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Advances in Experimental Medicine and... 2020Diffusion within bacteria is often thought of as a "simple" random process by which molecules collide and interact with each other. New research however shows that this... (Review)
Review
Diffusion within bacteria is often thought of as a "simple" random process by which molecules collide and interact with each other. New research however shows that this is far from the truth. Here we shed light on the complexity and importance of diffusion in bacteria, illustrating the similarities and differences of diffusive behaviors of molecules within different compartments of bacterial cells. We first describe common methodologies used to probe diffusion and the associated models and analyses. We then discuss distinct diffusive behaviors of molecules within different bacterial cellular compartments, highlighting the influence of metabolism, size, crowding, charge, binding, and more. We also explicitly discuss where further research and a united understanding of what dictates diffusive behaviors across the different compartments of the cell are required, pointing out new research avenues to pursue.
Topics: Bacteria; Biophysical Phenomena; Diffusion
PubMed: 32894475
DOI: 10.1007/978-3-030-46886-6_2 -
International Journal of Molecular... Oct 2022The mechanisms of transport of substances in the brain parenchyma have been a hot topic in scientific discussion in the past decade. This discussion was triggered by the... (Review)
Review
The mechanisms of transport of substances in the brain parenchyma have been a hot topic in scientific discussion in the past decade. This discussion was triggered by the proposed glymphatic hypothesis, which assumes a directed flow of cerebral fluid within the parenchyma, in contrast to the previous notion that diffusion is the main mechanism. However, when discussing the issue of "diffusion or non-diffusion", much less attention was given to the question that diffusion itself can have a different character. In our opinion, some of the recently published results do not fit into the traditional understanding of diffusion. In this regard, we outline the relevant new theoretical approaches on transport processes in complex random media such as concepts of diffusive diffusivity and time-dependent homogenization, which expands the understanding of the forms of transport of substances based on diffusion.
Topics: Extracellular Space; Brain; Diffusion; Biological Transport; Diffusion Magnetic Resonance Imaging
PubMed: 36293258
DOI: 10.3390/ijms232012401 -
Annual Review of Biophysics May 2023Diffusion is a pervasive process present in a broad spectrum of cellular reactions. Its mathematical description has existed for nearly two centuries and permits the... (Review)
Review
Diffusion is a pervasive process present in a broad spectrum of cellular reactions. Its mathematical description has existed for nearly two centuries and permits the construction of simple rules for evaluating the characteristic timescales of diffusive processes and some of their determinants. Although the term diffusion originally referred to random motions in three-dimensional (3D) media, several biological diffusion processes in lower dimensions have been reported. One-dimensional (1D) diffusions have been reported, for example, for translocations of various proteins along DNA or protein (e.g., microtubule) lattices and translation of helical peptides along the coiled-coil interface. Two-dimensional (2D) diffusion has been shown for dynamics of proteins along membranes. The microscopic mechanisms of these 1-3D diffusions may vary significantly depending on the nature of the diffusing molecules, the substrate, and the interactions between them. In this review, we highlight some key examples of 1-3D biomolecular diffusion processes and illustrate the roles that electrostatic interactions and intrinsic disorder may play in modulating these processes.
Topics: Static Electricity; DNA; Diffusion; Microtubules; Motion
PubMed: 36750250
DOI: 10.1146/annurev-biophys-111622-091220 -
Chemphyschem : a European Journal of... Jan 2009Diffusive transport of particles or, more generally, small objects, is a ubiquitous feature of physical and chemical reaction systems. In configurations containing... (Review)
Review
Diffusive transport of particles or, more generally, small objects, is a ubiquitous feature of physical and chemical reaction systems. In configurations containing confining walls or constrictions, transport is controlled both by the fluctuation statistics of the jittering objects and the phase space available to their dynamics. Consequently, the study of transport at the macro- and nanoscales must address both Brownian motion and entropic effects. Herein we report on recent advances in the theoretical and numerical investigation of stochastic transport occurring either in microsized geometries of varying cross sections or in narrow channels wherein the diffusing particles are hindered from passing each other (single-file diffusion). For particles undergoing biased diffusion in static suspension media enclosed by confining geometries, transport exhibits intriguing features such as 1) a decrease in nonlinear mobility with increasing temperature or also 2) a broad excess peak of the effective diffusion above the free diffusion limit. These paradoxical aspects can be understood in terms of entropic contributions resulting from the restricted dynamics in phase space. If, in addition, the suspension medium is subjected to external, time-dependent forcing, rectification or segregation of the diffusing Brownian particles becomes possible. Likewise, the diffusion in very narrow, spatially modulated channels is modified via contact particle-particle interactions, which induce anomalous sub-diffusion. The effective sub-diffusion constant for a driven single file also develops a resonance-like structure as a function of the confining coupling constant.
Topics: Algorithms; Diffusion; Ion Channels; Ion Transport; Models, Theoretical; Molecular Conformation
PubMed: 19025741
DOI: 10.1002/cphc.200800526 -
Physical Review Letters Nov 2022We investigate the dynamics of a single chiral active particle subject to an external torque due to the presence of a gravitational field. Our computer simulations...
We investigate the dynamics of a single chiral active particle subject to an external torque due to the presence of a gravitational field. Our computer simulations reveal an arbitrarily strong increase of the long-time diffusivity of the gravitactic agent when the external torque approaches the intrinsic angular drift. We provide analytic expressions for the mean-square displacement in terms of eigenfunctions and eigenvalues of the noisy-driven-pendulum problem. The pronounced maximum in the diffusivity is then rationalized by the vanishing of the lowest eigenvalues of the Fokker-Planck equation for the angular motion as the rotational diffusion decreases and the underlying classical bifurcation is approached. A simple harmonic-oscillator picture for the barrier-dominated motion provides a quantitative description for the onset of the resonance while its range of validity is determined by the crossover to a critical-fluctuation-dominated regime.
Topics: Diffusion; Computer Simulation; Motion
PubMed: 36493425
DOI: 10.1103/PhysRevLett.129.228003 -
Biophysical Journal Nov 2023To characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do...
To characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do so, we propose a machine-learning method to characterize diffusion processes with time-dependent properties at the experimental time resolution. Our approach operates at the single-trajectory level predicting the properties of interest, such as the diffusion coefficient or the anomalous diffusion exponent, at every time step of the trajectory. In this way, changes in the diffusive properties occurring along the trajectory emerge naturally in the prediction and thus allow the characterization without any prior knowledge or assumption about the system. We first benchmark the method on synthetic trajectories simulated under several conditions. We show that our approach can successfully characterize both abrupt and continuous changes in the diffusion coefficient or the anomalous diffusion exponent. Finally, we leverage the method to analyze experiments of single-molecule diffusion of two membrane proteins in living cells: the pathogen-recognition receptor DC-SIGN and the integrin α5β1. The analysis allows us to characterize physical parameters and diffusive states with unprecedented accuracy, shedding new light on the underlying mechanisms.
Topics: Deep Learning; Diffusion
PubMed: 37853693
DOI: 10.1016/j.bpj.2023.10.015 -
Biophysical Journal Feb 2021Diffusion is a fundamental mechanism for protein distribution in cell membranes. These membranes often exhibit complex shapes, which range from shallow domes to...
Diffusion is a fundamental mechanism for protein distribution in cell membranes. These membranes often exhibit complex shapes, which range from shallow domes to elongated tubular or pearl-like structures. Shape complexity of the membrane influences the diffusive spreading of proteins and molecules. Despite the importance membrane geometry plays in these diffusive processes, it is challenging to establish the dependence between diffusion and membrane morphology. We solve the diffusion equation numerically on various static curved shapes representative for experimentally observed membrane shapes. Our results show that membrane necks become diffusion barriers. We determine the diffusive half-time, i.e., the time that is required to reduce the amount of protein in the budded region by one half, and find a quadratic relation between the diffusive half-time and the averaged mean curvature of the membrane shape, which we rationalize by a scaling law. Our findings thus help estimate the characteristic diffusive timescale based on the simple measure of membrane mean curvature.
Topics: Cell Membrane; Diffusion; Membranes; Proteins
PubMed: 33359464
DOI: 10.1016/j.bpj.2020.12.014 -
Annual Review of Physiology 1987Membrane protein lateral diffusion can be constrained in several ways: Diffusion can be slower than that predicted for a simple, fluid lipid bilayer; diffusion can be... (Review)
Review
Membrane protein lateral diffusion can be constrained in several ways: Diffusion can be slower than that predicted for a simple, fluid lipid bilayer; diffusion can be confined to certain regions within the total membrane; and diffusion may not be equally probable in all directions, i.e. it may be anisotropic. We know that protein diffusion is reduced by increasing concentrations of membrane proteins and by interactions of the diffusant with structure(s) peripheral to the membrane. The molecular nature of such peripheral constraints has been difficult to pinpoint, but attention is now being directed to the extracellular matrix in addition to the membrane-associated cytoskeleton. There are many proteins that are confined to lateral domains in differentiated, isolated cells and in cells organized into tissue. The mechanisms that maintain such inhomogeneous distributions should be elucidated in the next few years. Whether lateral diffusion of membrane proteins over distances of a few micrometers is usually isotropic or anisotropic will be ascertained in the near future using imaging methods combined with photobleaching.
Topics: Diffusion; Lipid Bilayers; Membrane Proteins; Membranes
PubMed: 3551795
DOI: 10.1146/annurev.ph.49.030187.001115 -
Physical Review Letters Jan 2023Transport of deformable particles in a honeycomb network is studied numerically. It is shown that the particle deformability has a strong impact on their distribution in...
Transport of deformable particles in a honeycomb network is studied numerically. It is shown that the particle deformability has a strong impact on their distribution in the network. For sufficiently soft particles, we observe a short memory behavior from one bifurcation to the next, and the overall behavior consists in a random partition of particles, exhibiting a diffusionlike transport. On the contrary, stiff enough particles undergo a biased distribution whereby they follow a deterministic partition at bifurcations, due to long memory. This leads to a lateral ballistic drift in the network at small concentration and anomalous superdiffusion at larger concentration, even though the network is ordered. A further increase of concentration enhances particle-particle interactions which shorten the memory effect, turning the particle anomalous diffusion into a classical diffusion. We expect the drifting and diffusive regime transition to be generic for deformable particles.
Topics: Diffusion; Biological Transport
PubMed: 36669217
DOI: 10.1103/PhysRevLett.130.014001 -
Electrophoresis Dec 2023The temperature is often a critical factor affecting the diffusion of nanoparticles in complex physiological media, but its specific effects are still to be fully...
The temperature is often a critical factor affecting the diffusion of nanoparticles in complex physiological media, but its specific effects are still to be fully understood. Here, we constructed a temperature-regulated model of semidilute polymer solution and experimentally investigated the temperature-mediated diffusion of nanoparticles using the particle tracking method. By examining the ensemble-averaged mean square displacements (MSDs), we found that the MSD grows gradually as the temperature increases while the transition time from sublinear to linear stage in MSD decreases. Meanwhile, the temperature-dependent measured diffusivity of the nanoparticles shows an exponential growth. We revealed that these temperature-mediated changes are determined by the composite effect of the macroscale property of polymer solution and the microscale dynamics of polymer chain as well as nanoparticles. Furthermore, the measured non-Gaussian displacement probability distributions were found to exhibit non-Gaussian fat tails, and the tailed distribution is enhanced as the temperature increases. The non-Gaussianity was calculated and found to vary in the same trend with the tailed distribution, suggesting the occurrence of hopping events. This temperature-mediated non-Gaussian feature validates the recent theory of thermally induced activated hopping. Our results highlight the temperature-mediated changes in diffusive transport of nanoparticles in polymer solutions and may provide the possible strategy to improve drug delivery in physiological media.
Topics: Polymers; Temperature; Diffusion; Nanoparticles; Drug Delivery Systems
PubMed: 37736676
DOI: 10.1002/elps.202300054