1
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Singh A, Thutupalli S, Kumar M, Ameta S. Constrained dynamics of DNA oligonucleotides in phase-separated droplets. Biophys J 2024; 123:1458-1466. [PMID: 38169216 PMCID: PMC11163293 DOI: 10.1016/j.bpj.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Understanding the dynamics of biomolecules in complex environments is crucial for elucidating the effect of condensed and heterogeneous environments on their functional properties. A relevant environment-and one that can also be mimicked easily in vitro-is that of phase-separated droplets. While phase-separated droplet systems have been shown to compartmentalize a wide range of functional biomolecules, the effects of internal structuration of droplets on the dynamics and mobility of internalized molecules remain poorly understood. Here, we use fluorescence correlation spectroscopy to measure the dynamics of short oligonucleotides encapsulated within two representative kinds of uncharged and charged phase-separated droplets. We find that the internal structuration controls the oligonucleotide dynamics in these droplets, revealed by measuring physical parameters at high spatiotemporal resolution. By varying oligonucleotide length and salt concentrations (and thereby charge screening), we found that the dynamics are significantly affected in the noncharged droplets compared to the charged system. Our work lays the foundation for unraveling and quantifying the physical parameters governing biomolecular transport in the condensed environment.
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Affiliation(s)
- Anupam Singh
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India; International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Manoj Kumar
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
| | - Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India; Trivedi School of Biosciences, Ashoka University, Sonepat, India.
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2
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Fournier M, Leclerc P, Leray A, Champelovier D, Agbazahou F, Dahmani F, Bidaux G, Furlan A, Héliot L. Combined SPT and FCS methods reveal a mechanism of RNAP II oversampling in cell nuclei. Sci Rep 2023; 13:14633. [PMID: 37669988 PMCID: PMC10480184 DOI: 10.1038/s41598-023-38668-8] [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: 01/05/2023] [Accepted: 07/12/2023] [Indexed: 09/07/2023] Open
Abstract
Gene expression orchestration is a key question in fundamental and applied research. Different models for transcription regulation were proposed, yet the dynamic regulation of RNA polymerase II (RNAP II) activity remains a matter of debate. To improve our knowledge of this topic, we investigated RNAP II motility in eukaryotic cells by combining single particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) techniques, to take advantage of their different sensitivities in order to analyze together slow and fast molecular movements. Thanks to calibrated samples, we developed a benchmark for quantitative analysis of molecular dynamics, to eliminate the main potential instrumental biases. We applied this workflow to study the diffusion of RPB1, the catalytic subunit of RNAP II. By a cross-analysis of FCS and SPT, we could highlight different RPB1 motility states and identifyed a stationary state, a slow diffusion state, and two different modes of subdiffusion. Interestingly, our analysis also unveiled the oversampling by RPB1 of nuclear subdomains. Based on these data, we propose a novel model of spatio-temporal transcription regulation. Altogether, our results highlight the importance of combining microscopy approaches at different time scales to get a full insight into the real complexity of molecular kinetics in cells.
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Affiliation(s)
- Marie Fournier
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Pierre Leclerc
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Aymeric Leray
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS, Université de Bourgogne Franche Comte, Dijon, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Dorian Champelovier
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Florence Agbazahou
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Fatima Dahmani
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Gabriel Bidaux
- INSERM UMR 1060, CarMeN Laboratory, IHU OPERA, Hôpital Louis Pradel, Hospices Civils de Lyon, Univ Lyon1, Lyon, France
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France
| | - Alessandro Furlan
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France.
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 -CANTHER -Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, 59000, France.
- Unité Tumorigenèse et Résistance aux Traitements, Centre Oscar Lambret, 59000, Lille, France.
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France.
| | - Laurent Héliot
- Univ. Lille, CNRS, UMR 8523, PhLAM Laboratoire de Physique des Lasers, Atomes et Molécules, Lille, France.
- CNRS, Groupement de Recherche ImaBio, 59655, Villeneuve d'Ascq, France.
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3
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Yanagisawa M, Watanabe C, Yoshinaga N, Fujiwara K. Cell-Size Space Regulates the Behavior of Confined Polymers: From Nano- and Micromaterials Science to Biology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11811-11827. [PMID: 36125172 DOI: 10.1021/acs.langmuir.2c01397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polymer micromaterials in a liquid or gel phase covered with a surfactant membrane are widely used materials in pharmaceuticals, cosmetics, and foods. In particular, cell-sized micromaterials of biopolymer solutions covered with a lipid membrane have been studied as artificial cells to understand cells from a physicochemical perspective. The characteristics and phase transitions of polymers confined to a microscopic space often differ from those in bulk systems. The effect that causes this difference is referred to as the cell-size space effect (CSE), but the specific physicochemical factors remain unclear. This study introduces the analysis of CSE on molecular diffusion, nanostructure transition, and phase separation and presents their main factors, i.e., short- and long-range interactions with the membrane surface and small volume (finite element nature). This serves as a guide for determining the dominant factors of CSE. Furthermore, we also introduce other factors of CSE such as spatial closure and the relationships among space size, the characteristic length of periodicity, the structure size, and many others produced by biomolecular assemblies through the analysis of protein reaction-diffusion systems and biochemical reactions.
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Affiliation(s)
- Miho Yanagisawa
- Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
| | - Chiho Watanabe
- School of Integrated Arts and Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima 739-8521, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, National Institute of Advanced Industrial Science and Technology, Sendai 980-8577, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, Yokohama 223-8522, Japan
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4
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Maggs JE, Morales GJ. Time-integral iteration method for two-dimensional anomalous transport. Phys Rev E 2022; 106:045201. [PMID: 36397469 DOI: 10.1103/physreve.106.045201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
A methodology is developed to describe time-dependent phenomena associated with nonlocal transport in complex, two-dimensional geometries. It is an extension of the ''iterative method" introduced previously to solve steady-state transport problems [Maggs and Morales, Phys. Rev. E 99, 013307 (2019)10.1103/PhysRevE.99.013307], and it is based on the ''jumping particle" concepts associated with the continuous-time random walk (CTRW) model. The method presented explicitly evaluates the time integral contained in the CTRW master equation. A modified version of the Mittag-Leffler function is used for the waiting-time probability distributions to incorporate memory effects. Calculations of the propagation of ''anomalous transport waves" in various systems, with and without memory, illustrate the technique.
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Affiliation(s)
- J E Maggs
- Department of Physics and Astronomy, University of California, Los Angeles, California 90025, USA
| | - G J Morales
- Department of Physics and Astronomy, University of California, Los Angeles, California 90025, USA
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5
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Nieto Simavilla D, Ramakrishnan V, Smoukov SK, Venerus DC. Experimental investigation of anomalous molecular probe diffusion in entangled polymer melts. SOFT MATTER 2022; 18:6200-6208. [PMID: 35876110 DOI: 10.1039/d2sm00759b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Investigations on the diffusion of small molecules or particles in polymeric materials are important to numerous technologies and can also be used to gain insight on polymer chain dynamics. Systems where the probe size is comparable to (or smaller than) a characteristic length of the polymer chain, the tube diameter for example, are of particular interest because the diffusion coefficient of the probe can be orders of magnitude larger than the value predicted by the Stokes-Einstein relation. In the present study, we employ the optical technique known as forced Rayleigh scattering to study the diffusion of a molecular probe (dye) in several entangled polymer melts over a wide range of length and time scales. The probe size is much smaller than the tube diameter for the systems studied. We find the diffusion coefficient is larger by four to five orders of magnitude than the Stokes-Einstein prediction. More interestingly, we observe anomalous, non-Fickian, diffusion where the value of the measured diffusion coefficient can abruptly change by as much as 50%. We suggest that this unexpected behavior occurs when the time scale for diffusion is larger than the relaxation time associated with the constraint release mechanism for polymer chain dynamics.
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Affiliation(s)
- D Nieto Simavilla
- Basque Center for Applied Mathematics, 48009 Bilbao, Bizkaia (Basque-Country), Spain
| | - V Ramakrishnan
- SABIC, Plasticslaan 1, 4612PX Bergen op Zoom, The Netherlands
| | - S K Smoukov
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK
| | - D C Venerus
- Department of Chemical & Materials Engineering, New Jersey Institute of Technology, Newark, NJ 01072, USA.
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6
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Lu Y, Liu XY, Hu GH. Double-Spring Model for Nanoparticle Diffusion in a Polymer Network. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Lu
- School of Mechanics and Engineering Science, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200444, P. R. China
| | - Xin-Yue Liu
- School of Mechanics and Engineering Science, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200444, P. R. China
| | - Guo-Hui Hu
- School of Mechanics and Engineering Science, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200444, P. R. China
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7
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Molecular diffusion in ternary poly(vinyl alcohol) solutions. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-021-2121-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractThe diffusion kinetics of a molecular probe—rhodamine B—in ternary aqueous solutions containing poly(vinyl alcohol), glycerol, and surfactants was investigated using fluorescence correlation spectroscopy and dynamic light scattering. We show that the diffusion characteristics of rhodamine B in such complex systems is determined by a synergistic effect of molecular crowding and intermolecular interactions between chemical species. The presence of glycerol has no noticeable impact on rhodamine B diffusion at low concentration, but significantly slows down the diffusion of rhodamine B above 3.9% (w/v) due to a dominating steric inhibition effect. Furthermore, introducing surfactants (cationic/nonionic/anionic) to the system results in a decreased diffusion coefficient of the molecular probe. In solutions containing nonionic surfactant, this can be explained by an increased crowding effect. For ternary poly(vinyl alcohol) solutions containing cationic or anionic surfactant, surfactant—polymer and surfactant—rhodamine B interactions alongside the crowding effect of the molecules slow down the overall diffusivity of rhodamine B. The results advance our insight of molecular migration in a broad range of industrial complex formulations that incorporate multiple compounds, and highlight the importance of selecting the appropriate additives and surfactants in formulated products.
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8
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Yoshida S, Kisley L. Super-resolution fluorescence imaging of extracellular environments. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 257:119767. [PMID: 33862370 DOI: 10.1016/j.saa.2021.119767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
The extracellular matrix (ECM) is an important biophysical environment that plays a role in a number of physiological processes. The ECM is highly dynamic, with changes occurring as local, nanoscale, physicochemical variations in physical confinement and chemistry from the perspective of biological molecules. The length and time scale of ECM dynamics are challenging to measure with current spectroscopic techniques. Super-resolution fluorescence microscopy has the potential to probe local, nanoscale, physicochemical variations in the ECM. Here, we review super-resolution imaging and analysis methods and their application to study model nanoparticles and biomolecules within synthetic ECM hydrogels and the brain extracellular space (ECS). We provide a perspective of future directions for the field that can move super-resolution imaging of the ECM towards more biomedically-relevant samples. Overall, super-resolution imaging is a powerful tool that can increase our understanding of extracellular environments at new spatiotemporal scales to reveal ECM processes at the molecular-level.
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Affiliation(s)
- Shawn Yoshida
- Department of Physics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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9
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Mazzarotta A, Caputo TM, Raiola L, Battista E, Netti PA, Causa F. Small Oligonucleotides Detection in Three-Dimensional Polymer Network of DNA-PEG Hydrogels. Gels 2021; 7:90. [PMID: 34287281 PMCID: PMC8293047 DOI: 10.3390/gels7030090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 11/23/2022] Open
Abstract
The control of the three-dimensional (3D) polymer network structure is important for permselective materials when specific biomolecule detection is needed. Here we investigate conditions to obtain a tailored hydrogel network that combines both molecular filtering and molecular capture capabilities for biosensing applications. Along this line, short oligonucleotide detection in a displacement assay is set within PEGDA hydrogels synthetized by UV radical photopolymerization. To provide insights on the molecular filter capability, diffusion studies of several probes (sulforhodamine G and dextrans) with different hydrodynamic radii were carried out using NMR technique. Moreover, fluorometric analyses of hybridization of DNA oligonucleotides inside PEGDA hydrogels shed light on the mechanisms of recognition in 3D, highlighting that mesh size and crowding effect greatly impact the hybridization mechanism on a polymer network. Finally, we found the best probe density and diffusion transport conditions to allow the specific oligonucleotide capture and detection inside PEGDA hydrogels for oligonucleotide detection and the filtering out of higher molecular weight molecules.
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Affiliation(s)
- Alessia Mazzarotta
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy; (A.M.); (T.M.C.); (L.R.); (P.A.N.)
| | - Tania Mariastella Caputo
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy; (A.M.); (T.M.C.); (L.R.); (P.A.N.)
| | - Luca Raiola
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy; (A.M.); (T.M.C.); (L.R.); (P.A.N.)
| | - Edmondo Battista
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy;
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy; (A.M.); (T.M.C.); (L.R.); (P.A.N.)
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy;
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Filippo Causa
- Interdisciplinary Research Centre on Biomaterials (CRIB), Università degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy;
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI), University “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
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10
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Antenna Protein Clustering In Vitro Unveiled by Fluorescence Correlation Spectroscopy. Int J Mol Sci 2021; 22:ijms22062969. [PMID: 33804002 PMCID: PMC8000295 DOI: 10.3390/ijms22062969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 12/26/2022] Open
Abstract
Antenna protein aggregation is one of the principal mechanisms considered effective in protecting phototrophs against high light damage. Commonly, it is induced, in vitro, by decreasing detergent concentration and pH of a solution of purified antennas; the resulting reduction in fluorescence emission is considered to be representative of non-photochemical quenching in vivo. However, little is known about the actual size and organization of antenna particles formed by this means, and hence the physiological relevance of this experimental approach is questionable. Here, a quasi-single molecule method, fluorescence correlation spectroscopy (FCS), was applied during in vitro quenching of LHCII trimers from higher plants for a parallel estimation of particle size, fluorescence, and antenna cluster homogeneity in a single measurement. FCS revealed that, below detergent critical micelle concentration, low pH promoted the formation of large protein oligomers of sizes up to micrometers, and therefore is apparently incompatible with thylakoid membranes. In contrast, LHCII clusters formed at high pH were smaller and homogenous, and yet still capable of efficient quenching. The results altogether set the physiological validity limits of in vitro quenching experiments. Our data also support the idea that the small, moderately quenching LHCII oligomers found at high pH could be relevant with respect to non-photochemical quenching in vivo.
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11
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Otosu T, Yamaguchi S. Leaflet-specific Lipid Diffusion Revealed by Fluorescence Lifetime Correlation Analyses. CHEM LETT 2020. [DOI: 10.1246/cl.200539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
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12
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Li H, Zheng K, Yang J, Zhao J. Anomalous Diffusion Inside Soft Colloidal Suspensions Investigated by Variable Length Scale Fluorescence Correlation Spectroscopy. ACS OMEGA 2020; 5:11123-11130. [PMID: 32455234 PMCID: PMC7241028 DOI: 10.1021/acsomega.0c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/24/2020] [Indexed: 06/11/2023]
Abstract
The diffusion of molecules and particles inside the aqueous suspension of soft colloids (polymer microgels) is investigated using variable length scale fluorescence correlation spectroscopy (VLS-FCS). Carbopol 940 is chosen as the model matrix system, and two factors affecting diffusion are investigated: the spatial hindrance and the diffusant-matrix interaction. By studying diffusion of molecules and particles with different sizes inside the suspension, VLS-FCS reveals the restricted motion at a short length scale, that is, in the gaps between the microgels, and normal diffusion at a larger length scale. The information on the gap's length scale is also accessed. On the other hand, by tuning the pH value, the diffusant-matrix electrostatic attraction is adjusted and the results expose a short-time fast diffusion of probe molecules inside the gaps and a long-time restricted diffusion because of trapping inside the microgels. It is proved that VLS-FCS is a powerful method, investigating anomalous diffusion at different length scales and it is a promising approach to investigate diffusion in complex soft matter systems.
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Affiliation(s)
- Hengyi Li
- Beijing
National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The
University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaikai Zheng
- Beijing
National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The
University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Yang
- Beijing
National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The
University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Zhao
- Beijing
National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- The
University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Li Z, Yang J, Hollingsworth JV, Zhao J. Lateral diffusion of single polymer molecules at interfaces between water and oil. RSC Adv 2020; 10:16565-16569. [PMID: 35498844 PMCID: PMC9052869 DOI: 10.1039/d0ra02630a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/14/2020] [Indexed: 11/21/2022] Open
Abstract
Lateral diffusion of polymer molecules at the interfaces between immiscible oil and water is investigated at the single molecular level. The interfaces between water and alkanes are chosen as the model systems and polyethylene oxide (PEO) is the model polymer. Fluorescence correlation spectroscopy is used to measure the interfacial diffusion of fluorescence-labeled PEO with its molecular weight ranging over more than an order of magnitude. It is discovered that the interfacial diffusion coefficient scales with the molecular weight by the exponent of -0.5. Detailed analysis shows that the PEO chain takes an ideal two-dimensional random coil conformation at these fluidic interfaces and the bigger contribution from water's hydrodynamic friction is discovered.
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Affiliation(s)
- Zhuo Li
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | - Jingfa Yang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
| | | | - Jiang Zhao
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China .,University of Chinese Academy of Sciences Beijing 100049 China
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14
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Dong S, Tang X, Wang J, Zhang Z, Chen J, Lin Y, Xie S, Wang Z, Yang H. Self-assembly of lipid rafts revealed by fluorescence correlation spectroscopy in living breast cancer cells. JOURNAL OF BIOPHOTONICS 2020; 13:e201900214. [PMID: 31675171 DOI: 10.1002/jbio.201900214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 06/10/2023]
Abstract
Lipids and proteins in the plasma membrane are laterally heterogeneous and formalised as lipid rafts featuring unique biophysical properties. However, the self-assembly mechanism of lipid raft cannot be revealed even its physical properties and components were determined in specific physiological processes. In this study, two-photon generalised polarisation imaging and fluorescence correlation spectroscopy were used to study the fusion of lipid rafts through the membrane phase and the lateral diffusion of lipids in living breast cancer cells. A self-assembly model of lipid rafts associated with lipid diffusion and membrane phase was proposed to demonstrate the lipid sorting ability of lipid rafts in the plasma membrane. The results showed that the increased proportion of slow subdiffusion of GM1 -binding cholera toxin B-subunit (CT-B) was accompanied with an increased liquid-ordered domain during the β-estradiol-induced fusion of lipid rafts. And slow subdiffusion of CT-B was vanished with the depletion of lipid rafts. Whereas the dialkylindocarbocyanine (DiIC18 ) diffusion was not specifically regulated by lipid rafts. This study will open up a new insight for uncovering the self-assembly of lipid rafts in specific pathophysiological processes.
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Affiliation(s)
- Shiqing Dong
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Xiaoqiong Tang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Jiao Wang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Zhenghong Zhang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Jianling Chen
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Yao Lin
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Shusen Xie
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Hongqin Yang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, China
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15
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Dibak M, Fröhner C, Noé F, Höfling F. Diffusion-influenced reaction rates in the presence of pair interactions. J Chem Phys 2019; 151:164105. [PMID: 31675872 DOI: 10.1063/1.5124728] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi's volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction-diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction-diffusion equation in the steady state and derive semi-analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions.
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Affiliation(s)
- Manuel Dibak
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
| | - Christoph Fröhner
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
| | - Frank Noé
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
| | - Felix Höfling
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
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16
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Li X, Smith AW. Quantifying Lipid Mobility and Peptide Binding for Gram-Negative and Gram-Positive Model Supported Lipid Bilayers. J Phys Chem B 2019; 123:10433-10440. [DOI: 10.1021/acs.jpcb.9b09709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaosi Li
- Department of Chemistry, The University of Akron, 190 Buchtel Common, Akron, Ohio 44325-3601, United States
| | - Adam W. Smith
- Department of Chemistry, The University of Akron, 190 Buchtel Common, Akron, Ohio 44325-3601, United States
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17
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Aure RRL, Bernido CC, Carpio-Bernido MV, Bacabac RG. Damped White Noise Diffusion with Memory for Diffusing Microprobes in Ageing Fibrin Gels. Biophys J 2019; 117:1029-1036. [PMID: 31495446 PMCID: PMC6818180 DOI: 10.1016/j.bpj.2019.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 08/11/2019] [Accepted: 08/14/2019] [Indexed: 02/03/2023] Open
Abstract
From observations of colloidal tracer particles in fibrin undergoing gelation, we introduce an analytical framework that allows the determination of the probability density function for a stochastic process beyond fractional Brownian motion. Using passive microrheology via videomicroscopy, mean square displacements of tracer particles suspended in fibrin at different ageing times are obtained. The anomalous diffusion is then described by a damped white noise process with memory, with analytical results closely matching experimental plots of mean square displacements and probability density function. We further show that the white noise functional stochastic approach applied to passive microrheology reveals the existence of a gelation parameter μ which elucidates the dynamics of constrained tracer particles embedded in a time-dependent soft material. In addition, we found that microstructural heterogeneity of particle environments decreases as the ageing time increases. This study offers experimental insights on the ageing of fibrin gels while presenting a white noise functional stochastic approach that could be applied to other systems exhibiting non-Markovian diffusive behavior.
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Affiliation(s)
- Rev R L Aure
- Medical Biophysics Group, Department of Physics, University of San Carlos, Cebu City, Philippines; Department of Mathematics and Physics, Visayas State University, Baybay City, Leyte, Philippines
| | - Christopher C Bernido
- Theoretical and Computational Sciences and Engineering Group, Department of Physics, University of San Carlos, Cebu City, Philippines; Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol, Philippines.
| | - M Victoria Carpio-Bernido
- Theoretical and Computational Sciences and Engineering Group, Department of Physics, University of San Carlos, Cebu City, Philippines; Research Center for Theoretical Physics, Central Visayan Institute Foundation, Jagna, Bohol, Philippines
| | - Rommel G Bacabac
- Medical Biophysics Group, Department of Physics, University of San Carlos, Cebu City, Philippines
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18
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Gupta A, Sankaran J, Wohland T. Fluorescence correlation spectroscopy: The technique and its applications in soft matter. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2017-0104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
Fluorescence correlation spectroscopy (FCS) is a well-established single-molecule method used for the quantitative spatiotemporal analysis of dynamic processes in a wide range of samples. It possesses single-molecule sensitivity but provides ensemble averaged molecular parameters such as mobility, concentration, chemical reaction kinetics, photophysical properties and interaction properties. These parameters have been utilized to characterize a variety of soft matter systems. This review provides an overview of the basic principles of various FCS modalities, their instrumentation, data analysis, and the applications of FCS to soft matter systems.
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19
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Stolle MDN, Fradin C. Anomalous Diffusion in Inverted Variable-Lengthscale Fluorescence Correlation Spectroscopy. Biophys J 2019; 116:791-806. [PMID: 30782396 PMCID: PMC6400862 DOI: 10.1016/j.bpj.2019.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/12/2018] [Accepted: 01/14/2019] [Indexed: 11/24/2022] Open
Abstract
Using fluorescence correlation spectroscopy (FCS) to distinguish between different types of diffusion processes is often a perilous undertaking because the analysis of the resulting autocorrelation data is model dependant. Two recently introduced strategies, however, can help move toward a model-independent interpretation of FCS experiments: 1) the obtention of correlation data at different length scales and 2) their inversion to retrieve the mean-squared displacement associated with the process under study. We use computer simulations to examine the signature of several biologically relevant diffusion processes (simple diffusion, continuous-time random walk, caged diffusion, obstructed diffusion, two-state diffusion, and diffusing diffusivity) in variable-length-scale FCS. We show that, when used in concert, length-scale variation and data inversion permit us to identify non-Gaussian processes and, regardless of Gaussianity, to retrieve their mean-squared displacement over several orders of magnitude in time. This makes unbiased discrimination between different classes of diffusion models possible.
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Affiliation(s)
- Michael D N Stolle
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada.
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20
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Otosu T, Yamaguchi S. Quantifying the Diffusion of Lipids in the Proximal/Distal Leaflets of a Supported Lipid Bilayer by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy. J Phys Chem B 2018; 122:10315-10319. [DOI: 10.1021/acs.jpcb.8b08614] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Takuhiro Otosu
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Shoichi Yamaguchi
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
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21
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Zhokh A, Strizhak P. Non-Fickian Transport in Porous Media: Always Temporally Anomalous? Transp Porous Media 2018. [DOI: 10.1007/s11242-018-1066-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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22
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Kochmann S, Le ATH, Hili R, Krylov SN. Predicting efficiency of NECEEM‐based partitioning of protein binders from nonbinders in DNA‐encoded libraries. Electrophoresis 2018; 39:2991-2996. [DOI: 10.1002/elps.201800270] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Sven Kochmann
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - An T. H. Le
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular InteractionsYork University Toronto Ontario Canada
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23
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Hou R, Cherstvy AG, Metzler R, Akimoto T. Biased continuous-time random walks for ordinary and equilibrium cases: facilitation of diffusion, ergodicity breaking and ageing. Phys Chem Chem Phys 2018; 20:20827-20848. [PMID: 30066003 DOI: 10.1039/c8cp01863d] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We examine renewal processes with power-law waiting time distributions (WTDs) and non-zero drift via computing analytically and by computer simulations their ensemble and time averaged spreading characteristics. All possible values of the scaling exponent α are considered for the WTD ψ(t) ∼ 1/t1+α. We treat continuous-time random walks (CTRWs) with 0 < α < 1 for which the mean waiting time diverges, and investigate the behaviour of the process for both ordinary and equilibrium CTRWs for 1 < α < 2 and α > 2. We demonstrate that in the presence of a drift CTRWs with α < 1 are ageing and non-ergodic in the sense of the non-equivalence of their ensemble and time averaged displacement characteristics in the limit of lag times much shorter than the trajectory length. In the sense of the equivalence of ensemble and time averages, CTRW processes with 1 < α < 2 are ergodic for the equilibrium and non-ergodic for the ordinary situation. Lastly, CTRW renewal processes with α > 2-both for the equilibrium and ordinary situation-are always ergodic. For the situations 1 < α < 2 and α > 2 the variance of the diffusion process, however, depends on the initial ensemble. For biased CTRWs with α > 1 we also investigate the behaviour of the ergodicity breaking parameter. In addition, we demonstrate that for biased CTRWs the Einstein relation is valid on the level of the ensemble and time averaged displacements, in the entire range of the WTD exponent α.
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Affiliation(s)
- Ru Hou
- School of Mathematics and Statistics, Lanzhou University, Lanzhou 730000, China.
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24
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Harwardt MLIE, Dietz MS, Heilemann M, Wohland T. SPT and Imaging FCS Provide Complementary Information on the Dynamics of Plasma Membrane Molecules. Biophys J 2018; 114:2432-2443. [PMID: 29650369 PMCID: PMC6129459 DOI: 10.1016/j.bpj.2018.03.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/10/2018] [Accepted: 03/12/2018] [Indexed: 12/27/2022] Open
Abstract
The dynamics of biomolecules in the plasma membrane is of fundamental importance to understanding cellular processes. Cellular signaling often starts with extracellular ligand binding to a membrane receptor, which then transduces an intracellular signal. Ligand binding and receptor-complex activation often involve a complex rearrangement of proteins in the membrane, which results in changes in diffusion properties. Two widely used methods to characterize biomolecular diffusion are single-particle tracking (SPT) and imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS). Here, we compare the results of recovered diffusion coefficients and mean-square displacements of the two methods by simulations of free, domain-confined, or meshwork diffusion. We introduce, to our knowledge, a new method for the determination of confinement radii from ITIR-FCS data. We further establish and demonstrate simultaneous SPT/ITIR-FCS for direct comparison within living cells. Finally, we compare the results obtained by SPT and ITIR-FCS for the receptor tyrosine kinase MET. Our results show that SPT and ITIR-FCS yield complementary information on diffusion properties of biomolecules in cell membranes.
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Affiliation(s)
- Marie-Lena I E Harwardt
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Marina S Dietz
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt, Germany.
| | - Thorsten Wohland
- Departments of Biological Sciences and Chemistry, Center for Bioimaging Sciences, National University of Singapore, Singapore, Singapore.
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25
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Collini M, Bouzin M, Chirico G. Out of the Randomness: Correlating Noise in Biological Systems. Biophys J 2018; 114:2298-2307. [PMID: 29477335 PMCID: PMC6129560 DOI: 10.1016/j.bpj.2018.01.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 11/23/2022] Open
Abstract
The study of the dynamics of biological systems requires one to follow relaxation processes in time with micron-size spatial resolution. This need has led to the development of different fluorescence correlation techniques with high spatial resolution and a tremendous (from nanoseconds to seconds) temporal dynamic range. Spatiotemporal information can be obtained even on complex dynamic processes whose time evolution is not forecast by simple Brownian diffusion. Our discussion of the most recent applications of image correlation spectroscopy to the study of anomalous sub- or superdiffusion suggests that this field still requires the development of multidimensional image analyses based on analytical models or numerical simulations. We focus in particular on the framework of spatiotemporal image correlation spectroscopy and examine the critical steps in getting information on anomalous diffusive processes from the correlation maps. We point out how a dual space-time correlative analysis, in both the direct and the Fourier space, can provide quantitative information on superdiffusional processes when these are analyzed through an empirical model based on intermittent active dynamics. We believe that this dual space-time analysis, potentially amenable to mathematical treatment and to the exact fit of experimental data, could be extended to include the rich phenomenology of subdiffusive processes, thereby quantifying relevant parameters for the various motivating biological problems of interest.
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Affiliation(s)
- Maddalena Collini
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy; CNR-ISASI, Center for Complex Systems, Pozzuoli, Italy
| | - Margaux Bouzin
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Giuseppe Chirico
- Dipartimento di Fisica e Centro di Nanomedicina, Università degli Studi di Milano-Bicocca, Milan, Italy; CNR-ISASI, Center for Complex Systems, Pozzuoli, Italy.
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26
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Watanabe C, Yanagisawa M. Cell-size confinement effect on protein diffusion in crowded poly(ethylene)glycol solution. Phys Chem Chem Phys 2018. [PMID: 29542748 DOI: 10.1039/c7cp08199e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Micrometric membrane confinements and macromolecular crowding of cytoplasm are key factors that regulate molecular diffusion in live cells. Previous studies have shown that macromolecular crowding delays molecular diffusion. However, the effect of cell-size confinement on diffusion in the crowding environment is yet to be elucidated. Using fluorescence correlation spectroscopy (FCS), we analyzed protein diffusion in microdroplets containing polymer solution covered with lipid membranes that mimic cells. As a result, we found that a synergistic condition of crowding and micrometric confinement results in accelerated protein diffusion on a sub-millisecond time scale. This acceleration rate strongly depended on the size of the confined space and the degree of crowding. These findings indicate that cell-size confinement supports protein diffusion in highly crowded cytoplasm.
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Affiliation(s)
- Chiho Watanabe
- Department of Applied Physics, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
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27
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Nath P, Mangal R, Kohle F, Choudhury S, Narayanan S, Wiesner U, Archer LA. Dynamics of Nanoparticles in Entangled Polymer Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:241-249. [PMID: 29192503 DOI: 10.1021/acs.langmuir.7b03418] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mean square displacement ⟨r2⟩ of nanoparticle probes dispersed in simple isotropic liquids and in polymer solutions is interrogated using fluorescence correlation spectroscopy and single-particle tracking (SPT) experiments. Probe dynamics in different regimes of particle diameter (d), relative to characteristic polymer length scales, including the correlation length (ξ), the entanglement mesh size (a), and the radius of gyration (Rg), are investigated. In simple fluids and for polymer solutions in which d ≫ Rg, long-time particle dynamics obey random-walk statistics ⟨r2⟩:t, with the bulk zero-shear viscosity of the polymer solution determining the frictional resistance to particle motion. In contrast, in polymer solutions with d < Rg, polymer molecules in solution exert noncontinuum resistances to particle motion and nanoparticle probes appear to interact hydrodynamically only with a local fluid medium with effective drag comparable to that of a solution of polymer chain segments with sizes similar to those of the nanoparticle probes. Under these conditions, the nanoparticles exhibit orders of magnitude faster dynamics than those expected from continuum predictions based on the Stokes-Einstein relation. SPT measurements further show that when d > a, nanoparticle dynamics transition from diffusive to subdiffusive on long timescales, reminiscent of particle transport in a field with obstructions. This last finding is in stark contrast to the nanoparticle dynamics observed in entangled polymer melts, where X-ray photon correlation spectroscopy measurements reveal faster but hyperdiffusive dynamics. We analyze these results with the help of the hopping model for particle dynamics in polymers proposed by Cai et al. and, on that basis, discuss the physical origins of the local drag experienced by the nanoparticles in entangled polymer solutions.
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Affiliation(s)
| | - Rahul Mangal
- Department of Chemical Engineering, Indian Institute of Technology Kanpur , Kanpur, Uttar Pradesh 208016, India
| | | | | | - Suresh Narayanan
- Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60349, United States
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28
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Cherstvy AG, Nagel O, Beta C, Metzler R. Non-Gaussianity, population heterogeneity, and transient superdiffusion in the spreading dynamics of amoeboid cells. Phys Chem Chem Phys 2018; 20:23034-23054. [DOI: 10.1039/c8cp04254c] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
What is the underlying diffusion process governing the spreading dynamics and search strategies employed by amoeboid cells?
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Affiliation(s)
- Andrey G. Cherstvy
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Oliver Nagel
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Carsten Beta
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
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29
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Zhang X, Sisamakis E, Sozanski K, Holyst R. Nanoscopic Approach to Quantification of Equilibrium and Rate Constants of Complex Formation at Single-Molecule Level. J Phys Chem Lett 2017; 8:5785-5791. [PMID: 29131951 DOI: 10.1021/acs.jpclett.7b02742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Equilibrium and rate constants are key descriptors of complex-formation processes in a variety of chemical and biological reactions. However, these parameters are difficult to quantify, especially in the locally confined, heterogeneous, and dynamically changing living matter. Herein, we address this challenge by combining stimulated emission depletion (STED) nanoscopy with fluorescence correlation spectroscopy (FCS). STED reduces the length-scale of observation to tens of nanometres (2D)/attoliters (3D) and the time-scale to microseconds, with direct, gradual control. This allows one to distinguish diffusional and binding processes of complex-formation, even at reaction rates higher by an order of magnitude than in confocal FCS. We provide analytical autocorrelation formulas for probes undergoing diffusion-reaction processes under STED condition. We support the theoretical analysis of experimental STED-FCS data on a model system of dye-micelle, where we retrieve the equilibrium and rates constants. Our work paves a promising way toward quantitative characterization of molecular interactions in vivo.
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Affiliation(s)
- Xuzhu Zhang
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
| | | | - Krzysztof Sozanski
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
| | - Robert Holyst
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences , 01-224 Warsaw, Poland
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30
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Matse M, Chubynsky MV, Bechhoefer J. Test of the diffusing-diffusivity mechanism using near-wall colloidal dynamics. Phys Rev E 2017; 96:042604. [PMID: 29347613 DOI: 10.1103/physreve.96.042604] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 05/14/2023]
Abstract
The mechanism of diffusing diffusivity predicts that, in environments where the diffusivity changes gradually, the displacement distribution becomes non-Gaussian, even though the mean-square displacement grows linearly with time. Here, we report single-particle tracking measurements of the diffusion of colloidal spheres near a planar substrate. Because the local effective diffusivity is known, we have been able to carry out a direct test of this mechanism for diffusion in inhomogeneous media.
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Affiliation(s)
- Mpumelelo Matse
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Mykyta V Chubynsky
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - John Bechhoefer
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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31
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Fradin C. On the importance of protein diffusion in biological systems: The example of the Bicoid morphogen gradient. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1676-1686. [PMID: 28919007 DOI: 10.1016/j.bbapap.2017.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 08/16/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Morphogens are proteins that form concentration gradients in embryos and developing tissues, where they act as postal codes, providing cells with positional information and allowing them to behave accordingly. Bicoid was the first discovered morphogen, and remains one of the most studied. It regulates segmentation in flies, forming a striking exponential gradient along the anterior-posterior axis of early Drosophila embryos, and activating the transcription of multiple target genes in a concentration-dependent manner. In this review, the work done by us and by others to characterize the mobility of Bicoid in D. melanogaster embryos is presented. The central role played by the diffusion of Bicoid in both the establishment of the gradient and the activation of target genes is discussed, and placed in the context of the need for these processes to be all at once rapid, precise and robust. The Bicoid system, and morphogen gradients in general, remain amongst the most amazing examples of the coexistence, often observed in living systems, of small-scale disorder and large-scale spatial order. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Cécile Fradin
- Dept. of Physics and Astronomy, McMaster University, 1280 Main St W., Hamilton, ON L8S 4M1, Canada
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32
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33
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Jain R, Sebastian KL. Diffusing diffusivity: Rotational diffusion in two and three dimensions. J Chem Phys 2017; 146:214102. [PMID: 28576093 PMCID: PMC5453791 DOI: 10.1063/1.4984085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/11/2017] [Indexed: 11/14/2022] Open
Abstract
We consider the problem of calculating the probability distribution function (pdf) of angular displacement for rotational diffusion in a crowded, rearranging medium. We use the diffusing diffusivity model and following our previous work on translational diffusion [R. Jain and K. L. Sebastian, J. Phys. Chem. B 120, 3988 (2016)], we show that the problem can be reduced to that of calculating the survival probability of a particle undergoing Brownian motion, in the presence of a sink. We use the approach to calculate the pdf for the rotational motion in two and three dimensions. We also propose new dimensionless, time dependent parameters, αrot,2D and αrot,3D, which can be used to analyze the experimental/simulation data to find the extent of deviation from the normal behavior, i.e., constant diffusivity, and obtain explicit analytical expressions for them, within our model.
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Affiliation(s)
- Rohit Jain
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - K L Sebastian
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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34
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Ma YD, Luo KF. Anomalous and Normal Diffusion of Tracers in Crowded Environments: Effect of Size Disparity between Tracer and Crowders. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1609184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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35
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Krasowska M, Strzelewicz A, Dudek G, Cieśla M. Structure-diffusion relationship of polymer membranes with different texture. Phys Rev E 2017; 95:012155. [PMID: 28208504 DOI: 10.1103/physreve.95.012155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 11/07/2022]
Abstract
Two-dimensional diffusion in heterogenic composite membranes, i.e., materials comprising polymer with dispersed inorganic fillers, composed of ethylcellulose and magnetic powder is studied. In the experimental part, the morphology of membranes is described by the following characteristics: the amount of polymer matrix, the fractal dimension of polymer matrix, the average size of polymer matrix domains, the average number of obstacles in the proximity of each polymer matrix pixel. The simulation work concentrates on the motion of a particle in the membrane environment. The focus is set on the relationship between membranes morphology characterized by polymer matrix density, its fractal dimension, the average size of domains, and the average number of near obstacles and the characteristics of diffusive transport in them. The comparison of diffusion driven by Gaussian random walk and Lévy flights shows that the effective diffusion exponent at long time limits is subdiffusive and it does not depend on the details of the underlying random process causing diffusion. The analysis of the parameters describing the membrane structure shows that the most important factor for the diffusion character is the average size of a domain penetrated by diffusing particles. The presented results may be used in the design and preparation of membrane structures with specific diffusion properties.
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Affiliation(s)
- Monika Krasowska
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Ks. M. Strzody 9, 44-100 Gliwice, Poland
| | - Anna Strzelewicz
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Ks. M. Strzody 9, 44-100 Gliwice, Poland
| | - Gabriela Dudek
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, Ks. M. Strzody 9, 44-100 Gliwice, Poland
| | - Michał Cieśla
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-059 Kraków, Poland
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36
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Ernst M, John T, Guenther M, Wagner C, Schaefer UF, Lehr CM. A Model for the Transient Subdiffusive Behavior of Particles in Mucus. Biophys J 2017; 112:172-179. [PMID: 28076809 PMCID: PMC5233549 DOI: 10.1016/j.bpj.2016.11.900] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/28/2016] [Accepted: 11/21/2016] [Indexed: 10/20/2022] Open
Abstract
In this study we have applied a model to explain the reported subdiffusion of particles in mucus, based on the measured mean squared displacements (MSD). The model considers Brownian diffusion of particles in a confined geometry, made from permeable membranes. The applied model predicts a normal diffusive behavior at very short and long time lags, as observed in several experiments. In between these timescales, we find that the "subdiffusive" regime is only a transient effect, MSD∝τα,α<1. The only parameters in the model are the diffusion-coefficients at the limits of very short and long times, and the distance between the permeable membranes L. Our numerical results are in agreement with published experimental data for realistic assumptions of these parameters. Finally, we show that only particles with a diameter less than 40 nm are able to pass through a mucus layer by passive Brownian motion.
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Affiliation(s)
- Matthias Ernst
- Faculty of Engineering, Department of Applied Mathematics, University of Applied Sciences, Saarbrücken, Germany
| | - Thomas John
- Department of Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Marco Guenther
- Faculty of Engineering, Department of Applied Mathematics, University of Applied Sciences, Saarbrücken, Germany
| | - Christian Wagner
- Department of Experimental Physics, Saarland University, Saarbrücken, Germany; Physics and Materials Science Research Unit, University of Luxembourg, Luxembourg, Luxembourg
| | - Ulrich F Schaefer
- Department of Biopharmaceutics and Pharmaceutical Technology, Saarland University, Saarbrücken, Germany
| | - Claus-Michael Lehr
- Department of Biopharmaceutics and Pharmaceutical Technology, Saarland University, Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland, Saarland University, Saarbrücken, Germany.
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37
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Cherstvy AG, Metzler R. Anomalous diffusion in time-fluctuating non-stationary diffusivity landscapes. Phys Chem Chem Phys 2016; 18:23840-52. [DOI: 10.1039/c6cp03101c] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We investigate the diffusive and ergodic properties of massive and confined particles in a model disordered medium, in which the local diffusivity fluctuates in time while its mean has a power law dependence on the diffusion time.
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Affiliation(s)
- Andrey G. Cherstvy
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
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