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single particle analysis

Yu-Jiao Yang, Shuai Wang, Biao Zhang, Hong-Bin Shen
As a relatively new technology to solve the 3D structure of a protein or protein complex, the Single-Particle Reconstruction (SPR) of cryo-EM images shows much superiority and is in a rapidly developing stage. Resolution measurement in SPR, which evaluates the quality of a reconstructed 3D density map, plays a critical role for promoting methodology development of SPR and structural biology. Due to there is no benchmark map in a new structure generation, how to realize the resolution estimation of a new map is still an open problem...
May 21, 2018: Journal of Chemical Information and Modeling
Min Woo Sung, Rahamthulla Shaik, Allan D TerBush, Katherine W Osteryoung, Stanislav Vitha, Andreas Holzenburg
Chloroplasts host photosynthesis and fulfill other metabolic functions that are essential to plant life. They have to divide by binary fission to maintain their numbers throughout cycles of cell division. Chloroplast division is achieved by a complex ring-shaped division machinery located on both the inner (stromal) and the outer (cytosolic) side of the chloroplast envelope. The inner division ring (termed the Z ring) is formed by the assembly of tubulin-like FtsZ1 and FtsZ2 proteins. ARC6 is a key chloroplast division protein that interacts with the Z ring...
May 16, 2018: Journal of Biological Chemistry
Anuraj Kshirsagar, Tanaya Khanna, Vaishali Dhanwe, Kunal H Kate, Pawan K Khanna
Avoiding use of environmentally hazardous reducing agents and surfactants like sodium borohydride, hydrazine hydrate, alkyl amines and alkyl phosphines, the current article describes successful synthesis of silver nanoparticles via green synthesis by employing coconut, Indian gooseberry (amla), almond and mustard oils as capping as well as reducing agents. The presence of various fatty acids in such edible oils act as capping agents through their carboxylic acid functionality and control the growth of nanoparticles...
January 1, 2018: Journal of Nanoscience and Nanotechnology
Roland R Netz
An exactly solvable, Hamiltonian-based model of many massive particles that are coupled by harmonic potentials and driven by stochastic non-equilibrium forces is introduced. The stationary distribution and the fluctuation-dissipation relation are derived in closed form for the general non-equilibrium case. Deviations from equilibrium are on one hand characterized by the difference of the obtained stationary distribution from the Boltzmann distribution; this is possible because the model derives from a particle Hamiltonian...
May 14, 2018: Journal of Chemical Physics
Satori Tsuzuki, Daichi Yanagisawa, Katsuhiro Nishinari
This study proposes a model of a totally asymmetric simple exclusion process on a single-channel lane with functions of site assignments along the pit lane. The system model attempts to insert a new particle to the leftmost site at a certain probability by randomly selecting one of the empty sites in the pit lane, and reserving it for the particle. Thereafter, the particle is directed to stop at the site only once during its travel. Recently, the system was determined to show a self-deflection effect, in which the site usage distribution biases spontaneously toward the leftmost site, and the throughput becomes maximum when the site usage distribution is slightly biased to the rightmost site...
April 2018: Physical Review. E
Gustav Nystrom, Mario Arcari, Jozef Adamcik, Ivan Usov, Raffaele Mezzenga
Understanding how nanostructure and nanomechanics influence physical material properties on the micro- and macroscale is an essential goal in soft condensed matter research. Mechanisms governing fragmentation and chirality inversion of filamentous colloids are of specific interest because of their critical role in load-bearing and self-organizing functionalities of soft nanomaterials. Here we provide a fundamental insight into the self-organization across several length scales of nanocellulose, an important bio-colloid system with wide-ranging applications as structural, insulating and functional material...
May 14, 2018: ACS Nano
Ben Gi Spiegelberg, Brent A Lanting, James L Howard, Matthew G Teeter, Douglas Dr Naudie
BACKGROUND: There has been a trend in the evolution of total hip arthroplasty towards increased modularity; with this increase in modularity come some potentially harmful consequences. Modularity at the neck shaft junction has been linked to corrosion, adverse reaction to metal debris and pseudotumour formation. AIM: The aim of this retrieval study is to assess whether the surface integrity of the polyethylene (PE) liner is affected by metal wear debris in a single implant design series of THA revised for trunnionosis...
May 1, 2018: Hip International: the Journal of Clinical and Experimental Research on Hip Pathology and Therapy
James E Warner, Ryan B Norman, Steve R Blattnig
The deterministic radiation transport code HZETRN (High charge (Z) and Energy TRaNsport) was developed by NASA to study the effects of cosmic radiation on astronauts and instrumentation shielded by various materials. This work presents an analysis of computed differential flux from HZETRN compared with measurement data from three balloon-based experiments over a range of atmospheric depths, particle types, and energies. Model uncertainties were quantified using an interval-based validation metric that takes into account measurement uncertainty both in the flux and the energy at which it was measured...
May 2018: Life Sciences in Space Research
Philipp A M Schmidpeter, Xiaolong Gao, Vikrant Uphadyay, Jan Rheinberger, Crina M Nimigean
Cyclic nucleotide-modulated ion channels play several essential physiological roles. They are involved in signal transduction in photoreceptors and olfactory sensory neurons as well as pacemaking activity in the heart and brain. Investigations of the molecular mechanism of their actions, including structural and electrophysiological characterization, are restricted by the availability of stable, purified protein obtained from accessible systems. Here, we establish that SthK, a cyclic nucleotide-gated (CNG) channel from Spirochaeta thermophila , is an excellent model for investigating the gating of eukaryotic CNG channels at the molecular level...
May 11, 2018: Journal of General Physiology
Mahdi Hesari, Xianwen Mao, Peng Chen
Understanding the fundamental properties of charge carriers on the surface of semiconductor photo(electro)catalysts is key to the rational design of efficient photo(electro)catalytic devices for sunlight-driven energy conversion. Here high spatial resolution information is always desirable because of the ubiquitous heterogeneity in semiconductor particles. In this Perspective we review the latest advances in nanoscale imaging and quantitative analysis of charge carrier activities on individual semiconductor particles down to sub-particle resolution, covering the approaches of single-molecule super-resolution fluorescence imaging, scanning electron microscopy, and photoluminescence microscopy...
May 11, 2018: Journal of the American Chemical Society
Mridul K Thomas, Simone Fontana, Marta Reyes, Francesco Pomati
Scanning flow cytometry (SFCM) is characterized by the measurement of time-resolved pulses of fluorescence and scattering, enabling the high-throughput quantification of phytoplankton morphology and pigmentation. Quantifying variation at the single cell and colony level improves our ability to understand dynamics in natural communities. Automated high-frequency monitoring of these communities is presently limited by the absence of repeatable, rapid protocols to analyse SFCM datasets, where images of individual particles are not available...
2018: PloS One
Mohammad U Zahid, Liang Ma, Sung Jun Lim, Andrew M Smith
Inefficient delivery of macromolecules and nanoparticles to intracellular targets is a major bottleneck in drug delivery, genetic engineering, and molecular imaging. Here we apply live-cell single-quantum-dot imaging and tracking to analyze and classify nanoparticle states after intracellular delivery. By merging trajectory diffusion parameters with brightness measurements, multidimensional analysis reveals distinct and heterogeneous populations that are indistinguishable using single parameters alone. We derive new quantitative metrics of particle loading, cluster distribution, and vesicular release in single cells, and evaluate intracellular nanoparticles with diverse surfaces following osmotic delivery...
May 8, 2018: Nature Communications
Giovanni Garberoglio, Renzo Vallauri, Ubaldo Bafile
Extensive molecular dynamics simulations of liquid sodium have been carried out to evaluate correlation functions of several dynamical quantities. We report the results of a novel analysis of the longitudinal and transverse correlation functions obtained by evaluating directly their self- and distinct contributions at different wavevectors k. It is easily recognized that the self-contribution remains close to its k → 0 limit, which turns out to be exactly the autocorrelation function of the single particle velocity...
May 7, 2018: Journal of Chemical Physics
Arnaud Lesaine, Daniel Bonamy, Georges Gauthier, Cindy L Rountree, Véronique Lazarus
Layers obtained by drying a colloidal dispersion of silica spheres are found to be a good benchmark to test the elastic behaviour of porous media, in the challenging case of high porosities and nano-sized microstructures. Classically used for these systems, Kendall's approach explicitly considers the effect of surface adhesive forces onto the contact area between the particles. This approach provides the Young's modulus using a single adjustable parameter (the adhesion energy) but provides no further information on the tensorial nature and possible anisotropy of elasticity...
May 8, 2018: Soft Matter
Himanshu Bhatt, Sri Vishnu Kiran Rompicharla, Neeraja Komanduri, Aashma Shah, Sateja Paradkar, Balaram Ghosh, Swati Biswas
BACKGROUND: Solid lipid nanoparticles (SLNs) represent an affordable, easily scalable, stable and biocompatible drug delivery system with a high drug to lipid ratio which also improves solubility of poorly soluble drugs. OBJECTIVE: SLNs were developed by using glyceryl monostearate as the single lipid in presence of surfactant Poloxamer 188 and evaluated the efficiency of the SLNs to load the therapeutic cargo, curcumin (CUR). METHOD: The nano-formulation was optimized by Quality by Design approach to understand the effect of various process parameters on various quality attributes, including drug loadability, particle size and polydispersity...
May 3, 2018: Current Drug Delivery
Ákos Gellért, Tímea Pósa, Attila Fábián, László Szabó, Károly Bóka, Barbara Forró, Katalin Salánki, László Drahos, Eszter Tóth, Angéla Juhász, Ervin Balázs
A previous study showed that a single amino acid difference in the cucumber mosaic virus (CMV) capsid protein (CP) elicits unusual symptoms. The wild-type strain (CMV-R) induces green mosaic symptoms and malformation while the mutant strain (CMV-R3E79R) causes chlorotic lesions on inoculated leaves and strong stunting with necrosis on systemic leaves. Virion preparations of CMV-R and CMV-R3E79R were partially purified from Nicotiana clevelandii A. Gray and analysed by two-dimensional gel electrophoresis. Their separated protein patterns showed remarkable differences at the 50-75 kDa range, both in numbers and intensity of spots, with more protein spots for the mutant CMV...
May 3, 2018: Virus Research
Christopher A Little, Ruochen Xie, Christopher Batchelor-McAuley, Enno Kätelhön, Xiuting Li, Neil P Young, Richard G Compton
Herein we provide a generic framework for use in the acquisition and analysis of the electrochemical responses of individual nanoparticles, summarising aspects that must be considered to avoid mis-interpretation of data. Specifically, we threefold highlight the importance of the nanoparticle shape, the effect of the nanoparticle diffusion coefficient on the probability of it being observed and the influence of the used measurement bandwidth. Using the oxidation of silver nanoparticles as a model system, it is evidenced that when all of the above have been accounted for, the experimental data is consistent with being associated with the complete oxidation of the nanoparticles (50 nm diameter)...
May 4, 2018: Physical Chemistry Chemical Physics: PCCP
Nazia Khan, Ameeduzzafar, Kushagra Khanna, Aseem Bhatnagar, F J Ahmad, A Ali
PURPOSE: Enhancing the ocular hypotensive effect of forskolin (FK) by means of biodegradable chitosan (CS) coated poly lactic-co-glycolic acid (PLGA) nanoparticles (NP's). METHODS: One step emulsion-sonication process was employed for the formulation of CS-PLGA NP's with optimization being carried out by employing a four factor four level Box Behnken Design Expert. Physical and spectral characterization, drug release, permeation, confocal and ocular tolerance studies (ex-vivo & in vivo) were performed...
April 30, 2018: International Journal of Biological Macromolecules
Lyndsey Hendriks, Alexander Gundlach-Graham, Detlef Günther
Due to the rapid development of nanotechnologies, engineered nanomaterials (ENMs) and nanoparticles (ENPs) are becoming a part of everyday life: nanotechnologies are quickly migrating from laboratory benches to store shelves and industrial processes. As the use of ENPs continues to expand, their release into the environment is unavoidable; however, understanding the mechanisms and degree of ENP release is only possible through direct detection of these nanospecies in relevant matrices and at realistic concentrations...
April 25, 2018: Chimia
Tarek A Ameen, Hesameddin Ilatikhameneh, Archana Tankasala, Yuling Hsueh, James Charles, Jim Fonseca, Michael Povolotskyi, Jun Oh Kim, Sanjay Krishna, Monica S Allen, Jeffery W Allen, Rajib Rahman, Gerhard Klimeck
A detailed theoretical study of the optical absorption in doped self-assembled quantum dots is presented. A rigorous atomistic strain model as well as a sophisticated 20-band tight-binding model are used to ensure accurate prediction of the single particle states in these devices. We also show that for doped quantum dots, many-particle configuration interaction is also critical to accurately capture the optical transitions of the system. The sophisticated models presented in this work reproduce the experimental results for both undoped and doped quantum dot systems...
2018: Beilstein Journal of Nanotechnology
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