scholarly journals Brownian motion of inert tracer macromolecules in polymerized and spontaneously bundled mixtures of actin and filamin.

1990 ◽  
Vol 110 (5) ◽  
pp. 1645-1654 ◽  
Author(s):  
L Hou ◽  
K Luby-Phelps ◽  
F Lanni
Keyword(s):  
Brownian Motion ◽  
Large Scale ◽  
Three Dimensional ◽  
Structural Features ◽  
Polystyrene Latex ◽  
Rabbit Muscle ◽  
Optical Cell ◽  
Structural Result ◽  
Latex Particles ◽  
Filament Bundles

By use of light microscopy and fluorescence photobleaching recovery, we have studied (a) structures that form in a system composed of copolymerized rabbit muscle actin and chicken gizzard filamin and (b) the Brownian motion of inert tracer macromolecules in this matrix. We have used as tracers size-fractionated fluorescein-labeled ficoll and submicron polystyrene latex particles. In F-actin solutions, the relative diffusion coefficient of the tracer was a decreasing function of both tracer size and actin concentration. Also, a percolation transition for latex particle mobility was found to follow a form suggested by Ogston (Ogston, A. G. 1958. Trans. Faraday Soc. 54:1754-1757) for random filament matrices. The inclusion of filamin before polymerization resulted in increased tracer mobility. Below a filamin dimer-to-actin monomer ratio of 1:140, no structural features were observed in the light microscope. At or above this ratio for all actin concentrations tested, a three-dimensional network of filament bundles was clearly discriminated. Latex particles were always excluded from the bundles. By use of a dialysis optical cell in which polymerization could be initiated with very little hydrodynamic stress, we found that filamin can spontaneously bundle F-actin. A simple physical picture explains how dynamics can affect the structural result of coassembly and provides a further hypothesis on the balance between random filament cross-linking and large-scale bundling. Control of this balance may be important in cytoplasmic motile events.

scholarly journals Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
P. M. Pieczywek ◽  
W. Płaziński ◽  
A. Zdunek
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Large Scale ◽  
Dissipative Particle Dynamics ◽  
Three Dimensional ◽  
Structural Features ◽  
Particle Dynamics ◽  
Distribution Functions ◽  
Coarse Grained ◽  
Dynamics Model

Abstract In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.

Three-Dimensional Arrangements of Polystyrene Latex Particles with a Hyperbolic Quadruple Electrode System

Langmuir ◽  
2004 ◽  
Vol 20 (12) ◽  
pp. 5046-5051 ◽  
Author(s):  
Masahiko Abe ◽  
Masanori Orita ◽  
Hiroyuki Yamazaki ◽  
Shinya Tsukamoto ◽  
Yuki Teshima ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Electrode System ◽  
Polystyrene Latex ◽  
Latex Particles ◽  
Polystyrene Latex Particles

scholarly journals NeuroRetriever: Automatic Neuron Segmentation for Connectome Assembly

2021 ◽  
Vol 15 ◽  
Author(s):  
Chi-Tin Shih ◽  
Nan-Yow Chen ◽  
Ting-Yuan Wang ◽  
Guan-Wei He ◽  
Guo-Tzau Wang ◽  
...  
Keyword(s):  
Large Scale ◽  
Dynamic Range ◽  
Large Population ◽  
Three Dimensional ◽  
High Dynamic Range ◽  
Structural Features ◽  
Single Neurons ◽  
Brain Images ◽  
Human Segmentation ◽  
The Brain

Segmenting individual neurons from a large number of noisy raw images is the first step in building a comprehensive map of neuron-to-neuron connections for predicting information flow in the brain. Thousands of fluorescence-labeled brain neurons have been imaged. However, mapping a complete connectome remains challenging because imaged neurons are often entangled and manual segmentation of a large population of single neurons is laborious and prone to bias. In this study, we report an automatic algorithm, NeuroRetriever, for unbiased large-scale segmentation of confocal fluorescence images of single neurons in the adult Drosophila brain. NeuroRetriever uses a high-dynamic-range thresholding method to segment three-dimensional morphology of single neurons based on branch-specific structural features. Applying NeuroRetriever to automatically segment single neurons in 22,037 raw brain images, we successfully retrieved 28,125 individual neurons validated by human segmentation. Thus, automated NeuroRetriever will greatly accelerate 3D reconstruction of the single neurons for constructing the complete connectomes.

Three-Dimensional Structure and Evolution of the Moisture Field in the MJO

2015 ◽  
Vol 72 (10) ◽  
pp. 3733-3754 ◽  
Author(s):  
Ángel F. Adames ◽  
John M. Wallace
Keyword(s):  
Large Scale ◽  
Three Dimensional ◽  
Warm Pool ◽  
Structural Features ◽  
Dimensional Structure ◽  
Vertical Advection ◽  
Moisture Field ◽  
Moisture Advection ◽  
Pacific Warm Pool ◽  
Equatorial Wave

Abstract The large-scale circulation features that determine the structure and evolution of MJO-related moisture and precipitation fields are examined using a linear analysis protocol based on daily 850- minus 150-hPa global velocity potential data. The analysis is augmented by a compositing procedure that emphasizes the structural features over the Indo-Pacific warm pool sector (60°E–180°) that give rise to the eastward propagation of the enhanced moisture and precipitation. It is found that boundary layer (BL) convergence in the low-level easterlies to the east of the region of maximum ascent produces a deep but narrow plume of equatorial ascent that moistens the midtroposphere, while weakly diffluent flow above the BL spreads moisture away from the equator. Vertical advection of moisture from this plume of ascent accounts for the eastward propagation of the positive moisture anomalies across the Maritime Continent into the western Pacific. When the convection is first developing over the Indian Ocean, horizontal moisture advection contributes to both the eastward propagation and the amplification of the positive moisture anomalies along the equator to the east of the region of enhanced convection. Neither horizontal advection nor the net moistening from vertical advection and the apparent moisture sink exhibit significant westward tilt with height in the equatorial plane, but when they are superposed they explain the westward tilt of the moisture field. The strong spatial correlation between relative humidity and vertical velocity underscores the important role of equatorial wave dynamics in shaping the structure and evolution of the MJO.

Methods for making stereoslides and -prints, with freeze-etched olfactory epithelium as example

1984 ◽  
Vol 42 ◽  
pp. 704-705
Author(s):  
Bert Ph. M. Menco ◽  
Ido F. Menco ◽  
Frans L.T. Verdonk
Keyword(s):  
Electron Microscope ◽  
Olfactory Epithelium ◽  
Three Dimensional ◽  
Supporting Cell ◽  
Structural Features ◽  
Extensive Study ◽  
Sprague Dawley ◽  
Freezing Method ◽  
Respiratory Epithelia ◽  
Three Dimensional Presentation

Previously we presented an extensive study of the distributions of intramembranous particles of structures in apical surfaces of nasal olfactory and respiratory epithelia of the Sprague-Dawley rat. For the same structures these distributions were compared in samples which were i) chemically fixed and cryo-protected with glycerol before cryo-fixation, after excision, and ii)ultra-rapidly frozen by means of the slam-freezing method. Since a three-dimensional presentation markedly improves visualization of structural features micrographs were presented as stereopairs. Two exposures were made by tiling the sample stage of the electron microscope 6° in either direction with an eucentric goniometer. The negatives (Agfa Pan 25 Professional) were reversed with Kodak Technical Pan Film 2415 developed in D76 1:1. The prints were made from these reversed negatives. As an example tight-junctional features of an olfactory supporting cell in a region where this cell conjoined with two other cells are presented (Fig. 1).

Increased Protein Synthesis by Human Platelets during Phagocytosis of Latex Particles in Vitro

1976 ◽  
Vol 35 (02) ◽  
pp. 350-357 ◽  
Author(s):  
Hana Bessler ◽  
Galila Agam ◽  
Meir Djaldetti
Keyword(s):  
Protein Synthesis ◽  
Fold Increase ◽  
Human Platelets ◽  
Polystyrene Latex ◽  
Latex Particles ◽  
The Third ◽  
Platelet Protein ◽  
Dose Dependent ◽  
Phagocytotic Activity

SummaryA three-fold increase of protein synthesis by human platelets during in vitro phagocytosis of polystyrene latex particles was detected. During the first two hours of incubation, the percentage of phagocytizing platelets and the number of latex particles per platelet increased; by the end of the third hour, the first parameter remained stable, while the number of latex particles per cell had decreased.Vincristine (20 μg/ml of cell suspension) inhibited platelet protein synthesis. This effect was both time- and dose-dependent. The drug also caused a decrease in the number of phagocytizing cells, as well as in their phagocytotic activity.

Accelerated Discovery of High-Refractive-Index Polyimides via First-Principles Molecular Modeling, Virtual High-Throughput Screening, and Data Mining

2019 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Mojtaba Haghighatlari ◽  
Sai Prasad Ganesh ◽  
Chong Cheng ◽  
Johannes Hachmann
Keyword(s):  
Data Mining ◽  
Refractive Index ◽  
High Throughput ◽  
First Principles ◽  
High Throughput Screening ◽  
Large Scale ◽  
Computational Study ◽  
High Refractive Index ◽  
Structural Features ◽  
Learning Program

<div>We present a high-throughput computational study to identify novel polyimides (PIs) with exceptional refractive index (RI) values for use as optic or optoelectronic materials. Our study utilizes an RI prediction protocol based on a combination of first-principles and data modeling developed in previous work, which we employ on a large-scale PI candidate library generated with the ChemLG code. We deploy the virtual screening software ChemHTPS to automate the assessment of this extensive pool of PI structures in order to determine the performance potential of each candidate. This rapid and efficient approach yields a number of highly promising leads compounds. Using the data mining and machine learning program package ChemML, we analyze the top candidates with respect to prevalent structural features and feature combinations that distinguish them from less promising ones. In particular, we explore the utility of various strategies that introduce highly polarizable moieties into the PI backbone to increase its RI yield. The derived insights provide a foundation for rational and targeted design that goes beyond traditional trial-and-error searches.</div>

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