1
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Wozniak S, Feig M. Diffusion and Viscosity in Mixed Protein Solutions. J Phys Chem B 2024; 128:11676-11693. [PMID: 39560935 PMCID: PMC11613455 DOI: 10.1021/acs.jpcb.4c06877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2024] [Revised: 11/13/2024] [Accepted: 11/15/2024] [Indexed: 11/20/2024]
Abstract
The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately reproduced experimental trends across a wide range of protein concentrations, including highly crowded environments up to 300 g/L. Notably, viscosity increased with crowding but varied little between different crowder types, while diffusion rates were significantly reduced depending on protein-protein interaction strength. Analysis using the Stokes-Einstein relation indicated that the reduction in diffusion exceeded what was expected from viscosity changes alone, with the additional slow-down attributable to transient cluster formation driven by weakly attractive interactions. Contact kinetics analysis further revealed that longer-lived interactions contributed more significantly to reduced diffusion rates than short-lived interactions. This study also highlights the accuracy of current computational methodologies for capturing the dynamics of proteins in highly concentrated solutions and provides insights into the molecular mechanisms affecting protein mobility in crowded environments.
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Affiliation(s)
- Spencer Wozniak
- Department of Biochemistry
and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Michael Feig
- Department of Biochemistry
and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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2
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Wozniak S, Feig M. Diffusion and Viscosity in Mixed Protein Solutions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617612. [PMID: 39416204 PMCID: PMC11483061 DOI: 10.1101/2024.10.10.617612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
The viscosity and diffusion properties of crowded protein systems were investigated with molecular dynamics simulations of SH3 mixtures with different crowders, and results were compared with experimental data. The simulations accurately reproduced experimental trends across a wide range of protein concentrations, including highly crowded environments up to 300 g/L. Notably, viscosity increased with crowding but varied little between different crowder types, while diffusion rates were significantly reduced depending on protein-protein interaction strength. Analysis using the Stokes-Einstein relation indicated that the reduction in diffusion exceeded what was expected from viscosity changes alone, with the additional slow-down attributable to transient cluster formation driven by weakly attractive interactions. Contact kinetics analysis further revealed that longer-lived interactions contributed more significantly to reduced diffusion rates than short-lived interactions. This study also highlights the accuracy of current computational methodologies for capturing the dynamics of proteins in highly concentrated solutions and provides insights into the molecular mechanisms affecting protein mobility in crowded environments.
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Affiliation(s)
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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3
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Anthuparambil ND, Timmermann S, Dargasz M, Retzbach S, Senft MD, Begam N, Ragulskaya A, Paulus M, Zhang F, Westermeier F, Sprung M, Schreiber F, Gutt C. Salt induced slowdown of kinetics and dynamics during thermal gelation of egg-yolk. J Chem Phys 2024; 161:055102. [PMID: 39105556 DOI: 10.1063/5.0219004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/22/2024] [Indexed: 08/07/2024] Open
Abstract
We investigated the effect of the NaCl concentration (0.3-2M) on the structure and dynamics of hen egg yolk at room temperature and during thermal gelation at temperatures in the range of 66-90 °C utilizing low-dose x-ray photon correlation spectroscopy in ultra-small angle x-ray scattering geometry. With an increase in the salt concentration, we observe progressive structural and dynamic changes at room temperature, indicating the disruption of yolk components such as yolk-granules and yolk-plasma proteins. Temperature- and salt-dependent structural and dynamic investigations suggest a delay in the gel formation and aggregation of yolk low-density lipoproteins with increasing ionic strength. However, the time-temperature superposition relationship observed in all samples suggests an identical mechanism underlying protein aggregation-gelation with a temperature-dependent reaction rate. The sol-gel transition time extracted from kinetic and dynamic information follows Arrhenius's behavior, and the activation energy (460 kJ/mol) is found to be independent of the salt concentration.
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Affiliation(s)
| | | | | | - Sebastian Retzbach
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Maximilian D Senft
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Nafisa Begam
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | | | - Michael Paulus
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Fajun Zhang
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | | | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, 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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4
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Rajput S, Panigrahy S, Nayar D. In Silico View of Crowding: Biomolecular Processes to Nanomaterial Design. ACS OMEGA 2024; 9:29953-29965. [PMID: 39035939 PMCID: PMC11256109 DOI: 10.1021/acsomega.4c03344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024]
Abstract
It is widely accepted that deciphering biomolecular structure and function requires going beyond the single-molecule or single-complex paradigm. The densely packed macromolecules, cosolutes, and metabolites in the living cell impose crowding effects on the biomolecular structure and dynamics that need to be accounted for. Molecular simulations have proven to be a powerful tool to advance the current molecular-level understanding of such a highly concentrated, complex milieu. This Mini-Review focuses on summarizing the understanding achieved so far for the effects of crowding on biomolecular processes using computational methods, along with highlighting a new direction in employing crowding as a tool for tunable nanomaterial design. The two schools of thought that form the pillars of the current understanding of crowding effects are discussed. The investigation of crowded solutions using physics-based models that encompass different time and length scales to mimic the intracellular environment are described. The limitations and challenges faced by the current models and simulation methods are addressed, highlighting the gaps to be filled for better agreement with experiments. Crowding can also act as an effective tool to modulate the structure-property-function relationships of nanomaterials, leading to the development of novel functional materials. A few recent studies, mostly experimental, have been summarized in this direction. The Mini-Review concludes with an outlook for future developments in this field in order to enable accurate mimicking of the intracellular environment using simulations and to bridge the gap between biological processes and nanomaterial design.
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Affiliation(s)
- Satyendra Rajput
- Department of Materials Science
and Engineering, Indian Institute of Technology
Delhi, New Delhi 110016, India
| | - Sibasankar Panigrahy
- Department of Materials Science
and Engineering, Indian Institute of Technology
Delhi, New Delhi 110016, India
| | - Divya Nayar
- Department of Materials Science
and Engineering, Indian Institute of Technology
Delhi, New Delhi 110016, India
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5
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Saito M, Kobayashi M, Nishino H, Hiraki TN, Honjo Y, Kobayashi K, Joti Y, Ozaki K, Imai Y, Yamaga M, Abe T, Nagasawa N, Yoda Y, Mashita R, Hatsui T, Wakabayashi Y. Broadband Quasielastic Scattering Spectroscopy Using a Multiline Frequency Comblike Spectrum in the Hard X-Ray Region. PHYSICAL REVIEW LETTERS 2024; 132:256901. [PMID: 38996231 DOI: 10.1103/physrevlett.132.256901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/24/2024] [Accepted: 04/19/2024] [Indexed: 07/14/2024]
Abstract
We developed a novel quasielastic scattering spectroscopy system that uses a multiline frequency comblike resolution function to overcome the limit on the accessible timescale imposed by the inherent single-energy resolution of conventional spectroscopy systems. The new multiline system possesses multiple resolutions and can efficiently cover a wide time range, from 100 ps to 100 ns, where x-ray-based dynamic measurement techniques are being actively developed. It enables visualization of the relaxation shape and wave-number-dependent dynamic behavior using a two-dimensional detector, as demonstrated for the natural polymer polybutadine without deuteration.
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Affiliation(s)
- Makina Saito
- Department of Physics, Tohoku University, Sendai, Miyagi, 980-8578, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Masashi Kobayashi
- Department of Physics, Tohoku University, Sendai, Miyagi, 980-8578, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Haruki Nishino
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo, Hyogo, 679-5198, Japan
| | | | - Yoshiaki Honjo
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Kazuo Kobayashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Kyosuke Ozaki
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Yasuhiko Imai
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Mitsuhiro Yamaga
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Tetsuya Abe
- Department of Physics, Tohoku University, Sendai, Miyagi, 980-8578, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Nobumoto Nagasawa
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Yoshitaka Yoda
- Japan Synchrotron Radiation Research Institute (JASRI), 1-1-1, Kouto, Sayo, Hyogo, 679-5198, Japan
| | - Ryo Mashita
- Chemical Analysis Center, Sumitomo Rubber Industries Ltd., Kobe, Hyogo, 651-0071, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Yusuke Wakabayashi
- Department of Physics, Tohoku University, Sendai, Miyagi, 980-8578, Japan
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6
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Schulz F, Jain A, Dallari F, Markmann V, Lehmkühler F. In situ aggregation and early states of gelation of gold nanoparticle dispersions. SOFT MATTER 2024; 20:3836-3844. [PMID: 38651356 DOI: 10.1039/d4sm00080c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The aggregation and onset of gelation of PEGylated gold nanoparticles dispersed in a glycerol-water mixture is studied by small-angle X-ray scattering and X-ray photon correlation spectroscopy. Tracking structural dynamics with sub-ms time resolution over a total experimental time of 8 hours corresponding to a time windows larger than 108 Brownian times and varying the temperature between 298 K and 266 K we can identify three regimes. First, while cooling to 275 K the particles show Brownian motion that slows down due to the increasing viscosity. Second, upon further cooling the static structure changes significantly, indicated by a broad structure factor peak. We attribute this to the formation of aggregates while the dynamics are still dominated by single-particle diffusion. Finally, the relaxation functions become more and more stretched accompanied by an increased slow down of the dynamics. At the same time the structure changes continuously indicating the onset of gelation. Our observations further suggest that the colloidal aggregation and gelation is characterized first by structural changes with a subsequent slowing down of the systems dynamics. The analysis also reveals that the details of the gelation process and the gel structure strongly depend on the thickness of the PEG-coating of the gold nanoparticles.
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Affiliation(s)
- Florian Schulz
- Institute of Nanostructure and Solid State Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Avni Jain
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Francesco Dallari
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Verena Markmann
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
| | - Felix Lehmkühler
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany.
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7
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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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8
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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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9
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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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10
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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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11
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Bin M, Reiser M, Filianina M, Berkowicz S, Das S, Timmermann S, Roseker W, Bauer R, Öström J, Karina A, Amann-Winkel K, Ladd-Parada M, Westermeier F, Sprung M, Möller J, Lehmkühler F, Gutt C, Perakis F. Coherent X-ray Scattering Reveals Nanoscale Fluctuations in Hydrated Proteins. J Phys Chem B 2023. [PMID: 37209106 DOI: 10.1021/acs.jpcb.3c02492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress-relaxation in hydrated lysozyme proteins stimulated and probed by X-ray Photon Correlation Spectroscopy (XPCS). This approach allows us to access the nanoscale dynamics in the deeply supercooled regime (T = 180 K), which is typically not accessible through equilibrium methods. The observed stimulated dynamic response is attributed to collective stress-relaxation as the system transitions from a jammed granular state to an elastically driven regime. The relaxation time constants exhibit Arrhenius temperature dependence upon cooling with a minimum in the Kohlrausch-Williams-Watts exponent at T = 227 K. The observed minimum is attributed to an increase in dynamical heterogeneity, which coincides with enhanced fluctuations observed in the two-time correlation functions and a maximum in the dynamic susceptibility quantified by the normalized variance χT. The amplification of fluctuations is consistent with previous studies of hydrated proteins, which indicate the key role of density and enthalpy fluctuations in hydration water. Our study provides new insights into X-ray stimulated stress-relaxation and the underlying mechanisms behind spatiotemporal fluctuations in biological granular materials.
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Affiliation(s)
- Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Mariia Filianina
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sharon Berkowicz
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sudipta Das
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Sonja Timmermann
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Wojciech Roseker
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robert Bauer
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- Freiberg Water Research Center, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany
| | - Jonatan Öström
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Aigerim Karina
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Katrin Amann-Winkel
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute of Physics, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Marjorie Ladd-Parada
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Johannes Möller
- European X-Ray Free-Electron Laser Facility, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Felix Lehmkühler
- Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Christian Gutt
- Department Physik, Universität Siegen, Walter-Flex-Strasse 3, 57072 Siegen, Germany
| | - Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden
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12
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Wu M, Tikhonov E, Tudi A, Kruglov I, Hou X, Xie C, Pan S, Yang Z. Target-Driven Design of Deep-UV Nonlinear Optical Materials via Interpretable Machine Learning. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300848. [PMID: 36929243 DOI: 10.1002/adma.202300848] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/03/2023] [Indexed: 05/17/2023]
Abstract
The development of a data-driven science paradigm is greatly revolutionizing the process of materials discovery. Particularly, exploring novel nonlinear optical (NLO) materials with the birefringent phase-matching ability to deep-ultraviolet (UV) region is of vital significance for the field of laser technologies. Herein, a target-driven materials design framework combining high-throughput calculations (HTC), crystal structure prediction, and interpretable machine learning (ML) is proposed to accelerate the discovery of deep-UV NLO materials. Using a dataset generated from HTC, an ML regression model for predicting birefringence is developed for the first time, which exhibits a possibility of achieving fast and accurate prediction. Essentially, crystal structures are adopted as the only known input of this model to establish a close structure-property relationship mapping birefringence. Utilizing the ML-predicted birefringence which can affect the shortest phase-matching wavelength, a full list of potential chemical compositions based on an efficient screening strategy is identified. Further, eight structures with good stability are discovered to show potential applications in the deep-UV region, owing to their promising NLO-related properties. This study provides a new insight into the discovery of NLO materials and this design framework can identify desired materials with high performances in the broad chemical space at a low computational cost.
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Affiliation(s)
- Mengfan Wu
- Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi, 830011, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Evgenii Tikhonov
- Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi, 830011, China
| | - Abudukadi Tudi
- Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi, 830011, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ivan Kruglov
- Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi, 830011, China
| | - Xueling Hou
- Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi, 830011, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Congwei Xie
- Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi, 830011, China
| | - Shilie Pan
- Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi, 830011, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihua Yang
- Research Center for Crystal Materials, CAS Key Laboratory of Functional Materials and Devices for Special Environments, Xinjiang Technical Institute of Physics & Chemistry, CAS, Xinjiang Key Laboratory of Electronic Information Materials and Devices, 40-1 South Beijing Road, Urumqi, 830011, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
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13
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Begam N, Timmermann S, Ragulskaya A, Girelli A, Senft MD, Retzbach S, Anthuparambil ND, Akhundzadeh MS, Kowalski M, Reiser M, Westermeier F, Sprung M, Zhang F, Gutt C, Schreiber F. Effects of temperature and ionic strength on the microscopic structure and dynamics of egg white gels. J Chem Phys 2023; 158:074903. [PMID: 36813727 DOI: 10.1063/5.0130758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We investigate the thermal gelation of egg white proteins at different temperatures with varying salt concentrations using x-ray photon correlation spectroscopy in the geometry of ultra-small angle x-ray scattering. Temperature-dependent structural investigation suggests a faster network formation with increasing temperature, and the gel adopts a more compact network, which is inconsistent with the conventional understanding of thermal aggregation. The resulting gel network shows a fractal dimension δ, ranging from 1.5 to 2.2. The values of δ display a non-monotonic behavior with increasing amount of salt. The corresponding dynamics in the q range of 0.002-0.1 nm-1 is observable after major change of the gel structure. The extracted relaxation time exhibits a two-step power law growth in dynamics as a function of waiting time. In the first regime, the dynamics is associated with structural growth, whereas the second regime is associated with the aging of the gel, which is directly linked with its compactness, as quantified by the fractal dimension. The gel dynamics is characterized by a compressed exponential relaxation with a ballistic-type of motion. The addition of salt gradually makes the early stage dynamics faster. Both gelation kinetics and microscopic dynamics show that the activation energy barrier in the system systematically decreases with increasing salt concentration.
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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
| | - Maximilian D Senft
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | - Sebastian Retzbach
- Institut für Angewandte Physik, Universität Tübingen, 72076 Tübingen, Germany
| | | | | | - Marvin Kowalski
- Department Physik, Universität Siegen, 57072 Siegen, Germany
| | - Mario Reiser
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91 Stockholm, Sweden
| | - Fabian Westermeier
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Michael Sprung
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 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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14
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Chushkin Y, Gulotta A, Roosen-Runge F, Pal A, Stradner A, Schurtenberger P. Probing Cage Relaxation in Concentrated Protein Solutions by X-Ray Photon Correlation Spectroscopy. PHYSICAL REVIEW LETTERS 2022; 129:238001. [PMID: 36563210 DOI: 10.1103/physrevlett.129.238001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
Abstract
Diffusion of proteins on length scales of their size is crucial for understanding the machinery of living cells. X-ray photon correlation spectroscopy (XPCS) is currently the only way to access long-time collective diffusion on these length scales, but radiation damage so far limits the use in biological systems. We apply a new approach to use XPCS to measure cage relaxation in crowded α-crystallin solutions. This allows us to correct for radiation effects, obtain missing information on long time diffusion, and support the fundamental analogy between protein and colloid dynamical arrest.
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Affiliation(s)
- Yuriy Chushkin
- ESRF, The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble Cedex 9, France
| | - Alessandro Gulotta
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | - Felix Roosen-Runge
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
- Department of Biomedical Science and Biofilms Research Center for Biointerfaces (BRCB), Faculty of Health and Society, Malmö University, Sweden
| | - Antara Pal
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
| | - Anna Stradner
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
- Lund Institute of advanced Neutron and X-ray Science LINXS, Lund University, Lund, Sweden
| | - Peter Schurtenberger
- Division of Physical Chemistry, Lund University, Naturvetarvägen 14, 22100 Lund, Sweden
- Lund Institute of advanced Neutron and X-ray Science LINXS, Lund University, Lund, Sweden
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