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Journal of Biomechanical Engineering Jul 2023The cartilage endplates (CEPs) on the superior and inferior surfaces of the intervertebral disk (IVD), are the primary nutrient transport pathways between the disk and...
The cartilage endplates (CEPs) on the superior and inferior surfaces of the intervertebral disk (IVD), are the primary nutrient transport pathways between the disk and the vertebral body. Passive diffusion is responsible for transporting small nutrient and metabolite molecules through the avascular CEPs. The baseline solute diffusivities in healthy CEPs have been previously studied, however alterations in CEP diffusion associated with IVD degeneration remain unclear. This study aimed to quantitatively compare the solute diffusion in healthy and degenerated human CEPs using a fluorescence recovery after photobleaching (FRAP) approach. Seven healthy CEPs and 22 degenerated CEPs were collected from five fresh-frozen human cadaveric spines and 17 patients undergoing spine fusion surgery, respectively. The sodium fluorescein diffusivities in CEP radial and vertical directions were measured using the FRAP method. The CEP calcification level was evaluated by measuring the average X-ray attenuation. No difference was found in solute diffusivities between radial and axial directions in healthy and degenerated CEPs. Compared to healthy CEPs, the average solute diffusivity was 44% lower in degenerated CEPs (Healthy: 29.07 μm2/s (CI: 23.96-33.62 μm2/s); degenerated: 16.32 μm2/s (CI: 13.84-18.84 μm2/s), p < 0.001). The average solute diffusivity had an inverse relationship with the degree of CEP calcification as determined by the normalized X-ray attenuation values (ß = -22.19, R2 = 0.633; p < 0.001). This study suggests that solute diffusion through the disk and vertebral body interface is significantly hindered by CEP calcification, providing clues to help further understand the mechanism of IVD degeneration.
Topics: Humans; Cartilage; Intervertebral Disc; Intervertebral Disc Degeneration; Biological Transport; Diffusion; Calcinosis
PubMed: 36752723
DOI: 10.1115/1.4056871 -
Journal of Chromatography. A Jun 2022Taylor-Aris dispersion represents an undesired phenomenon in pressure-driven liquid chromatography, often responsible for the unchecked increase of the Height Equivalent...
Taylor-Aris dispersion represents an undesired phenomenon in pressure-driven liquid chromatography, often responsible for the unchecked increase of the Height Equivalent of the Theoretical Plate (HETP) when high throughput operating conditions are sought. Previous work on the subject showed how it is possible to contain the augmented dispersion in empty microchannels by inducing cross-sectional velocity components yielding an overall helical structure of the flow streamlines. Here, we explore the possibility of further reducing axial dispersion by devising flow conditions that give rise to chaotic streamlines. A three-dimensional steady flow generated by the combination of a pressure-driven Poiseuille flow and an electroosmotically-induced spatially periodic flow is used as a case study. Brenner's macrotransport approach is used to predict the axial dispersion coefficient of a diffusing solute in flows possessing regular, partially chaotic and globally chaotic kinematic features. Accurate Lagrangian-stochastic simulations of particle ensembles are used to validate the predictions obtained through Brenner's paradigm. Our findings suggest that the Taylor-Aris phenomenon can be altogether suppressed in the limit of globally chaotic kinematics. A theoretical interpretation of this outcome is developed by combining macrotransport theory with established results of the spectral approach to mixing in advecting-diffusing chaotic flows.
Topics: Cross-Sectional Studies; Diffusion; Solutions
PubMed: 35537353
DOI: 10.1016/j.chroma.2022.463110 -
Physical Review. E Feb 2020The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how...
The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how patterns can emerge from a homogenous steady state when two reactive components have different diffusivities (e.g., membrane-bound and cytosolic states). However, in nature, systems typically develop in a heterogeneous environment, where upstream protein patterns affect the formation of protein patterns downstream. Examples for this are the polarization of Cdc42 adjacent to the previous bud site in budding yeast and the formation of an actin-recruiter ring that forms around a PIP3 domain in macropinocytosis. This suggests that previously established protein patterns can serve as a template for downstream proteins and that these downstream proteins can "sense" the edge of the template. A mechanism for how this edge sensing may work remains elusive. Here we demonstrate and analyze a generic and robust edge-sensing mechanism, based on a two-component mass-conserving reaction-diffusion (McRD) model. Our analysis is rooted in a recently developed theoretical framework for McRD systems, termed local equilibria theory. We extend this framework to capture the spatially heterogeneous reaction kinetics due to the template. This enables us to graphically construct the stationary patterns in the phase space of the reaction kinetics. Furthermore, we show that the protein template can trigger a regional mass-redistribution instability near the template edge, leading to the accumulation of protein mass, which eventually results in a stationary peak at the template edge. We show that simple geometric criteria on the reactive nullcline's shape predict when this edge-sensing mechanism is operational. Thus, our results provide guidance for future studies of biological systems and for the design of synthetic pattern forming systems.
Topics: Diffusion; Models, Molecular; Protein Domains; Proteins
PubMed: 32168714
DOI: 10.1103/PhysRevE.101.022414 -
Journal of Mathematical Biology Apr 2022We consider a reaction-diffusion system of densities of two types of particles, introduced by Hannezo et al. (Cell 171(1):242-255.e27, 2017). It is a simple model for a...
We consider a reaction-diffusion system of densities of two types of particles, introduced by Hannezo et al. (Cell 171(1):242-255.e27, 2017). It is a simple model for a growth process: active, branching particles form the growing boundary layer of an otherwise static tissue, represented by inactive particles. The active particles diffuse, branch and become irreversibly inactive upon collision with a particle of arbitrary type. In absence of active particles, this system is in a steady state, without any a priori restriction on the amount of remaining inactive particles. Thus, while related to the well-studied FKPP-equation, this system features a game-changing continuum of steady state solutions, where each corresponds to a possible outcome of the growth process. However, simulations indicate that this system self-organizes: traveling fronts with fixed shape arise under a wide range of initial data. In the present work, we describe all positive and bounded traveling wave solutions, and obtain necessary and sufficient conditions for their existence. We find a surprisingly simple symmetry in the pairs of steady states which are joined via heteroclinic wave orbits. Our approach is constructive: we first prove the existence of almost constant solutions and then extend our results via a continuity argument along the continuum of limiting points.
Topics: Computer Simulation; Diffusion; Models, Biological
PubMed: 35482091
DOI: 10.1007/s00285-022-01753-z -
Journal of the American Chemical Society Oct 2022The kinetics of chemical reactions are determined by the law of mass action, which has been successfully applied to homogeneous, dilute mixtures. At nondilute...
The kinetics of chemical reactions are determined by the law of mass action, which has been successfully applied to homogeneous, dilute mixtures. At nondilute conditions, interactions among the components can give rise to coexisting phases, which can significantly alter the kinetics of chemical reactions. Here, we derive a theory for chemical reactions in coexisting phases at phase equilibrium. We show that phase equilibrium couples the rates of chemical reactions of components with their diffusive exchanges between the phases. Strikingly, the chemical relaxation kinetics can be represented as a flow along the phase equilibrium line in the phase diagram. A key finding of our theory is that differences in reaction rates between coexisting phases stem solely from phase-dependent reaction rate coefficients. Our theory is key to interpreting how concentration levels of reactive components in condensed phases control chemical reaction rates in synthetic and biological systems.
Topics: Kinetics; Diffusion
PubMed: 36241174
DOI: 10.1021/jacs.2c06265 -
Journal of the Royal Society, Interface Mar 2023How memory shapes animals' movement paths is a topic of growing interest in ecology, with connections to planning for conservation and climate change. Empirical studies...
How memory shapes animals' movement paths is a topic of growing interest in ecology, with connections to planning for conservation and climate change. Empirical studies suggest that memory has both temporal and spatial components, and can include both attractive and aversive elements. Here, we introduce reinforced diffusions (the continuous time counterpart of reinforced random walks) as a modelling framework for understanding the role that memory plays in determining animal movements. This framework includes reinforcement via functions of time before present and of distance away from a current location. Focusing on the interplay between memory and central place attraction (a component of home ranging behaviour), we explore patterns of space usage that result from the reinforced diffusion. Our efforts identify three qualitatively different behaviours: bounded wandering behaviour that does not collapse spatially, collapse to a very small area, and, most intriguingly, convergence to a cycle. Subsequent applications show how reinforced diffusion can create movement trajectories emulating the learning of movement routes by homing pigeons and consolidation of ant travel paths. The mathematically explicit manner with which assumptions about the structure of memory can be stated and subsequently explored provides linkages to biological concepts like an animal's 'immediate surroundings' and memory decay.
Topics: Animals; Ecology; Learning; Diffusion; Movement; Models, Biological
PubMed: 36987616
DOI: 10.1098/rsif.2022.0700 -
Journal of the Royal Society, Interface Mar 2021Swarming has been observed in various biological systems from collective animal movements to immune cells. In the cellular context, swarming is driven by the secretion...
Swarming has been observed in various biological systems from collective animal movements to immune cells. In the cellular context, swarming is driven by the secretion of chemotactic factors. Despite the critical role of chemotactic swarming, few methods to robustly identify and quantify this phenomenon exist. Here, we present a novel method for the analysis of time series of positional data generated from realizations of agent-based processes. We convert the positional data for each individual time point to a function measuring agent aggregation around a given area of interest, hence generating a functional time series. The functional time series, and a more easily visualized of agent aggregation derived from these functions, provide useful information regarding the evolution of the underlying process over time. We extend our method to build upon the modelling of collective motility using drift-diffusion partial differential equations (PDEs). Using a functional linear model, we are able to use the functional time series to estimate the drift and diffusivity terms associated with the underlying PDE. By producing an accurate estimate for the drift coefficient, we can infer the strength and range of attraction or repulsion exerted on agents, as in chemotaxis. Our approach relies solely on using agent positional data. The spatial distribution of diffusing chemokines is not required, nor do individual agents need to be tracked over time. We demonstrate our approach using random walk simulations of chemotaxis and experiments investigating cytotoxic T cells interacting with tumouroids.
Topics: Animals; Cell Tracking; Chemotactic Factors; Chemotaxis; Diffusion; Models, Biological; Movement
PubMed: 33715400
DOI: 10.1098/rsif.2020.0879 -
Magnetic Resonance Imaging Nov 2021Wood is a hygroscopic, multi-scale and anisotropic natural material composed of pores with different size and differently oriented. In particular, archaeologically...
Wood is a hygroscopic, multi-scale and anisotropic natural material composed of pores with different size and differently oriented. In particular, archaeologically excavated wood generally is waterlogged wood with very high moisture content (400%-800%) that need to have a rapid investigation at the microstructural level to obtain the best treatment with preservative agents. Time-dependent diffusion coefficient D(t) quantified by Pulse Field Gradient (PFG) Nuclear Magnetic Resonance (NMR) techniques provides useful information about complex porous media, such as the tortuosity (τ) describing pore connectivity and fluid transport through media, the average-pore size, the anisotropic degree (a). However, diffusion NMR is intrinsically limited since it is an indirect measure of medium microstructure and relies on inferences from models and estimation of relevant diffusion parameters. Therefore, it is necessary to validate the information obtained from NMR diffusion parameters through complementary investigations. In this work, the structures of five waterlogged wood species were studied by PFG of absorbed water. D(t) and τ of water diffusing along and perpendicular to vessels/tracheids main axes together with relaxation times and a were quantified. From these parameters, the pore sizes distribution and the wood microstructure characterization were obtained. Results among wood species were compared, validated and integrated by micro-imaging NMR (μ-MRI), environmental-scanning electron-microscope (ESEM) images, wood dry density and imbibition times measurement of all woods. The work suggests that a vs τ rather than the estimated pore size diversifies and characterize the different wood species. As a consequence diffusion-anisotropy vs tortuosity could be an alternative method to characterize and differentiate wood species of waterlogged wood when high resolution images (μ-MRI and ESEM) are not available. Moreover, the combined use of D(t) and micro-MRI expands the scale of dimensions observable by NMR covering all the interesting length scales of wood.
Topics: Diffusion; Magnetic Resonance Imaging; Magnetic Resonance Spectroscopy; Porosity; Wood
PubMed: 34454984
DOI: 10.1016/j.mri.2021.08.010 -
Journal of Contaminant Hydrology Oct 2021Diffusion coefficients for Na was measured in low-permeability samples (diameter of 3 cm and average length of 7 cm) from the deep disposal site of the Siberian...
Diffusion coefficients for Na was measured in low-permeability samples (diameter of 3 cm and average length of 7 cm) from the deep disposal site of the Siberian Chemical Combine (SCC) using the end-diffusion technique. The direction of diffusion was perpendicular to the direction of bedding. Special equipment was designed and constructed for the experiment. Two types of concentration observations were used. For non-sorbing Na, EC sensors and the length distribution of sorbed elements were used. The synthetic solution used in the experiments was a model of the low-activity contaminant of the SCC and consisted of NaNO (25 g/L) and nitrate compounds of Cs, Ni, Co, and Sr (100 mg/L each). The measured values of the effective diffusion coefficients D for Na from 1.92 × 10 to 1.70 × 10 m/s. The microstructure was studied with X-ray microtomography for the same cores. Image shooting was performed on undisturbed microsamples with a size of 0.91 mm (700 vox). Spatial correlation analysis was performed after the binarization of each obtained 3-D structure. This analysis showed that the spatial correlation scale of the indicator variogram is considerably smaller than the microsample length. Then, a numerical simulation of the Laplace equation with binary coefficients for each microsample was performed. The results were analysed in the form of a plot of the tortuosity versus the porosity. Pore-scale simulations show a nonlinear decrease in the tortuosity with decreasing porosity. Exponential values in the range between 1.8 and 2.4 were found by fitting this graph with Archie's model. Anisotropic tortuosity is also detected in the horizontal and vertical directions. The diffusion coefficients of non-sorbing Na measured in this study agree with those of the pore-scale diffusion simulation of the microtomography data.
Topics: Computer Simulation; Diffusion; Permeability; Porosity; Soil
PubMed: 34298490
DOI: 10.1016/j.jconhyd.2021.103858 -
Journal of Colloid and Interface Science Jan 2022The use of isotropic potential models of simple colloids for describing complex protein-protein interactions is a topic of ongoing debate in the biophysical community....
The use of isotropic potential models of simple colloids for describing complex protein-protein interactions is a topic of ongoing debate in the biophysical community. This contention stems from the unavailability of synthetic protein-like model particles that are amenable to systematic experimental characterization. In this article, we test the utility of colloidal theory to capture the solution structure, interactions and dynamics of novel globular protein-mimicking, computationally designed peptide assemblies called bundlemers that are programmable model systems at the intersection of colloids and proteins. Small-angle neutron scattering (SANS) measurements of semi-dilute bundlemer solutions in low and high ionic strength solution indicate that bundlemers interact locally via repulsive interactions that can be described by a screened repulsive potential. We also present neutron spin echo (NSE) spectroscopy results that show high-Q freely-diffusive dynamics of bundlemers. Importantly, formation of clusters due to short-range attractive, inter-bundlemer interactions is observed in SANS even at dilute bundlemer concentrations, which is indicative of the complexity of the bundlemer charged surface. The similarities and differences between bundlemers and simple colloidal as well as complex protein-protein interactions is discussed in detail.
Topics: Colloids; Diffusion; Peptides; Proteins; Scattering, Small Angle
PubMed: 34749446
DOI: 10.1016/j.jcis.2021.09.184