thermal displacement parameters, requires an accurate scattering model. Unfortunately, kinematical models are often inaccurate even for relativistic electron probes, especially for dense, oriented single crystals where strong channeling and multiple scattering
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Study of trioleoylglycerol two-layer and adiposome cross-section mimicking four-layer systems through atomic-level simulations Struct. Dyn. (IF 3.67) Pub Date : 2022-12-05 Ahmed Hammad Mirza
Adiposomes are artificially prepared lipid droplet (LD)-mimetic structures, which, unlike LDs, do not harbor proteins. The dynamics of interaction between triacylglycerols (TAGs), drug molecule, and phospholipids in adiposomes is currently not well-established. Trioleoylglycerol (TOG) molecule was divided into three parts: two oleoyl tails and one 2-monooleoylglycerol (MOG). Forcefield parameters for
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Expected resolution limits of x-ray free-electron laser single-particle imaging for realistic source and detector properties Struct. Dyn. (IF 3.67) Pub Date : 2022-11-16 Juncheng E, Y. Kim, J. Bielecki, M. Sikorski, R. de Wijn, C. Fortmann-Grote, J. Sztuk-Dambietz, J. C. P. Koliyadu, R. Letrun, H. J. Kirkwood, T. Sato, R. Bean, A. P. Mancuso, C. Kim
The unprecedented intensity of x-ray free-electron laser sources has enabled single-particle x-ray diffraction imaging (SPI) of various biological specimens in both two-dimensional projection and three dimensions (3D). The potential of studying protein dynamics in their native conditions, without crystallization or chemical staining, has encouraged researchers to aim for increasingly higher resolutions
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Charge-induced chemical dynamics in glycine probed with time-resolved Auger electron spectroscopy Struct. Dyn. (IF 3.67) Pub Date : 2022-11-08 David Schwickert, Marco Ruberti, Přemysl Kolorenč, Andreas Przystawik, Slawomir Skruszewicz, Malte Sumfleth, Markus Braune, Lars Bocklage, Luis Carretero, Marie Kristin Czwalinna, Dian Diaman, Stefan Düsterer, Marion Kuhlmann, Steffen Palutke, Ralf Röhlsberger, Juliane Rönsch-Schulenburg, Sven Toleikis, Sergey Usenko, Jens Viefhaus, Anton Vorobiov, Michael Martins, Detlef Kip, Vitali Averbukh, Jon
In the present contribution, we use x-rays to monitor charge-induced chemical dynamics in the photoionized amino acid glycine with femtosecond time resolution. The outgoing photoelectron leaves behind the cation in a coherent superposition of quantum mechanical eigenstates. Delayed x-ray pulses track the induced coherence through resonant x-ray absorption that induces Auger decay. Temporal modulation
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Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays Struct. Dyn. (IF 3.67) Pub Date : 2022-10-31 Sourav Banerjee, Zoltan Jurek, Malik Muhammad Abdullah, Robin Santra
The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo
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Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle Struct. Dyn. (IF 3.67) Pub Date : 2022-10-31 Daniel Sarabi, Lucija Ostojić, Robert Bosman, Adams Vallejos, Johanna-Barbara Linse, Michael Wulff, Matteo Levantino, Richard Neutze
Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging
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A machine learning photon detection algorithm for coherent x-ray ultrafast fluctuation analysis Struct. Dyn. (IF 3.67) Pub Date : 2022-10-17 Sathya R. Chitturi, Nicolas G. Burdet, Youssef Nashed, Daniel Ratner, Aashwin Mishra, T. J. Lane, Matthew Seaberg, Vincent Esposito, Chun Hong Yoon, Mike Dunne, Joshua J. Turner
X-ray free electron laser experiments have brought unique capabilities and opened new directions in research, such as creating new states of matter or directly measuring atomic motion. One such area is the ability to use finely spaced sets of coherent x-ray pulses to be compared after scattering from a dynamic system at different times. This enables the study of fluctuations in many-body quantum systems
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Ultrafast electron diffraction from transiently aligned asymmetric top molecules: Rotational dynamics and structure retrieval Struct. Dyn. (IF 3.67) Pub Date : 2022-10-17 Kyle J. Wilkin, Yanwei Xiong, Haoran Zhao, Sri Bhavya Muvva, Sajib Kumar Saha, Martin Centurion
Ultrafast electron diffraction (UED) from aligned molecules in the gas phase has successfully retrieved structures of both linear and symmetric top molecules. Alignment of asymmetric tops has been recorded with UED but no structural information was retrieved. We present here the extraction of two-dimensional structural information from simple transformations of experimental diffraction patterns of
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Picosecond infrared laser driven sample delivery for simultaneous liquid-phase and gas-phase electron diffraction studies Struct. Dyn. (IF 3.67) Pub Date : 2022-09-16 Zhipeng Huang, Meghanad Kayanattil, Stuart A. Hayes, R. J. Dwayne Miller
Here, we report on a new approach based on laser driven molecular beams that provides simultaneously nanoscale liquid droplets and gas-phase sample delivery for femtosecond electron diffraction studies. The method relies on Picosecond InfraRed Laser (PIRL) excitation of vibrational modes to strongly drive phase transitions under energy confinement by a mechanism referred to as Desorption by Impulsive
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Structure and dynamics of supercooled water in the hydration layer of poly(ethylene glycol) Struct. Dyn. (IF 3.67) Pub Date : 2022-09-08 Yuqing Li, Zehua Han, Changli Ma, Liang Hong, Yanwei Ding, Ye Chen, Junpeng Zhao, Dong Liu, Guangai Sun, Taisen Zuo, He Cheng, Charles C. Han
The statics and dynamics of supercooled water in the hydration layer of poly(ethylene glycol) (PEG) were studied by a combination of quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations. Two samples, that is, hydrogenated PEG/deuterated water (h-PEG/D2O) and fully deuterated PEG/hydrogenated water (d-PEG/H2O) with the same molar ratio of ethylene glycol (EG) monomer to water