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Physical Biology Sep 2022Morphogen gradients are a central concept in developmental biology. Their formation often involves the secretion of morphogens from a local source, that spread by...
Morphogen gradients are a central concept in developmental biology. Their formation often involves the secretion of morphogens from a local source, that spread by diffusion in the cell field, where molecules eventually get degraded. This implies limits to both the time and length scales over which morphogen gradients can form which are set by diffusion coefficients and degradation rates. Towards the goal of identifying plausible mechanisms capable of extending the gradient range, we here use theory to explore properties of a cell-to-cell signaling relay. Inspired by the millimeter-scale-expression and signaling gradients in flatworms, we consider morphogen-mediated morphogen production in the cell field. We show that such a relay can generate stable morphogen and signaling gradients that are oriented by a local, morphogen-independent source of morphogen at a boundary. This gradient formation can be related to an effective diffusion and an effective degradation that result from morphogen production due to signaling relay. If the secretion of morphogen produced in response to the relay is polarized, it further gives rise to an effective drift. We find that signaling relay can generate long-range gradients in relevant times without relying on extreme choices of diffusion coefficients or degradation rates, thus exceeding the limits set by physiological diffusion coefficients and degradation rates. A signaling relay is hence an attractive principle to conceptualize long-range gradient formation by slowly diffusing morphogens that are relevant for patterning in adult contexts such as regeneration and tissue turn-over.
Topics: Cell Communication; Diffusion; Models, Biological; Morphogenesis; Signal Transduction
PubMed: 35921820
DOI: 10.1088/1478-3975/ac86b4 -
Journal of Contaminant Hydrology Jun 2022Diffusion is the main transport process of water and solutes in clay-rich porous media owing to their very low permeability, so they are widely used as barriers against...
Diffusion is the main transport process of water and solutes in clay-rich porous media owing to their very low permeability, so they are widely used as barriers against contaminant spreading. However, the prediction of contaminant mobility can be very complicated when these media are partially water-saturated. We conducted diffusion experiments for water (HTO and HDO) and ions (Na and I) through partially water saturated compacted kaolinite, a weakly charged clay material, to quantify the distinct diffusive behavior of these species. The osmosis method was used to set kaolinite samples at 67, 86 and 100% saturation. The results showed that desaturation led to a sharp decrease in diffusive rates by factors of 6.5, 18 and 35 for HTO, I and Na, respectively, from 100 to 67% of the degree of saturation. Thus, to interpret water diffusivities, we proposed a model taking into account the diffusion of water in both gas and liquid phases, using diffusion data obtained for ions, considered as inert species. This model was capable of properly predicting water diffusive flux, especially at a low degree of saturation (67% saturation), for which the assumption made for the occurrence of air phase continuity throughout the sample appears to be more relevant than at 86% saturation.
Topics: Clay; Diffusion; Gases; Kaolin; Water
PubMed: 35306324
DOI: 10.1016/j.jconhyd.2022.103989 -
Physical Review. E Dec 2022A class of one-dimensional, discrete-time random walk models with memory, termed "random walk with n memory channels" (RWnMC), is proposed. In these models the...
A class of one-dimensional, discrete-time random walk models with memory, termed "random walk with n memory channels" (RWnMC), is proposed. In these models the information of n (n∈Z) previous steps from the walker's entire history is needed to decide a future step. Exact calculation of the mean and variance of position of the RW2MC (n=2) has been done, which shows that it can lead to asymptotic diffusive and superdiffusive behavior in different parameter regimes. A connection between RWnMC and a Pólya-type urn model evolving by drawing n balls at a time has also been reported. This connection for the RW2MC is discussed in detail and suggests the applicability of RW2MC in many population dynamics models with multiple competing species.
Topics: Diffusion; Walking; Population Dynamics; Diffusion Magnetic Resonance Imaging
PubMed: 36671173
DOI: 10.1103/PhysRevE.106.L062105 -
The Journal of Physical Chemistry. B Jan 2023The biological membrane is a complex two-dimensional fluid, in which various molecular interactions regulate the lateral diffusion of membrane-associated molecules....
The biological membrane is a complex two-dimensional fluid, in which various molecular interactions regulate the lateral diffusion of membrane-associated molecules. Pinning of membrane proteins or lipids by extra-membrane proteins impedes the diffusion. In addition, coupling between two monolayer leaflets within a phospholipid bilayer via interdigitation plays important roles, though this effect remains elusive. Here, we fabricate a substrate-supported model membrane with patterned bilayer/monolayer regions to explore the influences of interleaflet coupling. A patterned monolayer of polymerized diacetylene phospholipid, 1,2-bis(10,12-tricosadiynoyl)--glycero-3-phosphocholine (DiynePC), was lithographically generated and used to form patterned lipid bilayers and monolayers. A phospholipid monolayer was formed on top of the polymerized monolayer. The bilayer/monolayer hybrid membrane was continuous and fluid, but lateral diffusion in the monolayer region was significantly retarded, suggesting the influences of interleaflet coupling. We reconstituted photoreceptor rhodopsin (Rh) and G-protein transducin (G) as model transmembrane and peripheral proteins. Rh diffused laterally only in the bilayer region, whereas G diffused in both bilayer and monolayer regions. The patterned hybrid bilayer/monolayer membrane reproduces the retarded diffusion and confinement of membrane-bound molecules in a controlled manner and provides insight into the physicochemical and functional roles of semipermeable corrals in the cell membrane.
Topics: Phospholipids; Lipid Bilayers; Membrane Proteins; Rhodopsin; Diffusion
PubMed: 36598865
DOI: 10.1021/acs.jpcb.2c06053 -
Journal of Biological Physics Sep 2023We present an analysis of an epidemic spreading process on an Apollonian network that can describe an epidemic spreading in a non-sedentary population. We studied the...
We present an analysis of an epidemic spreading process on an Apollonian network that can describe an epidemic spreading in a non-sedentary population. We studied the modified diffusive epidemic process using the Monte Carlo method by computational analysis. Our model may be helpful for modeling systems closer to reality consisting of two classes of individuals: susceptible (A) and infected (B). The individuals can diffuse in a network according to constant diffusion rates [Formula: see text] and [Formula: see text], for the classes A and B, respectively, and obeying three diffusive regimes, i.e., [Formula: see text], [Formula: see text], and [Formula: see text]. Into the same site i, the reaction occurs according to the dynamical rule based on Gillespie's algorithm. Finite-size scaling analysis has shown that our model exhibits continuous phase transition to an absorbing state with a set of critical exponents given by [Formula: see text], [Formula: see text], and [Formula: see text] familiar to every investigated regime. In summary, the continuous phase transition, characterized by this set of critical exponents, does not have the same exponents of the mean-field universality class in both regular lattices and complex networks.
Topics: Humans; Computer Simulation; Algorithms; Epidemics; Models, Biological; Diffusion
PubMed: 37118345
DOI: 10.1007/s10867-023-09634-2 -
Soft Matter Apr 2020Diffusion is an essential and fundamental means of transport of substances on cell membranes, and the dynamics of biomembranes plays a crucial role in the regulation of... (Review)
Review
Diffusion is an essential and fundamental means of transport of substances on cell membranes, and the dynamics of biomembranes plays a crucial role in the regulation of numerous cellular processes. The understanding of the complex mechanisms and the nature of particle diffusion have a bearing on establishing guidelines for the design of efficient transport materials and unique therapeutic approaches. Herein, this review article highlights the most recent advances in investigating diffusion dynamics of nanoscale objects on biological membranes, focusing on the approaches of tailored computer simulations and theoretical analysis. Due to the presence of the complicated and heterogeneous environment on native cell membranes, the diffusive transport behaviors of nanoparticles exhibit unique and variable characteristics. The general aspects and basic theories of normal diffusion and anomalous diffusion have been introduced. In addition, the influence of a series of external and internal factors on the diffusion behaviors is discussed, including particle size, membrane curvature, particle-membrane interactions or particle-inclusion, and the crowding degree of membranes. Finally, we seek to identify open problems in the existing experimental, simulation, and theoretical research studies, and to propose challenges for future development.
Topics: Cell Membrane; Computer Simulation; Diffusion; Humans; Models, Biological; Nanostructures; Phospholipids
PubMed: 32236197
DOI: 10.1039/c9sm02338k -
Biophysical Journal Jun 2020Protein diffusion in lower-dimensional spaces is used for various cellular functions. For example, sliding on DNA is essential for proteins searching for their target...
Protein diffusion in lower-dimensional spaces is used for various cellular functions. For example, sliding on DNA is essential for proteins searching for their target sites, and protein diffusion on microtubules is important for proper cell division and neuronal development. On the one hand, these linear diffusion processes are mediated by long-range electrostatic interactions between positively charged proteins and negatively charged biopolymers and have similar characteristic diffusion coefficients. On the other hand, DNA and microtubules have different structural properties. Here, using computational approaches, we studied the mechanism of protein diffusion along DNA and microtubules by exploring the diffusion of both protein types on both biopolymers. We found that DNA-binding and microtubule-binding proteins can diffuse on each other's substrates; however, the adopted diffusion mechanism depends on the molecular properties of the diffusing proteins and the biopolymers. On the protein side, only DNA-binding proteins can perform rotation-coupled diffusion along DNA, with this being due to their higher net charge and its spatial organization at the DNA recognition helix. By contrast, the lower net charge on microtubule-binding proteins enables them to diffuse more quickly than DNA-binding proteins on both biopolymers. On the biopolymer side, microtubules possess intrinsically disordered, negatively charged C-terminal tails that interact with microtubule-binding proteins, thus supporting their diffusion. Thus, although both DNA-binding and microtubule-binding proteins can diffuse on the negatively charged biopolymers, the unique molecular features of the biopolymers and of their natural substrates are essential for function.
Topics: Biopolymers; DNA; Diffusion; Microtubules; Protein Binding; Static Electricity
PubMed: 32492371
DOI: 10.1016/j.bpj.2020.05.004 -
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 -
The European Respiratory Journal Jul 2022
Topics: Carbon Monoxide; Diffusion; Humans; Pulmonary Diffusing Capacity
PubMed: 35902101
DOI: 10.1183/13993003.00789-2022 -
Journal of the Royal Society, Interface Dec 2021Diffusion of water into plant materials is known to decrease their mechanical strength and stiffness but improve formability. Here, we characterize water diffusion...
Diffusion of water into plant materials is known to decrease their mechanical strength and stiffness but improve formability. Here, we characterize water diffusion through areca palm leaf-sheath-a model plant material, with hierarchical structure, used in eco-friendly foodware. The diffusion process is studied using mass gain measurements and imaging of water transport. By treating the areca sheath as homogeneous ensemble, and incorporating effects of material swelling due- to water absorption, a factor typically neglected in prior studies, the diffusion coefficient for water is estimated as (6.5 ± 2.2) × 10 mm s. It is shown that neglecting the swelling results in gross underestimation of . Microstructural effects (e.g. fibre, matrix) on the diffusion are characterized using imaging of the water transport at high resolution. The observations show that the water diffuses an order of magnitude faster in the matrix (8.63 × 10 mm s) than in the fibres (7.19 × 10 mm s). This non-uniformity is also reflected in the swelling-induced strain in the leaf, mapped by image correlation. Lastly, we vary salt concentration by controlled additions of NaCl and note a non-monotonic dependence of the diffusion on concentration. Implications of the results for improving foodware manufacturing processes and product life are discussed.
Topics: Biological Transport; Diffusion; Plant Leaves; Sodium Chloride; Water
PubMed: 34847794
DOI: 10.1098/rsif.2021.0483