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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 -
Science Advances Sep 2022Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species....
Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. Here, we design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.
Topics: Biological Transport; DNA; Diffusion; Nanopores; Nanotechnology
PubMed: 36070388
DOI: 10.1126/sciadv.abq4834 -
The Journal of Chemical Physics Aug 2022Real-time feedback-driven single-particle tracking is a technique that uses feedback control to enable single-molecule spectroscopy of freely diffusing particles in...
Real-time feedback-driven single-particle tracking is a technique that uses feedback control to enable single-molecule spectroscopy of freely diffusing particles in native or near-native environments. A number of different real-time feedback-driven single-particle tracking (RT-FD-SPT) approaches exist, and comparisons between methods based on experimental results are of limited use due to differences in samples and setups. In this study, we used statistical calculations and dynamical simulations to directly compare the performance of different methods. The methods considered were the orbital method, the knight's tour (grid scan) method, and MINFLUX, and we considered both fluorescence-based and interferometric scattering (iSCAT) approaches. There is a fundamental trade-off between precision and speed, with the knight's tour method being able to track the fastest diffusion but with low precision, and MINFLUX being the most precise but only tracking slow diffusion. To compare iSCAT and fluorescence, different biological samples were considered, including labeled and intrinsically fluorescent samples. The success of iSCAT as compared to fluorescence is strongly dependent on the particle size and the density and photophysical properties of the fluorescent particles. Using a wavelength for iSCAT that is negligibly absorbed by the tracked particle allows for an increased illumination intensity, which results in iSCAT providing better tracking for most samples. This work highlights the fundamental aspects of performance in RT-FD-SPT and should assist with the selection of an appropriate method for a particular application. The approach used can easily be extended to other RT-FD-SPT methods.
Topics: Diffusion; Feedback; Particle Size; Single Molecule Imaging
PubMed: 36050025
DOI: 10.1063/5.0096729 -
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 -
Journal of Hazardous Materials Oct 2023Antibiotics are recognized as effective medicine that has been extensively used in human and veterinary. Since the rate of releasing into the environment is stronger... (Review)
Review
Antibiotics are recognized as effective medicine that has been extensively used in human and veterinary. Since the rate of releasing into the environment is stronger than the rate of elimination, antibiotics are regarded as persistent or "pseudo-persistent" organic compounds that result in the development of microbial antibiotic resistance. Therefore, assessment for their ecological risks to the environment are essential. Diffusive gradients in thin films for organic compounds (o-DGT) have been adapted to investigate the environmental behaviors of antibiotics. Currently, more than 20 compounds have been tested by o-DGT in waters and soil environments. In this review, we explained the theoretical reason that o-DGT is feasible to determine the labile fraction of antibiotics in different environmental media. The most used agarose diffusive gel, and various binding agents such as resin, porous carbon and nano-scale materials have been compared to optimize the sampling of antibiotics by o-DGT. Results of deploying o-DGT devices in waters and soils from previous studies were discussed to understand the bioavailability and dynamic transport of antibiotics. Also, we provided the feasibility analysis of using o-DGT in sediments for antibiotics measurements, which is required to be carried out in future studies. To have a deep view on the development of o-DGT, its technical limitations and viable improvements were summarized in this study for further applications on antibiotics research.
Topics: Humans; Anti-Bacterial Agents; Biological Availability; Carbon; Diffusion; Porosity; Soil
PubMed: 37597396
DOI: 10.1016/j.jhazmat.2023.132279 -
Journal of Mathematical Biology May 2023The effects of habitat heterogeneity on a diffusing population are investigated here. We formulate a reaction-diffusion system of partial differential equations to...
The effects of habitat heterogeneity on a diffusing population are investigated here. We formulate a reaction-diffusion system of partial differential equations to analyze the effect of resource allocation in an ecosystem with resource having its own dynamics in space and time. We show a priori estimates to prove the existence of state solutions given a control. We formulate an optimal control problem of our ecosystem model such that the abundance of a single species is maximized while minimizing the cost of inflow resource allocation. In addition, we show the existence and uniqueness of the optimal control as well as the optimal control characterization. We also establish the existence of an optimal intermediate diffusion rate. Moreover, we illustrate several numerical simulations with Dirichlet and Neumann boundary conditions with the space domain in 1D and 2D.
Topics: Ecosystem; Population Dynamics; Models, Biological; Diffusion
PubMed: 37217639
DOI: 10.1007/s00285-023-01932-6 -
European Radiology Mar 2024Whether the alternation of the glymphatic system exists in neurodevelopmental disease still remains unclear. In this study, we investigated structural and functional...
OBJECTIVES
Whether the alternation of the glymphatic system exists in neurodevelopmental disease still remains unclear. In this study, we investigated structural and functional changes in the glymphatic system in the treatment-naïve attention-deficit/hyperactivity disorder (ADHD) children by quantitatively measuring the Virchow-Robin spaces (VRS) volume and diffusion tensor image-analysis along the perivascular space (DTI-ALPS).
METHODS
Forty-seven pediatric ADHD patients and 52 age- and gender-matched typically developing (TD) children were recruited in this prospective study. The VRS volume was calculated using a semi-automated approach in axial T2-weighted images. Diffusivities along the x-, y-, and z-axes in the projection, association, and subcortical neural fiber areas were measured. The ALPS index, a ratio that accentuated water diffusion along the perivascular space, was calculated. The Mann-Whitney U test was used to compare the quantitative parameters; Pearson's correlation was used to analyze the correlation with clinical symptoms.
RESULTS
The cerebral VRS volume (mean, 15.514 mL vs. 11.702 mL) and the VRS volume ratio in the ADHD group were larger than those in the TD group (all p < 0.001). The diffusivity along the x-axis in association fiber area and ALPS index were significantly smaller in the ADHD group vs. TD group (mean, 1.40 vs.1.59, p < 0.05 after false discovery rate adjustment). Besides, the ALPS index was related to inattention symptoms of ADHD (r = - 0.323, p < 0.05).
CONCLUSIONS
Our study suggests that the glymphatic system alternation may participate in the pathogenesis of ADHD, which may be a new research direction for exploring the mechanisms of psycho-behavioral developmental disorders. Moreover, the VRS volume and ALPS index could be used as the metrics for diagnosing ADHD.
CLINICAL RELEVANCE STATEMENT
Considering the potential relevance of the glymphatic system for exploring the mechanisms of attention deficit/hyperactivity, the Virchow-Robin spaces volume and the analysis along the perivascular space index could be used as additional metrics for diagnosing the disorder.
KEY POINTS
• Increased Virchow-Robin space volume and decreased analysis along the perivascular space index were found in the treatment-naïve attention-deficit/hyperactivity disorder children. • The results of this study indicate that the glymphatic system alternation may have a valuable role in the pathogenesis of attention-deficit/hyperactivity disorder. • The analysis along the perivascular space index is correlated with inattention symptoms of attention-deficit/hyperactivity disorder children.
Topics: Humans; Child; Attention Deficit Disorder with Hyperactivity; Prospective Studies; Benchmarking; Diffusion; Image Processing, Computer-Assisted
PubMed: 37673963
DOI: 10.1007/s00330-023-10220-2 -
Proceedings of the National Academy of... Sep 2022Understanding the physical principle that governs the stimuli-induced swelling and shrinking kinetics of hydrogels is indispensable for their applications. Here, we show...
Understanding the physical principle that governs the stimuli-induced swelling and shrinking kinetics of hydrogels is indispensable for their applications. Here, we show that the shrinking and swelling kinetics of self-healing hydrogels could be intrinsically asymmetric. The structure frustration, formed by the large difference in the heat and solvent diffusions, remarkably slows down the shrinking kinetics. The plateau modulus of viscoelastic gels is found to be a key parameter governing the formation of structure frustration and, in turn, the asymmetric swelling and shrinking kinetics. This work provides fundamental understandings on the temperature-triggered transient structure formation in self-healing hydrogels. Our findings will find broad use in diverse applications of self-healing hydrogels, where cooperative diffusion of water and gel network is involved. Our findings should also give insight into the molecular diffusion in biological systems that possess macromolecular crowding environments similar to self-healing hydrogels.
Topics: Diffusion; Hydrogels; Kinetics; Temperature; Water
PubMed: 36037384
DOI: 10.1073/pnas.2207422119 -
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 -
ELife Sep 2022Single-particle tracking (SPT) directly measures the dynamics of proteins in living cells and is a powerful tool to dissect molecular mechanisms of cellular regulation....
Single-particle tracking (SPT) directly measures the dynamics of proteins in living cells and is a powerful tool to dissect molecular mechanisms of cellular regulation. Interpretation of SPT with fast-diffusing proteins in mammalian cells, however, is complicated by technical limitations imposed by fast image acquisition. These limitations include short trajectory length due to photobleaching and shallow depth of field, high localization error due to the low photon budget imposed by short integration times, and cell-to-cell variability. To address these issues, we investigated methods inspired by Bayesian nonparametrics to infer distributions of state parameters from SPT data with short trajectories, variable localization precision, and absence of prior knowledge about the number of underlying states. We discuss the advantages and disadvantages of these approaches relative to other frameworks for SPT analysis.
Topics: Animals; Bayes Theorem; Diffusion; Mammals; Single Molecule Imaging
PubMed: 36066004
DOI: 10.7554/eLife.70169