163 research outputs found
Characterization of extracellular vesicles by IR spectroscopy: fast and simple classification based on amide and C-H stretching vibrations
Extracellular vesicles isolated by differential centrifugation from Jurkat T-cell line were investigated by attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FTIR). Amide and C-H stretching band intensity ratios calculated from IR bands, characteristic of protein and lipid components, proved to be distinctive for the different extracellular vesicle subpopulations. This proposed ’spectroscopic protein-to-lipid ratio’, combined with the outlined spectrum-analysis protocol is valid also for low sample concentrations (0.15-0.05 mg/ml total protein content) and can carry information about the presence of other non-vesicular formations such as aggregated proteins, lipoproteins and immune complexes. Detailed analysis of IR data reveals compositional changes of extracellular vesicles subpopulations: second derivative spectra suggest changes in protein composition from parent cell towards exosomes favoring proteins with -turns and unordered motifs at the expense of intermolecular -sheet structures. The IR-based protein-to-lipid assessment protocol was tested also for red blood cell derived microvesicles for which similar values were obtained. The potential applicability of this technique for fast and efficient characterization of vesicular components is high as the investigated samples require no further preparations and all the different molecular species can be determined in the same sample. The results indicate that ATR-FTIR measurements provide a simple and reproducible method for the screening of extracellular vesicle preparations. It is hoped that this sophisticated technique will have further impact in extracellular vesicle research
Fractal to Nonfractal Phase Transition in the Dielectric Breakdown Model
A fast method is presented for simulating the dielectric-breakdown model
using iterated conformal mappings. Numerical results for the dimension and for
corrections to scaling are in good agreement with the recent RG prediction of
an upper critical , at which a transition occurs between branching
fractal clusters and one-dimensional nonfractal clusters.Comment: 5 pages, 7 figures; corrections to scaling include
Diffusion limited aggregation as a Markovian process: site-sticking conditions
Cylindrical lattice diffusion limited aggregation (DLA), with a narrow width
N, is solved for site-sticking conditions using a Markovian matrix method
(which was previously developed for the bond-sticking case). This matrix
contains the probabilities that the front moves from one configuration to
another at each growth step, calculated exactly by solving the Laplace equation
and using the proper normalization. The method is applied for a series of
approximations, which include only a finite number of rows near the front. The
fractal dimensionality of the aggregate is extrapolated to a value near 1.68.Comment: 27 Revtex pages, 16 figure
Laplacian growth with separately controlled noise and anisotropy
Conformal mapping models are used to study competition of noise and
anisotropy in Laplacian growth. For that, a new family of models is introduced
with the noise level and directional anisotropy controlled independently.
Fractalization is observed in both anisotropic growth and the growth with
varying noise. Fractal dimension is determined from cluster size scaling with
its area. For isotropic growth we find d = 1.7, both at high and low noise. For
anisotropic growth with reduced noise the dimension can be as low as d = 1.5
and apparently is not universal. Also, we study fluctuations of particle areas
and observe, in agreement with previous studies, that exceptionally large
particles may appear during the growth, leading to pathologically irregular
clusters. This difficulty is circumvented by using an acceptance window for
particle areas.Comment: 13 pages, 15 figure
Conformal mapping methods for interfacial dynamics
The article provides a pedagogical review aimed at graduate students in
materials science, physics, and applied mathematics, focusing on recent
developments in the subject. Following a brief summary of concepts from complex
analysis, the article begins with an overview of continuous conformal-map
dynamics. This includes problems of interfacial motion driven by harmonic
fields (such as viscous fingering and void electromigration), bi-harmonic
fields (such as viscous sintering and elastic pore evolution), and
non-harmonic, conformally invariant fields (such as growth by
advection-diffusion and electro-deposition). The second part of the article is
devoted to iterated conformal maps for analogous problems in stochastic
interfacial dynamics (such as diffusion-limited aggregation, dielectric
breakdown, brittle fracture, and advection-diffusion-limited aggregation). The
third part notes that all of these models can be extended to curved surfaces by
an auxilliary conformal mapping from the complex plane, such as stereographic
projection to a sphere. The article concludes with an outlook for further
research.Comment: 37 pages, 12 (mostly color) figure
Characterization of the thermal and photoinduced reactions of photochromic spiropyrans in aqueous solution
Six water-soluble spiropyran derivatives have been characterized with respect to the thermal and photoinduced reactions over a broad pH-interval. A comprehensive kinetic model was formulated including the spiro- and the merocyanine isomers, the respective protonated forms, and the hydrolysis products. The experimental studies on the hydrolysis reaction mechanism were supplemented by calculations using quantum mechanical (QM) models employing density functional theory. The results show that (1) the substitution pattern dramatically influences the pKa-values of the protonated forms as well as the rates of the thermal isomerization reactions, (2) water is the nucleophile in the hydrolysis reaction around neutral pH, (3) the phenolate oxygen of the merocyanine form plays a key role in the hydrolysis reaction. Hence, the nonprotonated merocyanine isomer is susceptible to hydrolysis, whereas the corresponding protonated form is stable toward hydrolytic degradation
Basins of attraction on random topography
We investigate the consequences of fluid flowing on a continuous surface upon
the geometric and statistical distribution of the flow. We find that the
ability of a surface to collect water by its mere geometrical shape is
proportional to the curvature of the contour line divided by the local slope.
Consequently, rivers tend to lie in locations of high curvature and flat
slopes. Gaussian surfaces are introduced as a model of random topography. For
Gaussian surfaces the relation between convergence and slope is obtained
analytically. The convergence of flow lines correlates positively with drainage
area, so that lower slopes are associated with larger basins. As a consequence,
we explain the observed relation between the local slope of a landscape and the
area of the drainage basin geometrically. To some extent, the slope-area
relation comes about not because of fluvial erosion of the landscape, but
because of the way rivers choose their path. Our results are supported by
numerically generated surfaces as well as by real landscapes
Geometry of River Networks I: Scaling, Fluctuations, and Deviations
This article is the first in a series of three papers investigating the
detailed geometry of river networks. Large-scale river networks mark an
important class of two-dimensional branching networks, being not only of
intrinsic interest but also a pervasive natural phenomenon. In the description
of river network structure, scaling laws are uniformly observed. Reported
values of scaling exponents vary suggesting that no unique set of scaling
exponents exists. To improve this current understanding of scaling in river
networks and to provide a fuller description of branching network structure, we
report here a theoretical and empirical study of fluctuations about and
deviations from scaling. We examine data for continent-scale river networks
such as the Mississippi and the Amazon and draw inspiration from a simple model
of directed, random networks. We center our investigations on the scaling of
the length of sub-basin's dominant stream with its area, a characterization of
basin shape known as Hack's law. We generalize this relationship to a joint
probability density and show that fluctuations about scaling are substantial.
We find strong deviations from scaling at small scales which can be explained
by the existence of linear network structure. At intermediate scales, we find
slow drifts in exponent values indicating that scaling is only approximately
obeyed and that universality remains indeterminate. At large scales, we observe
a breakdown in scaling due to decreasing sample space and correlations with
overall basin shape. The extent of approximate scaling is significantly
restricted by these deviations and will not be improved by increases in network
resolution.Comment: 16 pages, 13 figures, Revtex4, submitted to PR
Stimuli-Responsive Membrane Anchor Peptide Nanofoils for Tunable Membrane Association and Lipid Bilayer Fusion
Self-assembled peptide nanostructures with stimuli-responsive features are promising as functional materials. Despite extensive research efforts, water-soluble supramolecular constructs that can interact with lipid membranes in a controllable way are still challenging to achieve. Here, we have employed a short membrane anchor protein motif (GLFD) and coupled it to a spiropyran photoswitch. Under physiological conditions, these conjugates assemble into ∼3.5 nm thick, foil-like peptide bilayer morphologies. Photoisomerization from the closed spiro (SP) form to the open merocyanine (MC) form of the photoswitch triggers rearrangements within the foils. This results in substantial changes in their membrane-binding properties, which also varies sensitively to lipid composition, ranging from reversible nanofoil reformation to stepwise membrane adsorption. The formed peptide layers in the assembly are also able to attach to various liposomes with different surface charges, enabling the fusion of their lipid bilayers. Here, SP-to-MC conversion can be used both to trigger and to modulate the liposome fusion efficiency
Unified View of Scaling Laws for River Networks
Scaling laws that describe the structure of river networks are shown to
follow from three simple assumptions. These assumptions are: (1) river networks
are structurally self-similar, (2) single channels are self-affine, and (3)
overland flow into channels occurs over a characteristic distance (drainage
density is uniform). We obtain a complete set of scaling relations connecting
the exponents of these scaling laws and find that only two of these exponents
are independent. We further demonstrate that the two predominant descriptions
of network structure (Tokunaga's law and Horton's laws) are equivalent in the
case of landscapes with uniform drainage density. The results are tested with
data from both real landscapes and a special class of random networks.Comment: 14 pages, 9 figures, 4 tables (converted to Revtex4, PRE ref added
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