Structurally Coloured Secondary Particles Composed of Black and White Colloidal Particles

PubMed Central

Takeoka, Yukikazu; Yoshioka, Shinya; Teshima, Midori; Takano, Atsushi; Harun-Ur-Rashid, Mohammad; Seki, Takahiro

2013-01-01

This study investigated the colourful secondary particles formed by controlling the aggregation states of colloidal silica particles and the enhancement of the structural colouration of the secondary particles caused by adding black particles. We obtained glossy, partially structurally coloured secondary particles in the absence of NaCl, but matte, whitish secondary particles were obtained in the presence of NaCl. When a small amount of carbon black was incorporated into both types of secondary particles, the incoherent multiple scattering of light from the amorphous region was considerably reduced. However, the peak intensities in the reflection spectra, caused by Bragg reflection and by coherent single wavelength scattering, were only slightly decreased. Consequently, a brighter structural colour of these secondary particles was observed with the naked eye. Furthermore, when magnetite was added as a black particle, the coloured secondary particles could be moved and collected by applying an external magnetic field. PMID:23917891

Single-shot imaging of trapped Fermi gas

NASA Astrophysics Data System (ADS)

Gajda, Mariusz; Mostowski, Jan; Sowiński, Tomasz; Załuska-Kotur, Magdalena

2016-07-01

Recently developed techniques allow for simultaneous measurements of the positions of all ultra-cold atoms in a trap with high resolution. Each such single-shot experiment detects one element of the quantum ensemble formed by the cloud of atoms. Repeated single-shot measurements can be used to determine all correlations between particle positions as opposed to standard measurements that determine particle density or two-particle correlations only. In this paper we discuss the possible outcomes of such single-shot measurements in the case of cloud of ultra-cold noninteracting Fermi atoms. We show that the Pauli exclusion principle alone leads to correlations between particle positions that originate from unexpected spatial structures formed by the atoms.

Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud.

PubMed

Cianfrocco, Michael A; Leschziner, Andres E

2015-05-08

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available 'off-the-shelf' computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16-480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.

Protein secondary structure determination by constrained single-particle cryo-electron tomography.

PubMed

Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

2012-12-05

Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series. Copyright © 2012 Elsevier Ltd. All rights reserved.

Molecular architecture of botulinum neurotoxin E revealed by single particle electron microscopy.

PubMed

Fischer, Audrey; Garcia-Rodriguez, Consuelo; Geren, Isin; Lou, Jianlong; Marks, James D; Nakagawa, Terunaga; Montal, Mauricio

2008-02-15

Clostridial botulinum neurotoxin (BoNT) causes a neuroparalytic condition recognized as botulism by arresting synaptic vesicle exocytosis. Although the crystal structures of full-length BoNT/A and BoNT/B holotoxins are known, the molecular architecture of the five other serotypes remains elusive. Here, we present the structures of BoNT/A and BoNT/E using single particle electron microscopy. Labeling of the particles with three different monoclonal antibodies raised against BoNT/E revealed the positions of their epitopes in the electron microscopy structure, thereby identifying the three hallmark domains of BoNT (protease, translocation, and receptor binding). Correspondingly, these antibodies selectively inhibit BoNT translocation activity as detected using a single molecule assay. The global structure of BoNT/E is strikingly different from that of BoNT/A despite strong sequence similarity. We postulate that the unique architecture of functionally conserved modules underlies the distinguishing attributes of BoNT/E and contributes to differences with BoNT/A.

Continuous structural evolution of calcium carbonate particles: a unifying model of copolymer-mediated crystallization.

PubMed

Kulak, Alex N; Iddon, Peter; Li, Yuting; Armes, Steven P; Cölfen, Helmut; Paris, Oskar; Wilson, Rory M; Meldrum, Fiona C

2007-03-28

Two double-hydrophilic block copolymers, each comprising a nonionic block and an anionic block comprising pendent aromatic sulfonate groups, were used as additives to modify the crystallization of CaCO3. Marked morphological changes in the CaCO3 particles were observed depending on the reaction conditions used. A poly(ethylene oxide)-b-poly(sodium 4-styrenesulfonate) diblock copolymer was particularly versatile in effecting a morphological change in calcite particles, and a continuous structural transition in the product particles from polycrystalline to mesocrystal to single crystal was observed with variation in the calcium concentration. The existence of this structural sequence provides unique insight into the mechanism of polymer-mediated crystallization. We propose that it reflects continuity in the crystallization mechanism itself, spanning the limits from nonoriented aggregation of nanoparticles to classical ion-by-ion growth. The various pathways to polycrystalline, mesocrystal, and single-crystal particles, which had previously been considered to be distinct, therefore all form part of a unifying crystallization framework based on the aggregation of precursor subunits.

Quantitatively probing propensity for structural transitions in engineered virus nanoparticles by single-molecule mechanical analysis

NASA Astrophysics Data System (ADS)

Castellanos, Milagros; Carrillo, Pablo J. P.; Mateu, Mauricio G.

2015-03-01

Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies.Viruses are increasingly being studied from the perspective of fundamental physics at the nanoscale as biologically evolved nanodevices with many technological applications. In viral particles of the minute virus of mice (MVM), folded segments of the single-stranded DNA genome are bound to the capsid inner wall and act as molecular buttresses that increase locally the mechanical stiffness of the particle. We have explored whether a quantitative linkage exists in MVM particles between their DNA-mediated stiffening and impairment of a heat-induced, virus-inactivating structural change. A series of structurally modified virus particles with disrupted capsid-DNA interactions and/or distorted capsid cavities close to the DNA-binding sites were engineered and characterized, both in classic kinetics assays and by single-molecule mechanical analysis using atomic force microscopy. The rate constant of the virus inactivation reaction was found to decrease exponentially with the increase in elastic constant (stiffness) of the regions closer to DNA-binding sites. The application of transition state theory suggests that the height of the free energy barrier of the virus-inactivating structural transition increases linearly with local mechanical stiffness. From a virological perspective, the results indicate that infectious MVM particles may have acquired the biological advantage of increased survival under thermal stress by evolving architectural elements that rigidify the particle and impair non-productive structural changes. From a nanotechnological perspective, this study provides proof of principle that determination of mechanical stiffness and its manipulation by protein engineering may be applied for quantitatively probing and tuning the conformational dynamics of virus-based and other protein-based nanoassemblies. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07046a

Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

PubMed Central

Cianfrocco, Michael A; Leschziner, Andres E

2015-01-01

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16–480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM. DOI: http://dx.doi.org/10.7554/eLife.06664.001 PMID:25955969

Cell structures caused by settling particles in turbulent Rayleigh-Bénard convection

NASA Astrophysics Data System (ADS)

Lee, Changhoon; Park, Sangro

2016-11-01

Turbulent thermal convection is an important phenomenon frequently found in nature and industrial processes, often with laden particles. In the last several decades, the vast majority of studies have addressed single phase convective flow with focus on the scaling relation of flow parameters associated with heat transfer. Particle-laden Rayleigh-Bénard convection, however, has not been sufficiently studied. In this study, modulation of cell structures by settling particles in turbulent Rayleigh-Bénard convection in a doubly periodic square channel is investigated using direct numerical simulation with a point particle approach. Flow parameters are fixed at Rayleigh number=106, Prandtl number=0.7, the aspect ratio=6, and Froude number=0.19. We report from the simulations that settling heavy particles modulate irregular large-scale thermal plume structures into organized polygonal cell structures. Different shapes of flow structures are obtained for different particle diameters and mass loadings. We found that polygonal cell structures arise due to asymmetric feedback force exerted by particles onto hot and cold plumes. Increasing the number of particles augments the asymmetry and the polygonal cell structures become smaller, eventually going to the hexagonal structures.

The effect of neutrally buoyant finite-size particles on channel flows in the laminar-turbulent transition regime

NASA Astrophysics Data System (ADS)

Loisel, Vincent; Abbas, Micheline; Masbernat, Olivier; Climent, Eric

2013-12-01

The presence of finite-size particles in a channel flow close to the laminar-turbulent transition is simulated with the Force Coupling Method which allows two-way coupling with the flow dynamics. Spherical particles with channel height-to-particle diameter ratio of 16 are initially randomly seeded in a fluctuating flow above the critical Reynolds number corresponding to single phase flow relaminarization. When steady-state is reached, the particle volume fraction is homogeneously distributed in the channel cross-section (ϕ ≅ 5%) except in the near-wall region where it is larger due to inertia-driven migration. Turbulence statistics (intensity of velocity fluctuations, small-scale vortical structures, wall shear stress) calculated in the fully coupled two-phase flow simulations are compared to single-phase flow data in the transition regime. It is observed that particles increase the transverse r.m.s. flow velocity fluctuations and they break down the flow coherent structures into smaller, more numerous and sustained eddies, preventing the flow to relaminarize at the single-phase critical Reynolds number. When the Reynolds number is further decreased and the suspension flow becomes laminar, the wall friction coefficient recovers the evolution of the laminar single-phase law provided that the suspension viscosity is used in the Reynolds number definition. The residual velocity fluctuations in the suspension correspond to a regime of particulate shear-induced agitation.

Representative volume element model of lithium-ion battery electrodes based on X-ray nano-tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashkooli, Ali Ghorbani; Amirfazli, Amir; Farhad, Siamak

For this, a new model that keeps all major advantages of the single-particle model of lithium-ion batteries (LIBs) and includes three-dimensional structure of the electrode was developed. Unlike the single spherical particle, this model considers a small volume element of an electrode, called the Representative Volume Element (RVE), which represent the real electrode structure. The advantages of using RVE as the model geometry was demonstrated for a typical LIB electrode consisting of nano-particle LiFePO 4 (LFP) active material. The three-dimensional morphology of the LFP electrode was reconstructed using a synchrotron X-ray nano-computed tomography at the Advanced Photon Source of themore » Argonne National. A 27 μm 3 cube from reconstructed structure was chosen as the RVE for the simulation purposes. The model was employed to predict the voltage curve in a half-cell during galvanostatic operations and validated with experimental data. The simulation results showed that the distribution of lithium inside the electrode microstructure is very different from the results obtained based on the single-particle model. The range of lithium concentration is found to be much greater, successfully illustrates the effect of microstructure heterogeneity.« less

Representative volume element model of lithium-ion battery electrodes based on X-ray nano-tomography

DOE PAGES

Kashkooli, Ali Ghorbani; Amirfazli, Amir; Farhad, Siamak; ...

2017-01-28

For this, a new model that keeps all major advantages of the single-particle model of lithium-ion batteries (LIBs) and includes three-dimensional structure of the electrode was developed. Unlike the single spherical particle, this model considers a small volume element of an electrode, called the Representative Volume Element (RVE), which represent the real electrode structure. The advantages of using RVE as the model geometry was demonstrated for a typical LIB electrode consisting of nano-particle LiFePO 4 (LFP) active material. The three-dimensional morphology of the LFP electrode was reconstructed using a synchrotron X-ray nano-computed tomography at the Advanced Photon Source of themore » Argonne National. A 27 μm 3 cube from reconstructed structure was chosen as the RVE for the simulation purposes. The model was employed to predict the voltage curve in a half-cell during galvanostatic operations and validated with experimental data. The simulation results showed that the distribution of lithium inside the electrode microstructure is very different from the results obtained based on the single-particle model. The range of lithium concentration is found to be much greater, successfully illustrates the effect of microstructure heterogeneity.« less

Simulating Biomass Fast Pyrolysis at the Single Particle Scale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ciesielski, Peter; Wiggins, Gavin; Daw, C Stuart

2017-07-01

Simulating fast pyrolysis at the scale of single particles allows for the investigation of the impacts of feedstock-specific parameters such as particle size, shape, and species of origin. For this reason particle-scale modeling has emerged as an important tool for understanding how variations in feedstock properties affect the outcomes of pyrolysis processes. The origins of feedstock properties are largely dictated by the composition and hierarchical structure of biomass, from the microstructural porosity to the external morphology of milled particles. These properties may be accounted for in simulations of fast pyrolysis by several different computational approaches depending on the level ofmore » structural and chemical complexity included in the model. The predictive utility of particle-scale simulations of fast pyrolysis can still be enhanced substantially by advancements in several areas. Most notably, considerable progress would be facilitated by the development of pyrolysis kinetic schemes that are decoupled from transport phenomena, predict product evolution from whole-biomass with increased chemical speciation, and are still tractable with present-day computational resources.« less

Nano-structured surface plasmon resonance sensor for sensitivity enhancement

NASA Astrophysics Data System (ADS)

Kim, Jae-Ho; Kim, Hyo-Sop; Kim, Jin-Ho; Choi, Sung-Wook; Cho, Yong-Jin

2008-08-01

A new nano-structured SPR sensor was devised to improve its sensitivity. Nano-scaled silica particles were used as the template to fabricate nano-structure. The surface of the silica particles was modified with thiol group and a single layer of the modified silica particles was attached on the gold or silver thin film using Langmuir-Blodgett (LB) method. Thereafter, gold or silver was coated on the template by an e-beam evaporator. Finally, the nano-structured surface with basin-like shape was obtained after removing the silica particles by sonication. Applying the new developed SPR sensor to a model food of alcoholic beverage, the sensitivities for the gold and silver nano-structured sensors, respectively, had 95% and 126% higher than the conventional one.

Optical amplification of photothermal therapy with gold nanoparticles and nanoclusters

NASA Astrophysics Data System (ADS)

Khlebtsov, Boris; Zharov, Vladimir; Melnikov, Andrei; Tuchin, Valery; Khlebtsov, Nikolai

2006-10-01

Recently, several groups (Anderson, Halas, Zharov, and their co-workers, 2003; El-Sayed and co-workers, 2006) demonstrated, through pioneering results, the great potential of photothermal (PT) therapy for the selective treatment of cancer cells, bacteria, viruses, and DNA targeted with gold nanospheres, nanoshells, nanorods, and nanosphere clusters. However, the current understanding of the relationship between the nanoparticle/cluster parameters (size, shape, particle/cluster structure, etc) and the efficiency of PT therapy is limited. Here, we report theoretical simulations aimed at finding the optimal single-particle and cluster structures to achieve its maximal absorption, which is crucial for PT therapeutic effects. To characterize the optical amplification in laser-induced thermal effects, we introduce relevant parameters such as the ratio of the absorption cross section to the gold mass of a single-particle structure and absorption amplification, defined as the ratio of cluster absorption to the total absorption of non-interacting particles. We consider the absorption efficiency of single nanoparticles (gold spheres, rods, and silica/gold nanoshells), linear chains, 2D lattice arrays, 3D random volume clusters, and the random aggregated N-particle ensembles on the outer surface of a larger dielectric sphere, which mimic aggregation of nanosphere bioconjugates on or within cancer cells. The cluster particles are bare or biopolymer-coated gold nanospheres. The light absorption of cluster structures is studied by using the generalized multiparticle Mie solution and the T-matrix method. The gold nanoshells with (silica core diameter)/(gold shell thickness) parameters of (50-100)/(3-8) nm and nanorods with minor/major sizes of (15-20)/(50-70) nm are shown to be more efficient PT labels and sensitizers than the equivolume solid single gold spheres. In the case of nanosphere clusters, the interparticle separations and the short linear-chain fragments are the main structural parameters determining the absorption efficiency and its spectral shifting to the red. Although we have not found a noticeable dependence of absorption amplification on the cluster sphere size, 20-40 nm particles are found to be most effective, in accordance with our experimental observations. The long-wavelength absorption efficiency of random clusters increases with the cluster particle number N at small N and reveals a saturation behaviour at N>20.

Morphological classification of bioaerosols from composting using scanning electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamer Vestlund, A.; FIRA International Ltd., Maxwell Road, Stevenage, Herts SG1 2EW; Al-Ashaab, R.

2014-07-15

Highlights: • Bioaerosols were captured using the filter method. • Bioaerosols were analysed using scanning electron microscope. • Bioaerosols were classified on the basis of morphology. • Single small cells were found more frequently than aggregates and larger cells. • Smaller cells may disperse further than heavier aggregate structures. - Abstract: This research classifies the physical morphology (form and structure) of bioaerosols emitted from open windrow composting. Aggregation state, shape and size of the particles captured are reported alongside the implications for bioaerosol dispersal after release. Bioaerosol sampling took place at a composting facility using personal air filter samplers. Samplesmore » were analysed using scanning electron microscopy. Particles were released mainly as small (<1 μm) single, spherical cells, followed by larger (>1 μm) single cells, with aggregates occurring in smaller proportions. Most aggregates consisted of clusters of 2–3 particles as opposed to chains, and were <10 μm in size. No cells were attached to soil debris or wood particles. These small single cells or small aggregates are more likely to disperse further downwind from source, and cell viability may be reduced due to increased exposure to environmental factors.« less

Nanotip analysis for dielectrophoretic concentration of nanosized viral particles.

PubMed

Yeo, Woon-Hong; Lee, Hyun-Boo; Kim, Jong-Hoon; Lee, Kyong-Hoon; Chung, Jae-Hyun

2013-05-10

Rapid and sensitive detection of low-abundance viral particles is strongly demanded in health care, environmental control, military defense, and homeland security. Current detection methods, however, lack either assay speed or sensitivity, mainly due to the nanosized viral particles. In this paper, we compare a dendritic, multi-terminal nanotip ('dendritic nanotip') with a single terminal nanotip ('single nanotip') for dielectrophoretic (DEP) concentration of viral particles. The numerical computation studies the concentration efficiency of viral particles ranging from 25 to 100 nm in radius for both nanotips. With DEP and Brownian motion considered, when the particle radius decreases by two times, the concentration time for both nanotips increases by 4-5 times. In the computational study, a dendritic nanotip shows about 1.5 times faster concentration than a single nanotip for the viral particles because the dendritic structure increases the DEP-effective area to overcome the Brownian motion. For the qualitative support of the numerical results, the comparison experiment of a dendritic nanotip and a single nanotip is conducted. Under 1 min of concentration time, a dendritic nanotip shows a higher sensitivity than a single nanotip. When the concentration time is 5 min, the sensitivity of a dendritic nanotip for T7 phage is 10(4) particles ml(-1). The dendritic nanotip-based concentrator has the potential for rapid identification of viral particles.

Nanotip analysis for dielectrophoretic concentration of nanosized viral particles

NASA Astrophysics Data System (ADS)

Yeo, Woon-Hong; Lee, Hyun-Boo; Kim, Jong-Hoon; Lee, Kyong-Hoon; Chung, Jae-Hyun

2013-05-01

Rapid and sensitive detection of low-abundance viral particles is strongly demanded in health care, environmental control, military defense, and homeland security. Current detection methods, however, lack either assay speed or sensitivity, mainly due to the nanosized viral particles. In this paper, we compare a dendritic, multi-terminal nanotip (‘dendritic nanotip’) with a single terminal nanotip (‘single nanotip’) for dielectrophoretic (DEP) concentration of viral particles. The numerical computation studies the concentration efficiency of viral particles ranging from 25 to 100 nm in radius for both nanotips. With DEP and Brownian motion considered, when the particle radius decreases by two times, the concentration time for both nanotips increases by 4-5 times. In the computational study, a dendritic nanotip shows about 1.5 times faster concentration than a single nanotip for the viral particles because the dendritic structure increases the DEP-effective area to overcome the Brownian motion. For the qualitative support of the numerical results, the comparison experiment of a dendritic nanotip and a single nanotip is conducted. Under 1 min of concentration time, a dendritic nanotip shows a higher sensitivity than a single nanotip. When the concentration time is 5 min, the sensitivity of a dendritic nanotip for T7 phage is 104 particles ml-1. The dendritic nanotip-based concentrator has the potential for rapid identification of viral particles.

Structural characterization and gas reactions of small metal particles by high resolution in-situ TEM (Transmission Electron Microscopy) and TED (Transmission Electron Diffraction)

NASA Technical Reports Server (NTRS)

Heinemann, K.

1987-01-01

The detection and size analysis of small metal particles supported on amorphous substrates becomes increasingly difficult when the particle size approaches that of the phase contrast background structures of the support. An approach of digital image analysis, involving Fourier transformation of the original image, filtering, and image reconstruction was studied with respect to the likelihood of unambiguously detecting particles of less than 1 nm diameter on amorphous substrates from a single electron micrograph.

Experimental study on pore structure and performance of sintered porous wick

NASA Astrophysics Data System (ADS)

He, Da; Wang, Shufan; Liu, Rutie; Wang, Zhubo; Xiong, Xiang; Zou, Jianpeng

2018-02-01

Porous wicks were prepared via powder metallurgy using NH4HCO3 powders as pore-forming agent. The pore-forming agent particle size was varied to control the pore structure and equivalent pore size distribution feature of porous wick. The effect of pore-forming agent particle size on the porosity, pore structures, equivalent pore size distribution and capillary pumping performance were investigated. Results show that with the particle size of pore-forming agent decrease, the green density and the volume shrinkage of the porous wicks gradually increase and the porosity reduces slightly. There are two types of pores inside the porous wick, large-sized prefabricated pores and small-sized gap pores. With the particle size of pore-forming agent decrease, the size of the prefabricated pores becomes smaller and the distribution tends to be uniform. Gap pores and prefabricated pores inside the wick can make up different types of pore channels. The equivalent pore size of wick is closely related to the structure of pore channels. Furthermore, the equivalent pore size distribution of wick shows an obvious double-peak feature when the pore-forming agent particle size is large. With the particle size of pore-forming agent decrease, the two peaks of equivalent pore size distribution approach gradually to each other, resulting in a single-peak feature. Porous wick with single-peak feature equivalent pore size distribution possesses the better capillary pumping performances.

Single particle tracking reveals spatial and dynamic organization of the Escherichia coli biofilm matrix

NASA Astrophysics Data System (ADS)

Birjiniuk, Alona; Billings, Nicole; Nance, Elizabeth; Hanes, Justin; Ribbeck, Katharina; Doyle, Patrick S.

2014-08-01

Biofilms are communities of surface-adherent bacteria surrounded by secreted polymers known as the extracellular polymeric substance. Biofilms are harmful in many industries, and thus it is of great interest to understand their mechanical properties and structure to determine ways to destabilize them. By performing single particle tracking with beads of varying surface functionalization it was found that charge interactions play a key role in mediating mobility within biofilms. With a combination of single particle tracking and microrheological concepts, it was found that Escherichia coli biofilms display height dependent charge density that evolves over time. Statistical analyses of bead trajectories and confocal microscopy showed inter-connecting micron scale channels that penetrate throughout the biofilm, which may be important for nutrient transfer through the system. This methodology provides significant insight into a particular biofilm system and can be applied to many others to provide comparisons of biofilm structure. The elucidation of structure provides evidence for the permeability of biofilms to microscale objects, and the ability of a biofilm to mature and change properties over time.

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

NASA Astrophysics Data System (ADS)

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; Samoylova, Liubov; Buzmakov, Alexey; Jurek, Zoltan; Ziaja, Beata; Santra, Robin; Loh, N. Duane; Tschentscher, Thomas; Mancuso, Adrian P.

2016-04-01

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.

Printing 1D Assembly Array of Single Particle Resolution for Magnetosensing.

PubMed

Gao, Meng; Kuang, Minxuan; Li, Lihong; Liu, Meijin; Wang, Libin; Song, Yanlin

2018-05-01

Magnetosensing is a ubiquitous ability for many organism species in nature. 1D assembly, especially that arranged in single-particle-resolution regulation, is able to sense the direction of magnetic field depending on the enhanced dipolar interaction in the linear orientation. Inspired by the magnetosome structure in magnetotactic bacteria, a 1D assembly array of single particle resolution with controlled length and well-behaved configuration is prepared via inkjet printing method assisted with magnetic guiding. In the fabrication process, chains in a "tip-to-tip" regulation with the desired number of particles are prepared in a confined tiny inkjet-printed droplet. By adjusting the receding angle of the substrate, the assembled 1D morphology is kept/deteriorated depending on the pinning/depinning behavior during ink evaporation, which leads to the formation of well-behaved 1D assembly/aggregated dot assembly. Owing to the high-aspect-ratio characteristic of the assembled structure, the as-prepared 1D arrays can be used for magnetic field sensing with anisotropic magnetization M // /M ⊥ up to 6.03. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Emerging opportunities in structural biology with X-ray free-electron lasers

PubMed Central

Schlichting, Ilme; Miao, Jianwei

2012-01-01

X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be “outrun” by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of “diffraction-before-destruction” has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical “phase problem” by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs. PMID:22922042

Controlled Synthesis and Fluorescence Tracking of Highly Uniform Poly(N-isopropylacrylamide) Microgels.

PubMed

Virtanen, Otto L J; Purohit, Ashvini; Brugnoni, Monia; Wöll, Dominik; Richtering, Walter

2016-09-08

Stimuli-sensitive poly(N-isopropylacrylamide) (PNIPAM) microgels have various prospective practical applications and uses in fundamental research. In this work, we use single particle tracking of fluorescently labeled PNIPAM microgels as a showcase for tuning microgel size by a rapid non-stirred precipitation polymerization procedure. This approach is well suited for prototyping new reaction compositions and conditions or for applications that do not require large amounts of product. Microgel synthesis, particle size and structure determination by dynamic and static light scattering are detailed in the protocol. It is shown that the addition of functional comonomers can have a large influence on the particle nucleation and structure. Single particle tracking by wide-field fluorescence microscopy allows for an investigation of the diffusion of labeled tracer microgels in a concentrated matrix of non-labeled microgels, a system not easily investigated by other methods such as dynamic light scattering.

Cryo-EM image alignment based on nonuniform fast Fourier transform.

PubMed

Yang, Zhengfan; Penczek, Pawel A

2008-08-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

PubMed Central

Yang, Zhengfan; Penczek, Pawel A.

2008-01-01

In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform Fast Fourier Transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis. PMID:18499351

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

NASA Astrophysics Data System (ADS)

Metere, Alfredo; Oleynikov, Peter; Dzugutov, Mikhail; O'Keeffe, Michael

2014-12-01

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.

Spectral structure of pressure measurements made in a combustion duct. [jet engine noise

NASA Technical Reports Server (NTRS)

Miles, J. H.; Raftopoulos, D. D.

1980-01-01

A model for acoustic plane wave propagation in a combustion duct through a confined, flowing gas containing soot particles is presented. The model takes into account only heat transfer between the gas and soot particles. As a result, the model depends on only a single parameter which can be written as the ratio of the soot particle thermal relaxation time to the soot particle mass fraction. The model yields expressions for the attenuation and dispersion of the plane wave which depends only on this single parameter. The model was used to calculate pressure spectra in a combustion duct. The results were compared with measured spectra. For particular values of the single free parameter, the calculated spectra resemble the measured spectra. Consequently, the model, to this extent, explains the experimental measurements and provides some insight into the number and type of particles.

Single-particle excitations in the level structure of 64Cu

NASA Astrophysics Data System (ADS)

Samanta, S.; Das, S.; Bhattacharjee, R.; Chatterjee, S.; Raut, R.; Ghugre, S. S.; Sinha, A. K.; Garg, U.; Neelam, Kumar, N.; Jones, P.; Laskar, Md. Sazedur R.; Babra, F. S.; Biswas, S.; Saha, S.; Singh, P.; Palit, R.

2018-01-01

Excited states of the 64Cu(Z =29 ,N =35 ) nucleus have been probed using heavy-ion-induced fusion evaporation reaction and an array of Compton-suppressed Clovers as detection system for the emitted γ rays. More than 50 new transitions have been identified and the level scheme of the nucleus has been established up to an excitation energy Ex˜6 MeV and spin ˜10 ℏ . The experimental results have been compared with those from large-basis shell-model calculations that facilitated an understanding of the single-particle configurations underlying the level structure of the nucleus.

Effects of complex internal structures on rheology of multiple emulsions particles in 2D from a boundary integral method.

PubMed

Wang, Jingtao; Liu, Jinxia; Han, Junjie; Guan, Jing

2013-02-08

A boundary integral method is developed to investigate the effects of inner droplets and asymmetry of internal structures on rheology of two-dimensional multiple emulsion particles with arbitrary numbers of layers and droplets within each layer. Under a modest extensional flow, the number increment of layers and inner droplets, and the collision among inner droplets subject the particle to stronger shears. In addition, the coalescence or release of inner droplets changes the internal structure of the multiple emulsion particles. Since the rheology of such particles is sensitive to internal structures and their change, modeling them as the core-shell particles to obtain the viscosity equation of a single particle should be modified by introducing the time-dependable volume fraction Φ(t) of the core instead of the fixed Φ. An asymmetric internal structure induces an oriented contact and merging of the outer and inner interface. The start time of the interface merging is controlled by adjusting the viscosity ratio and enhancing the asymmetry, which is promising in the controlled release of inner droplets through hydrodynamics for targeted drug delivery.

Probing the Single-Particle Character of Rotational States in F 19 Using a Short-Lived Isomeric Beam

DOE Office of Scientific and Technical Information (OSTI.GOV)

Santiago-Gonzalez, D.; Auranen, K.; Avila, M. L.

2018-03-01

A beam containing a substantial component of both the J(pi) = 5(+), T-1/2 = 162 ns isomeric state of F-18 and its 1(+), 109.77-min ground state is utilized to study members of the ground-state rotational band in F-19 through the neutron transfer reaction (d,p) in inverse kinematics. The resulting spectroscopic strengths confirm the single-particle nature of the 13/2(+) band-terminating state. The agreement between shell-model calculations using an interaction constructed within the sd shell, and our experimental results reinforces the idea of a single-particle-collective duality in the descriptions of the structure of atomic nuclei.

On-Chip Magnetic Platform for Single-Particle Manipulation with Integrated Electrical Feedback.

PubMed

Monticelli, Marco; Torti, Andrea; Cantoni, Matteo; Petti, Daniela; Albisetti, Edoardo; Manzin, Alessandra; Guerriero, Erica; Sordan, Roman; Gervasoni, Giacomo; Carminati, Marco; Ferrari, Giorgio; Sampietro, Marco; Bertacco, Riccardo

2016-02-17

Methods for the manipulation of single magnetic particles have become very interesting, in particular for in vitro biological studies. Most of these studies require an external microscope to provide the operator with feedback for controlling the particle motion, thus preventing the use of magnetic particles in high-throughput experiments. In this paper, a simple and compact system with integrated electrical feedback is presented, implementing in the very same device both the manipulation and detection of the transit of single particles. The proposed platform is based on zig-zag shaped magnetic nanostructures, where transverse magnetic domain walls are pinned at the corners and attract magnetic particles in suspension. By applying suitable external magnetic fields, the domain walls move to the nearest corner, thus causing the step by step displacement of the particles along the nanostructure. The very same structure is also employed for detecting the bead transit. Indeed, the presence of the magnetic particle in suspension over the domain wall affects the depinning field required for its displacement. This characteristic field can be monitored through anisotropic magnetoresistance measurements, thus implementing an integrated electrical feedback of the bead transit. In particular, the individual manipulation and detection of single 1-μm sized beads is demonstrated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

RNA secondary structures of the bacteriophage phi6 packaging regions.

PubMed

Pirttimaa, M J; Bamford, D H

2000-06-01

Bacteriophage phi6 genome consists of three segments of double-stranded RNA. During maturation, single-stranded copies of these segments are packaged into preformed polymerase complex particles. Only phi6 RNA is packaged, and each particle contains only one copy of each segment. An in vitro packaging and replication assay has been developed for phi6, and the packaging signals (pac sites) have been mapped to the 5' ends of the RNA segments. In this study, we propose secondary structure models for the pac sites of phi6 single-stranded RNA segments. Our models accommodate data from structure-specific chemical modifications, free energy minimizations, and phylogenetic comparisons. Previously reported pac site deletion studies are also discussed. Each pac site possesses a unique architecture, that, however, contains common structural elements.

Characterization of core–shell MOF particles by depth profiling experiments using on-line single particle mass spectrometry

DOE PAGES

Cahill, J. F.; Fei, H.; Cohen, S. M.; ...

2015-01-05

Materials with core-shell structures have distinct properties that lend themselves to a variety of potential applications. Characterization of small particle core-shell materials presents a unique analytical challenge. Herein, single particles of solid-state materials with core-shell structures were measured using on-line aerosol time-of-flight mass spectrometry (ATOFMS). Laser 'depth profiling' experiments verified the core-shell nature of two known core-shell particle configurations (< 2 mu m diameter) that possessed inverted, complimentary core-shell compositions (ZrO2@SiO2 versus SiO2@ZrO2). The average peak area ratios of Si and Zr ions were calculated to definitively show their core-shell composition. These ratio curves acted as a calibrant for anmore » uncharacterized sample - a metal-organic framework (MOF) material surround by silica (UiO-66(Zr)@SiO2; UiO = University of Oslo). ATOFMS depth profiling was used to show that these particles did indeed exhibit a core-shell architecture. The results presented here show that ATOFMS can provide unique insights into core-shell solid-state materials with particle diameters between 0.2-3 mu m.« less

IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure

PubMed Central

Zhang, Lei; Ren, Gang

2012-01-01

The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a “focused electron tomography reconstruction” (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single “snapshot” molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules. PMID:22291925

Expanding Single Particle Mass Spectrometer Analyses for the Identification of Microbe Signatures in Sea Spray Aerosol.

PubMed

Sultana, Camille M; Al-Mashat, Hashim; Prather, Kimberly A

2017-10-03

Ocean-derived microbes in sea spray aersosol (SSA) have the potential to influence climate and weather by acting as ice nucleating particles in clouds. Single particle mass spectrometers (SPMSs), which generate in situ single particle composition data, are excellent tools for characterizing aerosols under changing environmental conditions as they can provide high temporal resolution and require no sample preparation. While SPMSs have proven capable of detecting microbes, these instruments have never been utilized to definitively identify aerosolized microbes in ambient sea spray aersosol. In this study, an aerosol time-of-flight mass spectrometer was used to analyze laboratory generated SSA produced from natural seawater in a marine aerosol reference tank. We present the first description of a population of biological SSA mass spectra (BioSS), which closely match the ion signatures observed in previous terrestrial microbe studies. The fraction of BioSS dramatically increased in the largest supermicron particles, consistent with field and laboratory measurements of microbes ejected by bubble bursting, further supporting the assignment of BioSS mass spectra as microbes. Finally, as supported by analysis of inorganic ion signals, we propose that dry BioSS particles have heterogeneous structures, with microbes adhered to sodium chloride nodules surrounded by magnesium-enriched coatings. Consistent with this structure, chlorine-containing ion markers were ubiquitous in BioSS spectra and identified as possible tracers for distinguishing recently aerosolized marine from terrestrial microbes.

Problems in obtaining perfect images by single-particle electron cryomicroscopy of biological structures in amorphous ice.

PubMed

Henderson, Richard; McMullan, Greg

2013-02-01

Theoretical considerations together with simulations of single-particle electron cryomicroscopy images of biological assemblies in ice demonstrate that atomic structures should be obtainable from images of a few thousand asymmetric units, provided the molecular weight of the whole assembly being studied is greater than the minimum needed for accurate position and orientation determination. However, with present methods of specimen preparation and current microscope and detector technologies, many more particles are needed, and the alignment of smaller assemblies is difficult or impossible. Only larger structures, with enough signal to allow good orientation determination and with enough images to allow averaging of many hundreds of thousands or even millions of asymmetric units, have successfully produced high-resolution maps. In this review, we compare the contrast of experimental electron cryomicroscopy images of two smaller molecular assemblies, namely apoferritin and beta-galactosidase, with that expected from perfect simulated images calculated from their known X-ray structures. We show that the contrast and signal-to-noise ratio of experimental images still require significant improvement before it will be possible to realize the full potential of single-particle electron cryomicroscopy. In particular, although reasonably good orientations can be obtained for beta-galactosidase, we have been unable to obtain reliable orientation determination from experimental images of apoferritin. Simulations suggest that at least 2-fold improvement of the contrast in experimental images at ~10 Å resolution is needed and should be possible.

Single-particle states vs. collective modes: friends or enemies ?

NASA Astrophysics Data System (ADS)

Otsuka, T.; Tsunoda, Y.; Togashi, T.; Shimizu, N.; Abe, T.

2018-05-01

The quantum self-organization is introduced as one of the major underlying mechanisms of the quantum many-body systems. In the case of atomic nuclei as an example, two types of the motion of nucleons, single-particle states and collective modes, dominate the structure of the nucleus. The collective mode arises as the balance between the effect of the mode-driving force (e.g., quadrupole force for the ellipsoidal deformation) and the resistance power against it. The single-particle energies are one of the sources to produce such resistance power: a coherent collective motion is more hindered by larger spacings between relevant single particle states. Thus, the single-particle state and the collective mode are "enemies" against each other. However, the nuclear forces are rich enough so as to enhance relevant collective mode by reducing the resistance power by changing single-particle energies for each eigenstate through monopole interactions. This will be verified with the concrete example taken from Zr isotopes. Thus, the quantum self-organization occurs: single-particle energies can be self-organized by (i) two quantum liquids, e.g., protons and neutrons, (ii) monopole interaction (to control resistance). In other words, atomic nuclei are not necessarily like simple rigid vases containing almost free nucleons, in contrast to the naïve Fermi liquid picture. Type II shell evolution is considered to be a simple visible case involving excitations across a (sub)magic gap. The quantum self-organization becomes more important in heavier nuclei where the number of active orbits and the number of active nucleons are larger.

Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning

PubMed Central

Wu, Jiayi; Ma, Yong-Bei; Congdon, Charles; Brett, Bevin; Chen, Shuobing; Xu, Yaofang; Ouyang, Qi

2017-01-01

Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM) data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the assessment of structural heterogeneity. However, traditional algorithms for unsupervised classification, such as K-means clustering and maximum likelihood optimization, may classify images into wrong classes with decreasing signal-to-noise-ratio (SNR) in the image data, yet demand increased computational costs. Overcoming these limitations requires further development of clustering algorithms for high-performance cryo-EM data processing. Here we introduce an unsupervised single-particle clustering algorithm derived from a statistical manifold learning framework called generative topographic mapping (GTM). We show that unsupervised GTM clustering improves classification accuracy by about 40% in the absence of input references for data with lower SNRs. Applications to several experimental datasets suggest that our algorithm can detect subtle structural differences among classes via a hierarchical clustering strategy. After code optimization over a high-performance computing (HPC) environment, our software implementation was able to generate thousands of reference-free class averages within hours in a massively parallel fashion, which allows a significant improvement on ab initio 3D reconstruction and assists in the computational purification of homogeneous datasets for high-resolution visualization. PMID:28786986

Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.

PubMed

Wu, Jiayi; Ma, Yong-Bei; Congdon, Charles; Brett, Bevin; Chen, Shuobing; Xu, Yaofang; Ouyang, Qi; Mao, Youdong

2017-01-01

Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM) data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the assessment of structural heterogeneity. However, traditional algorithms for unsupervised classification, such as K-means clustering and maximum likelihood optimization, may classify images into wrong classes with decreasing signal-to-noise-ratio (SNR) in the image data, yet demand increased computational costs. Overcoming these limitations requires further development of clustering algorithms for high-performance cryo-EM data processing. Here we introduce an unsupervised single-particle clustering algorithm derived from a statistical manifold learning framework called generative topographic mapping (GTM). We show that unsupervised GTM clustering improves classification accuracy by about 40% in the absence of input references for data with lower SNRs. Applications to several experimental datasets suggest that our algorithm can detect subtle structural differences among classes via a hierarchical clustering strategy. After code optimization over a high-performance computing (HPC) environment, our software implementation was able to generate thousands of reference-free class averages within hours in a massively parallel fashion, which allows a significant improvement on ab initio 3D reconstruction and assists in the computational purification of homogeneous datasets for high-resolution visualization.

Growth of copper-zinc and copper-magnesium particles by gas-evaporation technique

NASA Astrophysics Data System (ADS)

Ohno, T.

1984-12-01

Fine particles of Cu-Zn and Cu-Mg systems of diameter less than 500 nm were prepared by evaporating the constituent metals simultaneously from two evaporation sources in an atmosphere of argon of 10 to 30 Torr. The composition, crystal structure and habit of the alloy particles were investigated by electron microscopy. The composition of the alloy particles varied depending on the growth zone of metal smoke and almost all phases known in Cu-Zn or Cu-Mg system were found at the same time. The particles with single phase showed generally well-defined crystal habits characteristic of their crystal structures. For the particles with two phases, a fixed lattice relation between the two phases was generally recognized. The formation process of the alloy particles is discussed through these observations.

Effects of nuclear structure in the spin-dependent scattering of weakly interacting massive particles

NASA Astrophysics Data System (ADS)

Nikolaev, M. A.; Klapdor-Kleingrothaus, H. V.

1993-06-01

We present calculations of the nuclear from factors for spin-dependent elastic scattering of dark matter WIMPs from123Te and131Xe isotopes, proposed to be used for dark matter detection. A method based on the theory of finite Fermi systems was used to describe the reduction of the single-particle spin-dependent matrix elements in the nuclear medium. Nucleon single-particle states were calculated in a realistic shell model potential; pairing effects were treated within the BCS model. The coupling of the lowest single-particle levels in123Te to collective 2+ excitations of the core was taken into account phenomenologically. The calculated nuclear form factors are considerably less then the single-particle ones for low momentum transfer. At high momentum transfer some dynamical amplification takes place due to the pion exchange term in the effective nuclear interaction. But as the momentum transfer increases, the difference disappears, the momentum transfer increases and the quenching effect disappears. The shape of the nuclear form factor for the131Xe isotope differs from the one obtained using an oscillator basis.

Particle decay of proton-unbound levels in N 12

DOE PAGES

Chipps, K. A.; Pain, S. D.; Greife, U.; ...

2017-04-24

Transfer reactions are a useful tool for studying nuclear structure, particularly in the regime of low level densities and strong single-particle strengths. Additionally, transfer reactions can populate levels above particle decay thresholds, allowing for the possibility of studying the subsequent decays and furthering our understanding of the nuclei being probed. In particular, the decay of loosely bound nuclei such as 12 N can help inform and improve structure models.The purpose of this paper is to learn about the decay of excited states in 12 N , to more generally inform nuclear structure models, particularly in the case of particle-unbound levelsmore » in low-mass systems which are within the reach of state-of-the-art ab initio calculations.« less

Microscopic insight into the structure of gallium isotopes

NASA Astrophysics Data System (ADS)

Verma, Preeti; Sharma, Chetan; Singh, Suram; Bharti, Arun; Khosa, S. K.

2012-07-01

Projected Shell Model technique has been applied to odd-A71-81Ga nuclei with the deformed single-particle states generated by the standard Nilsson potential. Various nuclear structure quantities have been calculated with this technique and compared with the available experimental data in the present work. The known experimental data of the yrast bands in these nuclei are persuasively described and the band diagrams obtained for these nuclei show that the yrast bands in these odd-A Ga isotopes don't belong to the single intrinsic state only but also have multi-particle states. The back-bending in moment of inertia and the electric quadrupole transitions are also calculated.

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

PubMed Central

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; Samoylova, Liubov; Buzmakov, Alexey; Jurek, Zoltan; Ziaja, Beata; Santra, Robin; Loh, N. Duane; Tschentscher, Thomas; Mancuso, Adrian P.

2016-01-01

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy and incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. We demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design. PMID:27109208

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy andmore » incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.« less

A comprehensive simulation framework for imaging single particles and biomolecules at the European X-ray Free-Electron Laser

DOE PAGES

Yoon, Chun Hong; Yurkov, Mikhail V.; Schneidmiller, Evgeny A.; ...

2016-04-25

The advent of newer, brighter, and more coherent X-ray sources, such as X-ray Free-Electron Lasers (XFELs), represents a tremendous growth in the potential to apply coherent X-rays to determine the structure of materials from the micron-scale down to the Angstrom-scale. There is a significant need for a multi-physics simulation framework to perform source-to-detector simulations for a single particle imaging experiment, including (i) the multidimensional simulation of the X-ray source; (ii) simulation of the wave-optics propagation of the coherent XFEL beams; (iii) atomistic modelling of photon-material interactions; (iv) simulation of the time-dependent diffraction process, including incoherent scattering; (v) assembling noisy andmore » incomplete diffraction intensities into a three-dimensional data set using the Expansion-Maximisation-Compression (EMC) algorithm and (vi) phase retrieval to obtain structural information. Furthermore, we demonstrate the framework by simulating a single-particle experiment for a nitrogenase iron protein using parameters of the SPB/SFX instrument of the European XFEL. This exercise demonstrably yields interpretable consequences for structure determination that are crucial yet currently unavailable for experiment design.« less

Single-particle cryo-EM-Improved ab initio 3D reconstruction with SIMPLE/PRIME.

PubMed

Reboul, Cyril F; Eager, Michael; Elmlund, Dominika; Elmlund, Hans

2018-01-01

Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over-the-counter laptops and CPU workstations is demonstrated. © 2017 The Protein Society.

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Donatelli, Jeffrey J.; Sethian, James A.; Zwart, Peter H.

Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithmmore » to reconstruct structural information from singleparticle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.« less

Reconstruction from limited single-particle diffraction data via simultaneous determination of state, orientation, intensity, and phase

DOE PAGES

Donatelli, Jeffrey J.; Sethian, James A.; Zwart, Peter H.

2017-06-26

Free-electron lasers now have the ability to collect X-ray diffraction patterns from individual molecules; however, each sample is delivered at unknown orientation and may be in one of several conformational states, each with a different molecular structure. Hit rates are often low, typically around 0.1%, limiting the number of useful images that can be collected. Determining accurate structural information requires classifying and orienting each image, accurately assembling them into a 3D diffraction intensity function, and determining missing phase information. Additionally, single particles typically scatter very few photons, leading to high image noise levels. We develop a multitiered iterative phasing algorithmmore » to reconstruct structural information from singleparticle diffraction data by simultaneously determining the states, orientations, intensities, phases, and underlying structure in a single iterative procedure. We leverage real-space constraints on the structure to help guide optimization and reconstruct underlying structure from very few images with excellent global convergence properties. We show that this approach can determine structural resolution beyond what is suggested by standard Shannon sampling arguments for ideal images and is also robust to noise.« less

Octupole deformation in neutron-rich actinides and superheavy nuclei and the role of nodal structure of single-particle wavefunctions in extremely deformed structures of light nuclei

NASA Astrophysics Data System (ADS)

Afanasjev, A. V.; Abusara, H.; Agbemava, S. E.

2018-03-01

Octupole deformed shapes in neutron-rich actinides and superheavy nuclei as well as extremely deformed shapes of the N∼ Z light nuclei have been investigated within the framework of covariant density functional theory. We confirmed the presence of new region of octupole deformation in neutron-rich actinides with the center around Z∼ 96,N∼ 196 but our calculations do not predict octupole deformation in the ground states of superheavy Z≥slant 108 nuclei. As exemplified by the study of 36Ar, the nodal structure of the wavefunction of occupied single-particle orbitals in extremely deformed structures allows to understand the formation of the α-clusters in very light nuclei, the suppression of the α-clusterization with the increase of mass number, the formation of ellipsoidal mean-field type structures and nuclear molecules.

Probing the Single-Particle Character of Rotational States in F 19 Using a Short-Lived Isomeric Beam

NASA Astrophysics Data System (ADS)

Santiago-Gonzalez, D.; Auranen, K.; Avila, M. L.; Ayangeakaa, A. D.; Back, B. B.; Bottoni, S.; Carpenter, M. P.; Chen, J.; Deibel, C. M.; Hood, A. A.; Hoffman, C. R.; Janssens, R. V. F.; Jiang, C. L.; Kay, B. P.; Kuvin, S. A.; Lauer, A.; Schiffer, J. P.; Sethi, J.; Talwar, R.; Wiedenhöver, I.; Winkelbauer, J.; Zhu, S.

2018-03-01

A beam containing a substantial component of both the Jπ=5+ , T1 /2=162 ns isomeric state of F 18 and its 1+, 109.77-min ground state is utilized to study members of the ground-state rotational band in F 19 through the neutron transfer reaction (d ,p ) in inverse kinematics. The resulting spectroscopic strengths confirm the single-particle nature of the 13 /2+ band-terminating state. The agreement between shell-model calculations using an interaction constructed within the s d shell, and our experimental results reinforces the idea of a single-particle-collective duality in the descriptions of the structure of atomic nuclei.

Characterization of a detector chain using a FPGA-based time-to-digital converter to reconstruct the three-dimensional coordinates of single particles at high flux

NASA Astrophysics Data System (ADS)

Nogrette, F.; Heurteau, D.; Chang, R.; Bouton, Q.; Westbrook, C. I.; Sellem, R.; Clément, D.

2015-11-01

We report on the development of a novel FPGA-based time-to-digital converter and its implementation in a detection chain that records the coordinates of single particles along three dimensions. The detector is composed of micro-channel plates mounted on top of a cross delay line and connected to fast electronics. We demonstrate continuous recording of the timing signals from the cross delay line at rates up to 4.1 × 106 s-1 and three-dimensional reconstruction of the coordinates up to 3.2 × 106 particles per second. From the imaging of a calibrated structure we measure the in-plane resolution of the detector to be 140(20) μm at a flux of 3 × 105 particles per second. In addition, we analyze a method to estimate the resolution without placing any structure under vacuum, a significant practical improvement. While we use UV photons here, the results of this work apply to the detection of other kinds of particles.

Relating structure and composition with accessibility of a single catalyst particle using correlative 3-dimensional micro-spectroscopy

DOE PAGES

Liu, Yijin; Meirer, Florian; Krest, Courtney M.; ...

2016-08-30

To understand how hierarchically structured functional materials operate, analytical tools are needed that can reveal small structural and chemical details in large sample volumes. Often, a single method alone is not sufficient to get a complete picture of processes happening at multiple length scales. Here we present a correlative approach combining three-dimensional X-ray imaging techniques at different length scales for the analysis of metal poisoning of an individual catalyst particle. The correlative nature of the data allowed establishing a macro-pore network model that interprets metal accumulations as a resistance to mass transport and can, by tuning the effect of metalmore » deposition, simulate the response of the network to a virtual ageing of the catalyst particle. In conclusion, the developed approach is generally applicable and provides an unprecedented view on dynamic changes in a material’s pore space, which is an essential factor in the rational design of functional porous materials.« less

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metere, Alfredo, E-mail: alfredo.metere@mmk.su.se; Oleynikov, Peter; Dzugutov, Mikhail

2014-12-21

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process,more » can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.« less

How temperature determines formation of maghemite nanoparticles

NASA Astrophysics Data System (ADS)

Girod, Matthias; Vogel, Stefanie; Szczerba, Wojciech; Thünemann, Andreas F.

2015-04-01

We report on the formation of polymer-stabilized superparamagnetic single-core and multi-core maghemite nanoparticles. The particle formation was carried out by coprecipitation of Fe(II) and Fe(III) sulfate in a continuous aqueous process using a micromixer system. Aggregates containing 50 primary particles with sizes of 2 nm were formed at a reaction temperature of 30 °C. These particles aggregated further with time and were not stable. In contrast, stable single-core particles with a diameter of 7 nm were formed at 80 °C as revealed by small-angle X-ray scattering (SAXS) coupled in-line with the micromixer for particle characterization. X-ray diffraction and TEM confirmed the SAXS results. X-ray absorption near-edge structure spectroscopy (XANES) identified the iron oxide phase as maghemite.

Counting polymers moving through a single ion channel

NASA Astrophysics Data System (ADS)

Bezrukov, Sergey M.; Vodyanoy, Igor; Parsegian, V. Adrian

1994-07-01

THE change in conductance of a small electrolyte-filled capillary owing to the passage of sub-micrometre-sized particles has long been used for particle counting and sizing. A commercial device for such measurements, the Coulter counter, is able to detect particles of sizes down to several tenths of a micrometre1-3. Nuclepore technology (in which pores are etched particle tracks) has extended the lower limit of size detection to 60-nm particles by using a capillary of diameter 0.45 μm (ref. 4). Here we show that natural channel-forming peptides incorporated into a bilayer lipid membrane can be used to detect the passage of single molecules with gyration radii as small as 5-15 Å. From our experiments with alamethicin pores we infer both the average number and the diffusion coefficients of poly(ethylene glycol) molecules in the pore. Our approach provides a means of observing the statistics and mechanics of flexible polymers moving within the confines of precisely defined single-molecule structures.

Plasmonic optical nanotweezers

NASA Astrophysics Data System (ADS)

Kotb, Rehab; El Maklizi, Mahmoud; Ismail, Yehea; Swillam, Mohamed A.

2017-02-01

Plasmonic grating structures can be used in many applications such as nanolithography and optical trapping. In this paper, we used plasmonic grating as optical tweezers to trap and manipulate dielectric nano-particles. Different plasmonic grating structures with single, double, and triple slits have been investigated and analyzed. The three configurations are optimized and compared to find the best candidate to trap and manipulate nanoparticles. The three optimized structures results in capability to super focusing and beaming the light effectively beyond the diffraction limit. A high transverse gradient optical force is obtained using the triple slit configuration that managed to significantly enhance the field and its gradient. Therefore, it has been chosen as an efficient optical tweezers. This structure managed to trap sub10nm particles efficiently. The resultant 50KT potential well traps the nano particles stably. The proposed structure is used also to manipulate the nano-particles by simply changing the angle of the incident light. We managed to control the movement of nano particle over an area of (5μm x 5μm) precisely. The proposed structure has the advantage of trapping and manipulating the particles outside the structure (not inside the structure such as the most proposed optical tweezers). As a result, it can be used in many applications such as drug delivery and biomedical analysis.

Chemical speciation of individual airborne particles by the combined use of quantitative energy-dispersive electron probe X-ray microanalysis and attenuated total reflection Fourier transform-infrared imaging techniques.

PubMed

Song, Young-Chul; Ryu, JiYeon; Malek, Md Abdul; Jung, Hae-Jin; Ro, Chul-Un

2010-10-01

In our previous work, it was demonstrated that the combined use of attenuated total reflectance (ATR) FT-IR imaging and quantitative energy-dispersive electron probe X-ray microanalysis (ED-EPMA), named low-Z particle EPMA, had the potential for characterization of individual aerosol particles. Additionally, the speciation of individual mineral particles was performed on a single particle level by the combined use of the two techniques, demonstrating that simultaneous use of the two single particle analytical techniques is powerful for the detailed characterization of externally heterogeneous mineral particle samples and has great potential for characterization of atmospheric mineral dust aerosols. These single particle analytical techniques provide complementary information on the physicochemical characteristics of the same individual particles, such as low-Z particle EPMA on morphology and elemental concentrations and the ATR-FT-IR imaging on molecular species, crystal structures, functional groups, and physical states. In this work, this analytical methodology was applied to characterize an atmospheric aerosol sample collected in Incheon, Korea. Overall, 118 individual particles were observed to be primarily NaNO(3)-containing, Ca- and/or Mg-containing, silicate, and carbonaceous particles, although internal mixing states of the individual particles proved complicated. This work demonstrates that more detailed physiochemical properties of individual airborne particles can be obtained using this approach than when either the low-Z particle EPMA or ATR-FT-IR imaging technique is used alone.

Probing the magnetic behavior of single nanodots.

PubMed

Neumann, Alexander; Thönnissen, Carsten; Frauen, Axel; Hesse, Simon; Meyer, Andreas; Oepen, Hans Peter

2013-05-08

In this paper, a method is presented that has the sensitivity to measure magnetization behavior of single nanostructures. It is demonstrated that the technique gives the ability to separate different signals of single nanodots from a small ensemble of structures. Our method is based on the anomalous Hall-Effect and allows for resolving signals from spherical nanoparticles with diameter down to 3.5 nm. The method gives access to magnetic properties of particles in a wide thermal and dynamical range. The potential of the technique is demonstrated utilizing particles that are created from Co films sandwiched by Pt layers.

Improved particle confinement in transition from multiple-helicity to quasi-single-helicity regimes of a reversed-field pinch.

PubMed

Frassinetti, L; Predebon, I; Koguchi, H; Yagi, Y; Hirano, Y; Sakakita, H; Spizzo, G; White, R B

2006-10-27

The quasi-single-helicity (QSH) state of a reversed-field pinch (RFP) plasma is a regime in which the RFP configuration can be sustained by a dynamo produced mainly by a single tearing mode and in which a helical structure with well-defined magnetic flux surfaces arises. In this Letter, we show that spontaneous transitions to the QSH regime enhance the particle confinement. This improvement is originated by the simultaneous and cooperative action of the increase of the magnetic island and the reduction of the magnetic stochasticity.

Attenuated total reflectance FT-IR imaging and quantitative energy dispersive-electron probe X-ray microanalysis techniques for single particle analysis of atmospheric aerosol particles.

PubMed

Ryu, JiYeon; Ro, Chul-Un

2009-08-15

This work demonstrates the practical applicability of the combined use of attenuated total reflectance (ATR) FT-IR imaging and low-Z particle electron probe X-ray microanalysis (EPMA) techniques for the characterization of individual aerosol particles. These two single particle analytical techniques provide complementary information on the physicochemical characteristics of the same individual particles, that is, the low-Z particle EPMA for the information on the morphology and elemental concentration and the ATR-FT-IR imaging on the functional group, molecular species, and crystal structure. It was confirmed that the ATR-FT-IR imaging technique can provide sufficient FT-IR absorption signals to perform molecular speciation of individual particles of micrometer size when applied to artificially generated aerosol particles such as ascorbic acid and NaNO(3) aerosols. An exemplar indoor atmospheric aerosol sample was investigated to demonstrate the practical feasibility of the combined application of ATR-FT-IR imaging and low-Z particle EPMA techniques for the characterization of individual airborne particles.

Coherent diffraction imaging: consistency of the assembled three-dimensional distribution.

PubMed

Tegze, Miklós; Bortel, Gábor

2016-07-01

The short pulses of X-ray free-electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. From the recorded diffraction patterns the structure of particles or molecules can be determined on the nano- or even atomic scale. In a coherent diffraction imaging experiment thousands of diffraction patterns of identical particles are recorded and assembled into a three-dimensional distribution which is subsequently used to solve the structure of the particle. It is essential to know, but not always obvious, that the assembled three-dimensional reciprocal-space intensity distribution is really consistent with the measured diffraction patterns. This paper shows that, with the use of correlation maps and a single parameter calculated from them, the consistency of the three-dimensional distribution can be reliably validated.

Crystalline structures of particles interacting through the harmonic-repulsive pair potential

NASA Astrophysics Data System (ADS)

Levashov, V. A.

2017-09-01

The behavior of identical particles interacting through the harmonic-repulsive pair potential has been studied in 3D using molecular dynamics simulations at a number of different densities. We found that at many densities, as the temperature of the systems decreases, the particles crystallize into complex structures whose formation has not been anticipated in previous studies on the harmonic-repulsive pair potential. In particular, at certain densities, crystallization into the structure I a 3 ¯ d (space group #230) with 16 particles in the unit cell occupying Wyckoff special positions (16b) was observed. This crystal structure has not been observed previously in experiments or in computer simulations of single component atomic or soft matter systems. At another density, we observed a liquid which is rather stable against crystallization. Yet, we observed crystallization of this liquid into the monoclinic C2/c (space group #15) structure with 32 particles in the unit cell occupying four different non-special Wyckoff (8f) sites. In this structure particles located at different Wyckoff sites have different energies. From the perspective of the local atomic environment, the organization of particles in this structure resembles the structure of some columnar quasicrystals. At a different value of the density, we did not observe crystallization at all despite rather long molecular dynamics runs. At two other densities, we observed the formation of the β S n distorted diamond structures instead of the expected diamond structure. Possibly, we also observed the formation of the R 3 ¯ c hexagonal lattice with 24 particles per unit cell occupying non-equivalent positions.

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

PubMed Central

Reddy, Hemanth K.N.; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A.; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G.; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A.; Kurta, Ruslan P.; Larsson, Daniel S.D.; Duane Loh, N.; Maia, Filipe R.N.C.; Mancuso, Adrian P.; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A.; Song, Changyong; Spence, John C.H.; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu

2017-01-01

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency. PMID:28654088

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source

DOE PAGES

Reddy, Hemanth K. N.; Yoon, Chun Hong; Aquila, Andrew; ...

2017-06-27

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65–70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. As a result, themore » data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.« less

Observing polymersome dynamics in controlled microscale flows

NASA Astrophysics Data System (ADS)

Kumar, Subhalakshmi; Shenoy, Anish; Schroeder, Charles

2015-03-01

Achieving an understanding of single particle rheology for large yet deformable particles with controlled membrane viscoelasticity is major challenge in soft materials. In this work, we directly visualize the dynamics of single polymersomes (~ 10 μm in size) in an extensional flow using optical microscopy. We generate polymer vesicular structures composed of polybutadiene-block-polyethylene oxide (PB-b-PEO) copolymers. Single polymersomes are confined near the stagnation point of a planar extensional flow using an automated microfluidic trap, thereby enabling the direct observation of polymersome dynamics under fluid flows with controlled strains and strain rates. In a series of experiments, we investigate the effect of varying elasticity in vesicular membranes on polymersome deformation, along with the impact of decreasing membrane fluidity upon increasing diblock copolymer molecular weight. Overall, we believe that this approach will enable precise characterization of the role of membrane properties on single particle rheology for deformable polymersomes.

Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source.

PubMed

Reddy, Hemanth K N; Yoon, Chun Hong; Aquila, Andrew; Awel, Salah; Ayyer, Kartik; Barty, Anton; Berntsen, Peter; Bielecki, Johan; Bobkov, Sergey; Bucher, Maximilian; Carini, Gabriella A; Carron, Sebastian; Chapman, Henry; Daurer, Benedikt; DeMirci, Hasan; Ekeberg, Tomas; Fromme, Petra; Hajdu, Janos; Hanke, Max Felix; Hart, Philip; Hogue, Brenda G; Hosseinizadeh, Ahmad; Kim, Yoonhee; Kirian, Richard A; Kurta, Ruslan P; Larsson, Daniel S D; Duane Loh, N; Maia, Filipe R N C; Mancuso, Adrian P; Mühlig, Kerstin; Munke, Anna; Nam, Daewoong; Nettelblad, Carl; Ourmazd, Abbas; Rose, Max; Schwander, Peter; Seibert, Marvin; Sellberg, Jonas A; Song, Changyong; Spence, John C H; Svenda, Martin; Van der Schot, Gijs; Vartanyants, Ivan A; Williams, Garth J; Xavier, P Lourdu

2017-06-27

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported ~600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

Liquid-liquid transition in the ST2 model of water

NASA Astrophysics Data System (ADS)

Debenedetti, Pablo

2013-03-01

We present clear evidence of the existence of a metastable liquid-liquid phase transition in the ST2 model of water. Using four different techniques (the weighted histogram analysis method with single-particle moves, well-tempered metadynamics with single-particle moves, weighted histograms with parallel tempering and collective particle moves, and conventional molecular dynamics), we calculate the free energy surface over a range of thermodynamic conditions, we perform a finite size scaling analysis for the free energy barrier between the coexisting liquid phases, we demonstrate the attainment of diffusive behavior, and we perform stringent thermodynamic consistency checks. The results provide conclusive evidence of a first-order liquid-liquid transition. We also show that structural equilibration in the sluggish low-density phase is attained over the time scale of our simulations, and that crystallization times are significantly longer than structural equilibration, even under deeply supercooled conditions. We place our results in the context of the theory of metastability.

The Correlation Entropy as a Measure of the Complexity of High-Lying Single-Particle Modes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoyanov, Chavdar; Zelevinsky, Vladimir; Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824-1321

Highly-excited single-particle states in nuclei are coupled with the excitations of a more complex character, first of all with collective phonon-like modes of the core. In the framework of the quasiparticle-phonon model we consider the structure of resulting complex configurations using the 1k17/2 orbital in 209Pb as an example. The eigenstates of the model carry significant degree of complexity that can be quantified with the aid of correlational invariant entropy. With artificially enhanced particle-core coupling, the system undergoes the doubling phase transition with the quasiparticle strength concentrated in two repelling peaks.

THE RELEASE OF IRON FROM DIFFERENT ASBESTOS STRUCTURES BY HYDROGEN PEROXIDE WITH CONCOMITANT O2 GENERATION

EPA Science Inventory

With the single exception of mercury, all metals in the atmosphere are associated with particles. The lungs are subsequently exposed to metals present in air pollution particles on a continuous basis. Because metal exposure can be associated with an oxidative stress, a mechanism ...

Detection of isolated protein-bound metal ions by single-particle cryo-STEM.

PubMed

Elad, Nadav; Bellapadrona, Giuliano; Houben, Lothar; Sagi, Irit; Elbaum, Michael

2017-10-17

Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography.

Detection of isolated protein-bound metal ions by single-particle cryo-STEM

PubMed Central

Elad, Nadav; Bellapadrona, Giuliano; Houben, Lothar; Sagi, Irit; Elbaum, Michael

2017-01-01

Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography. PMID:28973937

Special Features of the Structure of Single-Crystal Refractory Nickel Alloy Under Directed Crystallization

NASA Astrophysics Data System (ADS)

Bondarenko, Yu. A.; Echin, A. B.; Surova, V. A.; Kolodyazhnyi, M. Yu.

2017-05-01

The effect of the conditions of directed crystallization (the temperature gradient and the crystallization rate) on the dendrite spacing, on the size of the particles of the hardening γ'-phase in the arms and arm spaces of the dendrites, on the volume fraction and size of the pores, on the size of the particles of the eutectic γ/γ'-phase, and on the features of dendritic segregation in a single-crystal castable refractory alloy is studied.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

A manual and an automatic TERS based virus discrimination

NASA Astrophysics Data System (ADS)

Olschewski, Konstanze; Kämmer, Evelyn; Stöckel, Stephan; Bocklitz, Thomas; Deckert-Gaudig, Tanja; Zell, Roland; Cialla-May, Dana; Weber, Karina; Deckert, Volker; Popp, Jürgen

2015-02-01

Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%.Rapid techniques for virus identification are more relevant today than ever. Conventional virus detection and identification strategies generally rest upon various microbiological methods and genomic approaches, which are not suited for the analysis of single virus particles. In contrast, the highly sensitive spectroscopic technique tip-enhanced Raman spectroscopy (TERS) allows the characterisation of biological nano-structures like virions on a single-particle level. In this study, the feasibility of TERS in combination with chemometrics to discriminate two pathogenic viruses, Varicella-zoster virus (VZV) and Porcine teschovirus (PTV), was investigated. In a first step, chemometric methods transformed the spectral data in such a way that a rapid visual discrimination of the two examined viruses was enabled. In a further step, these methods were utilised to perform an automatic quality rating of the measured spectra. Spectra that passed this test were eventually used to calculate a classification model, through which a successful discrimination of the two viral species based on TERS spectra of single virus particles was also realised with a classification accuracy of 91%. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07033j

Characterization of a detector chain using a FPGA-based time-to-digital converter to reconstruct the three-dimensional coordinates of single particles at high flux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nogrette, F.; Chang, R.; Bouton, Q.

We report on the development of a novel FPGA-based time-to-digital converter and its implementation in a detection chain that records the coordinates of single particles along three dimensions. The detector is composed of micro-channel plates mounted on top of a cross delay line and connected to fast electronics. We demonstrate continuous recording of the timing signals from the cross delay line at rates up to 4.1 × 10{sup 6} s{sup −1} and three-dimensional reconstruction of the coordinates up to 3.2 × 10{sup 6} particles per second. From the imaging of a calibrated structure we measure the in-plane resolution of themore » detector to be 140(20) μm at a flux of 3 × 10{sup 5} particles per second. In addition, we analyze a method to estimate the resolution without placing any structure under vacuum, a significant practical improvement. While we use UV photons here, the results of this work apply to the detection of other kinds of particles.« less

Alignment error envelopes for single particle analysis.

PubMed

Jensen, G J

2001-01-01

To determine the structure of a biological particle to high resolution by electron microscopy, image averaging is required to combine information from different views and to increase the signal-to-noise ratio. Starting from the number of noiseless views necessary to resolve features of a given size, four general factors are considered that increase the number of images actually needed: (1) the physics of electron scattering introduces shot noise, (2) thermal motion and particle inhomogeneity cause the scattered electrons to describe a mixture of structures, (3) the microscope system fails to usefully record all the information carried by the scattered electrons, and (4) image misalignment leads to information loss through incoherent averaging. The compound effect of factors 2-4 is approximated by the product of envelope functions. The problem of incoherent image averaging is developed in detail through derivation of five envelope functions that account for small errors in 11 "alignment" parameters describing particle location, orientation, defocus, magnification, and beam tilt. The analysis provides target error tolerances for single particle analysis to near-atomic (3.5 A) resolution, and this prospect is shown to depend critically on image quality, defocus determination, and microscope alignment. Copyright 2001 Academic Press.

Ostwald ripening of clays and metamorphic minerals

USGS Publications Warehouse

Eberl, D.D.; Srodon, J.; Kralik, M.; Taylor, B.E.; Peterman, Z.E.

1990-01-01

Analyses of particle size distributions indicate that clay minerals and other diagenetic and metamorphic minerals commonly undergo recrystallization by Ostwald ripening. The shapes of their particle size distributions can yield the rate law for this process. One consequence of Ostwald ripening is that a record of the recrystallization process is preserved in the various particle sizes. Therefore, one can determine the detailed geologic history of clays and other recrystallized minerals by separating, from a single sample, the various particle sizes for independent chemical, structural, and isotopic analyses.

Kneelike Structure in the Spectrum of the Heavy Component of Cosmic Rays Observed with KASCADE-Grande

NASA Astrophysics Data System (ADS)

Apel, W. D.; Arteaga-Velázquez, J. C.; Bekk, K.; Bertaina, M.; Blümer, J.; Bozdog, H.; Brancus, I. M.; Buchholz, P.; Cantoni, E.; Chiavassa, A.; Cossavella, F.; Daumiller, K.; de Souza, V.; di Pierro, F.; Doll, P.; Engel, R.; Engler, J.; Finger, M.; Fuhrmann, D.; Ghia, P. L.; Gils, H. J.; Glasstetter, R.; Grupen, C.; Haungs, A.; Heck, D.; Hörandel, J. R.; Huber, D.; Huege, T.; Isar, P. G.; Kampert, K.-H.; Kang, D.; Klages, H. O.; Link, K.; Łuczak, P.; Ludwig, M.; Mathes, H. J.; Mayer, H. J.; Melissas, M.; Milke, J.; Mitrica, B.; Morello, C.; Navarra, G.; Oehlschläger, J.; Ostapchenko, S.; Over, S.; Palmieri, N.; Petcu, M.; Pierog, T.; Rebel, H.; Roth, M.; Schieler, H.; Schröder, F. G.; Sima, O.; Toma, G.; Trinchero, G. C.; Ulrich, H.; Weindl, A.; Wochele, J.; Wommer, M.; Zabierowski, J.

2011-10-01

We report the observation of a steepening in the cosmic ray energy spectrum of heavy primary particles at about 8×1016eV. This structure is also seen in the all-particle energy spectrum, but is less significant. Whereas the “knee” of the cosmic ray spectrum at 3-5×1015eV was assigned to light primary masses by the KASCADE experiment, the new structure found by the KASCADE-Grande experiment is caused by heavy primaries. The result is obtained by independent measurements of the charged particle and muon components of the secondary particles of extensive air showers in the primary energy range of 1016 to 1018eV. The data are analyzed on a single-event basis taking into account also the correlation of the two observables.

Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL.

PubMed

Nakano, Miki; Miyashita, Osamu; Jonic, Slavica; Song, Changyong; Nam, Daewoong; Joti, Yasumasa; Tama, Florence

2017-07-01

The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.

Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A.

PubMed

Markovic-Mueller, Sandra; Stuttfeld, Edward; Asthana, Mayanka; Weinert, Tobias; Bliven, Spencer; Goldie, Kenneth N; Kisko, Kaisa; Capitani, Guido; Ballmer-Hofer, Kurt

2017-02-07

Vascular endothelial growth factors (VEGFs) regulate blood and lymph vessel development upon activation of three receptor tyrosine kinases: VEGFR-1, -2, and -3. Partial structures of VEGFR/VEGF complexes based on single-particle electron microscopy, small-angle X-ray scattering, and X-ray crystallography revealed the location of VEGF binding and domain arrangement of individual receptor subdomains. Here, we describe the structure of the full-length VEGFR-1 extracellular domain in complex with VEGF-A at 4 Å resolution. We combined X-ray crystallography, single-particle electron microscopy, and molecular modeling for structure determination and validation. The structure reveals the molecular details of ligand-induced receptor dimerization, in particular of homotypic receptor interactions in immunoglobulin homology domains 4, 5, and 7. Functional analyses of ligand binding and receptor activation confirm the relevance of these homotypic contacts and identify them as potential therapeutic sites to allosterically inhibit VEGFR-1 activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination

DOE PAGES

Li, Xuanxuan; Spence, John C. H.; Hogue, Brenda G.; ...

2017-09-22

X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core–shell architecture were used as a model system for proof-of-principle coherentmore » diffractive single-particle imaging experiments. To deal with the heterogeneity of the core–shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core–shell architecture.« less

Merging single-shot XFEL diffraction data from inorganic nanoparticles: a new approach to size and orientation determination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xuanxuan; Spence, John C. H.; Hogue, Brenda G.

X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core–shell architecture were used as a model system for proof-of-principle coherentmore » diffractive single-particle imaging experiments. To deal with the heterogeneity of the core–shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core–shell architecture.« less

CLASHING BEAM PARTICLE ACCELERATOR

DOEpatents

Burleigh, R.J.

1961-04-11

A charged-particle accelerator of the proton synchrotron class having means for simultaneously accelerating two separate contra-rotating particle beams within a single annular magnet structure is reported. The magnet provides two concentric circular field regions of opposite magnetic polarity with one field region being of slightly less diameter than the other. The accelerator includes a deflector means straddling the two particle orbits and acting to collide the two particle beams after each has been accelerated to a desired energy. The deflector has the further property of returning particles which do not undergo collision to the regular orbits whereby the particles recirculate with the possibility of colliding upon subsequent passages through the deflector.

Colloid-colloid hydrodynamic interaction around a bend in a quasi-one-dimensional channel.

PubMed

Liepold, Christopher; Zarcone, Ryan; Heumann, Tibor; Rice, Stuart A; Lin, Binhua

2017-07-01

We report a study of how a bend in a quasi-one-dimensional (q1D) channel containing a colloid suspension at equilibrium that exhibits single-file particle motion affects the hydrodynamic coupling between colloid particles. We observe both structural and dynamical responses as the bend angle becomes more acute. The structural response is an increasing depletion of particles in the vicinity of the bend and an increase in the nearest-neighbor separation in the pair correlation function for particles on opposite sides of the bend. The dynamical response monitored by the change in the self-diffusion [D_{11}(x)] and coupling [D_{12}(x)] terms of the pair diffusion tensor reveals that the pair separation dependence of D_{12} mimics that of the pair correlation function just as in a straight q1D channel. We show that the observed behavior is a consequence of the boundary conditions imposed on the q1D channel: both the single-file motion and the hydrodynamic flow must follow the channel around the bend.

Quasifree (p, 2p) Reactions on Oxygen Isotopes: Observation of Isospin Independence of the Reduced Single-Particle Strength.

PubMed

Atar, L; Paschalis, S; Barbieri, C; Bertulani, C A; Díaz Fernández, P; Holl, M; Najafi, M A; Panin, V; Alvarez-Pol, H; Aumann, T; Avdeichikov, V; Beceiro-Novo, S; Bemmerer, D; Benlliure, J; Boillos, J M; Boretzky, K; Borge, M J G; Caamaño, M; Caesar, C; Casarejos, E; Catford, W; Cederkall, J; Chartier, M; Chulkov, L; Cortina-Gil, D; Cravo, E; Crespo, R; Dillmann, I; Elekes, Z; Enders, J; Ershova, O; Estrade, A; Farinon, F; Fraile, L M; Freer, M; Galaviz Redondo, D; Geissel, H; Gernhäuser, R; Golubev, P; Göbel, K; Hagdahl, J; Heftrich, T; Heil, M; Heine, M; Heinz, A; Henriques, A; Hufnagel, A; Ignatov, A; Johansson, H T; Jonson, B; Kahlbow, J; Kalantar-Nayestanaki, N; Kanungo, R; Kelic-Heil, A; Knyazev, A; Kröll, T; Kurz, N; Labiche, M; Langer, C; Le Bleis, T; Lemmon, R; Lindberg, S; Machado, J; Marganiec-Gałązka, J; Movsesyan, A; Nacher, E; Nikolskii, E Y; Nilsson, T; Nociforo, C; Perea, A; Petri, M; Pietri, S; Plag, R; Reifarth, R; Ribeiro, G; Rigollet, C; Rossi, D M; Röder, M; Savran, D; Scheit, H; Simon, H; Sorlin, O; Syndikus, I; Taylor, J T; Tengblad, O; Thies, R; Togano, Y; Vandebrouck, M; Velho, P; Volkov, V; Wagner, A; Wamers, F; Weick, H; Wheldon, C; Wilson, G L; Winfield, J S; Woods, P; Yakorev, D; Zhukov, M; Zilges, A; Zuber, K

2018-02-02

Quasifree one-proton knockout reactions have been employed in inverse kinematics for a systematic study of the structure of stable and exotic oxygen isotopes at the R^{3}B/LAND setup with incident beam energies in the range of 300-450  MeV/u. The oxygen isotopic chain offers a large variation of separation energies that allows for a quantitative understanding of single-particle strength with changing isospin asymmetry. Quasifree knockout reactions provide a complementary approach to intermediate-energy one-nucleon removal reactions. Inclusive cross sections for quasifree knockout reactions of the type ^{A}O(p,2p)^{A-1}N have been determined and compared to calculations based on the eikonal reaction theory. The reduction factors for the single-particle strength with respect to the independent-particle model were obtained and compared to state-of-the-art ab initio predictions. The results do not show any significant dependence on proton-neutron asymmetry.

Single-particle mapping of nonequilibrium nanocrystal transformations

DOE PAGES

Ye, Xingchen; Jones, Matthew R.; Frechette, Layne B.; ...

2016-11-18

Chemists have developed mechanistic insight into numerous chemical reactions by thoroughly characterizing nonequilibrium species. Although methods to probe these processes are well established for molecules, analogous techniques for understanding intermediate structures in nanomaterials have been lacking. For this study, we monitor the shape evolution of individual anisotropic gold nanostructures as they are oxidatively etched in a graphene liquid cell with a controlled redox environment. Short-lived, nonequilibrium nanocrystals are observed, structurally analyzed, and rationalized through Monte Carlo simulations. Understanding these reaction trajectories provides important fundamental insight connecting high-energy nanocrystal morphologies to the development of kinetically stabilized surface features and demonstrates themore » importance of developing tools capable of probing short-lived nanoscale species at the single-particle level.« less

Mapping Metals Incorporation of a Whole Single Catalyst Particle Using Element Specific X-ray Nanotomography

DOE PAGES

Meirer, Florian; Morris, Darius T.; Kalirai, Sam; ...

2015-01-02

Full-field transmission X-ray microscopy has been used to determine the 3D structure of a whole individual fluid catalytic cracking (FCC) particle at high spatial resolution and in a fast, noninvasive manner, maintaining the full integrity of the particle. Using X-ray absorption mosaic imaging to combine multiple fields of view, computed tomography was performed to visualize the macropore structure of the catalyst and its availability for mass transport. We mapped the relative spatial distributions of Ni and Fe using multiple-energy tomography at the respective X-ray absorption K-edges and correlated these distributions with porosity and permeability of an equilibrated catalyst (E-cat) particle.more » Both metals were found to accumulate in outer layers of the particle, effectively decreasing porosity by clogging of pores and eventually restricting access into the FCC particle.« less

Pyrolysis of ground pine chip and ground pellet particles

DOE PAGES

Rezaei, Hamid; Yazdanpanah, Fahimeh; Lim, C. Jim; ...

2016-08-04

In addition to particle size, biomass density influences heat and mass transfer rates during the thermal treatment processes. In this research, thermal behaviour of ground pine chip particles and ground pine pellet particles in the range of 0.25–5 mm was investigated. A single particle from ground pellets was almost 3 to 4 times denser than a single particle from ground chips at a similar size and volume of particle. Temperature was ramped up from room temperature (~25 °C) to 600 °C with heating rates of 10, 20, 30, and 50 °C/min. Pellet particles took 25–88 % longer time to drymore » than the chip particles. Microscopic examination of 3 mm and larger chip particles showed cracks during drying. No cracks were observed for pellet particles. The mass loss due to treatment at temperatures higher than 200 °C was about 80% both for chip and pellet particles. It took 4 min for chip and pellet particles to lose roughly 63% of their dry mass at a heating rate of 50 °C/min. The SEM structural analysis showed enlarged pores and cracks in cell walls of the pyrolyzed wood chips. As a result, these pores were not observed in pyrolyzed pellet particles.« less

Modeling of single film bubble and numerical study of the plateau structure in foam system

NASA Astrophysics Data System (ADS)

Sun, Zhong-guo; Ni, Ni; Sun, Yi-jie; Xi, Guang

2018-02-01

The single-film bubble has a special geometry with a certain amount of gas shrouded by a thin layer of liquid film under the surface tension force both on the inside and outside surfaces of the bubble. Based on the mesh-less moving particle semi-implicit (MPS) method, a single-film double-gas-liquid-interface surface tension (SDST) model is established for the single-film bubble, which characteristically has totally two gas-liquid interfaces on both sides of the film. Within this framework, the conventional surface free energy surface tension model is improved by using a higher order potential energy equation between particles, and the modification results in higher accuracy and better symmetry properties. The complex interface movement in the oscillation process of the single-film bubble is numerically captured, as well as typical flow phenomena and deformation characteristics of the liquid film. In addition, the basic behaviors of the coalescence and connection process between two and even three single-film bubbles are studied, and the cases with bubbles of different sizes are also included. Furthermore, the classic plateau structure in the foam system is reproduced and numerically proved to be in the steady state for multi-bubble connections.

Structural and magnetic studies of nanocrystalline Y{sub 2}Ir{sub 2}O{sub 7}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dwivedi, Vinod Kumar, E-mail: vinodd@iitk.ac.in; Mukhopadhyay, Soumik

2015-06-24

In this paper, we discuss synthesis of Y{sub 2}Ir{sub 2}O{sub 7} nanoparticles via chemical solution process. Structural analysis shows single cubic phase with Fd-3m space group symmetry. The particle size and distribution were studied by Transmission Electron Microscopy experiments. The average particle size turns out to be 50nm, which is in good agreement with the XRD results. Magnetic characterization shows no evidence of long range ordering even in presence of strong correlations.

Configuration of twins in glass-embedded silver nanoparticles of various origin

NASA Astrophysics Data System (ADS)

Hofmeister, H.; Dubiel, M.; Tan, G. L.; Schicke, K.-D.

2005-09-01

Structural characterization using high resolution electron microscopy and diffractogram analysis of silver nanoparticles embedded in glass by various routes of fabrication was aimed at revealing the characteristic features of twin faults occuring in such particles. Nearly spherical silver nanoparticles well below 10 nm size embedded in commercial soda-lime silicate float glass have been fabricated either by silver/sodium ion exchange or by Ag+ ion implantation. Twinned nanoparticles, besides single crystalline species, have frequently been observed for both fabrication routes, mainly at sizes above 5 nm, but also at smaller sizes, even around 1 nm. The variety of particle forms comprises single crystalline particles of nearly cuboctahedron shape, particles containing single twin faults, and multiply twinned particles containing parallel twin lamellae, or cyclic twinned segments arranged around axes of fivefold symmetry. Parallel twinning is distinctly favoured by ion implantation whereas cyclic twinning preferably occurs upon ion exchange processing. Regardless of single or repeated twinning, parallel or cyclic twin arrangement, one may classify simple twin faults of regular atomic configuration and compound twin faults whose irregular configuration consists of additional planar defects like associated stacking faults or secondary twin faults. Besides, a particular superstructure composed of parallel twin lamellae of only three atomic layers thickness is observed.

Inside versus Outside: Ion Redistribution in Nitric Acid Reacted Sea Spray Aerosol Particles as Determined by Single Particle Analysis (Invited)

NASA Astrophysics Data System (ADS)

Ault, A. P.; Guasco, T.; Ryder, O. S.; Baltrusaitis, J.; Cuadra-Rodriguez, L. A.; Collins, D. B.; Ruppel, M. J.; Bertram, T. H.; Prather, K. A.; Grassian, V. H.

2013-12-01

Sea spray aerosol (SSA) particles were generated under real-world conditions using natural seawater and a unique ocean-atmosphere facility equipped with actual breaking waves or a marine aerosol reference tank (MART) that replicates those conditions. The SSA particles were exposed to nitric acid in situ in a flow tube and the well-known chloride displacement and nitrate formation reaction was observed. However, as discussed here, little is known about how this anion displacement reaction affects the distribution of cations and other chemical constituents within and phase state of individual SSA particles. Single particle analysis of individual SSA particles shows that cations (Na+, K+, Mg2+ and Ca2+) within individual particles undergo a spatial redistribution after heterogeneous reaction with nitric acid, along with a more concentrated layer of organic matter at the surface of the particle. These data suggest that specific ion and aerosol pH effects play an important role in aerosol particle structure in ways that have not been previously recognized. The ordering of organic coatings can impact trace gas uptake, and subsequently impact trace gas budgets of O3 and NOx.

Centrifugation-assisted Assembly of Colloidal Silica into Crack-Free and Transferrable Films with Tunable Crystalline Structures

PubMed Central

Fan, Wen; Chen, Min; Yang, Shu; Wu, Limin

2015-01-01

Self-assembly of colloidal particles into colloidal films has many actual and potential applications. While various strategies have been developed to direct the assembly of colloidal particles, fabrication of crack-free and transferrable colloidal film with controllable crystal structures still remains a major challenge. Here we show a centrifugation-assisted assembly of colloidal silica spheres into free-standing colloidal film by using the liquid/liquid interfaces of three immiscible phases. Through independent control of centrifugal force and interparticle electrostatic repulsion, polycrystalline, single-crystalline and quasi-amorphous structures can be readily obtained. More importantly, by dehydration of silica particles during centrifugation, the spontaneous formation of capillary water bridges between particles enables the binding and pre-shrinkage of the assembled array at the fluid interface. Thus the assembled colloidal films are not only crack-free, but also robust and flexible enough to be easily transferred on various planar and curved substrates. PMID:26159121

SoAx: A generic C++ Structure of Arrays for handling particles in HPC codes

NASA Astrophysics Data System (ADS)

Homann, Holger; Laenen, Francois

2018-03-01

The numerical study of physical problems often require integrating the dynamics of a large number of particles evolving according to a given set of equations. Particles are characterized by the information they are carrying such as an identity, a position other. There are generally speaking two different possibilities for handling particles in high performance computing (HPC) codes. The concept of an Array of Structures (AoS) is in the spirit of the object-oriented programming (OOP) paradigm in that the particle information is implemented as a structure. Here, an object (realization of the structure) represents one particle and a set of many particles is stored in an array. In contrast, using the concept of a Structure of Arrays (SoA), a single structure holds several arrays each representing one property (such as the identity) of the whole set of particles. The AoS approach is often implemented in HPC codes due to its handiness and flexibility. For a class of problems, however, it is known that the performance of SoA is much better than that of AoS. We confirm this observation for our particle problem. Using a benchmark we show that on modern Intel Xeon processors the SoA implementation is typically several times faster than the AoS one. On Intel's MIC co-processors the performance gap even attains a factor of ten. The same is true for GPU computing, using both computational and multi-purpose GPUs. Combining performance and handiness, we present the library SoAx that has optimal performance (on CPUs, MICs, and GPUs) while providing the same handiness as AoS. For this, SoAx uses modern C++ design techniques such template meta programming that allows to automatically generate code for user defined heterogeneous data structures.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

PubMed Central

Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

2017-01-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

The HZE radiation problem. [highly-charged energetic galactic cosmic rays

NASA Technical Reports Server (NTRS)

Schimmerling, Walter

1990-01-01

Radiation-exposure limits have yet to be established for missions envisioned in the framework of the Space Exploration Initiative. The radiation threat outside the earth's magnetosphere encompasses protons from solar particle events and the highly charged energetic particles constituting galactic cosmic rays; radiation biology entails careful consideration of the extremely nonuniform patterns of such particles' energy deposition. The ability to project such biological consequences of exposure to energetic particles as carcinogenicity currently involves great uncertainties from: (1) different regions of space; (2) the effects of spacecraft structures; and (3) the dose-effect relationships of single traversals of energetic particles.

Single-particle cryo-electron microscopy of Rift Valley fever virus

PubMed Central

Sherman, Michael B.; Freiberg, Alexander N.; Holbrook, Michael R.; Watowich, Stanley J.

2009-01-01

Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human veterinary pathogen causing acute hepatitis in ruminants and has the potential to Single-particle cryo-EM reconstruction of RVFV MP-12 hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T=12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure provides a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit-vaccines. PMID:19304307

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

NASA Astrophysics Data System (ADS)

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang

2016-03-01

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtain 14 density maps at ~2-nm resolution. Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution

DOE PAGES

Zhang, Fan; Allen, Andrew J.; Levine, Lyle E.; ...

2017-02-24

We present an experimental study of the structural and dynamical properties of bimodal, micrometersized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXSbased X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5 % and systematically increased the volume fraction of the small particles from 0 % to 5 % to evaluate its effect on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can bemore » satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard sphere potential when the particle size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles does not exhibit significant variation with increasing volume fraction of small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of small particles. The dynamics of single-component large particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate strong dependence on the fraction of small particles. As a result, we also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with theoretical predictions, which suggest that the complex mutual interactions between large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.« less

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Fan; Allen, Andrew J.; Levine, Lyle E.

We present an experimental study of the structural and dynamical properties of bimodal, micrometersized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXSbased X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5 % and systematically increased the volume fraction of the small particles from 0 % to 5 % to evaluate its effect on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can bemore » satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard sphere potential when the particle size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles does not exhibit significant variation with increasing volume fraction of small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of small particles. The dynamics of single-component large particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate strong dependence on the fraction of small particles. As a result, we also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with theoretical predictions, which suggest that the complex mutual interactions between large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.« less

Dry-growth of silver single-crystal nanowires from porous Ag structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Chuantong, E-mail: chenchuantong@sanken.osaka-u.ac.jp; Nagao, Shijo; Jiu, Jinting

A fabrication method of single crystal Ag nanowires in large scale is introduced without any chemical synthesis in wet processes, which usually generates fivefold twinned nanowires of fcc metals. Dense single-crystal nanowires grow on a mechanically polished surface of micro-porous Ag structure, which is created from Ag micro-particles. The diameter and the length of the nanowires can be controlled simply by changing the temperature and the time of the heating during the nanowire growth in air. Unique growth mechanism is described in detail, based on stress-induced migration accelerated by the micro-porous structure where the origin of Ag nanowires growth ismore » incubated. Transmission electron microscopy analysis on the single crystal nanowires is also presented. This simple method offered an alternative preparation for metallic nanowires, especially with the single crystal structure in numerous applications.« less

Heavy ion action on single cells: Cellular inactivation capability of single accelerated heavy ions

NASA Technical Reports Server (NTRS)

Kost, M.; Pross, H.-D.; Russmann, C.; Schneider, E.; Kiefer, J.; Kraft, G.; Lenz, G.; Becher, W.

1994-01-01

Heavy ions (HZE-particles) constitute an important part of radiation in space. Although their number is small the high amount of energy transferred by individual particles may cause severe biological effects. Their investigation requires special techniques which were tested by experiments performed at the UNILAC at the GSI (Darmstadt). Diploid yeast was used which is a suitable eucaryotic test system because of its resistance to extreme conditions like dryness and vacuum. Cells were placed on nuclear track detector foils and exposed to ions of different atomic number and energy. To assess the action of one single ion on an individual cell, track parameters and the respective colony forming abilities (CFA) were determined with the help of computer aided image analysis. There is mounting evidence that not only the amount of energy deposited along the particle path, commonly given by the LET, is of importance but also the spatial problem of energy deposition at a submicroscopical scale. It is virtually impossible to investigate track structure effects in detail with whole cell populations and (globally applied) high particle fluences. It is, therefore, necessary to detect the action of simple ions in individual cells. The results show that the biological action depends on atomic number and specific energy of the impinging ions, which can be compared with model calculations of recent track structure models.

Chemical Structure, Ensemble and Single-Particle Spectroscopy of Thick-Shell InP-ZnSe Quantum Dots.

PubMed

Reid, Kemar R; McBride, James R; Freymeyer, Nathaniel J; Thal, Lucas B; Rosenthal, Sandra J

2018-02-14

Thick-shell (>5 nm) InP-ZnSe colloidal quantum dots (QDs) grown by a continuous-injection shell growth process are reported. The growth of a thick crystalline shell is attributed to the high temperature of the growth process and the relatively low lattice mismatch between the InP core and ZnSe shell. In addition to a narrow ensemble photoluminescence (PL) line-width (∼40 nm), ensemble and single-particle emission dynamics measurements indicate that blinking and Auger recombination are reduced in these heterostructures. More specifically, high single-dot ON-times (>95%) were obtained for the core-shell QDs, and measured ensemble biexciton lifetimes, τ 2x ∼ 540 ps, represent a 7-fold increase compared to InP-ZnS QDs. Further, high-resolution energy dispersive X-ray (EDX) chemical maps directly show for the first time significant incorporation of indium into the shell of the InP-ZnSe QDs. Examination of the atomic structure of the thick-shell QDs by high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) reveals structural defects in subpopulations of particles that may mitigate PL efficiencies (∼40% in ensemble), providing insight toward further synthetic refinement. These InP-ZnSe heterostructures represent progress toward fully cadmium-free QDs with superior photophysical properties important in biological labeling and other emission-based technologies.

Structure and morphology of magnetite anaerobically-produced by a marine magnetotactic bacterium and a dissimilatory iron-reducing bacterium

USGS Publications Warehouse

Sparks, N.H.C.; Mann, S.; Bazylinski, D.A.; Lovley, D.R.; Jannasch, H.W.; Frankel, R.B.

1990-01-01

Intracellular crystals of magnetite synthesized by cells of the magnetotactic vibroid organism, MV-1, and extracellular crystals of magnetite produced by the non-magnetotactic dissimilatory iron-reducing bacterium strain GS-15, were examined using high-resolution transmission electron microscopy, electron diffraction and 57Fe Mo??ssbauer spectroscopy. The magnetotactic bacterium contained a single chain of approximately 10 crystals aligned along the long axis of the cell. The crystals were essentially pure stoichiometric magnetite. When viewed along the crystal long axis the particles had a hexagonal cross-section whereas side-on they appeared as rectangules or truncated rectangles of average dimension, 53 ?? 35 nm. These findings are explained in terms of a three-dimensional morphology comprising a hexagonal prism of {110} faces which are capped and truncated by {111} end faces. Electron diffraction and lattice imaging studies indicated that the particles were structurally well-defined single crystals. In contrast, magnetite particles produced by the strain, GS-15 were irregular in shape and had smaller mean dimensions (14 nm). Single crystals were imaged but these were not of high structural perfection. These results highlight the influence of intracellular control on the crystallochemical specificity of bacterial magnetites. The characterization of these crystals is important in aiding the identification of biogenic magnetic materials in paleomagnetism and in studies of sediment magnetization. ?? 1990.

Magnetic shielding

DOEpatents

Kerns, J.A.; Stone, R.R.; Fabyan, J.

1985-02-12

A magnetically-conductive filler material bridges the gap between a multi-part magnetic shield structure which substantially encloses a predetermined volume so as to minimize the ingress or egress of magnetic fields with respect to that volume. The filler material includes a heavy concentration of single-magnetic-domain-sized particles of a magnetically conductive material (e.g. soft iron, carbon steel or the like) dispersed throughout a carrier material which is generally a non-magnetic material that is at least sometimes in a plastic or liquid state. The maximum cross-sectional particle dimension is substantially less than the nominal dimension of the gap to be filled. An epoxy base material (i.e. without any hardening additive) low volatility vacuum greases or the like may be used for the carrier material. The structure is preferably exposed to the expected ambient field while the carrier is in a plastic or liquid state so as to facilitate alignment of the single-magnetic-domain-sized particles with the expected magnetic field lines.

Magnetic shielding

DOEpatents

Kerns, J.A.; Stone, R.R.; Fabyan, J.

1987-10-06

A magnetically-conductive filler material bridges the gap between a multi-part magnetic shield structure which substantially encloses a predetermined volume so as to minimize the ingress or egress of magnetic fields with respect to that volume. The filler material includes a heavy concentration of single-magnetic-domain-sized particles of a magnetically conductive material (e.g. soft iron, carbon steel or the like) dispersed throughout a carrier material which is generally a non-magnetic material that is at least sometimes in a plastic or liquid state. The maximum cross-sectional particle dimension is substantially less than the nominal dimension of the gap to be filled. An epoxy base material (i.e. without any hardening additive) low volatility vacuum greases or the like may be used for the carrier material. The structure is preferably exposed to the expected ambient magnetic field while the carrier is in a plastic or liquid state so as to facilitate alignment of the single-magnetic-domain-sized particles with the expected magnetic field lines. 3 figs.

Magnetic shielding

DOEpatents

Kerns, John A.; Stone, Roger R.; Fabyan, Joseph

1987-01-01

A magnetically-conductive filler material bridges the gap between a multi-part magnetic shield structure which substantially encloses a predetermined volume so as to minimize the ingress or egress of magnetic fields with respect to that volume. The filler material includes a heavy concentration of single-magnetic-domain-sized particles of a magnetically conductive material (e.g. soft iron, carbon steel or the like) dispersed throughout a carrier material which is generally a non-magnetic material that is at least sometimes in a plastic or liquid state. The maximum cross-sectional particle dimension is substantially less than the nominal dimension of the gap to be filled. An epoxy base material (i.e. without any hardening additive) low volatility vacuum greases or the like may be used for the carrier material. The structure is preferably exposed to the expected ambient magnetic field while the carrier is in a plastic or liquid state so as to facilitate alignment of the single-magnetic-domain-sized particles with the expected magnetic field lines.

GraDeR: Membrane Protein Complex Preparation for Single-Particle Cryo-EM.

PubMed

Hauer, Florian; Gerle, Christoph; Fischer, Niels; Oshima, Atsunori; Shinzawa-Itoh, Kyoko; Shimada, Satoru; Yokoyama, Ken; Fujiyoshi, Yoshinori; Stark, Holger

2015-09-01

We developed a method, named GraDeR, which substantially improves the preparation of membrane protein complexes for structure determination by single-particle cryo-electron microscopy (cryo-EM). In GraDeR, glycerol gradient centrifugation is used for the mild removal of free detergent monomers and micelles from lauryl maltose-neopentyl glycol detergent stabilized membrane complexes, resulting in monodisperse and stable complexes to which standard processes for water-soluble complexes can be applied. We demonstrate the applicability of the method on three different membrane complexes, including the mammalian FoF1 ATP synthase. For this highly dynamic and fragile rotary motor, we show that GraDeR allows visualizing the asymmetry of the F1 domain, which matches the ground state structure of the isolated domain. Therefore, the present cryo-EM structure of FoF1 ATP synthase provides direct structural evidence for Boyer's binding change mechanism in the context of the intact enzyme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Innovative molecular-based fluorescent nanoparticles for multicolor single particle tracking in cells

NASA Astrophysics Data System (ADS)

Daniel, Jonathan; Godin, Antoine G.; Palayret, Matthieu; Lounis, Brahim; Cognet, Laurent; Blanchard-Desce, Mireille

2016-03-01

Based on an original molecular-based design, we present bright and photostable fluorescent organic nanoparticles (FONs) showing excellent colloidal stability in various aqueous environments. Complementary near-infrared emitting and green emitting FONs were prepared using a simple, fast and robust protocol. Both types of FONs could be simultaneously imaged at the single-particle level in solution as well as in biological environments using a monochromatic excitation and a dual-color fluorescence microscope. No evidence of acute cytotoxicity was found upon incubation of live cells with mixed solutions of FONs, and both types of nanoparticles were found internalized in the cells where their motion could be simultaneously tracked at video-rate up to minutes. These fluorescent organic nanoparticles open a novel non-toxic alternative to existing nanoparticles for imaging biological structures, compatible with live-cell experiments and specially fitted for multicolor single particle tracking.

Pauli structures arising from confined particles interacting via a statistical potential

NASA Astrophysics Data System (ADS)

Batle, Josep; Ciftja, Orion; Farouk, Ahmed; Alkhambashi, Majid; Abdalla, Soliman

2017-09-01

There have been suggestions that the Pauli exclusion principle alone can lead a non-interacting (free) system of identical fermions to form crystalline structures dubbed Pauli crystals. Single-shot imaging experiments for the case of ultra-cold systems of free spin-polarized fermionic atoms in a two-dimensional harmonic trap appear to show geometric arrangements that cannot be characterized as Wigner crystals. This work explores this idea and considers a well-known approach that enables one to treat a quantum system of free fermions as a system of classical particles interacting with a statistical interaction potential. The model under consideration, though classical in nature, incorporates the quantum statistics by endowing the classical particles with an effective interaction potential. The reasonable expectation is that possible Pauli crystal features seen in experiments may manifest in this model that captures the correct quantum statistics as a first order correction. We use the Monte Carlo simulated annealing method to obtain the most stable configurations of finite two-dimensional systems of confined particles that interact with an appropriate statistical repulsion potential. We consider both an isotropic harmonic and a hard-wall confinement potential. Despite minor differences, the most stable configurations observed in our model correspond to the reported Pauli crystals in single-shot imaging experiments of free spin-polarized fermions in a harmonic trap. The crystalline configurations observed appear to be different from the expected classical Wigner crystal structures that would emerge should the confined classical particles had interacted with a pair-wise Coulomb repulsion.

Online differentiation of mineral phase in aerosol particles by ion formation mechanism using a LAAP-TOF single-particle mass spectrometer

NASA Astrophysics Data System (ADS)

Marsden, Nicholas A.; Flynn, Michael J.; Allan, James D.; Coe, Hugh

2018-01-01

Mineralogy of silicate mineral dust has a strong influence on climate and ecosystems due to variation in physiochemical properties that result from differences in composition and crystal structure (mineral phase). Traditional offline methods of analysing mineral phase are labour intensive and the temporal resolution of the data is much longer than many atmospheric processes. Single-particle mass spectrometry (SPMS) is an established technique for the online size-resolved measurement of particle composition by laser desorption ionisation (LDI) followed by time-of-flight mass spectrometry (TOF-MS). Although non-quantitative, the technique is able to identify the presence of silicate minerals in airborne dust particles from markers of alkali metals and silicate molecular ions in the mass spectra. However, the differentiation of mineral phase in silicate particles by traditional mass spectral peak area measurements is not possible. This is because instrument function and matrix effects in the ionisation process result in variations in instrument response that are greater than the differences in composition between common mineral phases.In this study, we introduce a novel technique that enables the differentiation of mineral phase in silicate mineral particles by ion formation mechanism measured from subtle changes in ion arrival times at the TOF-MS detector. Using a combination of peak area and peak centroid measurements, we show that the arrangement of the interstitial alkali metals in the crystal structure, an important property in silicate mineralogy, influences the ion arrival times of elemental and molecular ion species in the negative ion mass spectra. A classification scheme is presented that allowed for the differentiation of illite-smectite, kaolinite and feldspar minerals on a single-particle basis. Online analysis of mineral dust aerosol generated from clay mineral standards produced mineral fractions that are in agreement with bulk measurements reported by traditional XRD (X-ray diffraction) analysis.

Bright-field electron tomography of individual inorganic fullerene-like structures

NASA Astrophysics Data System (ADS)

Bar Sadan, Maya; Wolf, Sharon G.; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties. Electronic supplementary information (ESI) available: Figs. S1 and S2 and movies S1-S6. See DOI: 10.1039/b9nr00251k

Imaging the microscopic structure of shear thinning and thickening colloidal suspensions.

PubMed

Cheng, Xiang; McCoy, Jonathan H; Israelachvili, Jacob N; Cohen, Itai

2011-09-02

The viscosity of colloidal suspensions varies with shear rate, an important effect encountered in many natural and industrial processes. Although this non-Newtonian behavior is believed to arise from the arrangement of suspended particles and their mutual interactions, microscopic particle dynamics are difficult to measure. By combining fast confocal microscopy with simultaneous force measurements, we systematically investigate a suspension's structure as it transitions through regimes of different flow signatures. Our measurements of the microscopic single-particle dynamics show that shear thinning results from the decreased relative contribution of entropic forces and that shear thickening arises from particle clustering induced by hydrodynamic lubrication forces. This combination of techniques illustrates an approach that complements current methods for determining the microscopic origins of non-Newtonian flow behavior in complex fluids.

Synthesis of ordered L10-type FeNi nanoparticles

DOEpatents

Pinkerton, Frederick E.

2015-09-22

Particles of iron and nickel are added to a flowing plasma stream which does not chemically alter the iron or nickel. The iron and nickel are heated and vaporized in the stream, and then a cryogenic fluid is added to the stream to rapidly cause the formation of nanometer size particles of iron and nickel. The particles are separated from the stream. The particles are preferably formed as single crystals in which the iron and nickel atoms are organized in a tetragonal L1.sub.0 crystal structure which displays magnetic anisotropy. A minor portion of an additive, such as titanium, vanadium, aluminum, boron, carbon, phosphorous, or sulfur, may be added to the plasma stream with the iron and nickel to enhance formation of the desired crystal structure.

Structure and Dynamics of Bimodal Colloidal Dispersions in a Low-Molecular-Weight Polymer Solution.

PubMed

Zhang, Fan; Allen, Andrew J; Levine, Lyle E; Tsai, De-Hao; Ilavsky, Jan

2017-03-21

We present an experimental study of the structural and dynamical properties of bimodal, micrometer-sized colloidal dispersions (size ratio ≈ 2) in an aqueous solution of low-molecular-weight polymer (polyethylene glycol 2000) using synchrotron ultra-small angle X-ray scattering (USAXS) and USAXS-based X-ray photon correlation spectroscopy. We fixed the volume fraction of the large particles at 5% and systematically increased the volume fraction of the small particles from 0 to 5% to evaluate their effects on the structure and dynamics. The bimodal dispersions were homogenous through the investigated parameter space. We found that the partial structure factors can be satisfactorily retrieved for the bimodal colloidal dispersions using a Percus-Yevick hard-sphere potential when the size distributions of the particles were taken into account. We also found that the partial structure factor between the large particles did not exhibit a significant variation with increasing volume fraction of the small particles, whereas the isothermal compressibility of the binary mixture was found to decrease with increasing volume fraction of the small particles. The dynamics of single-component large-particle dispersion obey the principles of de Gennes narrowing, where the wave vector dependence of the interparticle diffusion coefficient is inversely proportional to the interparticle structure factor. The dynamics of the bimodal dispersions demonstrate a strong dependence on the fraction of small particles. We also made a comparison between the experimental effective dynamic viscosity of the bimodal dispersion with the theoretical predictions, which suggest that the complex mutual interactions between the large and small particles have a strong effect on the dynamic behaviors of bimodal dispersions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hosseinizadeh, Ahmad; Mashayekhi, Ghoncheh; Copperman, Jeremy

Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. Furthermore, these results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.

Crosslinked polymer nanoparticles containing single conjugated polymer chains

NASA Astrophysics Data System (ADS)

Ponzio, Rodrigo A.; Marcato, Yésica L.; Gómez, María L.; Waiman, Carolina V.; Chesta, Carlos A.; Palacios, Rodrigo E.

2017-06-01

Conjugated polymer nanoparticles are widely used in fluorescent labeling and sensing, as they have mean radii between 5 and 100 nm, narrow size dispersion, high brightness, and are photochemically stable, allowing single particle detection with high spatial and temporal resolution. Highly crosslinked polymers formed by linking individual chains through covalent bonds yield high-strength rigid materials capable of withstanding dissolution by organic solvents. Hence, the combination of crosslinked polymers and conjugated polymers in a nanoparticulated material presents the possibility of interesting applications that require the combined properties of constituent polymers and nanosized dimension. In the present work, F8BT@pEGDMA nanoparticles composed of poly(ethylene glycol dimethacrylate) (pEGDMA; a crosslinked polymer) and containing the commercial conjugated polymer poly(9,9-dioctylfluorene-alt-benzothiadiazole) (F8BT) were synthesized and characterized. Microemulsion polymerization was applied to produce F8BT@pEDGMA particles with nanosized dimensions in a ∼25% yield. Photophysical and size distribution properties of F8BT@pEDGMA nanoparticles were evaluated by various methods, in particular single particle fluorescence microscopy techniques. The results demonstrate that the crosslinking/polymerization process imparts structural rigidity to the F8BT@pEDGMA particles by providing resistance against dissolution/disintegration in organic solvents. The synthesized fluorescent crosslinked nanoparticles contain (for the most part) single F8BT chains and can be detected at the single particle level, using fluorescence microscopy, which bodes well for their potential application as molecularly imprinted polymer fluorescent nanosensors with high spatial and temporal resolution.

Centrality dependence of dihadron correlations and azimuthal anisotropy harmonics in PbPb collisions at $$\\sqrt{s_{NN}}= 2.76\\ \\mbox{TeV}$$

DOE PAGES

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; ...

2012-05-30

Measurements from the CMS experiment at the LHC of dihadron correlations for charged particles produced in PbPb collisions at a nucleon-nucleon centre-of-mass energy of 2. 76 TeV are presented. The results are reported as a function of the particle transverse momenta (p T ) and collision centrality over a broad range in relative pseudorapidity (Δη) and the full range of relative azimuthal angle (Δmore » $$\\phi$$). The observed two-dimensional correlation structure in Δη and Δ$$\\phi$$ is characterised by a narrow peak at (Δη,Δ$$\\phi$$)≈(0,0) from jet-like correlations and a long-range structure that persists up to at least |Δη|=4. An enhancement of the magnitude of the short-range jet peak is observed with increasing centrality, especially for particles of p T around 1-2 GeV/c. The long-range azimuthal dihadron correlations are extensively studied using a Fourier decomposition analysis. The extracted Fourier coefficients are found to factorise into a product of single-particle azimuthal anisotropies up to p T ≈3-3. 5 GeV/c for at least one particle from each pair, except for the second-order harmonics in the most central PbPb events. Various orders of the single-particle azimuthal anisotropy harmonics are extracted for associated particle p T of 1-3 GeV/c, as a function of the trigger particle p T up to 20 GeV/c and over the full centrality range.« less

Second harmonic generation from small particle aggregates

NASA Astrophysics Data System (ADS)

Mochan, W. Luis; Ortiz, Guillermo P.; Mendoza, Bernardo S.; Brudny, Vera L.

2001-03-01

Novel nanofabrication techniques are capable of producing nanoparticles with controled structures which include small clusters, self-assembled particles, quantum dots, vesicles, etc. The non-linear optical scattering of these structures are important for applications, and can be used for their physical characterization. The second harmonic (SH) field radiated by a single small spherical particle has surface and bulk, dipolar and quadrupolar contributions of similar intensities and is strongly dependent of the local environment of the particle [1], in contrast to the linear case. In this work we calculate the nonlinear scattering by particle aggregates and we investigate the effects on the SH generation of the disorder induced field fluctuations and of the localization of light. We acknowledge the partial support from DGAPA-UNAM (grant IN110999), Conacyt (31120-E and 26651-E), CIP and UBACyT. [1] Vera L. Brudny, Bernardo S. Mendoza, and W. Luis Mochán, Phys. Rev. B 62, 11152 (2000).

Structural Studies of Silver Nanoparticles Obtained Through Single-Step Green Synthesis

NASA Astrophysics Data System (ADS)

Prasad Peddi, Siva; Abdallah Sadeh, Bilal

2015-10-01

Green synthesis of silver Nanoparticles (AGNP's) has been the most prominent among the metallic nanoparticles for research for over a decade and half now due to both the simplicity of preparation and the applicability of biological species with extensive applications in medicine and biotechnology to reduce and trap the particles. The current article uses Eclipta Prostrata leaf extract as the biological species to cap the AGNP's through a single step process. The characterization data obtained was used for the analysis of the sample structure. The article emphasizes the disquisition of their shape and size of the lattice parameters and proposes a general scheme and a mathematical model for the analysis of their dependence. The data of the synthesized AGNP's has been used to advantage through the introduction of a structural shape factor for the crystalline nanoparticles. The properties of the structure of the AGNP's proposed and evaluated through a theoretical model was undeviating with the experimental consequences. This modus operandi gives scope for the structural studies of ultrafine particles prepared using biological methods.

The structure of Escherichia coli signal recognition particle revealed by scanning transmission electron microscopy.

PubMed

Mainprize, Iain L; Beniac, Daniel R; Falkovskaia, Elena; Cleverley, Robert M; Gierasch, Lila M; Ottensmeyer, F Peter; Andrews, David W

2006-12-01

Structural studies on various domains of the ribonucleoprotein signal recognition particle (SRP) have not converged on a single complete structure of bacterial SRP consistent with the biochemistry of the particle. We obtained a three-dimensional structure for Escherichia coli SRP by cryoscanning transmission electron microscopy and mapped the internal RNA by electron spectroscopic imaging. Crystallographic data were fit into the SRP reconstruction, and although the resulting model differed from previous models, they could be rationalized by movement through an interdomain linker of Ffh, the protein component of SRP. Fluorescence resonance energy transfer experiments determined interdomain distances that were consistent with our model of SRP. Docking our model onto the bacterial ribosome suggests a mechanism for signal recognition involving interdomain movement of Ffh into and out of the nascent chain exit site and suggests how SRP could interact and/or compete with the ribosome-bound chaperone, trigger factor, for a nascent chain during translation.

Morphology and nano-structure analysis of soot particles sampled from high pressure diesel jet flames under diesel-like conditions

NASA Astrophysics Data System (ADS)

Jiang, Hao; Li, Tie; Wang, Yifeng; He, Pengfei

2018-04-01

Soot particles emitted from diesel engines have a significant impact on the atmospheric environment. Detailed understanding of soot formation and oxidation processes is helpful for reducing the pollution of soot particles, which requires information such as the size and nano-structure parameters of the soot primary particles sampled in a high-temperature and high-pressure diesel jet flame. Based on the thermophoretic principle, a novel sampling probe minimally disturbing the diesel jet flame in a constant volume combustion vessel is developed for analysing soot particles. The injected quantity of diesel fuel is less than 10 mg, and the soot particles sampled by carriers with a transmission electron microscope (TEM) grid and lacey TEM grid can be used to analyse the morphologies of soot aggregates and the nano-structure of the soot primary particles, respectively. When the quantity of diesel fuel is more than 10 mg, in order to avoid burning-off of the carriers in higher temperature and pressure conditions, single-crystal silicon chips are employed. Ultrasonic oscillations and alcohol extraction are then implemented to obtain high quality soot samples for observation using a high-resolution transmission electron microscope. An in-house Matlab-based code is developed to extract the nano-structure parameters of the soot particles. A complete sampling and analysis procedure of the soot particles is provided to study the formation and oxidation mechanism of soot.

Contributions of Organic Sources to Atmospheric Aerosol Particle Concentrations and Growth

NASA Astrophysics Data System (ADS)

Russell, L. M.

2017-12-01

Organic molecules are important contributors to aerosol particle mass and number concentrations through primary emissions as well as secondary growth in the atmosphere. New techniques for measuring organic aerosol components in atmospheric particles have improved measurements of this contribution in the last 20 years, including Scanning Transmission X-ray Microscopy Near Edge X-ray Absorption Fine Structure (STXM-NEXAFS), Fourier Transform Infrared spectroscopy (FTIR), and High-Resolution Aerosol Mass Spectrometry (AMS). STXM-NEXAFS individual aerosol particle composition illustrated the variety of morphology of organic components in marine aerosols, the inherent relationships between organic composition and shape, and the links between atmospheric aerosol composition and particles produced in smog chambers. This type of single particle microscopy has also added to size distribution measurements by providing evidence of how surface-controlled and bulk-controlled processes contribute to the growth of particles in the atmosphere. FTIR analysis of organic functional groups are sufficient to distinguish combustion, marine, and terrestrial organic particle sources and to show that each of those types of sources has a surprisingly similar organic functional group composition over four different oceans and four different continents. Augmenting the limited sampling of these off-line techniques with side-by-side inter-comparisons to online AMS provides complementary composition information and consistent quantitative attribution to sources (despite some clear method differences). Single-particle AMS techniques using light scattering and event trigger modes have now also characterized the types of particles found in urban, marine, and ship emission aerosols. Most recently, by combining with off-line techniques, single particle composition measurements have separated and quantified the contributions of organic, sulfate and salt components from ocean biogenic and sea spray emissions to particles, addressing the persistent question of the sources of cloud condensation nuclei in clean marine conditions.

Superfluid transition in the attractive Hofstadter-Hubbard model

NASA Astrophysics Data System (ADS)

Umucalılar, R. O.; Iskin, M.

2016-08-01

We consider a Fermi gas that is loaded onto a square optical lattice and subjected to a perpendicular artificial magnetic field, and determine its superfluid transition boundary by adopting a BCS-like mean-field approach in momentum space. The multiband structure of the single-particle Hofstadter spectrum is taken explicitly into account while deriving a generalized pairing equation. We present the numerical solutions as functions of the artificial magnetic flux, interaction strength, Zeeman field, chemical potential, and temperature, with a special emphasis on the roles played by the density of single-particle states and center-of-mass momentum of Cooper pairs.

Laser pyrolysis fabrication of ferromagnetic gamma'-Fe4N and FeC nanoparticles

NASA Technical Reports Server (NTRS)

Grimes, C. A.; Qian, D.; Dickey, E. C.; Allen, J. L.; Eklund, P. C.

2000-01-01

Using the laser pyrolysis method, single phase gamma'-Fe4N nanoparticles were prepared by a two step method involving preparation of nanoscale iron oxide and a subsequent gas-solid nitridation reaction. Single phase Fe3C and Fe7C3 could be prepared by laser pyrolysis from Fe(CO)5 and 3C2H4 directly. Characterization techniques such as XRD, TEM and vibrating sample magnetometer were used to measure phase structure, particle size and magnetic properties of these nanoscale nitride and carbide particles. c2000 American Journal of Physics.

Nonlocal screening in metal surfaces

NASA Technical Reports Server (NTRS)

Krotscheck, E.; Kohn, W.

1986-01-01

Due to the effect of the nonuniform environment on the static screening of the Coulomb potential, the local-density approximation for the particle-hole interaction is found to be inadequate to determine the surface energy of simple metals. Use of the same set of single-particle states, and thus the same one-body density and the same work function, has eliminated the single-electron states in favor of the structure of the short-ranged correlations as the basis of this effect. A posteriori simplifications of the Fermi hypernetted-chain theory may be found to allow the same calculational accuracy with simpler computational tools.

A stochastic model for density-dependent microwave Snow- and Graupel scattering coefficients of the NOAA JCSDA community radiative transfer model

NASA Astrophysics Data System (ADS)

Stegmann, Patrick G.; Tang, Guanglin; Yang, Ping; Johnson, Benjamin T.

2018-05-01

A structural model is developed for the single-scattering properties of snow and graupel particles with a strongly heterogeneous morphology and an arbitrary variable mass density. This effort is aimed to provide a mechanism to consider particle mass density variation in the microwave scattering coefficients implemented in the Community Radiative Transfer Model (CRTM). The stochastic model applies a bicontinuous random medium algorithm to a simple base shape and uses the Finite-Difference-Time-Domain (FDTD) method to compute the single-scattering properties of the resulting complex morphology.

DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

PubMed

Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

2016-09-01

Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural expansions for the ground state energy of a simple metal

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1973-01-01

A structural expansion for the static ground state energy of a simple metal is derived. An approach based on single particle band structure which treats the electron gas as a non-linear dielectric is presented, along with a more general many particle analysis using finite temperature perturbation theory. The two methods are compared, and it is shown in detail how band-structure effects, Fermi surface distortions, and chemical potential shifts affect the total energy. These are of special interest in corrections to the total energy beyond third order in the electron ion interaction, and hence to systems where differences in energies for various crystal structures are exceptionally small. Preliminary calculations using these methods for the zero temperature thermodynamic functions of atomic hydrogen are reported.

Life and death of a single catalytic cracking particle

PubMed Central

Meirer, Florian; Kalirai, Sam; Morris, Darius; Soparawalla, Santosh; Liu, Yijin; Mesu, Gerbrand; Andrews, Joy C.; Weckhuysen, Bert M.

2015-01-01

Fluid catalytic cracking (FCC) particles account for 40 to 45% of worldwide gasoline production. The hierarchical complex particle pore structure allows access of long-chain feedstock molecules into active catalyst domains where they are cracked into smaller, more valuable hydrocarbon products (for example, gasoline). In this process, metal deposition and intrusion is a major cause for irreversible catalyst deactivation and shifts in product distribution. We used x-ray nanotomography of industrial FCC particles at differing degrees of deactivation to quantify changes in single-particle macroporosity and pore connectivity, correlated to iron and nickel deposition. Our study reveals that these metals are incorporated almost exclusively in near-surface regions, severely limiting macropore accessibility as metal concentrations increase. Because macropore channels are “highways” of the pore network, blocking them prevents feedstock molecules from reaching the catalytically active domains. Consequently, metal deposition reduces conversion with time on stream because the internal pore volume, although itself unobstructed, becomes largely inaccessible. PMID:26601160

A single particle model to simulate the dynamics of entangled polymer melts.

PubMed

Kindt, P; Briels, W J

2007-10-07

We present a computer simulation model of polymer melts representing each chain as one single particle. Besides the position coordinate of each particle, we introduce a parameter n(ij) for each pair of particles i and j within a specified distance from each other. These numbers, called entanglement numbers, describe the deviation of the system of ignored coordinates from its equilibrium state for the given configuration of the centers of mass of the polymers. The deviations of the entanglement numbers from their equilibrium values give rise to transient forces, which, together with the conservative forces derived from the potential of mean force, govern the displacements of the particles. We have applied our model to a melt of C(800)H(1602) chains at 450 K and have found good agreement with experiments and more detailed simulations. Properties addressed in this paper are radial distribution functions, dynamic structure factors, and linear as well as nonlinear rheological properties.

Comparative analysis of breakdown mechanism in thin SiO2 oxide films in metal-oxide-semiconductor structures under the action of heavy charged particles and a pulsed voltage

NASA Astrophysics Data System (ADS)

Zinchenko, V. F.; Lavrent'ev, K. V.; Emel'yanov, V. V.; Vatuev, A. S.

2016-02-01

Regularities in the breakdown of thin SiO2 oxide films in metal-oxide-semiconductors structures of power field-effect transistors under the action of single heavy charged particles and a pulsed voltage are studied experimentally. Using a phenomenological approach, we carry out comparative analysis of physical mechanisms and energy criteria of the SiO2 breakdown in extreme conditions of excitation of the electron subsystem in the subpicosecond time range.

Structures of dynamic particle accumulation in Marangoni convection in half-zone liquid bridge

NASA Astrophysics Data System (ADS)

Tanaka, S.; Ueno, I.; Kawamura, H.

Thermocapillary convection is induced by the temperature difference T between two cylindrical rods sustaining liquid bridge. It is well known that the induced flow exhibits a transition from 2-D steady to 3-D time-dependent oscillatory flows with the increasing T. These convections can be visualized by using fine particles as tracers. In a certain flow condition, the particles were found to get accumulated. This is called PAS, particle accumulation structure, after Schwabe et al. (Microgravity, sci. technol. 1996). The authors group (Ueno et al, Proc. TSFP-2, 2001) categorized the induced flow fields into several regimes by the particle motion, structures and the surface temperature variation. Two sets of pulsating and rotating flows appeared. It was observed clearly that the particle gathered along a closed single path. This kind of structure was named as TL-PAS, Twisted-loop particle accumulation structure, (Tanaka et al, J. Japan Soc. Microgravity Appl, 2000). Special attention was paid for this kind of PAS in this study. The TL-PAS exhibited several types of closed path lines. Its detailed structure changed even in the same regime with a slight change of T and aspect ratio. The experimental setup consisted of the transparent crystal top and aluminum bottom rods. Flow fields were observed from top and side through two CCD cameras. A laser-light-sheet was employed in order to grasp the 3-D structures of TL-PAS. The liquid bridge of Silicone oil of 2 cSt was formed between rods of 5mm in diameter. Several kinds of particles were tested as tracer. The surface temperature variation was measured simultaneously by use of a 25μm thermocouple up to 50Hz, or 2.5μm CCT probe (constant current thermometry) up to 100Hz. By use of this apparatus, 3-D structure of TL-PAS and motions of individual particles were captured.

Transition Behaviors of Configurations of Colloidal Particles at a Curved Oil-Water Interface

PubMed Central

Lee, Mina; Xia, Ming; Park, Bum Jun

2016-01-01

We studied the transition behaviors of colloidal arrangements confined at a centro-symmetrically curved oil-water interface. We found that assemblies composed of several colloidal particles at the curved interface exhibit at least two unique patterns that can be attributed to two factors: heterogeneity of single-colloid self-potential and assembly kinetics. The presence of the two assembly structures indicates that an essential energy barrier between the two structures exists and that one of the structures is kinetically stable. This energy barrier can be overcome via external stimuli (e.g., convection and an optical force), leading to dynamic transitions of the assembly patterns. PMID:28773263

Bright-field electron tomography of individual inorganic fullerene-like structures.

PubMed

Bar Sadan, Maya; Wolf, Sharon G; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.

Tensile properties to 650 C and deformation structures in a precipitation strengthened titanium-aluminum alloy

NASA Technical Reports Server (NTRS)

Mendiratta, M. G.

1973-01-01

Appreciable strength levels were retained to 650 C in a Ti-10Al-1Si alloy aged in the (alpha + alpha sub 2) phase field to yield optimum room temperature strength and ductility. The aging treatment precipitated a uniform distribution of alpha sub 2-particles such that, at room temperature, dislocations bypassed instead of shearing the particles at low strains. Specimens fractured at room temperature exhibited fine uniform dimples even for those aging conditions that imparted no macroscopic ductility. The main crack appeared to propagate through the planar slip bands that had cut through the alpha sub 2-particles. A two-step aging process produced a higher volume fraction of bimodally distributed alpha sub 2-particles that led to higher strength levels at elevated temperatures. Both for the single size and the bimodal alpha sub 2-particle distributions, elevated-temperature deformation structures consisted mainly of planar slip bands that sheared through the alpha sub 2-particles.

Selective laser processing of ink-jet printed nano-scaled tin-clad copper particles

NASA Astrophysics Data System (ADS)

Yung, K. C.; Plura, T. S.

2010-11-01

The deposition of tin-clad nano-size copper particles was carried out by means of ink-jet printing. Curing the particles on Polyimide (PI) turned them into soldered structures using an Nd-YAG laser. Area coverage of 55% was achieved for a single-layer print. Subsequent laser sintering increased this value to 95%. A Butanol-based copper ink and an aqueous tin (Sn)-clad Copper (Cu) ink were produced and were ink-jetted in this work. These nano-metallic inks showed excellent suspension stability with particle weight concentrations as high as 5%. The ink components were examined by measuring the particle size distribution in a dispersed condition, and the melting temperature. A piezo ink-jet print head was used to deposit the inks onto a moveable substrate. The thermal effect of the laser irradiation allowed approaching and connecting adjacent particles by melting the particle’s tin coating. The results were examined with regard to structure and soldering properties using EDX, SEM and optical microscopy.

In Situ Visualization of the Growth and Fluctuations of Nanoparticle Superlattice in Liquids

NASA Astrophysics Data System (ADS)

Ou, Zihao; Shen, Bonan; Chen, Qian

We use liquid phase transmission electron microscopy to image and understand the crystal growth front and interfacial fluctuation of a nanoparticle superlattice. With single particle resolution and hundreds of nanoscale building blocks in view, we are able to identify the interface between ordered lattice and disordered structure and visualize the kinetics of single building block attachment at the lattice growth front. The spatial interfacial fluctuation profiles support the capillary wave theory, from which we derive a surface stiffness value consistent with scaling analysis. Our experiments demonstrate the potential of extending model study on collective systems to nanoscale with single particle resolution and testing fundamental theories of condensed matter at a length scale linking atoms and micron-sized colloids.

Chromatic patchy particles: Effects of specific interactions on liquid structure

DOE PAGES

Vasilyev, Oleg A.; Tkachenko, Alexei V.; Klumov, Boris A.

2015-07-13

We study the structural and thermodynamic properties of patchy particle liquids, with a special focus on the role of “color,” i.e., specific interactions between individual patches. A possible experimental realization of such “chromatic” interactions is by decorating the particle patches with single-stranded DNA linkers. The complementarity of the linkers can promote selective bond formation between predetermined pairs of patches. By using MD simulations, we compare the local connectivity, the bond orientation order, and other structural properties of the aggregates formed by the “colored” and “colorless” systems. The analysis is done for spherical particles with two different patch arrangements (tetrahedral andmore » cubic). It is found that the aggregated (liquid) phase of the “colorless” patchy particles is better connected, denser and typically has stronger local order than the corresponding “colored” one. This, in turn, makes the colored liquid less stable thermodynamically. Specifically, we predict that in a typical case the chromatic interactions should increase the relative stability of the crystalline phase with respect to the disordered liquid, thus expanding its region in the phase diagram.« less

Synthesis and characterization of monodispersed polymer/polydiacetylene nanocrystal composite particles.

PubMed

Wei, Zhong; Ujiiye-Ishii, Kento; Masuhara, Akito; Kasai, Hitoshi; Okada, Shuji; Matsune, Hideki; Asahi, Tsuyoshi; Masuhara, Hiroshi; Nakanishi, Hachiro

2005-06-01

Monodispersed polymer/polydiacetylenecomposite particles were synthesized by soap-free seeded emulsion polymerization of styrene andmethyl methacrylate; the products were characterized by XRD, SEM, TEM, UV-visible spectroscopy, and single particle scattering spectroscopy. In the synthesis process, polydiacetylene nanocrystals were found to act as inhibitor, and consequently a relatively low concentration was necessary. Different monomers lead to the differences in reaction condition and particle morphology; the PMMA composite particles were simpler in preparation than polystyrene particles, but the latter havebetter spherical morphology. The composite particles were composed of polymer shells and polydiacetylene cores, which kept their crystal structure and optical properties. A high percentage of cored particles could be achieved with optimized reaction conditions where the amount of seed was sufficient and the oily oligomer by-product was suppressed.

Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

DOE PAGES

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; ...

2016-03-30

DNA base pairing has been used for many years to direct the arrangement of inorganic nanocrystals into small groupings and arrays with tailored optical and electrical properties. The control of DNA-mediated assembly depends crucially on a better understanding of three-dimensional structure of DNA-nanocrystal-hybridized building blocks. Existing techniques do not allow for structural determination of these flexible and heterogeneous samples. Here we report cryo-electron microscopy and negative-staining electron tomography approaches to image, and three-dimensionally reconstruct a single DNA-nanogold conjugate, an 84-bp double-stranded DNA with two 5-nm nanogold particles for potential substrates in plasmon-coupling experiments. By individual-particle electron tomography reconstruction, we obtainmore » 14 density maps at ~ 2-nm resolution . Using these maps as constraints, we derive 14 conformations of dsDNA by molecular dynamics simulations. The conformational variation is consistent with that from liquid solution, suggesting that individual-particle electron tomography could be an expected approach to study DNA-assembling and flexible protein structure and dynamics.« less

Controlled phase evolution and the occurrence of single domain CoFe2O4 nanoparticles synthesized by PVA assisted sol-gel method

NASA Astrophysics Data System (ADS)

Srinivasa Rao, K.; Ranga Nayakulu, S. V.; Chaitanya Varma, M.; Choudary, G. S. V. R. K.; Rao, K. H.

2018-04-01

The present investigation describes the development of cobalt ferrite nanoparticles having size less than 10 nm, by a sol-gel method using polyvinyl alcohol as chelating agent. X-ray results show all the samples, annealed above 700 °C have spinel structure. The information about phase evolution with reaction temperatures was obtained by subjecting the as-prepared powder for DSC/TGA study. High saturation magnetization of 84.63 emu/g has been observed for a particle size of 8.1 nm, a rare event reported till date. The dM/dH versus H curves suggest that the transition from single domain state to multi-domain state occurs with increasing annealing temperature and the critical size for the single domain nature of CoFe2O4 is around 6.5 nm. The estimated critical diameter for single domain particle (6.7 nm) is in good agreement with that (6.5 nm) obtained from Transmission Electron Micrographs. The highest coercivity (1645 Oe) has been found for a particle of size 6.5 nm.

Photoresponsive Release from Azobenzene-Modified Single Cubic Crystal NaCl/Silica Particles

DOE PAGES

Jiang, Xingmao; Liu, Nanguo; Assink, Roger A.; ...

2011-01-01

Azobenzene ligands were uniformly anchored to the pore surfaces of nanoporous silica particles with single crystal NaCl using 4-(3-triethoxysilylpropylureido)azobenzene (TSUA). The functionalization delayed the release of NaCl significantly. The modified particles demonstrated a photocontrolled release by trans/cis isomerization of azobenzene moieties. The addition of amphiphilic solvents, propylene glycol (PG), propylene glycol propyl ether (PGPE), and dipropylene glycol propyl ether (DPGPE) delayed the release in water, although the wetting behavior was improved and the delay is the most for the block molecules with the longest carbon chain. The speedup by UV irradiation suggests a strong dependence of diffusion on the switchablemore » pore size. TGA, XRD, FTIR, and NMR techniques were used to characterize the structures.« less

Structure for Storing Properties of Particles (PoP)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patel, N. R.; Mattoon, C. M.; Beck, B. R.

2014-06-01

Some evaluated nuclear databases are critical for applications such as nuclear energy, nuclear medicine, homeland security, and stockpile stewardship. Particle masses, nuclear excitation levels, and other “Properties of Particles” are essential for making evaluated nuclear databases. Currently, these properties are obtained from various databases that are stored in outdated formats. Moreover, the “Properties of Particles” (PoP) structure is being designed that will allow storing all information for one or more particles in a single place, so that each evaluation, simulation, model calculation, etc. can link to the same data. Information provided in PoP will include properties of nuclei, gammas andmore » electrons (along with other particles such as pions, as evaluations extend to higher energies). Presently, PoP includes masses from the Atomic Mass Evaluation version 2003 (AME2003), and level schemes and gamma decays from the Reference Input Parameter Library (RIPL-3). The data are stored in a hierarchical structure. An example of how PoP stores nuclear masses and energy levels will be presented here.« less

Swelling, Structure, and Phase Stability of Soft, Compressible Microgels

NASA Astrophysics Data System (ADS)

Denton, Alan R.; Urich, Matthew

Microgels are soft colloidal particles that swell when dispersed in a solvent. The equilibrium particle size is governed by a delicate balance of osmotic pressures, which can be tuned by varying single-particle properties and externally controlled conditions, such as temperature, pH, ionic strength, and concentration. Because of their tunable size and ability to encapsulate dye or drug molecules, microgels have practical relevance for biosensing, drug delivery, carbon capture, and filtration. Using Monte Carlo simulation, we model suspensions of microgels that interact via Hertzian elastic interparticle forces and can expand or contract via trial size changes governed by the Flory-Rehner free energy of cross-linked polymer gels. We analyze the influence of particle compressibility and size fluctuations on bulk structural and thermal properties by computing swelling ratios, radial distribution functions, static structure factors, osmotic pressures, and freezing densities. With increasing density, microgels progressively deswell and their intrinsic polydispersity broadens, while compressibility acts to forestall crystallization. This work was supported by the National Science Foundation under Grant No. DMR- 1106331.

Structure for Storing Properties of Particles (PoP)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patel, N.R., E-mail: infinidhi@llnl.gov; Mattoon, C.M.; Beck, B.R.

2014-06-15

Evaluated nuclear databases are critical for applications such as nuclear energy, nuclear medicine, homeland security, and stockpile stewardship. Particle masses, nuclear excitation levels, and other “Properties of Particles” are essential for making evaluated nuclear databases. Currently, these properties are obtained from various databases that are stored in outdated formats. A “Properties of Particles” (PoP) structure is being designed that will allow storing all information for one or more particles in a single place, so that each evaluation, simulation, model calculation, etc. can link to the same data. Information provided in PoP will include properties of nuclei, gammas and electrons (alongmore » with other particles such as pions, as evaluations extend to higher energies). Presently, PoP includes masses from the Atomic Mass Evaluation version 2003 (AME2003), and level schemes and gamma decays from the Reference Input Parameter Library (RIPL-3). The data are stored in a hierarchical structure. An example of how PoP stores nuclear masses and energy levels will be presented here.« less

Single Aerosol Particle Studies Using Optical Trapping Raman And Cavity Ringdown Spectroscopy

NASA Astrophysics Data System (ADS)

Gong, Z.; Wang, C.; Pan, Y. L.; Videen, G.

2017-12-01

Due to the physical and chemical complexity of aerosol particles and the interdisciplinary nature of aerosol science that involves physics, chemistry, and biology, our knowledge of aerosol particles is rather incomplete; our current understanding of aerosol particles is limited by averaged (over size, composition, shape, and orientation) and/or ensemble (over time, size, and multi-particles) measurements. Physically, single aerosol particles are the fundamental units of any large aerosol ensembles. Chemically, single aerosol particles carry individual chemical components (properties and constituents) in particle ensemble processes. Therefore, the study of single aerosol particles can bridge the gap between aerosol ensembles and bulk/surface properties and provide a hierarchical progression from a simple benchmark single-component system to a mixed-phase multicomponent system. A single aerosol particle can be an effective reactor to study heterogeneous surface chemistry in multiple phases. Latest technological advances provide exciting new opportunities to study single aerosol particles and to further develop single aerosol particle instrumentation. We present updates on our recent studies of single aerosol particles optically trapped in air using the optical-trapping Raman and cavity ringdown spectroscopy.

Micro-Spectroscopic Chemical Imaging of Individual Identified Marine Biogenic and Ambient Organic Ice Nuclei (Invited)

NASA Astrophysics Data System (ADS)

Knopf, D. A.; Alpert, P. A.; Wang, B.; OBrien, R. E.; Moffet, R. C.; Aller, J. Y.; Laskin, A.; Gilles, M.

2013-12-01

Atmospheric ice formation represents one of the least understood atmospheric processes with important implications for the hydrological cycle and climate. Current freezing descriptions assume that ice active sites on the particle surface initiate ice nucleation, however, the nature of these sites remains elusive. Here, we present a new experimental method that allows us to relate physical and chemical properties of individual particles with observed water uptake and ice nucleation ability using a combination of micro-spectroscopic and optical single particle analytical techniques. We apply this method to field-collected particles and particles generated via bursting of bubbles produced by glass frit aeration and plunging water impingement jets in a mesocosm containing artificial sea water and bacteria and/or phytoplankton. The most efficient ice nuclei (IN) within a particle population are identified and characterized. Single particle characterization is achieved by computer controlled scanning electron microscopy with energy dispersive analysis of X-rays (CCSEM/EDX) and scanning transmission X-ray microscopy with near edge X-ray absorption fine structure spectroscopy. A vapor controlled cooling-stage coupled to an optical microscope is used to determine the onsets of water uptake, immersion freezing, and deposition ice nucleation of the individual particles as a function of temperature (T) as low as 200 K and relative humidity (RH) up to water saturation. In addition, we perform CCSEM/EDX to obtain on a single particle level the elemental composition of the entire particle population. Thus, we can determine if the IN are exceptional in nature or belong to a major particle type class with respect to composition and size. We find that ambient and sea spray particles are coated by organic material and can induce ice formation under tropospheric relevant conditions. Micro-spectroscopic single particle analysis of the investigated particle samples invokes a potential paradigm shift: Individual ice nucleating particle composition indicates that IN are similar to the majority of particles in the population and not exceptional. This suggests that composition alone may not be a determinant for IN identification. Furthermore, the results suggest that particle abundance may be a crucial parameter for IN efficiency when predicting cloud glaciation processes. These findings would have important consequences for cloud modeling, laboratory ice nucleation experiments, and field measurements.

Magnetic, hyperthermic and structural properties of zn substituted CaFe2O4 powders

NASA Astrophysics Data System (ADS)

Kheradmand, Abbas; Vahidi, Omid; Masoudpanah, S. M.

2018-03-01

In the present study, we have synthesized single phase Ca1 - x Zn x Fe2O4 powders by hydrothermal method. The cation distribution between the tetrahedral and octahedral sites in the spinel structure and the magnetic properties as a function of the zinc substitution have been investigated by X-ray diffraction (XRD), infrared spectroscopy and vibrating sample magnetometer methods. The obtained XRD pattern indicated that the synthesized particles had single phase cubic spinel structure with no impurity. The magnetic measurements showed that the saturation magnetization increased from 83 to 98 emu/g with the addition of zinc due to the decrease of inversity. The particle size observed by electron microscopy decreased from 1.38 to 0.97 µm with the increase of zinc addition. The Ca0.7Zn0.3Fe2O4 powders exhibited appropriate heating capability for hyperthermia applications with the maximum AC heating temperature of 20 °C and specific loss power of 9.29 W/g.

Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae

PubMed Central

Sõmera, Merike; Sarmiento, Cecilia; Truve, Erkki

2015-01-01

The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses. PMID:26083319

Structure of free radicals in irradiated acetyl-L-leucine single crystals at 77 K

DOE Office of Scientific and Technical Information (OSTI.GOV)

Almanov, G.A.; Bogdanchikov, G.A.; Usov, O.M.

1988-09-01

By using the EPR method, two types of radicals are observed, which are formed in acetyl-L-leucine single crystals irradiated at 77K. These are alkyl type radicals (CH/sub 3/)/sub 2/CCH/sub 2/CH(NHCOCH/sub 3/)COOH and peptide group radicals. When the crystals are defrozen to room temperatures, the radicals of the second type disappear without formation of paramagnetic particles. Two possible structures of the peptide group radicals were studied by the INDO method. On defreezing to room temperature, the alkyl group radical is retained, while the peptide radical disappears without formation of paramagnetic particles. For the protonated form of the anion-radical, a better agreementmore » is observed between the theoretically calculated and the experimentally obtained HFI constants. The quantum chemical analysis of the possible structures of the peptide group radicals indicates that the formation of the protonated form of the anion-radical is energetically favorable.« less

In-Flight Annealing of Magnetic Nanoparticles, Produced by the Particle Gun Technique

NASA Astrophysics Data System (ADS)

Stoyanov, S.; Skumryev, V.; Zhang, Y.; Huang, Y.; Hadjipanayis, G. C.

2003-03-01

The need of post annealing of nanocomposite structures aimed to form nanoparticles or to obtain a desired crystal structure often results in particles growth and/or a harmful alloying with the matrix material. In this study, we present a new technique to perform an in situ phase transformation of particles produced by the gas condensation process in a Particle Gun (PG). Particles are heat treated during their flight from the PG to the substrate, by absorption of light in a specially designed Heating Stage (HS), placed on the top of the PG. The total power of the light sources used is 2 kWatt. A simple model for the thermodynamic conditions in a single particle during the annealing process is developed. It is shown that the temperature of the particle depends on the light power and the size of the particle and can easily reach the required annealing values of 400 to 900^oC in a millisecond time scale. The versatility of this technique is demonstrated on the fabrication of high anisotropy FePt and SmCo particles, embedded in a carbon matrix. Work supported by NSF DMR9972035

Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.

PubMed

Fromm, S A; Sachse, C

2016-01-01

Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. © 2016 Elsevier Inc. All rights reserved.

Mini-thin filaments regulated by troponin–tropomyosin

PubMed Central

Gong, Huiyu; Hatch, Victoria; Ali, Laith; Lehman, William; Craig, Roger; Tobacman, Larry S.

2005-01-01

Striated muscle thin filaments contain hundreds of actin monomers and scores of troponins and tropomyosins. To study the cooperative mechanism of thin filaments, “mini-thin filaments” were generated by isolating particles nearly matching the minimal structural repeat of thin filaments: a double helix of actin subunits with each strand approximately seven actins long and spanned by a troponin–tropomyosin complex. One end of the particles was capped by a gelsolin (segment 1–3)–TnT fusion protein (substituting for normal TnT), and the other end was capped by tropomodulin. EM showed that the particles were 46 ± 9 nm long, with a knob-like mass attributable to gelsolin at one end. Average actin, tropomyosin, and gelsolin–troponin composition indicated one troponin–tropomyosin attached to each strand of the two-stranded actin filament. The minifilaments thus nearly represent single regulatory units of thin filaments. The myosin S1 MgATPase rate stimulated by the minifilaments was Ca2+-sensitive, indicating that single regulatory length particles are sufficient for regulation. Ca2+ bound cooperatively to cardiac TnC in conventional thin filaments but noncooperatively to cardiac TnC in minifilaments in the absence of myosin. This suggests that thin filament Ca2+-binding cooperativity reflects indirect troponin–troponin interactions along the long axis of conventional filaments, which do not occur in minifilaments. Despite noncooperative Ca2+ binding to minifilaments in the absence of myosin, Ca2+ cooperatively activated the myosin S1-particle ATPase rate. Two-stranded single regulatory units therefore may be sufficient for myosin-mediated Ca2+-binding cooperativity. Functional mini-thin filaments are well suited for biochemical and structural analysis of thin-filament regulation. PMID:15644437

Cryo-EM in drug discovery: achievements, limitations and prospects.

PubMed

Renaud, Jean-Paul; Chari, Ashwin; Ciferri, Claudio; Liu, Wen-Ti; Rémigy, Hervé-William; Stark, Holger; Wiesmann, Christian

2018-06-08

Cryo-electron microscopy (cryo-EM) of non-crystalline single particles is a biophysical technique that can be used to determine the structure of biological macromolecules and assemblies. Historically, its potential for application in drug discovery has been heavily limited by two issues: the minimum size of the structures it can be used to study and the resolution of the images. However, recent technological advances - including the development of direct electron detectors and more effective computational image analysis techniques - are revolutionizing the utility of cryo-EM, leading to a burst of high-resolution structures of large macromolecular assemblies. These advances have raised hopes that single-particle cryo-EM might soon become an important tool for drug discovery, particularly if they could enable structural determination for 'intractable' targets that are still not accessible to X-ray crystallographic analysis. This article describes the recent advances in the field and critically assesses their relevance for drug discovery as well as discussing at what stages of the drug discovery pipeline cryo-EM can be useful today and what to expect in the near future.

Heat and mass transfer at gas-phase ignition of grinded coal layer by several metal particles heated to a high temperature

NASA Astrophysics Data System (ADS)

Glushkov, D. O.; Kuznetsov, G. V.; Strizhak, P. A.

2017-07-01

Characteristics of gas-phase ignition of grinded brown coal (brand 2B, Shive-Ovoos deposit in Mongolia) layer by single and several metal particles heated to a high temperature (above 1000 K) have been investigated numerically. The developed mathematical model of the process takes into account the heating and thermal decomposition of coal at the expense of the heat supplied from local heat sources, release of volatiles, formation and heating of gas mixture and its ignition. The conditions of the joint effect of several hot particles on the main characteristic of the process-ignition delay time are determined. The relation of the ignition zone position in the vicinity of local heat sources and the intensity of combustible gas mixture warming has been elucidated. It has been found that when the distance between neighboring particles exceeds 1.5 hot particle size, an analysis of characteristics and regularities of coal ignition by several local heat sources can be carried out within the framework of the model of "single metal particle / grinded coal / air". Besides, it has been shown with the use of this model that the increase in the hot particle height leads, along with the ignition delay time reduction, to a reduction of the source initial temperatures required for solid fuel ignition. At an imperfect thermal contact at the interface hot particle / grinded coal due to the natural porosity of the solid fuel structure, the intensity of ignition reduces due to a less significant effect of radiation in the area of pores on the heat transfer conditions compared to heat transfer by conduction in the near-surface coal layer without regard to its heterogeneous structure.

Toward the theory of fermionic condensation

NASA Astrophysics Data System (ADS)

Khodel, V. A.

2017-04-01

The diagrammatic technique elaborated by Belyaev for the theory of a Fermi liquid has been implemented to analyze the behavior of Fermi systems beyond the topological phase transition point, where the fermionic condensate appears. It has been shown that the inclusion of the interaction between the condensate and above-condensate particles leads to the emergence of a gap in the single-particle excitation spectrum of these particles even in the absence of Cooper pairing. Hence, the emergence of this gap in homogeneous electron systems of silicon field-effect structures leads to a metal-insulator phase transition rather than to superconductivity. It has been shown that the same interaction explains the nature of the Fermi arc structure in twodimensional electron systems of cuprates.

Synthesis and structural characterization of transition metal doped MgO: Mg0.95Mn0.01TM0.04O (TM = Co, Ni, Cu)

NASA Astrophysics Data System (ADS)

Islam, Ishtihadah; Khandy, Shakeel Ahmad; Hafiz, Aurangzeb Khurram

2018-05-01

In the present work, preparation and characterization of transition metal doped MgO: Zn0.94Mn0.01TM0.05O (TM = Co, Ni and Cu) nano-particles have been reported. Transition metal doped samples of MgO were synthesized by Sol gel auto combustion method. Structural characterisation from XRD and SEM show the formation of single-phase primary particles, nearly of spherical shaped nano-crystallites. The crystallite size was found to be 78.2, 67.02, 78.11 and 64 nm for pure, Co, Cu and Ni doped MgMnO nano-particles, respectively. Hence, the average crystallite size increases monotonously from Co to Cu doping.

Determination of magnetic domain state of carbon coated iron nanoparticles via 57Fe zero-external-field NMR

NASA Astrophysics Data System (ADS)

Manjunatha, M.; Kumar, Rajeev; Sahoo, Balaram; Damle, Ramakrishna; Ramesh, K. P.

2018-05-01

The magnetic domain state of carbon coated iron nanopowder (Fe@C) was studied by the internal field nuclear magnetic resonance (IFNMR) at 77 K using the spin echo technique. The structure and magnetic properties of the sample were further characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), Mössbauer spectroscopy, vibrating sample magnetometry (VSM), thermogravimetric analysis (TGA) and Raman Spectroscopy. The obtained IFNMR results of Fe@C powder were compared with that of micron sized carbonyl iron (CI) and electrolytic iron (EI) powders. The calculated critical size of the single domain iron particles in Fe@C is ∼ 16 nm. A higher enhancement in echo amplitude was observed due to better response of the domain walls of multidomain particles in comparison to the single domain particles. The echo signal of CI and EI particles exhibit a single narrow intense peak corresponding to the domain walls, whereas Fe@C exhibits two low amplitude peaks at two different frequencies: a low frequency (46.6 MHz) peak corresponds to the response of the domain walls of the multidomain particles and the other high frequency (47.2 MHz) signal (a shoulder) corresponding to the response of the magnetic nuclei inside the domain. Our results help in determining the domain state of iron-based magnetic particles using 57Fe-IFNMR.

Ground-state energies of simple metals

NASA Technical Reports Server (NTRS)

Hammerberg, J.; Ashcroft, N. W.

1974-01-01

A structural expansion for the static ground-state energy of a simple metal is derived. Two methods are presented, one an approach based on single-particle band structure which treats the electron gas as a nonlinear dielectric, the other a more general many-particle analysis using finite-temperature perturbation theory. The two methods are compared, and it is shown in detail how band-structure effects, Fermi-surface distortions, and chemical-potential shifts affect the total energy. These are of special interest in corrections to the total energy beyond third order in the electron-ion interaction and hence to systems where differences in energies for various crystal structures are exceptionally small. Preliminary calculations using these methods for the zero-temperature thermodynamic functions of atomic hydrogen are reported.

Numerical investigation of field enhancement by metal nano-particles using a hybrid FDTD-PSTD algorithm.

PubMed

Pernice, W H; Payne, F P; Gallagher, D F

2007-09-03

We present a novel numerical scheme for the simulation of the field enhancement by metal nano-particles in the time domain. The algorithm is based on a combination of the finite-difference time-domain method and the pseudo-spectral time-domain method for dispersive materials. The hybrid solver leads to an efficient subgridding algorithm that does not suffer from spurious field spikes as do FDTD schemes. Simulation of the field enhancement by gold particles shows the expected exponential field profile. The enhancement factors are computed for single particles and particle arrays. Due to the geometry conforming mesh the algorithm is stable for long integration times and thus suitable for the simulation of resonance phenomena in coupled nano-particle structures.

Symplectic multi-particle tracking on GPUs

NASA Astrophysics Data System (ADS)

Liu, Zhicong; Qiang, Ji

2018-05-01

A symplectic multi-particle tracking model is implemented on the Graphic Processing Units (GPUs) using the Compute Unified Device Architecture (CUDA) language. The symplectic tracking model can preserve phase space structure and reduce non-physical effects in long term simulation, which is important for beam property evaluation in particle accelerators. Though this model is computationally expensive, it is very suitable for parallelization and can be accelerated significantly by using GPUs. In this paper, we optimized the implementation of the symplectic tracking model on both single GPU and multiple GPUs. Using a single GPU processor, the code achieves a factor of 2-10 speedup for a range of problem sizes compared with the time on a single state-of-the-art Central Processing Unit (CPU) node with similar power consumption and semiconductor technology. It also shows good scalability on a multi-GPU cluster at Oak Ridge Leadership Computing Facility. In an application to beam dynamics simulation, the GPU implementation helps save more than a factor of two total computing time in comparison to the CPU implementation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Levay, Peter; Nagy, Szilvia; Pipek, Janos

An elementary formula for the von Neumann and Renyi entropies describing quantum correlations in two-fermionic systems having four single-particle states is presented. An interesting geometric structure of fermionic entanglement is revealed. A connection with the generalized Pauli principle is established.

Presumed magnetic biosignatures observed in magnetite derived from abiotic reductive alteration of nanogoethite

NASA Astrophysics Data System (ADS)

Till, Jessica L.; Guyodo, Yohan; Lagroix, France; Morin, Guillaume; Menguy, Nicolas; Ona-Nguema, Georges

2017-03-01

The oriented chains of nanoscale Fe-oxide particles produced by magnetotactic bacteria are a striking example of biomineralization. Several distinguishing features of magnetite particles that comprise bacterial magnetosomes have been proposed to collectively constitute a biosignature of magnetotactic bacteria (Thomas-Keprta et al., 2001). These features include high crystallinity, chemical purity, a single-domain magnetic structure, well-defined crystal morphology, and arrangement of particles in chain structures. Here, we show that magnetite derived from the inorganic breakdown of nanocrystalline goethite exhibits magnetic properties and morphologies remarkably similar to those of biogenic magnetite from magnetosomes. During heating in reducing conditions, oriented nanogoethite aggregates undergo dehydroxylation and transform into stoichiometric magnetite. We demonstrate that highly crystalline single-domain magnetite with euhedral grain morphologies produced abiogenically from goethite meets several of the biogenicity criteria commonly used for the identification of magnetofossils. Furthermore, the suboxic conditions necessary for magnetofossil preservation in sediments are conducive to the reductive alteration of nanogoethite, as well as the preservation of detrital magnetite originally formed from goethite. The findings of this study have potential implications for the identification of biogenic magnetite, particularly in older sediments where diagenesis commonly disrupts the chain structure of magnetosomes. Our results indicate that isolated magnetofossils cannot be positively distinguished from inorganic magnetite on the basis of their magnetic properties and morphology, and that intact chain structures remain the only reliable distinguishing feature of fossil magnetosomes.

The single scattering properties of the aerosol particles as aggregated spheres

NASA Astrophysics Data System (ADS)

Wu, Y.; Gu, X.; Cheng, T.; Xie, D.; Yu, T.; Chen, H.; Guo, J.

2012-08-01

The light scattering and absorption properties of anthropogenic aerosol particles such as soot aggregates are complicated in the temporal and spatial distribution, which introduce uncertainty of radiative forcing on global climate change. In order to study the single scattering properties of anthorpogenic aerosol particles, the structures of these aerosols such as soot paticles and soot-containing mixtures with the sulfate or organic matter, are simulated using the parallel diffusion limited aggregation algorithm (DLA) based on the transmission electron microscope images (TEM). Then, the single scattering properties of randomly oriented aerosols, such as scattering matrix, single scattering albedo (SSA), and asymmetry parameter (AP), are computed using the superposition T-matrix method. The comparisons of the single scattering properties of these specific types of clusters with different morphological and chemical factors such as fractal parameters, aspect ratio, monomer radius, mixture mode and refractive index, indicate that these different impact factors can respectively generate the significant influences on the single scattering properties of these aerosols. The results show that aspect ratio of circumscribed shape has relatively small effect on single scattering properties, for both differences of SSA and AP are less than 0.1. However, mixture modes of soot clusters with larger sulfate particles have remarkably important effects on the scattering and absorption properties of aggregated spheres, and SSA of those soot-containing mixtures are increased in proportion to the ratio of larger weakly absorbing attachments. Therefore, these complex aerosols come from man made pollution cannot be neglected in the aerosol retrievals. The study of the single scattering properties on these kinds of aggregated spheres is important and helpful in remote sensing observations and atmospheric radiation balance computations.

Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

DOE PAGES

Fortmann-Grote, Carsten; Buzmakov, Alexey; Jurek, Zoltan; ...

2017-09-01

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. In conclusion, it is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fortmann-Grote, Carsten; Buzmakov, Alexey; Jurek, Zoltan

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. In conclusion, it is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

Single-particle tracking: applications to membrane dynamics.

PubMed

Saxton, M J; Jacobson, K

1997-01-01

Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.

Weak correlations between local density and dynamics near the glass transition.

PubMed

Conrad, J C; Starr, F W; Weitz, D A

2005-11-17

We perform experiments on two different dense colloidal suspensions with confocal microscopy to probe the relationship between local structure and dynamics near the glass transition. We calculate the Voronoi volume for our particles and show that this quantity is not a universal probe of glassy structure for all colloidal suspensions. We correlate the Voronoi volume to displacement and find that these quantities are only weakly correlated. We observe qualitatively similar results in a simulation of a polymer melt. These results suggest that the Voronoi volume does not predict dynamical behavior in experimental colloidal suspensions; a purely structural approach based on local single particle volume likely cannot describe the colloidal glass transition.

Fractal morphology, imaging and mass spectrometry of single aerosol particles in flight.

PubMed

Loh, N D; Hampton, C Y; Martin, A V; Starodub, D; Sierra, R G; Barty, A; Aquila, A; Schulz, J; Lomb, L; Steinbrener, J; Shoeman, R L; Kassemeyer, S; Bostedt, C; Bozek, J; Epp, S W; Erk, B; Hartmann, R; Rolles, D; Rudenko, A; Rudek, B; Foucar, L; Kimmel, N; Weidenspointner, G; Hauser, G; Holl, P; Pedersoli, E; Liang, M; Hunter, M S; Hunter, M M; Gumprecht, L; Coppola, N; Wunderer, C; Graafsma, H; Maia, F R N C; Ekeberg, T; Hantke, M; Fleckenstein, H; Hirsemann, H; Nass, K; White, T A; Tobias, H J; Farquar, G R; Benner, W H; Hau-Riege, S P; Reich, C; Hartmann, A; Soltau, H; Marchesini, S; Bajt, S; Barthelmess, M; Bucksbaum, P; Hodgson, K O; Strüder, L; Ullrich, J; Frank, M; Schlichting, I; Chapman, H N; Bogan, M J

2012-06-27

The morphology of micrometre-size particulate matter is of critical importance in fields ranging from toxicology to climate science, yet these properties are surprisingly difficult to measure in the particles' native environment. Electron microscopy requires collection of particles on a substrate; visible light scattering provides insufficient resolution; and X-ray synchrotron studies have been limited to ensembles of particles. Here we demonstrate an in situ method for imaging individual sub-micrometre particles to nanometre resolution in their native environment, using intense, coherent X-ray pulses from the Linac Coherent Light Source free-electron laser. We introduced individual aerosol particles into the pulsed X-ray beam, which is sufficiently intense that diffraction from individual particles can be measured for morphological analysis. At the same time, ion fragments ejected from the beam were analysed using mass spectrometry, to determine the composition of single aerosol particles. Our results show the extent of internal dilation symmetry of individual soot particles subject to non-equilibrium aggregation, and the surprisingly large variability in their fractal dimensions. More broadly, our methods can be extended to resolve both static and dynamic morphology of general ensembles of disordered particles. Such general morphology has implications in topics such as solvent accessibilities in proteins, vibrational energy transfer by the hydrodynamic interaction of amino acids, and large-scale production of nanoscale structures by flame synthesis.

Confocal Raman microscopy for monitoring chemical reactions on single optically trapped, solid-phase support particles.

PubMed

Houlne, Michael P; Sjostrom, Christopher M; Uibel, Rory H; Kleimeyer, James A; Harris, Joel M

2002-09-01

Optical trapping of small structures is a powerful tool for the manipulation and investigation of colloidal and particulate materials. The tight focus excitation requirements of optical trapping are well suited to confocal Raman microscopy. In this work, an inverted confocal Raman microscope is developed for studies of chemical reactions on single, optically trapped particles and applied to reactions used in solid-phase peptide synthesis. Optical trapping and levitation allow a particle to be moved away from the coverslip and into solution, avoiding fluorescence interference from the coverslip. More importantly, diffusion of reagents into the particle is not inhibited by a surface, so that reaction conditions mimic those of particles dispersed in solution. Optical trapping and levitation also maintain optical alignment, since the particle is centered laterally along the optical axis and within the focal plane of the objective, where both optical forces and light collection are maximized. Hour-long observations of chemical reactions on individual, trapped silica particles are reported. Using two-dimensional least-squares analysis methods, the Raman spectra collected during the course of a reaction can be resolved into component contributions. The resolved spectra of the time-varying species can be observed, as they bind to or cleave from the particle surface.

SAXS analysis of single- and multi-core iron oxide magnetic nanoparticles

PubMed Central

Szczerba, Wojciech; Costo, Rocio; Morales, Maria del Puerto; Thünemann, Andreas F.

2017-01-01

This article reports on the characterization of four superparamagnetic iron oxide nanoparticles stabilized with dimercaptosuccinic acid, which are suitable candidates for reference materials for magnetic properties. Particles p1 and p2 are single-core particles, while p3 and p4 are multi-core particles. Small-angle X-ray scattering analysis reveals a lognormal type of size distribution for the iron oxide cores of the particles. Their mean radii are 6.9 nm (p1), 10.6 nm (p2), 5.5 nm (p3) and 4.1 nm (p4), with narrow relative distribution widths of 0.08, 0.13, 0.08 and 0.12. The cores are arranged as a clustered network in the form of dense mass fractals with a fractal dimension of 2.9 in the multi-core particles p3 and p4, but the cores are well separated from each other by a protecting organic shell. The radii of gyration of the mass fractals are 48 and 44 nm, and each network contains 117 and 186 primary particles, respectively. The radius distributions of the primary particle were confirmed with transmission electron microscopy. All particles contain purely maghemite, as shown by X-ray absorption fine structure spectroscopy. PMID:28381973

Cryo-electron microscopy and cryo-electron tomography of nanoparticles.

PubMed

Stewart, Phoebe L

2017-03-01

Cryo-transmission electron microscopy (cryo-TEM or cryo-EM) and cryo-electron tomography (cryo-ET) offer robust and powerful ways to visualize nanoparticles. These techniques involve imaging of the sample in a frozen-hydrated state, allowing visualization of nanoparticles essentially as they exist in solution. Cryo-TEM grid preparation can be performed with the sample in aqueous solvents or in various organic and ionic solvents. Two-dimensional (2D) cryo-TEM provides a direct way to visualize the polydispersity within a nanoparticle preparation. Fourier transforms of cryo-TEM images can confirm the structural periodicity within a sample. While measurement of specimen parameters can be performed with 2D TEM images, determination of a three-dimensional (3D) structure often facilitates more spatially accurate quantization. 3D structures can be determined in one of two ways. If the nanoparticle has a homogeneous structure, then 2D projection images of different particles can be averaged using a computational process referred to as single particle reconstruction. Alternatively, if the nanoparticle has a heterogeneous structure, then a structure can be generated by cryo-ET. This involves collecting a tilt-series of 2D projection images for a defined region of the grid, which can be used to generate a 3D tomogram. Occasionally it is advantageous to calculate both a single particle reconstruction, to reveal the regular portions of a nanoparticle structure, and a cryo-electron tomogram, to reveal the irregular features. A sampling of 2D cryo-TEM images and 3D structures are presented for protein based, DNA based, lipid based, and polymer based nanoparticles. WIREs Nanomed Nanobiotechnol 2017, 9:e1417. doi: 10.1002/wnan.1417 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Stochastic Gain Degradation in III-V Heterojunction Bipolar Transistors due to Single Particle Displacement Damage

DOE PAGES

Vizkelethy, Gyorgy; Bielejec, Edward S.; Aguirre, Brandon A.

2017-11-13

As device dimensions decrease single displacement effects are becoming more important. We measured the gain degradation in III-V Heterojunction Bipolar Transistors due to single particles using a heavy ion microbeam. Two devices with different sizes were irradiated with various ion species ranging from oxygen to gold to study the effect of the irradiation ion mass on the gain change. From the single steps in the inverse gain (which is proportional to the number of defects) we calculated Cumulative Distribution Functions to help determine design margins. The displacement process was modeled using the Marlowe Binary Collision Approximation (BCA) code. The entiremore » structure of the device was modeled and the defects in the base-emitter junction were counted to be compared to the experimental results. While we found good agreement for the large device, we had to modify our model to reach reasonable agreement for the small device.« less

Stochastic Gain Degradation in III-V Heterojunction Bipolar Transistors due to Single Particle Displacement Damage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vizkelethy, Gyorgy; Bielejec, Edward S.; Aguirre, Brandon A.

As device dimensions decrease single displacement effects are becoming more important. We measured the gain degradation in III-V Heterojunction Bipolar Transistors due to single particles using a heavy ion microbeam. Two devices with different sizes were irradiated with various ion species ranging from oxygen to gold to study the effect of the irradiation ion mass on the gain change. From the single steps in the inverse gain (which is proportional to the number of defects) we calculated Cumulative Distribution Functions to help determine design margins. The displacement process was modeled using the Marlowe Binary Collision Approximation (BCA) code. The entiremore » structure of the device was modeled and the defects in the base-emitter junction were counted to be compared to the experimental results. While we found good agreement for the large device, we had to modify our model to reach reasonable agreement for the small device.« less

Chirality-controlled crystallization via screw dislocations.

PubMed

Sung, Baeckkyoung; de la Cotte, Alexis; Grelet, Eric

2018-04-11

Chirality plays an important role in science from enantiomeric separation in chemistry to chiral plasmonics in nanotechnology. However, the understanding of chirality amplification from chiral building blocks to ordered helical superstructures remains a challenge. Here, we demonstrate that topological defects, such as screw dislocations, can drive the chirality transfer from particle to supramolecular structure level during the crystallization process. By using a model system of chiral particles, which enables direct imaging of single particle incorporation into growing crystals, we show that the crystallization kinetic pathway is the key parameter for monitoring, via the defects, the chirality amplification of the crystalline structures from racemic to predominantly homohelical. We provide an explanation based on the interplay between geometrical frustration, racemization induced by thermal fluctuations, and particle chirality. Our results demonstrate that screw dislocations not only promote the growth, but also control the chiral morphology and therefore the functionality of crystalline states.

Torsion Profiling of Proteins Using Magnetic Particles

PubMed Central

van Reenen, A.; Gutiérrez-Mejía, F.; van IJzendoorn, L.J.; Prins, M.W.J.

2013-01-01

We report a method to profile the torsional spring properties of proteins as a function of the angle of rotation. The torque is applied by superparamagnetic particles and has been calibrated while taking account of the magnetization dynamics of the particles. We record and compare the torsional profiles of single Protein G-Immunoglobulin G (IgG) and IgG-IgG complexes, sandwiched between a substrate and a superparamagnetic particle, for torques in the range between 0.5 × 103 and 5 × 103 pN·nm. Both molecular systems show torsional stiffening for increasing rotation angle, but the elastic and inelastic torsion stiffnesses are remarkably different. We interpret the results in terms of the structural properties of the molecules. The torsion profiling technique opens new dimensions for research on biomolecular characterization and for research on bio-nanomechanical structure-function relationships. PMID:23473490

Quasilinear Line Broadened Model for Energetic Particle Transport

NASA Astrophysics Data System (ADS)

Ghantous, Katy; Gorelenkov, Nikolai; Berk, Herbert

2011-10-01

We present a self-consistent quasi-linear model that describes wave-particle interaction in toroidal geometry and computes fast ion transport during TAE mode evolution. The model bridges the gap between single mode resonances, where it predicts the analytically expected saturation levels, and the case of multiple modes overlapping, where particles diffuse across phase space. Results are presented in the large aspect ratio limit where analytic expressions are used for Fourier harmonics of the power exchange between waves and particles, . Implemention of a more realistic mode structure calculated by NOVAK code are also presented. This work is funded by DOE contract DE-AC02-09CH11466.

Beam-induced motion correction for sub-megadalton cryo-EM particles.

PubMed

Scheres, Sjors Hw

2014-08-13

In electron cryo-microscopy (cryo-EM), the electron beam that is used for imaging also causes the sample to move. This motion blurs the images and limits the resolution attainable by single-particle analysis. In a previous Research article (Bai et al., 2013) we showed that correcting for this motion by processing movies from fast direct-electron detectors allowed structure determination to near-atomic resolution from 35,000 ribosome particles. In this Research advance article, we show that an improved movie processing algorithm is applicable to a much wider range of specimens. The new algorithm estimates straight movement tracks by considering multiple particles that are close to each other in the field of view, and models the fall-off of high-resolution information content by radiation damage in a dose-dependent manner. Application of the new algorithm to four data sets illustrates its potential for significantly improving cryo-EM structures, even for particles that are smaller than 200 kDa. Copyright © 2014, Scheres.

Structure of Particle Networks in Capillary Suspensions with Wetting and Nonwetting Fluids

PubMed Central

2016-01-01

The mechanical properties of a suspension can be dramatically altered by adding a small amount of a secondary fluid that is immiscible with the bulk phase. The substantial changes in the strength of these capillary suspensions arise due to the capillary force inducing a percolating particle network. Spatial information on the structure of the particle networks is obtained using confocal microscopy. It is possible, for the first time, to visualize the different types of percolating structures of capillary suspensions in situ. These capillary networks are unique from other types of particulate networks due to the nature of the capillary attraction. We investigate the influence of the three-phase contact angle on the structure of an oil-based capillary suspension with silica microspheres. Contact angles smaller than 90° lead to pendular networks of particles connected with single capillary bridges or clusters comparable to the funicular state in wet granular matter, whereas a different clustered structure, the capillary state, forms for angles larger than 90°. Particle pair distribution functions are obtained by image analysis, which demonstrate differences in the network microstructures. When porous particles are used, the pendular conformation also appears for apparent contact angles larger than 90°. The complex shear modulus can be correlated to these microstructural changes. When the percolating structure is formed, the complex shear modulus increases by nearly three decades. Pendular bridges lead to stronger networks than the capillary state network conformations, but the capillary state clusters are nevertheless much stronger than pure suspensions without the added liquid. PMID:26807651

Shell Evolution towards 78Ni: Low-Lying States in 77Cu

NASA Astrophysics Data System (ADS)

Sahin, E.; Bello Garrote, F. L.; Tsunoda, Y.; Otsuka, T.; de Angelis, G.; Görgen, A.; Niikura, M.; Nishimura, S.; Xu, Z. Y.; Baba, H.; Browne, F.; Delattre, M.-C.; Doornenbal, P.; Franchoo, S.; Gey, G.; Hadyńska-KlÈ©k, K.; Isobe, T.; John, P. R.; Jung, H. S.; Kojouharov, I.; Kubo, T.; Kurz, N.; Li, Z.; Lorusso, G.; Matea, I.; Matsui, K.; Mengoni, D.; Morfouace, P.; Napoli, D. R.; Naqvi, F.; Nishibata, H.; Odahara, A.; Sakurai, H.; Schaffner, H.; Söderström, P.-A.; Sohler, D.; Stefan, I. G.; Sumikama, T.; Suzuki, D.; Taniuchi, R.; Taprogge, J.; Vajta, Z.; Watanabe, H.; Werner, V.; Wu, J.; Yagi, A.; Yalcinkaya, M.; Yoshinaga, K.

2017-06-01

The level structure of the neutron-rich 77Cu nucleus is investigated through β -delayed γ -ray spectroscopy at the Radioactive Isotope Beam Factory of the RIKEN Nishina Center. Ions of 77Ni are produced by in-flight fission, separated and identified in the BigRIPS fragment separator, and implanted in the WAS3ABi silicon detector array, surrounded by Ge cluster detectors of the EURICA array. A large number of excited states in 77Cu are identified for the first time by correlating γ rays with the β decay of 77Ni, and a level scheme is constructed by utilizing their coincidence relationships. The good agreement between large-scale Monte Carlo shell model calculations and experimental results allows for the evaluation of the single-particle structure near 78Ni and suggests a single-particle nature for both the 5 /21- and 3 /21- states in 77Cu, leading to doubly magic 78Ni.

High-lying single-particle modes, chaos, correlational entropy, and doubling phase transition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoyanov, Chavdar; Zelevinsky, Vladimir

Highly excited single-particle states in nuclei are coupled with the excitations of a more complex character, first of all with collective phononlike modes of the core. In the framework of the quasiparticle-phonon model, we consider the structure of resulting complex configurations, using the 1k{sub 17/2} orbital in {sup 209}Pb as an example. Although, on the level of one- and two-phonon admixtures, the fully chaotic Gaussian orthogonal ensemble regime is not reached, the eigenstates of the model carry a significant degree of complexity that can be quantified with the aid of correlational invariant entropy. With artificially enhanced particle-core coupling, the systemmore » undergoes the doubling phase transition with the quasiparticle strength concentrated in two repelling peaks. This phase transition is clearly detected by correlational entropy.« less

Detailed Surface Analysis Of Incremental Centrifugal Barrel Polishing (CBP) Of Single-Crystal Niobium Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palczewski, Ari D.; Tian, Hui; Trofimova, Olga

2011-07-01

We performed Centrifugal Barrel Polishing (CBP) on single crystal niobium samples/coupons housed in a stainless steel sample holder following the polishing recipe developed at Fermi Lab (FNAL) in 2011 \\cite{C. A. Cooper 2011}. Post CBP, the sample coupons were analyzed for surface roughness, crystal composition and structure, and particle contamination. Following the initial analysis each coupon was high pressure rinsed (HRP) and analyzed for the effectiveness of contamination removal. We were able to obtain the mirror like surface finish after the final stage of tumbling, although some defects and embedded particles remained. In addition, standard HPR appears to have littlemore » effect on removing embedded particles which remain after each tumbling step, although final polishing media removal was partially affected by standard/extended HPR.« less

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus

PubMed Central

Huynh, Nhung T.; Hesketh, Emma L.; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T.; Johnson, John E.; Ranson, Neil A.; Lomonossoff, George P.; Reddy, Vijay S.

2016-01-01

SUMMARY Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. PMID:27021160

Structure of a Venezuelan equine encephalitis virus assembly intermediate isolated from infected cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lamb, Kristen; Lokesh, G.L.; Sherman, Michael

2010-10-25

Venezuelan equine encephalitis virus (VEEV) is a prototypical enveloped ssRNA virus of the family Togaviridae. To better understand alphavirus assembly, we analyzed newly formed nucleocapsid particles (termed pre-viral nucleocapsids) isolated from infected cells. These particles were intermediates along the virus assembly pathway, and ultimately bind membrane-associated viral glycoproteins to bud as mature infectious virus. Purified pre-viral nucleocapsids were spherical with a unimodal diameter distribution. The structure of one class of pre-viral nucleocapsids was determined with single particle reconstruction of cryo-electron microscopy images. These studies showed that pre-viral nucleocapsids assembled into an icosahedral structure with a capsid stoichiometry similar to themore » mature nucleocapsid. However, the individual capsomers were organized significantly differently within the pre-viral and mature nucleocapsids. The pre-viral nucleocapsid structure implies that nucleocapsids are highly plastic and undergo glycoprotein and/or lipid-driven rearrangements during virus self-assembly. This mechanism of self-assembly may be general for other enveloped viruses.« less

Structural analyses of EBER1 and EBER2 ribonucleoprotein particles present in Epstein-Barr virus-infected cells.

PubMed Central

Glickman, J N; Howe, J G; Steitz, J A

1988-01-01

The ribonucleoprotein (RNP) particles containing the Epstein-Barr virus-associated small RNAs EBER1 and EBER2 were analyzed to determine their RNA secondary structures and sites of RNA-protein interaction. The secondary structures were probed with nucleases and by chemical modification with single-strand-specific reagents, and the sites of modification or cleavage were mapped by primer extension. These data were used to develop secondary structures for the two RNAs, and likely sites of close RNA-protein contact were identified by comparing modification patterns for naked RNA and RNA in RNP particles. In addition, sites of interaction between each Epstein-Barr virus-encoded RNA (EBER) and the La antigen were identified by analyzing RNA fragments resistant to digestion by RNase A or T1 after immunoprecipitation by an anti-La serum sample from a lupus patient. Our results confirm earlier findings that the La protein binds to the 3' terminus of each molecule. Possible functions for the EBER RNPs are discussed. Images PMID:2828685

Characterization of the crystal structure, kinematics, stresses and rotations in angular granular quartz during compaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurley, Ryan C.; Herbold, Eric B.; Pagan, Darren C.

Three-dimensional X-ray diffraction (3DXRD), a method for quantifying the position, orientation and elastic strain of large ensembles of single crystals, has recently emerged as an important tool for studying the mechanical response of granular materials during compaction. Applications have demonstrated the utility of 3DXRD and X-ray computed tomography (XRCT) for assessing strains, particle stresses and orientations, inter-particle contacts and forces, particle fracture mechanics, and porosity evolution in situ . Although past studies employing 3DXRD and XRCT have elucidated the mechanics of spherical particle packings and angular particle packings with a small number of particles, there has been limited effort tomore » date in studying angular particle packings with a large number of particles and in comparing the mechanics of these packings with those composed of a large number of spherical particles. Therefore, the focus of the present paper is on the mechanics of several hundred angular particles during compaction using in situ 3DXRD to study the crystal structure, kinematics, stresses and rotations of angular quartz grains. Comparisons are also made between the compaction response of angular grains and that of spherical grains, and stress-induced twinning within individual grains is discussed.« less

Characterization of the crystal structure, kinematics, stresses and rotations in angular granular quartz during compaction

DOE PAGES

Hurley, Ryan C.; Herbold, Eric B.; Pagan, Darren C.

2018-06-28

Three-dimensional X-ray diffraction (3DXRD), a method for quantifying the position, orientation and elastic strain of large ensembles of single crystals, has recently emerged as an important tool for studying the mechanical response of granular materials during compaction. Applications have demonstrated the utility of 3DXRD and X-ray computed tomography (XRCT) for assessing strains, particle stresses and orientations, inter-particle contacts and forces, particle fracture mechanics, and porosity evolution in situ . Although past studies employing 3DXRD and XRCT have elucidated the mechanics of spherical particle packings and angular particle packings with a small number of particles, there has been limited effort tomore » date in studying angular particle packings with a large number of particles and in comparing the mechanics of these packings with those composed of a large number of spherical particles. Therefore, the focus of the present paper is on the mechanics of several hundred angular particles during compaction using in situ 3DXRD to study the crystal structure, kinematics, stresses and rotations of angular quartz grains. Comparisons are also made between the compaction response of angular grains and that of spherical grains, and stress-induced twinning within individual grains is discussed.« less

Three kinds of particles on a single rationally parameterized world line

NASA Astrophysics Data System (ADS)

Kassandrov, V. V.; Markova, N. V.

2016-10-01

We consider the light cone (`retardation') equation (LCE) of an inertially moving observer and a single worldline parameterized by arbitrary rational functions. Then a set of apparent copies, R- or C-particles, defined by the (real or complex conjugate) roots of the LCE will be detected by the observer. For any rational worldline the collective R-C dynamics is manifestly Lorentz-invariant and conservative; the latter property follows directly from the structure of Vieta formulas for the LCE roots. In particular, two Lorentz invariants, the square of total 4-momentum and total rest mass, are distinct and both integer-valued. Asymptotically, at large values of the observer's proper time, one distinguishes three types of the LCE roots and associated R-C particles, with specific locations and evolutions; each of three kinds of particles can assemble into compact large groups - clusters. Throughout the paper, we make no use of differential equations of motion, field equations, etc.: the collective R-C dynamics is purely algebraic

Three-dimensional manipulation of single cells using surface acoustic waves.

PubMed

Guo, Feng; Mao, Zhangming; Chen, Yuchao; Xie, Zhiwei; Lata, James P; Li, Peng; Ren, Liqiang; Liu, Jiayang; Yang, Jian; Dao, Ming; Suresh, Subra; Huang, Tony Jun

2016-02-09

The ability of surface acoustic waves to trap and manipulate micrometer-scale particles and biological cells has led to many applications involving "acoustic tweezers" in biology, chemistry, engineering, and medicine. Here, we present 3D acoustic tweezers, which use surface acoustic waves to create 3D trapping nodes for the capture and manipulation of microparticles and cells along three mutually orthogonal axes. In this method, we use standing-wave phase shifts to move particles or cells in-plane, whereas the amplitude of acoustic vibrations is used to control particle motion along an orthogonal plane. We demonstrate, through controlled experiments guided by simulations, how acoustic vibrations result in micromanipulations in a microfluidic chamber by invoking physical principles that underlie the formation and regulation of complex, volumetric trapping nodes of particles and biological cells. We further show how 3D acoustic tweezers can be used to pick up, translate, and print single cells and cell assemblies to create 2D and 3D structures in a precise, noninvasive, label-free, and contact-free manner.

The effects of intraparticle and interparticle interactions on the magnetic hysteresis loop of frozen suspensions of bionized nanoferrite particles

NASA Astrophysics Data System (ADS)

Boekelheide, Zoe; Gruettner, Cordula; Dennis, Cindi

Bionized nano-ferrite (iron oxide/dextran) nanoparticles have been shown to have a large heating response in an alternating magnetic field, making them very promising for applications in magnetic nanoparticle hyperthermia cancer treatment. Magnetic hysteresis loop measurements of these particles provide insight into the magnetic reversal behavior of these particles, and thus their heating response. Measurements have been performed on frozen suspensions of nanoparticles dispersed in H2O, which have been frozen in a range of applied fields in order to tune the interparticle dipolar interactions through formation of linear chains. These experimental results are compared with micromagnetic models of both monolithic (single-domain) and internally structured (multi-grain) particles. It is found that the internal structure of the nanoparticles, which are made up of parallelepiped-shaped grains, is important for describing the magnetic reversal behavior of the particles and the resulting shape of the hysteresis loops. In addition to this, interparticle interactions between particles in a linear chain modify the reversal behavior and thus the shape of the hysteresis loop.

Super-resolution and super-localization microscopy: A novel tool for imaging chemical and biological processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Bin

2015-01-01

Optical microscopy imaging of single molecules and single particles is an essential method for studying fundamental biological and chemical processes at the molecular and nanometer scale. The best spatial resolution (~ λ/2) achievable in traditional optical microscopy is governed by the diffraction of light. However, single molecule-based super-localization and super-resolution microscopy imaging techniques have emerged in the past decade. Individual molecules can be localized with nanometer scale accuracy and precision for studying of biological and chemical processes.This work uncovered the heterogeneous properties of the pore structures. In this dissertation, the coupling of molecular transport and catalytic reaction at the singlemore » molecule and single particle level in multilayer mesoporous nanocatalysts was elucidated. Most previous studies dealt with these two important phenomena separately. A fluorogenic oxidation reaction of non-fluorescent amplex red to highly fluorescent resorufin was tested. The diffusion behavior of single resorufin molecules in aligned nanopores was studied using total internal reflection fluorescence microscopy (TIRFM).« less

Femtosecond pulsed laser micromachining of single crystalline 3C SiC structures based on a laser-induced defect-activation process

NASA Astrophysics Data System (ADS)

Dong, Yuanyuan; Zorman, Christian; Molian, Pal

2003-09-01

A femtosecond pulsed Ti:sapphire laser with a pulse width of 120 fs, a wavelength of 800 nm and a repetition rate of 1 kHz was employed for direct write patterning of single crystalline 3C-SiC thin films deposited on Si substrates. The ablation mechanism of SiC was investigated as a function of pulse energy. At high pulse energies (>1 µJ), ablation occurred via thermally dominated processes such as melting, boiling and vaporizing of single crystalline SiC. At low pulse energies, the ablation mechanism involved a defect-activation process that included the accumulation of defects, formation of nano-particles and vaporization of crystal boundaries, which contributed to well-defined and debris-free patterns in 3C-SiC thin films. The interactions between femtosecond laser pulses and the intrinsic lattice defects in epitaxially grown 3C-SiC films led to the generation of nano-particles. Micromechanical structures such as micromotor rotors and lateral resonators were patterned into 3C-SiC films using the defect-activation ablation mechanism.

Factor VIII organisation on nanodiscs with different lipid composition.

PubMed

Grushin, Kirill; Miller, Jaimy; Dalm, Daniela; Stoilova-McPhie, Svetla

2015-04-01

Nanodiscs (ND) are lipid bilayer membrane patches held by amphiphilic scaffolding proteins (MSP) of ~10 nm in diameter. Nanodiscs have been developed as lipid nanoplatforms for structural and functional studies of membrane and membrane associated proteins. Their size and monodispersity have rendered them unique for electron microscopy (EM) and single particle analysis studies of proteins and complexes either spanning or associated to the ND membrane. Binding of blood coagulation factors and complexes, such as the Factor VIII (FVIII) and the Factor VIIIa - Factor IXa (intrinsic tenase) complex to the negatively charged activated platelet membrane is required for normal haemostasis. In this study we present our work on optimising ND, specifically designed to bind FVIII at close to physiological conditions. The binding of FVIII to the negatively charged ND rich in phosphatidylserine (PS) was followed by electron microscopy at three different PS compositions and two different membrane scaffolding protein (MSP1D1) to lipid ratios. Our results show that the ND with highest PS content (80 %) and lowest MSP1D1 to lipid ratio (1:47) are the most suitable for structure determination of the membrane-bound FVIII by single particle EM. Our preliminary FVIII 3D reconstruction as bound to PS containing ND demonstrates the suitability of the optimised ND for structural studies by EM. Further assembly of the activated FVIII form (FVIIIa) and the whole FVIIIa-FIXa complex on ND, followed by EM and single particle reconstruction will help to identify the protein-protein and protein-membrane interfaces critical for the intrinsic tenase complex assembly and function.

Toroidal Optical Microresonators as Single-Particle Absorption Spectrometers

NASA Astrophysics Data System (ADS)

Heylman, Kevin D.

Single-particle and single-molecule measurements are invaluable tools for characterizing structural and energetic properties of molecules and nanomaterials. Photothermal microscopy in particular is an ultrasensitive technique capable of single-molecule resolution. In this thesis I introduce a new form of photothermal spectroscopy involving toroidal optical microresonators as detectors and a pair of non-interacting lasers as pump and probe for performing single-target absorption spectroscopy. The first three chapters will discuss the motivation, design principles, underlying theory, and fabrication process for the microresonator absorption spectrometer. With an early version of the spectrometer, I demonstrate photothermal mapping and all-optical tuning with toroids of different geometries in Chapter 4. In Chapter 5, I discuss photothermal mapping and measurement of the absolute absorption cross-sections of individual carbon nanotubes. For the next generation of measurements I incorporate all of the advances described in Chapter 2, including a double-modulation technique to improve detection limits and a tunable pump laser for spectral measurements on single gold nanoparticles. In Chapter 6 I observe sharp Fano resonances in the spectra of gold nanoparticles and describe them with a theoretical model. I continued to study this photonic-plasmonic hybrid system in Chapter 7 and explore the thermal tuning of the Fano resonance phase while quantifying the Fisher information. The new method of photothermal single-particle absorption spectroscopy that I will discuss in this thesis has reached record detection limits for microresonator sensing and is within striking distance of becoming the first single-molecule room-temperature absorption spectrometer.

Quantum self-organization and nuclear collectivities

NASA Astrophysics Data System (ADS)

Otsuka, T.; Tsunoda, Y.; Togashi, T.; Shimizu, N.; Abe, T.

2018-02-01

The quantum self-organization is introduced as one of the major underlying mechanisms of the quantum many-body systems. In the case of atomic nuclei as an example, two types of the motion of nucleons, single-particle states and collective modes, dominate the structure of the nucleus. The outcome of the collective mode is determined basically by the balance between the effect of the mode-driving force (e.g., quadrupole force for the ellipsoidal deformation) and the resistance power against it. The single-particle energies are one of the sources to produce such resistance power: a coherent collective motion is more hindered by larger gaps between relevant single particle states. Thus, the single-particle state and the collective mode are “enemies” each other. However, the nuclear forces are demonstrated to be rich enough so as to enhance relevant collective mode by reducing the resistance power by changing singleparticle energies for each eigenstate through monopole interactions. This will be verified with the concrete example taken from Zr isotopes. Thus, when the quantum self-organization occurs, single-particle energies can be self-organized, being enhanced by (i) two quantum liquids, e.g., protons and neutrons, (ii) two major force components, e.g., quadrupole interaction (to drive collective mode) and monopole interaction (to control resistance). In other words, atomic nuclei are not necessarily like simple rigid vases containing almost free nucleons, in contrast to the naïve Fermi liquid picture. Type II shell evolution is considered to be a simple visible case involving excitations across a (sub)magic gap. The quantum self-organization becomes more important in heavier nuclei where the number of active orbits and the number of active nucleons are larger. The quantum self-organization is a general phenomenon, and is expected to be found in other quantum systems.

Orientation Dependence of Functional Properties in Heterophase Single Crystals of the Ti36.5Ni51.0Hf12.5 and Ti48.5Ni51.5 Alloys

NASA Astrophysics Data System (ADS)

Panchenko, E. Yu.; Chumlyakov, Yu. I.; Surikov, N. Yu.; Tagiltsev, A. I.; Vetoshkina, N. G.; Osipovich, K. S.; Maier, H.; Sehitoglu, H.

2016-03-01

The features of orientation dependence of stress-induced thermoelastic B2-( R)- B19'-martensitic transformations in single crystals of the Ti48.5Ni51.5 and Ni51.0Ti36.5Hf12.5 (at.%) alloys, which contain disperse particles of the Ti3Ni4 and H-phase, respectively, are revealed along with those of their shape-memory effects (SME) and superelasticity (SE). It is experimentally demonstrated that irrespective of the crystal structure of disperse particles measuring more than 100 nm, for their volume fraction f > 16% there is a weaker orientation dependence of the reversible strain in the cases of manifestation of SME and SE. In the orientations of Class I, wherein martensitic detwinning introduces a considerable contribution into transformation strain, the values of SME |ɛ SME | and SE |ɛ SE | decrease by over a factor of two compared to the theoretical lattice strain value |ɛ tr0 | for a B2- B19'-transformation and the experimental values of reversible strain for quenched TiNi crystals. In the orientations of Class 2, wherein detwinning of the martensite is suppressed as is the case in quenched single-phase single crystals, the reversible strain is maintained close to its theoretical value |ɛ tr0 |. Micromechanical models of interaction between the martensite and the disperse particles are proposed, which account for the weaker orientation dependence of |ɛ SME | and |ɛ SE | due to suppression of detwinning of the B19'-martensite crystals by the particles and a transition from a single-variant evolution of the stress-induced martensitic transformations to a multiple-variant evolution of transformations in the cases of increased size of the particles and their larger volume fractions.

Development of solar flares and features of the fine structure of solar radio emission

NASA Astrophysics Data System (ADS)

Chernov, G. P.; Fomichev, V. V.; Yan, Y.; Tan, B.; Tan, Ch.; Fu, Q.

2017-11-01

The reason for the occurrence of different elements of the fine structure of solar radio bursts in the decimeter and centimeter wavelength ranges has been determined based on all available data from terrestrial and satellite observations. In some phenomena, fast pulsations, a zebra structre, fiber bursts, and spikes have been observed almost simultaneously. Two phenomena have been selected to show that the pulsations of radio emission are caused by particles accelerated in the magnetic reconnection region and that the zebra structure is excited in a source, such as a magnetic trap for fast particles. The complex combination of unusual fiber bursts, zebra structure, and spikes in the phenomenon on December 1, 2004, is associated with a single source, a magnetic island formed after a coronal mass ejection.

The role of BST2/tetherin in infection with the feline retroviruses

PubMed Central

Dietrich, Isabelle; Hosie, Margaret J.; Willett, Brian J.

2014-01-01

The recently identified host restriction factor tetherin (BST-2, CD317) potently inhibits the release of nascent retrovirus particles from infected cells. Recently, we reported the identification and characterization of tetherin as a novel feline retroviral restriction factor. Based on homology to human tetherin we identified a putative tetherin gene in the genome of the domestic cat (Felis catus) which was found to be expressed in different feline cell lines both prior to and post treatment with either type I or type II interferon (IFN). The predicted structure of feline tetherin (feTHN) was that of a type II single-pass transmembrane protein encoding an N-terminal transmembrane anchor, central predicted coiled-coil bearing extracellular domain to promote dimerization, and a C-terminal GPI-anchor, consistent with conservation of structure between human and feline tetherin. FeTHN displayed potent inhibition of feline immunodeficiency virus (FIV) and human immunodeficiency virus type 1 (HIV-1) particle release in single-cycle replication assays. Notably, feTHN activity was resistant to antagonism by HIV-1 Vpu. However, stable ectopic expression of feTHN mRNA in different feline cell lines had no inhibitory effect on the growth of diverse primary or cell culture-adapted strains of FIV. Hence, whereas feline tetherin efficiently blocks viral particle release in single-cycle replication assays, it might not prevent dissemination of feline retroviruses in vivo. PMID:21715020

Colloidal assembly directed by virtual magnetic moulds

NASA Astrophysics Data System (ADS)

Demirörs, Ahmet F.; Pillai, Pramod P.; Kowalczyk, Bartlomiej; Grzybowski, Bartosz A.

2013-11-01

Interest in assemblies of colloidal particles has long been motivated by their applications in photonics, electronics, sensors and microlenses. Existing assembly schemes can position colloids of one type relatively flexibly into a range of desired structures, but it remains challenging to produce multicomponent lattices, clusters with precisely controlled symmetries and three-dimensional assemblies. A few schemes can efficiently produce complex colloidal structures, but they require system-specific procedures. Here we show that magnetic field microgradients established in a paramagnetic fluid can serve as `virtual moulds' to act as templates for the assembly of large numbers (~108) of both non-magnetic and magnetic colloidal particles with micrometre precision and typical yields of 80 to 90 per cent. We illustrate the versatility of this approach by producing single-component and multicomponent colloidal arrays, complex three-dimensional structures and a variety of colloidal molecules from polymeric particles, silica particles and live bacteria and by showing that all of these structures can be made permanent. In addition, although our magnetic moulds currently resemble optical traps in that they are limited to the manipulation of micrometre-sized objects, they are massively parallel and can manipulate non-magnetic and magnetic objects simultaneously in two and three dimensions.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Understanding nanocellulose chirality and structure–properties relationship at the single fibril level

PubMed Central

Usov, Ivan; Nyström, Gustav; Adamcik, Jozef; Handschin, Stephan; Schütz, Christina; Fall, Andreas; Bergström, Lennart; Mezzenga, Raffaele

2015-01-01

Nanocellulose fibrils are ubiquitous in nature and nanotechnologies but their mesoscopic structural assembly is not yet fully understood. Here we study the structural features of rod-like cellulose nanoparticles on a single particle level, by applying statistical polymer physics concepts on electron and atomic force microscopy images, and we assess their physical properties via quantitative nanomechanical mapping. We show evidence of right-handed chirality, observed on both bundles and on single fibrils. Statistical analysis of contours from microscopy images shows a non-Gaussian kink angle distribution. This is inconsistent with a structure consisting of alternating amorphous and crystalline domains along the contour and supports process-induced kink formation. The intrinsic mechanical properties of nanocellulose are extracted from nanoindentation and persistence length method for transversal and longitudinal directions, respectively. The structural analysis is pushed to the level of single cellulose polymer chains, and their smallest associated unit with a proposed 2 × 2 chain-packing arrangement. PMID:26108282

Single-particle states in ^112Cd probed with the ^111Cd(d,p) reaction

NASA Astrophysics Data System (ADS)

Garrett, P. E.; Jamieson, D.; Demand, G. A.; Finlay, P.; Green, K. L.; Leach, K. G.; Phillips, A. A.; Sumithrarachchi, C. S.; Svensson, C. E.; Triambak, S.; Wong, J.; Ball, G. C.; Hertenberger, R.; Wirth, H.-F.; Kr"Ucken, R.; Faestermann, T.

2009-10-01

As part of a program of detailed spectroscopy of the Cd isotopes, the single-particle neutron states in ^112Cd have been probed with the ^111Cd(d,p) reaction. Beams of polarized 22 MeV deuterons, obtained from the LMU/TUM Tandem Accelerator, bombarded a target of ^111Cd. The protons from the reaction, corresponding to excitation energies up to 3 MeV in ^112Cd, were momentum analyzed with the Q3D spectrograph. Cross sections and analyzing powers were fit to results of DWBA calculations, and spectroscopic factors were determined. The results from the experiment, and implications for the structure of ^112Cd, will be presented.

Start-to-end simulation of single-particle imaging using ultra-short pulses at the European X-ray Free-Electron Laser

PubMed Central

Buzmakov, Alexey; Jurek, Zoltan; Loh, Ne-Te Duane; Samoylova, Liubov; Santra, Robin; Schneidmiller, Evgeny A.; Tschentscher, Thomas; Yakubov, Sergey; Yoon, Chun Hong; Yurkov, Michael V.; Ziaja-Motyka, Beata; Mancuso, Adrian P.

2017-01-01

Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs. PMID:28989713

Implementation of a flexible and scalable particle-in-cell method for massively parallel computations in the mantle convection code ASPECT

NASA Astrophysics Data System (ADS)

Gassmöller, Rene; Bangerth, Wolfgang

2016-04-01

Particle-in-cell methods have a long history and many applications in geodynamic modelling of mantle convection, lithospheric deformation and crustal dynamics. They are primarily used to track material information, the strain a material has undergone, the pressure-temperature history a certain material region has experienced, or the amount of volatiles or partial melt present in a region. However, their efficient parallel implementation - in particular combined with adaptive finite-element meshes - is complicated due to the complex communication patterns and frequent reassignment of particles to cells. Consequently, many current scientific software packages accomplish this efficient implementation by specifically designing particle methods for a single purpose, like the advection of scalar material properties that do not evolve over time (e.g., for chemical heterogeneities). Design choices for particle integration, data storage, and parallel communication are then optimized for this single purpose, making the code relatively rigid to changing requirements. Here, we present the implementation of a flexible, scalable and efficient particle-in-cell method for massively parallel finite-element codes with adaptively changing meshes. Using a modular plugin structure, we allow maximum flexibility of the generation of particles, the carried tracer properties, the advection and output algorithms, and the projection of properties to the finite-element mesh. We present scaling tests ranging up to tens of thousands of cores and tens of billions of particles. Additionally, we discuss efficient load-balancing strategies for particles in adaptive meshes with their strengths and weaknesses, local particle-transfer between parallel subdomains utilizing existing communication patterns from the finite element mesh, and the use of established parallel output algorithms like the HDF5 library. Finally, we show some relevant particle application cases, compare our implementation to a modern advection-field approach, and demonstrate under which conditions which method is more efficient. We implemented the presented methods in ASPECT (aspect.dealii.org), a freely available open-source community code for geodynamic simulations. The structure of the particle code is highly modular, and segregated from the PDE solver, and can thus be easily transferred to other programs, or adapted for various application cases.

ICTV Virus Taxonomy Profile: Virgaviridae

USDA-ARS?s Scientific Manuscript database

The family Virgaviridae is comprised of plant-infecting viruses with rod-shaped particles, single stranded RNA genomes with 3' terminal tRNA-like structures, and replication proteins typical of alphalike viruses. Differences in the number of genome components, genome organization and transmission m...

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

PubMed Central

Chen, F.-R.; Van Dyck, D.; Kisielowski, C.

2016-01-01

Resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we report a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose rate electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. We apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances. PMID:26887849

Low-energy electron holographic imaging of individual tobacco mosaic virions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Longchamp, Jean-Nicolas, E-mail: longchamp@physik.uzh.ch; Latychevskaia, Tatiana; Escher, Conrad

2015-09-28

Modern structural biology relies on Nuclear Magnetic Resonance (NMR), X-ray crystallography, and cryo-electron microscopy for gaining information on biomolecules at nanometer, sub-nanometer, or atomic resolution. All these methods, however, require averaging over a vast ensemble of entities, and hence knowledge on the conformational landscape of an individual particle is lost. Unfortunately, there are now strong indications that even X-ray free electron lasers will not be able to image individual molecules but will require nanocrystal samples. Here, we show that non-destructive structural biology of single particles has now become possible by means of low-energy electron holography. As an example, individual tobaccomore » mosaic virions deposited on ultraclean freestanding graphene are imaged at 1 nm resolution revealing structural details arising from the helical arrangement of the outer protein shell of the virus. Since low-energy electron holography is a lens-less technique and since electrons with a deBroglie wavelength of approximately 1 Å do not impose radiation damage to biomolecules, the method has the potential for Angstrom resolution imaging of single biomolecules.« less

Large scale structures in liquid crystal/clay colloids

NASA Astrophysics Data System (ADS)

van Duijneveldt, Jeroen S.; Klein, Susanne; Leach, Edward; Pizzey, Claire; Richardson, Robert M.

2005-04-01

Suspensions of three different clays in K15, a thermotropic liquid crystal, have been studied by optical microscopy and small angle x-ray scattering. The three clays were claytone AF, a surface treated natural montmorillonite, laponite RD, a synthetic hectorite, and mined sepiolite. The claytone and laponite were sterically stabilized whereas sepiolite formed a relatively stable suspension in K15 without any surface treatment. Micrographs of the different suspensions revealed that all three suspensions contained large scale structures. The nature of these aggregates was investigated using small angle x-ray scattering. For the clays with sheet-like particles, claytone and laponite, the flocs contain a mixture of stacked and single platelets. The basal spacing in the stacks was independent of particle concentration in the suspension and the phase of the solvent. The number of platelets in the stack and their percentage in the suspension varied with concentration and the aspect ratio of the platelets. The lath shaped sepiolite did not show any tendency to organize into ordered structures. Here the aggregates are networks of randomly oriented single rods.

Single-cycle high-intensity electromagnetic pulse generation in the interaction of a plasma wakefield with regular nonlinear structures.

PubMed

Bulanov, S S; Esirkepov, T Zh; Kamenets, F F; Pegoraro, F

2006-03-01

The interaction of regular nonlinear structures (such as subcycle solitons, electron vortices, and wake Langmuir waves) with a strong wake wave in a collisionless plasma can be exploited in order to produce ultrashort electromagnetic pulses. The electromagnetic field of the nonlinear structure is partially reflected by the electron density modulations of the incident wake wave and a single-cycle high-intensity electromagnetic pulse is formed. Due to the Doppler effect the length of this pulse is much shorter than that of the nonlinear structure. This process is illustrated with two-dimensional particle-in-cell simulations. The considered laser-plasma interaction regimes can be achieved in present day experiments and can be used for plasma diagnostics.

Snow particles extracted from X-ray computed microtomography imagery and their single-scattering properties

NASA Astrophysics Data System (ADS)

Ishimoto, Hiroshi; Adachi, Satoru; Yamaguchi, Satoru; Tanikawa, Tomonori; Aoki, Teruo; Masuda, Kazuhiko

2018-04-01

Sizes and shapes of snow particles were determined from X-ray computed microtomography (micro-CT) images, and their single-scattering properties were calculated at visible and near-infrared wavelengths using a Geometrical Optics Method (GOM). We analyzed seven snow samples including fresh and aged artificial snow and natural snow obtained from field samples. Individual snow particles were numerically extracted, and the shape of each snow particle was defined by applying a rendering method. The size distribution and specific surface area distribution were estimated from the geometrical properties of the snow particles, and an effective particle radius was derived for each snow sample. The GOM calculations at wavelengths of 0.532 and 1.242 μm revealed that the realistic snow particles had similar scattering phase functions as those of previously modeled irregular shaped particles. Furthermore, distinct dendritic particles had a characteristic scattering phase function and asymmetry factor. The single-scattering properties of particles of effective radius reff were compared with the size-averaged single-scattering properties. We found that the particles of reff could be used as representative particles for calculating the average single-scattering properties of the snow. Furthermore, the single-scattering properties of the micro-CT particles were compared to those of particle shape models using our current snow retrieval algorithm. For the single-scattering phase function, the results of the micro-CT particles were consistent with those of a conceptual two-shape model. However, the particle size dependence differed for the single-scattering albedo and asymmetry factor.

Nano-particle based scattering layers for optical efficiency enhancement of organic light-emitting diodes and organic solar cells

NASA Astrophysics Data System (ADS)

Chang, Hong-Wei; Lee, Jonghee; Hofmann, Simone; Hyun Kim, Yong; Müller-Meskamp, Lars; Lüssem, Björn; Wu, Chung-Chih; Leo, Karl; Gather, Malte C.

2013-05-01

The performance of both organic light-emitting diodes (OLEDs) and organic solar cells (OSC) depends on efficient coupling between optical far field modes and the emitting/absorbing region of the device. Current approaches towards OLEDs with efficient light-extraction often are limited to single-color emission or require expensive, non-standard substrates or top-down structuring, which reduces compatibility with large-area light sources. Here, we report on integrating solution-processed nano-particle based light-scattering films close to the active region of organic semiconductor devices. In OLEDs, these films efficiently extract light that would otherwise remain trapped in the device. Without additional external outcoupling structures, translucent white OLEDs containing these scattering films achieve luminous efficacies of 46 lm W-1 and external quantum efficiencies of 33% (both at 1000 cd m-2). These are by far the highest numbers ever reported for translucent white OLEDs and the best values in the open literature for any white device on a conventional substrate. By applying additional light-extraction structures, 62 lm W-1 and 46% EQE are reached. Besides universally enhancing light-extraction in various OLED configurations, including flexible, translucent, single-color, and white OLEDs, the nano-particle scattering film boosts the short-circuit current density in translucent organic solar cells by up to 70%.

iQIST v0.7: An open source continuous-time quantum Monte Carlo impurity solver toolkit

NASA Astrophysics Data System (ADS)

Huang, Li

2017-12-01

In this paper, we present a new version of the iQIST software package, which is capable of solving various quantum impurity models by using the hybridization expansion (or strong coupling expansion) continuous-time quantum Monte Carlo algorithm. In the revised version, the software architecture is completely redesigned. New basis (intermediate representation or singular value decomposition representation) for the single-particle and two-particle Green's functions is introduced. A lot of useful physical observables are added, such as the charge susceptibility, fidelity susceptibility, Binder cumulant, and autocorrelation time. Especially, we optimize measurement for the two-particle Green's functions. Both the particle-hole and particle-particle channels are supported. In addition, the block structure of the two-particle Green's functions is exploited to accelerate the calculation. Finally, we fix some known bugs and limitations. The computational efficiency of the code is greatly enhanced.

Physics of Alfvén waves and energetic particles in burning plasmas

NASA Astrophysics Data System (ADS)

Chen, Liu; Zonca, Fulvio

2016-01-01

Dynamics of shear Alfvén waves and energetic particles are crucial to the performance of burning fusion plasmas. This article reviews linear as well as nonlinear physics of shear Alfvén waves and their self-consistent interaction with energetic particles in tokamak fusion devices. More specifically, the review on the linear physics deals with wave spectral properties and collective excitations by energetic particles via wave-particle resonances. The nonlinear physics deals with nonlinear wave-wave interactions as well as nonlinear wave-energetic particle interactions. Both linear as well as nonlinear physics demonstrate the qualitatively important roles played by realistic equilibrium nonuniformities, magnetic field geometries, and the specific radial mode structures in determining the instability evolution, saturation, and, ultimately, energetic-particle transport. These topics are presented within a single unified theoretical framework, where experimental observations and numerical simulation results are referred to elucidate concepts and physics processes.

Interaction of a supersonic particle with a three-dimensional complex plasma

NASA Astrophysics Data System (ADS)

Zaehringer, E.; Schwabe, M.; Zhdanov, S.; Mohr, D. P.; Knapek, C. A.; Huber, P.; Semenov, I. L.; Thomas, H. M.

2018-03-01

The influence of a supersonic projectile on a three-dimensional complex plasma is studied. Micron sized particles in a low-temperature plasma formed a large undisturbed system in the new "Zyflex" chamber during microgravity conditions. A supersonic probe particle excited a Mach cone with Mach number M ≈ 1.5-2 and double Mach cone structure in the large weakly damped particle cloud. The speed of sound is measured with different methods and particle charge estimations are compared to the calculations from standard theories. The high image resolution enables the study of Mach cones in microgravity on the single particle level of a three-dimensional complex plasma and gives insight to the dynamics. A heating of the microparticles is discovered behind the supersonic projectile but not in the flanks of the Mach cone.

Monte Carlo simulation of light reflection from cosmetic powders on the skin

NASA Astrophysics Data System (ADS)

Okamoto, Takashi; Motoda, Masafumi; Igarashi, Takanori; Nakao, Keisuke

2011-07-01

The reflection and scattering properties of light incident on skin covered with powder particles have been investigated. A three-layer skin structure with a spot is modeled, and the propagation of light in the skin and the scattering of light by particles on the skin surface are simulated by means of a Monte Carlo method. Under the condition in which only single scattering of light occurs in the powder layer, the reflection spectra of light from the skin change dramatically with the size of powder particles. The color difference between normal skin and spots is found to diminish more when powder particles smaller than the wavelength of light are used. It is shown that particle polydispersity suppresses substantially the extreme spectral change caused by monodisperse particles with a size comparable to the light wavelength.

Spectrally reconfigurable integrated multi-spot particle trap.

PubMed

Leake, Kaelyn D; Olson, Michael A B; Ozcelik, Damla; Hawkins, Aaron R; Schmidt, Holger

2015-12-01

Optical manipulation of small particles in the form of trapping, pushing, or sorting has developed into a vast field with applications in the life sciences, biophysics, and atomic physics. Recently, there has been increasing effort toward integration of particle manipulation techniques with integrated photonic structures on self-contained optofluidic chips. Here, we use the wavelength dependence of multi-spot pattern formation in multimode interference (MMI) waveguides to create a new type of reconfigurable, integrated optical particle trap. Interfering lateral MMI modes create multiple trapping spots in an intersecting fluidic channel. The number of trapping spots can be dynamically controlled by altering the trapping wavelength. This novel, spectral reconfigurability is utilized to deterministically move single and multiple particles between different trapping locations along the channel. This fully integrated multi-particle trap can form the basis of high throughput biophotonic assays on a chip.

Electronic structure of alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ehrenreich, H.; Schwartz, L.M.

1976-01-01

The description of electronic properties of binary substitutional alloys within the single particle approximation is reviewed. Emphasis is placed on a didactic exposition of the equilibrium properties of the transport and magnetic properties of such alloys. Topics covered include: multiple scattering theory; the single band alloy; formal extensions of the theory; the alloy potential; realistic model state densities; the s-d model; and the muffin tin model. 43 figures, 3 tables, 151 references. (GHT)

Ionizing Radiation Environment on the International Space Station: Performance vs. Expectations for Avionics and Material

NASA Technical Reports Server (NTRS)

Koontz, Steven L.; Boeder, Paul A.; Pankop, Courtney; Reddell, Brandon

2005-01-01

The role of structural shielding mass in the design, verification, and in-flight performance of International Space Station (ISS), in both the natural and induced orbital ionizing radiation (IR) environments, is reported. Detailed consideration of the effects of both the natural and induced ionizing radiation environment during ISS design, development, and flight operations has produced a safe, efficient manned space platform that is largely immune to deleterious effects of the LEO ionizing radiation environment. The assumption of a small shielding mass for purposes of design and verification has been shown to be a valid worst-case approximation approach to design for reliability, though predicted dependences of single event effect (SEE) effects on latitude, longitude, SEP events, and spacecraft structural shielding mass are not observed. The Figure of Merit (FOM) method over predicts the rate for median shielding masses of about 10g/cm(exp 2) by only a factor of 3, while the Scott Effective Flux Approach (SEFA) method overestimated by about one order of magnitude as expected. The Integral Rectangular Parallelepiped (IRPP), SEFA, and FOM methods for estimating on-orbit (Single Event Upsets) SEU rates all utilize some version of the CREME-96 treatment of energetic particle interaction with structural shielding, which has been shown to underestimate the production of secondary particles in heavily shielded manned spacecraft. The need for more work directed to development of a practical understanding of secondary particle production in massive structural shielding for SEE design and verification is indicated. In contrast, total dose estimates using CAD based shielding mass distributions functions and the Shieldose Code provided a reasonable accurate estimate of accumulated dose in Grays internal to the ISS pressurized elements, albeit as a result of using worst-on-worst case assumptions (500 km altitude x 2) that compensate for ignoring both GCR and secondary particle production in massive structural shielding.

Formation and Structure of Calcium Carbonate Thin Films and Nanofibers Precipitated in the Presence of Poly(Allylamine Hydrochloride) and Magnesium Ions

PubMed Central

2013-01-01

That the cationic polyelectrolyte poly(allylamine hydrochloride) (PAH) exerts a significant influence on CaCO3 precipitation challenges the idea that only anionic additives have this effect. Here, we show that in common with anionic polyelectrolytes such as poly(aspartic acid), PAH supports the growth of calcite thin films and abundant nanofibers. While investigating the formation of these structures, we also perform the first detailed structural analysis of the nanofibers by transmission electron microscopy (TEM) and selected area electron diffraction. The nanofibers are shown to be principally single crystal, with isolated domains of polycrystallinity, and the single crystal structure is even preserved in regions where the nanofibers dramatically change direction. The formation mechanism of the fibers, which are often hundreds of micrometers long, has been the subject of intense speculation. Our results suggest that they form by aggregation of amorphous particles, which are incorporated into the fibers uniquely at their tips, before crystallizing. Extrusion of polymer during crystallization may inhibit particle addition at the fiber walls and result in local variations in the fiber nanostructure. Finally, we investigate the influence of Mg2+ on CaCO3 precipitation in the presence of PAH, which gives thinner and smoother films, together with fibers with more polycrystalline, granular structures. PMID:24489438

Formation and Structure of Calcium Carbonate Thin Films and Nanofibers Precipitated in the Presence of Poly(Allylamine Hydrochloride) and Magnesium Ions.

PubMed

Cantaert, Bram; Verch, Andreas; Kim, Yi-Yeoun; Ludwig, Henning; Paunov, Vesselin N; Kröger, Roland; Meldrum, Fiona C

2013-12-23

That the cationic polyelectrolyte poly(allylamine hydrochloride) (PAH) exerts a significant influence on CaCO 3 precipitation challenges the idea that only anionic additives have this effect. Here, we show that in common with anionic polyelectrolytes such as poly(aspartic acid), PAH supports the growth of calcite thin films and abundant nanofibers. While investigating the formation of these structures, we also perform the first detailed structural analysis of the nanofibers by transmission electron microscopy (TEM) and selected area electron diffraction. The nanofibers are shown to be principally single crystal, with isolated domains of polycrystallinity, and the single crystal structure is even preserved in regions where the nanofibers dramatically change direction. The formation mechanism of the fibers, which are often hundreds of micrometers long, has been the subject of intense speculation. Our results suggest that they form by aggregation of amorphous particles, which are incorporated into the fibers uniquely at their tips, before crystallizing. Extrusion of polymer during crystallization may inhibit particle addition at the fiber walls and result in local variations in the fiber nanostructure. Finally, we investigate the influence of Mg 2+ on CaCO 3 precipitation in the presence of PAH, which gives thinner and smoother films, together with fibers with more polycrystalline, granular structures.

The structure of human tripeptidyl peptidase II as determined by a hybrid approach.

PubMed

Schönegge, Anne-Marie; Villa, Elizabeth; Förster, Friedrich; Hegerl, Reiner; Peters, Jürgen; Baumeister, Wolfgang; Rockel, Beate

2012-04-04

Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the structure of human TPPII (HsTPPII) has been determined to subnanometer resolution by cryoelectron microscopy and single-particle analysis. The complex is built from two strands forming a quasihelical structure harboring a complex system of inner cavities. HsTPPII particles exhibit some polymorphism resulting in complexes consisting of nine or of eight dimers per strand. To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting. Analyses of the resulting hybrid structure of the HsTPPII holocomplex provide new insights into the mechanism of maturation and activation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Tuning Interfacial Properties and Processes by Controlling the Rheology and Structure of Poly( N-isopropylacrylamide) Particles at Air/Water Interfaces.

PubMed

Maestro, Armando; Jones, Daniel; Sánchez de Rojas Candela, Carmen; Guzman, Eduardo; Duits, Michel H G; Cicuta, Pietro

2018-06-05

By combining controlled experiments on single interfaces with measurements on solitary bubbles and liquid foams, we show that poly( N-isopropylacrylamide) (PNIPAM) microgels assembled at air/water interfaces exhibit a solid to liquid transition changing the temperature, and that this is associated with the change in the interfacial microstructure of the PNIPAM particles around their volume phase transition temperature. We show that the solid behaves as a soft 2D colloidal glass, and that the existence of this solid/liquid transition offers an ideal platform to tune the permeability of air bubbles covered by PNIPAM and to control macroscopic foam properties such as drainage, stability, and foamability. PNIPAM particles on fluid interfaces allow new tunable materials, for example foam structures with variable mechanical properties upon small temperature changes.

Coherent diffraction imaging analysis of shape-controlled nanoparticles with focused hard X-ray free-electron laser pulses.

PubMed

Takahashi, Yukio; Suzuki, Akihiro; Zettsu, Nobuyuki; Oroguchi, Tomotaka; Takayama, Yuki; Sekiguchi, Yuki; Kobayashi, Amane; Yamamoto, Masaki; Nakasako, Masayoshi

2013-01-01

We report the first demonstration of the coherent diffraction imaging analysis of nanoparticles using focused hard X-ray free-electron laser pulses, allowing us to analyze the size distribution of particles as well as the electron density projection of individual particles. We measured 1000 single-shot coherent X-ray diffraction patterns of shape-controlled Ag nanocubes and Au/Ag nanoboxes and estimated the edge length from the speckle size of the coherent diffraction patterns. We then reconstructed the two-dimensional electron density projection with sub-10 nm resolution from selected coherent diffraction patterns. This method enables the simultaneous analysis of the size distribution of synthesized nanoparticles and the structures of particles at nanoscale resolution to address correlations between individual structures of components and the statistical properties in heterogeneous systems such as nanoparticles and cells.

Fabrication of chitosan single-component microcapsules with a micrometer-thick and layered wall structure by stepwise core-mediated precipitation.

PubMed

Han, Yuanyuan; Tong, Weijun; Zhang, Yuying; Gao, Changyou

2012-02-27

Incubation of CaCO(3) microparticles in chitosan (CS) solution at pH 5.2 and following with ethylenediaminetetraacetic acid disodium salt (EDTA) treatment resulted in CS single-component microcapsules with an ultra-thick wall structure. Repeating the incubation caused stepwise increase of wall thickness and finally resulted in CS microcapsules with a layered structure. This unique method is mediated by precipitation of CS on the CaCO(3) particles as a result of pH increase caused by the partial dissolution of CaCO(3) . The obtained CS capsules are stable at neutral pH. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Controlled Release from Core-Shell Nanoporous Silica Particles for Corrosion Inhibition of Aluminum Alloys

DOE PAGES

Jiang, Xingmao; Jiang, Ying-Bing; Liu, Nanguo; ...

2011-01-01

Ceriumore » m (Ce) corrosion inhibitors were encapsulated into hexagonally ordered nanoporous silica particles via single-step aerosol-assisted self-assembly. The core/shell structured particles are effective for corrosion inhibition of aluminum alloy AA2024-T3. Numerical simulation proved that the core-shell nanostructure delays the release process. The effective diffusion coefficient elucidated from release data for monodisperse particles in water was 1.0 × 10 − 14  m 2 s for Ce 3+ compared to 2.5 × 10 − 13  m 2 s for NaCl. The pore size, pore surface chemistry, and the inhibitor solubility are crucial factors for the application. Microporous hydrophobic particles encapsulating a less soluble corrosion inhibitor are desirable for long-term corrosion inhibition.« less

Influence of Dispersant and Heat Treatment on the Morphology of Nanocrystalline Hydroxyapatite

NASA Astrophysics Data System (ADS)

Pan, Yusong; Xiong, Dangsheng

2010-10-01

Natural biological hard tissues are biocomposites of proteins and hydroxyapatite (HA) with superior strength. Nanometer scale HAp is the key material to manufacture bone substitute. In this work, nano-sized HA particles were synthesized by a wet method using orthophosphoric acid and calcium hydroxide as raw materials. The prepared nanocrystalline HAp was characterized for its phase purity and nano-scale morphological structure by XRD, TEM, and FTIR. The influences of heat treatment temperature and dispersant on the properties of HAp were also investigated. The results indicated that nano-particles were pure single-phase HAp with a diameter of 25-70 nm and length of 50-180 nm depending on heat treatment temperature. The morphology and crystallite size of HAp change with heat treatment temperature. After heat treating, the crystallinity of these nano-particles increased and its morphology transformed from needle-like to sphere-like structure. The dispersant is beneficial to prevent the growth of HA particles and provide a uniform particle size distribution. Moreover, the HAp tends to form small agglomerates in the absence of dispersant.

Composition and Morphology of Individual Combustion, Biomass Burning, and Secondary Organic Particle Types Obtained Using ATOFMS and STXM-NEXAFS Measurements (Invited)

NASA Astrophysics Data System (ADS)

Russell, L. M.; Bahadur, R.; Liu, S.; Takahama, S.; Prather, K. A.

2010-12-01

Complementary single particle measurements of organic aerosols using aerosol time-of-flight mass spectrometry (ATOFMS) and Scanning Transmission X-ray Microscopy—Near Edge X-ray Absorption Fine Structure (STXM-NEXAFS) are compared to examine the relationships between particle morphologies and chemical composition of particles having similar sources. ATOFMS measurements from field campaigns in polluted or urban (Riverside/SOAR 2005; Mexico City/MILAGRO 2006; Port of Long Beach 2007) and clean or marine (Arabian Sea/INDOEX 1999; Sea of Japan/ACE-Asia 2001; Trinidad Head/CIFEX 2004) locations illustrate regional differences in the amount and types of organic particles. The majority (≥ 85%) of the number of submicron particles are carbonaceous (including elemental and organic carbon), but represent less than 10% of the number of supermicron particles. Organic carbon (OC) particles are classified into three meta-classes corresponding to (1) combustion-generated OC/EC internalmixtures, (2) biomass burning generated K/OC mixtures, and (3) OC/High MassOC (HMOC) mixtures containing secondary markers of atmospheric processing. Normalized dot products are used to quantify similarity among fragment spectra and indicate that OC particle types are consistent across (and within) platforms. Single particle carbon STXM-NEXAFS measurements during ACE-Asia 2001 and MILAGRO 2006 yield similar source categories based on relative abundances of aromatic, alkane, and carboxylic acid functional groups. All three organic particle types correspond to a variety of very heterogeneous particle morphologies, although the highly oxygenated OC particles with likely secondary organic contributions frequently are nearly spherical, liquid-like particles. Similar particle types are observed at many other locations, including recent measurements at Bakersfield, Tijuana, and the R/V Atlantis as part of CalNex and CalMex. Size-resolved number fractions of the major ATOFMS organic particle types show qualitative agreement with OC particle types from STXM NEXAFS analysis, indicating a correspondence of the OC/EC type with the presence of strong aromatic groups, of the OC/HMOC type with high carboxylic acid groups, and of the biomass burning OC type with aromatic and carbonyl groups. The comparison shows that ATOFMS measurements can be used to establish robust statistics for offline single particle techniques, providing the atmospheric context for the functional group and morphological information obtained from STXM-NEXAFS for an improved understanding of the climate impact of organic aerosols.

Structural analysis of herpes simplex virus by optical super-resolution imaging

NASA Astrophysics Data System (ADS)

Laine, Romain F.; Albecka, Anna; van de Linde, Sebastian; Rees, Eric J.; Crump, Colin M.; Kaminski, Clemens F.

2015-01-01

Herpes simplex virus type-1 (HSV-1) is one of the most widespread pathogens among humans. Although the structure of HSV-1 has been extensively investigated, the precise organization of tegument and envelope proteins remains elusive. Here we use super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM) in combination with a model-based analysis of single-molecule localization data, to determine the position of protein layers within virus particles. We resolve different protein layers within individual HSV-1 particles using multi-colour dSTORM imaging and discriminate envelope-anchored glycoproteins from tegument proteins, both in purified virions and in virions present in infected cells. Precise characterization of HSV-1 structure was achieved by particle averaging of purified viruses and model-based analysis of the radial distribution of the tegument proteins VP16, VP1/2 and pUL37, and envelope protein gD. From this data, we propose a model of the protein organization inside the tegument.

Structural Changes in a Marine Podovirus Associated with Release of its Genome into Prochlorococcus

PubMed Central

Liu, Xiangan; Zhang, Qinfen; Murata, Kazuyoshi; Baker, Matthew L.; Sullivan, Matthew B.; Fu, Caroline; Dougherty, Matthew; Schmid, Michael F.; Osburne, Marcia S.; Chisholm, Sallie W.; Chiu, Wah

2010-01-01

Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single particle cryo-electron microscopy (cryo-EM) yields icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6 Å and 9 Å resolution, respectively. The asymmetric reconstruction reveals how symmetry mismatches are accommodated among 5 of the gene products at the portal vertex. Reconstructions of infectious and empty particles show a conformational change of the “valve” density in the nozzle, an orientation difference in the tail fibers, a disordering of the C-terminus of the portal protein, and disappearance of the core proteins. In addition, cryo-electron tomography (cryo-ET) of P-SSP7 infecting Prochlorococcus demonstrated the same tail fiber conformation as in empty particles. Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release. PMID:20543830

Stable optical trapping and sensitive characterization of nanostructures using standing-wave Raman tweezers

PubMed Central

Wu, Mu-ying; Ling, Dong-xiong; Ling, Lin; Li, William; Li, Yong-qing

2017-01-01

Optical manipulation and label-free characterization of nanoscale structures open up new possibilities for assembly and control of nanodevices and biomolecules. Optical tweezers integrated with Raman spectroscopy allows analyzing a single trapped particle, but is generally less effective for individual nanoparticles. The main challenge is the weak gradient force on nanoparticles that is insufficient to overcome the destabilizing effect of scattering force and Brownian motion. Here, we present standing-wave Raman tweezers for stable trapping and sensitive characterization of single isolated nanostructures with a low laser power by combining a standing-wave optical trap with confocal Raman spectroscopy. This scheme has stronger intensity gradients and balanced scattering forces, and thus can be used to analyze many nanoparticles that cannot be measured with single-beam Raman tweezers, including individual single-walled carbon nanotubes (SWCNT), graphene flakes, biological particles, SERS-active metal nanoparticles, and high-refractive semiconductor nanoparticles. This would enable sorting and characterization of specific SWCNTs and other nanoparticles based on their increased Raman fingerprints. PMID:28211526

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus.

PubMed

Huynh, Nhung T; Hesketh, Emma L; Saxena, Pooja; Meshcheriakova, Yulia; Ku, You-Chan; Hoang, Linh T; Johnson, John E; Ranson, Neil A; Lomonossoff, George P; Reddy, Vijay S

2016-04-05

Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Routine single particle CryoEM sample and grid characterization by tomography

PubMed Central

Noble, Alex J; Brasch, Julia; Chase, Jillian; Acharya, Priyamvada; Tan, Yong Zi; Zhang, Zhening; Kim, Laura Y; Scapin, Giovanna; Rapp, Micah; Eng, Edward T; Rice, William J; Cheng, Anchi; Negro, Carl J; Shapiro, Lawrence; Kwong, Peter D; Jeruzalmi, David; des Georges, Amedee; Potter, Clinton S

2018-01-01

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment. PMID:29809143

Recombinant Expression of Tandem-HBc Virus-Like Particles (VLPs).

PubMed

Stephen, Sam L; Beales, Lucy; Peyret, Hadrien; Roe, Amy; Stonehouse, Nicola J; Rowlands, David J

2018-01-01

The hepatitis B virus (HBV) core protein (HBc) has formed the building block for virus-like particle (VLP) production for more than 30 years. The ease of production of the protein, the robust ability of the core monomers to dimerize and assemble into intact core particles, and the strong immune responses they elicit when presenting antigenic epitopes all demonstrate its promise for vaccine development (reviewed in Pumpens and Grens (Intervirology 44: 98-114, 2001)). HBc has been modified in a number of ways in attempts to expand its potential as a novel vaccine platform. The HBc protein is predominantly α-helical in structure and folds to form an L-shaped molecule. The structural subunit of the HBc particle is a dimer of monomeric HBc proteins which together form an inverted T-shaped structure. In the assembled HBc particle the four-helix bundle formed at each dimer interface appears at the surface as a prominent "spike." The tips of the "spikes" are the preferred sites for the insertion of foreign sequences for vaccine purposes as they are the most highly exposed regions of the assembled particles. In the tandem-core modification two copies of the HBc protein are covalently linked by a flexible amino acid sequence which allows the fused dimer to fold correctly and assemble into HBc particles. The advantage of the modified structure is that the assembly of the dimeric subunits is defined and not formed by random association. This facilitates the introduction of single, larger sequences at the tip of each surface "spike," thus overcoming the conformational clashes contingent on insertion of large structures into monomeric HBc proteins.Differences in inserted sequences influence the assembly characteristics of the modified proteins, and it is important to optimize the design of each novel construct to maximize efficiency of assembly into regular VLPs. In addition to optimization of the construct, the expression system used can also influence the ability of recombinant structures to assemble into regular isometric particles. Here, we describe the production of recombinant tandem-core particles in bacterial, yeast and plant expression systems.

Guidelines for the formulation of Lagrangian stochastic models for particle simulations of single-phase and dispersed two-phase turbulent flows

NASA Astrophysics Data System (ADS)

Minier, Jean-Pierre; Chibbaro, Sergio; Pope, Stephen B.

2014-11-01

In this paper, we establish a set of criteria which are applied to discuss various formulations under which Lagrangian stochastic models can be found. These models are used for the simulation of fluid particles in single-phase turbulence as well as for the fluid seen by discrete particles in dispersed turbulent two-phase flows. The purpose of the present work is to provide guidelines, useful for experts and non-experts alike, which are shown to be helpful to clarify issues related to the form of Lagrangian stochastic models. A central issue is to put forward reliable requirements which must be met by Lagrangian stochastic models and a new element brought by the present analysis is to address the single- and two-phase flow situations from a unified point of view. For that purpose, we consider first the single-phase flow case and check whether models are fully consistent with the structure of the Reynolds-stress models. In the two-phase flow situation, coming up with clear-cut criteria is more difficult and the present choice is to require that the single-phase situation be well-retrieved in the fluid-limit case, elementary predictive abilities be respected and that some simple statistical features of homogeneous fluid turbulence be correctly reproduced. This analysis does not address the question of the relative predictive capacities of different models but concentrates on their formulation since advantages and disadvantages of different formulations are not always clear. Indeed, hidden in the changes from one structure to another are some possible pitfalls which can lead to flaws in the construction of practical models and to physically unsound numerical calculations. A first interest of the present approach is illustrated by considering some models proposed in the literature and by showing that these criteria help to assess whether these Lagrangian stochastic models can be regarded as acceptable descriptions. A second interest is to indicate how future developments can be safely built, which is also relevant for stochastic subgrid models for particle-laden flows in the context of Large Eddy Simulations.

Guidelines for the formulation of Lagrangian stochastic models for particle simulations of single-phase and dispersed two-phase turbulent flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minier, Jean-Pierre, E-mail: Jean-Pierre.Minier@edf.fr; Chibbaro, Sergio; Pope, Stephen B.

In this paper, we establish a set of criteria which are applied to discuss various formulations under which Lagrangian stochastic models can be found. These models are used for the simulation of fluid particles in single-phase turbulence as well as for the fluid seen by discrete particles in dispersed turbulent two-phase flows. The purpose of the present work is to provide guidelines, useful for experts and non-experts alike, which are shown to be helpful to clarify issues related to the form of Lagrangian stochastic models. A central issue is to put forward reliable requirements which must be met by Lagrangianmore » stochastic models and a new element brought by the present analysis is to address the single- and two-phase flow situations from a unified point of view. For that purpose, we consider first the single-phase flow case and check whether models are fully consistent with the structure of the Reynolds-stress models. In the two-phase flow situation, coming up with clear-cut criteria is more difficult and the present choice is to require that the single-phase situation be well-retrieved in the fluid-limit case, elementary predictive abilities be respected and that some simple statistical features of homogeneous fluid turbulence be correctly reproduced. This analysis does not address the question of the relative predictive capacities of different models but concentrates on their formulation since advantages and disadvantages of different formulations are not always clear. Indeed, hidden in the changes from one structure to another are some possible pitfalls which can lead to flaws in the construction of practical models and to physically unsound numerical calculations. A first interest of the present approach is illustrated by considering some models proposed in the literature and by showing that these criteria help to assess whether these Lagrangian stochastic models can be regarded as acceptable descriptions. A second interest is to indicate how future developments can be safely built, which is also relevant for stochastic subgrid models for particle-laden flows in the context of Large Eddy Simulations.« less

Synthesis of crystalline and amorphous, particle-agglomerated 3-D nanostructures of Al and Si oxides by femtosecond laser and the prediction of these particle sizes

NASA Astrophysics Data System (ADS)

Sivayoganathan, Mugunthan; Tan, Bo; Venkatakrishnan, Krishnan

2012-11-01

We report a single step technique of synthesizing particle-agglomerated, amorphous 3-D nanostructures of Al and Si oxides on powder-fused aluminosilicate ceramic plates and a simple novel method of wafer-foil ablation to fabricate crystalline nanostructures of Al and Si oxides at ambient conditions. We also propose a particle size prediction mechanism to regulate the size of vapor-condensed agglomerated nanoparticles in these structures. Size characterization studies performed on the agglomerated nanoparticles of fabricated 3-D structures showed that the size distributions vary with the fluence-to-threshold ratio. The variation in laser parameters leads to varying plume temperature, pressure, amount of supersaturation, nucleation rate, and the growth rate of particles in the plume. The novel wafer-foil ablation technique could promote the possibilities of fabricating oxide nanostructures with varying Al/Si ratio, and the crystallinity of these structures enhances possible applications. The fabricated nanostructures of Al and Si oxides could have great potentials to be used in the fabrication of low power-consuming complementary metal-oxide-semiconductor circuits and in Mn catalysts to enhance the efficiency of oxidation on ethylbenzene to acetophenone in the super-critical carbon dioxide.

Synthesis of crystalline and amorphous, particle-agglomerated 3-D nanostructures of Al and Si oxides by femtosecond laser and the prediction of these particle sizes.

PubMed

Sivayoganathan, Mugunthan; Tan, Bo; Venkatakrishnan, Krishnan

2012-11-09

We report a single step technique of synthesizing particle-agglomerated, amorphous 3-D nanostructures of Al and Si oxides on powder-fused aluminosilicate ceramic plates and a simple novel method of wafer-foil ablation to fabricate crystalline nanostructures of Al and Si oxides at ambient conditions. We also propose a particle size prediction mechanism to regulate the size of vapor-condensed agglomerated nanoparticles in these structures. Size characterization studies performed on the agglomerated nanoparticles of fabricated 3-D structures showed that the size distributions vary with the fluence-to-threshold ratio. The variation in laser parameters leads to varying plume temperature, pressure, amount of supersaturation, nucleation rate, and the growth rate of particles in the plume. The novel wafer-foil ablation technique could promote the possibilities of fabricating oxide nanostructures with varying Al/Si ratio, and the crystallinity of these structures enhances possible applications. The fabricated nanostructures of Al and Si oxides could have great potentials to be used in the fabrication of low power-consuming complementary metal-oxide-semiconductor circuits and in Mn catalysts to enhance the efficiency of oxidation on ethylbenzene to acetophenone in the super-critical carbon dioxide.

Synthesis of crystalline and amorphous, particle-agglomerated 3-D nanostructures of Al and Si oxides by femtosecond laser and the prediction of these particle sizes

PubMed Central

2012-01-01

We report a single step technique of synthesizing particle-agglomerated, amorphous 3-D nanostructures of Al and Si oxides on powder-fused aluminosilicate ceramic plates and a simple novel method of wafer-foil ablation to fabricate crystalline nanostructures of Al and Si oxides at ambient conditions. We also propose a particle size prediction mechanism to regulate the size of vapor-condensed agglomerated nanoparticles in these structures. Size characterization studies performed on the agglomerated nanoparticles of fabricated 3-D structures showed that the size distributions vary with the fluence-to-threshold ratio. The variation in laser parameters leads to varying plume temperature, pressure, amount of supersaturation, nucleation rate, and the growth rate of particles in the plume. The novel wafer-foil ablation technique could promote the possibilities of fabricating oxide nanostructures with varying Al/Si ratio, and the crystallinity of these structures enhances possible applications. The fabricated nanostructures of Al and Si oxides could have great potentials to be used in the fabrication of low power-consuming complementary metal-oxide-semiconductor circuits and in Mn catalysts to enhance the efficiency of oxidation on ethylbenzene to acetophenone in the super-critical carbon dioxide. PMID:23140103

TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA.

PubMed

Kobayashi, Amane; Sekiguchi, Yuki; Takayama, Yuki; Oroguchi, Tomotaka; Shirahama, Keiya; Torizuka, Yasufumi; Manoda, Masahiro; Nakasako, Masayoshi; Yamamoto, Masaki

2016-05-01

Coherent X-ray diffraction imaging (CXDI) is a technique for structure analyses of non-crystalline particles with dimensions ranging from micrometer to sub-micrometer. We have developed a diffraction apparatus named TAKASAGO-6 for use in single-shot CXDI experiments of frozen-hydrated non-crystalline biological particles at cryogenic temperature with X-ray free electron laser pulses provided at a repetition rate of 30 Hz from the SPring-8 Angstrom Compact free-electron LAser. Specimen particles are flash-cooled after being dispersed on thin membranes supported by specially designed disks. The apparatus is equipped with a high-speed translation stage with a cryogenic pot for raster-scanning of the disks at a speed higher than 25 μm/33 ms. In addition, we use devices assisting the easy transfer of cooled specimens from liquid-nitrogen storages to the cryogenic pot. In the current experimental procedure, more than 20 000 diffraction patterns can be collected within 1 h. Here we report the key components and performance of the diffraction apparatus. Based on the efficiency of the diffraction data collection and the structure analyses of metal particles, biological cells, and cellular organelles, we discuss the future application of this diffraction apparatus for structure analyses of biological specimens.

Formation of polymeric toroidal-spiral particles.

PubMed

Sharma, Vishal; Szymusiak, Magdalena; Shen, Hao; Nitsche, Ludwig C; Liu, Ying

2012-01-10

Compared to spherical matrices, particles with well-defined internal structure provide large surface to volume ratio and predictable release kinetics for the encapsulated payloads. We describe self-assembly of polymeric particles, whereby competitive kinetics of viscous sedimentation, diffusion, and cross-linking yield a controllable toroidal-spiral (T-S) structure. Precursor polymeric droplets are splashed through the surface of a less dense, miscible solution, after which viscous forces entrain the surrounding bulk solution into the sedimenting polymer drop to form T-S channels. The intricate structure forms because low interfacial tension between the two miscible solutions is dominated by viscous forces. The biocompatible polymer, poly(ethylene glycol) diacrylate (PEG-DA), is used to demonstrate the solidification of the T-S shapes at various configurational stages by UV-triggered cross-linking. The dimensions of the channels are controlled by Weber number during impact on the surface, and Reynolds number and viscosity ratio during subsequent sedimentation. We anticipate applications of the T-S particle in drug delivery, wherein diffusion through these T-S channels and the polymer matrix would offer parallel release pathways for molecules of different sizes. Polyphosphate, as a model macromolecule, is entrained in T-S particles during their formation. The in vitro release kinetics of polyphosphate from the T-S particles with various channel length and width is reported. In addition, self-assembly of T-S particles occurs in a single step under benign conditions for delicate macromolecules, and appears conducive to scaleup.

Characterisation of Black Carbon (BC) mixing state and flux in Beijing using single particle measurements.

NASA Astrophysics Data System (ADS)

Joshi, Rutambhara; Liu, Dantong; Allan, James; Coe, Hugh; Flynn, Michael; Broda, Kurtis; Olfert, Jason; Irwin, Martin; Sun, Yele; Fu, Pingqing; Wang, Junfeng; Ge, Xinlei; Langford, Ben; Nemitz, Eiko; Mullinger, Neil

2017-04-01

BC is generated by the incomplete combustion of carbonaceous fuels and it is an important component of fine PM2.5. In the atmosphere BC particles have a complex structure and its mixing state has crucial impact on optical properties. Quantifying the sources and emissions of black carbon in urban environments is important and presently uncertain, particularly in megacities undergoing rapid growth and change in emissions. During the winter of 2016 (10th Nov-10th Dec) the BC was characterised as part of a large joint UK-China field experiment in Beijing. This paper focuses on understanding the mixing state of BC as well as identification and quantification of BC sources. We used a combination of a Centrifugal Particle Mass Analyser (CPMA) and a Single Particle Soot Photometer (SP2) to uniquely quantify the morphology independent mass of single refractory BC particles and their coating content. The CPMA allows us to select pre-charged aerosol particles according to their mass to charge ratio and the SP2 provides information on the mass of refractory BC through a laser-induced incandescence method. Furthermore, another SP2 was used to measure the BC flux at 100m height using the Eddy Covariance method. We have successfully gathered 4 weeks of continuous measurements which include several severe pollution events in Beijing. Here we present preliminary results, characterising the distribution of coating mass on BC particles in Beijing and linking this to the main sources of BC in the city. We will provide initial estimates of the BC flux over a several kilometre footprint. Such analysis will provide important information for the further investigation of source distribution, emission, lifetime and optical properties of BC under complex environments in Beijing.

Effect of relative humidity on soot - secondary organic aerosol mixing: A case study from the Soot Aerosol Aging Study (PNNL-SAAS)

NASA Astrophysics Data System (ADS)

Sharma, N.; China, S.; Zaveri, R. A.; Shilling, J. E.; Pekour, M. S.; Liu, S.; Aiken, A. C.; Dubey, M. K.; Wilson, J. M.; Zelenyuk, A.; OBrien, R. E.; Moffet, R.; Gilles, M. K.; Gourihar, K.; Chand, D.; Sedlacek, A. J., III; Subramanian, R.; Onasch, T. B.; Laskin, A.; Mazzoleni, C.

2014-12-01

Atmospheric processing of fresh soot particles emitted by anthropogenic as well as natural sources alters their physical and chemical properties. For example, fresh and aged soot particles interact differently with incident solar radiation, resulting in different overall radiation budgets. Varying atmospheric chemical and meteorological conditions can result in complex soot mixing states. The Soot Aerosol Aging Study (SAAS) was conducted at the Pacific Northwest National Laboratory in November 2013 and January 2014 as a step towards understanding the evolution of mixing state of soot and its impact on climate-relevant properties. Aging experiments on diesel soot were carried out in a controlled laboratory chamber, and the effects of condensation and coagulation processes were systematically explored in separate sets of experiments. In addition to online measurement of aerosol properties, aerosol samples were collected for offline single particle analysis to investigate the evolution of the morphology, elemental composition and fine structure of sample particles from different experiments. Condensation experiments focused on the formation of α-pinene secondary organic aerosol on diesel soot aerosol seeds. Experiments were conducted to study the aging of soot under dry (RH < 2%) and humid conditions (RH ~ 80%). We present an analysis of the morphology of soot, its evolution, and its correlation with optical properties, as the condensation of α-pinene SOA is carried out for the two different RH conditions. The analysis was performed by using scanning electron microscopy, transmission electron microscopy, scanning transmission x-ray microscopy and atomic force microscopy for single particle characterization. In addition, particle size, mass, composition, shape, and density were characterized in-situ, as a function of organics condensed on soot seeds, using single particle mass spectrometer.

Possible layout solutions for the improvement of the dark rate of geiger mode avalanche structures in the GLOBALFOUNDRIES BCDLITE 0.18 μm CMOS technology

NASA Astrophysics Data System (ADS)

D'Ascenzo, N.; Xie, Q.

2018-04-01

Modern concepts of single photon or charged particle detection systems are based on geiger mode avalanche devices developed in CMOS technology. The key-problem encountered in the fabrication of these devices in CMOS is the dark rate level. The dark rate and single photon signal are not distinguishable. This sets also the limits of the application of geiger mode avalanche devices to single photon or charged particle detection systems. We report the design and fabrication of four possible layouts of these devices using the 0.18 μm BCDLite GLOBALFOUNDRIES process. The devices have an area of 50×50 μm2. They are characterized by a fast response time and an approximately 60 ns recovery time. The best topology exhibits an average dark rate as low as 3×103 kHz/mm2.

X-ray Vision for Aerosol Scientists: LCLS Snapshots of Soot (Narrated)

ScienceCinema

None

2018-01-26

This short conceptual animation depicts how scientists can now simultaneously capture fractal morphology (structure), chemical composition and nanoscale imagery of individual aerosol particles in flight. These particles, known as "PM2.5" because they are smaller than 2.5 microns in diameter, affect climate by interacting with sunlight and impact human health by entering the lungs. The single LCLS laser pulses travel to the Atomic, Molecular and Optical Sciences (AMO) laboratory in the Near Experimental Hall. As we zoom in, we see deep inside a simplified aerosol inlet, where the complex fractal structure of the soot particles, each one completely unique, is shown. Individual soot particles are then delivered into the pulses of the LCLS beam, which destroys them. X-rays are scattered to the detector before the particle is destroyed, giving information about the morphology of the particle. Ion fragments released in the explosion are sent into a mass spectrometer, which measures their mass-to-charge ratio -- giving scientists information about the chemical composition of the particle. Many different particles are analyzed in this manner, allowing scientists to probe variations in the particles due to changes in their environment before being sent through the aerosol inlet. The final visual of aerosols emitted from a factory is representative of the goal that such LCLS aerosol dynamics experiments can provide critical feedback into modeling and understanding combustion, aerosol processes in manufacturing or aerosol effects on climate change.

Single mimivirus particles intercepted and imaged with an X-ray laser

PubMed Central

Seibert, M. Marvin; Ekeberg, Tomas; Maia, Filipe R. N. C.; Svenda, Martin; Andreasson, Jakob; Jönsson, Olof; Odić, Duško; Iwan, Bianca; Rocker, Andrea; Westphal, Daniel; Hantke, Max; DePonte, Daniel P.; Barty, Anton; Schulz, Joachim; Gumprecht, Lars; Coppola, Nicola; Aquila, Andrew; Liang, Mengning; White, Thomas A.; Martin, Andrew; Caleman, Carl; Stern, Stephan; Abergel, Chantal; Seltzer, Virginie; Claverie, Jean-Michel; Bostedt, Christoph; Bozek, John D.; Boutet, Sébastien; Miahnahri, A. Alan; Messerschmidt, Marc; Krzywinski, Jacek; Williams, Garth; Hodgson, Keith O.; Bogan, Michael J.; Hampton, Christina Y.; Sierra, Raymond G.; Starodub, Dmitri; Andersson, Inger; Bajt, Saša; Barthelmess, Miriam; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Kirian, Richard; Hunter, Mark; Doak, R. Bruce; Marchesini, Stefano; Hau-Riege, Stefan P.; Frank, Matthias; Shoeman, Robert L.; Lomb, Lukas; Epp, Sascha W.; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Schmidt, Carlo; Foucar, Lutz; Kimmel, Nils; Holl, Peter; Rudek, Benedikt; Erk, Benjamin; Hömke, André; Reich, Christian; Pietschner, Daniel; Weidenspointner, Georg; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Schlichting, Ilme; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Chapman, Henry N.; Hajdu, Janos

2014-01-01

X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions1–4. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma1. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval2. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source5. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies. PMID:21293374

Programmable colloidal molecules from sequential capillarity-assisted particle assembly

PubMed Central

Ni, Songbo; Leemann, Jessica; Buttinoni, Ivo; Isa, Lucio; Wolf, Heiko

2016-01-01

The assembly of artificial nanostructured and microstructured materials which display structures and functionalities that mimic nature’s complexity requires building blocks with specific and directional interactions, analogous to those displayed at the molecular level. Despite remarkable progress in synthesizing “patchy” particles encoding anisotropic interactions, most current methods are restricted to integrating up to two compositional patches on a single “molecule” and to objects with simple shapes. Currently, decoupling functionality and shape to achieve full compositional and geometrical programmability remains an elusive task. We use sequential capillarity-assisted particle assembly which uniquely fulfills the demands described above. This is a new method based on simple, yet essential, adaptations to the well-known capillary assembly of particles over topographical templates. Tuning the depth of the assembly sites (traps) and the surface tension of moving droplets of colloidal suspensions enables controlled stepwise filling of traps to “synthesize” colloidal molecules. After deposition and mechanical linkage, the colloidal molecules can be dispersed in a solvent. The template’s shape solely controls the molecule’s geometry, whereas the filling sequence independently determines its composition. No specific surface chemistry is required, and multifunctional molecules with organic and inorganic moieties can be fabricated. We demonstrate the “synthesis” of a library of structures, ranging from dumbbells and triangles to units resembling bar codes, block copolymers, surfactants, and three-dimensional chiral objects. The full programmability of our approach opens up new directions not only for assembling and studying complex materials with single-particle-level control but also for fabricating new microscale devices for sensing, patterning, and delivery applications. PMID:27051882

Nuclear Structure Studies in the 132Sn Region: Safe Coulex with Carbon Targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allmond, James M; Stuchbery, Andrew E; Galindo-Uribarri, Alfredo

2015-01-01

The collective and single-particle structure of nuclei in the 132Sn region was recently studied by Coulomb excitation and heavy-ion induced transfer reactions using carbon, beryllium, and titanium targets. In particular, Coulomb excitation was used determine a complete set of electromagnetic moments for the first 2 + states and one-neutron transfer was used to probe the purity and evolution of single-neutron states. These recent experiments were conducted at the Holifield Radioactive Ion Beam Facility at ORNL using a CsI-HPGe detector array (BareBall- CLARION) to detect scattered particles and emitted gamma rays from the in-beam reactions. A Bragg-curve detector was used tomore » measure the energy loss of the various beams through the targets and to measure the radioactive beam compositions. A sample of the Coulomb excitation results is presented here with an emphasis placed on 116Sn. In particular, the safe Coulex criterion for carbon targets will be analyzed and discussed.« less

Three-dimensional manipulation of single cells using surface acoustic waves

PubMed Central

Guo, Feng; Mao, Zhangming; Chen, Yuchao; Xie, Zhiwei; Lata, James P.; Li, Peng; Ren, Liqiang; Liu, Jiayang; Yang, Jian; Dao, Ming; Suresh, Subra; Huang, Tony Jun

2016-01-01

The ability of surface acoustic waves to trap and manipulate micrometer-scale particles and biological cells has led to many applications involving “acoustic tweezers” in biology, chemistry, engineering, and medicine. Here, we present 3D acoustic tweezers, which use surface acoustic waves to create 3D trapping nodes for the capture and manipulation of microparticles and cells along three mutually orthogonal axes. In this method, we use standing-wave phase shifts to move particles or cells in-plane, whereas the amplitude of acoustic vibrations is used to control particle motion along an orthogonal plane. We demonstrate, through controlled experiments guided by simulations, how acoustic vibrations result in micromanipulations in a microfluidic chamber by invoking physical principles that underlie the formation and regulation of complex, volumetric trapping nodes of particles and biological cells. We further show how 3D acoustic tweezers can be used to pick up, translate, and print single cells and cell assemblies to create 2D and 3D structures in a precise, noninvasive, label-free, and contact-free manner. PMID:26811444

Live Imaging of Cellular Internalization of Single Colloidal Particle by Combined Label-Free and Fluorescence Total Internal Reflection Microscopy.

PubMed

Byrne, Gerard D; Vllasaliu, Driton; Falcone, Franco H; Somekh, Michael G; Stolnik, Snjezana

2015-11-02

In this work we utilize the combination of label-free total internal reflection microscopy and total internal reflectance fluorescence (TIRM/TIRF) microscopy to achieve a simultaneous, live imaging of single, label-free colloidal particle endocytosis by individual cells. The TIRM arm of the microscope enables label free imaging of the colloid and cell membrane features, while the TIRF arm images the dynamics of fluorescent-labeled clathrin (protein involved in endocytosis via clathrin pathway), expressed in transfected 3T3 fibroblasts cells. Using a model polymeric colloid and cells with a fluorescently tagged clathrin endocytosis pathway, we demonstrate that wide field TIRM/TIRF coimaging enables live visualization of the process of colloidal particle interaction with the labeled cell structure, which is valuable for discerning the membrane events and route of colloid internalization by the cell. We further show that 500 nm in diameter model polystyrene colloid associates with clathrin, prior to and during its cellular internalization. This association is not apparent with larger, 1 μm in diameter colloids, indicating an upper particle size limit for clathrin-mediated endocytosis.

Neutral Mass Spectrometry of Mega-Dalton Particles with Single-Particle Resolution using a Nano-Electromechanical System

NASA Astrophysics Data System (ADS)

Kelber, Scott; Hanay, Mehmet; Naik, Akshay; Chi, Derrick; Hentz, Sebastien; Bullard, Caryn; Collinet, Eric; Duraffourg, Laurent; Roukes, Michael

2012-02-01

Nanoelectromechanical systems (NEMS) enable mass sensing with unprecedented sensitivity and mass dynamic range. Previous works have relied on statistical analysis of multiple landing events to assemble mass spectra. Here we demonstrate the utility of using multiple modes of the NEMS device in determining the mass of individual molecules landing on the NEMS. Analyte particles in vapor form are produced using matrix assisted laser desorption ionization. Resonant frequencies of the first two modes of a single NEMS device, placed in close proximity to the analyte source, are tracked using parallel phase locked loops. Each analyte molecule landing on the NEMS generates a distinct frequency shift in the two modes. These time correlated frequency jumps are used to evaluate the mass of each analyte particle landing on the NEMS and thus generate mass spectra. We present the latest experimental results using this scheme and also demonstrate the utility for mass spectrometry of large biomolecules. This NEMS-Mass Spec. system offers a new tool for structural biology and pathology for the analysis of large proteins, protein complexes, and viruses.

EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing.

PubMed

Berndsen, Zachary; Bowman, Charles; Jang, Haerin; Ward, Andrew B

2017-12-01

The Electron Microscopy Hole Punch (EMHP) is a streamlined suite of tools for quick assessment, sorting and hole masking of electron micrographs. With recent advances in single-particle electron cryo-microscopy (cryo-EM) data processing allowing for the rapid determination of protein structures using a smaller computational footprint, we saw the need for a fast and simple tool for data pre-processing that could run independent of existing high-performance computing (HPC) infrastructures. EMHP provides a data preprocessing platform in a small package that requires minimal python dependencies to function. https://www.bitbucket.org/chazbot/emhp Apache 2.0 License. bowman@scripps.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Optimization of pore structure and particle morphology of mesoporous silica for antibody adsorption for use in affinity chromatography

NASA Astrophysics Data System (ADS)

Hikosaka, Ryouichi; Nagata, Fukue; Tomita, Masahiro; Kato, Katsuya

2016-10-01

Antibodies have received significant attention for use as antibody drugs, because they bind the objective protein (antigen) via antigen-antibody reactions. Recently, many reports have appeared on various monoclonal antibodies that recognize a single antigen. In this study, monoclonal antibodies are used as adsorbates on mesoporous silica (MPS) for affinity chromatography. MPS has high surface area and large pore volume; moreover, pore diameter, pore structure, and particle morphology are relatively easy to tune by adjusting the conditions of synthesis. The pore structure (two-dimensional (2D) hexagonal and three-dimensional cubic) and particle morphology (spherical and polyhedral) of MPS are optimized for use in a monoclonal antibody/MPS composite. When anti-IgG (one of the monoclonal antibodies) adsorbs on the MPS material and IgG (antigen) binds to anti-IgG/MPS composites, MCM-41p with a 2D-hexagonal pore structure and polyhedral particle morphology has the highest IgG binding efficiency. In addition, the antibody/MPS composites remain stable in chaotropic and low-pH solutions and can be cycled at least five times without decreasing IgG elution. In purification and removal tests, the use of the antibody/MPS composites allows only the objective protein from protein mixtures to be bound and eluted.

[Design and study of parallel computing environment of Monte Carlo simulation for particle therapy planning using a public cloud-computing infrastructure].

PubMed

Yokohama, Noriya

2013-07-01

This report was aimed at structuring the design of architectures and studying performance measurement of a parallel computing environment using a Monte Carlo simulation for particle therapy using a high performance computing (HPC) instance within a public cloud-computing infrastructure. Performance measurements showed an approximately 28 times faster speed than seen with single-thread architecture, combined with improved stability. A study of methods of optimizing the system operations also indicated lower cost.

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.

PubMed

Baird, Nathan J; Ludtke, Steven J; Khant, Htet; Chiu, Wah; Pan, Tao; Sosnick, Tobin R

2010-11-24

RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.

Single file diffusion into a semi-infinite tube.

PubMed

Farrell, Spencer G; Brown, Aidan I; Rutenberg, Andrew D

2015-11-23

We investigate single file diffusion (SFD) of large particles entering a semi-infinite tube, such as luminal diffusion of proteins into microtubules or flagella. While single-file effects have no impact on the evolution of particle density, we report significant single-file effects for individually tracked tracer particle motion. Both exact and approximate ordering statistics of particles entering semi-infinite tubes agree well with our stochastic simulations. Considering initially empty semi-infinite tubes, with particles entering at one end starting from an initial time t = 0, tracked particles are initially super-diffusive after entering the system, but asymptotically diffusive at later times. For finite time intervals, the ratio of the net displacement of individual single-file particles to the average displacement of untracked particles is reduced at early times and enhanced at later times. When each particle is numbered, from the first to enter (n = 1) to the most recent (n = N), we find good scaling collapse of this distance ratio for all n. Experimental techniques that track individual particles, or local groups of particles, such as photo-activation or photobleaching of fluorescently tagged proteins, should be able to observe these single-file effects. However, biological phenomena that depend on local concentration, such as flagellar extension or luminal enzymatic activity, should not exhibit single-file effects.

Glucose transporter distribution in the vessels of the central nervous system of the axolotl Ambystoma mexicanum (Urodela: Ambystomatidae).

PubMed

Lazzari, Maurizio; Bettini, Simone; Ciani, Franco; Franceschini, Valeria

2008-10-01

The GLUT-1 isoform of the glucose transporter is commonly considered a reliable molecular marker of blood-brain barrier endothelia in the neural vasculature organized in a three-dimensional network of single vessels. The central nervous system of the axolotl Ambystoma mexicanum is characterized by a vascular architecture that contains both single and paired vessels. The presence and distribution of the GLUT-1 transporter are studied in this urodele using both immunoperoxidase histochemistry and immunogold technique. Light microscopy reveals immunopositivity in both parenchymal and meningeal vessels. The transverse-sectioned pairs of vessels do not show the same size. Furthermore, in the same pair, the two elements often differ in diameter. The main regions of the central nervous system show a different percentage of the paired structures. Only immunogold cytochemistry reveals different staining intensity in the two adjoined elements of a vascular pair. Colloidal gold particles show an asymmetric distribution in the endothelia of both single and paired vessels. These particles are more numerous on the abluminal surface than on the luminal one. The particle density is calculated in both vascular types. The different values could indicate functional differences between single and paired vessels and between the two adjoined elements of a pair, regarding glucose transport.

Correlating capacity and Li content in layered material for Li-ion battery using XRD and particle size distribution measurements

NASA Astrophysics Data System (ADS)

Al-Tabbakh, A. A. A.; Al-Zubaidi, A. B.; Kamarulzaman, N.

2016-03-01

A lithiated transition-metal oxide material was successfully synthesized by a combustion method for Li-ion battery. The material was characterized using thermogravimetric and particle size analyzers, scanning electron microscope and X-ray diffractometer. The calcined powders of the material exhibited a finite size distribution and a single phase of pure layered structure of space group Roverline{3} m . An innovative method was developed to calculate the material electrochemical capacity based on considerations of the crystal structure and contributions of Li ions from specified unit cells at the surfaces and in the interiors of the material particles. Results suggested that most of the Li ions contributing to the electrochemical current originated from the surface region of the material particles. It was possible to estimate the thickness of the most delithiated region near the particle surfaces at any delithiation depth accurately. Furthermore, results suggested that the core region of the particles remained electrochemically inaccessible in the conventional applied voltages. This result was justified by direct quantitative comparison of specific capacity values calculated from the particle size distribution with those measured experimentally. The present analysis is believed to be of some value for estimation of the failure mechanism in cathode compounds, thus assisting the development of Li-ion batteries.

Microspectroscopic Analysis of Anthropogenic- and Biogenic-Influenced Aerosol Particles during the SOAS Field Campaign

NASA Astrophysics Data System (ADS)

Ault, A. P.; Bondy, A. L.; Nhliziyo, M. V.; Bertman, S. B.; Pratt, K.; Shepson, P. B.

2013-12-01

During the summer, the southeastern United States experiences a cooling haze due to the interaction of anthropogenic and biogenic aerosol sources. An objective of the summer 2013 Southern Oxidant and Aerosol Study (SOAS) was to improve our understanding of how trace gases and aerosols are contributing to this relative cooling through light scattering and absorption. To improve understanding of biogenic-anthropogenic interactions through secondary organic aerosol (SOA) formation on primary aerosol cores requires detailed physicochemical characterization of the particles after uptake and processing. Our measurements focus on single particle analysis of aerosols in the accumulation mode (300-1000 nm) collected using a multi orifice uniform deposition impactor (MOUDI) at the Centreville, Alabama SEARCH site. Particles were characterized using an array of microscopic and spectroscopic techniques, including: scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive X-ray analysis (EDX), and Raman microspectroscopy. These analyses provide detailed information on particle size, morphology, elemental composition, and functional groups. This information is combined with mapping capabilities to explore individual particle spatial patterns and how that impacts structural characteristics. The improved understanding will be used to explore how sources and processing (such as SOA coating of soot) change particle structure (i.e. core shell) and how the altered optical properties impact air quality/climate effects on a regional scale.

Mechanisms of Current Transfer in Electrodeposited Layers of Submicron Semiconductor Particles

NASA Astrophysics Data System (ADS)

Zhukov, N. D.; Mosiyash, D. S.; Sinev, I. V.; Khazanov, A. A.; Smirnov, A. V.; Lapshin, I. V.

2017-12-01

Current-voltage ( I- V) characteristics of conductance in multigrain layers of submicron particles of silicon, gallium arsenide, indium arsenide, and indium antimonide have been studied. Nanoparticles of all semiconductors were obtained by processing initial single crystals in a ball mill and applied after sedimentation onto substrates by means of electrodeposition. Detailed analysis of the I- V curves of electrodeposited layers shows that their behavior is determined by the mechanism of intergranular tunneling emission from near-surface electron states of submicron particles. Parameters of this emission process have been determined. The proposed multigrain semiconductor structures can be used in gas sensors, optical detectors, IR imagers, etc.

Rapid structural analysis of nanomaterials in aqueous solutions

NASA Astrophysics Data System (ADS)

Ryuzaki, Sou; Tsutsui, Makusu; He, Yuhui; Yokota, Kazumichi; Arima, Akihide; Morikawa, Takanori; Taniguchi, Masateru; Kawai, Tomoji

2017-04-01

Rapid structural analysis of nanoscale matter in a liquid environment represents innovative technologies that reveal the identities and functions of biologically important molecules. However, there is currently no method with high spatio-temporal resolution that can scan individual particles in solutions to gain structural information. Here we report the development of a nanopore platform realizing quantitative structural analysis for suspended nanomaterials in solutions with a high z-axis and xy-plane spatial resolution of 35.8 ± 1.1 and 12 nm, respectively. We used a low thickness-to-diameter aspect ratio pore architecture for achieving cross sectional areas of analyte (i.e. tomograms). Combining this with multiphysics simulation methods to translate ionic current data into tomograms, we demonstrated rapid structural analysis of single polystyrene (Pst) beads and single dumbbell-like Pst beads in aqueous solutions.

Colloidal heteroaggregation: a strategy to prepare composite materials

NASA Astrophysics Data System (ADS)

López-López, J. M.; Schmitt, A.; Moncho-Jordá, A.; Hidalgo-Álvarez, R.

2009-01-01

In this work, we make use of single-cluster light-scattering (SCLS) experiments and Brownian dynamics (BD) simulations in order to investigate the formation of binary clusters of oppositely-charged colloidal particles by heteroaggregation processes. Two parameters determinate the stability, size and structure of the clusters: the relative concentration of both species x and the range of the particle-particle interactions κa. SCLS experiments reveal that stable binary clusters arise in asymmetric systems when particle-particle interactions are long-ranged. These stable aggregates group in bell-shaped distributions that correspond to compact clusters with different orders, i.e., with a given number of minority particles. It is found that x controls the distribution of the clusters among the different orders and κa determine the average size of the clusters belonging to each order. Finally, BD simulations allow us to interpret all these results within the the frame of the classic Hogg-Healy-Fuersternau theory.

Patchy Particles of Block Copolymers from Interface-Engineered Emulsions

NASA Astrophysics Data System (ADS)

Ku, Kang Hee; Kim, Yongjoo; Yi, Gi-Ra; Jung, Yeon Sik; Kim, Bumjoon

A simple method for creating soft patchy particles with a variety of three-dimensional shapes has been developed through the evaporation-induced assembly of polystyrene-b-poly(4-vinylpyridine) (PS-b-P4VP) block copolymer (BCP) in an oil-in-water emulsion. Depending on the particle volume, a series of patchy particles in the shapes of snowmen, dumbbells, triangles, tetrahedra, and raspberry can be prepared, which are then precisely tuned by modulating the interfacial interaction at the particle/water interface using a mixture of two different surfactants. Moreover, for a given interfacial interaction, the stretching penalty of the BCPs in the patchy particles can be systematically controlled by adding P4VP homopolymers, which decreases the number of patches of soft particles from multiple patches to a single patch but increases the size of the patch. Calculations based on the strong segregation theory supported the experimental observation of various soft patchy particles and identified the underlying principles of their formation with tunable 3D structures.

The Rapid Distortion of Two-Way Coupled Particle-Laden Turbulence

NASA Astrophysics Data System (ADS)

Kasbaoui, Mohamed; Koch, Donald; Desjardins, Olivier

2017-11-01

The modulation of sheared turbulence by dispersed particles is addressed in the two-way coupling regime. The preferential sampling of the straining regions of the flow by inertial particles in turbulence leads to the formation of clusters. These fast sedimenting particle structures cause the anisotropic alteration of turbulence at small scales in the direction of gravity. These effects are investigated in a revisited Rapid Distortion Theory (RDT), extended for two-way coupled particle-laden flows. To make the analysis tractable, we assume that particles have small but non-zero inertia. In the classical results for single-phase flows, the RDT assumption of fast shearing compared to the turbulence time scales leads to the distortion of ``frozen'' turbulence. In particle-laden turbulence, the coupling between the two phases remains strong even under fast shearing and leads to a dynamic modulation of the turbulence spectrum. Turbulence statistics obtained from RDT are compared with Euler-Lagrange simulations of homogeneously sheared particle-laden turbulence.

Optoelectronic tweezers for microparticle and cell manipulation

NASA Technical Reports Server (NTRS)

Wu, Ming Chiang (Inventor); Chiou, Pei Yu (Inventor); Ohta, Aaron T. (Inventor)

2009-01-01

An optical image-driven light induced dielectrophoresis (DEP) apparatus and method are described which provide for the manipulation of particles or cells with a diameter on the order of 100 .mu.m or less. The apparatus is referred to as optoelectric tweezers (OET) and provides a number of advantages over conventional optical tweezers, in particular the ability to perform operations in parallel and over a large area without damage to living cells. The OET device generally comprises a planar liquid-filled structure having one or more portions which are photoconductive to convert incoming light to a change in the electric field pattern. The light patterns are dynamically generated to provide a number of manipulation structures that can manipulate single particles and cells or groups of particles/cells. The OET preferably includes a microscopic imaging means to provide feedback for the optical manipulation, such as detecting position and characteristics wherein the light patterns are modulated accordingly.

Optoelectronic Tweezers for Microparticle and Cell Manipulation

NASA Technical Reports Server (NTRS)

Wu, Ming Chiang (Inventor); Chiou, Pei-Yu (Inventor); Ohta, Aaron T. (Inventor)

2014-01-01

An optical image-driven light induced dielectrophoresis (DEP) apparatus and method are described which provide for the manipulation of particles or cells with a diameter on the order of 100 micromillimeters or less. The apparatus is referred to as optoelectric tweezers (OET) and provides a number of advantages over conventional optical tweezers, in particular the ability to perform operations in parallel and over a large area without damage to living cells. The OET device generally comprises a planar liquid-filled structure having one or more portions which are photoconductive to convert incoming light to a change in the electric field pattern. The light patterns are dynamically generated to provide a number of manipulation structures that can manipulate single particles and cells or group of particles/cells. The OET preferably includes a microscopic imaging means to provide feedback for the optical manipulation, such as detecting position and characteristics wherein the light patterns are modulated accordingly.

Microgels: Structure, Dynamics, and Possible Applications.

NASA Astrophysics Data System (ADS)

McKenna, John; Streletzky, Kiril

2007-03-01

We cross-linked Hydropxypropylcellulose (HPC) polymer chains to produce microgel nanoparticles and studied their structure and dynamics using Dynamic Light Scattering spectroscopy. The complex nature of the fluid and large size distribution of the particles renders typical characterization algorithm CONTIN ineffective and inconsistent. Instead, the particles spectra have been fit to a sum of stretched exponentials. Each term offers three parameters for analysis and represents a single mode. The results of this analysis show that the microgels undergo a transition to a fewer modes around 41C. The CONTIN size distribution analysis shows similar results, but these come with much less consistency and resolution. Our experiments prove that microgel particles shrink under volume phase transition. The shrinkage is reversible and depends on the amount of cross-linker, salt and polymer concentrations and rate of heating. Reversibility of microgel volume phase transition property might be particularly useful for a controlled drug delivery and release.

Time Crystal Platform: From Quasicrystal Structures in Time to Systems with Exotic Interactions.

PubMed

Giergiel, Krzysztof; Miroszewski, Artur; Sacha, Krzysztof

2018-04-06

Time crystals are quantum many-body systems that, due to interactions between particles, are able to spontaneously self-organize their motion in a periodic way in time by analogy with the formation of crystalline structures in space in condensed matter physics. In solid state physics properties of space crystals are often investigated with the help of external potentials that are spatially periodic and reflect various crystalline structures. A similar approach can be applied for time crystals, as periodically driven systems constitute counterparts of spatially periodic systems, but in the time domain. Here we show that condensed matter problems ranging from single particles in potentials of quasicrystal structure to many-body systems with exotic long-range interactions can be realized in the time domain with an appropriate periodic driving. Moreover, it is possible to create molecules where atoms are bound together due to destructive interference if the atomic scattering length is modulated in time.

Time Crystal Platform: From Quasicrystal Structures in Time to Systems with Exotic Interactions

NASA Astrophysics Data System (ADS)

Giergiel, Krzysztof; Miroszewski, Artur; Sacha, Krzysztof

2018-04-01

Time crystals are quantum many-body systems that, due to interactions between particles, are able to spontaneously self-organize their motion in a periodic way in time by analogy with the formation of crystalline structures in space in condensed matter physics. In solid state physics properties of space crystals are often investigated with the help of external potentials that are spatially periodic and reflect various crystalline structures. A similar approach can be applied for time crystals, as periodically driven systems constitute counterparts of spatially periodic systems, but in the time domain. Here we show that condensed matter problems ranging from single particles in potentials of quasicrystal structure to many-body systems with exotic long-range interactions can be realized in the time domain with an appropriate periodic driving. Moreover, it is possible to create molecules where atoms are bound together due to destructive interference if the atomic scattering length is modulated in time.

A data set from flash X-ray imaging of carboxysomes

NASA Astrophysics Data System (ADS)

Hantke, Max F.; Hasse, Dirk; Ekeberg, Tomas; John, Katja; Svenda, Martin; Loh, Duane; Martin, Andrew V.; Timneanu, Nicusor; Larsson, Daniel S. D.; van der Schot, Gijs; Carlsson, Gunilla H.; Ingelman, Margareta; Andreasson, Jakob; Westphal, Daniel; Iwan, Bianca; Uetrecht, Charlotte; Bielecki, Johan; Liang, Mengning; Stellato, Francesco; Deponte, Daniel P.; Bari, Sadia; Hartmann, Robert; Kimmel, Nils; Kirian, Richard A.; Seibert, M. Marvin; Mühlig, Kerstin; Schorb, Sebastian; Ferguson, Ken; Bostedt, Christoph; Carron, Sebastian; Bozek, John D.; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Epp, Sascha W.; Chapman, Henry N.; Barty, Anton; Andersson, Inger; Hajdu, Janos; Maia, Filipe R. N. C.

2016-08-01

Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

How good can cryo-EM become?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glaeser, Robert M.

The suddenness with which single-particle cryo-electron microscopy (cryo-EM) has emerged as a method for determining high-resolution structures of biological macromolecules invites the questions, how much better can this technology get, and how fast is that likely to happen? While we can rightly celebrate the maturation of cryo-EM as a high-resolution structure-determination tool, I believe there still are many developments to look forward to.

Single particle electrochemical sensors and methods of utilization

DOEpatents

Schoeniger, Joseph [Oakland, CA; Flounders, Albert W [Berkeley, CA; Hughes, Robert C [Albuquerque, NM; Ricco, Antonio J [Los Gatos, CA; Wally, Karl [Lafayette, CA; Kravitz, Stanley H [Placitas, NM; Janek, Richard P [Oakland, CA

2006-04-04

The present invention discloses an electrochemical device for detecting single particles, and methods for using such a device to achieve high sensitivity for detecting particles such as bacteria, viruses, aggregates, immuno-complexes, molecules, or ionic species. The device provides for affinity-based electrochemical detection of particles with single-particle sensitivity. The disclosed device and methods are based on microelectrodes with surface-attached, affinity ligands (e.g., antibodies, combinatorial peptides, glycolipids) that bind selectively to some target particle species. The electrodes electrolyze chemical species present in the particle-containing solution, and particle interaction with a sensor element modulates its electrolytic activity. The devices may be used individually, employed as sensors, used in arrays for a single specific type of particle or for a range of particle types, or configured into arrays of sensors having both these attributes.

Experimental Study of Acid Treatment Toward Characterization of Structural, Optical, and Morphological Properties of TiO2-SnO2 Composite Thin Film

NASA Astrophysics Data System (ADS)

Fajar, M. N.; Hidayat, R.; Triwikantoro; Endarko

2018-04-01

The TiO2-SnO2 thin film with single and double-layer structure has successfully synthesized on FTO (Fluorine-doped Tin Oxide) substrate using the screen printing technique. The structural, optical, and morphological properties of the film were investigated by XRD, UV-Vis, and SEM, respectively. The results showed that the single and double-layer structure of TiO2-SnO2 thin film has mixed phase with a strong formation of casseritte phase. The acid treatment effect on TiO2-SnO2 thin film decreases the peak intensity of anatase phase formation and thin film’s absorbance values. The morphological study is also revealed that the single layer TiO2-SnO2 thin film had a more porous nature and decreased particle size distribution after acid treatment, while the double-layer TiO2-SnO2 thin film Eroded due to acid treatment.

Applications of a global nuclear-structure model to studies of the heaviest elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moeller, P.; Nix, J.R.

1993-10-01

We present some new results on heavy-element nuclear-structure properties calculated on the basis of the finite-range droplet model and folded-Yukawa single-particle potential. Specifically, we discuss calculations of nuclear ground-state masses and microscopic corrections, {alpha}-decay properties, {beta}-decay properties, fission potential-energy surfaces, and spontaneous-fission half-lives. These results, obtained in a global nuclear-structure approach, are particularly reliable for describing the stability properties of the heaviest elements.

The synthesis of Ba2+ doped multiferroic BiFeO3 nanoparticles by using a hydrothermal approach in the presence of different surface activators and the investigation of structural and magnetic features

NASA Astrophysics Data System (ADS)

Mardani, Reza

2017-05-01

In this work, Bi1-x Ba x FeO3 nanoparticles were synthesized by a hydrothermal method in the presence of various surface activators, and different amounts of barium were inserted in a bismuth ferrite (x  =  0.1, 0.15, 0.2) structure instead of bismuth. The structural and magnetic properties, morphology, and size of the synthesized nanoparticles were investigated by XRD, FT-IR, FE-SEM, TEM, DLS and VSM. The XRD analysis results reveal that the synthetic nanoparticles have a single phase. A phase shift from a rhombohedral structure to a tetragonal structure occurs due to the enhanced barium amount in the bismuth ferrite structure. The SEM analysis exhibits a uniform shape of the Bi0.85Ba0.15FeO3 particles and the image observed by TEM clarifies the size of the particles as 11 nm. Furthermore, the effect of the diverse surfaces of activators in the synthesis of Bi0.85Ba0.15FeO3 nanoparticles was studied, revealing that when sugar was used as a surfactant, the particle size reduced and the magnetic properties increased notably.

Structure and magnetic properties of Nd2Fe14B fine particles produced by spark erosion

NASA Astrophysics Data System (ADS)

Wan, H.; Berkowitz, A. E.

1994-11-01

At present Nd2Fe14B is the best permanent magnet because of its extremely high coercivity and energy product. Optimum properties of Nd2Fe14B magnets can be attained by producing single domain particles, and then aligning and compacting them. Due to the reactivity of the Nd constitutent, it is challenging to produce and handle a large amount of fine particles of this material. We have prepared fine particles of Nd2Fe14B by spark erosion with various dielectric media. Yield, size, size distribution, structure, and magnetic properties are discussed. The Nd2Fe14B particles were made by the sharker pot spark erosion method. Relaxation oscillators or a pulse generator were used to power the park erosion. Commercial Neomax 35 was employed as the primary material. The dielectric media were liquid Ar, Ar gas, and hydrocarbons, which provided an oxygen free environment. Structure and size were studied by transmission electron microscopy (TEM), scanning electron microscopy (SEM), and x-ray diffraction. Magnetic properties were measured by vibrating sample magnetometer (VSM) with temperatures in range of 4.2-1200 K. The particles produced in these three different dielectric media had different microstructures and crystal structures. The particles made in Ar gas were pure Nd2Fe14B phase. The particles made in liquid Ar were a mixture of amorphous and crystalline Nd2Fe14B, because the liquid Ar provided a much higher quench rate than Ar gas, which produced some amorphous Nd2Fe14B. Upon annealing, the amorphous particles became crystalline. The fine particles produced in hydrocarbons, such as pentane and dodecane, had more complex mixed phases, since the rare earth reacted with the hydrocarbons during the sparking process. The phases were NdC2, alpha-Fe, and amorphous and crystalline Nd2Fe14B. The effects of power parameters, such as voltage and capacitance, on particle size were investigated. Particle sizes from 20 nm to 50 microns were obtained.

Physical chemistry of Nanogap-Enhanced Raman Scattering (NERS)

NASA Astrophysics Data System (ADS)

Suh, Yung Doug; Kim, Hyun Woo

2017-08-01

Plasmonically coupled electromagnetic field localization has generated a variety of new concepts and applications, and this has been one of the hottest topics in nanoscience, materials science, chemistry, physics and engineering and increasingly more important over the last decade. In particular, plasmonically coupled nanostructures with ultra-small gap ( 1-nm or smaller) gap have been of special interest due to their ultra-strong optical properties that can be useful for a variety of signal enhancements such surface-enhanced Raman scattering (SERS) and nanoantenna. These promising nanostructures with extraordinarily strong optical signal, however, have rendered a limited success in widespread use and commercialization largely due to the lack of designing principles, high-yield synthetic strategies with nm-level structural controllability and reproducibility and lack of systematic single-molecule and single-particle level studies. All these are extremely important challenges because even small changes ( 1 nm) of the coupled nanogap structures can significant affect plasmon mode and signal intensity and therefore structural and signal reproducibility and controllability can be in question. The plasmonic nanogap-enhanced Raman scattering (NERS) is defined as the plasmonic nanogap-based Raman signal enhancement within plasmonic nanogap particles with 1 nm gap and a Raman dye positioned inside the gap.

Synthesis, Optical and Structural Properties of Copper Sulfide Nanocrystals from Single Molecule Precursors

PubMed Central

Ajibade, Peter A.; Botha, Nandipha L.

2017-01-01

We report the synthesis and structural studies of copper sulfide nanocrystals from copper (II) dithiocarbamate single molecule precursors. The precursors were thermolysed in hexadecylamine (HDA) to prepare HDA-capped CuS nanocrystals. The optical properties of the nanocrystals studied using UV–visible and photoluminescence spectroscopy showed absorption band edges at 287 nm that are blue shifted, and the photoluminescence spectra show emission curves that are red-shifted with respect to the absorption band edges. These shifts are as a result of the small crystallite sizes of the nanoparticles leading to quantum size effects. The structural studies were carried out using powder X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), and atomic force microscopy. The XRD patterns indicates that the CuS nanocrystals are in hexagonal covellite crystalline phases with estimated particles sizes of 17.3–18.6 nm. The TEM images showed particles with almost spherical or rod shapes, with average crystallite sizes of 3–9.8 nm. SEM images showed morphology with ball-like microspheres on the surfaces, and EDS spectra confirmed the presence of CuS nanoparticles. PMID:28336865

Characterization of aerosols containing Zn, Pb, and Cl from an industrial region of Mexico City.

PubMed

Moffet, Ryan C; Desyaterik, Yury; Hopkins, Rebecca J; Tivanski, Alexei V; Gilles, Mary K; Wang, Y; Shutthanandan, V; Molina, Luisa T; Abraham, Rodrigo Gonzalez; Johnson, Kirsten S; Mugica, Violeta; Molina, Mario J; Laskin, Alexander; Prather, Kimberly A

2008-10-01

Recent ice core measurements show lead concentrations increasing since 1970, suggesting new nonautomobile-related sources of Pb are becoming important worldwide (1). Developing a full understanding of the major sources of Pb and other metals is critical to controlling these emissions. During the March, 2006 MILAGRO campaign, single particle measurements in Mexico City revealed the frequent appearance of particles internally mixed with Zn, Pb, Cl, and P. Pb concentrations were as high as 1.14 microg/m3 in PM10 and 0.76 microg/m3 in PM2.5. Real time measurements were used to select time periods of interest to perform offline analysis to obtain detailed aerosol speciation. Many Zn-rich particles had needle-like structures and were found to be composed of ZnO and/or Zn(NO3)2 x 6H2O. The internally mixed Pb-Zn-Cl particles represented as much as 73% of the fine mode particles (by number) in the morning hours between 2-5 am. The Pb-Zn-Cl particles were primarily in the submicrometer size range and typically mixed with elemental carbon suggesting a combustion source. The unique single particle chemical associations measured in this study closely match signatures indicative of waste incineration. Our findings also show these industrial emissions play an important role in heterogeneous processing of NO(y) species. Primary emissions of metal and sodium chloride particles emitted by the same source underwent heterogeneous transformations into nitrate particles as soon as photochemical production of nitric acid began each day at approximately 7 am.

Transitions in eigenvalue and wavefunction structure in (1+2) -body random matrix ensembles with spin.

PubMed

Vyas, Manan; Kota, V K B; Chavda, N D

2010-03-01

Finite interacting Fermi systems with a mean-field and a chaos generating two-body interaction are modeled by one plus two-body embedded Gaussian orthogonal ensemble of random matrices with spin degree of freedom [called EGOE(1+2)-s]. Numerical calculations are used to demonstrate that, as lambda , the strength of the interaction (measured in the units of the average spacing of the single-particle levels defining the mean-field), increases, generically there is Poisson to GOE transition in level fluctuations, Breit-Wigner to Gaussian transition in strength functions (also called local density of states) and also a duality region where information entropy will be the same in both the mean-field and interaction defined basis. Spin dependence of the transition points lambda_{c} , lambdaF, and lambdad , respectively, is described using the propagator for the spectral variances and the formula for the propagator is derived. We further establish that the duality region corresponds to a region of thermalization. For this purpose we compared the single-particle entropy defined by the occupancies of the single-particle orbitals with thermodynamic entropy and information entropy for various lambda values and they are very close to each other at lambda=lambdad.

Single-particle studies of band alignment effects on electron transfer dynamics from semiconductor hetero-nanostructures to single-walled carbon nanotubes.

PubMed

Yuan, Chi-Tsu; Wang, Yong-Gang; Huang, Kuo-Yen; Chen, Ting-Yu; Yu, Pyng; Tang, Jau; Sitt, Amit; Banin, Uri; Millo, Oded

2012-01-24

We utilize single-molecule spectroscopy combined with time-correlated single-photon counting to probe the electron transfer (ET) rates from various types of semiconductor hetero-nanocrystals, having either type-I or type-II band alignment, to single-walled carbon nanotubes. A significantly larger ET rate was observed for type-II ZnSe/CdS dot-in-rod nanostructures as compared to type-I spherical CdSe/ZnS core/shell quantum dots and to CdSe/CdS dot-in-rod structures. Furthermore, such rapid ET dynamics can compete with both Auger and radiative recombination processes, with significance for effective photovoltaic operation. © 2011 American Chemical Society

Complex refractive index of Martian dust - Wavelength dependence and composition

NASA Technical Reports Server (NTRS)

Pang, K.; Ajello, J. M.

1977-01-01

The size distribution and complex refractive index of Martian dust-cloud particles observed in 1971 with the Mariner 9 UV spectrometer are determined by matching the observed single-scattering albedo and phase function with Mie-scattering calculations for size distributions of spheres. Values of phase function times single-scattering albedo are presented for 12 wavelength intervals in the range from 190 to 350 nm, and best-fit values are obtained for the absorption index. It is found that the absorption index of the dust particles increases with decreasing wavelength from 350 to about 210 nm and then drops off shortward of 210 nm, with a structural shoulder occurring in the absorption spectrum between 240 and 250 nm. A search for a candidate material that can explain the strong UV absorption yields TiO2, whose anatase polymorph has an absorption spectrum matching that of the Martian dust. The TiO2 content of the dust particles is estimated to be a few percent or less.

Formation and structure of stable aggregates in binary diffusion-limited cluster-cluster aggregation processes

NASA Astrophysics Data System (ADS)

López-López, J. M.; Moncho-Jordá, A.; Schmitt, A.; Hidalgo-Álvarez, R.

2005-09-01

Binary diffusion-limited cluster-cluster aggregation processes are studied as a function of the relative concentration of the two species. Both, short and long time behaviors are investigated by means of three-dimensional off-lattice Brownian Dynamics simulations. At short aggregation times, the validity of the Hogg-Healy-Fuerstenau approximation is shown. At long times, a single large cluster containing all initial particles is found to be formed when the relative concentration of the minority particles lies above a critical value. Below that value, stable aggregates remain in the system. These stable aggregates are composed by a few minority particles that are highly covered by majority ones. Our off-lattice simulations reveal a value of approximately 0.15 for the critical relative concentration. A qualitative explanation scheme for the formation and growth of the stable aggregates is developed. The simulations also explain the phenomenon of monomer discrimination that was observed recently in single cluster light scattering experiments.

Single and double multiphoton ionization of Li and Be atoms by strong laser fields

NASA Astrophysics Data System (ADS)

Telnov, Dmitry; Heslar, John; Chu, Shih-I.

2011-05-01

The time-dependent density functional theory with self-interaction correction and proper asymptotic long-range potential is extended for nonperturbative treatment of multiphoton single and double ionization of Li and Be atoms by strong 800 nm laser fields. We make use of the time-dependent Krieger-Li-Iafrate (TDKLI) exchange-correlation potential with the integer discontinuity which improves the description of the double ionization process. However, we have found that the discontinuity of the TDKLI potential is not sufficient to reproduce the characteristic feature of double ionization. This may happen because the discontinuity of the TDKLI potential is related to the spin particle numbers only and not to the total particle number. Introducing a discontinuity with respect to the total particle number to the exchange-correlation potential, we were able to obtain the knee structure in the intensity dependence of the double ionization probability of Be. This work was partially supported by DOE and NSF and by NSC-Taiwan.

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

DOE PAGES

Chen, F. -R.; Van Dyck, D.; Kisielowski, C.

2016-02-18

We report that resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we show a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose ratemore » electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. Lastly, we apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances.« less

Gamma-ray spectroscopy of 131Sn81 via the (9Be, 8Be γ) reaction

NASA Astrophysics Data System (ADS)

Burcher, Sean; Bey, A.; Jones, K.; Ahn, S. H.; Ayres, A.; Schmitt, K. T.; Allmond, J.; Galindo-Urribari, A.; Radford, D. C.; Liang, J. F.; Neseraja, C. D.; Pain, S. D.; Pittman, S. T.; Smith, M. S.; Stracener, D. W.; Varner, R. L.; Bardayan, D. W.; O'Malley, P. D.; Cizewski, J. A.; Howard, M. E.; Manning, B. M.; Garcia Ruiz, R. F.; Kozub, R. L.; Matos, M.; Padilla-Rodal, E.

2016-09-01

Nuclear data in the region of the doubly-magic nucleus 132Sn82 is useful for benchmarking nuclear structure theories due to the clean single-particle nature of the nuclear wavefunction near the closed shells. At the Holifield Radioactive Ion Beam Facility (HRIBF) neutron-rich beams in the 132Sn82 region were produced via proton-induced fission of a Uranium-Carbide target. The CLARION array of HPGe detectors was coupled with the HyBall array of CsI detectors to allow for particle-gamma coincidence measurements. The gamma-ray de-excitation of the four lowest lying single-neutron states has been observed for the first time via the (9Be,8Be γ) reaction. The excitation energy of these states have been measured to higher precision than was possible with the previous charged particle measurement. This work was supported in part by the U.S. Department of Energy and the National Science Foundation.

Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic)

NASA Astrophysics Data System (ADS)

Ortega-Retuerta, E.; Joux, F.; Jeffrey, W. H.; Ghiglione, J.-F.

2012-12-01

We explored the patterns of total and active bacterial community structure in a gradient covering surface waters from the Mackenzie River to the coastal Beaufort Sea, Canadian Arctic Ocean, with a particular focus on free-living vs. particle-attached communities. Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) showed significant differences when comparing river, coast and open sea bacterial community structures. In contrast to the river and coastal waters, total (16S rDNA-based) and active (16S rRNA-based) communities in the open sea samples were not significantly different, suggesting that most present bacterial groups were equally active in this area. Additionally, we observed significant differences between particle-attached (PA) and free-living (FL) bacterial communities in the open sea, but similar structure in the two fractions for coastal and river samples. Direct multivariate statistical analyses showed that total community structure was mainly driven by salinity (proxy of DOC and CDOM), suspended particles, amino acids and chlorophyll a. 16S rRNA genes pyrosequencing of selected samples confirmed these significant differences from river to sea and also between PA and FL fractions only in open sea samples, and PA samples generally showed higher diversity (Shannon, Simpson and Chao indices) than FL samples. At the class level, Opitutae was most abundant in the PA fraction of the sea sample, followed by Flavobacteria and Gammaproteobacteria, while the FL sea sample was dominated by Alphaproteobacteria. Finally, the coast and river samples, both PA and FL fractions, were dominated by Betaproteobacteria, Alphaproteobacteria and Actinobacteria. These results highlight the coexistence of particle specialists and generalists and the role of particle quality in structuring bacterial communities in the area. These results may also serve as a~basis to predict further changes in bacterial communities should climate change lead to further increases in river discharge and related particles load.

Influence of neighboring particles on the drag of a particle suspended in laminar flows

NASA Astrophysics Data System (ADS)

Roig, Adam Vincent

Understanding particle-fluid flows is very important for the areas of sedimentation in river beds, fluidized bed reactors, and other fields of multiphase flow. The effect of one particle on another in a fluid flow is not very well understood nor does a correlation exist to describe the behavior of the drag coefficient between particles. The use of Proteus was validated by comparison to previous studies to the result obtained through simulations in Proteus, including analysis of the wake structure of a single sphere. Two particles were then analyzed for various Reynolds numbers less than 250 but greater than 5 and for the dimensionless gap of L/D ≥ 2, where L is the distance between the two particle centers and D is the diameter of the particles. Two arrangements were used for simulation, with the particles spaced horizontally or vertically within the fluid flow. Both orientations were evaluated for the effects of the dimensionless gap on the drag coefficient. The wake structure at higher Reynolds numbers were also evaluated for effects due to neighboring particles. A correlation was developed for the case of the horizontal particles at a dimensionless gap, L/D ≥ 2 for the range of Reynolds numbers described. The orientation effect is then studied at a fixed distance for offsets of thirty, forty-five and sixty degrees from the horizontal. Results are also presented to evaluate the effect of the diameter of a neighboring particle. The current results are restricted to the case described in the work. Future studies may build on the current work to extend the work to other effects of neighboring particles and multiple particle influence.

Acetate- and thiol-capped monodisperse ruthenium nanoparticles: XPS, XAS, and HRTEM studies.

PubMed

Chakroune, Nassira; Viau, Guillaume; Ammar, Souad; Poul, Laurence; Veautier, Delphine; Chehimi, Mohamed M; Mangeney, Claire; Villain, Françoise; Fiévet, Fernand

2005-07-19

Monodisperse ruthenium nanoparticles were prepared by reduction of RuCl3 in 1,2-propanediol. The mean particle size was controlled by appropriate choice of the reduction temperature and the acetate ion concentration. Colloidal solutions in toluene were obtained by coating the metal particles with dodecanethiol. High-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), and X-ray absorption spectroscopy (XANES and EXAFS for the Ru K-absorption edge) were performed on particles of two different diameters, 2 and 4 nm, and in different environments, polyol/acetate or thiol. For particles stored in polyol/acetate XPS studies revealed superficial oxidation limited to one monolayer and a surface coating containing mostly acetate ions. Analysis of the EXAFS spectra showed both oxygen and ruthenium atoms around the ruthenium atoms with a Ru-Ru coordination number N smaller than the bulk value, as expected for fine particles. In the case of 2 nm acetate-capped particles N is consistent with particles made up of a metallic core and an oxidized monolayer. For 2 nm thiol-coated particles, a Ru-S bond was evidenced by XPS and XAS. For the 4 nm particles XANES and XPS studies showed that most of the ruthenium atoms are in the zerovalent state. Nevertheless, in both cases, when capped with thiol, the Ru-Ru coordination number inferred from EXAFS is much smaller than for particles of the same size stored in polyol. This is attributed to a structural disorganization of the particles by thiol chemisorption. HRTEM studies confirm the marked dependence of the structural properties of the ruthenium particles on their chemical environment; they show the acetate-coated particles to be single crystals, whereas the thiol-coated particles appear to be polycrystalline.

The influence of different processing stages on particle size, microstructure, and appearance of dark chocolate.

PubMed

Glicerina, Virginia; Balestra, Federica; Dalla Rosa, Marco; Bergenhstål, Bjorn; Tornberg, Eva; Romani, Santina

2014-07-01

The effect of different process stages on microstructural and visual properties of dark chocolate was studied. Samples were obtained at each phase of the manufacture process: mixing, prerefining, refining, conching, and tempering. A laser light diffraction technique and environmental scanning electron microscopy (ESEM) were used to study the particle size distribution (PSD) and to analyze modifications in the network structure. Moreover, colorimetric analyses (L*, h°, and C*) were performed on all samples. Each stage influenced in stronger way the microstructural characteristic of products and above all the PSD. Sauter diameter (D [3.2]) decreased from 5.44 μm of mixed chocolate sample to 3.83 μm, of the refined one. ESEM analysis also revealed wide variations in the network structure of samples during the process, with an increase of the aggregation and contact point between particles from mixing to refining stage. Samples obtained from the conching and tempering were characterized by small PS, and a less dense aggregate structure. From color results, samples with the finest particles, having larger specific surface area and the smallest diameter, appeared lighter and more saturated than those with coarse particles. Final quality of food dispersions is affected by network and particles characteristics. The deep knowledge of the influence of single processing stage on chocolate microstructural properties is useful in order to improve or modify final product characteristics. ESEM and laser diffraction are suitable techniques to study changes in chocolate microstructure. © 2014 Institute of Food Technologists®

Single-wall nanohorn structure and distribution of incorporated materials

NASA Astrophysics Data System (ADS)

Maigne, Alan; Gloter, Alexandre; Ajima, Kumiko; Colliex, Christian; Iijima, Sumio

2005-03-01

Single-wall carbon nanohorns (SWNHs) are unique spherical-aggregates of single-wall carbon quasi-nanotubes. So far, the observable area has been limited to the aggregate surfaces. We studied core-region structure with TEM using thickness measurement method, EELS, and EDS, and found that carbon density was uniform over the whole aggregate. This result allows to modelize the core-region and to clarify previous models of SWNHs. We used same tools to investigate the incorporation of materials such as fullerenes or platinium compounds. We found that particles can even be incorporated in the core-region and that their distribution in the aggregate depends on their concentration. The information available with these models should be useful in the study of SWNH applications to, for example, drug delivery system.

A parallel direct-forcing fictitious domain method for simulating microswimmers

NASA Astrophysics Data System (ADS)

Gao, Tong; Lin, Zhaowu

2017-11-01

We present a 3D parallel direct-forcing fictitious domain method for simulating swimming micro-organisms at small Reynolds numbers. We treat the motile micro-swimmers as spherical rigid particles using the ``Squirmer'' model. The particle dynamics are solved on the moving Larangian meshes that overlay upon a fixed Eulerian mesh for solving the fluid motion, and the momentum exchange between the two phases is resolved by distributing pseudo body-forces over the particle interior regions which constrain the background fictitious fluids to follow the particle movement. While the solid and fluid subproblems are solved separately, no inner-iterations are required to enforce numerical convergence. We demonstrate the accuracy and robustness of the method by comparing our results with the existing analytical and numerical studies for various cases of single particle dynamics and particle-particle interactions. We also perform a series of numerical explorations to obtain statistical and rheological measurements to characterize the dynamics and structures of Squirmer suspensions. NSF DMS 1619960.

Particle Deposition in Human Lungs due to Varying Cross-Sectional Ellipticity of Left and Right Main Bronchi

NASA Astrophysics Data System (ADS)

Roth, Steven; Oakes, Jessica; Shadden, Shawn

2015-11-01

Particle deposition in the human lungs can occur with every breathe. Airbourne particles can range from toxic constituents (e.g. tobacco smoke and air pollution) to aerosolized particles designed for drug treatment (e.g. insulin to treat diabetes). The effect of various realistic airway geometries on complex flow structures, and thus particle deposition sites, has yet to be extensively investigated using computational fluid dynamics (CFD). In this work, we created an image-based geometric airway model of the human lung and performed CFD simulations by employing multi-domain methods. Following the flow simulations, Lagrangian particle tracking was used to study the effect of cross-sectional shape on deposition sites in the conducting airways. From a single human lung model, the cross-sectional ellipticity (the ratio of major and minor diameters) of the left and right main bronchi was varied systematically from 2:1 to 1:1. The influence of the airway ellipticity on the surrounding flow field and particle deposition was determined.

A novel sheet-like virus particle array is a hallmark of Zika virus infection.

PubMed

Liu, Jun; Kline, Brandon A; Kenny, Tara A; Smith, Darci R; Soloveva, Veronica; Beitzel, Brett; Pang, Song; Lockett, Stephen; Hess, Harald F; Palacios, Gustavo; Kuhn, Jens H; Sun, Mei G; Zeng, Xiankun

2018-04-25

Zika virus (ZIKV) is an emerging flavivirus that caused thousands of human infections in recent years. Compared to other human flaviviruses, ZIKV replication is not well understood. Using fluorescent, transmission electron, and focused ion beam-scanning electron microscopy, we examined ZIKV replication dynamics in Vero 76 cells and in the brains of infected laboratory mice. We observed the progressive development of a perinuclear flaviviral replication factory both in vitro and in vivo. In vitro, we illustrated the ZIKV lifecycle from particle cell entry to egress. ZIKV particles assembled and aggregated in an induced convoluted membrane structure and ZIKV strain-specific membranous vesicles. While most mature virus particles egressed via membrane budding, some particles also likely trafficked through late endosomes and egressed through membrane abscission. Interestingly, we consistently observed a novel sheet-like virus particle array consisting of a single layer of ZIKV particles. Our study further defines ZIKV replication and identifies a novel hallmark of ZIKV infection.

Aggregation in particle rich environments: a textural study of examples from volcanic eruptions, meteorite impacts, and fluidized bed processing

NASA Astrophysics Data System (ADS)

Mueller, Sebastian B.; Kueppers, Ulrich; Huber, Matthew S.; Hess, Kai-Uwe; Poesges, Gisela; Ruthensteiner, Bernhard; Dingwell, Donald B.

2018-04-01

Aggregation is a common process occurring in many diverse particulate gas mixtures (e.g. those derived from explosive volcanic eruptions, meteorite impact events, and fluid bed processing). It results from the collision and sticking of particles suspended in turbulent gas/air. To date, there is no generalized model of the underlying physical processes. Here, we investigate aggregates from 18 natural deposits (16 volcanic deposits and two meteorite impact deposits) as well as aggregates produced experimentally via fluidized bed techniques. All aggregates were analyzed for their size, internal structuring, and constituent particle size distribution. Commonalities and differences between the aggregate types are then used to infer salient features of the aggregation process. Average core to rim ratios of internally structured aggregates (accretionary lapilli) is found to be similar for artificial and volcanic aggregates but up to an order of magnitude different than impact-related aggregates. Rim structures of artificial and volcanic aggregates appear to be physically similar (single, sub-spherical, regularly-shaped rims) whereas impact-related aggregates more often show multiple or irregularly shaped rims. The particle size distributions (PSDs) of all three aggregate types are similar (< 200 μm). This proves that in all three environments, aggregation occurs under broadly similar conditions despite the significant differences in source conditions (particle volume fraction, particle size distribution, particle composition, temperature), residence times, plume conditions (e.g., humidity and temperature), and dynamics of fallout and deposition. Impact-generated and volcanic aggregates share many similarities, and in some cases may be indistinguishable without their stratigraphic context.

Aggregation in particle rich environments: a textural study of examples from volcanic eruptions, meteorite impacts, and fluidized bed processing.

PubMed

Mueller, Sebastian B; Kueppers, Ulrich; Huber, Matthew S; Hess, Kai-Uwe; Poesges, Gisela; Ruthensteiner, Bernhard; Dingwell, Donald B

2018-01-01

Aggregation is a common process occurring in many diverse particulate gas mixtures (e.g. those derived from explosive volcanic eruptions, meteorite impact events, and fluid bed processing). It results from the collision and sticking of particles suspended in turbulent gas/air. To date, there is no generalized model of the underlying physical processes. Here, we investigate aggregates from 18 natural deposits (16 volcanic deposits and two meteorite impact deposits) as well as aggregates produced experimentally via fluidized bed techniques. All aggregates were analyzed for their size, internal structuring, and constituent particle size distribution. Commonalities and differences between the aggregate types are then used to infer salient features of the aggregation process. Average core to rim ratios of internally structured aggregates (accretionary lapilli) is found to be similar for artificial and volcanic aggregates but up to an order of magnitude different than impact-related aggregates. Rim structures of artificial and volcanic aggregates appear to be physically similar (single, sub-spherical, regularly-shaped rims) whereas impact-related aggregates more often show multiple or irregularly shaped rims. The particle size distributions (PSDs) of all three aggregate types are similar (< 200 μm). This proves that in all three environments, aggregation occurs under broadly similar conditions despite the significant differences in source conditions (particle volume fraction, particle size distribution, particle composition, temperature), residence times, plume conditions (e.g., humidity and temperature), and dynamics of fallout and deposition. Impact-generated and volcanic aggregates share many similarities, and in some cases may be indistinguishable without their stratigraphic context.

Single particle mass spectral signatures from vehicle exhaust particles and the source apportionment of on-line PM2.5 by single particle aerosol mass spectrometry.

PubMed

Yang, Jian; Ma, Shexia; Gao, Bo; Li, Xiaoying; Zhang, Yanjun; Cai, Jing; Li, Mei; Yao, Ling'ai; Huang, Bo; Zheng, Mei

2017-09-01

In order to accurately apportion the many distinct types of individual particles observed, it is necessary to characterize fingerprints of individual particles emitted directly from known sources. In this study, single particle mass spectral signatures from vehicle exhaust particles in a tunnel were performed. These data were used to evaluate particle signatures in a real-world PM 2.5 apportionment study. The dominant chemical type originating from average positive and negative mass spectra for vehicle exhaust particles are EC species. Four distinct particle types describe the majority of particles emitted by vehicle exhaust particles in this tunnel. Each particle class is labeled according to the most significant chemical features in both average positive and negative mass spectral signatures, including ECOC, NaK, Metal and PAHs species. A single particle aerosol mass spectrometry (SPAMS) was also employed during the winter of 2013 in Guangzhou to determine both the size and chemical composition of individual atmospheric particles, with vacuum aerodynamic diameter (d va ) in the size range of 0.2-2μm. A total of 487,570 particles were chemically analyzed with positive and negative ion mass spectra and a large set of single particle mass spectra was collected and analyzed in order to identify the speciation. According to the typical tracer ions from different source types and classification by the ART-2a algorithm which uses source fingerprints for apportioning ambient particles, the major sources of single particles were simulated. Coal combustion, vehicle exhaust, and secondary ion were the most abundant particle sources, contributing 28.5%, 17.8%, and 18.2%, respectively. The fraction with vehicle exhaust species particles decreased slightly with particle size in the condensation mode particles. Copyright © 2017 Elsevier B.V. All rights reserved.

Emergence of reconfigurable wires and spinners via dynamic self-assembly

DOE PAGES

Kokot, Gasper; Piet, David; Whitesides, George M.; ...

2015-03-26

Dissipative colloidal materials use energy to generate and maintain structural complexity. The energy injection rate, and properties of the environment are important control parameters that influence the outcome of dynamic self-assembly. Here we demonstrate that dispersions of magnetic microparticles confined at the air-liquid interface, and energized by a uniaxial in-plane alternating magnetic field, self-assemble into a variety of structures that range from pulsating clusters and single-particle-thick wires to dynamic arrays of spinners (self-assembled short chains) rotating in either direction. The spinners emerge via spontaneous breaking of the uniaxial symmetry of the energizing magnetic field. Demonstration of the formation and disaggregationmore » of particle assemblies suggests strategies to form new meso-scale structures with the potential to perform functions such as mixing and sensing.« less

Spin interactions in InAs quantum dots

NASA Astrophysics Data System (ADS)

Doty, M. F.; Ware, M. E.; Stinaff, E. A.; Scheibner, M.; Bracker, A. S.; Gammon, D.; Ponomarev, I. V.; Reinecke, T. L.; Korenev, V. L.

2006-03-01

Fine structure splittings in optical spectra of self-assembled InAs quantum dots (QDs) generally arise from spin interactions between particles confined in the dots. We present experimental studies of the fine structure that arises from multiple charges confined in a single dot [1] or in molecular orbitals of coupled pairs of dots. To probe the underlying spin interactions we inject particles with a known spin orientation (by using polarized light to perform photoluminescence excitation spectroscopy experiments) or use a magnetic field to orient and/or mix the spin states. We develop a model of the spin interactions that aids in the development of quantum information processing applications based on controllable interactions between spins confined to QDs. [1] Polarized Fine Structure in the Photoluminescence Excitation Spectrum of a Negatively Charged Quantum Dot, Phys. Rev. Lett. 95, 177403 (2005)

Investigating radiation induced damage processes with femtosecond x-ray pulses (Conference Presentation)

NASA Astrophysics Data System (ADS)

Song, Changyong

2017-05-01

Interest in high-resolution structure investigation has been zealous, especially with the advent of X-ray free electron lasers (XFELs). The intense and ultra-short X-ray laser pulses ( 10 GW) pave new routes to explore structures and dynamics of single macromolecules, functional nanomaterials and complex electronic materials. In the last several years, we have developed XFEL single-shot diffraction imaging by probing ultrafast phase changes directly. Pump-probe single-shot imaging was realized by synchronizing femtosecond (<10 fs in FWHM) X-ray laser (probe) with femtosecond (50 fs) IR laser (pump) at better than 1 ps resolution. Nanoparticles under intense fs-laser pulses were investigated with fs XFEL pulses to provide insight into the irreversible particle damage processes with nanoscale resolution. Research effort, introduced, aims to extend the current spatio-temporal resolution beyond the present limit. We expect this single-shot dynamic imaging to open new science opportunity with XFELs.

Theory of Fermi Liquid with Flat Bands

NASA Astrophysics Data System (ADS)

Khodel, V. A.

2018-04-01

A self-consistent theory of Fermi systems hosting flat bands is developed. Compared with an original model of fermion condensation, its key point consists in proper accounting for mixing between condensate and non-condensate degrees of freedom that leads to formation of a non-BCS gap Υ (p) in the single-particle spectrum. The results obtained explain: (1) the two-gap structure of spectra of single-particle excitations of electron systems of copper oxides, revealed in ARPES studies, (2) the role of violation of the topological stability of the Landau state in the arrangement of the T-x phase diagram of this family of high-T_c superconductors, (3) the topological nature of a metal-insulator transition, discovered in homogeneous two-dimensional low-density electron liquid of MOSFETs more than 20 years ago.

Dynamic fracture behavior of single and contacting Poly(methyl methacrylate) particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parab, Niranjan D.; Guo, Zherui; Hudspeth, Matthew C.

Fracture behaviors of single, two, and multiple contacting spherical Poly (methyl methacrylate) (PMMA) particles were recorded using high speed synchrotron X-ray phase contrast imaging. A miniaturized Kolsky bar setup was used to apply dynamic compressive loading on the PMMA particles. In both single and two particle experiments, cracking initiated near the center of the particles and propagated towards the contacts. The crack bifurcated near the contact points for single particle experiments, thus forming conical fragments. The crack bifurcation and subsequent conical fragment formation was observed only at the particle-particle contact for two particle experiments. The particles were observed to fracturemore » in hemispherical fragments normal to the contact plane in the multiparticle experiments. The observed failure mechanisms strongly suggest that the maximum tensile stress near the center of the particle is the critical parameter governing fracture of the particles. Moreover, the compressive stress under the contact areas led to the bifurcation and subsequent conical fragment formation.« less

Dynamic fracture behavior of single and contacting Poly(methyl methacrylate) particles

DOE PAGES

Parab, Niranjan D.; Guo, Zherui; Hudspeth, Matthew C.; ...

2017-09-19

Fracture behaviors of single, two, and multiple contacting spherical Poly (methyl methacrylate) (PMMA) particles were recorded using high speed synchrotron X-ray phase contrast imaging. A miniaturized Kolsky bar setup was used to apply dynamic compressive loading on the PMMA particles. In both single and two particle experiments, cracking initiated near the center of the particles and propagated towards the contacts. The crack bifurcated near the contact points for single particle experiments, thus forming conical fragments. The crack bifurcation and subsequent conical fragment formation was observed only at the particle-particle contact for two particle experiments. The particles were observed to fracturemore » in hemispherical fragments normal to the contact plane in the multiparticle experiments. The observed failure mechanisms strongly suggest that the maximum tensile stress near the center of the particle is the critical parameter governing fracture of the particles. Moreover, the compressive stress under the contact areas led to the bifurcation and subsequent conical fragment formation.« less

Multiscale modeling of particle in suspension with smoothed dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Bian, Xin; Litvinov, Sergey; Qian, Rui; Ellero, Marco; Adams, Nikolaus A.

2012-01-01

We apply smoothed dissipative particle dynamics (SDPD) [Español and Revenga, Phys. Rev. E 67, 026705 (2003)] to model solid particles in suspension. SDPD is a thermodynamically consistent version of smoothed particle hydrodynamics (SPH) and can be interpreted as a multiscale particle framework linking the macroscopic SPH to the mesoscopic dissipative particle dynamics (DPD) method. Rigid structures of arbitrary shape embedded in the fluid are modeled by frozen particles on which artificial velocities are assigned in order to satisfy exactly the no-slip boundary condition on the solid-liquid interface. The dynamics of the rigid structures is decoupled from the solvent by solving extra equations for the rigid body translational/angular velocities derived from the total drag/torque exerted by the surrounding liquid. The correct scaling of the SDPD thermal fluctuations with the fluid-particle size allows us to describe the behavior of the particle suspension on spatial scales ranging continuously from the diffusion-dominated regime typical of sub-micron-sized objects towards the non-Brownian regime characterizing macro-continuum flow conditions. Extensive tests of the method are performed for the case of two/three dimensional bulk particle-system both in Brownian/ non-Brownian environment showing numerical convergence and excellent agreement with analytical theories. Finally, to illustrate the ability of the model to couple with external boundary geometries, the effect of confinement on the diffusional properties of a single sphere within a micro-channel is considered, and the dependence of the diffusion coefficient on the wall-separation distance is evaluated and compared with available analytical results.

X-ray Vision for Aerosol Scientists: LCLS Snapshots of Soot (Narrated)

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

2012-10-22

This short conceptual animation depicts how scientists can now simultaneously capture fractal morphology (structure), chemical composition and nanoscale imagery of individual aerosol particles in flight. These particles, known as "PM2.5" because they are smaller than 2.5 microns in diameter, affect climate by interacting with sunlight and impact human health by entering the lungs. The single LCLS laser pulses travel to the Atomic, Molecular and Optical Sciences (AMO) laboratory in the Near Experimental Hall. As we zoom in, we see deep inside a simplified aerosol inlet, where the complex fractal structure of the soot particles, each one completely unique, is shown.more » Individual soot particles are then delivered into the pulses of the LCLS beam, which destroys them. X-rays are scattered to the detector before the particle is destroyed, giving information about the morphology of the particle. Ion fragments released in the explosion are sent into a mass spectrometer, which measures their mass-to-charge ratio -- giving scientists information about the chemical composition of the particle. Many different particles are analyzed in this manner, allowing scientists to probe variations in the particles due to changes in their environment before being sent through the aerosol inlet. The final visual of aerosols emitted from a factory is representative of the goal that such LCLS aerosol dynamics experiments can provide critical feedback into modeling and understanding combustion, aerosol processes in manufacturing or aerosol effects on climate change.« less

Fluorescence imaging of single-molecule retention trajectories in reversed-phase chromatographic particles.

PubMed

Cooper, Justin T; Peterson, Eric M; Harris, Joel M

2013-10-01

Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. The simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized.

Three-dimensional cryoEM reconstruction of native LDL particles to 16Å resolution at physiological body temperature.

PubMed

Kumar, Vibhor; Butcher, Sarah J; Öörni, Katariina; Engelhardt, Peter; Heikkonen, Jukka; Kaski, Kimmo; Ala-Korpela, Mika; Kovanen, Petri T

2011-05-09

Low-density lipoprotein (LDL) particles, the major carriers of cholesterol in the human circulation, have a key role in cholesterol physiology and in the development of atherosclerosis. The most prominent structural components in LDL are the core-forming cholesteryl esters (CE) and the particle-encircling single copy of a huge, non-exchangeable protein, the apolipoprotein B-100 (apoB-100). The shape of native LDL particles and the conformation of native apoB-100 on the particles remain incompletely characterized at the physiological human body temperature (37 °C). To study native LDL particles, we applied cryo-electron microscopy to calculate 3D reconstructions of LDL particles in their hydrated state. Images of the particles vitrified at 6 °C and 37 °C resulted in reconstructions at ~16 Å resolution at both temperatures. 3D variance map analysis revealed rigid and flexible domains of lipids and apoB-100 at both temperatures. The reconstructions showed less variability at 6 °C than at 37 °C, which reflected increased order of the core CE molecules, rather than decreased mobility of the apoB-100. Compact molecular packing of the core and order in a lipid-binding domain of apoB-100 were observed at 6 °C, but not at 37 °C. At 37 °C we were able to highlight features in the LDL particles that are not clearly separable in 3D maps at 6 °C. Segmentation of apoB-100 density, fitting of lipovitellin X-ray structure, and antibody mapping, jointly revealed the approximate locations of the individual domains of apoB-100 on the surface of native LDL particles. Our study provides molecular background for further understanding of the link between structure and function of native LDL particles at physiological body temperature.

A novel method to study single-particle dynamics by the resistive pulse technique

NASA Astrophysics Data System (ADS)

Berge, L. I.; Feder, J.; Jøssang, T.

1989-08-01

We have developed a new method, a pressure-reversal technique, which extends the uses of the resistive pulse (Coulter counter) technique to single-particle dynamics. The resistive pulse technique measures the increase in resistance when particles suspended in an electrolyte are transported through a current-carrying aperture. By the new method, the pressure is reversed when a particle exits the pore. A trigger signal, derived from the particle pulses, is used to activate two miniature solenoid valves which serve as pressure switches. In this way, the particle reenters the pore. A single particle flowing back and forth may be studied over a long period of time. The time the particle spends outside the pore between reversals is variable from a few milliseconds to several seconds. We have so far used pore diameters in the range of 3-30 μm. The new technique enables us to study single-particle dissolution and single-particle flow dynamics. The experimental arrangement and the details of the new method are described together with some illustrative measurements.

Exploiting MIC architectures for the simulation of channeling of charged particles in crystals

NASA Astrophysics Data System (ADS)

Bagli, Enrico; Karpusenko, Vadim

2016-08-01

Coherent effects of ultra-relativistic particles in crystals is an area of science under development. DYNECHARM + + is a toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures. The particle trajectory in a crystal is computed through numerical integration of the equation of motion. The code was revised and improved in order to exploit parallelization on multi-cores and vectorization of single instructions on multiple data. An Intel Xeon Phi card was adopted for the performance measurements. The computation time was proved to scale linearly as a function of the number of physical and virtual cores. By enabling the auto-vectorization flag of the compiler a three time speedup was obtained. The performances of the card were compared to the Dual Xeon ones.

Proceedings of the 14th International Conference on the Numerical Simulation of Plasmas

NASA Astrophysics Data System (ADS)

Partial Contents are as follows: Numerical Simulations of the Vlasov-Maxwell Equations by Coupled Particle-Finite Element Methods on Unstructured Meshes; Electromagnetic PIC Simulations Using Finite Elements on Unstructured Grids; Modelling Travelling Wave Output Structures with the Particle-in-Cell Code CONDOR; SST--A Single-Slice Particle Simulation Code; Graphical Display and Animation of Data Produced by Electromagnetic, Particle-in-Cell Codes; A Post-Processor for the PEST Code; Gray Scale Rendering of Beam Profile Data; A 2D Electromagnetic PIC Code for Distributed Memory Parallel Computers; 3-D Electromagnetic PIC Simulation on the NRL Connection Machine; Plasma PIC Simulations on MIMD Computers; Vlasov-Maxwell Algorithm for Electromagnetic Plasma Simulation on Distributed Architectures; MHD Boundary Layer Calculation Using the Vortex Method; and Eulerian Codes for Plasma Simulations.

Site-Specific Colloidal Crystal Nucleation by Template-enhanced Particle Transport

NASA Astrophysics Data System (ADS)

Mishra, Chandan K.; Sood, A. K.; Ganapathy, Rajesh

The deliberate positioning of nano- and microstructures on surfaces is often a prerequisite for fabricating functional devices. While template-assisted nucleation is a promising route to self-assemble these structures, its success hinges on particles reaching target sites prior to nucleation and for nano/microscale particles, this is hampered by their small surface mobilities. We tailored surface features, which in the presence of attractive depletion interactions not only directed micrometer-sized colloids to specific sites but also subsequently guided their growth into ordered crystalline arrays of well-defined size and symmetry. By following the nucleation kinetics with single-particle resolution, we demonstrate control over nucleation density in a growth regime that has hitherto remained inaccessible. Our findings pave the way towards realizing non-trivial surface architectures composed of complex colloids/nanoparticles as well.

Suitability and perspectives on using recombinant insect cells for the production of virus-like particles.

PubMed

Yamaji, Hideki

2014-03-01

Virus-like particles (VLPs) can be produced in recombinant protein production systems by expressing viral surface proteins that spontaneously assemble into particulate structures similar to authentic viral or subviral particles. VLPs serve as excellent platforms for the development of safe and effective vaccines and diagnostic antigens. Among various recombinant protein production systems, the baculovirus-insect cell system has been used extensively for the production of a wide variety of VLPs. This system is already employed for the manufacture of a licensed human papillomavirus-like particle vaccine. However, the baculovirus-insect cell system has several inherent limitations including contamination of VLPs with progeny baculovirus particles. Stably transformed insect cells have emerged as attractive alternatives to the baculovirus-insect cell system. Different types of VLPs, with or without an envelope and composed of either single or multiple structural proteins, have been produced in stably transformed insect cells. VLPs produced by stably transformed insect cells have successfully elicited immune responses in vivo. In some cases, the yield of VLPs attained with recombinant insect cells was comparable to, or higher than, that obtained by baculovirus-infected insect cells. Recombinant insect cells offer a promising approach to the development and production of VLPs.

Fabrication of Polyhedral Particles from Spherical Colloids and Their Self-Assembly into Rotator Phases**

PubMed Central

Vutukuri, Hanumantha Rao; Imhof, Arnout; van Blaaderen, Alfons

2014-01-01

Particle shape is a critical parameter that plays an important role in self-assembly, for example, in designing targeted complex structures with desired properties. Over the last decades, an unprecedented range of monodisperse nanoparticle systems with control over the shape of the particles have become available. In contrast, the choice of micrometer-sized colloidal building blocks of particles with flat facets, that is, particles with polygonal shapes, is significantly more limited. This can be attributed to the fact that in contrast to nanoparticles, the larger colloids are significantly harder to synthesize as single crystals. It is now shown that a very simple building block, such as a micrometer-sized polymeric spherical colloidal particle, is already enough to fabricate particles with regularly placed flat facets, including completely polygonal shapes with sharp edges. As an illustration that the yields are high enough for further self-assembly studies, the formation of three-dimensional rotator phases of fluorescently labelled, micrometer-sized, and charged rhombic dodecahedron particles was demonstrated. This method for fabricating polyhedral particles opens a new avenue for designing new materials. PMID:25366869

Simulation and Experimental Study on Surface Formation Mechanism in Machining of SiCp/Al Composites

NASA Astrophysics Data System (ADS)

Du, Jinguang; Zhang, Haizhen; He, Wenbin; Ma, Jun; Ming, Wuyi; Cao, Yang

2018-03-01

To intuitively reveal the surface formation mechanism in machining of SiCp/Al composites, in this paper the removal mode of reinforced particle and aluminum matrix, and their influence on surface formation mechanism were analyzed by single diamond grit cutting simulation and single diamond grit scratch experiment. Simulation and experiment results show that when the depth of cut is small, the scratched surface of the workpiece is relatively smooth; however, there are also irregular pits on the machined surface. When increasing the depth of cut, there are many obvious laminar structures on the scratched surface, and the surface appearance becomes coarser. When the cutting speed is small, the squeezing action of abrasive grit on SiC particles plays a dominant role in the extrusion of SiC particles. When increasing the cutting speed, SiC particles also occur broken or fractured; but the machined surface becomes smooth. When machining SiCp/Al composites, the SiC may happen in such removal ways, such as fracture, debonding, broken, sheared, pulled into and pulled out, etc. By means of reasonably developing micro cutting finite element simulation model of SiCp/Al composites could be used to analyze the surface formation process and particle removal way in different machining conditions.

Colloid-probe AFM studies of the interaction forces of proteins adsorbed on colloidal crystals.

PubMed

Singh, Gurvinder; Bremmell, Kristen E; Griesser, Hans J; Kingshott, Peter

2015-04-28

In recent years, colloid-probe AFM has been used to measure the direct interaction forces between colloidal particles of different size or surface functionality in aqueous media, as one can study different forces in symmerical systems (i.e., sphere-sphere geometry). The present study investigates the interaction between protein coatings on colloid probes and hydrophilic surfaces decorated with hexagonally close packed single particle layers that are either uncoated or coated with proteins. Controlled solvent evaporation from aqueous suspensions of colloidal particles (coated with or without lysozyme and albumin) produces single layers of close-packed colloidal crystals over large areas on a solid support. The measurements have been carried out in an aqueous medium at different salt concentrations and pH values. The results show changes in the interaction forces as the surface charge of the unmodified or modified particles, and ionic strength or pH of the solution is altered. At high ionic strength or pH, electrostatic interactions are screened, and a strong repulsive force at short separation below 5 nm dominates, suggesting structural changes in the absorbed protein layer on the particles. We also study the force of adhesion, which decreases with an increment in the salt concentration, and the interaction between two different proteins indicating a repulsive interaction on approach and adhesion on retraction.

TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kobayashi, Amane; Sekiguchi, Yuki; Oroguchi, Tomotaka

Coherent X-ray diffraction imaging (CXDI) is a technique for structure analyses of non-crystalline particles with dimensions ranging from micrometer to sub-micrometer. We have developed a diffraction apparatus named TAKASAGO-6 for use in single-shot CXDI experiments of frozen-hydrated non-crystalline biological particles at cryogenic temperature with X-ray free electron laser pulses provided at a repetition rate of 30 Hz from the SPring-8 Angstrom Compact free-electron LAser. Specimen particles are flash-cooled after being dispersed on thin membranes supported by specially designed disks. The apparatus is equipped with a high-speed translation stage with a cryogenic pot for raster-scanning of the disks at a speedmore » higher than 25 μm/33 ms. In addition, we use devices assisting the easy transfer of cooled specimens from liquid-nitrogen storages to the cryogenic pot. In the current experimental procedure, more than 20 000 diffraction patterns can be collected within 1 h. Here we report the key components and performance of the diffraction apparatus. Based on the efficiency of the diffraction data collection and the structure analyses of metal particles, biological cells, and cellular organelles, we discuss the future application of this diffraction apparatus for structure analyses of biological specimens.« less

Microfabricated particle focusing device

DOEpatents

Ravula, Surendra K.; Arrington, Christian L.; Sigman, Jennifer K.; Branch, Darren W.; Brener, Igal; Clem, Paul G.; James, Conrad D.; Hill, Martyn; Boltryk, Rosemary June

2013-04-23

A microfabricated particle focusing device comprises an acoustic portion to preconcentrate particles over large spatial dimensions into particle streams and a dielectrophoretic portion for finer particle focusing into single-file columns. The device can be used for high throughput assays for which it is necessary to isolate and investigate small bundles of particles and single particles.

Characterization of Two Unique Cholesterol-Rich Lipid Particles Isolated from Human Atherosclerotic Lesions

PubMed Central

Chao, Fei-Fei; Blanchette-Mackie, E. Joan; Chen, Ya-Jun; Dickens, Benjamin F.; Berlin, Elliott; Amende, Lynn M.; Skarlatos, Sonia I.; Gamble, Wilbert; Resau, James H.; Mergner, Wolfgang T.; Kruth, Howard S.

1990-01-01

The authors' laboratory, using histochemicalmethods, previously identified two types of cholesterol-containing lipid particles in the extracellular spaces of human atherosclerotic lesions, one particle enriched in esterified cholesterol and the other particle enriched in unesterified cholesterol. The authors isolated and characterized these lipid particles. The esterified cholesterol-rich lipid particle was a small lipid droplet and differed from intracellular lipid dropletsfound in foam cells with respect to size and chemical composition. It had an esterified cholesterol core surrounded by aphospholipidunesterified cholesterol monolayer. Some aqueous spaces were seen within the particle core. Unesterified cholesterol-rich lipid particles were multilamellated, solid structures and vesicles comprised of single or multiple lamellas. The esterified cholesterol-rich particle had a density <1.01 g/ml, whereas the unesterified cholesterol-rich particle had a density between 1.03 and 1.05 g/ml. Both particles were similar in size fraction, whereas palmitate, stearate, oleate, and linoleate were predominant in the phospholipid fraction. The origins and the role of these two unusual lipid particles in vessel wall cholesterol metabolism remain to be determined. ImagesFigure 1Figure 3Figure 4Figure 5 PMID:2297045

NanoXCT: a novel technique to probe the internal architecture of pharmaceutical particles.

PubMed

Wong, Jennifer; D'Sa, Dexter; Foley, Matthew; Chan, John Gar Yan; Chan, Hak-Kim

2014-11-01

To demonstrate the novel application of nano X-ray computed tomography (NanoXCT) for visualizing and quantifying the internal structures of pharmaceutical particles. An Xradia NanoXCT-100, which produces ultra high-resolution and non-destructive imaging that can be reconstructed in three-dimensions (3D), was used to characterize several pharmaceutical particles. Depending on the particle size of the sample, NanoXCT was operated in Zernike Phase Contrast (ZPC) mode using either: 1) large field of view (LFOV), which has a two-dimensional (2D) spatial resolution of 172 nm; or 2) high resolution (HRES) that has a resolution of 43.7 nm. Various pharmaceutical particles with different physicochemical properties were investigated, including raw (2-hydroxypropyl)-beta-cyclodextrin (HβCD), poly (lactic-co-glycolic) acid (PLGA) microparticles, and spray-dried particles that included smooth and nanomatrix bovine serum albumin (BSA), lipid-based carriers, and mannitol. Both raw HβCD and PLGA microparticles had a network of voids, whereas spray-dried smooth BSA and mannitol generally had a single void. Lipid-based carriers and nanomatrix BSA particles resulted in low quality images due to high noise-to-signal ratio. The quantitative capabilities of NanoXCT were also demonstrated where spray-dried mannitol was found to have an average void volume of 0.117 ± 0.247 μm(3) and average void-to-material percentage of 3.5%. The single PLGA particle had values of 1993 μm(3) and 59.3%, respectively. This study reports the first series of non-destructive 3D visualizations of inhalable pharmaceutical particles. Overall, NanoXCT presents a powerful tool to dissect and observe the interior of pharmaceutical particles, including those of a respirable size.

Topology and geometry of the dark matter web

NASA Astrophysics Data System (ADS)

Ramachandra, Nesar; Shandarin, Sergei

2017-01-01

Topological connections in the single-streaming voids and multi-streaming filaments and walls reveal a cosmic web structure different from traditional mass density fields. A single void structure not only percolates the multi-stream field in all the directions, but also occupies over 99 per cent of all the single-streaming regions. Sub-grid analyses on scales smaller than simulation resolution reveal tiny pockets of voids that are isolated by membranes of the structure. For the multi-streaming excursion sets, the percolating structure is much thinner than the filaments in over-density excursion approach. We also introduce, for the first time, a framework to detect dark matter haloes in multi-stream fields. Closed compact regions hosting local maxima of the multi-stream field are detected using local geometrical conditions and properties of the Lagrangian sub-manifold. All the halo particles are guaranteed to be completely outside void regions of the Universe. Majority of the halo candidates are embedded in the largest structure that percolates the entire volume. The University of Kansas FY 2017 Competition General Research Fund, GRF Award 2301155.

Structural and Magnetic Studies of Thermally Treated NiFe2O4 Nanoparticles

NASA Astrophysics Data System (ADS)

Ghosh, Surajit; Patel, Prayas Chandra; Gangopadhyay, Debraj; Sharma, Poornima; Singh, Ranjan K.; Srivastava, P. C.

2017-12-01

The heat treatment of nanoparticles can have a direct effect on their particle sizes, which, in turn, can influence many of their structural and magnetic properties. Here, we report the effect of sintering temperature on the chemically synthesized high-quality NiFe2O4 nanoparticles. The structural studies show the formation of pure NiFe2O4 nanoparticles with the space group Fd{\\bar{3}}m . The inverse spinel structure was also confirmed from the lattice vibrations analyzed from Raman and Fourier transform infrared spectroscopy (FTIR) spectra. The presence of strong exchange interactions was detected from the temperature-dependent magnetization study. Moreover, at higher sintering temperatures, the grain growth due to fusion of several smaller particles by coalescing their surfaces enhances the crystallinity and its magnetocrystalline anisotropy. Coercivity and saturation magnetization were found to depend significantly on the sintering temperature, which was understood in the realm of the formation of single-domain-like structure and change in magnetocrystalline anisotropy at higher sintering temperatures.

Structural and magnetic characteristics of PVA/CoFe{sub 2}O{sub 4} nano-composites prepared via mechanical alloying method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rashidi, S.; Ataie, A., E-mail: aataie@ut.ac.ir

Highlights: • Single phase CoFe{sub 2}O{sub 4} nano-particles synthesized in one step by mechanical alloying. • PVA/CoFe{sub 2}O{sub 4} magnetic nano-composites were fabricated via mechanical milling. • FTIR confirmed the interaction between PVA and magnetic CoFe{sub 2}O{sub 4} particles. • Increasing in milling time and PVA amount led to well dispersion of CoFe{sub 2}O{sub 4}. - Abstract: In this research, polyvinyl alcohol/cobalt ferrite nano-composites were successfully synthesized employing a two-step procedure: the spherical single-phase cobalt ferrite of 20 ± 4 nm mean particle size was synthesized via mechanical alloying method and then embedded into polymer matrix by intensive milling. Themore » results revealed that increase in polyvinyl alcohol content and milling time causes cobalt ferrite particles disperse more homogeneously in polymer matrix, while the mean particle size and shape of cobalt ferrite have not been significantly affected. Transmission electron microscope images indicated that polyvinyl alcohol chains have surrounded the cobalt ferrite nano-particles; also, the interaction between polymer and cobalt ferrite particles in nano-composite samples was confirmed. Magnetic properties evaluation showed that saturation magnetization, coercivity and anisotropy constant values decreased in nano-composite samples compared to pure cobalt ferrite. However, the coercivity values of related nano-composite samples enhanced by increasing PVA amount due to domain wall mechanism.« less

Methods for forming particles from single source precursors

DOEpatents

Fox, Robert V [Idaho Falls, ID; Rodriguez, Rene G [Pocatello, ID; Pak, Joshua [Pocatello, ID

2011-08-23

Single source precursors are subjected to carbon dioxide to form particles of material. The carbon dioxide may be in a supercritical state. Single source precursors also may be subjected to supercritical fluids other than supercritical carbon dioxide to form particles of material. The methods may be used to form nanoparticles. In some embodiments, the methods are used to form chalcopyrite materials. Devices such as, for example, semiconductor devices may be fabricated that include such particles. Methods of forming semiconductor devices include subjecting single source precursors to carbon dioxide to form particles of semiconductor material, and establishing electrical contact between the particles and an electrode.

Method of forming silicon structures with selectable optical characteristics

NASA Technical Reports Server (NTRS)

Fathauer, Robert W. (Inventor); Schowalter, Leo (Inventor)

1993-01-01

Silicon and metal are coevaporated onto a silicon substrate in a molecular beam epitaxy system with a larger than stoichiometric amount of silicon so as to epitaxially grow particles of metal silicide embedded in a matrix of single crystal epitaxially grown silicon. The particles interact with incident photons by resonant optical absorption at the surface plasmon resonance frequency. Controlling the substrate temperature and deposition rate and time allows the aspect ratio of the particles to be tailored to desired wavelength photons and polarizations. The plasmon energy may decay as excited charge carriers or phonons, either of which can be monitored to indicate the amount of incident radiation at the selected frequency and polarization.

In situ observation of the formation of hollow zinc oxide shells

DOE PAGES

Tringe, J. W.; Levie, H. W.; El-Dasher, B. S.; ...

2011-06-14

Single crystal zinc particles, 1–2 μm1–2 μm in diameter, were observed in situ with transmission electron microscopy during sublimation. The rate of sublimation is strongly dependent on the presence of a surface oxide layer. Near 375°, minimally oxidized Zn surfaces sublime in tens of seconds, consistent with a model in which the particle behaves similarly to an isolated microscale effusion cell. By contrast, zinc particles fully enclosed by oxide sublime less than one-tenth as quickly. Here these results provide new insight into the synthesis mechanisms of hollow ZnO microspheres and related structures formed from metallic zinc at elevated temperatures.

Perspectives on individual to ensembles of ambient fine and ultrafine particles and their sources

NASA Astrophysics Data System (ADS)

Bein, Keith James

By combining Rapid Single-ultrafine-particle Mass Spectrometry (RSMS) measurements during the Pittsburgh Supersite experiment with a large array of concurrent PM, gas and meteorological data, a synthesis of data and analyses is employed to characterize sources, emission trends and dynamics of ambient fine and ultrafine particles. Combinatorial analyses elicit individual to ensemble descriptions of particles, their sources, their changes in state from atmospheric processing and the scales of motion driving their transport and dynamics. Major results include (1) Particle size and composition are strong indicators of sources/source categories and real-time measurements allow source attribution at the single particle and point source level. (2) Single particle source attribution compares well to factor analysis of chemically-speciated bulk phase data and both resulted in similar conclusions but independently revealed new sources. (3) RSMS data can quantitatively estimate composition-resolved, number-based particle size distribution. Comparison to mass-based data yielded new information about physical and chemical properties of particles and instrument sensitivity. (4) Source-specific signatures and real-time monitoring allow passing plumes to be tracked and characterized. (5) The largest of three identified coal combustion sources emits ˜ 2.4 x 10 17 primary submicron particles per second. (6) Long-range transport has a significant impact on the eastern U.S. including specific influences of eight separate wildfire events. (7) Pollutant dynamics in the Pittsburgh summertime air shed, and Northeastern U.S., is characterized by alternating periods of stagnation and cleansing. The eight wildfire events were detected in between seven successive stagnation events. (8) Connections exist between boreal fire activity, southeast subsiding transport of the emissions, alternating periods of stagnation and cleansing at the receptor and the structure and propagation of extratropical waves. (9) Wildfire emissions can severely impact preexisting pollutant concentrations and physical and chemical processes at the receptor. (10) High-severity crown fires in boreal Canada emit ˜ 1.2 x 1015 particles/kg biomass burned. (11) In 1998, wildfire activity in the circumpolar boreal forest emitted ˜ 8 x 1026 particles, representing ˜ 14% of global wildland fire emissions. Results and conclusions address future scientific objectives in understanding effects of particles on human health and global climate change.

Effects of Number Scaling on Entangled States in Quantum Mechanics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Benioff, Paul

A summary of number structure scaling is followed by a description of the effects of number scaling in nonrelativistic quantum mechanics. The description extends earlier work to include the effects on the states of two or more interacting particles. Emphasis is placed on the effects on entangled states. The resulting scaling field is generalized to describe the effects on these states. It is also seen that one can use fiber bundles with fibers associated with single locations of the underlying space to describe the effects of scaling on arbitrary numbers of particles.

Microradiography with Semiconductor Pixel Detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jakubek, Jan; Cejnarova, Andrea; Dammer, Jiri

High resolution radiography (with X-rays, neutrons, heavy charged particles, ...) often exploited also in tomographic mode to provide 3D images stands as a powerful imaging technique for instant and nondestructive visualization of fine internal structure of objects. Novel types of semiconductor single particle counting pixel detectors offer many advantages for radiation imaging: high detection efficiency, energy discrimination or direct energy measurement, noiseless digital integration (counting), high frame rate and virtually unlimited dynamic range. This article shows the application and potential of pixel detectors (such as Medipix2 or TimePix) in different fields of radiation imaging.

Single particle characterization using a light scattering module coupled to a time-of-flight aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Cross, E. S.; Onasch, T. B.; Canagaratna, M.; Jayne, J. T.; Kimmel, J.; Yu, X.-Y.; Alexander, M. L.; Worsnop, D. R.; Davidovits, P.

2008-12-01

We present the first single particle results obtained using an Aerodyne time-of-flight aerosol mass spectrometer coupled with a light scattering module (LS-ToF-AMS). The instrument was deployed at the T1 ground site approximately 40 km northeast of the Mexico City Metropolitan Area (MCMA) as part of the MILAGRO field study in March of 2006. The instrument was operated as a standard AMS from 12-30 March, acquiring average chemical composition and size distributions for the ambient aerosol, and in single particle mode from 27-30 March. Over a 75-h sampling period, 12 853 single particle mass spectra were optically triggered, saved, and analyzed. The correlated optical and chemical detection allowed detailed examination of single particle collection and quantification within the LS-ToF-AMS. The single particle data enabled the mixing states of the ambient aerosol to be characterized within the context of the size-resolved ensemble chemical information. The particulate mixing states were examined as a function of sampling time and most of the particles were found to be internal mixtures containing many of the organic and inorganic species identified in the ensemble analysis. The single particle mass spectra were deconvolved, using techniques developed for ensemble AMS data analysis, into HOA, OOA, NH4NO3, (NH4)2SO4, and NH4Cl fractions. Average single particle mass and chemistry measurements are shown to be in agreement with ensemble MS and PTOF measurements. While a significant fraction of ambient particles were internal mixtures of varying degrees, single particle measurements of chemical composition allowed the identification of time periods during which the ambient ensemble was externally mixed. In some cases the chemical composition of the particles suggested a likely source. Throughout the full sampling period, the ambient ensemble was an external mixture of combustion-generated HOA particles from local sources (e.g. traffic), with number concentrations peaking during morning rush hour (04:00-08:00 LT) each day, and more processed particles of mixed composition from nonspecific sources. From 09:00-12:00 LT all particles within the ambient ensemble, including the locally produced HOA particles, became coated with NH4NO3 due to photochemical production of HNO3. The number concentration of externally mixed HOA particles remained low during daylight hours. Throughout the afternoon the OOA component dominated the organic fraction of the single particles, likely due to secondary organic aerosol formation and condensation. Single particle mass fractions of (NH4)2SO4 were lowest during the day and highest during the night. In one instance, gas-to-particle condensation of (NH4)2SO4 was observed on all measured particles within a strong SO2 plume arriving at T1 from the northwest. Particles with high NH4Cl mass fractions were identified during early morning periods. A limited number of particles (~5% of the total number) with mass spectral features characteristic of biomass burning were also identified.

Magnetic Properties of Copper Doped Nickel Ferrite Nanoparticles Synthesized by Co Precipitation Method

NASA Astrophysics Data System (ADS)

Anjana, V.; John, Sara; Prakash, Pooja; Nair, Amritha M.; Nair, Aravind R.; Sambhudevan, Sreedha; Shankar, Balakrishnan

2018-02-01

Nickel ferrite nanoparticles with copper atoms as dopant have been prepared using co-precipitation method with general formula Ni1-xCuxFe2O4 (x=0.2, 0.4, 0.6, 0.8 and 1) and are sintered at quite ambient temperature. Structural and magnetic properties were examined using Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffraction method (XRD) and Vibrating Sample Magnetometer (VSM) to study the influence of copper doping in nickel ferrite magnetic nanoparticles. X-ray studies proves that the particles are possessing single phase spinel structure with an average particle size calculated using Debye Scherer formula. Magnetic measurements reveal that saturation magnetization value (Ms) decreases while magnetic coercivity (Hc) increases upon doping.

Large Colloids in Cholesteric Liquid Crystals

NASA Astrophysics Data System (ADS)

Stratford, K.; Gray, A.; Lintuvuori, J. S.

2015-12-01

We describe a coarse-grained Landau-de Gennes model of liquid crystals (LCs) including hydrodynamics based on the Beris-Edwards equations. The model is employed to study the impact of large colloids on the long range LC defect structure in the cholesteric LC blue phases. `Large' here means that the particle size is comparable to the cholesteric pitch, the length scale on which the LC order undergoes a helical twist. We investigate the case of a single particle, with either normal or degenerate planar anchoring, placed initially in an equilibrium blue phase LC. It is found that in some cases, well defined steady disclination structure emerges at the particle surface, while in other cases no clear steady state is reached in the simulations, and disclination reorganisation appears to proliferate through the bulk LC. These systems are of potential interest in the context of using LCs to template self-assembly of colloid structure, e.g., for opto-electronic devices. Computationally, we demonstrate a parallel approach using mixed message-passing and threaded model on graphical processing units allows effective and efficient progress for this problem.

Variations in the structure of nexuses in the myocardium of the golden hamster Mesocricetus auratus.

PubMed Central

Skepper, J N; Navaratnam, V

1986-01-01

The structure of nexuses in the atrioventricular node of the golden hamster was studied with the transmission electron microscope, using thin sections and freeze-fracture replicas, and was compared with that of nexuses in the working myocardium of the right ventricular wall. Whereas ventricular myocardium contained macular nexuses only, nodal tissue contained annular and linear configurations as well as maculae of varying size. The significance of such variations in nexus pattern is not clear although several hypotheses are discussed in the literature. Measurements made on electron micrographs, after allowing for tilt of the specimen, yielded a particle diameter of 10.59 nm for nodal myocardium and 10.95 nm for ventricular myocardium, both measurements being substantially higher than figures generally cited in the literature. In each area the measurements had a normal distribution suggesting a single type of particle. The small but significant difference in particle size between the two areas is more likely to be caused by dissimilarities in packing arrangement rather than by differences in intrinsic structure or in functional state. Images Fig. 1 Fig. 3 PMID:3693102

Structural dissection of Ebola virus and its assembly determinants using cryo-electron tomography.

PubMed

Bharat, Tanmay A M; Noda, Takeshi; Riches, James D; Kraehling, Verena; Kolesnikova, Larissa; Becker, Stephan; Kawaoka, Yoshihiro; Briggs, John A G

2012-03-13

Ebola virus is a highly pathogenic filovirus causing severe hemorrhagic fever with high mortality rates. It assembles heterogenous, filamentous, enveloped virus particles containing a negative-sense, single-stranded RNA genome packaged within a helical nucleocapsid (NC). We have used cryo-electron microscopy and tomography to visualize Ebola virus particles, as well as Ebola virus-like particles, in three dimensions in a near-native state. The NC within the virion forms a left-handed helix with an inner nucleoprotein layer decorated with protruding arms composed of VP24 and VP35. A comparison with the closely related Marburg virus shows that the N-terminal region of nucleoprotein defines the inner diameter of the Ebola virus NC, whereas the RNA genome defines its length. Binding of the nucleoprotein to RNA can assemble a loosely coiled NC-like structure; the loose coil can be condensed by binding of the viral matrix protein VP40 to the C terminus of the nucleoprotein, and rigidified by binding of VP24 and VP35 to alternate copies of the nucleoprotein. Four proteins (NP, VP24, VP35, and VP40) are necessary and sufficient to mediate assembly of an NC with structure, symmetry, variability, and flexibility indistinguishable from that in Ebola virus particles released from infected cells. Together these data provide a structural and architectural description of Ebola virus and define the roles of viral proteins in its structure and assembly.

Microprobe studies of microtomed particles of white druse salts in shergottite EETA 79001

NASA Technical Reports Server (NTRS)

Lindstrom, D. J.

1991-01-01

The white druse material in Antarctic shergottite EETA 79001 has attracted much attention as a possible sample fo Martian aqueous deposits. Instrumental Neutron Activation Analysis (INAA) was used to determine trace element analyses of small particles of this material obtained by handpicking of likely grains from broken surfaces of the meteorite. Electron microprobe work was attempted on grain areas as large as 150x120 microns. Backscattered electron images show considerable variations in brightness, and botryoidal structures were observed. Microprobe analyses showed considerable variability both within single particles and between different particles. Microtomed surfaces of small selected particles were shown to be very useful in obtaining information on the texture and composition of rare lithologies like the white druse of EETA 79001. This material is clearly heterogeneous on all distance scales, so a large number of further analyses will be required to characterize it.

Geometric phase coded metasurface: from polarization dependent directive electromagnetic wave scattering to diffusion-like scattering.

PubMed

Chen, Ke; Feng, Yijun; Yang, Zhongjie; Cui, Li; Zhao, Junming; Zhu, Bo; Jiang, Tian

2016-10-24

Ultrathin metasurface compromising various sub-wavelength meta-particles offers promising advantages in controlling electromagnetic wave by spatially manipulating the wavefront characteristics across the interface. The recently proposed digital coding metasurface could even simplify the design and optimization procedures due to the digitalization of the meta-particle geometry. However, current attempts to implement the digital metasurface still utilize several structural meta-particles to obtain certain electromagnetic responses, and requiring time-consuming optimization especially in multi-bits coding designs. In this regard, we present herein utilizing geometric phase based single structured meta-particle with various orientations to achieve either 1-bit or multi-bits digital metasurface. Particular electromagnetic wave scattering patterns dependent on the incident polarizations can be tailored by the encoded metasurfaces with regular sequences. On the contrast, polarization insensitive diffusion-like scattering can also been successfully achieved by digital metasurface encoded with randomly distributed coding sequences leading to substantial suppression of backward scattering in a broadband microwave frequency. The proposed digital metasurfaces provide simple designs and reveal new opportunities for controlling electromagnetic wave scattering with or without polarization dependence.

Geometric phase coded metasurface: from polarization dependent directive electromagnetic wave scattering to diffusion-like scattering

PubMed Central

Chen, Ke; Feng, Yijun; Yang, Zhongjie; Cui, Li; Zhao, Junming; Zhu, Bo; Jiang, Tian

2016-01-01

Ultrathin metasurface compromising various sub-wavelength meta-particles offers promising advantages in controlling electromagnetic wave by spatially manipulating the wavefront characteristics across the interface. The recently proposed digital coding metasurface could even simplify the design and optimization procedures due to the digitalization of the meta-particle geometry. However, current attempts to implement the digital metasurface still utilize several structural meta-particles to obtain certain electromagnetic responses, and requiring time-consuming optimization especially in multi-bits coding designs. In this regard, we present herein utilizing geometric phase based single structured meta-particle with various orientations to achieve either 1-bit or multi-bits digital metasurface. Particular electromagnetic wave scattering patterns dependent on the incident polarizations can be tailored by the encoded metasurfaces with regular sequences. On the contrast, polarization insensitive diffusion-like scattering can also been successfully achieved by digital metasurface encoded with randomly distributed coding sequences leading to substantial suppression of backward scattering in a broadband microwave frequency. The proposed digital metasurfaces provide simple designs and reveal new opportunities for controlling electromagnetic wave scattering with or without polarization dependence. PMID:27775064

One-pot fabrication of graphene oxide-patched hollow-structured microgel particles in a microcapillary device

NASA Astrophysics Data System (ADS)

Byun, Aram; Jeong, Eun Seon; Kim, Jin Woong

2014-03-01

Microgels are colloidal gel particles that consist of chemically cross-linked three-dimensional polymer networks. They play an essential role in delivery and release of active ingredients in medicine, cosmetics, food, and even autonomic self-healing applications. Despite their wide applicability, permeability control through the hydrogel phase is limited due to its intrinsic loose network nature. Herein, we introduce generation of hollow-structured microgel particles whose interfaces were patched with graphene oxide (GO) sheets. The whole fabrication procedure was carried out in a microcapillary device in a single step. GO sheets have an ability to adhere to both O/W and W/O interfaces. Taking advantages of this behavior, we generated monodisperse O/W/O double emulsion whose interfaces were patched with GO sheets. Solidification of the aqueous middle phase to the hydrogel phase gave rise to uniform GO-patched microgel shell particles. Furthermore, we demonstrated that the permeation of molecules through the shell could be controlled even to small molecular length scales due to the adsorption of GO.

New apparatus of single particle trap system for aerosol visualization

NASA Astrophysics Data System (ADS)

Higashi, Hidenori; Fujioka, Tomomi; Endo, Tetsuo; Kitayama, Chiho; Seto, Takafumi; Otani, Yoshio

2014-08-01

Control of transport and deposition of charged aerosol particles is important in various manufacturing processes. Aerosol visualization is an effective method to directly observe light scattering signal from laser-irradiated single aerosol particle trapped in a visualization cell. New single particle trap system triggered by light scattering pulse signal was developed in this study. The performance of the device was evaluated experimentally. Experimental setup consisted of an aerosol generator, a differential mobility analyzer (DMA), an optical particle counter (OPC) and the single particle trap system. Polystylene latex standard (PSL) particles (0.5, 1.0 and 2.0 μm) were generated and classified according to the charge by the DMA. Singly charged 0.5 and 1.0 μm particles and doubly charged 2.0 μm particles were used as test particles. The single particle trap system was composed of a light scattering signal detector and a visualization cell. When the particle passed through the detector, trigger signal with a given delay time sent to the solenoid valves upstream and downstream of the visualization cell for trapping the particle in the visualization cell. The motion of particle in the visualization cell was monitored by CCD camera and the gravitational settling velocity and the electrostatic migration velocity were measured from the video image. The aerodynamic diameter obtained from the settling velocity was in good agreement with Stokes diameter calculated from the electrostatic migration velocity for individual particles. It was also found that the aerodynamic diameter obtained from the settling velocity was a one-to-one function of the scattered light intensity of individual particles. The applicability of this system will be discussed.

Particle-fluid interactions for flow measurements

NASA Technical Reports Server (NTRS)

Berman, N. S.

1973-01-01

Study has been made of the motion of single particle and of group of particles, emphasizing solid particles in gaseous fluid. Velocities of fluid and particle are compared for several conditions of physical interest. Mean velocity and velocity fluctuations are calculated for single particle, and some consideration is given to multiparticle systems.

Insights into DNA-mediated interparticle interactions from a coarse-grained model

NASA Astrophysics Data System (ADS)

Ding, Yajun; Mittal, Jeetain

2014-11-01

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking

PubMed Central

von Diezmann, Alex; Shechtman, Yoav; Moerner, W. E.

2017-01-01

Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers, or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information of single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field-dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems. PMID:28151646

Effect of cobalt doping on crystallinity, stability, magnetic and optical properties of magnetic iron oxide nano-particles

NASA Astrophysics Data System (ADS)

Anjum, Safia; Tufail, Rabia; Rashid, Khalid; Zia, Rehana; Riaz, S.

2017-06-01

This paper is dedicated to investigate the effect of Co2+ ions in magnetite Fe3O4 nano-particles with stoichiometric formula CoxFe3-xO4 where (x = 0, 0.05, 0.1 and 0.15) prepared by co-precipitation method. The structural, thermal, morphological, magnetic and optical properties of magnetite and Co2+ doped magnetite nanoparticles have been carried out using X-ray Diffractometer, Fourier Transform Infrared Spectroscopy, Themogravimetric Analysis, Scanning Electron Microscopy, Vibrating Sample Magnetometer (VSM) and UV-Vis Spectrometer (UV-Vis) respectively. Structural analysis verified the formation of single phase inverse spinel cubic structure with decrease in lattice parameters due to increase in cobalt content. FTIR analysis confirms the single phase of CoxFe3-xO4 nanoparticles with the major band at 887 cm-1, which might be due to the stretching vibrations of metal-oxide bond. The DSC results corroborate the finding of an increase in the maghemite to hematite phase transition temperature with increase in Co2+ content. The decrease in enthalpy with increase in Co2+ concentration attributed to the fact that the degree of conversion from maghemite to hematite decrease which shows that the stability increases with increasing Co2+ content in B-site of Fe3O4 structure. SEM analysis demonstrated the formation of spherical shaped nanoparticles with least agglomeration. The magnetic measurements enlighten that the coercivity and anisotropy of CoxFe3-xO4 nanoparticles are significantly increased. From UV-Vis analysis it is revealed that band gap energy increases with decreasing particle size. This result has a great interest for magnetic fluid hyperthermia application (MPH).

Dosimetry of heavy ions by use of CCD detectors

NASA Technical Reports Server (NTRS)

Schott, J. U.

1994-01-01

The design and the atomic composition of Charge Coupled Devices (CCD's) make them unique for investigations of single energetic particle events. As detector system for ionizing particles they detect single particles with local resolution and near real time particle tracking. In combination with its properties as optical sensor, particle transversals of single particles are to be correlated to any objects attached to the light sensitive surface of the sensor by simple imaging of their shadow and subsequent image analysis of both, optical image and particle effects, observed in affected pixels. With biological objects it is possible for the first time to investigate effects of single heavy ions in tissue or extinguished organs of metabolizing (i.e. moving) systems with a local resolution better than 15 microns. Calibration data for particle detection in CCD's are presented for low energetic protons and heavy ions.

A Defect Structure for 6-Line Ferrihydrite Nanoparticles (Invited)

NASA Astrophysics Data System (ADS)

Gilbert, B.; Spagnoli, D.; Fakra, S.; Petkov, V.; Penn, R. L.; Banfield, J. F.; Waychunas, G.

2010-12-01

Ferrihydrite is an environmental iron oxyhydroxide mineral that is only found in the form of nanoscale particles yet exerts significant impacts on the biogeochemistry of soils, sediments and surface waters. This material has remained poorly characterized due to significant experimental challenges in determining stoichiometry and structure. In a breakthrough, Michel et al., Science 316, 1726 (2007), showed that real-space pair distribution function (PDF) data from ferrihydrite samples with a range of particle sizes could be modeled by a single newly proposed crystal phase. However, ambiguity remained as to the relationship between this model and real ferrihydrite structure because that model does not perfectly reproduce the reciprocal-space X-ray diffraction data (XRD). Subsequently, Michel et al. PNAS 107, 2787 (2010), demonstrated that ferrihydrite could be thermally coarsened to form an annealed nanomaterial for which both XRD and PDF data are reproduced by a refined version of their original structure. These findings confirmed that the Michel et al. structure is a true mineral phase, but do not resolve the question of how to adequately describe the structure of ferrihydrite nanoparticles formed by low-temperature precipitation in surface waters. There is agreement that a model based upon a single unit cell cannot capture the structural diversity present in real nanoparticles, which can include defects, vacancies and disorder, particularly surface strain. However, for the Michel et al. model of ferrihydrite the disagreement between simulated and experimental XRD is significant, indicating either that the underlying structural model is incorrect; that the assumption that a single phase is sufficient to describe the nanomaterial is not valid; or that ferrihydrite nanoparticles possess an unusually large amount of disorder that must be characterized. Thus, quantitative tests of explicit structural configurations are essential to understand the real nanoparticle disorder and to test the correctness of an underlying phase described by a single unit cell. We reviewed the crystal chemistry of the Michel et al. structure and alternatives and developed hypotheses for plausible structural defects. We developed a novel reverse Monte Carlo (RMC) algorithm that generates defects and disorder within full-nanoparticle structural models and simulates the corresponding PDF and wide-angle XRD patterns for comparison with experimental data. This successfully generated full-nanoparticle structures that are in agreement with both real- and reciprocal-space X-ray scattering data. RMC-derived structures may be incorrect, and are not unique, and must therefore be evaluated for chemical plausibility as emphasized by Manceau, Clay Minerals 44, 19 (2009). Nevertheless, the results show that the inclusion of disorder and defects in full-nanoparticle model of ferrihydrite can resolve the discrepancy between XRD and PDF results found for a model based upon a single unit cell.

Microstructure and rheology of particle stabilized emulsions: Effects of particle shape and inter-particle interactions.

PubMed

Katepalli, Hari; John, Vijay T; Tripathi, Anubhav; Bose, Arijit

2017-01-01

Using fumed and spherical silica particles of similar hydrodynamic size, we investigated the effects of particle shape and inter-particle interactions on the formation, stability and rheology of bromohexadecane-in-water Pickering emulsions. The interparticle interactions were varied from repulsive to attractive by modifying the salt concentration in the aqueous phase. Optical microscope images revealed smaller droplet sizes for the fumed silica stabilized emulsions. All the emulsions remained stable for several weeks. Cryo-SEM images of the emulsion droplets showed a hexagonally packed single layer of particles at oil-water interfaces in emulsions stabilized with silica spheres, irrespective of the nature of the inter-particle interactions. Thus, entropic, excluded volume interactions dominate the fate of spherical particles at oil-water interfaces. On the other hand, closely packed layers of particles were observed at oil-water interfaces for the fumed silica stabilized emulsions for both attractive and repulsive interparticle interactions. At the high salt concentrations, attractive inter-particles interactions led to aggregation of fumed silica particles, and multiple layers of these particles were then observed on the droplet surfaces. A network of fumed silica particles was also observed between the emulsion droplets, suggesting that enthalpic interactions are responsible for the determining particle configurations at oil-water interfaces as well as in the aqueous phase. Steady shear viscosity measurements over a range of shear stresses, as well as oscillatory shear measurements at 1Hz confirm the presence of a network in fumed silica suspensions and emulsions, and the lack of such a network when spherical particles are used. The fractal structure of fumed silica leads to several contact points and particle interlocking in the water as well as on the bromohexadecane-water interfaces, with corresponding effects on the structure and rheology of the emulsions. The attenuation of droplet motion due to the formation of a particle network can be exploited for stabilizing emulsions and for modulating their rheology. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways.

PubMed

Bhatia, Dhiraj; Arumugam, Senthil; Nasilowski, Michel; Joshi, Himanshu; Wunder, Christian; Chambon, Valérie; Prakash, Ved; Grazon, Chloé; Nadal, Brice; Maiti, Prabal K; Johannes, Ludger; Dubertret, Benoit; Krishnan, Yamuna

2016-12-01

Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

Oleic acid coated magnetic nano-particles: Synthesis and characterizations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panda, Biswajit, E-mail: bpanda@mes.ac.in; Goyal, P. S.

2015-06-24

Magnetic nano particles of Fe{sub 3}O{sub 4} coated with oleic acid were synthesized using wet chemical route, which involved co-precipitation of Fe{sup 2+} and Fe{sup 3+} ions. The nano particles were characterized using XRD, TEM, FTIR, TGA and VSM. X-ray diffraction studies showed that nano particles consist of single phase Fe{sub 3}O{sub 4} having inverse spinel structure. The particle size obtained from width of Bragg peak is about 12.6 nm. TEM analysis showed that sizes of nano particles are in range of 6 to 17 nm with a dominant population at 12 - 14 nm. FTIR and TGA analysis showed that -COOH groupmore » of oleic acid is bound to the surface of Fe{sub 3}O{sub 4} particles and one has to heat the sample to 278° C to remove the attached molecule from the surface. Further it was seen that Fe{sub 3}O{sub 4} particles exhibit super paramagnetism with a magnetization of about 53 emu/ gm.« less

Amine-Amine Exchange in Aminium-Methanesulfonate Aerosols

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dawson, Matthew L.; Varner, Mychel E.; Perraud, Veronique M.

2014-12-18

Aerosol particles are ubiquitous in the atmosphere and have been shown to impact the Earth’s climate, reduce visibility, and adversely affect human health. Modeling the evolution of aerosol systems requires an understanding of the species and mechanisms involved in particle growth, including the complex interactions between particle- and gas-phase species. Here we report studies of displacement of amines (methylamine, dimethylamine or trimethylamine) in methanesulfonate salt particles by exposure to a different gas-phase amine, using a single particle mass spectrometer, SPLAT II. The variation of the displacement with the nature of the amine suggests that behavior is dependent on water inmore » or on the particles. Small clusters of methanesulfonic acid with amines are used as a model in quantum chemical calculations to identify key structural elements that are expected to influence water uptake, and hence the efficiency of displacement by gas-phase molecules in the aminium salts. Such molecular-level understanding of the processes affecting the ability of gas-phase amines to displace particle-phase aminium species is important for modeling the growth of particles and their impacts in the atmosphere.« less

Dealing with indistinguishable particles and their entanglement.

PubMed

Compagno, Giuseppe; Castellini, Alessia; Lo Franco, Rosario

2018-07-13

Here, we discuss a particle-based approach to deal with systems of many identical quantum objects (particles) that never employs labels to mark them. We show that it avoids both methodological problems and drawbacks in the study of quantum correlations associated with the standard quantum mechanical treatment of identical particles. The core of this approach is represented by the multiparticle probability amplitude, whose structure in terms of single-particle amplitudes we derive here by first principles. To characterize entanglement among the identical particles, this new method uses the same notions, such as partial trace, adopted for non-identical ones. We highlight the connection between our approach and second quantization. We also define spin-exchanged multipartite states which contain a generalization of W states to identical particles. We prove that particle spatial overlap plays a role in the distributed entanglement within multipartite systems and is responsible for the appearance of non-local quantum correlations.This article is part of a discussion meeting issue 'Foundations of quantum mechanics and their impact on contemporary society'. © 2018 The Author(s).

Non-plane-wave Hartree-Fock states and nuclear homework potentials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gutierrez, G.; Plastino, A.; de Llano, M.

1979-12-01

It is shown that non-plane-wave single-particle Hartree-Fock orbitals giving rise to a ''spin-density-wave-like'' structure give lower energy than plane waves beyond a certain relatively low density in both nuclear and neutron matter with homework pair potentials v/sub 1/ and v/sub 2/.

Nanoscopic compartmentalization of membrane protein motion at the axon initial segment.

PubMed

Albrecht, David; Winterflood, Christian M; Sadeghi, Mohsen; Tschager, Thomas; Noé, Frank; Ewers, Helge

2016-10-10

The axon initial segment (AIS) is enriched in specific adaptor, cytoskeletal, and transmembrane molecules. During AIS establishment, a membrane diffusion barrier is formed between the axonal and somatodendritic domains. Recently, an axonal periodic pattern of actin, spectrin, and ankyrin forming 190-nm-spaced, ring-like structures has been discovered. However, whether this structure is related to the diffusion barrier function is unclear. Here, we performed single-particle tracking time-course experiments on hippocampal neurons during AIS development. We analyzed the mobility of lipid-anchored molecules by high-speed single-particle tracking and correlated positions of membrane molecules with the nanoscopic organization of the AIS cytoskeleton. We observe a strong reduction in mobility early in AIS development. Membrane protein motion in the AIS plasma membrane is confined to a repetitive pattern of ∼190-nm-spaced segments along the AIS axis as early as day in vitro 4, and this pattern alternates with actin rings. Mathematical modeling shows that diffusion barriers between the segments significantly reduce lateral diffusion along the axon. © 2016 Albrecht et al.

Solid-phase diffusion mechanism for GaAs nanowire growth.

PubMed

Persson, Ann I; Larsson, Magnus W; Stenström, Stig; Ohlsson, B Jonas; Samuelson, Lars; Wallenberg, L Reine

2004-10-01

Controllable production of nanometre-sized structures is an important field of research, and synthesis of one-dimensional objects, such as nanowires, is a rapidly expanding area with numerous applications, for example, in electronics, photonics, biology and medicine. Nanoscale electronic devices created inside nanowires, such as p-n junctions, were reported ten years ago. More recently, hetero-structure devices with clear quantum-mechanical behaviour have been reported, for example the double-barrier resonant tunnelling diode and the single-electron transistor. The generally accepted theory of semiconductor nanowire growth is the vapour-liquid-solid (VLS) growth mechanism, based on growth from a liquid metal seed particle. In this letter we suggest the existence of a growth regime quite different from VLS. We show that this new growth regime is based on a solid-phase diffusion mechanism of a single component through a gold seed particle, as shown by in situ heating experiments of GaAs nanowires in a transmission electron microscope, and supported by highly resolved chemical analysis and finite element calculations of the mass transport and composition profiles.

Lagrangian single-particle turbulent statistics through the Hilbert-Huang transform.

PubMed

Huang, Yongxiang; Biferale, Luca; Calzavarini, Enrico; Sun, Chao; Toschi, Federico

2013-04-01

The Hilbert-Huang transform is applied to analyze single-particle Lagrangian velocity data from numerical simulations of hydrodynamic turbulence. The velocity trajectory is described in terms of a set of intrinsic mode functions C(i)(t) and of their instantaneous frequency ω(i)(t). On the basis of this decomposition we define the ω-conditioned statistical moments of the C(i) modes, named q-order Hilbert spectra (HS). We show that such quantities have enhanced scaling properties as compared to traditional Fourier transform- or correlation-based (structure functions) statistical indicators, thus providing better insights into the turbulent energy transfer process. We present clear empirical evidence that the energylike quantity, i.e., the second-order HS, displays a linear scaling in time in the inertial range, as expected from a dimensional analysis. We also measure high-order moment scaling exponents in a direct way, without resorting to the extended self-similarity procedure. This leads to an estimate of the Lagrangian structure function exponents which are consistent with the multifractal prediction in the Lagrangian frame as proposed by Biferale et al. [Phys. Rev. Lett. 93, 064502 (2004)].

The Microwave Radiative Properties of Falling Snow Derived from Nonspherical Ice Particle Models. Part II: Initial Testing Using Radar, Radiometer and In Situ Observations

NASA Technical Reports Server (NTRS)

Olson, William S.; Tian, Lin; Grecu, Mircea; Kuo, Kwo-Sen; Johnson, Benjamin; Heymsfield, Andrew J.; Bansemer, Aaron; Heymsfield, Gerald M.; Wang, James R.; Meneghini, Robert

2016-01-01

In this study, two different particle models describing the structure and electromagnetic properties of snow are developed and evaluated for potential use in satellite combined radar-radiometer precipitation estimation algorithms. In the first model, snow particles are assumed to be homogeneous ice-air spheres with single-scattering properties derived from Mie theory. In the second model, snow particles are created by simulating the self-collection of pristine ice crystals into aggregate particles of different sizes, using different numbers and habits of the collected component crystals. Single-scattering properties of the resulting nonspherical snow particles are determined using the discrete dipole approximation. The size-distribution-integrated scattering properties of the spherical and nonspherical snow particles are incorporated into a dual-wavelength radar profiling algorithm that is applied to 14- and 34-GHz observations of stratiform precipitation from the ER-2 aircraft-borne High-Altitude Imaging Wind and Rain Airborne Profiler (HIWRAP) radar. The retrieved ice precipitation profiles are then input to a forward radiative transfer calculation in an attempt to simulate coincident radiance observations from the Conical Scanning Millimeter-Wave Imaging Radiometer (CoSMIR). Much greater consistency between the simulated and observed CoSMIR radiances is obtained using estimated profiles that are based upon the nonspherical crystal/aggregate snow particle model. Despite this greater consistency, there remain some discrepancies between the higher moments of the HIWRAP-retrieved precipitation size distributions and in situ distributions derived from microphysics probe observations obtained from Citation aircraft underflights of the ER-2. These discrepancies can only be eliminated if a subset of lower-density crystal/aggregate snow particles is assumed in the radar algorithm and in the interpretation of the in situ data.

Saha equation, single and two particle states

NASA Technical Reports Server (NTRS)

Kraeft, W. D.; Girardeau, M. D.; Strege, B.

1990-01-01

Single- and two-particle properties in a dense plasma are discussed in connection with their role in the mass action law for a partially ionized plasma. The two-particle-bound states are nearly density independent, while the continuum is essentially shifted. The single-particle states are damped, and their energy has a negative shift and a parabolic behavior for small momenta.

Quantum chemical molecular dynamics simulation of single-walled carbon nanotube cap nucleation on an iron particle.

PubMed

Ohta, Yasuhito; Okamoto, Yoshiko; Page, Alister J; Irle, Stephan; Morokuma, Keiji

2009-11-24

The atomic scale details of single-walled carbon nanotube (SWNT) nucleation on metal catalyst particles are elusive to experimental observations. Computer simulation of metal-catalyzed SWNT nucleation is a challenging topic but potentially of great importance to understand the factors affecting SWNT diameters, chirality, and growth efficiency. In this work, we use nonequilibrium density functional tight-binding molecular dynamics simulations and report nucleation of sp(2)-carbon cap structures on an iron particle consisting of 38 atoms. One C(2) molecule was placed every 1.0 ps around an Fe(38) cluster for 30 ps, after which a further 410 ps of annealing simulation without carbon supply was performed. We find that sp(2)-carbon network nucleation and annealing processes occur in three sequential and repetitive stages: (A) polyyne chains on the metal surface react with each other to evolve into a Y-shaped polyyne junction, which preferentially form a five-membered ring as a nucleus; (B) polyyne chains on the first five-membered ring form an additional fused five- or six-membered ring; and (C) pentagon-to-hexagon self-healing rearrangement takes place with the help of short-lived polyyne chains, stabilized by the mobile metal atoms. The observed nucleation process resembles the formation of a fullerene cage. However, the metal particle plays a key role in differentiating the nucleation process from fullerene cage formation, most importantly by keeping the growing cap structure from closing into a fullerene cage and by keeping the carbon edge "alive" for the addition of new carbon material.

Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics.

PubMed

Sevink, G J A; Schmid, F; Kawakatsu, T; Milano, G

2017-02-22

We have extended an existing hybrid MD-SCF simulation technique that employs a coarsening step to enhance the computational efficiency of evaluating non-bonded particle interactions. This technique is conceptually equivalent to the single chain in mean-field (SCMF) method in polymer physics, in the sense that non-bonded interactions are derived from the non-ideal chemical potential in self-consistent field (SCF) theory, after a particle-to-field projection. In contrast to SCMF, however, MD-SCF evolves particle coordinates by the usual Newton's equation of motion. Since collisions are seriously affected by the softening of non-bonded interactions that originates from their evaluation at the coarser continuum level, we have devised a way to reinsert the effect of collisions on the structural evolution. Merging MD-SCF with multi-particle collision dynamics (MPCD), we mimic particle collisions at the level of computational cells and at the same time properly account for the momentum transfer that is important for a realistic system evolution. The resulting hybrid MD-SCF/MPCD method was validated for a particular coarse-grained model of phospholipids in aqueous solution, against reference full-particle simulations and the original MD-SCF model. We additionally implemented and tested an alternative and more isotropic finite difference gradient. Our results show that efficiency is improved by merging MD-SCF with MPCD, as properly accounting for hydrodynamic interactions considerably speeds up the phase separation dynamics, with negligible additional computational costs compared to efficient MD-SCF. This new method enables realistic simulations of large-scale systems that are needed to investigate the applications of self-assembled structures of lipids in nanotechnologies.

Colloidal gold-labeled insulin complex. Characterization and binding to adipocytes.

PubMed

Moll, U M; Thun, C; Pfeiffer, E F

1986-01-01

Biologically active insulin gold complex was used as an ultrastructural marker to study insulin binding sites, uptake, and internalization in isolated rat adipocytes. The preparation conditions for monodispersed particles, ca. 16 nm in diameter and loaded with approximately 100 insulin molecules, are reported. The complex is stable for at least six weeks. Single particles or small clusters were scattered across the cell membrane. The distribution of unbound receptors seemed to be independent of the extensive system of pre-existing surface connected vesicles in adipocytes. The uptake of particles took place predominantly via non-coated pinocytotic invaginations; clathrin-coated pits did not seem to be important for this process. Lysosome-like structures contained aggregates of 10-15 particles. These data suggest that insulin gold complex is a useful marker for the specific labeling of insulin binding sites.

Dose limited reliability of quantitative annular dark field scanning transmission electron microscopy for nano-particle atom-counting.

PubMed

De Backer, A; Martinez, G T; MacArthur, K E; Jones, L; Béché, A; Nellist, P D; Van Aert, S

2015-04-01

Quantitative annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique to characterise nano-particles on an atomic scale. Because of their limited size and beam sensitivity, the atomic structure of such particles may become extremely challenging to determine. Therefore keeping the incoming electron dose to a minimum is important. However, this may reduce the reliability of quantitative ADF STEM which will here be demonstrated for nano-particle atom-counting. Based on experimental ADF STEM images of a real industrial catalyst, we discuss the limits for counting the number of atoms in a projected atomic column with single atom sensitivity. We diagnose these limits by combining a thorough statistical method and detailed image simulations. Copyright © 2014 Elsevier B.V. All rights reserved.

Encoding the structure of many-body localization with matrix product operators

NASA Astrophysics Data System (ADS)

Pekker, David; Clark, Bryan K.

2015-03-01

Anderson insulators are non-interacting disordered systems which have localized single particle eigenstates. The interacting analogue of Anderson insulators are the Many-Body Localized (MBL) phases. The natural language for representing the spectrum of the Anderson insulator is that of product states over the single-particle modes. We show that product states over Matrix Product Operators of small bond dimension is the corresponding natural language for describing the MBL phases. In this language all of the many-body eigenstates are encode by Matrix Product States (i.e. DMRG wave function) consisting of only two sets of low bond-dimension matrices per site: the Gi matrix corresponding to the local ground state on site i and the Ei matrix corresponding to the local excited state. All 2 n eigenstates can be generated from all possible combinations of these matrices.

SubspaceEM: A Fast Maximum-a-posteriori Algorithm for Cryo-EM Single Particle Reconstruction

PubMed Central

Dvornek, Nicha C.; Sigworth, Fred J.; Tagare, Hemant D.

2015-01-01

Single particle reconstruction methods based on the maximum-likelihood principle and the expectation-maximization (E–M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300. PMID:25839831

Extracting Spectroscopic Factors of Argon Isotopes from Transfer Reactions

NASA Astrophysics Data System (ADS)

Manfredi, Juan; Lee, J.; Tsang, M. B.; Lynch, W. G.; Barney, J.; Estee, J.; Sweany, S.; Brown, K. W.; Cerizza, G.; Anderson, C.; Setiawan, H.; Loelius, C.; Xu, Z.; Rogers, A. M.; Pruitt, C.; Sobotka, L. G.; Elson, J. M.; Langer, C.; Chajecki, Z.; Chen, G.; Jones, K. L.; Smith, K.; Xiao, Z.; Li, Z.; Winkelbauer, J. R.

2017-01-01

A spectroscopic factor (SF) quantifies the single particle occupancy of a given state in a nucleus. For the argon isotopes, there is a discrepancy of the SF between studies that use transfer reactions and knockout reactions. Understanding the SFs of these isotopes, and in particular how the SF changes across the isotopic chain, is important for understanding how single particle structure changes with neutron number. The transfer reactions 34Ar(p,d) and 46Ar(p,d) were measured at the National Superconducting Cyclotron Laboratory (NSCL) using the same beam energy (70 MeV/u) as from the previous knockout measurement. Spectroscopic factors were extracted from measured angular distributions via ADWA calculations. Preliminary findings will be presented. The National Superconducting Cyclotron Laboratory is supported by the NSF (PHY 1102511), and Juan Manfredi is supported by the DOE NNSA Stewardship Science Graduate Fellowship.

Dragonfly: an implementation of the expand-maximize-compress algorithm for single-particle imaging.

PubMed

Ayyer, Kartik; Lan, Ti-Yen; Elser, Veit; Loh, N Duane

2016-08-01

Single-particle imaging (SPI) with X-ray free-electron lasers has the potential to change fundamentally how biomacromolecules are imaged. The structure would be derived from millions of diffraction patterns, each from a different copy of the macromolecule before it is torn apart by radiation damage. The challenges posed by the resultant data stream are staggering: millions of incomplete, noisy and un-oriented patterns have to be computationally assembled into a three-dimensional intensity map and then phase reconstructed. In this paper, the Dragonfly software package is described, based on a parallel implementation of the expand-maximize-compress reconstruction algorithm that is well suited for this task. Auxiliary modules to simulate SPI data streams are also included to assess the feasibility of proposed SPI experiments at the Linac Coherent Light Source, Stanford, California, USA.

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction.

PubMed

Pittman, Nikéa; Misseldine, Adam; Geilen, Lorena; Halder, Sujata; Smith, J Kennon; Kurian, Justin; Chipman, Paul; Janssen, Mandy; Mckenna, Robert; Baker, Timothy S; D'Abramo, Anthony; Cotmore, Susan; Tattersall, Peter; Agbandje-McKenna, Mavis

2017-10-30

LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism.

Micrometer-sized TPM emulsion droplets with surface-mobile binding groups

NASA Astrophysics Data System (ADS)

van der Wel, Casper; van de Stolpe, Guido L.; Verweij, Ruben W.; Kraft, Daniela J.

2018-03-01

Colloids coated with lipid membranes have been widely employed for fundamental studies of lipid membrane processes, biotechnological applications such as drug delivery and biosensing, and more recently, for self-assembly. The latter has been made possible by inserting DNA oligomers with covalently linked hydrophobic anchors into the membrane. The lateral mobility of the DNA linkers on micrometer-sized droplets and solid particles has opened the door to creating structures with unprecedented structural flexibility. Here, we investigate micro-emulsions of TPM (3-(trimethoxysilyl)propyl methacrylate) as a platform for lipid monolayers and further functionalization with proteins and DNA oligonucleotides. TPM droplets can be produced with a narrow size distribution and are polymerizable, thus providing supports for model lipid membranes with controlled size and curvature. With fluorescence recovery after photobleaching, we observed that droplet-attached lipids, NeutrAvidin proteins, as well as DNA oligonucleotides all show mobility on the surface. We explored the assembly of micron-sized particles on TPM-droplets by exploiting either avidin-biotin interactions or double-stranded DNA with complementary single-stranded end groups. While the single molecules are mobile, the particles that are attached to them are not. We propose that this is caused by the heterogeneous nature of emulsified TPM, which forms an oligomer network that limits the collective motion of linkers, but allows the surface mobility of individual molecules.

Aging induced changes on NEXAFS fingerprints in individual combustion particles

NASA Astrophysics Data System (ADS)

Zelenay, V.; Mooser, R.; Tritscher, T.; Křepelová, A.; Heringa, M. F.; Chirico, R.; Prévôt, A. S. H.; Weingartner, E.; Baltensperger, U.; Dommen, J.; Watts, B.; Raabe, J.; Huthwelker, T.; Ammann, M.

2011-11-01

Soot particles can significantly influence the Earth's climate by absorbing and scattering solar radiation as well as by acting as cloud condensation nuclei. However, despite their environmental (as well as economic and political) importance, the way these properties are affected by atmospheric processing of the combustion exhaust gases is still a subject of discussion. In this work, individual soot particles emitted from two different vehicles, a EURO 2 transporter, a EURO 3 passenger car, and a wood stove were investigated on a single-particle basis. The emitted exhaust, including the particulate and the gas phase, was processed in a smog chamber with artificial solar radiation. Single particle specimens of both unprocessed and aged soot were characterized using near edge X-ray absorption fine structure spectroscopy (NEXAFS) and scanning electron microscopy. Comparison of NEXAFS spectra from the unprocessed particles and those resulting from exhaust photooxidation in the chamber revealed changes in the carbon functional group content. For the wood stove emissions, these changes were minor, related to the relatively mild oxidation conditions. For the EURO 2 transporter emissions, the most apparent change was that of carboxylic carbon from oxidized organic compounds condensing on the primary soot particles. For the EURO 3 car emissions oxidation of primary soot particles upon photochemical aging has likely contributed as well. Overall, the changes in the NEXAFS fingerprints were in qualitative agreement with data from an aerosol mass spectrometer. Furthermore, by taking full advantage of our in situ microreactor concept, we show that the soot particles from all three combustion sources changed their ability to take up water under humid conditions upon photochemical aging of the exhaust. Due to the selectivity and sensitivity of the NEXAFS technique for the water mass, also small amounts of water taken up into the internal voids of agglomerated particles could be detected. Because such small amounts of water uptake do not lead to measurable changes in particle diameter, it may remain beyond the limits of volume growth measurements, especially for larger agglomerated particles.

High sensitivity fluorescent single particle and single molecule detection apparatus and method

DOEpatents

Mathies, Richard A.; Peck, Konan; Stryer, Lubert

1990-01-01

Apparatus is described for ultrasensitive detection of single fluorescent particles down to the single fluorescent molecule limit in a fluid or on a substrate comprising means for illuminating a predetermined volume of the fluid or area of the substrate whereby to emit light including background light from the fluid and burst of photons from particles residing in the area. The photon burst is detected in real time to generate output representative signal. The signal is received and the burst of energy from the fluorescent particles is distinguished from the background energy to provide an indication of the number, location or concentration of the particles or molecules.

Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components

PubMed Central

Zivanovic, Yvan; Confalonieri, Fabrice; Ponchon, Luc; Lurz, Rudi; Chami, Mohamed; Flayhan, Ali; Renouard, Madalena; Huet, Alexis; Decottignies, Paulette; Davidson, Alan R.; Breyton, Cécile

2014-01-01

Bacteriophage T5 represents a large family of lytic Siphoviridae infecting Gram-negative bacteria. The low-resolution structure of T5 showed the T=13 geometry of the capsid and the unusual trimeric organization of the tail tube, and the assembly pathway of the capsid was established. Although major structural proteins of T5 have been identified in these studies, most of the genes encoding the morphogenesis proteins remained to be identified. Here, we combine a proteomic analysis of T5 particles with a bioinformatic study and electron microscopic immunolocalization to assign function to the genes encoding the structural proteins, the packaging proteins, and other nonstructural components required for T5 assembly. A head maturation protease that likely accounts for the cleavage of the different capsid proteins is identified. Two other proteins involved in capsid maturation add originality to the T5 capsid assembly mechanism: the single head-to-tail joining protein, which closes the T5 capsid after DNA packaging, and the nicking endonuclease responsible for the single-strand interruptions in the T5 genome. We localize most of the tail proteins that were hitherto uncharacterized and provide a detailed description of the tail tip composition. Our findings highlight novel variations of viral assembly strategies and of virion particle architecture. They further recommend T5 for exploring phage structure and assembly and for deciphering conformational rearrangements that accompany DNA transfer from the capsid to the host cytoplasm. PMID:24198424

Beyond the single-file fluid limit using transfer matrix method: Exact results for confined parallel hard squares

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gurin, Péter; Varga, Szabolcs

2015-06-14

We extend the transfer matrix method of one-dimensional hard core fluids placed between confining walls for that case where the particles can pass each other and at most two layers can form. We derive an eigenvalue equation for a quasi-one-dimensional system of hard squares confined between two parallel walls, where the pore width is between σ and 3σ (σ is the side length of the square). The exact equation of state and the nearest neighbor distribution functions show three different structures: a fluid phase with one layer, a fluid phase with two layers, and a solid-like structure where the fluidmore » layers are strongly correlated. The structural transition between differently ordered fluids develops continuously with increasing density, i.e., no thermodynamic phase transition occurs. The high density structure of the system consists of clusters with two layers which are broken with particles staying in the middle of the pore.« less

Single particles measured by a light scattering module coupled to a time-of-flight aerosol mass spectrometer onboard the NOAA P-3 aircraft during SENEX

NASA Astrophysics Data System (ADS)

Liao, J.; Middlebrook, A. M.; Welti, A.; Sueper, D.; Murphy, D. M.

2014-12-01

Single particles in the eastern US were characterized by a light scattering module coupled to a time-of-flight aerosol mass spectrometer (LS-ToF-AMS) onboard the NOAA P-3 aircraft during the Southeastern Nexus (SENEX) campaign. Single particle data were collected for 30 seconds every 5 minutes. Aerosols larger than 200-300 nm in vacuum aerodynamic diameter can be optically detected by the 405 nm crystal laser and trigger the saving of single particle mass spectra. The measured single particles are internally-mixed as expected. The single particles were classified as prompt, delayed, and null based on the chemical ion signal arrival time difference between prediction from the light scattering signal and measurement by mass spectrometer and the presence or absence of a mass spectrum. On average the number fraction of particles detected as prompt, delayed, and null (no spectrum) is about 30%, 10%, and 60%. The number fraction of these three particle types varied with aerosol size, chemical composition and the investigation region and will be discussed in detail. For example, the number fraction of prompt particles was significantly higher for the flight to the Pennsylvania natural gas shale region on July 6, 2013, which is probably related to the chemical composition (more acidic) and phase of the ambient particles. These particle types and detection efficiency are related to the bouncing effect on the vaporizer and may provide insight into the non-unit AMS collection efficiency. Moreover, most of the particles larger than 800 nm in vacuum aerodynamic diameter sized with the traditional AMS PToF mode are delayed particles and their mass spectral signals appear to be affected by this process.

Numerical analysis of a 3D optical sensor based on single mode fiber to multimode interference graphene design

NASA Astrophysics Data System (ADS)

Mutter, Kussay N.; Jafri, Zubir M.; Tan, Kok Chooi

2016-04-01

In this paper, the simulation and design of a waveguide for water turbidity sensing are presented. The structure of the proposed sensor uses a 2x2 array of multimode interference (MMI) coupler based on micro graphene waveguide for high sensitivity. The beam propagation method (BPM) are used to efficiently design the sensor structure. The structure is consist of an array of two by two elements of sensors. Each element has three sections of single mode for field input tapered to MMI as the main core sensor without cladding which is graphene based material, and then a single mode fiber as an output. In this configuration MMI responses to any change in the environment. We validate and present the results by implementing the design on a set of sucrose solution and showing how these samples lead to a sensitivity change in the sensor based on the MMI structures. Overall results, the 3D design has a feasible and effective sensing by drawing topographical distribution of suspended particles in the water.

Quantum cryptography using single-particle entanglement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jae-Weon; Lee, Eok Kyun; Chung, Yong Wook

2003-07-01

A quantum cryptography scheme based on entanglement between a single-particle state and a vacuum state is proposed. The scheme utilizes linear optics devices to detect the superposition of the vacuum and single-particle states. Existence of an eavesdropper can be detected by using a variant of Bell's inequality.

Single step, pH induced gold nanoparticle chain formation in lecithin/water system.

PubMed

Sharma, Damyanti

2013-07-01

Gold nanoparticle (AuNP) chains have been formed by a single step method in a lecithin/water system where lecithin itself plays the role of a reductant and a template for AuNP chain formation. Two preparative strategies were explored: (1) evaporating lecithin solution with aqueous gold chloride (HAuCl4) at different pHs and (2) dispersing lecithin vesicles in aqueous HAuCl4 solutions of various pHs in the range of 2.5-11.3. In method 1, at initial pH 2.5, 20-50 nm AuNPs are found attached to lecithin vesicles. When pH is raised to 5.5 there are no vesicles present and 20 nm monodisperse particles are found aggregating. Chain formation of fine nanoparticles (3-5 nm) is observed from neutral to basic pH, between 6.5-10.3 The chains formed are hundreds of nanometers to micrometer long and are usually 2-3 nanoparticles wide. On further increasing pH to 11.3, particles form disk-like or raft-like structures. When method (ii) was used a little chain formation was observed. Most of the nanoparticles formed were found either sitting together as raft like structures or scattered on lecithin structures. Copyright © 2013 Elsevier B.V. All rights reserved.

Direct visualization of the thermomagnetic behavior of pseudo-single-domain magnetite particles.

PubMed

Almeida, Trevor P; Muxworthy, Adrian R; Kovács, András; Williams, Wyn; Brown, Paul D; Dunin-Borkowski, Rafal E

2016-04-01

The study of the paleomagnetic signal recorded by rocks allows scientists to understand Earth's past magnetic field and the formation of the geodynamo. The magnetic recording fidelity of this signal is dependent on the magnetic domain state it adopts. The most prevalent example found in nature is the pseudo-single-domain (PSD) structure, yet its recording fidelity is poorly understood. Here, the thermoremanent behavior of PSD magnetite (Fe3O4) particles, which dominate the magnetic signatures of many rock lithologies, is investigated using electron holography. This study provides spatially resolved magnetic information from individual Fe3O4 grains as a function of temperature, which has been previously inaccessible. A small exemplar Fe3O4 grain (~150 nm) exhibits dynamic movement of its magnetic vortex structure above 400°C, recovering its original state upon cooling, whereas a larger exemplar Fe3O4 grain (~250 nm) is shown to retain its vortex state on heating to 550°C, close to the Curie temperature of 580°C. Hence, we demonstrate that Fe3O4 grains containing vortex structures are indeed reliable recorders of paleodirectional and paleointensity information, and the presence of PSD magnetic signals does not preclude the successful recovery of paleomagnetic signals.

Direct visualization of the thermomagnetic behavior of pseudo–single-domain magnetite particles

PubMed Central

Almeida, Trevor P.; Muxworthy, Adrian R.; Kovács, András; Williams, Wyn; Brown, Paul D.; Dunin-Borkowski, Rafal E.

2016-01-01

The study of the paleomagnetic signal recorded by rocks allows scientists to understand Earth’s past magnetic field and the formation of the geodynamo. The magnetic recording fidelity of this signal is dependent on the magnetic domain state it adopts. The most prevalent example found in nature is the pseudo–single-domain (PSD) structure, yet its recording fidelity is poorly understood. Here, the thermoremanent behavior of PSD magnetite (Fe3O4) particles, which dominate the magnetic signatures of many rock lithologies, is investigated using electron holography. This study provides spatially resolved magnetic information from individual Fe3O4 grains as a function of temperature, which has been previously inaccessible. A small exemplar Fe3O4 grain (~150 nm) exhibits dynamic movement of its magnetic vortex structure above 400°C, recovering its original state upon cooling, whereas a larger exemplar Fe3O4 grain (~250 nm) is shown to retain its vortex state on heating to 550°C, close to the Curie temperature of 580°C. Hence, we demonstrate that Fe3O4 grains containing vortex structures are indeed reliable recorders of paleodirectional and paleointensity information, and the presence of PSD magnetic signals does not preclude the successful recovery of paleomagnetic signals. PMID:27152353

Mass spectra features of biomass burning boiler and coal burning boiler emitted particles by single particle aerosol mass spectrometer.

PubMed

Xu, Jiao; Li, Mei; Shi, Guoliang; Wang, Haiting; Ma, Xian; Wu, Jianhui; Shi, Xurong; Feng, Yinchang

2017-11-15

In this study, single particle mass spectra signatures of both coal burning boiler and biomass burning boiler emitted particles were studied. Particle samples were suspended in clean Resuspension Chamber, and analyzed by ELPI and SPAMS simultaneously. The size distribution of BBB (biomass burning boiler sample) and CBB (coal burning boiler sample) are different, as BBB peaks at smaller size, and CBB peaks at larger size. Mass spectra signatures of two samples were studied by analyzing the average mass spectrum of each particle cluster extracted by ART-2a in different size ranges. In conclusion, BBB sample mostly consists of OC and EC containing particles, and a small fraction of K-rich particles in the size range of 0.2-0.5μm. In 0.5-1.0μm, BBB sample consists of EC, OC, K-rich and Al_Silicate containing particles; CBB sample consists of EC, ECOC containing particles, while Al_Silicate (including Al_Ca_Ti_Silicate, Al_Ti_Silicate, Al_Silicate) containing particles got higher fractions as size increase. The similarity of single particle mass spectrum signatures between two samples were studied by analyzing the dot product, results indicated that part of the single particle mass spectra of two samples in the same size range are similar, which bring challenge to the future source apportionment activity by using single particle aerosol mass spectrometer. Results of this study will provide physicochemical information of important sources which contribute to particle pollution, and will support source apportionment activities. Copyright © 2017. Published by Elsevier B.V.

Micrometeorite penetration effects in gold foil

NASA Technical Reports Server (NTRS)

Hallgren, D. S.; Radigan, W.; Hemenway, C. L.

1976-01-01

Penetration structures revealed by a Skylab experiment dealing with exposure of single and double layers of 500-800 A thick gold foil to micrometeorites are examined. Examination of all double-layered gold foils revealed that particles producing holes of any type greater than 5 microns in diameter in the first foil break up into many fragments which in turn produce many more holes in the second foil. Evidence of an original particle is not found on any stainless steel plate below the foils, except in one instance. A precise relationship between the size of the event and the mass of the particle producing it could not be determined due to the extreme morphological variety in penetration effects. Fluxes from gold foil and crater experiments are briefly discussed.

Comparison of morphology and phase composition of hydroxyapatite nanoparticles sonochemically synthesized with dual- or single-frequency ultrasonic reactor

NASA Astrophysics Data System (ADS)

Deng, Shi-ting; Yu, Hong; Liu, Di; Bi, Yong-guang

2017-10-01

To investigate how a dual- or single-frequency ultrasonic reactor changes the morphology and phase composition of hydroxyapatite nanoparticles (nHAPs), we designed and constructed the preparation of nHAPs using dual- or single-frequency ultrasonic devices, i.e., the single frequency ultrasonic generator with ultrasonic horn (25 kHz), the ultrasonic bath (40 kHz) and the dual-frequency sonochemical systems combined with the ultrasonic horn and the ultrasonic bath simultaneously (25 + 40 kHz). The results showed that the sonicated samples displayed a more uniform shape with less agglomeration than non-sonicated sample. The rod-shaped particles with 1.66 stoichiometry and without a second phase were synthesized successfully in the ultrasonic bath or horn systems. The nHAPs obtained from the dual-frequency ultrasonic systems exhibited a regular rod-shaped structure with better dispersion and more uniform shapes than those of obtained in either ultrasonic bath or horn systems. Additionally, the size of rod-shaped particles obtained in the dual-frequency ultrasound with a mean width of 35 nm and a mean length of 64 nm was smaller than other samples. A possible mechanism is that the dual-frequency ultrasound significantly enhances the cavitation yield over single frequency ultrasound and thus improves the dispersion of particles and reduces the size of the crystals. In addition, irregular holes can be observed in the nanoparticles obtained in the dual-frequency ultrasound. Therefore, the dual-frequency ultrasonic systems are expected to become a convenient, efficient and environmentally friendly synthetic technology to obtain well-defined nHAPs for specific biomedical applications.

Modeling photoacoustic spectral features of micron-sized particles

NASA Astrophysics Data System (ADS)

Strohm, Eric M.; Gorelikov, Ivan; Matsuura, Naomi; Kolios, Michael C.

2014-10-01

The photoacoustic signal generated from particles when irradiated by light is determined by attributes of the particle such as the size, speed of sound, morphology and the optical absorption coefficient. Unique features such as periodically varying minima and maxima are observed throughout the photoacoustic signal power spectrum, where the periodicity depends on these physical attributes. The frequency content of the photoacoustic signals can be used to obtain the physical attributes of unknown particles by comparison to analytical solutions of homogeneous symmetric geometric structures, such as spheres. However, analytical solutions do not exist for irregularly shaped particles, inhomogeneous particles or particles near structures. A finite element model (FEM) was used to simulate photoacoustic wave propagation from four different particle configurations: a homogeneous particle suspended in water, a homogeneous particle on a reflecting boundary, an inhomogeneous particle with an absorbing shell and non-absorbing core, and an irregularly shaped particle such as a red blood cell. Biocompatible perfluorocarbon droplets, 3-5 μm in diameter containing optically absorbing nanoparticles were used as the representative ideal particles, as they are spherical, homogeneous, optically translucent, and have known physical properties. The photoacoustic spectrum of micron-sized single droplets in suspension and on a reflecting boundary were measured over the frequency range of 100-500 MHz and compared directly to analytical models and the FEM. Good agreement between the analytical model, FEM and measured values were observed for a droplet in suspension, where the spectral minima agreed to within a 3.3 MHz standard deviation. For a droplet on a reflecting boundary, spectral features were correctly reproduced using the FEM but not the analytical model. The photoacoustic spectra from other common particle configurations such as particle with an absorbing shell and a biconcave-shaped red blood cell were also investigated, where unique features in the power spectrum could be used to identify them.

An equivalent method for optimization of particle tuned mass damper based on experimental parametric study

NASA Astrophysics Data System (ADS)

Lu, Zheng; Chen, Xiaoyi; Zhou, Ying

2018-04-01

A particle tuned mass damper (PTMD) is a creative combination of a widely used tuned mass damper (TMD) and an efficient particle damper (PD) in the vibration control area. The performance of a one-storey steel frame attached with a PTMD is investigated through free vibration and shaking table tests. The influence of some key parameters (filling ratio of particles, auxiliary mass ratio, and particle density) on the vibration control effects is investigated, and it is shown that the attenuation level significantly depends on the filling ratio of particles. According to the experimental parametric study, some guidelines for optimization of the PTMD that mainly consider the filling ratio are proposed. Furthermore, an approximate analytical solution based on the concept of an equivalent single-particle damper is proposed, and it shows satisfied agreement between the simulation and experimental results. This simplified method is then used for the preliminary optimal design of a PTMD system, and a case study of a PTMD system attached to a five-storey steel structure following this optimization process is presented.

Compression-induced texture change in NiMnGa-polymer composites observed by synchrotron radiation

NASA Astrophysics Data System (ADS)

Scheerbaum, Nils; Hinz, Dietrich; Gutfleisch, Oliver; Skrotzki, Werner; Schultz, Ludwig

2007-05-01

Composites consisting of magnetic shape memory (MSM) particles embedded in a polyester matrix were prepared. Single-crystalline MSM particles were obtained by mortar grinding of melt-extracted and subsequently annealed Ni50.9Mn27.1Ga22.0 (at. %) fibers. The crystal structure of the martensite is tetragonal (5M) with c

Nonlinear dynamics of resonant electrons interacting with coherent Langmuir waves

NASA Astrophysics Data System (ADS)

Tobita, Miwa; Omura, Yoshiharu

2018-03-01

We study the nonlinear dynamics of resonant particles interacting with coherent waves in space plasmas. Magnetospheric plasma waves such as whistler-mode chorus, electromagnetic ion cyclotron waves, and hiss emissions contain coherent wave structures with various discrete frequencies. Although these waves are electromagnetic, their interaction with resonant particles can be approximated by equations of motion for a charged particle in a one-dimensional electrostatic wave. The equations are expressed in the form of nonlinear pendulum equations. We perform test particle simulations of electrons in an electrostatic model with Langmuir waves and a non-oscillatory electric field. We solve equations of motion and study the dynamics of particles with different values of inhomogeneity factor S defined as a ratio of the non-oscillatory electric field intensity to the wave amplitude. The simulation results demonstrate deceleration/acceleration, thermalization, and trapping of particles through resonance with a single wave, two waves, and multiple waves. For two-wave and multiple-wave cases, we describe the wave-particle interaction as either coherent or incoherent based on the probability of nonlinear trapping.

Single-molecule detection of proteins with antigen-antibody interaction using resistive-pulse sensing of submicron latex particles

NASA Astrophysics Data System (ADS)

Takakura, T.; Yanagi, I.; Goto, Y.; Ishige, Y.; Kohara, Y.

2016-03-01

We developed a resistive-pulse sensor with a solid-state pore and measured the latex agglutination of submicron particles induced by antigen-antibody interaction for single-molecule detection of proteins. We fabricated the pore based on numerical simulation to clearly distinguish between monomer and dimer latex particles. By measuring single dimers agglutinated in the single-molecule regime, we detected single human alpha-fetoprotein molecules. Adjusting the initial particle concentration improves the limit of detection (LOD) to 95 fmol/l. We established a theoretical model of the LOD by combining the reaction kinetics and the counting statistics to explain the effect of initial particle concentration on the LOD. The theoretical model shows how to improve the LOD quantitatively. The single-molecule detection studied here indicates the feasibility of implementing a highly sensitive immunoassay by a simple measurement method using resistive-pulse sensing.

Single exposure three-dimensional imaging of dusty plasma clusters.

PubMed

Hartmann, Peter; Donkó, István; Donkó, Zoltán

2013-02-01

We have worked out the details of a single camera, single exposure method to perform three-dimensional imaging of a finite particle cluster. The procedure is based on the plenoptic imaging principle and utilizes a commercial Lytro light field still camera. We demonstrate the capabilities of our technique on a single layer particle cluster in a dusty plasma, where the camera is aligned and inclined at a small angle to the particle layer. The reconstruction of the third coordinate (depth) is found to be accurate and even shadowing particles can be identified.

Multi-party quantum summation without a trusted third party based on single particles

NASA Astrophysics Data System (ADS)

Zhang, Cai; Situ, Haozhen; Huang, Qiong; Yang, Pingle

We propose multi-party quantum summation protocols based on single particles, in which participants are allowed to compute the summation of their inputs without the help of a trusted third party and preserve the privacy of their inputs. Only one participant who generates the source particles needs to perform unitary operations and only single particles are needed in the beginning of the protocols.

Plenoptic particle image velocimetry with multiple plenoptic cameras

NASA Astrophysics Data System (ADS)

Fahringer, Timothy W.; Thurow, Brian S.

2018-07-01

Plenoptic particle image velocimetry was recently introduced as a viable three-dimensional, three-component velocimetry technique based on light field cameras. One of the main benefits of this technique is its single camera configuration allowing the technique to be applied in facilities with limited optical access. The main drawback of this configuration is decreased accuracy in the out-of-plane dimension. This work presents a solution with the addition of a second plenoptic camera in a stereo-like configuration. A framework for reconstructing volumes with multiple plenoptic cameras including the volumetric calibration and reconstruction algorithms, including: integral refocusing, filtered refocusing, multiplicative refocusing, and MART are presented. It is shown that the addition of a second camera improves the reconstruction quality and removes the ‘cigar’-like elongation associated with the single camera system. In addition, it is found that adding a third camera provides minimal improvement. Further metrics of the reconstruction quality are quantified in terms of a reconstruction algorithm, particle density, number of cameras, camera separation angle, voxel size, and the effect of common image noise sources. In addition, a synthetic Gaussian ring vortex is used to compare the accuracy of the single and two camera configurations. It was determined that the addition of a second camera reduces the RMSE velocity error from 1.0 to 0.1 voxels in depth and 0.2 to 0.1 voxels in the lateral spatial directions. Finally, the technique is applied experimentally on a ring vortex and comparisons are drawn from the four presented reconstruction algorithms, where it was found that MART and multiplicative refocusing produced the cleanest vortex structure and had the least shot-to-shot variability. Filtered refocusing is able to produce the desired structure, albeit with more noise and variability, while integral refocusing struggled to produce a coherent vortex ring.

Effects of Energetic and Inert Nano Particles on Burning Liquid Ethanol Droplets

NASA Astrophysics Data System (ADS)

Plascencia, Miguel; Sim, Hyung Sub; Vargas, Andres; Smith, Owen; Karagozian, Ann

2017-11-01

This study explores the effects of nano particulate additives on ethanol fuel droplet combustion in a quiescent environment. Two different types of droplet combustion experiments were performed: one involving the classic single droplet suspended from a quartz fiber and the other involving a burning droplet that has continual fuel delivery via a quartz capillary. Two alternative nano particles were explored here to demonstrate the effect of energetic additives: reactive nano aluminum (nAl) and inert nano silicon dioxide (nSiO2), each with average diameter 80 nm. Simultaneous high speed visible and OH* chemiluminescence images were taken to determine burning rate constants (K) and to study flame and droplet characteristics with varying particulate concentrations. Particle/vapor ejections were seen in continuously fed droplet experiments, while rod-suspended burning droplets showed limited particle ejection. The nSiO2 -laden, rod-suspended droplets formed a porous, shell-like structure resembling the shape of a droplet at higher nSiO2 concentrations, in contrast to smaller residue structures for nAl-laden droplets. Changes in K depended on concentrations of nAl and nSiO2 as well as the method of droplet formation, and TEM images of particle residue revealed additional insights. Supported by AFOSR Grant FA9550-15-1-0339.

Surface structural evolution of AuAg/TiO2 catalyst in the transformation of benzyl alcohol to sodium benzoate

NASA Astrophysics Data System (ADS)

Cui, Yuanyuan; Wang, Ying; Fan, Kangnian; Dai, Wei-Lin

2013-08-01

A series of AuAg/TiO2 catalysts calcined at different temperatures were used for single-pot, solvent-free synthesis of sodium benzoate and benzoic acid through the green oxidation of benzyl alcohol. The best catalytic performance, which produced a sodium benzoate yield of up to 85%, was obtained over the AuAg/TiO2 catalyst calcined at 623 K. Systematic characterizations including BET, XRD, TEM, XPS, and UV-vis DRS and ICP were carried out to investigate the influence of calcined temperature on the structural evolution of the bimetallic AuAg/TiO2 catalysts. TEM images showed that both low (473 K) and high calcinations temperatures (973 K) resulted in larger particles. The smallest particles (8.2 nm) were obtained at 623 K. This decrease in particle size may have been induced by the re-dispersion and interaction of the bimetallic species. XRD and XPS results showed that proper calcination temperature (623 K) could promote interactions between the bimetallic particles and the TiO2 support as well as the dispersion of active bimetallic species. The higher catalytic performance of the 623 K calcined catalyst could be attributed to the smaller particle size and the synergetic interaction between nano-bimetallic gold and silver species.

Biocompatible Er, Yb co-doped fluoroapatite upconversion nanoparticles for imaging applications

NASA Astrophysics Data System (ADS)

Anjana, R.; K. M., Kurias; M. K., Jayaraj

2017-08-01

Upconversion luminescence, visible emission on infra red (IR) excitation was achieved in a biocompatible material, fluoroapatite. Fluoroapatite crystals are well known biomaterials, which is a component of tooth enamel. Also it can be considered as an excellent host material for lanthanide doping since the ionic radii of lanthanide is similar to that of calcium ion(Ca2+) hence successful incorporation of dopants within the lattice is possible. Erbium (Er), Ytterbium (Yb) co-doped fluorapatite (FAp) nanoparticles were prepared by precipitation method. The particles show intense visible emission when excited with 980 nm laser. Since upconversion luminescence is a multiphoton process the excitation power dependence on emission will give number of photons involved in the emission of single photon. Excitation power dependence studies show that two photons are involved in the emission of single photons. The value of slope was different for different emission peak because of the difference in intermediate energy level involved. The crystal structure and morphology of the particle were determined using X-ray diffractometer (XRD) and field emission scanning electron microscope (FESEM). These particles with surface functionalisation can be used for live cell imaging.

Laser- and Particle-Beam Chemical Processes on Surfaces. Volume 129

DTIC Science & Technology

1989-12-26

explosive decomposition of organometallic compounds with single pulse laser irradiation . This new... ultrashort , meaning ultra high intensity , excimer laser pulses , two-photon absorption becomes important and limits the penetration depth of the laser ...requires a higher photon load before suffering damage to its chemical structure. With extremely high light intensities , ultrashort excimer laser pulses

Single α-particle irradiation permits real-time visualization of RNF8 accumulation at DNA damaged sites

NASA Astrophysics Data System (ADS)

Muggiolu, Giovanna; Pomorski, Michal; Claverie, Gérard; Berthet, Guillaume; Mer-Calfati, Christine; Saada, Samuel; Devès, Guillaume; Simon, Marina; Seznec, Hervé; Barberet, Philippe

2017-01-01

As well as being a significant source of environmental radiation exposure, α-particles are increasingly considered for use in targeted radiation therapy. A better understanding of α-particle induced damage at the DNA scale can be achieved by following their tracks in real-time in targeted living cells. Focused α-particle microbeams can facilitate this but, due to their low energy (up to a few MeV) and limited range, α-particles detection, delivery, and follow-up observations of radiation-induced damage remain difficult. In this study, we developed a thin Boron-doped Nano-Crystalline Diamond membrane that allows reliable single α-particles detection and single cell irradiation with negligible beam scattering. The radiation-induced responses of single 3 MeV α-particles delivered with focused microbeam are visualized in situ over thirty minutes after irradiation by the accumulation of the GFP-tagged RNF8 protein at DNA damaged sites.

Data processing software suite SITENNO for coherent X-ray diffraction imaging using the X-ray free-electron laser SACLA.

PubMed

Sekiguchi, Yuki; Oroguchi, Tomotaka; Takayama, Yuki; Nakasako, Masayoshi

2014-05-01

Coherent X-ray diffraction imaging is a promising technique for visualizing the structures of non-crystalline particles with dimensions of micrometers to sub-micrometers. Recently, X-ray free-electron laser sources have enabled efficient experiments in the `diffraction before destruction' scheme. Diffraction experiments have been conducted at SPring-8 Angstrom Compact free-electron LAser (SACLA) using the custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors. In the experiments, ten thousands of single-shot diffraction patterns can be collected within several hours. Then, diffraction patterns with significant levels of intensity suitable for structural analysis must be found, direct-beam positions in diffraction patterns determined, diffraction patterns from the two CCD detectors merged, and phase-retrieval calculations for structural analyses performed. A software suite named SITENNO has been developed to semi-automatically apply the four-step processing to a huge number of diffraction data. Here, details of the algorithm used in the suite are described and the performance for approximately 9000 diffraction patterns collected from cuboid-shaped copper oxide particles reported. Using the SITENNO suite, it is possible to conduct experiments with data processing immediately after the data collection, and to characterize the size distribution and internal structures of the non-crystalline particles.

Data processing software suite SITENNO for coherent X-ray diffraction imaging using the X-ray free-electron laser SACLA

PubMed Central

Sekiguchi, Yuki; Oroguchi, Tomotaka; Takayama, Yuki; Nakasako, Masayoshi

2014-01-01

Coherent X-ray diffraction imaging is a promising technique for visualizing the structures of non-crystalline particles with dimensions of micrometers to sub-micrometers. Recently, X-ray free-electron laser sources have enabled efficient experiments in the ‘diffraction before destruction’ scheme. Diffraction experiments have been conducted at SPring-8 Angstrom Compact free-electron LAser (SACLA) using the custom-made diffraction apparatus KOTOBUKI-1 and two multiport CCD detectors. In the experiments, ten thousands of single-shot diffraction patterns can be collected within several hours. Then, diffraction patterns with significant levels of intensity suitable for structural analysis must be found, direct-beam positions in diffraction patterns determined, diffraction patterns from the two CCD detectors merged, and phase-retrieval calculations for structural analyses performed. A software suite named SITENNO has been developed to semi-automatically apply the four-step processing to a huge number of diffraction data. Here, details of the algorithm used in the suite are described and the performance for approximately 9000 diffraction patterns collected from cuboid-shaped copper oxide particles reported. Using the SITENNO suite, it is possible to conduct experiments with data processing immediately after the data collection, and to characterize the size distribution and internal structures of the non-crystalline particles. PMID:24763651

Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports

PubMed Central

Meyerson, Joel R.; Rao, Prashant; Kumar, Janesh; Chittori, Sagar; Banerjee, Soojay; Pierson, Jason; Mayer, Mark L.; Subramaniam, Sriram

2014-01-01

Poor partitioning of macromolecules into the holes of holey carbon support grids frequently limits structural determination by single particle cryo-electron microscopy (cryo-EM). Here, we present a method to deposit, on gold-coated carbon grids, a self-assembled monolayer whose surface properties can be controlled by chemical modification. We demonstrate the utility of this approach to drive partitioning of ionotropic glutamate receptors into the holes, thereby enabling 3D structural analysis using cryo-EM methods. PMID:25403871

The effect of single-horn glaze ice on the vortex structures in the wake of a horizontal axis wind turbine

NASA Astrophysics Data System (ADS)

Jin, Zhe-Yan; Dong, Qiao-Tian; Yang, Zhi-Gang

2015-02-01

The present study experimentally investigated the effect of a simulated single-horn glaze ice accreted on rotor blades on the vortex structures in the wake of a horizontal axis wind turbine by using the stereoscopic particle image velocimetry (Stereo-PIV) technique. During the experiments, four horizontal axis wind turbine models were tested, and both "free-run" and "phase-locked" Stereo-PIV measurements were carried out. Based on the "free-run" measurements, it was found that because of the simulated single-horn glaze ice, the shape, vorticity, and trajectory of tip vortices were changed significantly, and less kinetic energy of the airflow could be harvested by the wind turbine. In addition, the "phase-locked" results indicated that the presence of simulated single-horn glaze ice resulted in a dramatic reduction of the vorticity peak of the tip vortices. Moreover, as the length of the glaze ice increased, both root and tip vortex gaps were found to increase accordingly.

Two-particle problem in comblike structures

NASA Astrophysics Data System (ADS)

Agliari, Elena; Cassi, Davide; Cattivelli, Luca; Sartori, Fabio

2016-05-01

Encounters between walkers performing a random motion on an appropriate structure can describe a wide variety of natural phenomena ranging from pharmacokinetics to foraging. On homogeneous structures the asymptotic encounter probability between two walkers is (qualitatively) independent of whether both walkers are moving or one is kept fixed. On infinite comblike structures this is no longer the case and here we deepen the mechanisms underlying the emergence of a finite probability that two random walkers will never meet, while one single random walker is certain to visit any site. In particular, we introduce an analytical approach to address this problem and even more general problems such as the case of two walkers with different diffusivity, particles walking on a finite comb and on arbitrary bundled structures, possibly in the presence of loops. Our investigations are both analytical and numerical and highlight that, in general, the outcome of a reaction involving two reactants on a comblike architecture can strongly differ according to whether both reactants are moving (no matter their relative diffusivities) or only one is moving and according to the density of shortcuts among the branches.

Structure analysis of turbulent liquid phase by POD and LSE techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munir, S., E-mail: shahzad-munir@comsats.edu.pk; Muthuvalu, M. S.; Siddiqui, M. I.

2014-10-24

In this paper, vortical structures and turbulence characteristics of liquid phase in both single liquid phase and two-phase slug flow in pipes were studied. Two dimensional velocity vector fields of liquid phase were obtained by Particle image velocimetry (PIV). Two cases were considered one single phase liquid flow at 80 l/m and second slug flow by introducing gas at 60 l/m while keeping liquid flow rate same. Proper orthogonal decomposition (POD) and Linear stochastic estimation techniques were used for the extraction of coherent structures and analysis of turbulence in liquid phase for both cases. POD has successfully revealed large energymore » containing structures. The time dependent POD spatial mode coefficients oscillate with high frequency for high mode numbers. The energy distribution of spatial modes was also achieved. LSE has pointed out the coherent structured for both cases and the reconstructed velocity fields are in well agreement with the instantaneous velocity fields.« less

Synthesis and characterization of pure strontium apatite particles and nanoporous scaffold prepared by dextrose-templated method

NASA Astrophysics Data System (ADS)

Ma, Xiaoyu; Liu, Yongjia; Zhu, Bangshang

2018-02-01

Strontium shows an increasing interest on bone formation and bone resorption prevention. Here, pure apatite strontium (Ap-SrOH) [Sr5(PO4)3(OH), strontium hydroxyapatite] particles were prepared by the precipitation method using Sr(NO3)2 · 6H2O and (NH4)2HPO4 as reagents. Scanning electron microscope, transmission electron microscope combined with electron diffraction, X-ray diffraction, Fourier transform infrared spectra (FTIR), variable temperature FTIR and thermo gravimetric analysis were employed to evaluate the crystalline structure, chemical composition, and thermal stability of the Ap-SrOH particles. The results show that phase pure Ap-SrOH particles were prepared by wet precipitation. The obtained Ap-SrOH particles are single crystal in phase structure, they have hexagonal fusiform shape, and their size is about 30-180 nm in diameter, and 0.4-2.5 μm in length. The cell MTT assay evaluations indicate that Ap-SrOH particles have very low cytotoxicity. Furthermore, nanoporous Ap-SrOH scaffolds were synthesized by anhydrous dextrose template method. After mixed 5-10 wt% of anhydrous dextrose with Ap-SrOH particles, pressed into discs, and sintered in microwave muffle furnace at 600 °C, the scaffolds with both nanoporous and nanotopography were formed. Cell culture of MC3T3-E1 osteoblasts in vitro show cells grow well on nanoporous Ap-SrOH scaffold. Therefore, Ap-SrOH particles and their nanoporous scaffolds are promising biomaterials for bone repairing and bone disease (e.g. osteoporosis) healing.

Ultrasonically assisted single screw extrusion, film blowing and film casting of LLDPE/clay and PA6/clay nanocomposites

NASA Astrophysics Data System (ADS)

Niknezhad, Setareh

The major objective of this study was to investigate the effect of ultrasonic treatment on the dispersion of modified clay particles in LLDPE and PA6 matrices and the final properties of nanocomposites. LLDPE and PA6 are two polymers that are widely used in packaging industry. Blown and cast films were manufactured from the prepared nanocomposites. To achieve one step film processing, an online ultrasonic film casting was developed. Ultrasonic waves caused high-energy mixing and dispersion due to the acoustic cavitation, causing the clay agglomorates to separate into individual platelets in polymer matrix. Ultrasonic waves also broke down the polymer molecular chains reducing viscosity of the melt, facilating dispersion of the clay platelets throughout the matrix. Ultrasound also led to a breakage of the clay platelets reducing the particle size and improving their distribution. Clay particles acted as a heterogenous nucleation agent generating smaller size polymer crystals. In turn, these improved different properties including mechanical properties, oxygen permeability and transparency of films. In LLDPE/clay 20A nanocomposites, the effect of ultrasound was more obvious at higher clay loadings. Exfoliated structure for ultrasonically treated nanocomposites containing 2.5, 5 and 7.5 wt% of clay 20A and highly intercalated structure for ultrasonically treated nanocomposites containing 10 wt% of clay 20A were achieved. However, in blown films, the exfoliated structure transferred to the intercalated structure due to the addition of more shear and thermal degradation of surfactants of the clay particles. While, manufacturing cast films using the new developed online ultrasonic cast film machine revealed the exfoliated structure with ultrasonic treatment till 7.5 wt% of clay loadings. Cast films of nanocomposites containing 5 wt% of clay loadings were also prepared with addition of different compatibilizers. The compatibilizer containing higher amount of grafted maleic anhydride (MA) affected mechanical properties and oxygen permeability with ultrasonic treatment to higher extent. However, use of compatibilizers led to a higher die pressure and resulted in opaque cast films. The mechanical properties were in agreement with crystallinity of samples. The exfoliated structure was achieved for PA6/clay 30B nanocomposites prepared using ultrasonically assisted single screw extrusion except for untreated nanocomposites containing 10 wt% of clay 30B. Untreated 92.5/7.5 and 90/10 PA6/clay 30B blown films showed the intercalated structure, but the exfoliated structure was achieved with ultrasonic treatment. All cast films of PA6/clay 30B showed the exfoliated structure. FTIR spectroscopy along with XRD results confirmed the existence of alpha and gamma-type crystals in the cast films, with clay particles favoring the formation of gamma-type crystals, and ultrasonic treatment favoring the formation of alpha-type crystals. Both parameters increased crystallinity of cast films improving their mechanical properties and oxygen permeability.

Molecular dynamics simulation of fast particle irradiation on the single crystal CeO2

NASA Astrophysics Data System (ADS)

Sasajima, Y.; Ajima, N.; Osada, T.; Ishikawa, N.; Iwase, A.

2013-11-01

We used a molecular dynamics method to simulate structural relaxation caused by the high-energy-ion irradiation of single crystal CeO2. As the initial condition, we assumed high thermal energy was supplied to the individual atoms within a cylindrical region of nanometer-order diameter located in the center of the single crystal. The potential proposed by Inaba et al. was utilized to calculate interactions between atoms [H. Inaba, R. Sagawa, H. Hayashi, K. Kawamura, Solid State Ionics 122 (1999) 95-103]. The supplied thermal energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it was dissipated in the crystal. We compared the obtained results with those of computer simulations for UO2 and found that CeO2 was more stable than UO2 when supplied with high thermal energy.

Temperature dependent and applied field strength dependent magnetic study of cobalt nickel ferrite nano particles: Synthesized by an environmentally benign method

NASA Astrophysics Data System (ADS)

Sontu, Uday Bhasker; G, Narsinga Rao; Chou, F. C.; M, V. Ramana Reddy

2018-04-01

Spinel ferrites have come a long way in their versatile applications. The ever growing applications of these materials demand detailed study of material properties and environmental considerations in their synthesis. In this article, we report the effect of temperature and applied magnetic field strength on the magnetic behavior of the cobalt nickel ferrite nano powder samples. Basic structural properties of spinel ferrite nano particles, that are synthesized by an environmentally benign method of auto combustion, are characterized through XRD, TEM, RAMAN spectroscopy. Diffuse Reflectance Spectroscopy (DRS) is done to understand the nickel substitution effect on the optical properties of cobalt ferrite nano particles. Thermo magnetic studies using SQUID in the temperature range 5 K to 400 K and room temperature (300 K) VSM studies are performed on these samples. Fields of 0Oe (no applied field: ZF), 1 kOe (for ZFC and FC curves), 5 kOe (0.5 T), 50 kOe (5T) (for M-H loop study) are used to study the magnetic behavior of these nano particles. The XRD,TEM analysis suggest 40 nm crystallites that show changes in the cation distribution and phase changes in the spinel structure with nickel substitution. Raman micrographs support phase purity changes and cation redistributions with nickel substitution. Diffuse reflectance study on powder samples suggests two band gap values for nickel rich compounds. The Magnetic study of these sample nano particles show varied magnetic properties from that of hard magnetic, positive multi axial anisotropy and single-magnetic-domain structures at 5 K temperature to soft magnetic core shell like structures at 300 K temperature. Nickel substitution effect is non monotonous. Blocking temperature of all the samples is found to be higher than the values suggested in the literature.

Monte Carlo simulation of ionizing radiation induced DNA strand breaks utilizing coarse grained high-order chromatin structures.

PubMed

Liang, Ying; Yang, Gen; Liu, Feng; Wang, Yugang

2016-01-07

Ionizing radiation threatens genome integrity by causing DNA damage. Monte Carlo simulation of the interaction of a radiation track structure with DNA provides a powerful tool for investigating the mechanisms of the biological effects. However, the more or less oversimplification of the indirect effect and the inadequate consideration of high-order chromatin structures in current models usually results in discrepancies between simulations and experiments, which undermine the predictive role of the models. Here we present a biophysical model taking into consideration factors that influence indirect effect to simulate radiation-induced DNA strand breaks in eukaryotic cells with high-order chromatin structures. The calculated yields of single-strand breaks and double-strand breaks (DSBs) for photons are in good agreement with the experimental measurements. The calculated yields of DSB for protons and α particles are consistent with simulations by the PARTRAC code, whereas an overestimation is seen compared with the experimental results. The simulated fragment size distributions for (60)Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with (60)Co irradiation validates our model in simulating photon irradiation. The general agreement found in α particle irradiation encourages model applicability in the high linear energy transfer range. Moreover, we demonstrate the importance of chromatin high-order structures in shaping the spectrum of initial damage.

Average crystal structure(s) of the embedded meta stable η‧-phase in the Al-Mg-Zn system

NASA Astrophysics Data System (ADS)

Bøvik Larsen, Helge; Thorkildsen, Gunnar; Natland, Sølvi; Pattison, Philip

2014-05-01

Meta stable embedded nano-sized ?-particles within a single grain extracted from an alloy having the nominal composition ? have been examined with X-ray diffraction. By applying the orientational and metric relationships that exist between the hexagonal unit cell of the ?-particles and the cubic unit cell of the Al-matrix, it has been proven possible to directly collect diffracted intensity data from the ?-particle ensemble. This has been done using synchrotron radiation and a ?-diffractometer having a scintillator point detector setup. The approach has resulted in improved data quality compared to previous experiments. The interpretation of the data set, based on a combination of Patterson syntheses, direct methods and geometrical restraints, yielded two possible average structural representations: one Al-rich with the approximate stoichiometric composition ? and one Al-depleted with approximate stoichiometric composition ?. Both structures are realized in the same space group, ?, and are most probably superimposed in the crystalline system examined. The geometries are discussed within the atomic environment approach where icosahedral or near-icosahedral configurations are encountered. Comparison with previous published models and the equilibrium structure reveals a main difference related to the distribution of the Zn-sites in the unit cell. A possible transformation path is also suggested. Various aspects and challenges regarding data collection, data reduction and data quality are specifically addressed.

Characterizing physical properties and heterogeneous chemistry of single particles in air using optical trapping-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Gong, Z.; Wang, C.; Pan, Y. L.; Videen, G.

2017-12-01

Heterogeneous reactions of solid particles in a gaseous environment are of increasing interest; however, most of the heterogeneous chemistry studies of airborne solids were conducted on particle ensembles. A close examination on the heterogeneous chemistry between single particles and gaseous-environment species is the key to elucidate the fundamental mechanisms of hydroscopic growth, cloud nuclei condensation, secondary aerosol formation, etc., and reduce the uncertainty of models in radiative forcing, climate change, and atmospheric chemistry. We demonstrate an optical trapping-Raman spectroscopy (OT-RS) system to study the heterogeneous chemistry of the solid particles in air at single-particle level. Compared to other single-particle techniques, optical trapping offers a non-invasive, flexible, and stable method to isolate single solid particle from substrates. Benefited from two counter-propagating hollow beams, the optical trapping configuration is adaptive to trap a variety of particles with different materials from inorganic substitution (carbon nanotubes, silica, etc.) to organic, dye-doped polymers and bioaerosols (spores, pollen, etc.), with different optical properties from transparent to strongly absorbing, with different sizes from sub-micrometers to tens of microns, or with distinct morphologies from loosely packed nanotubes to microspheres and irregular pollen grains. The particles in the optical trap may stay unchanged, surface degraded, or optically fragmented according to different laser intensity, and their physical and chemical properties are characterized by the Raman spectra and imaging system simultaneously. The Raman spectra is able to distinguish the chemical compositions of different particles, while the synchronized imaging system can resolve their physical properties (sizes, shapes, morphologies, etc.). The temporal behavior of the trapped particles also can be monitored by the OT-RS system at an indefinite time with a resolution from 10 ms to 5 min, which can be further applied to monitor the dynamics of heterogeneous reactions. The OT-RS system provides a flexible method to characterize and monitor the physical properties and heterogeneous chemistry of optically trapped solid particles in gaseous environment at single-particle level.

Impact gages for detecting meteoroid and other orbital debris impacts on space vehicles.

NASA Technical Reports Server (NTRS)

Mastandrea, J. R.; Scherb, M. V.

1973-01-01

Impacts on space vehicles have been simulated using the McDonnell Douglas Aerophysics Laboratory (MDAL) Light-Gas Guns to launch particles at hypervelocity speeds into scaled space structures. Using impact gages and a triangulation technique, these impacts have been detected and accurately located. This paper describes in detail the various types of impact gages (piezoelectric PZT-5A, quartz, electret, and off-the-shelf plastics) used. This description includes gage design and experimental results for gages installed on single-walled scaled payload carriers, multiple-walled satellites and space stations, and single-walled full-scale Delta tank structures. A brief description of the triangulation technique, the impact simulation, and the data acquisition system are also included.

Sequential Quantum Secret Sharing Using a Single Qudit

NASA Astrophysics Data System (ADS)

Bai, Chen-Ming; Li, Zhi-Hui; Li, Yong-Ming

2018-05-01

In this paper we propose a novel and efficient quantum secret sharing protocol using d-level single particle, which it can realize a general access structure via the thought of concatenation. In addition, Our scheme includes all advantages of Tavakoli’s scheme [Phys. Rev. A 92 (2015) 030302(R)]. In contrast to Tavakoli’s scheme, the efficiency of our scheme is 1 for the same situation, and the access structure is more general and has advantages in practical significance. Furthermore, we also analyze the security of our scheme in the primary quantum attacks. Sponsored by the National Natural Science Foundation of China under Grant Nos. 61373150 and 61602291, and Industrial Research and Development Project of Science and Technology of Shaanxi Province under Grant No. 2013k0611

Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic)

NASA Astrophysics Data System (ADS)

Ortega-Retuerta, E.; Joux, F.; Jeffrey, W. H.; Ghiglione, J. F.

2013-04-01

We explored the patterns of total and active bacterial community structure in a gradient covering surface waters from the Mackenzie River to the coastal Beaufort Sea in the Canadian Arctic Ocean, with a particular focus on free-living (FL) vs. particle-attached (PA) communities. Capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) showed significant differences when comparing river, coast and open sea bacterial community structures. In contrast to the river and coastal waters, total (16S rDNA-based) and active (16S rRNA-based) communities in the open sea samples were not significantly different, suggesting that most present bacterial groups were equally active in this area. Additionally, we observed significant differences between PA and FL bacterial community structure in the open sea, but similar structure in the two fractions for coastal and river samples. Direct multivariate statistical analyses showed that total community structure was mainly driven by salinity (a proxy of dissolved organic carbon and chromophoric dissolved organic matter), suspended particles, amino acids and chlorophyll a. Pyrosequencing of 16S rRNA genes from selected samples confirmed significant differences between river, coastal and sea samples. The PA fraction was only different (15.7% similarity) from the FL one in the open sea sample. Furthermore, PA samples generally showed higher diversity (Shannon, Simpson and Chao indices) than FL samples. At the class level, Opitutae was most abundant in the PA fraction of the sea sample, followed by Flavobacteria and Gammaproteobacteria, while the FL sea sample was dominated by Alphaproteobacteria. Finally, for the coast and river samples and both PA and FL fractions, Betaproteobacteria, Alphaproteobacteria and Actinobacteria were dominant. These results highlight the coexistence of particle specialists and generalists and the role of particle quality in structuring bacterial communities in the area. These results may also serve as a basis to predict further changes in bacterial communities should climate change lead to further increases in river discharge and related particle loads.

Anti-Brownian ELectrokinetic (ABEL) Trapping of Single High Density Lipoprotein (HDL) Particles

NASA Astrophysics Data System (ADS)

Bockenhauer, Samuel; Furstenberg, Alexandre; Wang, Quan; Devree, Brian; Jie Yao, Xiao; Bokoch, Michael; Kobilka, Brian; Sunahara, Roger; Moerner, W. E.

2010-03-01

The ABEL trap is a novel device for trapping single biomolecules in solution for extended observation. The trap estimates the position of a fluorescently-labeled object as small as ˜10 nm in solution and then applies a feedback electrokinetic drift every 20 us to trap the object by canceling its Brownian motion. We use the ABEL trap to study HDL particles at the single-copy level. HDL particles, essential in regulation of ``good'' cholesterol in humans, comprise a small (˜10 nm) lipid bilayer disc bounded by a belt of apolipoproteins. By engineering HDL particles with single fluorescent donor/acceptor probes and varying lipid compositions, we are working to study lipid diffusion on small length scales. We also use HDL particles as hosts for single transmembrane receptors, which should enable study of receptor conformational dynamics on long timescales.

Real-time airborne particle analyzer

DOEpatents

Reilly, Peter T.A.

2012-10-16

An aerosol particle analyzer includes a laser ablation chamber, a gas-filled conduit, and a mass spectrometer. The laser ablation chamber can be operated at a low pressure, which can be from 0.1 mTorr to 30 mTorr. The ablated ions are transferred into a gas-filled conduit. The gas-filled conduit reduces the electrical charge and the speed of ablated ions as they collide and mix with buffer gases in the gas-filled conduit. Preferably, the gas filled-conduit includes an electromagnetic multipole structure that collimates the nascent ions into a beam, which is guided into the mass spectrometer. Because the gas-filled conduit allows storage of vast quantities of the ions from the ablated particles, the ions from a single ablated particle can be analyzed multiple times and by a variety of techniques to supply statistically meaningful analysis of composition and isotope ratios.

Experimental investigation of nearly monodispersed ternary Mn_{0.5}Zn_{0.5}Fe_{2}O_{4} magnetic fluid

NASA Astrophysics Data System (ADS)

Parekh, K.; Upadhyay, R. V.; Mehta, R. V.; Aswal, V. K.

2008-03-01

The experimental investigations of a nearly monodispersed magnetic fluid, containing a ternary Mn_{0.5}Zn_{0.5}Fe_{2}O_{4} (MZ5) magnetic fluid, are carried out using XRD, TEM, Small Angle Neutron Scattering (SANS) and a SQUID magnetometer. The XRD and TEM measurements give the particle size to be 7.5 and 8.4 nm respectively, and confirms the single phase cubic spinel structure. The size distribution retrieved from TEM is found to be very narrow (<10{%}). Room temperature magnetic measurement fits with the Langevin's function modified for the particle size distribution as well as for the particle-particle interaction parameter. M(H)-measurements as a function of field for different temperatures show that the system is superparamagnetic at room temperature and develops coercivity at 5 K. Figs 4, Refs 12.

Mobile spin impurity in an optical lattice

NASA Astrophysics Data System (ADS)

Duncan, C. W.; Bellotti, F. F.; Öhberg, P.; Zinner, N. T.; Valiente, M.

2017-07-01

We investigate the Fermi polaron problem in a spin-1/2 Fermi gas in an optical lattice for the limit of both strong repulsive contact interactions and one dimension. In this limit, a polaronic-like behaviour is not expected, and the physics is that of a magnon or impurity. While the charge degrees of freedom of the system are frozen, the resulting tight-binding Hamiltonian for the impurity’s spin exhibits an intriguing structure that strongly depends on the filling factor of the lattice potential. This filling dependency also transfers to the nature of the interactions for the case of two magnons and the important spin balanced case. At low filling, and up until near unit filling, the single impurity Hamiltonian faithfully reproduces a single-band, quasi-homogeneous tight-binding problem. As the filling is increased and the second band of the single particle spectrum of the periodic potential is progressively filled, the impurity Hamiltonian, at low energies, describes a single particle trapped in a multi-well potential. Interestingly, once the first two bands are fully filled, the impurity Hamiltonian is a near-perfect realisation of the Su-Schrieffer-Heeger model. Our studies, which go well beyond the single-band approximation, that is, the Hubbard model, pave the way for the realisation of interacting one-dimensional models of condensed matter physics.

Boxes of Model Building and Visualization.

PubMed

Turk, Dušan

2017-01-01

Macromolecular crystallography and electron microscopy (single-particle and in situ tomography) are merging into a single approach used by the two coalescing scientific communities. The merger is a consequence of technical developments that enabled determination of atomic structures of macromolecules by electron microscopy. Technological progress in experimental methods of macromolecular structure determination, computer hardware, and software changed and continues to change the nature of model building and visualization of molecular structures. However, the increase in automation and availability of structure validation are reducing interactive manual model building to fiddling with details. On the other hand, interactive modeling tools increasingly rely on search and complex energy calculation procedures, which make manually driven changes in geometry increasingly powerful and at the same time less demanding. Thus, the need for accurate manual positioning of a model is decreasing. The user's push only needs to be sufficient to bring the model within the increasing convergence radius of the computing tools. It seems that we can now better than ever determine an average single structure. The tools work better, requirements for engagement of human brain are lowered, and the frontier of intellectual and scientific challenges has moved on. The quest for resolution of new challenges requires out-of-the-box thinking. A few issues such as model bias and correctness of structure, ongoing developments in parameters defining geometric restraints, limitations of the ideal average single structure, and limitations of Bragg spot data are discussed here, together with the challenges that lie ahead.

Nano-imaging of single cells using STIM

NASA Astrophysics Data System (ADS)

Minqin, Ren; van Kan, J. A.; Bettiol, A. A.; Daina, Lim; Gek, Chan Yee; Huat, Bay Boon; Whitlow, H. J.; Osipowicz, T.; Watt, F.

2007-07-01

Scanning transmission ion microscopy (STIM) is a technique which utilizes the energy loss of high energy (MeV) ions passing through a sample to provide structural images. In this paper, we have successfully demonstrated STIM imaging of single cells at the nano-level using the high resolution capability of the proton beam writing facility at the Centre for Ion Beam Applications, National University of Singapore. MCF-7 breast cancer cells (American Type Culture Collection [ATCC]) were seeded on to silicon nitride windows, backed by a Hamamatsu pin diode acting as a particle detector. A reasonable contrast was obtained using 1 MeV protons and excellent contrast obtained using 1 MeV alpha particles. In a further experiment, nano-STIM was also demonstrated using cells seeded on to the pin diode directly, and high quality nano-STIM images showing the nucleus and multiple nucleoli were extracted before the detector was significantly damaged.

Encoding the structure of many-body localization with matrix product operators

NASA Astrophysics Data System (ADS)

Pekker, David; Clark, Bryan K.

2017-01-01

Anderson insulators are noninteracting disordered systems which have localized single-particle eigenstates. The interacting analog of Anderson insulators are the many-body localized (MBL) phases. The spectrum of the many-body eigenstates of an Anderson insulator is efficiently represented as a set of product states over the single-particle modes. We show that product states over matrix product operators of small bond dimension is the corresponding efficient description of the spectrum of an MBL insulator. In this language all of the many-body eigenstates are encoded by matrix product states (i.e., density matrix renormalization group wave functions) consisting of only two sets of low bond dimension matrices per site: the Gi matrices corresponding to the local ground state on site i and the Ei matrices corresponding to the local excited state. All 2n eigenstates can be generated from all possible combinations of these sets of matrices.

A Method for the Alignment of Heterogeneous Macromolecules from Electron Microscopy

PubMed Central

Shatsky, Maxim; Hall, Richard J.; Brenner, Steven E.; Glaeser, Robert M.

2009-01-01

We propose a feature-based image alignment method for single-particle electron microscopy that is able to accommodate various similarity scoring functions while efficiently sampling the two-dimensional transformational space. We use this image alignment method to evaluate the performance of a scoring function that is based on the Mutual Information (MI) of two images rather than one that is based on the cross-correlation function. We show that alignment using MI for the scoring function has far less model-dependent bias than is found with cross-correlation based alignment. We also demonstrate that MI improves the alignment of some types of heterogeneous data, provided that the signal to noise ratio is relatively high. These results indicate, therefore, that use of MI as the scoring function is well suited for the alignment of class-averages computed from single particle images. Our method is tested on data from three model structures and one real dataset. PMID:19166941

Photoacoustic-Based Multimodal Nanoprobes: from Constructing to Biological Applications.

PubMed

Gao, Duyang; Yuan, Zhen

2017-01-01

Multimodal nanoprobes have attracted intensive attentions since they can integrate various imaging modalities to obtain complementary merits of single modality. Meanwhile, recent interest in laser-induced photoacoustic imaging is rapidly growing due to its unique advantages in visualizing tissue structure and function with high spatial resolution and satisfactory imaging depth. In this review, we summarize multimodal nanoprobes involving photoacoustic imaging. In particular, we focus on the method to construct multimodal nanoprobes. We have divided the synthetic methods into two types. First, we call it "one for all" concept, which involves intrinsic properties of the element in a single particle. Second, "all in one" concept, which means integrating different functional blocks in one particle. Then, we simply introduce the applications of the multifunctional nanoprobes for in vivo imaging and imaging-guided tumor therapy. At last, we discuss the advantages and disadvantages of the present methods to construct the multimodal nanoprobes and share our viewpoints in this area.

First total-absorption spectroscopy measurement on the neutron-rich Cu isotopes

NASA Astrophysics Data System (ADS)

Naqvi, F.; Spyrou, A.; Liddick, S. N.; Larsen, A. C.; Guttormsen, M.; Bleuel, D. L.; Campo, L. C.; Couture, A.; Crider, B. P.; Dombos, A. C.; Ginter, T.; Lewis, R.; Mosby, S.; Perdikakis, G.; Prokop, C. P.; Quinn, S. J.; Renstrom, T.; Rubio, B.; Siem, S.

2015-10-01

The first beta-decay studies of 73-71Cu isotopes using the Total Absorption Spectroscopy (TAS) will be reported. The Cu isotopes have one proton outside the Z = 28 shell and hence are good candidates to probe the single-particle structure in the region.Theories predict weakening of the Z = 28 shell gap due to the tensor interaction between the valence πν single-particle orbitals. Comparing the beta-decay strength distributions in the daughter Zn isotopes to the theoretical calculations will provide a stringent test of the predictions. The experiment was performed at the National Superconducting Cyclotron Laboratory (NSCL) employing the TAS technique with the Summing NaI(Tl) detector, while beta decays were measured in the NSCL beta-counting system. The experimentally obtained total absorption spectra for the neutron-rich Cu isotopes will be presented and the implications of the extracted beta-feeding intensities will be discussed.

Holographic acoustic elements for manipulation of levitated objects.

PubMed

Marzo, Asier; Seah, Sue Ann; Drinkwater, Bruce W; Sahoo, Deepak Ranjan; Long, Benjamin; Subramanian, Sriram

2015-10-27

Sound can levitate objects of different sizes and materials through air, water and tissue. This allows us to manipulate cells, liquids, compounds or living things without touching or contaminating them. However, acoustic levitation has required the targets to be enclosed with acoustic elements or had limited manoeuvrability. Here we optimize the phases used to drive an ultrasonic phased array and show that acoustic levitation can be employed to translate, rotate and manipulate particles using even a single-sided emitter. Furthermore, we introduce the holographic acoustic elements framework that permits the rapid generation of traps and provides a bridge between optical and acoustical trapping. Acoustic structures shaped as tweezers, twisters or bottles emerge as the optimum mechanisms for tractor beams or containerless transportation. Single-beam levitation could manipulate particles inside our body for applications in targeted drug delivery or acoustically controlled micro-machines that do not interfere with magnetic resonance imaging.

Holographic acoustic elements for manipulation of levitated objects

NASA Astrophysics Data System (ADS)

Marzo, Asier; Seah, Sue Ann; Drinkwater, Bruce W.; Sahoo, Deepak Ranjan; Long, Benjamin; Subramanian, Sriram

2015-10-01

Sound can levitate objects of different sizes and materials through air, water and tissue. This allows us to manipulate cells, liquids, compounds or living things without touching or contaminating them. However, acoustic levitation has required the targets to be enclosed with acoustic elements or had limited manoeuvrability. Here we optimize the phases used to drive an ultrasonic phased array and show that acoustic levitation can be employed to translate, rotate and manipulate particles using even a single-sided emitter. Furthermore, we introduce the holographic acoustic elements framework that permits the rapid generation of traps and provides a bridge between optical and acoustical trapping. Acoustic structures shaped as tweezers, twisters or bottles emerge as the optimum mechanisms for tractor beams or containerless transportation. Single-beam levitation could manipulate particles inside our body for applications in targeted drug delivery or acoustically controlled micro-machines that do not interfere with magnetic resonance imaging.

Holographic acoustic elements for manipulation of levitated objects

PubMed Central

Marzo, Asier; Seah, Sue Ann; Drinkwater, Bruce W.; Sahoo, Deepak Ranjan; Long, Benjamin; Subramanian, Sriram

2015-01-01

Sound can levitate objects of different sizes and materials through air, water and tissue. This allows us to manipulate cells, liquids, compounds or living things without touching or contaminating them. However, acoustic levitation has required the targets to be enclosed with acoustic elements or had limited manoeuvrability. Here we optimize the phases used to drive an ultrasonic phased array and show that acoustic levitation can be employed to translate, rotate and manipulate particles using even a single-sided emitter. Furthermore, we introduce the holographic acoustic elements framework that permits the rapid generation of traps and provides a bridge between optical and acoustical trapping. Acoustic structures shaped as tweezers, twisters or bottles emerge as the optimum mechanisms for tractor beams or containerless transportation. Single-beam levitation could manipulate particles inside our body for applications in targeted drug delivery or acoustically controlled micro-machines that do not interfere with magnetic resonance imaging. PMID:26505138

High-energy anomalies in covalent high-Tc cuprates with large Hubbard Ud on copper

NASA Astrophysics Data System (ADS)

Barišić, O. S.; Barišić, S.

2015-03-01

A large Ud theory is constructed for the metallic state of high-Tc cuprates. The Emery three-band model, extended with Ox-Oy hopping tpp, and with Ud → ∞, is mapped on slave fermions. The Dyson time-dependent diagrammatic theory in terms of the Cu-O hopping tpd, starting from the nondegenerate unperturbed ground state, is translationally and asymptotically locally gauge invariant. The small parameter of the theory is the average hole occupation of Cu sites nd. The lowest order of the theory generates the single particle propagators of the hybridized pdp- and dpd-fermions with the exact covalent three band structure. The leading many-body effect is band narrowing, accompanied by Landau-like damping of the single particle propagation, due to incoherent local charge Cu-O fluctuations. The corresponding continuum is found below and above the Fermi level.

Thermal and damping behaviour of magnetic shape memory alloy composites

NASA Astrophysics Data System (ADS)

Glock, Susanne; Michaud, Véronique

2015-06-01

Single crystals of ferromagnetic shape memory alloys (MSMA) exhibit magnetic field and stress induced strains via energy dissipating twinning. Embedding single crystalline MSMA particles into a polymer matrix could thus produce composites with enhanced energy dissipation, suitable for damping applications. Composites of ferromagnetic, martensitic or austenitic Ni-Mn-Ga powders embedded in a standard epoxy matrix were produced by casting. The martensitic powder composites showed a crystal structure dependent damping behaviour that was more dissipative than that of austenitic powder or Cu-Ni reference powder composites and than that of the pure matrix. The loss ratio also increased with increasing strain amplitude and decreasing frequency, respectively. Furthermore, Ni-Mn-Ga powder composites exhibited an increased damping behaviour at the martensite/austenite transformation temperature of the Ni-Mn-Ga particles in addition to that at the glass transition temperature of the epoxy matrix, creating possible synergetic effects.

Opto-electrochemical In Situ Monitoring of the Cathodic Formation of Single Cobalt Nanoparticles.

PubMed

Brasiliense, Vitor; Clausmeyer, Jan; Dauphin, Alice L; Noël, Jean-Marc; Berto, Pascal; Tessier, Gilles; Schuhmann, Wolfgang; Kanoufi, Fréderic

2017-08-21

Single-particle electrochemistry at a nanoelectrode is explored by dark-field optical microscopy. The analysis of the scattered light allows in situ dynamic monitoring of the electrodeposition of single cobalt nanoparticles down to a radius of 65 nm. Larger sub-micrometer particles are directly sized optically by super-localization of the edges and the scattered light contains complementary information concerning the particle redox chemistry. This opto-electrochemical approach is used to derive mechanistic insights about electrocatalysis that are not accessible from single-particle electrochemistry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

The structure of particle-laden jets and nonevaporating sprays

NASA Technical Reports Server (NTRS)

Shuen, J. S.; Solomon, A. S. P.; Zhang, Q. F.; Faeth, G. M.

1983-01-01

Mean and fluctuating gas velocities, liquid mass fluxes and drop sizes were in nonevaporating sprays. These results, as well as existing measurements in solid particle-laden jets, were used to evaluate models of these processes. The following models were considered: (1) a locally homogeneous flow (LHF) model, where slip between the phases was neglected; (2) a deterministic separated flow (DSF) model, where slip was considered but effects of particle dispersion by turbulence were ignored; and (3) a stochastic separated flow (SSF) model, where effects of interphase slip and turbulent dispersion were considered using random-walk computations for particle motion. The LHF and DSF models did not provide very satisfactory predictions over the present data base. In contrast, the SSF model performed reasonably well - including conditions in nonevaporating sprays where enhanced dispersion of particles by turbulence caused the spray to spread more rapidly than single-phase jets for comparable conditions. While these results are encouraging, uncertainties in initial conditions limit the reliability of the evaluation. Current work is seeking to eliminate this deficiency.

Optimisation of powders for pulmonary delivery using supercritical fluid technology.

PubMed

Rehman, Mahboob; Shekunov, Boris Y; York, Peter; Lechuga-Ballesteros, David; Miller, Danforth P; Tan, Trixie; Colthorpe, Paul

2004-05-01

Supercritical fluid technology exploited in this work afforded single-step production of respirable particles of terbutaline sulphate (TBS). Different crystal forms of TBS were produced consistently, including two polymorphs, a stoichiometric monohydrate and amorphous material as well as particles with different degrees of crystallinity, size, and morphology. Different solid-state and surface characterisation techniques were applied in conjunction with measurements of powder flow properties using AeroFlow device and aerosol performance by Andersen Cascade Impactor tests. Improved fine particle fraction (FPF) was demonstrated for some powders produced by the SCF process when compared to the micronised material. Such enhanced flow properties and dispersion correlated well with the reduced surface energy parameters demonstrated by these powders. It is shown that semi-crystalline particles exhibited lower specific surface energy leading to a better performance in the powder flow and aerosol tests than crystalline materials. This difference of the surface and bulk crystal structure for selected powder batches is explained by the mechanism of precipitation in SCF which can lead to surface conditioning of particles produced.

Localization and force analysis at the single virus particle level using atomic force microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Chih-Hao; Horng, Jim-Tong; Chang, Jeng-Shian

2012-01-06

Highlights: Black-Right-Pointing-Pointer Localization of single virus particle. Black-Right-Pointing-Pointer Force measurements. Black-Right-Pointing-Pointer Force mapping. -- Abstract: Atomic force microscopy (AFM) is a vital instrument in nanobiotechnology. In this study, we developed a method that enables AFM to simultaneously measure specific unbinding force and map the viral glycoprotein at the single virus particle level. The average diameter of virus particles from AFM images and the specificity between the viral surface antigen and antibody probe were integrated to design a three-stage method that sets the measuring area to a single virus particle before obtaining the force measurements, where the influenza virus was usedmore » as the object of measurements. Based on the purposed method and performed analysis, several findings can be derived from the results. The mean unbinding force of a single virus particle can be quantified, and no significant difference exists in this value among virus particles. Furthermore, the repeatability of the proposed method is demonstrated. The force mapping images reveal that the distributions of surface viral antigens recognized by antibody probe were dispersed on the whole surface of individual virus particles under the proposed method and experimental criteria; meanwhile, the binding probabilities are similar among particles. This approach can be easily applied to most AFM systems without specific components or configurations. These results help understand the force-based analysis at the single virus particle level, and therefore, can reinforce the capability of AFM to investigate a specific type of viral surface protein and its distributions.« less

Extinction cross section measurements for a single optically trapped particle

NASA Astrophysics Data System (ADS)

Cotterell, Michael I.; Preston, Thomas C.; Mason, Bernard J.; Orr-Ewing, Andrew J.; Reid, Jonathan P.

2015-08-01

Bessel beam (BB) optical traps have become widely used to confine single and multiple aerosol particles across a broad range of sizes, from a few microns to < 200 nm in radius. The radiation pressure force exerted by the core of a single, zeroth-order BB incident on a particle can be balanced by a counter-propagating gas flow, allowing a single particle to be trapped indefinitely. The pseudo non-diffracting nature of BBs enables particles to be confined over macroscopic distances along the BB core propagation length; the position of the particle along this length can be finely controlled by variation of the BB laser power. This latter property is exploited to optimize the particle position at the center of the TEM00 mode of a high finesse optical cavity, allowing cavity ring-down spectroscopy (CRDS) to be performed on single aerosol particles and their optical extinction cross section, σext, measured. Further, the variation in the light from the illuminating BB elastically scattered by the particle is recorded as a function of scattering angle. Such intensity distributions are fitted to Lorenz-Mie theory to determine the particle radius. The trends in σext with particle radius are modelled using cavity standing wave Mie simulations and a particle's varying refractive index with changing relative humidity is determined. We demonstrate σext measurements on individual sub-micrometer aerosol particles and determine the lowest limit in particle size that can be probed by this technique. The BB-CRDS method will play a key role in reducing the uncertainty associated with atmospheric aerosol radiative forcing, which remains among the largest uncertainties in climate modelling.

Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation

PubMed Central

Śledź, Paweł; Unverdorben, Pia; Beck, Florian; Pfeifer, Günter; Schweitzer, Andreas; Förster, Friedrich; Baumeister, Wolfgang

2013-01-01

The 26S proteasome is a 2.5-MDa, ATP-dependent multisubunit proteolytic complex that processively destroys proteins carrying a degradation signal. The proteasomal ATPase heterohexamer is a key module of the 19S regulatory particle; it unfolds substrates and translocates them into the 20S core particle where degradation takes place. We used cryoelectron microscopy single-particle analysis to obtain insights into the structural changes of 26S proteasome upon the binding and hydrolysis of ATP. The ATPase ring adopts at least two distinct helical staircase conformations dependent on the nucleotide state. The transition from the conformation observed in the presence of ATP to the predominant conformation in the presence of ATP-γS induces a sliding motion of the ATPase ring over the 20S core particle ring leading to an alignment of the translocation channels of the ATPase and the core particle gate, a conformational state likely to facilitate substrate translocation. Two types of intersubunit modules formed by the large ATPase domain of one ATPase subunit and the small ATPase domain of its neighbor exist. They resemble the contacts observed in the crystal structures of ClpX and proteasome-activating nucleotidase, respectively. The ClpX-like contacts are positioned consecutively and give rise to helical shape in the hexamer, whereas the proteasome-activating nucleotidase-like contact is required to close the ring. Conformational switching between these forms allows adopting different helical conformations in different nucleotide states. We postulate that ATP hydrolysis by the regulatory particle ATPase (Rpt) 5 subunit initiates a cascade of conformational changes, leading to pulling of the substrate, which is primarily executed by Rpt1, Rpt2, and Rpt6. PMID:23589842

Low-Energy Bead-Mill Dispersion of Agglomerated Core-Shell α-Fe/Al₂O₃ and α″-Fe₁₆N₂/Al₂O₃ Ferromagnetic Nanoparticles in Toluene.

PubMed

Zulhijah, Rizka; Suhendi, Asep; Yoshimi, Kazuki; Kartikowati, Christina Wahyu; Ogi, Takashi; Iwaki, Toru; Okuyama, Kikuo

2015-06-09

Magnetic materials such as α″-Fe16N2 and α-Fe, which have the largest magnetic moment as hard and soft magnetic materials, are difficult to produce as single domain magnetic nanoparticles (MNPs) because of quasistable state and high reactivity, respectively. The present work reports dispersion of agglomerated plasma-synthesized core-shell α″-Fe16N2/Al2O3 and α-Fe/Al2O3 in toluene by a new bead-mill with very fine beads to prepare single domain MNPs. As a result, optimization of the experimental conditions (bead size, rotation speed, and dispersion time) enables the break-up of agglomerated particles into primary particles without destroying the particle structure. Slight deviation from the optimum conditions, i.e., lower or higher dispersion energy, gives undispersed or broken particles due to fragile core-shell structure against stress or impact force of beads. The dispersibility of α″-Fe16N2/Al2O3 is more restricted than that of α-Fe/Al2O3, because of the preparation conditions. Especially for α″-Fe16N2/Al2O3, no change on crystallinity (98% α″-Fe16N2) or magnetization saturation after dispersion was observed, showing that this method is appropriate to disperse α″-Fe16N2/Al2O3 MNPs. A different magnetic hysteresis behavior is observed for well-dispersed α″-Fe16N2/Al2O3 MNPs, and the magnetic coercivity of these NPs is constricted when the magnetic field close to zero due to magnetic dipole coupling among dispersed α″-Fe16N2 MNPs.

Synthesis of u-channelled spherical Fex(CoyNi1-y)100-x Janus colloidal particles with excellent electromagnetic wave absorption performance.

PubMed

Li, Hao; Cao, Zhenming; Lin, Jiayao; Zhao, Hui; Jiang, Qiaorong; Jiang, Zhiyuan; Liao, Honggang; Kuang, Qin; Xie, Zhaoxiong

2018-01-25

Due to their distinctive structure, inherently anisotropic properties and broad applications, Janus colloidal particles have attracted tremendous attention and it is significant to synthesize high yield Janus colloidal particles in a cost-effective and reliable way. On the other hand, due to the expanded electromagnetic interference problems, it is highly desired to develop excellent electromagnetic wave absorbing materials with an ultra-wide absorption bandwidth for practical application. Herein, a confined liquid-solid redox reaction strategy has been developed to fabricate a series of Fe x (Co y Ni 1-y ) 100-x ternary alloy particles. The as-prepared particles are in the form of u-channelled noncentrosymmetric spheres, one kind of Janus colloidal particles which have been rarely observed. Due to the combination and synergy effects of multi-magnetic metals, the polycrystalline structure and their specific morphology, the as-prepared particles possess multiple magnetic resonance and multiple dielectric relaxation processes, and therefore show excellent electromagnetic wave absorption performances. In particular, the strongest reflection loss (RL) of the Fe 15 (Co 0.2 Ni 0.8 ) 85 Janus colloidal particles is up to -36.9 dB with a thickness of 2.5 mm, and the effective absorption (RL < -10 dB) bandwidth can reach 9.2 GHz (8-17.2 GHz) with a thickness of 2 mm. Such a wide bandwidth has barely been reported for magnetic metal alloys under a single thickness. These results suggest that the Fe x (Co y Ni 1-y ) 100-x Janus particles could be a promising candidate for highly efficient electromagnetic wave absorbing materials for practical application.

The oxygen isotopes

NASA Astrophysics Data System (ADS)

Alex Brown, B.

The properties of the oxygen isotopes provide diverse examples of progress made in experiments and theory. This chain of isotopes has been studied from beyond the proton drip line in 12O to beyond the neutron drip line in 25,26O. This short survey starts with the microscopic G matrix approach for 18O of Kuo and Brown in the 1960's and shows how theory has evolved. The nuclear structure around the doubly-magic nucleus 24O is particularly simple in terms of the nuclear shell model. The nuclear structure around the doubly-magic nucleus 16O exhibits the coexistence of single-particle and collective structure.

Semiclassical Origin of Superdeformed Shell Structure in the Spheroidal Cavity Model

NASA Astrophysics Data System (ADS)

Arita, K.; Sugita, A.; Matsuyanagi, K.

1998-12-01

Classical periodic orbits responsible for emergence of the superdeformed shell structures of single-particle motion in spheroidal cavities are identified and their relative contributions to the shell structures are evaluated. Both prolate and oblate superdeformations (axis ratio approximately 2:1) as well as prolate hyperdeformation (axis ratio approximately 3:1) are investigated. Fourier transforms of quantum spectra clearly show that three-dimensional periodic orbits born out of bifurcations of planar orbits in the equatorial plane become predominant at large prolate deformations, while butterfly-shaped planar orbits bifurcated from linear orbits along the minor axis are important at large oblate deformations.

Tuning structural motifs and alloying of bulk immiscible Mo-Cu bimetallic nanoparticles by gas-phase synthesis

NASA Astrophysics Data System (ADS)

Krishnan, Gopi; Verheijen, Marcel A.; Ten Brink, Gert H.; Palasantzas, George; Kooi, Bart J.

2013-05-01

Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still remains a formidable challenge. Hence, we present here a general methodology for gas phase synthesis of bimetallic NPs with distinctively different structural motifs ranging at a single particle level from a fully mixed alloy to core-shell, to onion (multi-shell), and finally to a Janus/dumbbell, with the same overall particle composition. These concepts are illustrated for Mo-Cu NPs, where the precise control of the bimetallic NPs with various degrees of chemical ordering, including different shapes from spherical to cube, is achieved by tailoring the energy and thermal environment that the NPs experience during their production. The initial state of NP growth, either in the liquid or in the solid state phase, has important implications for the different structural motifs and shapes of synthesized NPs. Finally we demonstrate that we are able to tune the alloying regime, for the otherwise bulk immiscible Mo-Cu, by achieving an increase of the critical size, below which alloying occurs, closely up to an order of magnitude. It is discovered that the critical size of the NP alloy is not only affected by controlled tuning of the alloying temperature but also by the particle shape.Nowadays bimetallic nanoparticles (NPs) have emerged as key materials for important modern applications in nanoplasmonics, catalysis, biodiagnostics, and nanomagnetics. Consequently the control of bimetallic structural motifs with specific shapes provides increasing functionality and selectivity for related applications. However, producing bimetallic NPs with well controlled structural motifs still remains a formidable challenge. Hence, we present here a general methodology for gas phase synthesis of bimetallic NPs with distinctively different structural motifs ranging at a single particle level from a fully mixed alloy to core-shell, to onion (multi-shell), and finally to a Janus/dumbbell, with the same overall particle composition. These concepts are illustrated for Mo-Cu NPs, where the precise control of the bimetallic NPs with various degrees of chemical ordering, including different shapes from spherical to cube, is achieved by tailoring the energy and thermal environment that the NPs experience during their production. The initial state of NP growth, either in the liquid or in the solid state phase, has important implications for the different structural motifs and shapes of synthesized NPs. Finally we demonstrate that we are able to tune the alloying regime, for the otherwise bulk immiscible Mo-Cu, by achieving an increase of the critical size, below which alloying occurs, closely up to an order of magnitude. It is discovered that the critical size of the NP alloy is not only affected by controlled tuning of the alloying temperature but also by the particle shape. Electronic supplementary information (ESI) available: Experimental details including schematics of the gas phase synthesis set up, target arrangement, synthesis condition for various structures, and TEM images of alloy, core-shell and Mo-Cu-Mo onion nanoparticles. See DOI: 10.1039/c3nr00565h

Determination of the structure and composition of Au-Ag bimetallic spherical nanoparticles using single particle ICP-MS measurements performed with normal and high temporal resolution.

PubMed

Kéri, Albert; Kálomista, Ildikó; Ungor, Ditta; Bélteki, Ádám; Csapó, Edit; Dékány, Imre; Prohaska, Thomas; Galbács, Gábor

2018-03-01

In this study, the information that can be obtained by combining normal and high resolution single particle ICP-MS (spICP-MS) measurements for spherical bimetallic nanoparticles (BNPs) was assessed. One commercial certified core-shell Au-Ag nanoparticle and three newly synthesized and fully characterized homogenous alloy Au-Ag nanoparticle batches of different composition were used in the experiments as BNP samples. By scrutinizing the high resolution spICP-MS signal time profiles, it was revealed that the width of the signal peak linearly correlates with the diameter of nanoparticles. It was also observed that the width of the peak for same-size nanoparticles is always significantly larger for Au than for Ag. It was also found that it can be reliably determined whether a BNP is of homogeneus alloy or core-shell structure and that, in the case of the latter, the core comprises of which element. We also assessed the performance of several ICP-MS based analytical methods in the analysis of the quantitative composition of bimetallic nanoparticles. Out of the three methods (normal resolution spICP-MS, direct NP nebulization with solution-mode ICP-MS, and solution-mode ICP-MS after the acid dissolution of the nanoparticles), the best accuracy and precision was achieved by spICP-MS. This method allows the determination of the composition with less than 10% relative inaccuracy and better than 3% precision. The analysis is fast and only requires the usual standard colloids for size calibration. Combining the results from both quantitative and structural analyses, the core diameter and shell thickness of core-shell particles can also be calculated. Copyright © 2017 Elsevier B.V. All rights reserved.

Characterization of vertical aerosol flows by single particle mass spectrometry for micrometeorological analysis

NASA Astrophysics Data System (ADS)

Gelhausen, Elmar; Hinz, Klaus-Peter; Schmidt, Andres; Spengler, Bernhard

2011-10-01

A single particle mass spectrometer LAMPAS 2 (Laser Mass Analyzer for Particles in the Airborne State) was combined with an ultrasonic anemometer to provide a measurement system for monitoring environmental substance exchange as caused by emission/deposition of aerosol particles. For this study, 681 mass spectra of detected particles were sorted into groups of similarity by a clustering algorithm leading to five classes of different particle types. Each single mass spectrum was correlated to corresponding anemometer data (vertical wind vector and wind speed) in a time-resolved analysis. Due to sampling constraints time-resolution was limited to 36 s, as a result of transition time distributions through the sampling tube. Vertical particle flow (emission/deposition) was determined for all particles based on these data as acquired during a measuring campaign in Giessen, Germany. For a selected particle class a detailed up- and downwards flow consideration was performed to prove the developed approach. Particle flow of that class was dominated by an emission trend as expected. The presented combination of single-particle mass spectrometry and ultrasonic anemometry provides for the possibility to correlate chemical particle data and wind data in a distinct assignment for the description of turbulent particle behavior near earth surface. Results demonstrate the ability to apply the method to real micrometeorological systems, if sampling issues are properly considered for an intended time resolution.

Direct writing of metal nanostructures: lithographic tools for nanoplasmonics research.

PubMed

Leggett, Graham J

2011-03-22

Continued progress in the fast-growing field of nanoplasmonics will require the development of new methods for the fabrication of metal nanostructures. Optical lithography provides a continually expanding tool box. Two-photon processes, as demonstrated by Shukla et al. (doi: 10.1021/nn103015g), enable the fabrication of gold nanostructures encapsulated in dielectric material in a simple, direct process and offer the prospect of three-dimensional fabrication. At higher resolution, scanning probe techniques enable nanoparticle particle placement by localized oxidation, and near-field sintering of nanoparticulate films enables direct writing of nanowires. Direct laser "printing" of single gold nanoparticles offers a remarkable capability for the controlled fabrication of model structures for fundamental studies, particle-by-particle. Optical methods continue to provide a powerful support for research into metamaterials.

Landau Levels of Majorana Fermions in a Spin Liquid.

PubMed

Rachel, Stephan; Fritz, Lars; Vojta, Matthias

2016-04-22

Majorana fermions, originally proposed as elementary particles acting as their own antiparticles, can be realized in condensed-matter systems as emergent quasiparticles, a situation often accompanied by topological order. Here we propose a physical system which realizes Landau levels-highly degenerate single-particle states usually resulting from an orbital magnetic field acting on charged particles-for Majorana fermions. This is achieved in a variant of a quantum spin system due to Kitaev which is distorted by triaxial strain. This strained Kitaev model displays a spin-liquid phase with charge-neutral Majorana-fermion excitations whose spectrum corresponds to that of Landau levels, here arising from a tailored pseudomagnetic field. We show that measuring the dynamic spin susceptibility reveals the Landau-level structure by a remarkable mechanism of probe-induced bound-state formation.

Biological applications of phase-contrast electron microscopy.

PubMed

Nagayama, Kuniaki

2014-01-01

Here, I review the principles and applications of phase-contrast electron microscopy using phase plates. First, I develop the principle of phase contrast based on a minimal model of microscopy, introducing a double Fourier-transform process to mathematically formulate the image formation. Next, I explain four phase-contrast (PC) schemes, defocus PC, Zernike PC, Hilbert differential contrast, and schlieren optics, as image-filtering processes in the context of the minimal model, with particular emphases on the Zernike PC and corresponding Zernike phase plates. Finally, I review applications of Zernike PC cryo-electron microscopy to biological systems such as protein molecules, virus particles, and cells, including single-particle analysis to delineate three-dimensional (3D) structures of protein and virus particles and cryo-electron tomography to reconstruct 3D images of complex protein systems and cells.

REVIEWS OF TOPICAL PROBLEMS: Acceleration of cosmic rays by shock waves

NASA Astrophysics Data System (ADS)

Berezhko, E. G.; Krymskiĭ, G. F.

1988-01-01

Theoretical work on various processes by which shock waves accelerate cosmic rays is reviewed. The most efficient of these processes, Fermi acceleration, is singled out for special attention. A linear theory for this process is presented. The results found on the basis of nonlinear models of Fermi acceleration, which incorporate the modification of the structure caused by the accelerated particles, are reported. There is a discussion of various possibilities for explaining the generation of high-energy particles observed in interplanetary and interstellar space on the basis of a Fermi acceleration mechanism. The acceleration by shock waves from supernova explosions is discussed as a possible source of galactic cosmic rays. The most important unresolved questions in the theory of acceleration of charged particles by shock waves are pointed out.

Particle Trapping Mechanisms Are Different in Spatially Ordered and Disordered Interacting Gels.

PubMed

Hansing, Johann; Netz, Roland R

2018-06-05

Using stochastic simulations, we study the influence of spatial disorder on the diffusion of a single particle through a gel that consists of rigid, straight fibers. The interaction between the particle and the gel fibers consists of an invariant short-range repulsion, the steric part, and an interaction part that can be attractive or repulsive and of varying range. The effect that spatial disorder of the gel structure has on the particle diffusivity depends crucially on the presence of nonsteric interactions. For attractive interactions, disorder slows down diffusion, because in disordered gels, the particle becomes strongly trapped in regions of locally increased fiber density. For repulsive interactions, the diffusivity is minimal for intermediate disorder strength, because highly disordered lattices exhibit abundant passageways of locally low fiber density. The comparison with experimental data on protein and fluorophore diffusion through various hydrogels is favorable. Our findings shed light on particle-diffusion mechanisms in biogels and thus on biological barrier properties, which can be helpful for the optimal design of synthetic diffusors as well as synthetic mucus constructs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Visualizing Ebolavirus Particles Using Single-Particle Interferometric Reflectance Imaging Sensor (SP-IRIS).

PubMed

Carter, Erik P; Seymour, Elif Ç; Scherr, Steven M; Daaboul, George G; Freedman, David S; Selim Ünlü, M; Connor, John H

2017-01-01

This chapter describes an approach for the label-free imaging and quantification of intact Ebola virus (EBOV) and EBOV viruslike particles (VLPs) using a light microscopy technique. In this technique, individual virus particles are captured onto a silicon chip that has been printed with spots of virus-specific capture antibodies. These captured virions are then detected using an optical approach called interference reflectance imaging. This approach allows for the detection of each virus particle that is captured on an antibody spot and can resolve the filamentous structure of EBOV VLPs without the need for electron microscopy. Capture of VLPs and virions can be done from a variety of sample types ranging from tissue culture medium to blood. The technique also allows automated quantitative analysis of the number of virions captured. This can be used to identify the virus concentration in an unknown sample. In addition, this technique offers the opportunity to easily image virions captured from native solutions without the need for additional labeling approaches while offering a means of assessing the range of particle sizes and morphologies in a quantitative manner.

Relative size selection of a conjugated polyelectrolyte in virus-like protein structures.

PubMed

Brasch, Melanie; Cornelissen, Jeroen J L M

2012-02-01

A conjugated polyelectrolyte poly[(2-methoxy-5-propyloxy sulfonate)-phenyl-ene vinylene] (MPS-PPV) drives the assembly of virus capsid proteins to form single virus-like particles (VLPs) and aggregates with more than two VLPs, with a relative selection of high molecular weight polymer in the latter. This journal is © The Royal Society of Chemistry 2012

Bio-inspired formation of functional calcite/metal oxide nanoparticle composites.

PubMed

Kim, Yi-Yeoun; Schenk, Anna S; Walsh, Dominic; Kulak, Alexander N; Cespedes, Oscar; Meldrum, Fiona C

2014-01-21

Biominerals are invariably composite materials, where occlusion of organic macromolecules within single crystals can significantly modify their properties. In this article, we take inspiration from this biogenic strategy to generate composite crystals in which magnetite (Fe3O4) and zincite (ZnO) nanoparticles are embedded within a calcite single crystal host, thereby endowing it with new magnetic or optical properties. While growth of crystals in the presence of small molecules, macromolecules and particles can lead to their occlusion within the crystal host, this approach requires particles with specific surface chemistries. Overcoming this limitation, we here precipitate crystals within a nanoparticle-functionalised xyloglucan gel, where gels can also be incorporated within single crystals, according to their rigidity. This method is independent of the nanoparticle surface chemistry and as the gel maintains its overall structure when occluded within the crystal, the nanoparticles are maintained throughout the crystal, preventing, for example, their movement and accumulation at the crystal surface during crystal growth. This methodology is expected to be quite general, and could be used to endow a wide range of crystals with new functionalities.

The UPSF code: a metaprogramming-based high-performance automatically parallelized plasma simulation framework

NASA Astrophysics Data System (ADS)

Gao, Xiatian; Wang, Xiaogang; Jiang, Binhao

2017-10-01

UPSF (Universal Plasma Simulation Framework) is a new plasma simulation code designed for maximum flexibility by using edge-cutting techniques supported by C++17 standard. Through use of metaprogramming technique, UPSF provides arbitrary dimensional data structures and methods to support various kinds of plasma simulation models, like, Vlasov, particle in cell (PIC), fluid, Fokker-Planck, and their variants and hybrid methods. Through C++ metaprogramming technique, a single code can be used to arbitrary dimensional systems with no loss of performance. UPSF can also automatically parallelize the distributed data structure and accelerate matrix and tensor operations by BLAS. A three-dimensional particle in cell code is developed based on UPSF. Two test cases, Landau damping and Weibel instability for electrostatic and electromagnetic situation respectively, are presented to show the validation and performance of the UPSF code.

Online single particle measurement of fireworks pollution during Chinese New Year in Nanning.

PubMed

Li, Jingyan; Xu, Tingting; Lu, Xiaohui; Chen, Hong; Nizkorodov, Sergey A; Chen, Jianmin; Yang, Xin; Mo, Zhaoyu; Chen, Zhiming; Liu, Huilin; Mao, Jingying; Liang, Guiyun

2017-03-01

Time-resolved single-particle measurements were conducted during Chinese New Year in Nanning, China. Firework displays resulted in a burst of SO 2 , coarse mode, and accumulation mode (100-500nm) particles. Through single particle mass spectrometry analysis, five different types of particles (fireworks-metal, ash, dust, organic carbon-sulfate (OC-sulfate), biomass burning) with different size distributions were identified as primary emissions from firework displays. The fireworks-related particles accounted for more than 70% of the total analyzed particles during severe firework detonations. The formation of secondary particulate sulfate and nitrate during firework events was investigated on single particle level. An increase of sulfite peak (80SO 3 - ) followed by an increase of sulfate peaks (97HSO 4 - +96SO 4 - ) in the mass spectra during firework displays indicated the aqueous uptake and oxidation of SO 2 on particles. High concentration of gaseous SO 2 , high relative humidity and high particle loading likely promoted SO 2 oxidation. Secondary nitrate formed through gas-phase oxidation of NO 2 to nitric acid, followed by the condensation into particles as ammonium nitrate. This study shows that under worm, humid conditions, both primary and secondary aerosols contribute to the particulate air pollution during firework displays. Copyright © 2016. Published by Elsevier B.V.

Self-Assembly of DNA-Coated Particles: Experiment, Simulation and Theory

NASA Astrophysics Data System (ADS)

Song, Minseok

The bottom-up assembly of material architectures with tunable complexity, function, composition, and structure is a long sought goal in rational materials design. One promising approach aims to harnesses the programmability and specificity of DNA hybridization in order to direct the assembly of oligonucleotide-functionalized nano- and micro-particles by tailoring, in part, interparticle interactions. DNA-programmable assembly into three-dimensionally ordered structures has attracted extensive research interest owing to emergent applications in photonics, plasmonics and catalysis and potentially many other areas. Progress on the rational design of DNA-mediated interactions to create useful two-dimensional structures (e.g., structured films), on the other hand, has been rather slow. In this thesis, we establish strategies to engineer a diversity of 2D crystalline arrangements by designing and exploiting DNA-programmable interparticle interactions. We employ a combination of simulation, theory and experiments to predict and confirm accessibility of 2D structural diversity in an effort to establish a rational approach to 2D DNA-mediated particle assembly. We start with the experimental realization of 2D DNA-mediated assembly by decorating micron-sized silica particles with covalently attached single-stranded DNA through a two-step reaction. Subsequently, we elucidate sensitivity and ultimate controllability of DNA-mediated assembly---specifically the melting transition from dispersed singlet particles to aggregated or assembled structures---through control of the concentration of commonly employed nonionic surfactants. We relate the observed tunability to an apparent coupling with the critical micelle temperature in these systems. Also, both square and hexagonal 2D ordered particle arrangements are shown to evolve from disordered aggregates under appropriate annealing conditions defined based upon pre-established melting profiles. Subsequently, the controlled mixing of complementary ssDNA functionality on individual particles ('multi-flavoring') as opposed to functionalization of particles with the same type of ssDNA ('uni-flavoring') is explored as a possible design handle for tuning interparticle interactions and, thereby, accessing diverse structures. We employ a combination of simulations, theory, and experimental validation toward establishing 'multi-flavoring' as a rational design strategy. Firstly, MD simulations are carried out using effective pair potentials to describe interparticle interactions that are representative of different degrees of ssDNA 'multi-flavoring'. These simulations reveal the template-free assembly of a diversity of 2D crystal polymorphs that is apparently tunable by controlling the relative attractive strengths between like and unlike functionalized particles. The resulting phase diagrams predict conditions (i.e., strengths of relative interparticle interactions) for obtaining crystalline phases with lattice symmetries ranging among square, alternating string hexagonal, random hexagonal, rhombic, honeycomb, and even kagome. Finally, these model findings are translated to experiments, in which binary microparticles are decorated with a tailored mixture of two different complementary ssDNA strands as a straight-forward means to realize tunable particle interactions. Guided by simple statistical mechanics and the detailed MD simulations, 'multi-flavoring' and control of solution phase particle stoichiometry resulted in experimental realization of structurally diverse 2D microparticle assemblies consistent with predictions, such as square, pentagonal and hexagonal lattices (honeycomb, kagome). The combined simulation, theory, and experimental findings reveal how control of interparticle interactions via DNA-functionalized particle "multi-flavoring" can lead to an even wider range of accessible colloidal crystal structures. The 2D experiments coupled with the model predictions may be used to provide new fundamental insight into nano- or microparticle assembly in three dimensions.

Improved hybrid optimization algorithm for 3D protein structure prediction.

PubMed

Zhou, Changjun; Hou, Caixia; Wei, Xiaopeng; Zhang, Qiang

2014-07-01

A new improved hybrid optimization algorithm - PGATS algorithm, which is based on toy off-lattice model, is presented for dealing with three-dimensional protein structure prediction problems. The algorithm combines the particle swarm optimization (PSO), genetic algorithm (GA), and tabu search (TS) algorithms. Otherwise, we also take some different improved strategies. The factor of stochastic disturbance is joined in the particle swarm optimization to improve the search ability; the operations of crossover and mutation that are in the genetic algorithm are changed to a kind of random liner method; at last tabu search algorithm is improved by appending a mutation operator. Through the combination of a variety of strategies and algorithms, the protein structure prediction (PSP) in a 3D off-lattice model is achieved. The PSP problem is an NP-hard problem, but the problem can be attributed to a global optimization problem of multi-extremum and multi-parameters. This is the theoretical principle of the hybrid optimization algorithm that is proposed in this paper. The algorithm combines local search and global search, which overcomes the shortcoming of a single algorithm, giving full play to the advantage of each algorithm. In the current universal standard sequences, Fibonacci sequences and real protein sequences are certified. Experiments show that the proposed new method outperforms single algorithms on the accuracy of calculating the protein sequence energy value, which is proved to be an effective way to predict the structure of proteins.

Atomic Resolution Structure of the Oncolytic Parvovirus LuIII by Electron Microscopy and 3D Image Reconstruction

PubMed Central

Misseldine, Adam; Geilen, Lorena; Halder, Sujata; Smith, J. Kennon; Kurian, Justin; Chipman, Paul; Janssen, Mandy; Mckenna, Robert; Baker, Timothy S.; D’Abramo, Anthony; Cotmore, Susan; Tattersall, Peter; Agbandje-McKenna, Mavis

2017-01-01

LuIII, a protoparvovirus pathogenic to rodents, replicates in human mitotic cells, making it applicable for use to kill cancer cells. This virus group includes H-1 parvovirus (H-1PV) and minute virus of mice (MVM). However, LuIII displays enhanced oncolysis compared to H-1PV and MVM, a phenotype mapped to the major capsid viral protein 2 (VP2). This suggests that within LuIII VP2 are determinants for improved tumor lysis. To investigate this, the structure of the LuIII virus-like-particle was determined using single particle cryo-electron microscopy and image reconstruction to 3.17 Å resolution, and compared to the H-1PV and MVM structures. The LuIII VP2 structure, ordered from residue 37 to 587 (C-terminal), had the conserved VP topology and capsid morphology previously reported for other protoparvoviruses. This includes a core β-barrel and α-helix A, a depression at the icosahedral 2-fold and surrounding the 5-fold axes, and a single protrusion at the 3-fold axes. Comparative analysis identified surface loop differences among LuIII, H-1PV, and MVM at or close to the capsid 2- and 5-fold symmetry axes, and the shoulder of the 3-fold protrusions. The 2-fold differences cluster near the previously identified MVM sialic acid receptor binding pocket, and revealed potential determinants of protoparvovirus tumor tropism. PMID:29084163

Source apportionment of lead-containing aerosol particles in Shanghai using single particle mass spectrometry.

PubMed

Zhang, Yaping; Wang, Xiaofei; Chen, Hong; Yang, Xin; Chen, Jianmin; Allen, Jonathan O

2009-01-01

Lead (Pb) in individual aerosol particles was measured using single particle aerosol mass spectrometer (ATOFMS) in the summer of 2007 in Shanghai, China. Pb was found in 3% of particles with diameters in the range 0.1-2.0 microm. Single particle data were analyzed focusing on the particles with high Pb content which were mostly submicron. Using the ART-2a neural network algorithm, these fine Pb-rich particles were classified into eight main classes by their mass spectral patterns. Based on the size distribution, temporal variation of number density, chemical composition and the correlation between different chemical species for each class, three major emission sources were identified. About 45% of the Pb-rich particles contained organic or elemental carbon and were attributed to the emission from coal combustion; particles with good correlation between Cl and Pb content were mostly attributed to waste incineration. One unique class of particles was identified by strong phosphate and Pb signals, which were assigned to emissions from phosphate industry. Other Pb-rich particles included aged sea salt and particles from metallurgical processes.

Multifunctional metal-polymer nanoagglomerates from single-pass aerosol self-assembly

NASA Astrophysics Data System (ADS)

Byeon, Jeong Hoon

2016-08-01

In this study, gold (Au)-iron (Fe) nanoagglomerates were capped by a polymer mixture (PM) consisting of poly(lactide-co-glycolic acid), protamine sulfate, and poly-l-lysine via floating self-assembly in a single-pass aerosol configuration as multibiofunctional nanoplatforms. The Au-Fe nanoagglomerates were directly injected into PM droplets (PM dissolved in dichloromethane) in a collison atomizer and subsequently heat-treated to liberate the solvent from the droplets, resulting in the formation of PM-capped Au-Fe nanoagglomerates. Measured in vitro, the cytotoxicities of the nanoagglomerates (>98.5% cell viability) showed no significant differences compared with PM particles alone (>98.8%), thus implying that the nanoagglomerates are suitable for further testing of biofunctionalities. Measurements of gene delivery performance revealed that the incorporation of the Au-Fe nanoagglomerates enhanced the gene delivery performance (3.2 × 106 RLU mg-1) of the PM particles alone (2.1 × 106 RLU mg-1), which may have been caused by the PM structural change from a spherical to a hairy structure (i.e., the change followed the agglomerated backbone). Combining the X-ray-absorbing ability of Au and the magnetic property of Fe led to magnetic resonance (MR)-computed tomography (CT) contrast ability in a phantom; and the signal intensities [which reached 64 s-1 T2-relaxation in MR and 194 Hounsfield units (HUs) in CT at 6.0 mg mL-1] depended on particle concentration (0.5-6.0 mg mL-1).

Impact of agglomeration state of nano- and submicron sized gold particles on pulmonary inflammation

PubMed Central

2010-01-01

Background Nanoparticle (NP) toxicity testing comes with many challenges. Characterization of the test substance is of crucial importance and in the case of NPs, agglomeration/aggregation state in physiological media needs to be considered. In this study, we have addressed the effect of agglomerated versus single particle suspensions of nano- and submicron sized gold on the inflammatory response in the lung. Rats were exposed to a single dose of 1.6 mg/kg body weight (bw) of spherical gold particles with geometric diameters of 50 nm or 250 nm diluted either by ultrapure water or by adding phosphate buffered saline (PBS). A single dose of 1.6 mg/kg bw DQ12 quartz was used as a positive control for pulmonary inflammation. Extensive characterization of the particle suspensions has been performed by determining the zetapotential, pH, gold concentration and particle size distribution. Primary particle size and particle purity has been verified using transmission electron microscopy (TEM) techniques. Pulmonary inflammation (total cell number, differential cell count and pro-inflammatory cytokines), cell damage (total protein and albumin) and cytotoxicity (alkaline phosphatase and lactate dehydrogenase) were determined in bronchoalveolar lavage fluid (BALF) and acute systemic effects in blood (total cell number, differential cell counts, fibrinogen and C-reactive protein) 3 and 24 hours post exposure. Uptake of gold particles in alveolar macrophages has been determined by TEM. Results Particles diluted in ultrapure water are well dispersed, while agglomerates are formed when diluting in PBS. The particle size of the 50 nm particles was confirmed, while the 250 nm particles appear to be 200 nm using tracking analysis and 210 nm using TEM. No major differences in pulmonary and systemic toxicity markers were observed after instillation of agglomerated versus single gold particles of different sizes. Both agglomerated as well as single nanoparticles were taken up by macrophages. Conclusion Primary particle size, gold concentration and particle purity are important features to check, since these characteristics may deviate from the manufacturer's description. Suspensions of well dispersed 50 nm and 250 nm particles as well as their agglomerates produced very mild pulmonary inflammation at the same mass based dose. We conclude that single 50 nm gold particles do not pose a greater acute hazard than their agglomerates or slightly larger gold particles when using pulmonary inflammation as a marker for toxicity. PMID:21126342

Novel algorithm and MATLAB-based program for automated power law analysis of single particle, time-dependent mean-square displacement

NASA Astrophysics Data System (ADS)

Umansky, Moti; Weihs, Daphne

2012-08-01

In many physical and biophysical studies, single-particle tracking is utilized to reveal interactions, diffusion coefficients, active modes of driving motion, dynamic local structure, micromechanics, and microrheology. The basic analysis applied to those data is to determine the time-dependent mean-square displacement (MSD) of particle trajectories and perform time- and ensemble-averaging of similar motions. The motion of particles typically exhibits time-dependent power-law scaling, and only trajectories with qualitatively and quantitatively comparable MSD should be ensembled. Ensemble averaging trajectories that arise from different mechanisms, e.g., actively driven and diffusive, is incorrect and can result inaccurate correlations between structure, mechanics, and activity. We have developed an algorithm to automatically and accurately determine power-law scaling of experimentally measured single-particle MSD. Trajectories can then categorized and grouped according to user defined cutoffs of time, amplitudes, scaling exponent values, or combinations. Power-law fits are then provided for each trajectory alongside categorized groups of trajectories, histograms of power laws, and the ensemble-averaged MSD of each group. The codes are designed to be easily incorporated into existing user codes. We expect that this algorithm and program will be invaluable to anyone performing single-particle tracking, be it in physical or biophysical systems. Catalogue identifier: AEMD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 25 892 No. of bytes in distributed program, including test data, etc.: 5 572 780 Distribution format: tar.gz Programming language: MATLAB (MathWorks Inc.) version 7.11 (2010b) or higher, program should also be backwards compatible. Symbolic Math Toolboxes (5.5) is required. The Curve Fitting Toolbox (3.0) is recommended. Computer: Tested on Windows only, yet should work on any computer running MATLAB. In Windows 7, should be used as administrator, if the user is not the administrator the program may not be able to save outputs and temporary outputs to all locations. Operating system: Any supporting MATLAB (MathWorks Inc.) v7.11 / 2010b or higher. Supplementary material: Sample output files (approx. 30 MBytes) are available. Classification: 12 External routines: Several MATLAB subfunctions (m-files), freely available on the web, were used as part of and included in, this code: count, NaN suite, parseArgs, roundsd, subaxis, wcov, wmean, and the executable pdfTK.exe. Nature of problem: In many physical and biophysical areas employing single-particle tracking, having the time-dependent power-laws governing the time-averaged meansquare displacement (MSD) of a single particle is crucial. Those power laws determine the mode-of-motion and hint at the underlying mechanisms driving motion. Accurate determination of the power laws that describe each trajectory will allow categorization into groups for further analysis of single trajectories or ensemble analysis, e.g. ensemble and time-averaged MSD. Solution method: The algorithm in the provided program automatically analyzes and fits time-dependent power laws to single particle trajectories, then group particles according to user defined cutoffs. It accepts time-dependent trajectories of several particles, each trajectory is run through the program, its time-averaged MSD is calculated, and power laws are determined in regions where the MSD is linear on a log-log scale. Our algorithm searches for high-curvature points in experimental data, here time-dependent MSD. Those serve as anchor points for determining the ranges of the power-law fits. Power-law scaling is then accurately determined and error estimations of the parameters and quality of fit are provided. After all single trajectory time-averaged MSDs are fit, we obtain cutoffs from the user to categorize and segment the power laws into groups; cutoff are either in exponents of the power laws, time of appearance of the fits, or both together. The trajectories are sorted according to the cutoffs and the time- and ensemble-averaged MSD of each group is provided, with histograms of the distributions of the exponents in each group. The program then allows the user to generate new trajectory files with trajectories segmented according to the determined groups, for any further required analysis. Additional comments: README file giving the names and a brief description of all the files that make-up the package and clear instructions on the installation and execution of the program is included in the distribution package. Running time: On an i5 Windows 7 machine with 4 GB RAM the automated parts of the run (excluding data loading and user input) take less than 45 minutes to analyze and save all stages for an 844 trajectory file, including optional PDF save. Trajectory length did not affect run time (tested up to 3600 frames/trajectory), which was on average 3.2±0.4 seconds per trajectory.

An orientation analysis method for protein immobilized on quantum dot particles

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Inoue, Masae

2009-11-01

The evaluation of orientation of biomolecules immobilized on nanodevices is crucial for the development of high performance devices. Such analysis requires ultra high sensitivity so as to be able to detect less than one molecular layer on a device. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has sufficient sensitivity to evaluate the uppermost surface structure of a single molecular layer. The objective of this study is to develop an orientation analysis method for proteins immobilized on nanomaterials such as quantum dot particles, and to evaluate the orientation of streptavidin immobilized on quantum dot particles by means of TOF-SIMS. In order to detect fragment ions specific to the protein surface, a monoatomic primary ion source (Ga +) and a cluster ion source (Au 3+) were employed. Streptavidin-immobilized quantum dot particles were immobilized on aminosilanized ITO glass plates at amino groups by covalent bonding. The reference samples streptavidin directly immobilized on ITO plates were also prepared. All samples were dried with a freeze dryer before TOF-SIMS measurement. The positive secondary ion spectra of each sample were obtained using TOF-SIMS with Ga + and Au 3+, respectively, and then they were compared so as to characterize each sample and detect the surface structure of the streptavidin immobilized with the biotin-immobilized quantum dots. The chemical structures of the upper surface of the streptavidin molecules immobilized on the quantum dot particles were evaluated with TOF-SIMS spectra analysis. The indicated surface side of the streptavidin molecules immobilized on the quantum dots includes the biotin binding site.

Mixed Calcium Dust and Carbonaceous Particles from Asia Contributing to Precipitation Changes in California

NASA Astrophysics Data System (ADS)

Kristensen, L.; Cornwell, G.; Sedlacek, A. J., III; Prather, K. A.

2016-12-01

Mineral dust particles can serve as cloud condensation nuclei (CCN), with enhanced CCN activity observed when the dust is mixed with additional soluble species. Long range atmospheric transport can change the composition of dust particles through aging, cloud processing and mixing with other particles. The CalWater2 campaign measured single particles and cloud dynamics to investigate the influence aerosols have on the hydrological cycle in California. An Aircraft Aerosol Time-of-Flight Mass Spectrometer (ATOFMS) was used to characterize and identify single particles within clouds potentially acting as ice and cloud nuclei. Two matching flights over California's mountains in March 2015 detected significantly different particle types that resulted in different precipitation totals. Calcium dust dominated the particle composition during the first flight which had an observed decrease in orographic precipitation. Particle composition and air mass back trajectories indicate an Asian desert origin. The calcium dust particles contained secondary acids, in particular oxalic acid, acquired during transport from Asia to California. This chemical processing likely increased the solubility of the dust, enabling the particles to act as more effective CCN. The chemical composition also showed oligomeric carbonaceous species were mixed with the calcium dust particles, potentially further increasing the solubility the particles. A single particle soot photometer (SP2) measured black carbon concurrently and returned intense incandescence when calcium dust was present, confirming the calcium dust particles were internally mixed with a carbonaceous species. Dust particles were greatly reduced during the second flight with local biomass burning particles the dominant type. Observed precipitation in California were within forecast levels during the second flight. These single particle measurements from CalWater2 show that dust particles from Asia can affect cloud process and thus precipitation in California.

Automated data collection in single particle electron microscopy

PubMed Central

Tan, Yong Zi; Cheng, Anchi; Potter, Clinton S.; Carragher, Bridget

2016-01-01

Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed. PMID:26671944

Microprocessor-based single particle calibration of scintillation counter

NASA Technical Reports Server (NTRS)

Mazumdar, G. K. D.; Pathak, K. M.

1985-01-01

A microprocessor-base set-up is fabricated and tested for the single particle calibration of the plastic scintillator. The single particle response of the scintillator is digitized by an A/D converter, and a 8085 A based microprocessor stores the pulse heights. The digitized information is printed. Facilities for CRT display and cassette storing and recalling are also made available.

Single-Particle Mobility Edge in a One-Dimensional Quasiperiodic Optical Lattice

NASA Astrophysics Data System (ADS)

Lüschen, Henrik P.; Scherg, Sebastian; Kohlert, Thomas; Schreiber, Michael; Bordia, Pranjal; Li, Xiao; Das Sarma, S.; Bloch, Immanuel

2018-04-01

A single-particle mobility edge (SPME) marks a critical energy separating extended from localized states in a quantum system. In one-dimensional systems with uncorrelated disorder, a SPME cannot exist, since all single-particle states localize for arbitrarily weak disorder strengths. However, in a quasiperiodic system, the localization transition can occur at a finite detuning strength and SPMEs become possible. In this Letter, we find experimental evidence for the existence of such a SPME in a one-dimensional quasiperiodic optical lattice. Specifically, we find a regime where extended and localized single-particle states coexist, in good agreement with theoretical simulations, which predict a SPME in this regime.

Fabrication of large binary colloidal crystals with a NaCl structure

PubMed Central

Vermolen, E. C. M.; Kuijk, A.; Filion, L. C.; Hermes, M.; Thijssen, J. H. J.; Dijkstra, M.; van Blaaderen, A.

2009-01-01

Binary colloidal crystals offer great potential for tuning material properties for applications in, for example, photonics, semiconductors and spintronics, because they allow the positioning of particles with quite different characteristics on one lattice. For micrometer-sized colloids, it is believed that gravity and slow crystallization rates hinder the formation of high-quality binary crystals. Here, we present methods for growing binary colloidal crystals with a NaCl structure from relatively heavy, hard-sphere-like, micrometer-sized silica particles by exploring the following external fields: electric, gravitational, and dielectrophoretic fields and a structured surface (colloidal epitaxy). Our simulations show that the free-energy difference between the NaCl and NiAs structures, which differ in their stacking of the hexagonal planes of the larger spheres, is very small (≈0.002 kBT). However, we demonstrate that the fcc stacking of the large spheres, which is crucial for obtaining the pure NaCl structure, can be favored by using a combination of the above-mentioned external fields. In this way, we have successfully fabricated large, 3D, oriented single crystals having a NaCl structure without stacking disorder. PMID:19805259

Probing quantum entanglement in the Schwarzschild space-time beyond the single-mode approximation

NASA Astrophysics Data System (ADS)

He, Juan; Ding, Zhi-Yong; Ye, Liu

2018-05-01

In this paper, we deduce the vacuum structure for Dirac fields in the background of Schwarzschild space-time beyond the single-mode approximation and discuss the performance of quantum entanglement between particle and antiparticle modes of a Dirac field with Hawking effect. It is shown that Hawking radiation does not always destroy the physically accessible entanglement, and entanglement amplification may happen in some cases. This striking result is different from that of the single-mode approximation, which holds that the Hawking radiation can only destroy entanglement. Lastly, we analyze the physically accessible entanglement relation outside the event horizon and demonstrate that the monogamy inequality is constantly established regardless of the choice of given parameters.

Fluorescence enhancement on silver nanostructures: studies of components of ribosomal translation in vitro

NASA Astrophysics Data System (ADS)

Mandecki, Wlodek; Bharill, Shashank; Borejdo, Julian; Cabral, Diana; Cooperman, Barry S.; Farrell, Ian; Fetter, Linus; Goldman, Emanuel; Gryczynski, Zygmunt; Jakubowski, Hieronim; Liu, Hanqing; Luchowski, Rafal; Matveeva, Evgenia; Pan, Dongli; Qin, Haiou; Tennant, Donald; Gryczynski, Ignacy

2008-02-01

Metallic particles, silver in particular, can significantly enhance the fluorescence of dye molecules in the immediate vicinity (5-20 nm) of the particle. This magnifying effect can be theoretically explained/predicted by considering the change of photonic mode density near the fluorophore due to coupling to the conducting surface. We are using this method to observe fluorescence from a single ribosomal particle in a project aimed at acquiring sequence information from the translating ribosome (NIH's $1000 Genome Initiative). Several quartz slides with silver nanostructures were made using electron beam lithography techniques. The structures were approximately 50 nm high silver tiles measuring 400-700 nm on the side, and were spaced differently over a total area of 1 mm x 1 mm on any given quartz slide. In a preliminary experiment, we coated this surface with the Alexa 647-labeled antibodies and collected single molecule images using the MicroTime 200 (PicoQuant) confocal system. We showed that the fluorescence intensity measured over the silver islands film was more than 100-fold higher than fluorescence from a comparable site on uncoated section of the quartz slide. No noticeable photobleaching was seen. The fluorescence lifetime was very short, about 200 ps or less (this is the resolution limit of the system). The method has great promise for investigations of biologically relevant single molecules.

Double-slit experiment with single wave-driven particles and its relation to quantum mechanics.

PubMed

Andersen, Anders; Madsen, Jacob; Reichelt, Christian; Rosenlund Ahl, Sonja; Lautrup, Benny; Ellegaard, Clive; Levinsen, Mogens T; Bohr, Tomas

2015-07-01

In a thought-provoking paper, Couder and Fort [Phys. Rev. Lett. 97, 154101 (2006)] describe a version of the famous double-slit experiment performed with droplets bouncing on a vertically vibrated fluid surface. In the experiment, an interference pattern in the single-particle statistics is found even though it is possible to determine unambiguously which slit the walking droplet passes. Here we argue, however, that the single-particle statistics in such an experiment will be fundamentally different from the single-particle statistics of quantum mechanics. Quantum mechanical interference takes place between different classical paths with precise amplitude and phase relations. In the double-slit experiment with walking droplets, these relations are lost since one of the paths is singled out by the droplet. To support our conclusions, we have carried out our own double-slit experiment, and our results, in particular the long and variable slit passage times of the droplets, cast strong doubt on the feasibility of the interference claimed by Couder and Fort. To understand theoretically the limitations of wave-driven particle systems as analogs to quantum mechanics, we introduce a Schrödinger equation with a source term originating from a localized particle that generates a wave while being simultaneously guided by it. We show that the ensuing particle-wave dynamics can capture some characteristics of quantum mechanics such as orbital quantization. However, the particle-wave dynamics can not reproduce quantum mechanics in general, and we show that the single-particle statistics for our model in a double-slit experiment with an additional splitter plate differs qualitatively from that of quantum mechanics.

Asymmetric Bidirectional Controlled Quantum Information Transmission via Seven-Particle Entangled State

NASA Astrophysics Data System (ADS)

Sang, Ming-huang; Nie, Li-ping

2017-11-01

We demonstrate that a seven-particle entangled state can be used to realize the deterministic asymmetric bidirectional controlled quantum information transmission by performing only Bell-state measurement and two-particle projective measurement and single-particle measurement. In our protocol, Alice can teleport an arbitrary unknown single-particle state to Bob and at the same time Bob can remotely prepare an arbitrary known two-particle state for Alice via the control of the supervisor Charlie.

A surface structural model for ferrihydrite I: Sites related to primary charge, molar mass, and mass density

NASA Astrophysics Data System (ADS)

Hiemstra, Tjisse; Van Riemsdijk, Willem H.

2009-08-01

A multisite surface complexation (MUSIC) model for ferrihydrite (Fh) has been developed. The surface structure and composition of Fh nanoparticles are described in relation to ion binding and surface charge development. The site densities of the various reactive surface groups, the molar mass, the mass density, the specific surface area, and the particle size are quantified. As derived theoretically, molecular mass and mass density of nanoparticles will depend on the types of surface groups and the corresponding site densities and will vary with particle size and surface area because of a relatively large contribution of the surface groups in comparison to the mineral core of nanoparticles. The nano-sized (˜2.6 nm) particles of freshly prepared 2-line Fh as a whole have an increased molar mass of M ˜ 101 ± 2 g/mol Fe, a reduced mass density of ˜3.5 ± 0.1 g/cm 3, both relatively to the mineral core. The specific surface area is ˜650 m 2/g. Six-line Fh (5-6 nm) has a molar mass of M ˜ 94 ± 2 g/mol, a mass density of ˜3.9 ± 0.1 g/cm 3, and a surface area of ˜280 ± 30 m 2/g. Data analysis shows that the mineral core of Fh has an average chemical composition very close to FeOOH with M ˜ 89 g/mol. The mineral core has a mass density around ˜4.15 ± 0.1 g/cm 3, which is between that of feroxyhyte, goethite, and lepidocrocite. These results can be used to constrain structural models for Fh. Singly-coordinated surface groups dominate the surface of ferrihydrite (˜6.0 ± 0.5 nm -2). These groups can be present in two structural configurations. In pairs, the groups either form the edge of a single Fe-octahedron (˜2.5 nm -2) or are present at a single corner (˜3.5 nm -2) of two adjacent Fe octahedra. These configurations can form bidentate surface complexes by edge- and double-corner sharing, respectively, and may therefore respond differently to the binding of ions such as uranyl, carbonate, arsenite, phosphate, and others. The relatively low PZC of ferrihydrite can be rationalized based on the estimated proton affinity constant for singly-coordinated surface groups. Nanoparticles have an enhanced surface charge. The charging behavior of Fh nanoparticles can be described satisfactory using the capacitance of a spherical Stern layer condenser in combination with a diffuse double layer for flat plates.

An electrostatic Particle-In-Cell code on multi-block structured meshes

NASA Astrophysics Data System (ADS)

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; Vernon, Louis J.; Moulton, J. David

2017-12-01

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. Despite the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where an arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma-material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. Compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.

An electrostatic Particle-In-Cell code on multi-block structured meshes

DOE PAGES

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; ...

2017-09-14

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less

Assessing the concept of structure sensitivity or insensitivity for sub-nanometer catalyst materials

NASA Astrophysics Data System (ADS)

Crampton, Andrew S.; Rötzer, Marian D.; Ridge, Claron J.; Yoon, Bokwon; Schweinberger, Florian F.; Landman, Uzi; Heiz, Ueli

2016-10-01

The nature of the nano-catalyzed hydrogenation of ethylene, yielding benchmark information pertaining to the concept of structure sensitivity/insensitivity and its applicability at the bottom of the catalyst particle size-range, is explored with experiments on size-selected Ptn (n = 7-40) clusters soft-landed on MgO, in conjunction with first-principles simulations. As in the case of larger particles both the direct ethylene hydrogenation channel and the parallel hydrogenation-dehydrogenation ethylidyne-producing route must be considered, with the fundamental uncovering that at the < 1 nm size-scale the reaction exhibits characteristics consistent with structure sensitivity, in contrast to the structure insensitivity found for larger particles. In this size-regime, the chemical properties can be modulated and tuned by a single atom, reflected by the onset of low temperature hydrogenation at T > 150 K catalyzed by Ptn (n ≥ 10) clusters, with maximum room temperature reactivity observed for Pt13 using a pulsed molecular beam technique. Structure insensitive behavior, inherent for specific cluster sizes at ambient temperatures, can be induced in the more active sizes, e.g. Pt13, by a temperature increase, up to 400 K, which opens dehydrogenation channels leading to ethylidyne formation. This reaction channel was, however found to be attenuated on Pt20, as catalyst activity remained elevated after the 400 K step. Pt30 displayed behavior which can be understood from extrapolating bulk properties to this size range; in particular the calculated d-band center. In the non-scalable sub-nanometer size regime, however, precise control of particle size may be used for atom-by-atom tuning and manipulation of catalyzed hydrogenation activity and selectivity.

An electrostatic Particle-In-Cell code on multi-block structured meshes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less

Active Brownian particles escaping a channel in single file.

PubMed

Locatelli, Emanuele; Baldovin, Fulvio; Orlandini, Enzo; Pierno, Matteo

2015-02-01

Active particles may happen to be confined in channels so narrow that they cannot overtake each other (single-file conditions). This interesting situation reveals nontrivial physical features as a consequence of the strong interparticle correlations developed in collective rearrangements. We consider a minimal two-dimensional model for active Brownian particles with the aim of studying the modifications introduced by activity with respect to the classical (passive) single-file picture. Depending on whether their motion is dominated by translational or rotational diffusion, we find that active Brownian particles in single file may arrange into clusters that are continuously merging and splitting (active clusters) or merely reproduce passive-motion paradigms, respectively. We show that activity conveys to self-propelled particles a strategic advantage for trespassing narrow channels against external biases (e.g., the gravitational field).

Active Brownian particles escaping a channel in single file

NASA Astrophysics Data System (ADS)

Locatelli, Emanuele; Baldovin, Fulvio; Orlandini, Enzo; Pierno, Matteo

2015-02-01

Active particles may happen to be confined in channels so narrow that they cannot overtake each other (single-file conditions). This interesting situation reveals nontrivial physical features as a consequence of the strong interparticle correlations developed in collective rearrangements. We consider a minimal two-dimensional model for active Brownian particles with the aim of studying the modifications introduced by activity with respect to the classical (passive) single-file picture. Depending on whether their motion is dominated by translational or rotational diffusion, we find that active Brownian particles in single file may arrange into clusters that are continuously merging and splitting (active clusters) or merely reproduce passive-motion paradigms, respectively. We show that activity conveys to self-propelled particles a strategic advantage for trespassing narrow channels against external biases (e.g., the gravitational field).

Portraits of colloidal hybrid nanostructures: controlled synthesis and potential applications.

PubMed

Nguyen, Thanh-Dinh

2013-03-01

Inorganic hybrid nanostructures containing two or more nanocomponents have been emerging in many areas of materials science in recent years. The particle-particle interactions in a hybrid particle system could significantly improve existing local electronic structure and induce tunable physiochemical responses. The current work reviews the diverse inorganic hybrid nanostructures formed by adhesion of the different single components via seed-mediated method. The hybrid nanomaterials have great potentials for real applications in many other fields. The nanohybrids have been used as efficient heterocatalysts for carbon monoxide conversion and photodegradation of organic contaminants. The enhanced catalytic activity of these hybrid nanocatalysts could be attributed the formation of oxygen vacancies and electron transfer across the structural junction in a hybrid system as a result of the interfacial particle-particle interactions. The synergistic combination of up-converting and semiconducting properties in an up-converting semiconducting hybrid particle results in appearance of sub-band-gap photoconductivity. This behavior has a great significance for the design of photovoltaic devices for effective solar energy conversion. The functionalization and subsequent bioconjugation of the hybrid nanostructures to afford the multifunctional nanomedical platforms for simultaneous diagnosis and therapy are reviewed. The conjugated multifunctional hybrid nanostructures exhibit high biocompatibility and highly selective binding with functional groups-fabricated alive organs through delivering them to the tumor sites. The clever combinations of multifunctional features and antibody conjugation within these vehicles make them to generally offer new opportunities for clinical diagnostics and therapeutics. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Speciation of individual mineral particles of micrometer size by the combined use of attenuated total reflectance-Fourier transform-infrared imaging and quantitative energy-dispersive electron probe X-ray microanalysis techniques.

PubMed

Jung, Hae-Jin; Malek, Md Abdul; Ryu, JiYeon; Kim, BoWha; Song, Young-Chul; Kim, HyeKyeong; Ro, Chul-Un

2010-07-15

Our previous work demonstrated for the first time the potential of the combined use of two techniques, attenuated total reflectance FT-IR (ATR-FT-IR) imaging and a quantitative energy-dispersive electron probe X-ray microanalysis, low-Z particle EPMA, for the characterization of individual aerosol particles. In this work, the speciation of mineral particles was performed on a single particle level for 24 mineral samples, including kaolinite, montmorillonite, vermiculite, talc, quartz, feldspar, calcite, gypsum, and apatite, by the combined use of ATR-FT-IR imaging and low-Z particle EPMA techniques. These two single particle analytical techniques provide complementary information, the ATR-FT-IR imaging on mineral types and low-Z particle EPMA on the morphology and elemental concentrations, on the same individual particles. This work demonstrates that the combined use of the two single particle analytical techniques can powerfully characterize externally heterogeneous mineral particle samples in detail and has great potential for the characterization of airborne mineral dust particles.

Prolate spheroidal hematite particles equatorially belt with drug-carrying layered double hydroxide disks: Ring Nebula-like nanocomposites.

PubMed

Nedim Ay, Ahmet; Konuk, Deniz; Zümreoglu-Karan, Birgul

2011-02-03

A new nanocomposite architecture is reported which combines prolate spheroidal hematite nanoparticles with drug-carrying layered double hydroxide [LDH] disks in a single structure. Spindle-shaped hematite nanoparticles with average length of 225 nm and width of 75 nm were obtained by thermal decomposition of hydrothermally synthesized hematite. The particles were first coated with Mg-Al-NO3-LDH shell and then subjected to anion exchange with salicylate ions. The resulting bio-nanohybrid displayed a close structural resemblance to that of the Ring Nebula. Scanning electron microscope and transmission electron microscopy images showed that the LDH disks are stacked around the equatorial part of the ellipsoid extending along the main axis. This geometry possesses great structural tunability as the composition of the LDH and the nature of the interlayer region can be tailored and lead to novel applications in areas ranging from functional materials to medicine by encapsulating various guest molecules.

Prolate spheroidal hematite particles equatorially belt with drug-carrying layered double hydroxide disks: Ring Nebula-like nanocomposites

PubMed Central

2011-01-01

A new nanocomposite architecture is reported which combines prolate spheroidal hematite nanoparticles with drug-carrying layered double hydroxide [LDH] disks in a single structure. Spindle-shaped hematite nanoparticles with average length of 225 nm and width of 75 nm were obtained by thermal decomposition of hydrothermally synthesized hematite. The particles were first coated with Mg-Al-NO3-LDH shell and then subjected to anion exchange with salicylate ions. The resulting bio-nanohybrid displayed a close structural resemblance to that of the Ring Nebula. Scanning electron microscope and transmission electron microscopy images showed that the LDH disks are stacked around the equatorial part of the ellipsoid extending along the main axis. This geometry possesses great structural tunability as the composition of the LDH and the nature of the interlayer region can be tailored and lead to novel applications in areas ranging from functional materials to medicine by encapsulating various guest molecules. PMID:21711652

Collective and non-collective structures in nuclei of mass region A ≈ 125

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, A. K.; Collaboration: INGA Collaboration; Gammasphere Collaboration

Generation of angular momentum in nuclei is a key question in nuclear structure studies. In single particle model, it is due to alignment of spin of individual nucleon available in the valence space, whereas coherent motion of nucleons are assumed in the collective model. The nuclei near the closed shell at Z = 50 with mass number A ≈ 120-125 represent ideal cases to explore the interplay between these competing mechanisms and the transition from non-collective to collective behavior or vice versa. Recent spectroscopic studies of nuclei in this region reveal several non-collective maximally aligned states representing the first kindmore » of excitation mechanism, where 8-12 particles above the {sup 114}Sn align their spins to generate these states. Deformed rotational bands feeding the non-collective states in the spin range I=20-25 and excitation energies around 10 MeV have also been observed. Structure of the collective and non-collective states are discussed in the framework of Cranked-Nilsson-Strutinsky model.« less

Small-angle X-ray and neutron scattering demonstrates that cell-free expression produces properly formed disc-shaped nanolipoprotein particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cleveland, Thomas E.; He, Wei; Evans, Angela C.

Nanolipoprotein particles (NLPs), composed of membrane scaffold proteins and lipids, have been used to support membrane proteins in a native-like bilayer environment for biochemical and structural studies. Traditionally, these NLPs have been prepared by the controlled removal of detergent from a detergent-solubilized protein-lipid mixture. Recently, an alternative method has been developed using direct cell-free expression of the membrane scaffold protein in the presence of preformed lipid vesicles, which spontaneously produces NLPs without the need for detergent at any stage. Using SANS/SAXS, we show here that NLPs produced by this cell-free expression method are structurally indistinguishable from those produced using detergentmore » removal methodologies. This further supports the utility of single step cell-free methods for the production of lipid binding proteins. Lastly, in addition, detailed structural information describing these NLPs can be obtained by fitting a capped core-shell cylinder type model to all SANS/SAXS data simultaneously.« less

Small-angle X-ray and neutron scattering demonstrates that cell-free expression produces properly formed disc-shaped nanolipoprotein particles

DOE PAGES

Cleveland, Thomas E.; He, Wei; Evans, Angela C.; ...

2018-02-13

Nanolipoprotein particles (NLPs), composed of membrane scaffold proteins and lipids, have been used to support membrane proteins in a native-like bilayer environment for biochemical and structural studies. Traditionally, these NLPs have been prepared by the controlled removal of detergent from a detergent-solubilized protein-lipid mixture. Recently, an alternative method has been developed using direct cell-free expression of the membrane scaffold protein in the presence of preformed lipid vesicles, which spontaneously produces NLPs without the need for detergent at any stage. Using SANS/SAXS, we show here that NLPs produced by this cell-free expression method are structurally indistinguishable from those produced using detergentmore » removal methodologies. This further supports the utility of single step cell-free methods for the production of lipid binding proteins. Lastly, in addition, detailed structural information describing these NLPs can be obtained by fitting a capped core-shell cylinder type model to all SANS/SAXS data simultaneously.« less

Molecular architecture of the TRAPPII complex and implications for vesicle tethering.

PubMed

Yip, Calvin K; Berscheminski, Julia; Walz, Thomas

2010-11-01

Multisubunit tethering complexes participate in the process of vesicle tethering--the initial interaction between transport vesicles and their acceptor compartments. TRAPPII (named for transport protein particle II) is a highly conserved tethering complex that functions in the late Golgi apparatus and consists of all of the subunits of TRAPPI and three additional, specific subunits. We have purified native yeast TRAPPII and characterized its structure and subunit organization by single-particle EM. Our data show that the nine TRAPPII components form a core complex that dimerizes into a three-layered, diamond-shaped structure. The TRAPPI subunits assemble into TRAPPI complexes that form the outer layers. The three TRAPPII-specific subunits cap the ends of TRAPPI and form the middle layer, which is responsible for dimerization. TRAPPII binds the Ypt1 GTPase and probably uses the TRAPPI catalytic core to promote guanine nucleotide exchange. We discuss the implications of the structure of TRAPPII for coat interaction and TRAPPII-associated human pathologies.