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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 -
European Biophysics Journal : EBJ Dec 2022The intracellular diffusive movement of molecular substances that are buffered by diffusing chelators is often modeled as movement between compartments with constant...
The intracellular diffusive movement of molecular substances that are buffered by diffusing chelators is often modeled as movement between compartments with constant concentrations within which the buffering occurs. Here, an algorithm to solve such a system of time-dependent differential equations is presented. This Dynamic and Balanced Operator Splitting Scheme (DABOSS) combines dynamic time stepping and operator splitting techniques. The time stepping minimizes the number of time steps while bounding local errors. The balanced operator splitting separates the diffusion and reaction components (each of which is solved efficiently) in a way that preserves the correct steady-state behavior. Analysis shows that DABOSS scales almost linearly in the number of compartments and remains accurate over very long simulations. Moreover, DABOSS works efficiently for nanometer-sized compartments with sources of flux, showing that it is applicable to situations where more spatial resolution is desired.
Topics: Diffusion; Algorithms; Movement
PubMed: 36376400
DOI: 10.1007/s00249-022-01622-z -
The Journal of Chemical Physics Apr 2022A quantitative model of the mobility of ligand-presenting particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this...
A quantitative model of the mobility of ligand-presenting particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles featuring ligands that selectively bind receptors decorating an interface. The formation of a ligand-receptor complex leads to a molecular bridge anchoring the particle to the surface. We consider systems with reversible bridges in which ligand-receptor pairs bind/unbind with finite reaction rates. For a given set of bridges, the particle can explore a tiny fraction of the surface as the extensivity of the bridges is finite. We show how, at timescales longer than the bridges' lifetime, the average position of the particle diffuses away from its initial value. We distill our findings into two analytic equations for the sliding diffusion constant of particles carrying mobile and fixed ligands. We quantitatively validate our theoretical predictions using reaction-diffusion simulations. We compare our findings with results from recent literature studies and discuss the molecular parameters that likely affect the particle's mobility most. Our results, along with recent literature studies, will allow inferring the microscopic parameters at play in complex biological systems from experimental trajectories.
Topics: Cell Membrane; Diffusion; Ligands
PubMed: 35490015
DOI: 10.1063/5.0084848 -
Journal of the American Chemical Society Apr 2024Recent microscopy and nuclear magnetic resonance (NMR) studies have noticed substantial suppression of intracellular diffusion for positively charged proteins,...
Recent microscopy and nuclear magnetic resonance (NMR) studies have noticed substantial suppression of intracellular diffusion for positively charged proteins, suggesting an overlooked role of electrostatic attraction in nonspecific protein interactions in a predominantly negatively charged intracellular environment. Utilizing single-molecule detection and statistics, here, we quantify in aqueous solutions how protein diffusion, in the limit of low diffuser concentration to avoid aggregate/coacervate formation, is modulated by differently charged interactor proteins over wide concentration ranges. We thus report substantially suppressed diffusion when oppositely charged interactors are added at parts per million levels, yet unvaried diffusivities when same-charge interactors are added beyond 1%. The electrostatic attraction-driven suppression of diffusion is sensitive to the protein net charge states, as probed by varying the solution pH and ionic strength or chemically modifying the proteins and is robust across different diffuser-interactor pairs. By converting the measured diffusivities to diffuser diameters, we further show that in the limit of excess interactors, a positively charged diffuser molecule effectively drags along just one monolayer of negatively charged interactors, where further interactions stop. We thus unveil ubiquitous, net charge-driven protein-protein interactions and shed new light on the mechanism of charge-based diffusion suppression in living cells.
Topics: Proteins; Diffusion; Osmolar Concentration
PubMed: 38576203
DOI: 10.1021/jacs.4c02475 -
The Journal of Chemical Physics Apr 2015In this paper, we study biased diffusion of point Brownian particles in a three-dimensional comb-like structure formed by a main cylindrical tube with identical periodic...
In this paper, we study biased diffusion of point Brownian particles in a three-dimensional comb-like structure formed by a main cylindrical tube with identical periodic cylindrical dead ends. It is assumed that the dead ends are thin cylinders whose radius is much smaller than both the radius of the main tube and the distance between neighboring dead ends. It is also assumed that in the main tube, the particle, in addition to its regular diffusion, moves with a uniform constant drift velocity. For such a system, we develop a formalism that allows us to derive analytical expressions for the Laplace transforms of the first two moments of the particle displacement along the main tube axis. Inverting these Laplace transforms numerically, one can find the time dependences of the two moments for arbitrary values of both the drift velocity and the dead-end length, including the limiting case of infinitely long dead ends, where the unbiased diffusion becomes anomalous at sufficiently long times. The expressions for the Laplace transforms are used to find the effective drift velocity and diffusivity of the particle as functions of its drift velocity in the main tube and the tube geometric parameters. As might be expected from common-sense arguments, the effective drift velocity monotonically decreases from the initial drift velocity to zero as the dead-end length increases from zero to infinity. The effective diffusivity is a more complex, non-monotonic function of the dead-end length. As this length increases from zero to infinity, the effective diffusivity first decreases, reaches a minimum, and then increases approaching a plateau value which is proportional to the square of the particle drift velocity in the main tube.
Topics: Algorithms; Diffusion; Models, Chemical; Motion
PubMed: 25854222
DOI: 10.1063/1.4916310 -
The Journal of Chemical Physics Jul 2011We present the detailed analysis of the diffusive transport of spatially inhomogeneous fluid mixtures and the interplay between structural and dynamical properties...
We present the detailed analysis of the diffusive transport of spatially inhomogeneous fluid mixtures and the interplay between structural and dynamical properties varying on the atomic scale. The present treatment is based on different areas of liquid state theory, namely, kinetic and density functional theory and their implementation as an effective numerical method via the lattice Boltzmann approach. By combining the first two methods, it is possible to obtain a closed set of kinetic equations for the singlet phase space distribution functions of each species. The interactions among particles are considered within a self-consistent approximation and the resulting effective molecular fields are analyzed. We focus on multispecies diffusion in systems with short-range hard-core repulsion between particles of unequal sizes and weak attractive long-range interactions. As a result, the attractive part of the potential does not contribute explicitly to viscosity but to diffusivity and the thermodynamic properties. Finally, we obtain a practical scheme to solve the kinetic equations by employing a discretization procedure derived from the lattice Boltzmann approach. Within this framework, we present numerical data concerning the mutual diffusion properties both in the case of a quiescent bulk fluid and shear flow inducing Taylor dispersion.
Topics: Diffusion; Hydrodynamics; Kinetics; Models, Chemical; Nanostructures
PubMed: 21806087
DOI: 10.1063/1.3608416 -
ACS Biomaterials Science & Engineering Sep 2021Synthetic hydrogels formed from poly(ethylene glycol) (PEG) are widely used to study how cells interact with their extracellular matrix. These -like 3D environments...
Synthetic hydrogels formed from poly(ethylene glycol) (PEG) are widely used to study how cells interact with their extracellular matrix. These -like 3D environments provide a basis for tissue engineering and cell therapies but also for research into fundamental biological questions and disease modeling. The physical properties of PEG hydrogels can be modulated to provide mechanical cues to encapsulated cells; however, the impact of changing hydrogel stiffness on the diffusivity of solutes to and from encapsulated cells has received only limited attention. This is particularly true in selectively cross-linked "tetra-PEG" hydrogels, whose design limits network inhomogeneities. Here, we used a combination of theoretical calculations, predictive modeling, and experimental measurements of hydrogel swelling, rheological behavior, and diffusion kinetics to characterize tetra-PEG hydrogels' permissiveness to the diffusion of molecules of biologically relevant size as we changed polymer concentration, and thus hydrogel mechanical strength. Our models predict that hydrogel mesh size has little effect on the diffusivity of model molecules and instead predicts that diffusion rates are more highly dependent on solute size. Indeed, our model predicts that changes in hydrogel mesh size only begin to have a non-negligible impact on the concentration of a solute that diffuses out of hydrogels for the smallest mesh sizes and largest diffusing solutes. Experimental measurements characterizing the diffusion of fluorescein isothiocyanate (FITC)-labeled dextran molecules of known size aligned well with modeling predictions and suggest that doubling the polymer concentration from 2.5% (w/v) to 5% produces stiffer gels with faster gelling kinetics without affecting the diffusivity of solutes of biologically relevant size but that 10% hydrogels can slow their diffusion. Our findings provide confidence that the stiffness of tetra-PEG hydrogels can be modulated over a physiological range without significantly impacting the transport rates of solutes to and from encapsulated cells.
Topics: Biocompatible Materials; Diffusion; Hydrogels; Polyethylene Glycols; Tissue Engineering
PubMed: 34151570
DOI: 10.1021/acsbiomaterials.0c01723 -
Advances in Experimental Medicine and... 1991The rotational mobility of paramagnetic solutes dispersed in partially hydrated macromolecules (proteins, polysaccharides, synthetic polymers) was measured using... (Review)
Review
The rotational mobility of paramagnetic solutes dispersed in partially hydrated macromolecules (proteins, polysaccharides, synthetic polymers) was measured using Electron Spin Resonance. A critical minimum amount of water was observed to be necessary for these molecules to reach a level of mobility of the same order as in dilute solutions. This amount of water depended on the size of the diffusing solute and on the microporosity of the macromolecule. Above this critical moisture range, a progressive increase of the proportion of mobile solute occurred over a hydration range determined by the size of the diffusing solute. At the same time, the rotational diffusivity of the mobile solute increased linearly with water content. The mobilization pattern of spin-labelled side chains of caseinates was observed to be similar to that of the solute. Results are discussed with reference to free volume theory.
Topics: Caseins; Chemical Phenomena; Chemistry, Physical; Diffusion; Electron Spin Resonance Spectroscopy; Food; Polymers; Water
PubMed: 1660672
DOI: 10.1007/978-1-4899-0664-9_5 -
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 -
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