1
|
Bujdák J. Controversial Issues Related to Dye Adsorption on Clay Minerals: A Critical Review. Molecules 2023; 28:6951. [PMID: 37836793 PMCID: PMC10574638 DOI: 10.3390/molecules28196951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
This critical review points out the most serious and problematic issues to be found in the literature on the adsorption of dyes on clay minerals. The introduction draws attention to the fundamental problems, namely the insufficient characterization of adsorbents, the influence of impurities on the adsorption of dyes, and the choice of inappropriate models for the description of the very complex systems that clay minerals and their systems represent. This paper discusses the main processes accompanying adsorption in colloidal systems of clay minerals. The relationship between the stability of the colloidal systems and the adsorption of dye molecules is analyzed. The usual methodological procedures for determining and evaluating the adsorption of dyes are critically reviewed. A brief overview and examples of modified clay minerals and complex systems for the adsorption of organic dyes are summarized. This review is a guide for avoiding some faults in characterizing the adsorption of organic dyes on clay minerals, to improve the procedure for determining adsorption, to evaluate results correctly, and to find an appropriate theoretical interpretation. The main message of this article is a critical analysis of the current state of the research in this field, but at the same time, it is a guide on how to avoid the most common problems and mistakes.
Collapse
Affiliation(s)
- Juraj Bujdák
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15 Bratislava, Slovakia; ; Tel.: +421-2-9014-9602
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, 845 36 Bratislava, Slovakia
| |
Collapse
|
2
|
Huang TX, Dong B, Filbrun SL, Okmi AA, Cheng X, Yang M, Mansour N, Lei S, Fang N. Single-molecule photocatalytic dynamics at individual defects in two-dimensional layered materials. SCIENCE ADVANCES 2021; 7:eabj4452. [PMID: 34597131 PMCID: PMC10938566 DOI: 10.1126/sciadv.abj4452] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
The insightful comprehension of in situ catalytic dynamics at individual structural defects of two-dimensional (2D) layered material, which is crucial for the design of high-performance catalysts via defect engineering, is still missing. Here, we resolved single-molecule trajectories resulted from photocatalytic activities at individual structural features (i.e., basal plane, edge, wrinkle, and vacancy) in 2D layered indium selenide (InSe) in situ to quantitatively reveal heterogeneous photocatalytic dynamics and surface diffusion behaviors. The highest catalytic activity was found at vacancy in a four-layer InSe, up to ~30× higher than that on the basal plane. Moreover, lower adsorption strength of reactant and slower dissociation/diffusion rates of product were found at more photocatalytic active defects. These distinct dynamic properties are determined by lattice structures/electronic energy levels of defects and layer thickness of supported InSe. Our findings shed light on the fundamental understanding of photocatalysis at defects and guide the rational defect engineering.
Collapse
Affiliation(s)
- Teng-Xiang Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Bin Dong
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Seth L. Filbrun
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Aisha Ahmad Okmi
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Xiaodong Cheng
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Meek Yang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Nourhan Mansour
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Sidong Lei
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| |
Collapse
|
3
|
Çam M, Lichter S, Goedde CG. Kink propagation and solute partitioning in an atomic monolayer on a substrate. Phys Rev E 2021; 104:L022801. [PMID: 34525584 DOI: 10.1103/physreve.104.l022801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 11/07/2022]
Abstract
When a monolayer of Lennard-Jones atoms is driven by an external force over an atomically spaced lattice, the atoms do not move in the direction of the force. By considering monolayers containing a solvent and two different solutes, we show that the different atomic species follow distinct directions and so partition from one another and from the solvent. The strength of the driving force is chosen so that at any instant, most atoms are stationary while only a small fraction propagates as solitary waves. In this regime, the mean velocity of the layer is due to the nonzero contribution from merely a few atoms. We also present a simple theory, based on the probability that an atom in the monolayer will hop from one equilibrium location to the next, that explains the distinct directions of atomic migration.
Collapse
Affiliation(s)
- Metehan Çam
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Seth Lichter
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Christopher G Goedde
- Department of Physics and Astrophysics, DePaul University, Chicago, Illinois 60614, USA
| |
Collapse
|
4
|
Kosztołowicz T. Boundary conditions at a thin membrane that generate non-Markovian normal diffusion. Phys Rev E 2020; 102:022123. [PMID: 32942412 DOI: 10.1103/physreve.102.022123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
We show that some boundary conditions assumed at a thin membrane may result in normal diffusion not being the stochastic Markov process. We consider boundary conditions defined in terms of the Laplace transform in which there is a linear combination of probabilities and probability fluxes defined on both membrane surfaces. The coefficients of the combination may depend on the Laplace transform parameter. Such boundary conditions are most commonly used when considering diffusion in a membrane system unless collective or nonlocal processes in particles diffusion occur. We find Bachelier-Smoluchowski-Chapmann-Kolmogorov (BSCK) equation in terms of the Laplace transform and we derive the criterion to check whether the boundary conditions lead to fundamental solutions of diffusion equation satisfying this equation. If the BSCK equation is not met, then the Markov property is broken. When a probability flux is continuous at the membrane, the general forms of the boundary conditions for which the fundamental solutions meet the BSCK equation are derived. A measure of broken of semi-group property is also proposed. The relation of this measure to the non-Markovian property measure is discussed.
Collapse
Affiliation(s)
- Tadeusz Kosztołowicz
- Institute of Physics, Jan Kochanowski University, Uniwersytecka 7, 25-406 Kielce, Poland
| |
Collapse
|
5
|
Hedayati M, Kipper MJ, Krapf D. Anomalous protein kinetics on low-fouling surfaces. Phys Chem Chem Phys 2020; 22:5264-5271. [PMID: 32095800 DOI: 10.1039/d0cp00326c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, protein-surface interactions were probed in terms of adsorption and desorption of a model protein, bovine serum albumin, on a low-fouling surface with single-molecule localization microscopy. Single-molecule experiments enable precise determination of both adsorption and desorption rates. Strikingly the experimental data show anomalous desorption kinetics, evident as a surface dwell time that exhibits a power-law distribution, i.e. a heavy-tailed rather than the expected exponential distribution. As a direct consequence of this heavy-tailed distribution, the average desorption rate depends upon the time scale of the experiment and the protein surface concentration does not reach equilibrium. Further analysis reveals that the observed anomalous desorption emerges due to the reversible formation of a small fraction of soluble protein multimers (small oligomers), such that each one desorbs from the surface with a different rate. The overall kinetics can be described by a series of elementary reactions, yielding simple scaling relations that predict experimental observations. This work reveals a mechanistic origin for anomalous desorption kinetics that can be employed to interpret observations where low-protein fouling surfaces eventually foul when in long-term contact with protein solutions. The work also provides new insights that can be used to define design principles for non-fouling surfaces and to predict their performance.
Collapse
Affiliation(s)
- Mohammadhasan Hedayati
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | - Matt J Kipper
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523, USA. and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA. and School of Advanced Materials Discovery, Colorado State University, Fort Collins, CO 80523, USA
| | - Diego Krapf
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA. and School of Advanced Materials Discovery, Colorado State University, Fort Collins, CO 80523, USA and Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
6
|
Masoliver J, Lindenberg K. Two-dimensional telegraphic processes and their fractional generalizations. Phys Rev E 2020; 101:012137. [PMID: 32069616 DOI: 10.1103/physreve.101.012137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Indexed: 11/07/2022]
Abstract
We study the planar motion of telegraphic processes. We derive the two-dimensional telegrapher's equation for isotropic and uniform motions starting from a random walk model which is the two-dimensional version of the multistate random walk with a continuum number of states representing the spatial directions. We generalize the isotropic model and the telegrapher's equation to include planar fractional motions. Earlier, we worked with the one-dimensional version [Masoliver, Phys. Rev. E 93, 052107 (2016)PREHBM2470-004510.1103/PhysRevE.93.052107] and derived the three-dimensional version [Masoliver, Phys. Rev. E 96, 022101 (2017)PREHBM2470-004510.1103/PhysRevE.96.022101]. An important lesson is that we cannot obtain the two-dimensional version from the three-dimensional or the one-dimensional one from the two-dimensional result. Each dimension must be approached starting from an appropriate random walk model for that dimension.
Collapse
Affiliation(s)
- Jaume Masoliver
- Department of Condensed Matter Physics and Institute of Complex Systems (UBICS), University of Barcelona, 08028 Catalonia, Spain
| | - Katja Lindenberg
- Department of Chemistry and Biochemistry and BioCircuits Institute, University of California, San Diego 92093-0340, USA
| |
Collapse
|
7
|
Chien FT, Lin PK, Chien W, Hung CH, Yu MH, Chou CF, Chen YL. Crowding-facilitated macromolecular transport in attractive micropost arrays. Sci Rep 2017; 7:1340. [PMID: 28465594 PMCID: PMC5430964 DOI: 10.1038/s41598-017-01248-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/27/2017] [Indexed: 11/18/2022] Open
Abstract
Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium. Furthermore, we employed hidden Markov analysis to determine the transition of macromolecular adsorption-desorption on posts and hopping between posts. The apparent free energy barriers are comparable to theoretical estimates determined from polymer conformational fluctuations.
Collapse
Affiliation(s)
- Fan-Tso Chien
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC.,Department of Life Science, National Dong Hwa University, Hualien, Taiwan, ROC
| | - Po-Keng Lin
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC
| | - Wei Chien
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC.,Department of Physics, National Taiwan University, Taipei, Taiwan, ROC
| | - Cheng-Hsiang Hung
- Department of Physics, National Taiwan University, Taipei, Taiwan, ROC
| | - Ming-Hung Yu
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC
| | - Chia-Fu Chou
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC
| | - Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan, ROC. .,Department of Physics, National Taiwan University, Taipei, Taiwan, ROC. .,Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan, ROC.
| |
Collapse
|
8
|
Piscitelli A, Pica Ciamarra M. Escape rate and diffusion of a Stochastically Driven particle. Sci Rep 2017; 7:41442. [PMID: 28120904 PMCID: PMC5264591 DOI: 10.1038/srep41442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/19/2016] [Indexed: 02/03/2023] Open
Abstract
The dynamical properties of a tracer repeatedly colliding with heat bath particles can be described within a Langevin framework provided that the tracer is more massive than the bath particles, and that the collisions are frequent. Here we consider the escape of a particle from a potential well, and the diffusion coefficient in a periodic potential, without making these assumptions. We have thus investigated the dynamical properties of a Stochastically Driven particle that moves under the influence of the confining potential in between successive collisions with the heat bath. In the overdamped limit, both the escape rate and the diffusion coefficient coincide with those of a Langevin particle. Conversely, in the underdamped limit the two dynamics have a different temperature dependence. In particular, at low temperature the Stochastically Driven particle has a smaller escape rate, but a larger diffusion coefficient.
Collapse
Affiliation(s)
- Antonio Piscitelli
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Massimo Pica Ciamarra
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore.,CNR-SPIN, Dipartimento di Scienze Fisiche, Università di Napoli Federico II, I-80126, Napoli, Italy
| |
Collapse
|
9
|
Krapf D, Campagnola G, Nepal K, Peersen OB. Strange kinetics of bulk-mediated diffusion on lipid bilayers. Phys Chem Chem Phys 2016; 18:12633-41. [PMID: 27095275 PMCID: PMC4861227 DOI: 10.1039/c6cp00937a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Diffusion at solid-liquid interfaces is crucial in many technological and biophysical processes. Although its behavior seems to be deceivingly simple, recent studies showing passive superdiffusive transport suggest that diffusion on surfaces may hide rich complexities. In particular, bulk-mediated diffusion occurs when molecules are transiently released from the surface to perform three-dimensional excursions into the liquid bulk. This phenomenon bears the dichotomy where a molecule always return to the surface but the mean jump length is infinite. Such behavior is associated with a breakdown of the central limit theorem and weak ergodicity breaking. Here, we use single-particle tracking to study the statistics of bulk-mediated diffusion on a supported lipid bilayer. We find that the time-averaged mean square displacement (MSD) of individual trajectories, the archetypal measure in diffusion processes, does not converge to the ensemble MSD but it remains a random variable, even in the long observation-time limit. The distribution of time averages is shown to agree with a Lévy flight model. Our results also unravel intriguing anomalies in the statistics of displacements. The time-averaged MSD is shown to depend on experimental time and investigations of fractional moments show a scaling 〈|r(t)|(q)〉∼t(qν(q)) with non-linear exponents, i.e. ν(q) ≠ const. This type of behavior is termed strong anomalous diffusion and is rare among experimental observations.
Collapse
Affiliation(s)
- Diego Krapf
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO 80523, USA.
| | | | | | | |
Collapse
|
10
|
Wang D, Chin HY, He C, Stoykovich MP, Schwartz DK. Polymer Surface Transport Is a Combination of in-Plane Diffusion and Desorption-Mediated Flights. ACS Macro Lett 2016; 5:509-514. [PMID: 35607234 DOI: 10.1021/acsmacrolett.6b00183] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous studies of polymer motion at solid/liquid interfaces described the transport in the context of a continuous time random walk (CTRW) process, in which diffusion switches between desorption-mediated "flights" (i.e., hopping) and surface-adsorbed waiting-time intervals. However, it has been unclear whether the waiting times represented periods of complete immobility or times during which molecules engaged in a different (e.g., slower or confined) mode of interfacial transport. Here we designed high-throughput, single-molecule tracking measurements to address this question. Specifically, we studied polymer dynamics on either chemically homogeneous or nanopatterned surfaces (hexagonal diblock copolymer films) with chemically distinct domains, where polymers were essentially excluded from the low-affinity domains, eliminating the possibility of significant continuous diffusion in the absence of desorption-mediated flights. Indeed, the step-size distributions on homogeneous surfaces exhibited an additional diffusive mode that was missing on the chemically heterogeneous nanopatterned surfaces, confirming the presence of a slow continuous mode due to 2D in-plane diffusion. Kinetic Monte Carlo simulations were performed to test this model and, with the theoretical in-plane diffusion coefficient of D2D = 0.20 μm2/s, we found a good agreement between simulations and experimental data on both chemically homogeneous and nanopatterned surfaces.
Collapse
Affiliation(s)
- Dapeng Wang
- Department of Chemical and
Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Huai-Ying Chin
- Department of Chemical and
Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Chunlin He
- Department of Chemical and
Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Mark P. Stoykovich
- Department of Chemical and
Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Daniel K. Schwartz
- Department of Chemical and
Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| |
Collapse
|
11
|
Matsuda Y, Hanasaki I, Iwao R, Yamaguchi H, Niimi T. Faster Convergence of Diffusion Anisotropy Detection by Three-Step Relation of Single-Particle Trajectory. Anal Chem 2016; 88:4502-7. [PMID: 26980574 DOI: 10.1021/acs.analchem.6b00390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We focus on the issue of limited number of samples in the single particle tracking (SPT) when trying to extract the diffusion anisotropy that originates from the particle asymmetry. We propose a novel evaluation technique of SPT making use of the relation of the consecutive three steps. More specifically, the trend of the angle comprised of the three positions and the displacements are plotted on a scatter diagram. The particle anisotropy dependence of the shape of the scatter diagram is examined through the data from the standard numerical model of anisotropic two-dimensional Brownian motion. Comparison with the existing method reveals the faster convergence in the evaluation. In particular, our proposed method realizes the detection of diffusion anisotropy under the conditions of not only less number of data but also larger time steps. This is of practical importance not only when the abundant data is hard to achieve but also when the rotational diffusion is fast compared to the frame rate of the camera equipment, which tends to be more common for smaller particles or molecules of interest.
Collapse
Affiliation(s)
- Yu Matsuda
- Institute of Materials and Systems for Sustainability, Nagoya University , Furo-cho, Chikusa, Nagoya, Aichi 464-8603, Japan
| | - Itsuo Hanasaki
- Department of Mechanical Systems Engineering, Tokyo University of Agriculture and Technology , Naka-cho 2-24-16, Koganei, Tokyo 184-8588, Japan
| | - Ryo Iwao
- Department of Micro-Nano Systems Engineering, Nagoya University , Furo-cho, Chikusa, Nagoya, Aichi 464-8603, Japan
| | - Hiroki Yamaguchi
- Department of Micro-Nano Systems Engineering, Nagoya University , Furo-cho, Chikusa, Nagoya, Aichi 464-8603, Japan
| | - Tomohide Niimi
- Department of Micro-Nano Systems Engineering, Nagoya University , Furo-cho, Chikusa, Nagoya, Aichi 464-8603, Japan
| |
Collapse
|
12
|
Cherstvy AG, Metzler R. Ergodicity breaking and particle spreading in noisy heterogeneous diffusion processes. J Chem Phys 2016; 142:144105. [PMID: 25877560 DOI: 10.1063/1.4917077] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We study noisy heterogeneous diffusion processes with a position dependent diffusivity of the form D(x) ∼ D0|x|(α0) in the presence of annealed and quenched disorder of the environment, corresponding to an effective variation of the exponent α in time and space. In the case of annealed disorder, for which effectively α0 = α0(t), we show how the long time scaling of the ensemble mean squared displacement (MSD) and the amplitude variation of individual realizations of the time averaged MSD are affected by the disorder strength. For the case of quenched disorder, the long time behavior becomes effectively Brownian after a number of jumps between the domains of a stratified medium. In the latter situation, the averages are taken over both an ensemble of particles and different realizations of the disorder. As physical observables, we analyze in detail the ensemble and time averaged MSDs, the ergodicity breaking parameter, and higher order moments of the time averages.
Collapse
Affiliation(s)
- Andrey G Cherstvy
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| |
Collapse
|
13
|
Weltz JS, Schwartz DK, Kaar JL. Surface-Mediated Protein Unfolding as a Search Process for Denaturing Sites. ACS NANO 2016; 10:730-738. [PMID: 26580418 DOI: 10.1021/acsnano.5b05787] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Surface-induced protein denaturation has important implications for the development of materials that are resistant and/or innocuous to biomolecules. Here, we studied the mechanism of lysozyme (T4L) unfolding on fused silica (FS) using single-molecule methods that provided direct insight into the cause of denaturation. Unfolding of T4L was monitored by Förster resonance energy transfer while simultaneously tracking the adsorption, diffusion, and desorption of individual molecules at the solid-solution interface. Results of high-throughput single-molecule analysis suggested that the unfolding of T4L on FS was mediated by surface diffusion and occurred on isolated nanoscale sites, which were relatively rare and distinct from the majority of the surface. These observations suggest that surface-mediated protein unfolding is a search process that is based on the exploration for denaturing sites by the protein. Ultimately, these findings have important implications for the design of protein-compatible surfaces.
Collapse
Affiliation(s)
- James S Weltz
- Department of Chemical and Biological Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado , Boulder, Colorado 80309, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado , Boulder, Colorado 80309, United States
| |
Collapse
|
14
|
Mardoukhi Y, Jeon JH, Metzler R. Geometry controlled anomalous diffusion in random fractal geometries: looking beyond the infinite cluster. Phys Chem Chem Phys 2015; 17:30134-47. [PMID: 26503611 DOI: 10.1039/c5cp03548a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We investigate the ergodic properties of a random walker performing (anomalous) diffusion on a random fractal geometry. Extensive Monte Carlo simulations of the motion of tracer particles on an ensemble of realisations of percolation clusters are performed for a wide range of percolation densities. Single trajectories of the tracer motion are analysed to quantify the time averaged mean squared displacement (MSD) and to compare this with the ensemble averaged MSD of the particle motion. Other complementary physical observables associated with ergodicity are studied, as well. It turns out that the time averaged MSD of individual realisations exhibits non-vanishing fluctuations even in the limit of very long observation times as the percolation density approaches the critical value. This apparent non-ergodic behaviour concurs with the ergodic behaviour on the ensemble averaged level. We demonstrate how the non-vanishing fluctuations in single particle trajectories are analytically expressed in terms of the fractal dimension and the cluster size distribution of the random geometry, thus being of purely geometrical origin. Moreover, we reveal that the convergence scaling law to ergodicity, which is known to be inversely proportional to the observation time T for ergodic diffusion processes, follows a power-law ∼T(-h) with h < 1 due to the fractal structure of the accessible space. These results provide useful measures for differentiating the subdiffusion on random fractals from an otherwise closely related process, namely, fractional Brownian motion. Implications of our results on the analysis of single particle tracking experiments are provided.
Collapse
Affiliation(s)
- Yousof Mardoukhi
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany.
| | | | | |
Collapse
|
15
|
Sun X, Xiao S, Deng H, Hu W. Diffusion mechanisms at the Pb solid–liquid interface: Atomic level point of view. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.05.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
16
|
Akimoto T, Seki K. Transition from distributional to ergodic behavior in an inhomogeneous diffusion process: Method revealing an unknown surface diffusivity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022114. [PMID: 26382351 DOI: 10.1103/physreve.92.022114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Indexed: 06/05/2023]
Abstract
Diffusion of molecules in cells plays an important role in providing a biological reaction on the surface by finding a target on the membrane surface. The water retardation (slow diffusion) near the target assists the searching molecules to recognize the target. Here, we consider effects of the surface diffusivity on the effective diffusivity, where diffusion on the surface is slower than that in bulk. We show that the ensemble-averaged mean-square displacements increase linearly with time when the desorption rate from the surface is finite, which is valid even when the diffusion on the surface is anomalous (subdiffusion). Moreover, this slow diffusion on the surface affects the fluctuations of the time-averaged mean-square displacements (TAMSDs). We find that fluctuations of the TAMSDs remain large when the measurement time is smaller than a characteristic time, and decays according to an increase of the measurement time for a relatively large measurement time. Therefore, we find a transition from nonergodic (distributional) to ergodic diffusivity in a target search process. Moreover, this fluctuation analysis provides a method to estimate an unknown surface diffusivity.
Collapse
Affiliation(s)
- Takuma Akimoto
- Department of Mechanical Engineering, Keio University, Yokohama, 223-8522, Japan
| | - Kazuhiko Seki
- Nanosystem Research Institute, AIST, Tsukuba, 305-8565, Japan
| |
Collapse
|
17
|
Metzler R, Jeon JH, Cherstvy AG, Barkai E. Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking. Phys Chem Chem Phys 2014; 16:24128-64. [DOI: 10.1039/c4cp03465a] [Citation(s) in RCA: 1046] [Impact Index Per Article: 104.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This Perspective summarises the properties of a variety of anomalous diffusion processes and provides the necessary tools to analyse and interpret recorded anomalous diffusion data.
Collapse
Affiliation(s)
- Ralf Metzler
- Institute of Physics and Astronomy
- University of Potsdam
- Potsdam-Golm, Germany
- Physics Department
- Tampere University of Technology
| | - Jae-Hyung Jeon
- Physics Department
- Tampere University of Technology
- Tampere, Finland
- Korean Institute for Advanced Study (KIAS)
- Seoul, Republic of Korea
| | - Andrey G. Cherstvy
- Institute of Physics and Astronomy
- University of Potsdam
- Potsdam-Golm, Germany
| | - Eli Barkai
- Physics Department and Institute of Nanotechnology and Advanced Materials
- Bar-Ilan University
- Ramat Gan, Israel
| |
Collapse
|
18
|
Jeon JH, Chechkin AV, Metzler R. Scaled Brownian motion: a paradoxical process with a time dependent diffusivity for the description of anomalous diffusion. Phys Chem Chem Phys 2014; 16:15811-7. [DOI: 10.1039/c4cp02019g] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|