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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 -
Biochimica Et Biophysica Acta Oct 2016Cellular membranes are typically decorated with a plethora of embedded and adsorbed macromolecules, e.g. proteins, that participate in numerous vital processes. With... (Review)
Review
Cellular membranes are typically decorated with a plethora of embedded and adsorbed macromolecules, e.g. proteins, that participate in numerous vital processes. With typical surface densities of 30,000 proteins per μm(2) cellular membranes are indeed crowded places that leave only few nanometers of private space for individual proteins. Here, we review recent advances in our understanding of protein crowding in membrane systems. We first give a brief overview on state-of-the-art approaches in experiment and simulation that are frequently used to study crowded membranes. After that, we review how crowding can affect diffusive transport of proteins and lipids in membrane systems. Next, we discuss lipid and protein sorting in crowded membrane systems, including effects like protein cluster formation, phase segregation, and lipid droplet formation. Subsequently, we highlight recent progress in uncovering crowding-induced conformational changes of membranes, e.g. membrane budding and vesicle formation. Finally, we give a short outlook on potential future developments in the field of crowded membrane systems. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Topics: Cell Membrane; Diffusion; Membrane Lipids; Membrane Proteins; Molecular Conformation
PubMed: 26724385
DOI: 10.1016/j.bbamem.2015.12.021 -
Biophysical Journal Nov 2015A large number (tens of thousands) of single molecular trajectories on a cell membrane can now be collected by superresolution methods. The data contains information... (Review)
Review
A large number (tens of thousands) of single molecular trajectories on a cell membrane can now be collected by superresolution methods. The data contains information about the diffusive motion of molecule, proteins, or receptors and here we review methods for its recovery by statistical analysis of the data. The information includes the forces, organization of the membrane, the diffusion tensor, the long-time behavior of the trajectories, and more. To recover the long-time behavior and statistics of long trajectories, a stochastic model of their nonequilibrium motion is required. Modeling and data analysis serve extracting novel biophysical features at an unprecedented spatiotemporal resolution. The review presents data analysis, modeling, and stochastic simulations applied in particular on surface receptors evolving in neuronal cells.
Topics: Data Interpretation, Statistical; Diffusion; Models, Molecular; Motion; Neurons; Stochastic Processes
PubMed: 26536253
DOI: 10.1016/j.bpj.2015.09.003 -
Scientific Reports Nov 2022Accurate and efficient forward models of photon migration in heterogeneous geometries are important for many applications of light in medicine because many biological...
Accurate and efficient forward models of photon migration in heterogeneous geometries are important for many applications of light in medicine because many biological tissues exhibit a layered structure of independent optical properties and thickness. However, closed form analytical solutions are not readily available for layered tissue-models, and often are modeled using computationally expensive numerical techniques or theoretical approximations that limit accuracy and real-time analysis. Here, we develop an open-source accurate, efficient, and stable numerical routine to solve the diffusion equation in the steady-state and time-domain for a layered cylinder tissue model with an arbitrary number of layers and specified thickness and optical coefficients. We show that the steady-state ([Formula: see text] ms) and time-domain ([Formula: see text] ms) fluence (for an 8-layer medium) can be calculated with absolute numerical errors approaching machine precision. The numerical implementation increased computation speed by 3 to 4 orders of magnitude compared to previously reported theoretical solutions in layered media. We verify our solutions asymptotically to homogeneous tissue geometries using closed form analytical solutions to assess convergence and numerical accuracy. Approximate solutions to compute the reflected intensity are presented which can decrease the computation time by an additional 2-3 orders of magnitude. We also compare our solutions for 2, 3, and 5 layered media to gold-standard Monte Carlo simulations in layered tissue models of high interest in biomedical optics (e.g. skin/fat/muscle and brain). The presented routine could enable more robust real-time data analysis tools in heterogeneous tissues that are important in many clinical applications such as functional brain imaging and diffuse optical spectroscopy.
Topics: Scattering, Radiation; Diffusion; Photons; Monte Carlo Method; Optics and Photonics
PubMed: 36347893
DOI: 10.1038/s41598-022-22649-4 -
Journal of Biophotonics Feb 2018Quantitative measurements of intravascular microscopic dynamics, such as absolute blood flow velocity, shear stress and the diffusion coefficient of red blood cells...
Quantitative measurements of intravascular microscopic dynamics, such as absolute blood flow velocity, shear stress and the diffusion coefficient of red blood cells (RBCs), are fundamental in understanding the blood flow behavior within the microcirculation, and for understanding why diffuse correlation spectroscopy (DCS) measurements of blood flow are dominantly sensitive to the diffusive motion of RBCs. Dynamic light scattering-optical coherence tomography (DLS-OCT) takes the advantages of using DLS to measure particle flow and diffusion within an OCT resolution-constrained three-dimensional volume, enabling the simultaneous measurements of absolute RBC velocity and diffusion coefficient with high spatial resolution. In this work, we applied DLS-OCT to measure both RBC velocity and the shear-induced diffusion coefficient within penetrating venules of the somatosensory cortex of anesthetized mice. Blood flow laminar profile measurements indicate a blunted laminar flow profile and the degree of blunting decreases with increasing vessel diameter. The measured shear-induced diffusion coefficient was proportional to the flow shear rate with a magnitude of ~0.1 to 0.5 × 10 mm . These results provide important experimental support for the recent theoretical explanation for why DCS is dominantly sensitive to RBC diffusive motion.
Topics: Algorithms; Animals; Biomechanical Phenomena; Diffusion; Dynamic Light Scattering; Erythrocytes; Female; Mechanical Phenomena; Mice; Tomography, Optical Coherence
PubMed: 28700129
DOI: 10.1002/jbio.201700070 -
Biophysical Journal Jun 2021From nutrient uptake to chemoreception to synaptic transmission, many systems in cell biology depend on molecules diffusing and binding to membrane receptors....
From nutrient uptake to chemoreception to synaptic transmission, many systems in cell biology depend on molecules diffusing and binding to membrane receptors. Mathematical analysis of such systems often neglects the fact that receptors process molecules at finite kinetic rates. A key example is the celebrated formula of Berg and Purcell for the rate that cell surface receptors capture extracellular molecules. Indeed, this influential result is only valid if receptors transport molecules through the cell wall at a rate much faster than molecules arrive at receptors. From a mathematical perspective, ignoring receptor kinetics is convenient because it makes the diffusing molecules independent. In contrast, including receptor kinetics introduces correlations between the diffusing molecules because, for example, bound receptors may be temporarily blocked from binding additional molecules. In this work, we present a modeling framework for coupling bulk diffusion to surface receptors with finite kinetic rates. The framework uses boundary homogenization to couple the diffusion equation to nonlinear ordinary differential equations on the boundary. We use this framework to derive an explicit formula for the cellular uptake rate and show that the analysis of Berg and Purcell significantly overestimates uptake in some typical biophysical scenarios. We confirm our analysis by numerical simulations of a many-particle stochastic system.
Topics: Diffusion; Kinetics; Ligands; Models, Biological; Receptors, Cell Surface
PubMed: 33794148
DOI: 10.1016/j.bpj.2021.03.021 -
PloS One 2019Fluorescence fluctuation spectroscopy (FFS) refers to techniques that analyze fluctuations in the fluorescence emitted by fluorophores diffusing in a small volume and...
Fluorescence fluctuation spectroscopy (FFS) refers to techniques that analyze fluctuations in the fluorescence emitted by fluorophores diffusing in a small volume and can be used to distinguish between populations of molecules that exhibit differences in brightness or diffusion. For example, fluorescence correlation spectroscopy (FCS) resolves species through their diffusion by analyzing correlations in the fluorescence over time; photon counting histograms (PCH) and related methods based on moment analysis resolve species through their brightness by analyzing fluctuations in the photon counts. Here we introduce correlated photon counting histograms (cPCH), which uses both types of information to simultaneously resolve fluorescent species by their brightness and diffusion. We define the cPCH distribution by the probability to detect both a particular number of photons at the current time and another number at a later time. FCS and moment analysis are special cases of the moments of the cPCH distribution, and PCH is obtained by summing over the photon counts in either channel. cPCH is inherently a dual channel technique, and the expressions we develop apply to the dual colour case. Using simulations, we demonstrate that two species differing in both their diffusion and brightness can be better resolved with cPCH than with either FCS or PCH. Further, we show that cPCH can be extended both to longer dwell times to improve the signal-to-noise and to the analysis of images. By better exploiting the information available in fluorescence fluctuation spectroscopy, cPCH will be an enabling methodology for quantitative biology.
Topics: Algorithms; Diffusion; Fluorescent Dyes; Models, Theoretical; Photons; Spectrometry, Fluorescence
PubMed: 31887113
DOI: 10.1371/journal.pone.0226063 -
Physical Chemistry Chemical Physics :... Oct 2022Living organisms employ chemical self-organization to build structures, and inspire new strategies to design synthetic systems that spontaneously take a particular form,... (Review)
Review
Living organisms employ chemical self-organization to build structures, and inspire new strategies to design synthetic systems that spontaneously take a particular form, a combination of integrated chemical reactions, assembly pathways and physicochemical processes. However, spatial programmability that is required to direct such self-organization is a challenge to control. Thermodynamic equilibrium typically brings about a homogeneous solution, or equilibrium structures such as supramolecular complexes and crystals. This perspective addresses out-of-equilibrium gradients that can be driven by coupling chemical reaction, diffusion and hydrodynamics, and provide spatial differentiation in the self-organization of molecular, ionic or colloidal building blocks in solution. These physicochemical gradients are required to (1) direct the organization from the starting conditions ( a homogeneous solution), and (2) sustain the organization, to prevent it from decaying towards thermodynamic equilibrium. We highlight four different concepts that can be used as a design principle to establish such self-organization, using chemical reactions as a driving force to sustain the gradient and, ultimately, program the characteristics of the gradient: (1) reaction-diffusion coupling; (2) reaction-convection; (3) the Marangoni effect and (4) diffusiophoresis. Furthermore, we outline their potential as attractive pathways to translate chemical reactions and molecular/colloidal assembly into organization of patterns in solution, (dynamic) self-assembled architectures and collectively moving swarms at the micro-, meso- and macroscale, exemplified by recent demonstrations in the literature.
Topics: Diffusion; Hydrodynamics; Thermodynamics
PubMed: 36172850
DOI: 10.1039/d2cp02542f -
Respiratory Physiology & Neurobiology Jul 2017Roughton and Forster (RF) proposed to split the lung diffusing capacity into two contributions describing first, diffusion to red blood cells (RBC), and second, capture...
Roughton and Forster (RF) proposed to split the lung diffusing capacity into two contributions describing first, diffusion to red blood cells (RBC), and second, capture by diffusion from the RBC surface and reaction with haemoglobin. Solving the diffusion-reaction equations for simplified capillary-RBC structures, we investigate the RF interpretation. This reveals first that the conventional extrapolation to zero pressure of 1/DLCO on PO is not a correct measure of the diffusive component. Consequently the capillary volumes deduced from this extrapolation are erroneous. Secondly, capture mechanisms are different for CO and NO: while DLCO characterizes "volume absorption" in the RBC and is correlated with hematocrit, DLNO quantifies "surface absorption" and provide information about the morphology of the space between the alveolar surface and the RBC surfaces. In conclusion, the RF approach may lead to erroneous physiological interpretations of DLCO; nevertheless, the measurement of DLCO and DLNO bring different types of information that give the potential for a better understanding of respiratory diseases.
Topics: Capillaries; Carbon Monoxide; Diffusion; Erythrocytes; Humans; Lung; Models, Cardiovascular; Nitric Oxide; Pulmonary Diffusing Capacity
PubMed: 28049017
DOI: 10.1016/j.resp.2016.12.014 -
Magnetic Resonance in Medicine Jun 2020In diffusion MRI, the actual b-value played out on the scanner may deviate from the nominal value due to magnetic field imperfections. A simple image-based correction...
PURPOSE
In diffusion MRI, the actual b-value played out on the scanner may deviate from the nominal value due to magnetic field imperfections. A simple image-based correction method for this problem is presented.
METHODS
The apparent diffusion constant (ADC) of a water phantom was measured voxel-wise along 64 diffusion directions at b = 1000 s/mm . The true diffusion constant of water was estimated, considering the phantom temperature. A voxel-wise correction factor, providing an effective b-value including any magnetic field deviations, was determined for each diffusion direction by relating the measured ADC to the true diffusion constant. To test the method, the measured b-value map was used to calculate the corrected voxel-wise ADC for additionally acquired diffusion data sets on the same water phantom and data sets acquired on a small water phantom at three different positions. Diffusion tensor was estimated by applying the measured b-value map to phantom and in vivo data sets.
RESULTS
The b-value-corrected ADC maps of the phantom showed the expected spatial uniformity as well as a marked improvement in consistency across diffusion directions. The b-value correction for the brain data resulted in a 5.8% and 5.5% decrease in mean diffusivity and angular differences of the primary diffusion direction of 2.71° and 0.73° inside gray and white matter, respectively.
CONCLUSION
The actual b-value deviates significantly from its nominal setting, leading to a spatially variable error in the common diffusion outcome measures. The suggested method measures and corrects these artifacts.
Topics: Artifacts; Diffusion; Diffusion Magnetic Resonance Imaging; Phantoms, Imaging; Reproducibility of Results
PubMed: 31840300
DOI: 10.1002/mrm.28078