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European Biophysics Journal : EBJ Dec 2015An equation of motion is derived from fractal analysis of the Brownian particle trajectory in which the asymptotic fractal dimension of the trajectory has a required...
An equation of motion is derived from fractal analysis of the Brownian particle trajectory in which the asymptotic fractal dimension of the trajectory has a required value. The formula makes it possible to calculate the time dependence of the mean square displacement for both short and long periods when the molecule diffuses anomalously. The anomalous diffusion which occurs after long periods is characterized by two variables, the transport coefficient and the anomalous diffusion exponent. An explicit formula is derived for the transport coefficient, which is related to the diffusion constant, as dependent on the Brownian step time, and the anomalous diffusion exponent. The model makes it possible to deduce anomalous diffusion properties from experimental data obtained even for short time periods and to estimate the transport coefficient in systems for which the diffusion behavior has been investigated. The results were confirmed for both sub and super-diffusion.
Topics: Diffusion; Fractals; Lipid Bilayers; Models, Theoretical
PubMed: 26129728
DOI: 10.1007/s00249-015-1054-5 -
Comparative Biochemistry and... Mar 2021The capillary bed constitutes the obligatory pathway for almost all oxygen (O) and substrate molecules as they pass from blood to individual cells. As the largest organ,... (Review)
Review
The capillary bed constitutes the obligatory pathway for almost all oxygen (O) and substrate molecules as they pass from blood to individual cells. As the largest organ, by mass, skeletal muscle contains a prodigious surface area of capillaries that have a critical role in metabolic homeostasis and must support energetic requirements that increase as much as 100-fold from rest to maximal exercise. In 1919 Krogh's 3 papers, published in the Journal of Physiology, brilliantly conflated measurements of muscle capillary function at rest and during contractions with Agner K. Erlang's mathematical model of O diffusion. These papers single-handedly changed the perception of capillaries from passive vessels serving at the mercy of their upstream arterioles into actively contracting vessels that were recruited during exercise to elevate blood-myocyte O flux. Although seminal features of Krogh's model have not withstood the test of time and subsequent technological developments, Krogh is credited with helping found the field of muscle microcirculation and appreciating the role of the capillary bed and muscle O diffusing capacity in facilitating blood-myocyte O flux. Today, thanks in large part to Krogh, it is recognized that comprehending the role of the microcirculation, as it supports perfusive and diffusive O conductances, is fundamental to understanding skeletal muscle plasticity with exercise training and resolving the mechanistic bases by which major pathologies including heart failure and diabetes cripple exercise tolerance and cerebrovascular dysfunction predicates impaired executive function.
Topics: Animals; Capillaries; Diffusion; Humans; Muscle Cells; Muscles; Oxygen
PubMed: 33242636
DOI: 10.1016/j.cbpa.2020.110852 -
Magnetic Resonance in Medicine Jun 2022To address the long echo times and relatively weak diffusion sensitization that typically limit oscillating gradient spin-echo (OGSE) experiments, an OGSE implementation...
PURPOSE
To address the long echo times and relatively weak diffusion sensitization that typically limit oscillating gradient spin-echo (OGSE) experiments, an OGSE implementation combining spiral readouts, gap-filled oscillating gradient shapes providing stronger diffusion encoding, and a high-performance gradient system is developed here and utilized to investigate the tradeoff between b-value and maximum OGSE frequency in measurements of diffusion dispersion (i.e., the frequency dependence of diffusivity) in the in vivo human brain. In addition, to assess the effects of the marginal flow sensitivity introduced by these OGSE waveforms, flow-compensated variants are devised for experimental comparison.
METHODS
Using DTI sequences, OGSE acquisitions were performed on three volunteers at b-values of 300, 500, and 1000 s/mm and frequencies up to 125, 100, and 75 Hz, respectively; scans were performed for gap-filled oscillating gradient shapes with and without flow sensitivity. Pulsed gradient spin-echo DTI acquisitions were also performed at each b-value. Upon reconstruction, mean diffusivity (MD) maps and maps of the diffusion dispersion rate were computed.
RESULTS
The power law diffusion dispersion model was found to fit best to MD measurements acquired at b = 1000 s/mm despite the associated reduction of the spectral range; this observation was consistent with Monte Carlo simulations. Furthermore, diffusion dispersion rates without flow sensitivity were slightly higher than flow-sensitive measurements.
CONCLUSION
The presented OGSE implementation provided an improved depiction of diffusion dispersion and demonstrated the advantages of measuring dispersion at higher b-values rather than higher frequencies within the regimes employed in this study.
Topics: Brain; Diffusion; Diffusion Magnetic Resonance Imaging; Humans; Monte Carlo Method
PubMed: 35049104
DOI: 10.1002/mrm.29161 -
Biophysical Journal Jan 1985Phospholipid bilayers have been formed on glass, quartz, and silicon surfaces by a sequential transfer of two monolayers at a pressure of approximately 40 dyn/cm from... (Comparative Study)
Comparative Study
Phospholipid bilayers have been formed on glass, quartz, and silicon surfaces by a sequential transfer of two monolayers at a pressure of approximately 40 dyn/cm from the air-water interface to the solid substrates. Lateral diffusion measurements of L-alpha-dipalmitoylphosphatidylcholine (DPPC) bilayers supported on oxidized silicon wafers reveal two sharp phase transitions at temperatures similar to those found in multilayer systems with several different techniques. The diffusion measurements obtained using fluorescence recovery after pattern photobleaching provide evidence for the existence of an intermediate (probably P beta' or ripple) phase in single bilayers. While in the intermediate and high temperature (liquid-crystalline L alpha) phase, the diffusion coefficients do not vary very much with temperature, a strong temperature dependence is observed in the low temperature (gel L beta') phase. This is attributed to defect-mediated diffusion. Lipids in silicon supported bilayers made from L-alpha-dioleoylphosphatidylcholine (DOPC) or L-alpha-dimyristoylphosphatidylcholine (DMPC) diffuse rapidly above their respective chain-melting transition temperatures. Arrhenius plots show straight lines with activation energies of 40.9 and 43.7 kJ/mol, respectively. Supported DPPC bilayers on oxidized silicon form long tubular liposomes when heated through their oxidized silicon form long tubular liposomes when heated through their chain-melting-phase transition, as viewed with epifluorescence microscopy. It is suggested that this is a consequence of the expansion of the lipid on the fixed solid support. Conversely, DOPC bilayers form large void areas on this substrate upon cooling. Large circular membrane defects (holes) are observed under rapid coating conditions. The formation of these defects is modulated by including small amounts of lyso-L-palmitoyl phosphatidylcholine in the DMPC-supported bilayers. A simple model describes the dependence of hole size and hole number on the concentration of lysolecithin.
Topics: Diffusion; Lipid Bilayers; Phospholipids; Physical Phenomena; Physics
PubMed: 3978184
DOI: 10.1016/S0006-3495(85)83882-0 -
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 -
Biophysical Journal May 2019Rebinding kinetics of molecular ligands plays a key role in the operation of biomachinery, from regulatory networks to protein transcription, and is also a key factor in...
Rebinding kinetics of molecular ligands plays a key role in the operation of biomachinery, from regulatory networks to protein transcription, and is also a key factor in design of drugs and high-precision biosensors. In this study, we investigate initial release and rebinding of ligands to their binding sites grafted on a planar surface, a situation commonly observed in single-molecule experiments and that occurs in vivo, e.g., during exocytosis. Via scaling arguments and molecular dynamic simulations, we analyze the dependence of nonequilibrium rebinding kinetics on two intrinsic length scales: the average separation distance between the binding sites and the total diffusible volume (i.e., height of the experimental reservoir in which diffusion takes place or average distance between receptor-bearing surfaces). We obtain time-dependent scaling laws for on rates and for the cumulative number of rebinding events. For diffusion-limited binding, the (rebinding) on rate decreases with time via multiple power-law regimes before the terminal steady-state (constant on-rate) regime. At intermediate times, when particle density has not yet become uniform throughout the diffusible volume, the cumulative number of rebindings exhibits a novel, to our knowledge, plateau behavior because of the three-dimensional escape process of ligands from binding sites. The duration of the plateau regime depends on the average separation distance between binding sites. After the three-dimensional diffusive escape process, a one-dimensional diffusive regime describes on rates. In the reaction-limited scenario, ligands with higher affinity to their binding sites (e.g., longer residence times) delay entry to the power-law regimes. Our results will be useful for extracting hidden timescales in experiments such as kinetic rate measurements for ligand-receptor interactions in microchannels, as well as for cell signaling via diffusing molecules.
Topics: Binding Sites; Diffusion; Kinetics; Ligands; Molecular Dynamics Simulation; Protein Binding; Protein Conformation; Proteins
PubMed: 31029377
DOI: 10.1016/j.bpj.2019.02.033 -
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 -
Journal of Biomechanical Engineering Nov 2022Due to lack of full vascularization, the meniscus relies on diffusion through the extracellular matrix to deliver small (e.g., nutrients) and large (e.g., proteins) to...
Due to lack of full vascularization, the meniscus relies on diffusion through the extracellular matrix to deliver small (e.g., nutrients) and large (e.g., proteins) to resident cells. Under normal physiological conditions, the meniscus undergoes up to 20% compressive strains. While previous studies characterized solute diffusivity in the uncompressed meniscus, to date, little is known about the diffusive transport under physiological strain levels. This information is crucial to fully understand the pathophysiology of the meniscus. The objective of this study was to investigate strain-dependent diffusive properties of the meniscus fibrocartilage. Tissue samples were harvested from the central portion of porcine medial menisci and tested via fluorescence recovery after photobleaching to measure diffusivity of fluorescein (332 Da) and 40 K Da dextran (D40K) under 0%, 10%, and 20% compressive strain. Specifically, average diffusion coefficient and anisotropic ratio, defined as the ratio of the diffusion coefficient in the direction of the tissue collagen fibers to that orthogonal, were determined. For all the experimental conditions investigated, fluorescein diffusivity was statistically faster than that of D40K. Also, for both molecules, diffusion coefficients significantly decreased, up to ∼45%, as the strain increased. In contrast, the anisotropic ratios of both molecules were similar and not affected by the strain applied to the tissue. This suggests that compressive strains used in this study did not alter the diffusive pathways in the meniscus. Our findings provide new knowledge on the transport properties of the meniscus fibrocartilage that can be leveraged to further understand tissue pathophysiology and approaches to tissue restoration.
Topics: Animals; Anisotropy; Diffusion; Fibrocartilage; Fluoresceins; Meniscus; Swine
PubMed: 35789377
DOI: 10.1115/1.4054931 -
Nature Methods Jun 2022Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is...
Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes.
Topics: Diffusion; Microscopy, Fluorescence; Nanoparticles; Nanotechnology
PubMed: 35637303
DOI: 10.1038/s41592-022-01491-6