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Biophysical Journal Mar 2019Using fluorescence correlation spectroscopy (FCS) to distinguish between different types of diffusion processes is often a perilous undertaking because the analysis of...
Using fluorescence correlation spectroscopy (FCS) to distinguish between different types of diffusion processes is often a perilous undertaking because the analysis of the resulting autocorrelation data is model dependant. Two recently introduced strategies, however, can help move toward a model-independent interpretation of FCS experiments: 1) the obtention of correlation data at different length scales and 2) their inversion to retrieve the mean-squared displacement associated with the process under study. We use computer simulations to examine the signature of several biologically relevant diffusion processes (simple diffusion, continuous-time random walk, caged diffusion, obstructed diffusion, two-state diffusion, and diffusing diffusivity) in variable-length-scale FCS. We show that, when used in concert, length-scale variation and data inversion permit us to identify non-Gaussian processes and, regardless of Gaussianity, to retrieve their mean-squared displacement over several orders of magnitude in time. This makes unbiased discrimination between different classes of diffusion models possible.
Topics: Diffusion; Models, Theoretical; Spectrometry, Fluorescence
PubMed: 30782396
DOI: 10.1016/j.bpj.2019.01.024 -
Physical Review Letters Jun 2023We introduce a simple model of diffusive jump process where a fee is charged for each jump. The nonlinear cost function is such that slow jumps incur a flat fee, while...
We introduce a simple model of diffusive jump process where a fee is charged for each jump. The nonlinear cost function is such that slow jumps incur a flat fee, while for fast jumps the cost is proportional to the velocity of the jump. The model-inspired by the way taxi meters work-exhibits a very rich behavior. The cost for trajectories of equal length and equal duration exhibits giant fluctuations at a critical value of the scaled distance traveled. Furthermore, the full distribution of the cost until the target is reached exhibits an interesting "freezing" transition in the large-deviation regime. All the analytical results are corroborated by numerical simulations. Our results also apply to elastic systems near the depinning transition, when driven by a random force.
Topics: Diffusion; Algorithms
PubMed: 37354426
DOI: 10.1103/PhysRevLett.130.237102 -
Small (Weinheim An Der Bergstrasse,... Apr 2023The rapid development of microscopic techniques over the past decades enables the establishment of single molecule fluorescence imaging as a powerful tool in biological...
The rapid development of microscopic techniques over the past decades enables the establishment of single molecule fluorescence imaging as a powerful tool in biological and biomedical sciences. Single molecule fluorescence imaging allows to study the chemical, physicochemical, and biological properties of target molecules or particles by tracking their molecular position in the biological environment and determining their dynamic behavior. However, the precise determination of particle distribution and diffusivities is often challenging due to high molecule/particle densities, fast diffusion, and photobleaching/blinking of the fluorophore. A novel, accurate, and fast statistical analysis tool, Diffusion Analysis of NAnoscopic Ensembles (DANAE), that solves all these obstacles is introduced. DANAE requires no approximations or any a priori input regarding unknown system-inherent parameters, such as background distributions; a requirement that is vitally important when studying the behavior of molecules/particles in living cells. The superiority of DANAE with various data from simulations is demonstrated. As experimental applications of DANAE, membrane receptor diffusion in its natural membrane environment, and cargo mobility/distribution within nanostructured lipid nanoparticles are presented. Finally, the method is extended to two-color channel fluorescence microscopy.
Topics: Microscopy, Fluorescence; Single Molecule Imaging; Nanotechnology; Diffusion
PubMed: 36670094
DOI: 10.1002/smll.202206722 -
The Journal of Physical Chemistry. B Apr 2016It has been found in many experiments that the mean square displacement of a Brownian particle x(T) diffusing in a rearranging environment is strictly Fickian, obeying...
It has been found in many experiments that the mean square displacement of a Brownian particle x(T) diffusing in a rearranging environment is strictly Fickian, obeying ⟨(x(T))(2)⟩ ∝ T, but the probability distribution function for the displacement is not Gaussian. An explanation of this is that the diffusivity of the particle itself is changing as a function of time. Models for this diffusing diffusivity have been solved analytically in the limit of small time, but simulations were necessary for intermediate and large times. We show that one of the diffusing diffusivity models is equivalent to Brownian motion in the presence of a sink and introduce a class of models for which it is possible to find analytical solutions. Our solution gives ⟨(x(T))(2)⟩ ∝ T for all times and at short times the probability distribution function of the displacement is exponential which crosses over to a Gaussian in the limit of long times and large displacements.
Topics: Diffusion; Models, Theoretical; Normal Distribution
PubMed: 27029607
DOI: 10.1021/acs.jpcb.6b01527 -
Science (New York, N.Y.) Feb 1964Fluorescein-sodium, a fluorescent tracer whose molecular weight is 376, diffuses rather freely from the interior of one cell to another in a gland epithelium...
Fluorescein-sodium, a fluorescent tracer whose molecular weight is 376, diffuses rather freely from the interior of one cell to another in a gland epithelium (Drosophila) but does not diffuse along the intercellular space to the exterior. The permeability of the junctional surfaces of the cell membranes appears to be high, in contrast to the nonjunctional surfaces and intercellular spaces which represent strong diffusion barriers.
Topics: Animals; Cell Biology; Cell Membrane; Diffusion; Drosophila; Epithelium; Fluoresceins; Research; Salivary Glands
PubMed: 14090146
DOI: 10.1126/science.143.3609.959 -
Analytical and Bioanalytical Chemistry Oct 2002The physical and chemical properties of complex non-oxide ceramic materials require advanced methods of diffusivity determination. In this study, we present a method... (Review)
Review
The physical and chemical properties of complex non-oxide ceramic materials require advanced methods of diffusivity determination. In this study, we present a method based on the high-dose ion implantation of stable tracers in combination with secondary ion mass spectroscopy for depth profiling. The analytical basics, advantages and problems of the method are discussed for two examples of complex materials, the Si-B-C-N precursor ceramics and the Ti-based transition metal diborides. We demonstrate that is possible to measure the temperature dependence of diffusivities, especially for ceramic systems with low diffusivities, for systems that contain elements for which no suitable radioactive tracers exist for extended measurements.
Topics: Ceramics; Diffusion; Radioactive Tracers; Spectrometry, Mass, Secondary Ion; Temperature
PubMed: 12397474
DOI: 10.1007/s00216-002-1536-z -
Electrophoresis May 2020Diffusion of colored dye on water saturated paper substrates has been traditionally exploited with great skill by renowned water color artists. The same physics finds...
Diffusion of colored dye on water saturated paper substrates has been traditionally exploited with great skill by renowned water color artists. The same physics finds more recent practical applications in paper-based diagnostic devices deploying chemicals that react with a bodily fluid yielding colorimetric signals for disease detection. During spontaneous imbibition through the tortuous pathways of a porous electrolyte saturated paper matrix, a dye molecule undergoes diffusion in a complex network of pores. The advancing front forms a strongly correlated interface that propagates diffusively but with an enhanced effective diffusivity. We measure this effective diffusivity and show that it is several orders of magnitude greater than the free solution diffusivity and has a significant dependence on the solution pH and salt concentration in the background electrolyte. We attribute this to electrically mediated interfacial interactions between the ionic species in the liquid dye and spontaneous surface charges developed at porous interfaces, and introduce a simple theory to explain this phenomenon.
Topics: Capillary Action; Colorimetry; Coloring Agents; Diffusion; Electrolytes; Electrophoresis; Paper; Porosity
PubMed: 31991501
DOI: 10.1002/elps.201900409 -
The Journal of Cell Biology May 2023Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis...
Single-particle tracking microscopy is a powerful technique to investigate how proteins dynamically interact with their environment in live cells. However, the analysis of tracks is confounded by noisy molecule localization, short tracks, and rapid transitions between different motion states, notably between immobile and diffusive states. Here, we propose a probabilistic method termed ExTrack that uses the full spatio-temporal information of tracks to extract global model parameters, to calculate state probabilities at every time point, to reveal distributions of state durations, and to refine the positions of bound molecules. ExTrack works for a wide range of diffusion coefficients and transition rates, even if experimental data deviate from model assumptions. We demonstrate its capacity by applying it to slowly diffusing and rapidly transitioning bacterial envelope proteins. ExTrack greatly increases the regime of computationally analyzable noisy single-particle tracks. The ExTrack package is available in ImageJ and Python.
Topics: Bacterial Proteins; Diffusion; Kinetics; Microscopy
PubMed: 36880553
DOI: 10.1083/jcb.202208059 -
Physical Review Letters Aug 2015Using random walk simulations we explore diffusive transport through monodisperse sphere packings over a range of packing fractions ϕ in the vicinity of the jamming...
Using random walk simulations we explore diffusive transport through monodisperse sphere packings over a range of packing fractions ϕ in the vicinity of the jamming transition at ϕ(c). Various diffusion properties are computed over several orders of magnitude in both time and packing pressure. Two well-separated regimes of normal "Fickian" diffusion, where the mean squared displacement is linear in time, are observed. The first corresponds to diffusion inside individual spheres, while the latter is the long-time bulk diffusion. The intermediate anomalous diffusion regime and the long-time value of the diffusion coefficient are both shown to be controlled by particle contacts, which in turn depend on proximity to ϕ(c). The time required to recover normal diffusion t* scales as (ϕ-ϕ(c))(-0.5) and the long-time diffusivity D(∞)∼(ϕ-ϕ(c))0.5, or D(∞)∼1/t*. It is shown that the distribution of mean first passage times associated with the escape of random walkers between neighboring particles controls both t* and D(∞) in the limit ϕ→ϕ(c).
Topics: Algorithms; Biological Transport; Diffusion; Models, Biological; Models, Theoretical; Stochastic Processes
PubMed: 26340211
DOI: 10.1103/PhysRevLett.115.088002 -
Proceedings of the National Academy of... Mar 2020Protein mobility at solid-liquid interfaces can affect the performance of applications such as bioseparations and biosensors by facilitating reorganization of adsorbed...
Protein mobility at solid-liquid interfaces can affect the performance of applications such as bioseparations and biosensors by facilitating reorganization of adsorbed protein, accelerating molecular recognition, and informing the fundamentals of adsorption. In the case of ion-exchange chromatographic beads with small, tortuous pores, where the existence of surface diffusion is often not recognized, slow mass transfer can result in lower resin capacity utilization. We demonstrate that accounting for and exploiting protein surface diffusion can alleviate the mass-transfer limitations on multiple significant length scales. Although the surface diffusivity has previously been shown to correlate with ionic strength (IS) and binding affinity, we show that the dependence is solely on the binding affinity, irrespective of pH, IS, and resin ligand density. Different surface diffusivities give rise to different protein distributions within the resin, as characterized using confocal microscopy and small-angle neutron scattering (length scales of micrometer and nanometer, respectively). The binding dependence of surface diffusion inspired a protein-loading approach in which the binding affinity, and hence the surface diffusivity, is modulated by varying IS. Such gradient loading increased the protein uptake efficiency by up to 43%, corroborating the importance of protein surface diffusion in protein transport in ion-exchange chromatography.
Topics: Diffusion; Ion Exchange Resins; Models, Chemical; Proteins
PubMed: 32179691
DOI: 10.1073/pnas.1921499117