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Journal of the American Chemical Society Aug 2022
Editorial Summary of the Comment and Responses on "Following Molecular Mobility during Chemical Reactions: No Evidence for Active Propulsion" and "Molecular Diffusivity of Click Reaction Components: The Diffusion Enhancement Question".
Topics: Diffusion
PubMed: 35919984
DOI: 10.1021/jacs.2c05873 -
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 -
Applied Optics Sep 2012We investigate the use of the Mellin-Laplace transform for reconstructing optical parameters from time-resolved optical tomography in diffusive media. We present here...
We investigate the use of the Mellin-Laplace transform for reconstructing optical parameters from time-resolved optical tomography in diffusive media. We present here its definition, its mathematical properties, and its sensitivity to variations of optical properties. The method was validated on two-dimensional reconstructions from simulation in the reflection geometry. We conclude that reconstructions based on the Mellin-Laplace transform are more robust to noise than the methods using first moments.
Topics: Algorithms; Computer Simulation; Diffusion; Models, Theoretical; Phantoms, Imaging; Tomography, Optical
PubMed: 22945142
DOI: 10.1364/AO.51.005978 -
Physical Review Letters Aug 2010A concentration difference of particles across a membrane perforated by pores will induce a diffusive flux. If the diffusing objects are of the same length scale as the...
A concentration difference of particles across a membrane perforated by pores will induce a diffusive flux. If the diffusing objects are of the same length scale as the pores, diffusion may not be simple; objects can move into the pore in a configuration that requires them to back up in order to continue forward. A configuration that blocks flow through the pore may be statistically preferred, an attracting metastable state of the system. This effect is purely kinetic, and not dependent on potentials, friction, or dissipation. We discuss several geometries which generate this effect, and introduce a heuristic model which captures the qualitative features.
Topics: Biological Transport; Diffusion; Membranes; Molecular Dynamics Simulation; Porosity; Probability
PubMed: 20868199
DOI: 10.1103/PhysRevLett.105.098102 -
Advanced Drug Delivery Reviews Mar 2019Mucus is a dynamic barrier which covers and protects the underlying mucosal epithelial membrane against bacteria and foreign particles. This protection mechanism extends... (Review)
Review
Mucus is a dynamic barrier which covers and protects the underlying mucosal epithelial membrane against bacteria and foreign particles. This protection mechanism extends to include therapeutic macromolecules and nanoparticles (NPs) through trapping of these particles. Mucus is not only a physical barrier that limiting particles movements based on their sizes but it selectively binds with particles through both hydrophilic and lipophilic interactions. Therefore, nano-carriers for mucosal delivery should be designed to eliminate entrapment by the mucus barrier. For this reason, different strategies have been approached for both solid nano-carriers and liquid core nano-carriers to synthesise muco-diffusive nano-carrier. Among these nano-strategies, Self-Emulsifying Drug Delivery System (SEDDS) was recognised as very promising nano-carrier for mucus delivery. The system was introduced to enhance the dissolution and bioavailability of orally administered insoluble drugs. SEDDS has shown high stability against intestinal enzymatic activity and more importantly, relatively rapid permeation characteristics across mucus barrier. The high diffusivity of SEDDS has been tested using various in vitro measurement techniques including both bulk and individual measurement of droplets diffusion within mucus. The selection and processing of an optimum in vitro technique is of great importance to avoid misinterpretation of the diffusivity of SEDDS through mucus barrier. In conclusion, SEDDS is a system with high capacity to diffuse through intestinal mucus even though this system has not been studied to the same extent as solid nano-carriers.
Topics: Animals; Diffusion; Drug Delivery Systems; Emulsions; Humans; Mucus; Nanotechnology; Permeability
PubMed: 30974131
DOI: 10.1016/j.addr.2019.04.001 -
The Journal of Physical Chemistry. B May 2022We demonstrate a novel application of the time-temperature superposition (TTS) principle to predict solute diffusivity in glassy polymers using atomistic molecular...
We demonstrate a novel application of the time-temperature superposition (TTS) principle to predict solute diffusivity in glassy polymers using atomistic molecular dynamics simulations. Our TTS approach incorporates the Debye-Waller factor ⟨⟩, a measure of solute caging, along with concepts from thermodynamic scaling methods, allowing us to balance contributions to the dynamics from temperature and ⟨⟩ using adjustable parameters. Our approach rescales the solute mean-squared displacement curves at several temperatures into a master curve that approximates the diffusive dynamics at a reference temperature, effectively extending the simulation time scale from nanoseconds to seconds and beyond. With a set of "universal" parameters, this TTS approach predicts with reasonable accuracy in a broad range of polymer/solute systems. Using TTS greatly reduces the computational cost compared to standard MD simulations. Thus, our method offers a means to rapidly and routinely provide order-of-magnitude estimates of using simulations.
Topics: Diffusion; Molecular Dynamics Simulation; Polymers; Solutions; Temperature
PubMed: 35583328
DOI: 10.1021/acs.jpcb.2c00057 -
Mathematical Biosciences Dec 2022The bulk-surface wave pinning model is a reaction-diffusion system for studying cell polarisation. It is constituted by a surface reaction-diffusion equation, coupled to...
The bulk-surface wave pinning model is a reaction-diffusion system for studying cell polarisation. It is constituted by a surface reaction-diffusion equation, coupled to a bulk diffusion equation with a non-linear boundary condition. Cell polarisation arises as the surface component develops specific patterns. Since proteins diffuse much faster in the cell interior than on the membrane, in the literature, the bulk component is often assumed to be spatially homogeneous. Therefore, the model can be reduced to a single surface equation. However, in real applications a spatially non-uniform bulk component might be an important player to take into account. In this paper, we study, through numerical computations, the role of the bulk component and, more specifically, how different bulk diffusion rates might affect the polarisation response. We find that the bulk component is indeed a key factor in determining the surface polarisation response. Moreover, for certain geometries, it is the spatial heterogeneity of the bulk component that triggers the polarisation response, which might not be possible in a reduced model. Understanding how polarisation depends on bulk diffusivity might be crucial when studying models of migrating cells, which are naturally subject to domain deformation.
Topics: Diffusion; Cell Polarity
PubMed: 36397641
DOI: 10.1016/j.mbs.2022.108925 -
Biophysical Journal Feb 2014Biological systems often have to measure extremely low concentrations of chemicals with high precision. When dealing with such small numbers of molecules, the inevitable...
Biological systems often have to measure extremely low concentrations of chemicals with high precision. When dealing with such small numbers of molecules, the inevitable randomness of physical transport processes and binding reactions will limit the precision with which measurements can be made. An important question is what the lower bound on the noise would be in such measurements. Using the theory of diffusion-influenced reactions, we derive an analytical expression for the precision of concentration estimates that are obtained by monitoring the state of a receptor to which a diffusing ligand can bind. The variance in the estimate consists of two terms, one resulting from the intrinsic binding kinetics and the other from the diffusive arrival of ligand at the receptor. The latter term is identical to the fundamental limit derived by Berg and Purcell (Biophys. J., 1977), but disagrees with a more recent expression by Bialek and Setayeshgar. Comparing the theoretical predictions against results from particle-based simulations confirms the accuracy of the resulting expression and reaffirms the fundamental limit established by Berg and Purcell.
Topics: Diffusion; Kinetics; Ligands; Models, Chemical; Protein Binding; Receptors, Cell Surface
PubMed: 24560000
DOI: 10.1016/j.bpj.2013.12.030 -
Proceedings of the National Academy of... Oct 2022Remitted waves are used for sensing and imaging in diverse diffusive media from the Earth's crust to the human brain. Separating the source and detector increases the...
Remitted waves are used for sensing and imaging in diverse diffusive media from the Earth's crust to the human brain. Separating the source and detector increases the penetration depth of light, but the signal strength decreases rapidly, leading to a poor signal-to-noise ratio. Here, we show, experimentally and numerically, that wavefront shaping a laser beam incident on a diffusive sample enables an enhancement of remission by an order of magnitude at depths of up to 10 transport mean free paths. We develop a theoretical model which predicts the maximal remission enhancement. Our analysis reveals a significant improvement in the sensitivity of remitted waves to local changes of absorption deep inside diffusive media. This work illustrates the potential of coherent wavefront control for noninvasive diffuse wave imaging applications, such as diffuse optical tomography and functional near-infrared spectroscopy.
Topics: Brain; Diffusion; Humans; Signal-To-Noise Ratio
PubMed: 36191199
DOI: 10.1073/pnas.2207089119 -
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