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Biotechnology and Bioengineering Aug 1998Experimental measurements of effective diffusive permeabilities and effective diffusion coefficients in biofilms are reviewed. Effective diffusive permeabilities, the... (Review)
Review
Experimental measurements of effective diffusive permeabilities and effective diffusion coefficients in biofilms are reviewed. Effective diffusive permeabilities, the parameter appropriate to the analysis of reaction-diffusion interactions, depend on solute type and biofilm density. Three categories of solute physical chemistry with distinct diffusive properties were distinguished by the present analysis. In order of descending mean relative effective diffusive permeability (De/Daq) these were inorganic anions or cations (0.56), nonpolar solutes with molecular weights of 44 or less (0.43), and organic solutes of molecular weight greater than 44 (0.29). Effective diffusive permeabilities decrease sharply with increasing biomass volume fraction suggesting a serial resistance model of diffusion in biofilms as proposed by Hinson and Kocher (1996). A conceptual model of biofilm structure is proposed in which each cell is surrounded by a restricted permeability envelope. Effective diffusion coefficients, which are appropriate to the analysis of transient penetration of nonreactive solutes, are generally similar to effective diffusive permeabilities in biofilms of similar composition. In three studies that examine diffusion of very large molecular weight solutes (>5000) in biofilms, the average ratio of the relative effective diffusion coefficient of the large solute to the relative effective diffusion coefficient of either sucrose or fluorescein was 0.64, 0.61, and 0.36. It is proposed that large solutes are effectively excluded from microbial cells, that small solutes partition into and diffuse within cells, and that ionic solutes are excluded from cells but exhibit increased diffusive permeability (but decreased effective diffusion coefficients) due to sorption to the biofilm matrix.
Topics: Biofilms; Biotechnology; Diffusion; Models, Theoretical; Permeability
PubMed: 10099336
DOI: 10.1002/(sici)1097-0290(19980805)59:3<261::aid-bit1>3.0.co;2-9 -
Nature Communications Oct 2018Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid...
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid rearrangements of the medium constantly change the effective diffusivity felt locally by a diffusing particle and thus impact the distribution of the first-passage time to a reaction event. Here, we investigate the effect of these dynamic spatiotemporal heterogeneities onto diffusion-limited reactions. We describe a general mathematical framework to translate many results for ordinary homogeneous Brownian motion to heterogeneous diffusion. In particular, we derive the probability density of the first-passage time to a reaction event and show how the dynamic disorder broadens the distribution and increases the likelihood of both short and long trajectories to reactive targets. While the disorder slows down reaction kinetics on average, its dynamic character is beneficial for a faster search and realization of an individual reaction event triggered by a single molecule.
Topics: Diffusion; Models, Theoretical; Time Factors
PubMed: 30353010
DOI: 10.1038/s41467-018-06610-6 -
Journal of Environmental Management Jan 2023Significant amounts of heat can be generated during the initial stages after wastes are deposited in landfills, primarily due to decomposition of food waste. Objectives... (Review)
Review
Significant amounts of heat can be generated during the initial stages after wastes are deposited in landfills, primarily due to decomposition of food waste. Objectives of this study are to compile, examine and compare thermal properties of municipal solid waste (MSW) components, and liquid and gas phases in MSW landfills and their thermal responses that effect temperature increases in gas and leachate. Specific thermal properties examined include thermal conductivity, thermal diffusivity, and specific heat of waste materials deposited in landfills, liquids (water), and gases present. Compilation of these properties will allow in depth thermal analyses to evaluate heat transfer dynamics in landfills with different waste compositions. Examination of thermal characteristics of MSW components indicate that heat generated during decomposition of waste components would primarily be transferred to liquid (leachate) due to formation of water and gaseous components and their high specific heats. As a result, both the leachate and gases released from a landfill during the initial stages after wastes are deposited and when some oxygen is present as an electron acceptor will be warmer. Except for the metals and construction waste, it is likely that most waste components will have a significant temperature gradient during warming up and cooling off stages due to their low thermal conductivities and low thermal diffusivities. Even when the gas phase is at higher temperatures, it will take long time for waste materials (other than food waste and metals) to come to a uniform temperature during the heat generation (primarily due to decomposition of food waste) in a landfill.
Topics: Solid Waste; Refuse Disposal; Hot Temperature; Food; Thermal Diffusion; Waste Disposal Facilities; Gases; Water
PubMed: 36343401
DOI: 10.1016/j.jenvman.2022.116651 -
Journal of the American Chemical Society Aug 2022
Editorial Summary of the Comment and Responses on "Following Molecular Mobility during Chemical Reactions: No Evidence for Active Propulsion" and "Molecular Diffusivity of Click Reaction Components: The Diffusion Enhancement Question".
Topics: Diffusion
PubMed: 35919984
DOI: 10.1021/jacs.2c05873 -
Physical Review Letters Feb 2016Active fluids such as swarming bacteria and motile colloids exhibit exotic properties different from conventional equilibrium materials. As a peculiar example, a...
Active fluids such as swarming bacteria and motile colloids exhibit exotic properties different from conventional equilibrium materials. As a peculiar example, a spherical tracer immersed inside active fluids shows an enhanced translational diffusion, orders of magnitude stronger than its intrinsic Brownian motion. Here, rather than spherical tracers, we investigate the diffusion of isolated ellipsoids in a quasi-two-dimensional bacterial bath. Our study shows a nonlinear enhancement of both translational and rotational diffusions of ellipsoids. More importantly, we uncover an anomalous coupling between particles' translation and rotation that is strictly prohibited in Brownian diffusion. The coupling reveals a counterintuitive anisotropic particle diffusion, where an ellipsoid diffuses fastest along its minor axis in its body frame. Combining experiments with theoretical modeling, we show that such an anomalous diffusive behavior arises from the generic straining flow of swimming bacteria. Our work illustrates an unexpected feature of active fluids and deepens our understanding of transport processes in microbiological systems.
Topics: Bacterial Physiological Phenomena; Diffusion; Escherichia coli; Models, Biological; Suspensions
PubMed: 26919019
DOI: 10.1103/PhysRevLett.116.068303 -
Nano Letters Mar 2023Using single-molecule displacement/diffusivity mapping (SMM), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of...
Using single-molecule displacement/diffusivity mapping (SMM), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients in both organelles are ∼40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, hence a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
Topics: Animals; Proteins; Endoplasmic Reticulum; Diffusion; Mitochondria; Nanotechnology; Mammals
PubMed: 36802676
DOI: 10.1021/acs.nanolett.2c04379 -
Magnetic Resonance in Medicine Aug 2020We investigate the importance of high gradient-amplitude and high slew-rate on oscillating gradient spin echo (OGSE) diffusion imaging for human brain imaging and...
PURPOSE
We investigate the importance of high gradient-amplitude and high slew-rate on oscillating gradient spin echo (OGSE) diffusion imaging for human brain imaging and evaluate human brain imaging with OGSE on the MAGNUS head-gradient insert (200 mT/m amplitude and 500 T/m/s slew rate).
METHODS
Simulations with cosine-modulated and trapezoidal-cosine OGSE at various gradient amplitudes and slew rates were performed. Six healthy subjects were imaged with the MAGNUS gradient at 3T with OGSE at frequencies up to 100 Hz and b = 450 s/mm . Comparisons were made against standard pulsed gradient spin echo (PGSE) diffusion in vivo and in an isotropic diffusion phantom.
RESULTS
Simulations show that to achieve high frequency and b-value simultaneously for OGSE, high gradient amplitude, high slew rates, and high peripheral nerve stimulation limits are required. A strong linear trend for increased diffusivity (mean: 8-19%, radial: 9-27%, parallel: 8-15%) was observed in normal white matter with OGSE (20 Hz to 100 Hz) as compared to PGSE. Linear fitting to frequency provided excellent correlation, and using a short-range disorder model provided radial long-term diffusivities of D = 911 ± 72 µm /s, D = 1519 ± 164 µm /s, and D = 640 ± 111 µm /s and correlation lengths of l = 0.802 ± 0.156 µm, l = 0.837 ± 0.172 µm, and l = 0.780 ± 0.174 µm. Diffusivity changes with OGSE frequency were negligible in the phantom, as expected.
CONCLUSION
The high gradient amplitude, high slew rate, and high peripheral nerve stimulation thresholds of the MAGNUS head-gradient enables OGSE acquisition for in vivo human brain imaging.
Topics: Brain; Diffusion; Diffusion Magnetic Resonance Imaging; Humans; Neuroimaging; Phantoms, Imaging
PubMed: 32011027
DOI: 10.1002/mrm.28180 -
International Journal of Pharmaceutics Oct 2011Mathematical models for the release of drug from both non-degradable and degradable slab matrices in which the initial drug loading is greater than the solubility are... (Review)
Review
Mathematical models for the release of drug from both non-degradable and degradable slab matrices in which the initial drug loading is greater than the solubility are presented in this paper. Taking the anomalous diffusions in the drug release processes into account, the fractional calculus is introduced to model the related phenomena. To describe different kinds of anomalous diffusions, corresponding fractional diffusion equations are adopted. By employing the integral transform methods, similarity solution method and perturbation method, exact and approximation solutions to the models are obtained.
Topics: Delayed-Action Preparations; Diffusion; Mathematics; Models, Theoretical; Solubility
PubMed: 21163340
DOI: 10.1016/j.ijpharm.2010.12.009 -
Biophysical Journal Mar 2021We develop a theoretical foundation for a time-series analysis method suitable for revealing the spectrum of diffusion coefficients in mixed Brownian systems, for which...
We develop a theoretical foundation for a time-series analysis method suitable for revealing the spectrum of diffusion coefficients in mixed Brownian systems, for which no prior knowledge of particle distinction is required. This method is directly relevant for particle tracking in biological systems, in which diffusion processes are often nonuniform. We transform Brownian data onto the logarithmic domain, in which the coefficients for individual modes of diffusion appear as distinct spectral peaks in the probability density. We refer to the method as the logarithmic measure of diffusion, or simply as the logarithmic measure. We provide a general protocol for deriving analytical expressions for the probability densities on the logarithmic domain. The protocol is applicable for any number of spatial dimensions with any number of diffusive states. The analytical form can be fitted to data to reveal multiple diffusive modes. We validate the theoretical distributions and benchmark the accuracy and sensitivity of the method by extracting multimodal diffusion coefficients from two-dimensional Brownian simulations of polydisperse filament bundles. Bundling the filaments allows us to control the system nonuniformity and hence quantify the sensitivity of the method. By exploiting the anisotropy of the simulated filaments, we generalize the logarithmic measure to rotational diffusion. By fitting the analytical forms to simulation data, we confirm the method's theoretical foundation. An error analysis in the single-mode regime shows that the proposed method is comparable in accuracy to the standard mean-squared displacement approach for evaluating diffusion coefficients. For the case of multimodal diffusion, we compare the logarithmic measure against other, more sophisticated methods, showing that both model selectivity and extraction accuracy are comparable for small data sets. Therefore, we suggest that the logarithmic measure, as a method for multimodal diffusion coefficient extraction, is ideally suited for small data sets, a condition often confronted in the experimental context. Finally, we critically discuss the proposed benefits of the method and its information content.
Topics: Anisotropy; Computer Simulation; Diffusion
PubMed: 33453269
DOI: 10.1016/j.bpj.2021.01.001 -
Journal of Colloid and Interface Science Feb 2011Colloidosomes are aqueous cores surrounded by a shell composed of packed colloidal particles. Recent studies suggest that these colloidal shells reduce, or even inhibit,...
Colloidosomes are aqueous cores surrounded by a shell composed of packed colloidal particles. Recent studies suggest that these colloidal shells reduce, or even inhibit, the transport of molecular species (diffusants). However, the effect of the colloidal shell on transport is unclear: In some cases, the reduction in transport of diffusants through the shell was found to be independent of the size of the colloidal particles composing the shell. Other studies find, however, that shells composed of small colloidal particles of order 100nm or less hindered transport of diffusants more than those composed of micro-scale colloidal particles. In this paper we present a simple diffusion model that accounts for three processes that reduce diffusant transport through the shell: (i) a reduction in the penetrable volume available for transport, which also increases the tortuousity of the diffusional path, (ii) narrow pore size which may hinder transport for larger diffusants through size exclusion, and (iii) a reduction in interfacial area due to 'blocking' of the surface by the adsorbed particles. We find that the colloidal particle size does not affect the reduction in transport through the colloidal shell when the shell is a monolayer. However, in closely packed, thick layers where the thickness of the multi-layer shell is fixed, the rate of transport decreases significantly with colloidal particle dimensions. These results are in excellent agreement with previously published experimental results.
Topics: Colloids; Diffusion; Models, Chemical; Particle Size
PubMed: 21122874
DOI: 10.1016/j.jcis.2010.11.011