1
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Martinelli A, Baglioni J, Sun P, Dallari F, Pineda E, Duan Y, Spitzbart-Silberer T, Westermeier F, Sprung M, Monaco G. A new experimental setup for combined fast differential scanning calorimetry and X-ray photon correlation spectroscopy. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:557-565. [PMID: 38656773 DOI: 10.1107/s1600577524002510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/16/2024] [Indexed: 04/26/2024]
Abstract
Synchrotron-radiation-based techniques are a powerful tool for the investigation of materials. In particular, the availability of highly brilliant sources has opened the possibility to develop techniques sensitive to dynamics at the atomic scale such as X-ray photon correlation spectroscopy (XPCS). XPCS is particularly relevant in the study of glasses, which have been often investigated at the macroscopic scale by, for example, differential scanning calorimetry. Here, we show how to adapt a Flash calorimeter to combine XPCS and calorimetric scans. This setup paves the way to novel experiments requiring dynamical and thermodynamic information, ranging from the study of the crystallization kinetics to the study of the glass transition in systems that can be vitrified thanks to the high cooling rates reachable with an ultrafast calorimeter.
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Affiliation(s)
- Alessandro Martinelli
- University of Padova, Department of Physics and Astronomy `Galileo Galilei', Via F. Marzolo 8, 35131 Padova, Italy
| | - Jacopo Baglioni
- University of Padova, Department of Physics and Astronomy `Galileo Galilei', Via F. Marzolo 8, 35131 Padova, Italy
| | - Peihao Sun
- University of Padova, Department of Physics and Astronomy `Galileo Galilei', Via F. Marzolo 8, 35131 Padova, Italy
| | - Francesco Dallari
- University of Padova, Department of Physics and Astronomy `Galileo Galilei', Via F. Marzolo 8, 35131 Padova, Italy
| | - Eloi Pineda
- Department of Physics, Institute of Energy Technologies, Universitat Politècnica de Catalunya - BarcelonaTech, 08019 Barcelona, Spain
| | - Yajuan Duan
- Department of Physics, Institute of Energy Technologies, Universitat Politècnica de Catalunya - BarcelonaTech, 08019 Barcelona, Spain
| | | | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Giulio Monaco
- University of Padova, Department of Physics and Astronomy `Galileo Galilei', Via F. Marzolo 8, 35131 Padova, Italy
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2
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Dallari F, Lokteva I, Möller J, Roseker W, Goy C, Westermeier F, Boesenberg U, Hallmann J, Rodriguez-Fernandez A, Scholz M, Shayduk R, Madsen A, Grübel G, Lehmkühler F. Real-time swelling-collapse kinetics of nanogels driven by XFEL pulses. SCIENCE ADVANCES 2024; 10:eadm7876. [PMID: 38640237 PMCID: PMC11029799 DOI: 10.1126/sciadv.adm7876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
Stimuli-responsive polymers are an important class of materials with many applications in nanotechnology and drug delivery. The most prominent one is poly-N-isopropylacrylamide (PNIPAm). The characterization of the kinetics of its change after a temperature jump is still a lively research topic, especially at nanometer-length scales where it is not possible to rely on conventional microscopic techniques. Here, we measured in real time the collapse of a PNIPAm shell on silica nanoparticles with megahertz x-ray photon correlation spectroscopy at the European XFEL. We characterize the changes of the particles diffusion constant as a function of time and consequently local temperature on sub-microsecond timescales. We developed a phenomenological model to describe the observed data and extract the characteristic times associated to the swelling and collapse processes. Different from previous studies tracking the turbidity of PNIPAm dispersions and using laser heating, we find collapse times below microsecond timescales and two to three orders of magnitude slower swelling times.
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Affiliation(s)
- Francesco Dallari
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- Department of Physics and Astronmy, University of Padua, Via Marzolo 8, 35131 Padova, Italy
| | - Irina Lokteva
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Wojciech Roseker
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Claudia Goy
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Ulrike Boesenberg
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Jörg Hallmann
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Markus Scholz
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Roman Shayduk
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Anders Madsen
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Gerhard Grübel
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Felix Lehmkühler
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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3
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Li H, Ladd-Parada M, Karina A, Dallari F, Reiser M, Perakis F, Striker NN, Sprung M, Westermeier F, Grübel G, Steffen W, Lehmkühler F, Amann-Winkel K. Intrinsic Dynamics of Amorphous Ice Revealed by a Heterodyne Signal in X-ray Photon Correlation Spectroscopy Experiments. J Phys Chem Lett 2023; 14:10999-11007. [PMID: 38039400 PMCID: PMC10726389 DOI: 10.1021/acs.jpclett.3c02470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/04/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023]
Abstract
Unraveling the mechanism of water's glass transition and the interconnection between amorphous ices and liquid water plays an important role in our overall understanding of water. X-ray photon correlation spectroscopy (XPCS) experiments were conducted to study the dynamics and the complex interplay between the hypothesized glass transition in high-density amorphous ice (HDA) and the subsequent transition to low-density amorphous ice (LDA). Our XPCS experiments demonstrate that a heterodyne signal appears in the correlation function. Such a signal is known to originate from the interplay of a static component and a dynamic component. Quantitative analysis was performed on this heterodyne signal to extract the intrinsic dynamics of amorphous ice during the HDA-LDA transition. An angular dependence indicates non-isotropic, heterogeneous dynamics in the sample. Using the Stokes-Einstein relation to extract diffusion coefficients, the data are consistent with the scenario of static LDA islands floating within a diffusive matrix of high-density liquid water.
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Affiliation(s)
- Hailong Li
- Max-Planck-Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- State
Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Marjorie Ladd-Parada
- Department
of Physics, AlbaNova University Center, Stockholm University, Roslagstullsbacken 21, SE-10691 Stockholm, Sweden
- Department
of Chemistry, KTH Royal Institute of Technology, Roslagstullsbacken 21, 11421 Stockholm, Sweden
| | - Aigerim Karina
- Department
of Physics, AlbaNova University Center, Stockholm University, Roslagstullsbacken 21, SE-10691 Stockholm, Sweden
| | - Francesco Dallari
- Deutsches
Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mario Reiser
- Department
of Physics, AlbaNova University Center, Stockholm University, Roslagstullsbacken 21, SE-10691 Stockholm, Sweden
| | - Fivos Perakis
- Department
of Physics, AlbaNova University Center, Stockholm University, Roslagstullsbacken 21, SE-10691 Stockholm, Sweden
| | - Nele N. Striker
- Deutsches
Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches
Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Fabian Westermeier
- Deutsches
Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Gerhard Grübel
- Deutsches
Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg
Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- European
X-ray Free-Electron Laser, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Werner Steffen
- Max-Planck-Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Felix Lehmkühler
- Deutsches
Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Hamburg
Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Katrin Amann-Winkel
- Max-Planck-Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Physics, AlbaNova University Center, Stockholm University, Roslagstullsbacken 21, SE-10691 Stockholm, Sweden
- Institute
of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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4
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Czajka T, Neuhaus C, Alfken J, Stammer M, Chushkin Y, Pontoni D, Hoffmann C, Milovanovic D, Salditt T. Lipid vesicle pools studied by passive X-ray microrheology. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:123. [PMID: 38060069 PMCID: PMC10703982 DOI: 10.1140/epje/s10189-023-00375-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Vesicle pools can form by attractive interaction in a solution, mediated by proteins or divalent ions such as calcium. The pools, which are alternatively also denoted as vesicle clusters, form by liquid-liquid phase separation (LLPS) from an initially homogeneous solution. Due to the short range liquid-like order of vesicles in the pool or cluster, the vesicle-rich phase can also be regarded as a condensate, and one would like to better understand not only the structure of these systems, but also their dynamics. The diffusion of vesicles, in particular, is expected to change when vesicles are arrested in a pool. Here we investigate whether passive microrheology based on X-ray photon correlation spectroscopy (XPCS) is a suitable tool to study model systems of artificial lipid vesicles exhibiting LLPS, and more generally also other heterogeneous biomolecular fluids. We show that by adding highly scattering tracer particles to the solution, valuable information on the single vesicle as well as collective dynamics can be inferred. While the correlation functions reveal freely diffusing tracer particles in solutions at low CaCl[Formula: see text] concentrations, the relaxation rate [Formula: see text] shows a nonlinear dependence on [Formula: see text] at a higher concentration of around 8 mM CaCl[Formula: see text], characterised by two linear regimes with a broad cross-over. We explain this finding based on arrested diffusion in percolating vesicle clusters.
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Affiliation(s)
- Titus Czajka
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - Charlotte Neuhaus
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - Jette Alfken
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - Moritz Stammer
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, 37077, Göttingen, Germany
| | - Yuriy Chushkin
- European Synchrotron Radiation Facility, 38043, Grenoble Cedex 9, France
| | - Diego Pontoni
- European Synchrotron Radiation Facility, 38043, Grenoble Cedex 9, France
| | - Christian Hoffmann
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117, Berlin, Germany
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117, Berlin, Germany
| | - Tim Salditt
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, 37077, Göttingen, Germany.
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5
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Anthuparambil ND, Girelli A, Timmermann S, Kowalski M, Akhundzadeh MS, Retzbach S, Senft MD, Dargasz M, Gutmüller D, Hiremath A, Moron M, Öztürk Ö, Poggemann HF, Ragulskaya A, Begam N, Tosson A, Paulus M, Westermeier F, Zhang F, Sprung M, Schreiber F, Gutt C. Exploring non-equilibrium processes and spatio-temporal scaling laws in heated egg yolk using coherent X-rays. Nat Commun 2023; 14:5580. [PMID: 37696830 PMCID: PMC10495384 DOI: 10.1038/s41467-023-41202-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The soft-grainy microstructure of cooked egg yolk is the result of a series of out-of-equilibrium processes of its protein-lipid contents; however, it is unclear how egg yolk constituents contribute to these processes to create the desired microstructure. By employing X-ray photon correlation spectroscopy, we investigate the functional contribution of egg yolk constituents: proteins, low-density lipoproteins (LDLs), and yolk-granules to the development of grainy-gel microstructure and microscopic dynamics during cooking. We find that the viscosity of the heated egg yolk is solely determined by the degree of protein gelation, whereas the grainy-gel microstructure is controlled by the extent of LDL aggregation. Overall, protein denaturation-aggregation-gelation and LDL-aggregation follows Arrhenius-type time-temperature superposition (TTS), indicating an identical mechanism with a temperature-dependent reaction rate. However, above 75 °C TTS breaks down and temperature-independent gelation dynamics is observed, demonstrating that the temperature can no longer accelerate certain non-equilibrium processes above a threshold value.
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Affiliation(s)
- Nimmi Das Anthuparambil
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany.
- Department Physik, Universität Siegen, 57072, Siegen, Germany.
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | | | - Marvin Kowalski
- Department Physik, Universität Siegen, 57072, Siegen, Germany
| | | | - Sebastian Retzbach
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Maximilian D Senft
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | | | - Dennis Gutmüller
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Anusha Hiremath
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Marc Moron
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Özgül Öztürk
- Department Physik, Universität Siegen, 57072, Siegen, Germany
| | | | | | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Amir Tosson
- Department Physik, Universität Siegen, 57072, Siegen, Germany
| | - Michael Paulus
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, 72076, Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, 57072, Siegen, Germany.
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6
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Timmermann S, Anthuparambil ND, Girelli A, Begam N, Kowalski M, Retzbach S, Senft MD, Akhundzadeh MS, Poggemann HF, Moron M, Hiremath A, Gutmüller D, Dargasz M, Öztürk Ö, Paulus M, Westermeier F, Sprung M, Ragulskaya A, Zhang F, Schreiber F, Gutt C. X-ray driven and intrinsic dynamics in protein gels. Sci Rep 2023; 13:11048. [PMID: 37422480 PMCID: PMC10329714 DOI: 10.1038/s41598-023-38059-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023] Open
Abstract
We use X-ray photon correlation spectroscopy to investigate how structure and dynamics of egg white protein gels are affected by X-ray dose and dose rate. We find that both, changes in structure and beam-induced dynamics, depend on the viscoelastic properties of the gels with soft gels prepared at low temperatures being more sensitive to beam-induced effects. Soft gels can be fluidized by X-ray doses of a few kGy with a crossover from stress relaxation dynamics (Kohlrausch-Williams-Watts exponents [Formula: see text] to 2) to typical dynamical heterogeneous behavior ([Formula: see text]1) while the high temperature egg white gels are radiation-stable up to doses of 15 kGy with [Formula: see text]. For all gel samples we observe a crossover from equilibrium dynamics to beam induced motion upon increasing X-ray fluence and determine the resulting fluence threshold values [Formula: see text]. Surprisingly small threshold values of [Formula: see text] s[Formula: see text] nm[Formula: see text] can drive the dynamics in the soft gels while for stronger gels this threshold is increased to [Formula: see text] s[Formula: see text] nm[Formula: see text]. We explain our observations with the viscoelastic properties of the materials and can connect the threshold dose for structural beam damage with the dynamic properties of beam-induced motion. Our results suggest that soft viscoelastic materials can display pronounced X-ray driven motion even for low X-ray fluences. This induced motion is not detectable by static scattering as it appears at dose values well below the static damage threshold. We show that intrinsic sample dynamics can be separated from X-ray driven motion by measuring the fluence dependence of the dynamical properties.
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Affiliation(s)
- Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Str. 3, 57072, Siegen, Germany.
| | - Nimmi Das Anthuparambil
- Department Physik, Universität Siegen, Walter-Flex-Str. 3, 57072, Siegen, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Marvin Kowalski
- Department Physik, Universität Siegen, Walter-Flex-Str. 3, 57072, Siegen, Germany
| | - Sebastian Retzbach
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Maximilian Darius Senft
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | | | | | - Marc Moron
- Fakultät Physik/DELTA, TU Dortmund, Maria-Goeppert-Mayer-Str. 2, 44227, Dortmund, Germany
| | - Anusha Hiremath
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Dennis Gutmüller
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Michelle Dargasz
- Department Physik, Universität Siegen, Walter-Flex-Str. 3, 57072, Siegen, Germany
| | - Özgül Öztürk
- Department Physik, Universität Siegen, Walter-Flex-Str. 3, 57072, Siegen, Germany
| | - Michael Paulus
- Fakultät Physik/DELTA, TU Dortmund, Maria-Goeppert-Mayer-Str. 2, 44227, Dortmund, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Anastasia Ragulskaya
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076, Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Str. 3, 57072, Siegen, Germany.
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7
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Schnappinger T, Jadoun D, Gudem M, Kowalewski M. Time-resolved X-ray and XUV based spectroscopic methods for nonadiabatic processes in photochemistry. Chem Commun (Camb) 2022; 58:12763-12781. [PMID: 36317595 PMCID: PMC9671098 DOI: 10.1039/d2cc04875b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/21/2022] [Indexed: 11/03/2023]
Abstract
The photochemistry of numerous molecular systems is influenced by conical intersections (CIs). These omnipresent nonadiabatic phenomena provide ultra-fast radiationless relaxation channels by creating degeneracies between electronic states and decide over the final photoproducts. In their presence, the Born-Oppenheimer approximation breaks down, and the timescales of the electron and nuclear dynamics become comparable. Due to the ultra-fast dynamics and the complex interplay between nuclear and electronic degrees of freedom, the direct experimental observation of nonadiabatic processes close to CIs remains challenging. In this article, we give a theoretical perspective on novel spectroscopic techniques capable of observing clear signatures of CIs. We discuss methods that are based on ultra-short laser pulses in the extreme ultraviolet and X-ray regime, as their spectral and temporal resolution allow for resolving the ultra-fast dynamics near CIs.
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Affiliation(s)
- Thomas Schnappinger
- Department of Physics, Stockholm University, Albanova University Centre, SE-106 91 Stockholm, Sweden.
| | - Deependra Jadoun
- Department of Physics, Stockholm University, Albanova University Centre, SE-106 91 Stockholm, Sweden.
| | - Mahesh Gudem
- Department of Physics, Stockholm University, Albanova University Centre, SE-106 91 Stockholm, Sweden.
| | - Markus Kowalewski
- Department of Physics, Stockholm University, Albanova University Centre, SE-106 91 Stockholm, Sweden.
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8
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Vescovi R, Chard R, Saint ND, Blaiszik B, Pruyne J, Bicer T, Lavens A, Liu Z, Papka ME, Narayanan S, Schwarz N, Chard K, Foster IT. Linking scientific instruments and computation: Patterns, technologies, and experiences. PATTERNS (NEW YORK, N.Y.) 2022; 3:100606. [PMID: 36277824 PMCID: PMC9583115 DOI: 10.1016/j.patter.2022.100606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/07/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022]
Abstract
Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly discarding some data elements or by directing instruments to relevant areas of experimental space. Thus, methods are required for configuring and running distributed computing pipelines—what we call flows—that link instruments, computers (e.g., for analysis, simulation, artificial intelligence [AI] model training), edge computing (e.g., for analysis), data stores, metadata catalogs, and high-speed networks. We review common patterns associated with such flows and describe methods for instantiating these patterns. We present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages powerful computers for data inversion,model training, or other purposes. We also discuss implications of such methods for operators and users of scientific facilities. Patterns for linking instruments and computers for online analysis are reviewed Methods are presented for capturing such “flows” in reusable forms The use of Globus automation services to run flows is described Implications of these methods for scientists and facilities are discussed
The industrial revolution transformed society via large-scale automation of manufacturing. Today, AI- and robotics-driven automation of scientific research seems set to usher in a new era of accelerated discovery. But just as the industrial revolution depended on new replicable and scalable manufacturing processes and methods for delivering the copious mechanical power required by those processes, so the automated discovery revolution demands new methods for implementing research automation processes and for connecting those processes to computing and data power. We present here new methods that address these essential needs by allowing scientists to capture common automation patterns in reusable flows and to embed such flows in a global trust, data, and computing fabric that enables instant access to powerful AI, simulation, and other computational capabilities. We use examples from synchrotron light sources to show how these methods can be realized in software and applied at scale.
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Affiliation(s)
- Rafael Vescovi
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Ryan Chard
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Nickolaus D Saint
- Globus, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
| | - Ben Blaiszik
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Globus, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
| | - Jim Pruyne
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Globus, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
| | - Tekin Bicer
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Alex Lavens
- Structural Biology Center, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Zhengchun Liu
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Michael E Papka
- Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Department of Computer Science, University of Illinois Chicago, 1200 W. Harrison St., Chicago, IL 60607, USA
| | - Suresh Narayanan
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Nicholas Schwarz
- X-ray Science Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Kyle Chard
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Department of Computer Science, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
| | - Ian T Foster
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA.,Department of Computer Science, University of Chicago, 5730 S. Ellis Ave., Chicago, IL 60615, USA
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9
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Timmermann S, Starostin V, Girelli A, Ragulskaya A, Rahmann H, Reiser M, Begam N, Randolph L, Sprung M, Westermeier F, Zhang F, Schreiber F, Gutt C. Automated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn-Hilliard-type simulations using auto-encoder networks. J Appl Crystallogr 2022; 55:751-757. [PMID: 35974741 PMCID: PMC9348880 DOI: 10.1107/s1600576722004435] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/26/2022] [Indexed: 11/10/2022] Open
Abstract
Machine learning methods are used for an automated classification of experimental two-time X-ray photon correlation maps from an arrested liquid-liquid phase separation of a protein solution. The correlation maps are matched with correlation maps generated with Cahn-Hilliard-type simulations of liquid-liquid phase separations according to two simulation parameters and in the last step interpreted in the framework of the simulation. The matching routine employs an auto-encoder network and a differential evolution based algorithm. The method presented here is a first step towards handling large amounts of dynamic data measured at high-brilliance synchrotron and X-ray free-electron laser sources, facilitating fast comparison with phase field models of phase separation.
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Affiliation(s)
- Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Vladimir Starostin
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Anastasia Ragulskaya
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Hendrik Rahmann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Lisa Randolph
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
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10
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Wan G, Zhang G, Chen JZ, Toney MF, Miller JT, Tassone CJ. Reaction-Mediated Transformation of Working Catalysts. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Gang Wan
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Guanghui Zhang
- State Key Laboratory of Fine Chemicals, PSU-DUT Joint Center for Energy Research, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, People’s Republic of China
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Johnny Zhu Chen
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Michael F. Toney
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Jeffrey T. Miller
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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11
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Moron M, Al-Masoodi A, Lovato C, Reiser M, Randolph L, Surmeier G, Bolle J, Westermeier F, Sprung M, Winter R, Paulus M, Gutt C. Gelation Dynamics upon Pressure-Induced Liquid-Liquid Phase Separation in a Water-Lysozyme Solution. J Phys Chem B 2022; 126:4160-4167. [PMID: 35594491 DOI: 10.1021/acs.jpcb.2c01947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Employing X-ray photon correlation spectroscopy, we measure the kinetics and dynamics of a pressure-induced liquid-liquid phase separation (LLPS) in a water-lysozyme solution. Scattering invariants and kinetic information provide evidence that the system reaches the phase boundary upon pressure-induced LLPS with no sign of arrest. The coarsening slows down with increasing quench depths. The g2 functions display a two-step decay with a gradually increasing nonergodicity parameter typical for gelation. We observe fast superdiffusive (γ ≥ 3/2) and slow subdiffusive (γ < 0.6) motion associated with fast viscoelastic fluctuations of the network and a slow viscous coarsening process, respectively. The dynamics age linearly with time τ ∝ tw, and we observe the onset of viscoelastic relaxation for deeper quenches. Our results suggest that the protein solution gels upon reaching the phase boundary.
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Affiliation(s)
- M Moron
- Fakultät Physik/DELTA, TU Dortmund, 44221 Dortmund, Germany
| | - A Al-Masoodi
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
| | - C Lovato
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
| | - M Reiser
- Department of Physics, Stockholm University, 10691 Stockholm, Sweden
| | - L Randolph
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
| | - G Surmeier
- Fakultät Physik/DELTA, TU Dortmund, 44221 Dortmund, Germany
| | - J Bolle
- Fakultät Physik/DELTA, TU Dortmund, 44221 Dortmund, Germany
| | - F Westermeier
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - M Sprung
- Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany
| | - R Winter
- Fakultät Chemie und Chemische Biologie, Physikalische Chemie, TU Dortmund, 44227 Dortmund, Germany
| | - M Paulus
- Fakultät Physik/DELTA, TU Dortmund, 44221 Dortmund, Germany
| | - C Gutt
- Department Physik, Naturwissenschaftlich-Technische Fakultät, Universität Siegen, 57068 Siegen, Germany
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12
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Senses E, Kitchens CL, Faraone A. Viscosity reduction in polymer nanocomposites: Insights from dynamic neutron and X‐ray scattering. JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1002/pol.20210320] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Erkan Senses
- Department of Chemical and Biological Engineering Koc University Istanbul Turkey
| | - Christopher L. Kitchens
- Department of Chemical and Biomolecular Engineering Clemson University Clemson South Carolina USA
| | - Antonio Faraone
- Center for Neutron Research National Institute of Standards and Technology Gaithersburg Maryland USA
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13
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Gore M, Narvekar A, Bhagwat A, Jain R, Dandekar P. Macromolecular cryoprotectants for the preservation of mammalian cell culture: lessons from crowding, overview and perspectives. J Mater Chem B 2021; 10:143-169. [PMID: 34913462 DOI: 10.1039/d1tb01449h] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Cryopreservation is a process used for the storage of mammalian cells at a very low temperature, in a state of 'suspended animation.' Highly effective and safe macromolecular cryoprotectants (CPAs) have gained significant attention as they obviate the toxicity of conventional CPAs like dimethyl sulfoxide (DMSO) and reduce the risks involved in the storage of cultures at liquid nitrogen temperatures. These agents provide cryoprotection through multiple mechanisms, involving extracellular and intracellular macromolecular crowding, thereby impacting the biophysical and biochemical dynamics of the freezing medium and the cryopreserved cells. These CPAs vary in their structures and physicochemical properties, which influence their cryoprotective activities. Moreover, the introduction of polymeric crowders in the cryopreservation media enables serum-free storage at low-DMSO concentrations and high-temperature vitrification of frozen cultures (-80 °C). This review highlights the need for macromolecular CPAs and describes their mechanisms of cryopreservation, by elucidating the role of crowding effects. It also classifies the macromolecules based on their chemistry and their structure-activity relationships. Furthermore, this article provides perspectives on the factors that may influence the outcomes of the cell freezing process or may help in designing and evaluating prospective macromolecules. This manuscript also includes case studies about cellular investigations that have been conducted to demonstrate the cryoprotective potential of macromolecular CPAs. Ultimately, this review provides essential directives that will further improve the cell cryopreservation process and may encourage the use of macromolecular CPAs to fortify basic, applied, and translational research.
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Affiliation(s)
- Manish Gore
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Aditya Narvekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Advait Bhagwat
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Mumbai, 400 019, India.
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, 400 019, India.
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14
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Berkowicz S, Perakis F. Exploring the validity of the Stokes-Einstein relation in supercooled water using nanomolecular probes. Phys Chem Chem Phys 2021; 23:25490-25499. [PMID: 34494639 DOI: 10.1039/d1cp02866a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The breakdown of Stokes-Einstein relation in liquid water is one of the many anomalies that take place upon cooling and indicates the decoupling of diffusion and viscosity. It is hypothesized that these anomalies manifest due to the appearance of nanometer-scale spatial fluctuations, which become increasingly pronounced in the supercooled regime. Here, we explore the validity of the Stokes-Einstein relation in supercooled water using nanomolecular probes. We capture the diffusive dynamics of the probes using dynamic light scattering and target dynamics at different length scales by varying the probe size, from ≈100 nm silica spheres to molecular-sized polyhydroxylated fullerenes (≈1 nm). We find that all the studied probes, independent of size, display similar diffusive dynamics with an Arrhenius activation energy of ≈23 kJ mol-1. Analysis of the diffusion coefficient further indicates that the probes, independent of their size, experience similar dynamic environment, which coincides with the macroscopic viscosity, while single water molecules effectively experience a comparatively lower viscosity. Finally, we conclude that our results indicate that the Stokes-Einstein relation is preserved for diffusion of probes in supercooled water T ≥ 260 K with size as small as ≈1 nm.
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Affiliation(s)
- Sharon Berkowicz
- Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 Stockholm, Sweden.
| | - Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, SE-10691 Stockholm, Sweden.
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15
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Bin M, Yousif R, Berkowicz S, Das S, Schlesinger D, Perakis F. Wide-angle X-ray scattering and molecular dynamics simulations of supercooled protein hydration water. Phys Chem Chem Phys 2021; 23:18308-18313. [PMID: 34269785 DOI: 10.1039/d1cp02126e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the mechanism responsible for the protein low-temperature crossover observed at T≈ 220 K can help us improve current cryopreservation technologies. This crossover is associated with changes in the dynamics of the system, such as in the mean-squared displacement, whereas experimental evidence of structural changes is sparse. Here we investigate hydrated lysozyme proteins by using a combination of wide-angle X-ray scattering and molecular dynamics (MD) simulations. Experimentally we suppress crystallization by accurate control of the protein hydration level, which allows access to temperatures down to T = 175 K. The experimental data indicate that the scattering intensity peak at Q = 1.54 Å-1, attributed to interatomic distances, exhibits temperature-dependent changes upon cooling. In the MD simulations it is possible to decompose the water and protein contributions and we observe that, while the protein component is nearly temperature independent, the hydration water peak shifts in a fashion similar to that of bulk water. The observed trends are analysed by using the water-water and water-protein radial distribution functions, which indicate changes in the local probability density of hydration water.
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Affiliation(s)
- Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden.
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16
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From Femtoseconds to Hours—Measuring Dynamics over 18 Orders of Magnitude with Coherent X-rays. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11136179] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
X-ray photon correlation spectroscopy (XPCS) enables the study of sample dynamics between micrometer and atomic length scales. As a coherent scattering technique, it benefits from the increased brilliance of the next-generation synchrotron radiation and Free-Electron Laser (FEL) sources. In this article, we will introduce the XPCS concepts and review the latest developments of XPCS with special attention on the extension of accessible time scales to sub-μs and the application of XPCS at FELs. Furthermore, we will discuss future opportunities of XPCS and the related technique X-ray speckle visibility spectroscopy (XSVS) at new X-ray sources. Due to its particular signal-to-noise ratio, the time scales accessible by XPCS scale with the square of the coherent flux, allowing to dramatically extend its applications. This will soon enable studies over more than 18 orders of magnitude in time by XPCS and XSVS.
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17
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Begam N, Ragulskaya A, Girelli A, Rahmann H, Chandran S, Westermeier F, Reiser M, Sprung M, Zhang F, Gutt C, Schreiber F. Kinetics of Network Formation and Heterogeneous Dynamics of an Egg White Gel Revealed by Coherent X-Ray Scattering. PHYSICAL REVIEW LETTERS 2021; 126:098001. [PMID: 33750145 DOI: 10.1103/physrevlett.126.098001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
The kinetics of heat-induced gelation and the microscopic dynamics of a hen egg white gel are probed using x-ray photon correlation spectroscopy along with ultrasmall-angle x-ray scattering. The kinetics of structural growth reveals a reaction-limited aggregation process with a gel fractal dimension of ≈2 and an average network mesh size of ca. 400 nm. The dynamics probed at these length scales reveals an exponential growth of the characteristic relaxation times followed by an intriguing steady state in combination with a compressed exponential correlation function and a temporal heterogeneity. The degree of heterogeneity increases with decreasing length scale. We discuss our results in the broader context of experiments and models describing attractive colloidal gels.
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Affiliation(s)
- Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | | | - Anita Girelli
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Hendrik Rahmann
- Department Physik, Universität Siegen, 57072 Siegen, Germany
| | - Sivasurender Chandran
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mario Reiser
- Department Physik, Universität Siegen, 57072 Siegen, Germany
- European X-ray Free-Electron Laser GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, 57072 Siegen, Germany
| | - Frank Schreiber
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
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