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Computers in Biology and Medicine Sep 2022We develop a lumped parameter model to describe and predict the mass release of (absorption from) an arbitrary shaped body of any dimension in a large environment....
We develop a lumped parameter model to describe and predict the mass release of (absorption from) an arbitrary shaped body of any dimension in a large environment. Through the one-to-one analogy between diffusion-dominated mass transfer systems and electrical circuits we provide exact solutions in terms of averaged concentrations and mass released. An estimate of the equivalent resistance and of the release time is also given, and shown to be inversely proportional to the diffusivity. The proposed electrical analogue approach allows a time constant to be defined and provides an easy extension to a multi-layer and multi-phase cases in planar and spherical geometries. The simulation results are compared with those obtained from the solution of the corresponding analytical, numerical and experimental solutions, showing a satisfactory accuracy and a good agreement.
Topics: Computer Simulation; Diffusion; Electricity; Mathematics
PubMed: 35834969
DOI: 10.1016/j.compbiomed.2022.105774 -
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 -
Physical Review. E May 2023The effect of helicity in magnetohydrodynamic turbulence on the effective turbulent magnetic diffusion is considered here. The helical correction to turbulent...
The effect of helicity in magnetohydrodynamic turbulence on the effective turbulent magnetic diffusion is considered here. The helical correction to turbulent diffusivity is analytically calculated with the use of the renormalization group approach. In agreement with previous numerical findings, this correction is shown to be negative and proportional to the second power of the magnetic Reynolds number, when the latter is small. In addition, the helical correction to turbulent diffusivity is found to obey a power-law-type dependence on the wave number of the most energetic turbulent eddies, k_{ℓ}, of the form k_{ℓ}^{-10/3}.
Topics: Physical Phenomena; Diffusion; Magnetic Phenomena
PubMed: 37329043
DOI: 10.1103/PhysRevE.107.055205 -
Nanoscale Jul 2014In contrast to adenosine triphosphate (ATP)-dependent motor enzymes, other enzymes are little-known as "motors" or "pumps", that is, for their ability to induce motion.... (Review)
Review
In contrast to adenosine triphosphate (ATP)-dependent motor enzymes, other enzymes are little-known as "motors" or "pumps", that is, for their ability to induce motion. The enhanced diffusive movement of enzyme molecules, the self-propulsion of enzyme-based nanomotors, and liquid pumping with enzymatic micropumps were indeed only recently reported. Enzymatically induced motion can be achieved in mild conditions and without the use of external fields. It is thus better suited for use in living systems (from single-cell to whole-body) than most other ways to achieve motion at small scales. Enzymatically induced motion is thus not only new but also important. Therefore, the present work reviews the most significant discoveries in enzymatically induced motion. As we will learn, freely diffusing enzymes enhance their diffusive movement by nonreciprocal conformational changes which parallel their catalytic cycles. Meanwhile, enzyme-modified nano- and micro-objects turn chemical energy into kinetic energy through mechanisms such as bubble recoil propulsion, self-electrophoresis, and self-diffusiophoresis. Enzymatically induced motion of small objects ranges from enhanced diffusive movement to directed motion at speeds as high as 1 cm s(-1). In spite of the progress made in understanding how the energy of enzyme reactions is turned into motion, most enzymatically powered devices remain inefficient and need improvements before we will witness their application in real world environments.
Topics: Actins; Diffusion; Enzymes; Enzymes, Immobilized; Nanotechnology; Polymers
PubMed: 24931666
DOI: 10.1039/c4nr01760a -
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 Sep 2020The effect of bead and ligand structure on protein adsorption was investigated for multimodal anion exchangers combining a quaternary ammonium ion group with hydrophobic...
The effect of bead and ligand structure on protein adsorption was investigated for multimodal anion exchangers combining a quaternary ammonium ion group with hydrophobic moieties: Nuvia aPrime 1 and aPrime 2, based on a 54 μm diameter polymeric bead, and Capto Adhere ImpRes and Capto Adhere, based on agarose beads 51 and 78 μm diameter, respectively. Bovine serum albumin (BSA) monomer, BSA dimer, and thyroglobulin (Tg) were used as model proteins. Based on TEM imaging and iSEC, the Nuvia resins have a microgranular structure and large pores (110 nm radius), while the Capto resins have a fibrous structure and smaller pores (32-36 nm radius). Comparable binding capacities (80-110 mg/mL), decreasing as salt is added, are observed for all three proteins on the Nuvia resins. Higher capacities (110-130 mg/mL), also decreasing as salt is added, are observed for BSA monomer and dimer on the Capto resins. However, the Tg binding capacity is very low in this case and increases as salt is added. Confocal laser scanning microscopy show that the kinetics are controlled by pore diffusion for all four resins, but with diffusivities that decrease as the protein size increases especially for the Capto resins. For Tg at low salt, binding is restricted to a thin shell close to the bead surface for both Capto resins. The ratio of effective and free diffusivity is about 0.30, 0.18, and 0.08 for BSA monomer, BSA dimer, and Tg, respectively, on the Nuvia resin. These values decrease to about 0.11, 0.04, and 0.01, respectively, for the Capto resins as a result of diffusional hindrance. Dynamic binding capacities are consistent with the equilibrium and rate behaviors.
Topics: Adsorption; Anion Exchange Resins; Anions; Chromatography, Ion Exchange; Diffusion; Hydrophobic and Hydrophilic Interactions; Kinetics; Ligands; Polymers; Proteins; Sepharose; Serum Albumin, Bovine
PubMed: 32822983
DOI: 10.1016/j.chroma.2020.461444 -
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 -
Soft Matter Jul 2018The displacements of ensembles of colloids at the interface between oil and suspensions of the bacterium Pseudomonas aeruginosa PA14ΔpelA indicate enhanced colloid...
The displacements of ensembles of colloids at the interface between oil and suspensions of the bacterium Pseudomonas aeruginosa PA14ΔpelA indicate enhanced colloid mobilities and apparently diffusive motion driven by interactions with the bacteria. However, inspection of individual trajectories of ∼500 particles reveals prolonged, directed displacements inconsistent with purely hydrodynamic interactions between swimming bacteria and colloids. Analysis of the properties of colloid paths indicates trajectories can be sorted into four distinct categories, including diffusive, persistent, curly, and mixed trajectory types. Non-diffusive trajectories are the norm, comprising 2/3 of the observed trajectories. Imaging of colloids in the interface reveals anisotropic assemblies formed by colloids decorated with one or more adhered bacteria that drive the colloids along these paths. The trajectories and enhanced transport result from individual colloids being moved as cargo by these adhered bacteria. The implications of these structures and open questions for interfacial transport are discussed and related to the active colloid literature.
Topics: Bacterial Adhesion; Diffusion; Models, Biological; Movement; Pseudomonas aeruginosa
PubMed: 29943791
DOI: 10.1039/c8sm00481a -
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 -
Biophysical Journal Nov 2015The efficient treatment of many ocular diseases depends on the rapid diffusive distribution of solutes such as drugs or drug delivery vehicles through the vitreous...
The efficient treatment of many ocular diseases depends on the rapid diffusive distribution of solutes such as drugs or drug delivery vehicles through the vitreous humor. However, this multicomponent hydrogel possesses selective permeability properties, which allow for the diffusion of certain molecules and particles, whereas others are immobilized. In this study, we perform an interspecies comparison showing that the selective permeability properties of the vitreous are conserved across several mammalian species. We identify the polyanionic glycosaminoglycans hyaluronic acid and heparan sulfate as two key macromolecules that establish this selective permeability. We show that electrostatic interactions between the polyanionic macromolecules and diffusing solutes can be weakened by charge screening or enzymatic glycosaminoglycan digestion. Furthermore, molecule penetration into the vitreous is also charge-dependent and only efficient as long as the net charge of the molecule does not exceed a certain threshold.
Topics: Animals; Cattle; Diffusion; Heparitin Sulfate; Humans; Hyaluronic Acid; Permeability; Sheep; Swine; Vitreous Body
PubMed: 26588575
DOI: 10.1016/j.bpj.2015.10.002