1
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Kol R, Nachtergaele P, De Somer T, D’hooge DR, Achilias DS, De Meester S. Toward More Universal Prediction of Polymer Solution Viscosity for Solvent-Based Recycling. Ind Eng Chem Res 2022; 61:10999-11011. [PMID: 35941852 PMCID: PMC9354514 DOI: 10.1021/acs.iecr.2c01487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022]
Abstract
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The viscosity of polymer solutions is important for both
polymer
synthesis and recycling. Polymerization reactions can become hampered
by diffusional limitations once a viscosity threshold is reached,
and viscous solutions complicate the cleaning steps during the dissolution–precipitation
technique. Available experimental data is limited, which is more severe
for green solvents, justifying dedicated viscosity data recording
and interpretation. In this work, a systematic study is therefore
performed on the viscosity of polystyrene solutions, considering different
concentrations, temperatures, and conventional and green solvents.
The results show that for the shear rate range of 1–1000 s–1, the solutions with concentrations between 5 and
39 wt % display mainly Newtonian behavior, which is further confirmed
by the applicability of the segment-based Eyring-NRTL and Eyring-mNRF
models. Moreover, multivariate data analysis successfully predicts
the viscosity of polystyrene solutions under different conditions.
This approach will facilitate future data recording for other polymer–solvent
combinations while minimizing experimental effort.
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Affiliation(s)
- Rita Kol
- Laboratory for Circular Process Engineering (LCPE), Department of Green Chemistry and Technology, Ghent University, Graaf Karel De Goedelaan 5, 8500 Kortrijk, Belgium
- Laboratory of Polymer Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Pieter Nachtergaele
- Research Group STEN, Department of Green Chemistry & Technology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Tobias De Somer
- Laboratory for Circular Process Engineering (LCPE), Department of Green Chemistry and Technology, Ghent University, Graaf Karel De Goedelaan 5, 8500 Kortrijk, Belgium
| | - Dagmar R. D’hooge
- Laboratory for Chemical Technology (LCT) and Centre for Textiles Science and Engineering (CTSE), Department of Materials, Textiles and Chemical Engineering, Faculty of Engineering and Architecture, Ghent University, Technologiepark 125 and 70a, 9052 Zwijnaarde, Belgium
| | - Dimitris S. Achilias
- Laboratory of Polymer Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Steven De Meester
- Laboratory for Circular Process Engineering (LCPE), Department of Green Chemistry and Technology, Ghent University, Graaf Karel De Goedelaan 5, 8500 Kortrijk, Belgium
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2
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Karpińska A, Zgorzelska A, Kwapiszewska K, Hołyst R. Entanglement of polymer chains in hypertonic medium enhances the delivery of DNA and other biomacromolecules into cells. J Colloid Interface Sci 2022; 627:270-282. [PMID: 35849860 DOI: 10.1016/j.jcis.2022.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/08/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022]
Abstract
HYPOTHESIS Most experimental procedures applied in modern biology involve cargo delivering into cells. One of the ways to cargo introduction is osmotic-mediated intracellular vesicle swelling. However, its widespread use was hindered due to cargo size (<10 nm) and cell-type-related restrictions. We addressed the issue of the composition of colloidal loading solution to enhance the efficiency of cellular delivery. EXPERIMENTS We examined the effectiveness of colloidal loading solutions of varied compositions, including various types and sizes of polymers building osmotic pressure. We used confocal imaging coupled with fluorescence correlation spectroscopy to evaluate the introduction of polymers, proteins, nanoparticles, and DNA plasmids (cargos of sizes 1-175 nm) to cells representing eight cell lines: cancer, normal, epithelial, and mesenchymal ones. FINDINGS We found that cellular delivery effectiveness strongly correlates with the size and concentration of osmotic pressure building polymers and not with the high value of the osmotic pressure itself. We show that polymer solutions at the entangled regime of concentrations enhance the delivery of large biomacromolecules even of size 200 nm (DNA plasmids) into cells, including MDA-MB-231 cells - so far resistant to the osmotic procedure. We show that the colloid loading medium based on entangled polymer chains is a versatile cargo delivery tool for molecular biology.
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Affiliation(s)
- Aneta Karpińska
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
| | - Alicja Zgorzelska
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
| | - Karina Kwapiszewska
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
| | - Robert Hołyst
- Department of Soft Condensed Matter, Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland.
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3
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Kalwarczyk T, Bielec K, Burdzy K, Holyst R. Influence of molecular rebinding on the reaction rate of complex formation. Phys Chem Chem Phys 2021; 23:19343-19351. [PMID: 34524310 DOI: 10.1039/d1cp02820k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We simulated Brownian diffusion and reaction-diffusion processes to study the influence of molecular rebinding on the reaction rates of bimolecular reactions. We found that the number of rebinding events, Nreb, is proportional to the target's size and inversely proportional to the diffusion coefficient D and simulation time-step Δt. We found the proportionality constant close to π-1/2. We confirmed that Nreb is defined as a ratio of the activation-limited rate constant ka to the diffusion-limited rate constant, kD. We provide the formula describing the reactivity coefficient κ, modelling the transient-native complex transition for the activation-controlled reaction rates. We show that κ is proportional to (D/Δt)1/2. Finally, we apply our rebinding-including reaction rate model to the real reactions of photoacid dissociation and protein association. Based on literature data for both types of reactions, we found the Δt time-scale. We show that for the photodissociation of a proton, the Δt is equal to 171 ± 18 fs and the average number of rebinding events is approximately equal to 40. For proteins, Δt is of the order of 100 ps with around 20 rebinding events. In both cases the timescale is similar to the timescale of fluctuation of the solvent molecules surrounding the reactants; vibrations and bending in the case of photoacid dissociation and diffusional motion for proteins.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Bielec
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Burdzy
- Department of Mathematics, Box 354350, University of Washington, Seattle, WA 98195, USA
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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4
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Hutchinson RB, Chen X, Zhou N, Cavagnero S. Fluorescence Anisotropy Decays and Microscale-Volume Viscometry Reveal the Compaction of Ribosome-Bound Nascent Proteins. J Phys Chem B 2021; 125:6543-6558. [PMID: 34110829 PMCID: PMC8741338 DOI: 10.1021/acs.jpcb.1c04473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This work introduces a technology that combines fluorescence anisotropy decay with microscale-volume viscometry to investigate the compaction and dynamics of ribosome-bound nascent proteins. Protein folding in the cell, especially when nascent chains emerge from the ribosomal tunnel, is poorly understood. Previous investigations based on fluorescence anisotropy decay determined that a portion of the ribosome-bound nascent protein apomyoglobin (apoMb) forms a compact structure. This work, however, could not assess the size of the compact region. The combination of fluorescence anisotropy with microscale-volume viscometry, presented here, enables identifying the size of compact nascent-chain subdomains using a single fluorophore label. Our results demonstrate that the compact region of nascent apoMb contains 57-83 amino acids and lacks residues corresponding to the two native C-terminal helices. These amino acids are necessary for fully burying the nonpolar residues in the native structure, yet they are not available for folding before ribosome release. Therefore, apoMb requires a significant degree of post-translational folding for the generation of its native structure. In summary, the combination of fluorescence anisotropy decay and microscale-volume viscometry is a powerful approach to determine the size of independently tumbling compact regions of biomolecules. This technology is of general applicability to compact macromolecules linked to larger frameworks.
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Affiliation(s)
| | - Xi Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ningkun Zhou
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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5
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Agasty A, Wisniewska A, Kalwarczyk T, Koynov K, Holyst R. Macroscopic Viscosity of Polymer Solutions from the Nanoscale Analysis. ACS APPLIED POLYMER MATERIALS 2021; 3:2813-2822. [PMID: 34056617 PMCID: PMC8159165 DOI: 10.1021/acsapm.1c00348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 03/31/2021] [Indexed: 06/12/2023]
Abstract
The effective viscosity in polymer solutions probed by diffusion of nanoparticles depends on their size. It is a well-defined function of the probe size, the radius of gyration, mesh size (correlation length), activation energy, and its parameters. As the nanoparticle's size exceeds the radius of gyration of polymer coils, the effective viscosity approaches its macroscopic limiting value. Here, we apply the equation for effective viscosity in the macroscopic limit to the following polymer solutions: hydroxypropyl cellulose (HPC) in water, polymethylmethacrylate (PMMA) in toluene, and polyacrylonitrile (PAN) in dimethyl sulfoxide (DMSO). We compare them with previous data for PEG/PEO in water and PDMS in ethyl acetate. We determine polymer parameters from the measurements of the macroscopic viscosity in a wide range of average polymer molecular weights (24-300 kg/mol), temperatures (283-303 K), and concentrations (0.005-1.000 g/cm3). In addition, the polydispersity of polymers is taken into account in the appropriate molecular weight averaging functions. We provide the model applicable for the study of nanoscale probe diffusion in polymer solutions and macroscopic characterization of different polymer materials via rheological measurements.
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Affiliation(s)
- Airit Agasty
- Department
of Soft Matter, Institute of Physical Chemistry,
Polish Academy of Science, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Agnieszka Wisniewska
- Department
of Soft Matter, Institute of Physical Chemistry,
Polish Academy of Science, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Kalwarczyk
- Department
of Soft Matter, Institute of Physical Chemistry,
Polish Academy of Science, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Kaloian Koynov
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Robert Holyst
- Department
of Soft Matter, Institute of Physical Chemistry,
Polish Academy of Science, Kasprzaka 44/52, 01-224 Warsaw, Poland
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6
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Bubak G, Kwapiszewska K, Kalwarczyk T, Bielec K, Andryszewski T, Iwan M, Bubak S, Hołyst R. Quantifying Nanoscale Viscosity and Structures of Living Cells Nucleus from Mobility Measurements. J Phys Chem Lett 2021; 12:294-301. [PMID: 33346672 DOI: 10.1021/acs.jpclett.0c03052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the mobility of nano-objects in the eukaryotic cell nucleus, at multiple length-scales, is essential for dissecting nuclear structure-function relationships both in space and in time. Here, we demonstrate, using single-molecule fluorescent correlation spectroscopies, that motion of inert probes (proteins, polymers, or nanoparticles) with diameters ranging from 2.6 to 150 nm is mostly unobstructed in a nucleus. Supported by the analysis of electron tomography images, these results advocate the ∼150 nm-wide interchromosomal channels filled with the aqueous diluted protein solution. The nucleus is percolated by these channels to allow various cargos to migrate freely at the nanoscale. We determined the volume of interchromosomal channels in the HeLa cell nucleus to 237 ± 61 fL, which constitutes 34% of the cell nucleus volume. The volume fraction of mobile proteins in channels equals 16% ± 4%, and the concentration is 1 mM.
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Affiliation(s)
- Grzegorz Bubak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Bielec
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Andryszewski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Michalina Iwan
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Szymon Bubak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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7
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Potier M, Tea L, Benyahia L, Nicolai T, Renou F. Viscosity of Aqueous Polysaccharide Solutions and Selected Homogeneous Binary Mixtures. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c02157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mathieu Potier
- Le Mans Université, IMMM UMR-CNRS 6283, 72085 Le Mans Cedex 9, France
| | - Lingsam Tea
- Le Mans Université, IMMM UMR-CNRS 6283, 72085 Le Mans Cedex 9, France
| | - Lazhar Benyahia
- Le Mans Université, IMMM UMR-CNRS 6283, 72085 Le Mans Cedex 9, France
| | - Taco Nicolai
- Le Mans Université, IMMM UMR-CNRS 6283, 72085 Le Mans Cedex 9, France
| | - Frederic Renou
- Le Mans Université, IMMM UMR-CNRS 6283, 72085 Le Mans Cedex 9, France
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8
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Hess M, Gratz M, Remmer H, Webers S, Landers J, Borin D, Ludwig F, Wende H, Odenbach S, Tschöpe A, Schmidt AM. Scale-dependent particle diffusivity and apparent viscosity in polymer solutions as probed by dynamic magnetic nanorheology. SOFT MATTER 2020; 16:7562-7575. [PMID: 32716420 DOI: 10.1039/c9sm00747d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In several upcoming rheological approaches, including methods of micro- and nanorheology, the measurement geometry is of critical impact on the interpretation of the results. The relative size of the probe objects employed (as compared to the intrinsic length scales of the sample to be investigated) becomes of crucial importance, and there is increasing interest to investigate the dynamic processes and mobility in nanostructured materials. A combination of different rheological approaches based on the rotation of magnetically blocked nanoprobes is used to systematically investigate the size-dependent diffusion behavior in aqueous poly(ethylene glycol) (PEG) solutions with special attention paid to the relation of probe size to characteristic length scales within the polymer solutions. We employ two types of probe particles: nickel rods of hydrodynamic length Lh between 200 nm and 650 nm, and cobalt ferrite spheres with diameter dh between 13 nm and 23 nm, and examine the influence of particle size and shape on the nanorheological information obtained in model polymer solutions based on two related, dynamic-magnetic approaches. The results confirm that as long as the investigated solutions are not entangled, and the particles are much larger than the macromolecular correlation length, a good accordance between macroscopic and nanoscopic results, whereas a strong size-dependent response is observed in cases where the particles are of similar size or smaller than the radius of gyration Rg or the correlation length ξ of the polymer solution.
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Affiliation(s)
- Melissa Hess
- Institute of Physical Chemistry, Chemistry Department, Faculty of Mathematics and Natural Sciences, University of Cologne, Luxemburger Str. 116, D-50939 Köln, Germany.
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9
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Kwapiszewska K, Szczepański K, Kalwarczyk T, Michalska B, Patalas-Krawczyk P, Szymański J, Andryszewski T, Iwan M, Duszyński J, Hołyst R. Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines. J Phys Chem Lett 2020; 11:6914-6920. [PMID: 32787203 PMCID: PMC7450658 DOI: 10.1021/acs.jpclett.0c01748] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Metabolic reactions in living cells are limited by diffusion of reagents in the cytoplasm. Any attempt to quantify the kinetics of biochemical reactions in the cytosol should be preceded by careful measurements of the physical properties of the cellular interior. The cytoplasm is a complex, crowded fluid characterized by effective viscosity dependent on its structure at a nanoscopic length scale. In this work, we present and validate the model describing the cytoplasmic nanoviscosity, based on measurements in seven human cell lines, for nanoprobes ranging in diameters from 1 to 150 nm. Irrespective of cell line origin (epithelial-mesenchymal, cancerous-noncancerous, male-female, young-adult), we obtained a similar dependence of the viscosity on the size of the nanoprobes, with characteristic length-scales of 20 ± 11 nm (hydrodynamic radii of major crowders in the cytoplasm) and 4.6 ± 0.7 nm (radii of intercrowder gaps). Moreover, we revealed that the cytoplasm behaves as a liquid for length scales smaller than 100 nm and as a physical gel for larger length scales.
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Affiliation(s)
- Karina Kwapiszewska
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Krzysztof Szczepański
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Tomasz Kalwarczyk
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Bernadeta Michalska
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | | | - Jędrzej Szymański
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | - Tomasz Andryszewski
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Michalina Iwan
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Jerzy Duszyński
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | - Robert Hołyst
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
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10
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Agasty A, Wisniewska A, Kalwarczyk T, Koynov K, Holyst R. Scaling equation for viscosity of polydimethylsiloxane in ethyl acetate: From dilute to concentrated solutions. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Yeh JW, Taloni A, Sriram KK, Shen JP, Kao DY, Chou CF. Nanoconfinement-Induced DNA Reptating Motion and Analogy to Fluctuating Interfaces. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b02074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jia-Wei Yeh
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Alessandro Taloni
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- CNR-Consiglio Nazionale delle Ricerche, ISC, Via dei Taurini 19, 00185 Roma, Italy
| | - K. K. Sriram
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Jie-Pan Shen
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Der-You Kao
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Fu Chou
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
- Research Centre for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
- Genomics Research Centre, Academia Sinica, Taipei 11529, Taiwan
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12
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Makuch K, Hołyst R, Kalwarczyk T, Garstecki P, Brady JF. Diffusion and flow in complex liquids. SOFT MATTER 2020; 16:114-124. [PMID: 31702751 DOI: 10.1039/c9sm01119f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thermal motion of particles and molecules in liquids underlies many chemical and biological processes. Liquids, especially in biology, are complex due to structure at multiple relevant length scales. While diffusion in homogeneous simple liquids is well understood through the Stokes-Einstein relation, this equation fails completely in describing diffusion in complex media. Modeling, understanding, engineering and controlling processes at the nanoscale, most importantly inside living cells, requires a theoretical framework for the description of viscous response to allow predictions of diffusion rates in complex fluids. Here we use a general framework with the viscosity η(k) described by a function of wave vector in reciprocal space. We introduce a formulation that allows one to relate the rotational and translational diffusion coefficients and determine the viscosity η(k) directly from experiments. We apply our theory to provide a database for rotational diffusion coefficients of proteins/protein complexes in the bacterium E. coli. We also provide a database for the diffusion coefficient of proteins sliding along major grooves of DNA in E. coli. These parameters allow predictions of rate constants for association of proteins. In addition to constituting a theoretical framework for description of diffusion of probes and viscosity in complex fluids, the formulation that we propose should decrease substantially the cost of numerical simulations of transport in complex media by replacing the simulation of individual crowding particles with a continuous medium characterized by a wave-length dependent viscosity η(k).
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Affiliation(s)
- Karol Makuch
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland. and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - John F Brady
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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13
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Hess M, Roeben E, Rochels P, Zylla M, Webers S, Wende H, Schmidt AM. Size effects on rotational particle diffusion in complex fluids as probed by Magnetic Particle Nanorheology. Phys Chem Chem Phys 2019; 21:26525-26539. [PMID: 31778132 DOI: 10.1039/c9cp04083h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rheological approaches based on micro- or nanoscopic probe objects are of interest due to the low volume requirement, the option of spatially resolved probing, and the minimal-invasive nature often connected to such probes. For the study of microstructured systems or biological environments, such methods show potential for investigating the local, size-dependent diffusivity and particle-matrix interactions. For the latter, the relative length scale of the used probes compared to the size of the structural units of the matrix becomes relevant. In this study, a rotational-dynamic approach based on Magnetic Particle Nanorheology (MPN) is used to extract size- and frequency-dependent nanorheological properties by using an otherwise well-established polymer model system. We use magnetically blocked CoFe2O4 nanoparticles as tracers and systematically vary their hydrodynamic size by coating them with a silica shell. On the polymer side, we employ aqueous solutions of poly(ethylene glycol) (PEG) by varying molar mass M and volume fraction φ. The complex Brownian relaxation behavior of the tracer particles in solutions of systematically varied composition is investigated by means of AC susceptometry (ACS), and the results provide access to frequency dependent rheological properties. The size-dependent particle diffusivity is evaluated based on theoretical descriptions and macroscopic measurements. The results allow the classification of the investigated compositions into three regimes, taking into account the probe particle size and the length scales of the polymer solution. While a fuzzy cross-over is indicated between the well-known macroscopic behavior and structurally dominated spectra, where the hydrodynamic radius is equal to the radius of gyration of the polymer (rh ∼ Rg), the frequency-related scaling behavior is dominated by the correlation length ξ respectively by the tube diameter a in entangled solutions for rh < Rg.
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Affiliation(s)
- Melissa Hess
- Institute of Physical Chemistry, Chemistry Department, Faculty of Mathematics and Natural Sciences, University of Cologne, Luxemburger Str. 116, D-50939 Köln, Germany.
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14
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Gratz M, Tschöpe A. Size Effects in the Oscillatory Rotation Dynamics of Ni Nanorods in Poly(ethylene oxide) Solutions. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00788] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Micha Gratz
- Experimentalphysik, Universität des Saarlandes, Campus D2 2, 66123 Saarbrücken, Germany
| | - Andreas Tschöpe
- Experimentalphysik, Universität des Saarlandes, Campus D2 2, 66123 Saarbrücken, Germany
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15
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Qing J, Chen A, Zhao N. Quantifying the protein-protein association rate in polymer solutions: crowding-induced diffusion and energy modifications. Phys Chem Chem Phys 2019; 20:27937-27948. [PMID: 30379153 DOI: 10.1039/c8cp05203d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A theoretical framework is developed to study protein-protein association in polymer solutions under diffusion-limited conditions. Starting from the basal association rate, two fundamental aspects concerning macromolecular crowding are particularly taken into account. One is the effect of microviscosity on protein diffusion. The length-scale dependent relations of translational and rotational diffusion coefficients are incorporated. Another is relevant to the crowding-induced effective interaction between the pair of proteins. The resultant energy modifications to the basal association rate are properly introduced, following an instructive classification with increasing crowder size: repulsive interaction dominant, repulsive and attractive interactions competitive, and attractive interaction prevailing. With specific energy modification terms, we are able to investigate the deviations of the association rate from the Stokes-Einstein (SE) behavior (i.e., the linear relationship with respect to the reciprocal of macroviscosity) in a quantitative manner. Our theory is applied to study the association of TEM1-β-lactamase (TEM) and the β-lactamase inhibitor protein (BLIP) in polyethylene glycol (PEG) solutions, with varying concentration and polymerization. We explicitly evaluate the relative association rate constant as a function of the solution macroviscosity. The theoretical results demonstrate very good agreement with the experimental data. Moreover, the complicated non-trivial deviations, either positive (slower than SE) or negative (faster than SE), are systematically rationalized. The precise role of energy modifications and the microviscosity effect on diffusion, in particular on rotational diffusion, are clearly unraveled.
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Affiliation(s)
- Jing Qing
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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16
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Bian Y, Yan R, Li P, Zhao N. Unusual crowding-induced chain looping kinetics in hard-sphere fluids: a contrastive study with polymer solutions. SOFT MATTER 2019; 15:4976-4988. [PMID: 31173026 DOI: 10.1039/c9sm00400a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A theoretical framework is developed to investigate the looping kinetics of a chain in hard-sphere (HS) fluids, based on a generalized Smoluchowski diffusion-reaction equation. A contrastive study with polymer solutions is performed. The crowding-associated effective viscosity and collapse effects are properly taken into account, which obey different scaling relations in HS and polymer fluids. We examine the dependence of the looping time on both concentration and size of crowders, demonstrating unusual and distinct discrepancies in the two crowded media. Firstly, in the solution of large polymers, the looping rate grows monotonically with polymer concentration. On the other hand, in the solution of large HSs, a caging regime can be observed, where the looping time tends to the value in the absence of crowders. Secondly, polymers in moderate size generally impede chain looping due to the enhanced viscosity. However, in HS fluids, the looping time exhibits a rather complicated variation with increasing HS size. We show a possible mechanism where in the case of small crowders with a relatively strong compaction in the probed chain, the looping kinetics can be facilitated. As the crowder size increases, the collapse effect is reduced and looping is dominated by viscosity-induced inhibition. Simultaneously, our theory rationalizes another possibility of the mechanism observed by recent simulation work. We conclude that the looping kinetics in specific systems actually should be governed by the critical competition between the two crowding factors. By giving reasonable measurements of effective viscosity and collapse, our theoretical framework can provide a unified strategy to analyze crowding effects on the looping rate in a systematic manner.
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Affiliation(s)
- Yukun Bian
- College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
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17
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Yuan C, Chen A, Zhang B, Zhao N. Activity–crowding coupling effect on the diffusion dynamics of a self-propelled particle in polymer solutions. Phys Chem Chem Phys 2019; 21:24112-24125. [DOI: 10.1039/c9cp04498a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The anomalous diffusion dynamics of an active particle in polymer solutions is studied based on a Langevin Brownian dynamics simulation.
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Affiliation(s)
- Chengli Yuan
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Anpu Chen
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Bingjie Zhang
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Nanrong Zhao
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
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18
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Bian Y, Cao X, Li P, Zhao N. Understanding chain looping kinetics in polymer solutions: crowding effects of microviscosity and collapse. SOFT MATTER 2018; 14:8060-8072. [PMID: 30255917 DOI: 10.1039/c8sm01499j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A theoretical framework based on a generalized Langevin equation with fractional Gaussian noise is presented to describe the looping kinetics of chains in polymer solutions. Particular attention is paid to quantitatively revealing crowding effects on the loop formation rate in terms of microviscosity and collapse. By the aid of empirical relations for these two crowding associated physical quantities, we explicitly investigate the relationship between the looping rate and polymer concentration, the degree of polymerization, and system parameters. According to our analysis, the dependence of the looping rate on the crowder volume fraction exhibits three typical regimes: monotonic decreasing, a non-monotonic trend and monotonic increasing. We reveal that these non-trivial behaviors can be attributed to the competition between the two opposing factors of viscosity-associated inhibition and collapse-induced facilitation of loop formation. We apply our theory to analyze the kinetics of single-stranded DNA hairpin base pairing in polyethylene glycol solutions. The theoretical results can reproduce the experimental data on the closing rate of hairpins quantitatively to a certain degree with reasonable fitting parameters. The unexpected increase of the closing rate upon the addition of increasing amounts of polymer is well rationalised. Such good agreements clearly demonstrate the validity of our theory, appropriately addressing the very role of crowding effects in the relevant kinetics.
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Affiliation(s)
- Yukun Bian
- College of Physical Science and Technology, Sichuan University, Chengdu 610064, China
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19
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Abstract
The motion of small probe molecules in a two-dimensional system containing frozen polymer chains was studied by means of Monte Carlo simulations. The model macromolecules were coarse-grained and restricted to vertices of a triangular lattice. The cooperative motion algorithm was used to generate representative configurations of macromolecular systems of different polymer concentrations. The remaining unoccupied lattice sites of the system were filled with small molecules. The structure of the polymer film, especially near the percolation threshold, was determined. The dynamic lattice liquid algorithm was then employed for studies of the dynamics of small objects in the polymer matrix. The influence of chain length and polymer concentration on the mobility and the character of motion of small molecules were studied. Short- and long-time dynamic behaviors of solvent molecules were also described. Conditions of anomalous diffusions' appearance in such systems are discussed. The influence of the structure of the matrix of obstacles on the molecular transport was discussed.
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Affiliation(s)
- Piotr Polanowski
- Department of Molecular Physics, Technical University of Łódź, 90-924 Łódź, Poland
| | - Andrzej Sikorski
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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20
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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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21
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Chen A, Zhao N, Hou Z. The effect of hydrodynamic interactions on nanoparticle diffusion in polymer solutions: a multiparticle collision dynamics study. SOFT MATTER 2017; 13:8625-8635. [PMID: 29115361 DOI: 10.1039/c7sm01854a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The diffusion of nanoparticles (NPs) in polymer solutions is studied by a combination of a mesoscale simulation method, multiparticle collision dynamics (MPCD), and molecular dynamics (MD) simulations. We investigate the long-time diffusion coefficient D as well as the subdiffusive behavior in the intermediate time region. The dependencies of both D and subdiffusion factor α on NP size and polymer concentration, respectively, are explicitly calculated. Particular attention is paid to the role of hydrodynamic interaction (HI) in the NP diffusion dynamics. Our simulation results show that the long-time diffusion coefficients satisfy perfectly the scaling relation found by experimental observations. Meanwhile, the subdiffusive factor decreases with the increase in polymer concentration but is of little relevance to the NP size. By parallel simulations with and without HI, we reveal that HI will generally enhance D, while the enhancement effect is non-monotonous with increasing polymer concentration, and it becomes most pronounced at semidilute concentrations. With the aid of a scaling law based on the diffusive activation energy model, we understand that HI affects diffusion through decreasing the diffusive activation energy on the one hand while increasing the effective diffusion size on the other. In addition, HI will certainly influence the subdiffusive behavior of the NP, leading to a larger subdiffusion exponent.
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Affiliation(s)
- Anpu Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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22
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Maldonado-Camargo L, Yang C, Rinaldi C. Scale-dependent rotational diffusion of nanoparticles in polymer solutions. NANOSCALE 2017; 9:12039-12050. [PMID: 28795729 DOI: 10.1039/c7nr01603d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
It is shown that the rotational diffusivity of nanoparticles in polymer solutions spanning the dilute to semi-dilute regimes deviates from the predictions of the Stokes-Einstein (SE) relationship, and that this deviation can be explained by the existence of a polymer depletion layer with the viscosity of the bath solvent. The measurements of the rotational diffusion coefficient of poly(ethylene glycol) (PEG) grafted magnetic nanoparticles in PEG solutions spanning the dilute to semi-dilute regimes and a wide range of polymer molecular weights were obtained from the dynamic magnetic response of the nanoparticles to alternating magnetic fields. Experimental rotational diffusion coefficient values were compared with those predicted by the SE relation using the macroscopic viscosity of the polymer solutions and the hydrodynamic radius of the nanoparticles. Deviations between experimental and SE rotational diffusivity values were observed for nanoparticles in polymer solutions where the radius of gyration of the polymer exceeded the hydrodynamic radius of the particles. A simple model for the rotational hydrodynamic drag on a particle surrounded by a polymer depletion layer was found to describe the experimental rotational diffusivities well, suggesting that the observed phenomenon arises due to the formation of a polymer depletion layer around the nanoparticles.
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Affiliation(s)
- Lorena Maldonado-Camargo
- Department of Chemical Engineering, University of Florida, P.O. Box 116005, Gainesville, FL 32603, USA.
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23
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Wisniewska A, Sozanski K, Kalwarczyk T, Kedra-Krolik K, Holyst R. Scaling Equation for Viscosity of Polymer Mixtures in Solutions with Application to Diffusion of Molecular Probes. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00545] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Agnieszka Wisniewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Sozanski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Karolina Kedra-Krolik
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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24
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Qing J, Chen A, Zhao N. A new scaling for the rotational diffusion of molecular probes in polymer solutions. Phys Chem Chem Phys 2017; 19:32687-32697. [DOI: 10.1039/c7cp07047k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present work, we propose a new scaling form for the rotational diffusion coefficient of molecular probes in semi-dilute polymer solutions, based on a theoretical study.
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Affiliation(s)
- Jing Qing
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Anpu Chen
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
| | - Nanrong Zhao
- College of Chemistry
- Sichuan University
- Chengdu 610064
- China
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25
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Rheological properties of graphene/nylon 6 nanocomposites prepared by masterbatch melt mixing. JOURNAL OF POLYMER RESEARCH 2016. [DOI: 10.1007/s10965-016-1144-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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26
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Feng X, Chen A, Wang J, Zhao N, Hou Z. Understanding Protein Diffusion in Polymer Solutions: A Hydration with Depletion Model. J Phys Chem B 2016; 120:10114-10123. [DOI: 10.1021/acs.jpcb.6b06248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Xiaoqing Feng
- College
of Chemistry, Sichuan University, Chengdu 610064, China
| | - Anpu Chen
- College
of Chemistry, Sichuan University, Chengdu 610064, China
| | - Juan Wang
- College
of Chemistry, Sichuan University, Chengdu 610064, China
| | - Nanrong Zhao
- College
of Chemistry, Sichuan University, Chengdu 610064, China
| | - Zhonghuai Hou
- Hefei National Laboratory for Physical Sciences at the Microscale & Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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27
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Motion of Molecular Probes and Viscosity Scaling in Polyelectrolyte Solutions at Physiological Ionic Strength. PLoS One 2016; 11:e0161409. [PMID: 27536866 PMCID: PMC4990340 DOI: 10.1371/journal.pone.0161409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/04/2016] [Indexed: 11/19/2022] Open
Abstract
We investigate transport properties of model polyelectrolyte systems at physiological ionic strength (0.154 M). Covering a broad range of flow length scales-from diffusion of molecular probes to macroscopic viscous flow-we establish a single, continuous function describing the scale dependent viscosity of high-salt polyelectrolyte solutions. The data are consistent with the model developed previously for electrically neutral polymers in a good solvent. The presented approach merges the power-law scaling concepts of de Gennes with the idea of exponential length scale dependence of effective viscosity in complex liquids. The result is a simple and applicable description of transport properties of high-salt polyelectrolyte solutions at all length scales, valid for motion of single molecules as well as macroscopic flow of the complex liquid.
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28
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Keshavarz M, Engelkamp H, Xu J, Braeken E, Otten MBJ, Uji-I H, Schwartz E, Koepf M, Vananroye A, Vermant J, Nolte RJM, De Schryver F, Maan JC, Hofkens J, Christianen PCM, Rowan AE. Nanoscale Study of Polymer Dynamics. ACS NANO 2016; 10:1434-1441. [PMID: 26688072 DOI: 10.1021/acsnano.5b06931] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The thermal motion of polymer chains in a crowded environment is anisotropic and highly confined. Whereas theoretical and experimental progress has been made, typically only indirect evidence of polymer dynamics is obtained either from scattering or mechanical response. Toward a complete understanding of the complicated polymer dynamics in crowded media such as biological cells, it is of great importance to unravel the role of heterogeneity and molecular individualism. In the present work, we investigate the dynamics of synthetic polymers and the tube-like motion of individual chains using time-resolved fluorescence microscopy. A single fluorescently labeled polymer molecule is observed in a sea of unlabeled polymers, giving access to not only the dynamics of the probe chain itself but also to that of the surrounding network. We demonstrate that it is possible to extract the characteristic time constants and length scales in one experiment, providing a detailed understanding of polymer dynamics at the single chain level. The quantitative agreement with bulk rheology measurements is promising for using local probes to study heterogeneity in complex, crowded systems.
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Affiliation(s)
- Masoumeh Keshavarz
- High Field Magnet Laboratory (HFML - EMFL), Radboud University , Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
- Institute for Molecules and Materials, Department of Molecular Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans Engelkamp
- High Field Magnet Laboratory (HFML - EMFL), Radboud University , Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200 F, B-3001 Heverlee, Belgium
| | - Jialiang Xu
- Institute for Molecules and Materials, Department of Molecular Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Els Braeken
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200 F, B-3001 Heverlee, Belgium
| | - Matthijs B J Otten
- Institute for Molecules and Materials, Department of Molecular Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hiroshi Uji-I
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200 F, B-3001 Heverlee, Belgium
| | - Erik Schwartz
- Institute for Molecules and Materials, Department of Molecular Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Matthieu Koepf
- Institute for Molecules and Materials, Department of Molecular Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Anja Vananroye
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200 F, B-3001 Heverlee, Belgium
| | - Jan Vermant
- Department of Chemical Engineering, Katholieke Universiteit Leuven , de Croylaan 46, B-3001 Heverlee, Belgium
- Department of Materials - Hönggerberg, ETH Zürich , Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| | - Roeland J M Nolte
- Institute for Molecules and Materials, Department of Molecular Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Frans De Schryver
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200 F, B-3001 Heverlee, Belgium
| | - Jan C Maan
- High Field Magnet Laboratory (HFML - EMFL), Radboud University , Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Johan Hofkens
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven , Celestijnenlaan 200 F, B-3001 Heverlee, Belgium
- Nano-Science Center/Department of Chemistry, University of Copenhagen , Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Peter C M Christianen
- High Field Magnet Laboratory (HFML - EMFL), Radboud University , Toernooiveld 7, NL-6525 ED Nijmegen, The Netherlands
| | - Alan E Rowan
- Institute for Molecules and Materials, Department of Molecular Materials, Radboud University , Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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29
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Sozański K, Ruhnow F, Wiśniewska A, Tabaka M, Diez S, Hołyst R. Small Crowders Slow Down Kinesin-1 Stepping by Hindering Motor Domain Diffusion. PHYSICAL REVIEW LETTERS 2015; 115:218102. [PMID: 26636875 DOI: 10.1103/physrevlett.115.218102] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Indexed: 05/23/2023]
Abstract
The dimeric motor protein kinesin-1 moves processively along microtubules against forces of up to 7 pN. However, the mechanism of force generation is still debated. Here, we point to the crucial importance of diffusion of the tethered motor domain for the stepping of kinesin-1: small crowders stop the motor at a viscosity of 5 mPa·s-corresponding to a hydrodynamic load in the sub-fN (~10^{-4} pN) range-whereas large crowders have no impact even at viscosities above 100 mPa·s. This indicates that the scale-dependent, effective viscosity experienced by the tethered motor domain is a key factor determining kinesin's functionality. Our results emphasize the role of diffusion in the kinesin-1 stepping mechanism and the general importance of the viscosity scaling paradigm in nanomechanics.
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Affiliation(s)
- Krzysztof Sozański
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Felix Ruhnow
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstrasse 18, 01307 Dresden, Germany
| | - Agnieszka Wiśniewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Stefan Diez
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Arnoldstrasse 18, 01307 Dresden, Germany
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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30
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Kalwarczyk T, Sozanski K, Ochab-Marcinek A, Szymanski J, Tabaka M, Hou S, Holyst R. Motion of nanoprobes in complex liquids within the framework of the length-scale dependent viscosity model. Adv Colloid Interface Sci 2015; 223:55-63. [PMID: 26189602 DOI: 10.1016/j.cis.2015.06.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 06/27/2015] [Accepted: 06/27/2015] [Indexed: 01/12/2023]
Abstract
This paper deals with the recent phenomenological model of the motion of nanoscopic objects (colloidal particles, proteins, nanoparticles, molecules) in complex liquids. We analysed motion in polymer, micellar, colloidal and protein solutions and the cytoplasm of living cells using the length-scale dependent viscosity model. Viscosity monotonically approaches macroscopic viscosity as the size of the object increases and thus gives a single, coherent picture of motion at the nano and macro scale. The model includes interparticle interactions (solvent-solute), temperature and the internal structure of a complex liquid. The depletion layer ubiquitously occurring in complex liquids is also incorporated into the model. We also discuss the biological aspects of crowding in terms of the length-scale dependent viscosity model.
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Affiliation(s)
- Tomasz Kalwarczyk
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Sozanski
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Anna Ochab-Marcinek
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Jedrzej Szymanski
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; State Key Laboratory of Medicinal Chemical Biology, Nankai University, China
| | - Robert Holyst
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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