Nodal Diffusion Burnable Poison Treatment for Prismatic Reactor Cores

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

A. M. Ougouag; R. M. Ferrer

2010-10-01

The prismatic block version of the High Temperature Reactor (HTR) considered as a candidate Very High Temperature Reactor (VHTR)design may use burnable poison pins in locations at some corners of the fuel blocks (i.e., assembly equivalent structures). The presence of any highly absorbing materials, such as these burnable poisons, within fuel blocks for hexagonal geometry, graphite-moderated High Temperature Reactors (HTRs) causes a local inter-block flux depression that most nodal diffusion-based method have failed to properly model or otherwise represent. The location of these burnable poisons near vertices results in an asymmetry in the morphology of the assemblies (or blocks). Hencemore » the resulting inadequacy of traditional homogenization methods, as these “spread” the actually local effect of the burnable poisons throughout the assembly. Furthermore, the actual effect of the burnable poison is primarily local with influence in its immediate vicinity, which happens to include a small region within the same assembly as well as similar regions in the adjacent assemblies. Traditional homogenization methods miss this artifact entirely. This paper presents a novel method for treating the local effect of the burnable poison explicitly in the context of a modern nodal method.« less

Continuous needleless electrospinning of magnetic nanofibers from magnetization-induced self-assembling PVA/ferrofluid cone array

NASA Astrophysics Data System (ADS)

Wang, Hongjian; Liu, Bin; Huang, Weilong; Lin, Zi; Luo, Jie; Li, Yan; Zhuang, Lin; Wang, Wei; Jiang, Lelun

2018-04-01

A novel approach, continuous needleless electrospinning from the tips of magnetization-induced self-assembling PVA/ferrofluid cone array, was proposed to prepare magnetic nanofibers. A PVA/ferrofluid was synthesized, the needleless electrospinning process was observed, and the morphology and magnetic properties of magnetic nanofibers were investigated. The results showed that the PVA/ferrofluid could remain stable and homogeneous for 21 days under the magnetic field gradient (2.2 mT/mm). "Taylor cone" array of PVA/ferrofluid was self-assembled under both the magnetic and electric fields. As the electric voltage reached 25 kV, the jets were emitted from the "Taylor cone" array, resulting in needleless electrospinning of magnetic nanofibers. Magnetic nanofibers were homogeneous and continuous with an average diameter of 73.6 nm. Magnetic nanofibers showed a good magnetic response property and relatively high saturated magnetization (1.71 emu/g), which is expected to be applied in the biomedical field.

Preparing Synthetic Aβ in Different Aggregation States

PubMed Central

Stine, W. Blaine; Jungbauer, Lisa; Yu, Chunjiang; LaDu, Mary Jo

2013-01-01

This chapter outlines protocols that produce homogenous preparations of oligomeric and fibrillar amyloid -β peptide (Aβ). While there are several isoforms of this peptide, the 42 amino acid form is the focus because of its genetic and pathological link to Alzheimer’s disease (AD). Past decades of AD research highlight the dependence of Aβ42 function on its structural assembly state. Biochemical, cellular and in vivo studies of Aβ42 usually begin with purified peptide obtained by chemical synthesis or recombinant expression. The initial steps to solubilize and prepare these purified dry peptide stocks are critical to controlling the structural assembly of Aβ. To develop homogenous Aβ42 assemblies, we initially monomerize the peptide, erasing any “structural history” that could seed aggregation, by using a strong solvent. It is this starting material that has allowed us to define and optimize conditions that consistently produce homogenous solutions of soluble oligomeric and fibrillar Aβ42 assemblies. These preparations have been developed and characterized by using atomic force microscopy (AFM) to identify the structurally discrete species formed by Aβ42 under specific solution conditions. These preparations have been used extensively to demonstrate a variety of functional differences between oligomeric and fibrillar Aβ42. We also present a protocol for fluorescently labeling oligomeric Aβ42 that does not affect structure, as measured by AFM, or function, as measured by a cellular uptake assay. These reagents are critical experimental tools that allow for defining specific structure/function connections. PMID:20967580

Inoculation of Scrapie with the Self-Assembling RADA-Peptide Disrupts Prion Accumulation and Extends Hamster Survival

USDA-ARS?s Scientific Manuscript database

Intercerebral inoculation of 263K Scrapie brain homogenate (PrPsc) with a self-assembling RADA-peptide (RADA) significantly delayed disease onset and increased hamster survival. Time of survival was dependent on the dose of RADA and pre-incubation with PrPsc prior to inoculation. RADA treatment resu...

Electrostatic Self-Assembly of Diamond Nanoparticles onto Al- and N-Polar Sputtered Aluminum Nitride Surfaces

PubMed Central

Yoshikawa, Taro; Reusch, Markus; Zuerbig, Verena; Cimalla, Volker; Lee, Kee-Han; Kurzyp, Magdalena; Arnault, Jean-Charles; Nebel, Christoph E.; Ambacher, Oliver; Lebedev, Vadim

2016-01-01

Electrostatic self-assembly of diamond nanoparticles (DNPs) onto substrate surfaces (so-called nanodiamond seeding) is a notable technique, enabling chemical vapor deposition (CVD) of nanocrystalline diamond thin films on non-diamond substrates. In this study, we examine this technique onto differently polarized (either Al- or N-polar) c-axis oriented sputtered aluminum nitride (AlN) film surfaces. This investigation shows that Al-polar films, as compared to N-polar ones, obtain DNPs with higher density and more homogeneously on their surfaces. The origin of these differences in density and homogeneity is discussed based on the hydrolysis behavior of AlN surfaces in aqueous suspensions. PMID:28335345

Controlled graphene oxide assembly on silver nanocube monolayers for SERS detection: dependence on nanocube packing procedure

PubMed Central

Banchelli, Martina; Tiribilli, Bruno; Pini, Roberto; Dei, Luigi

2016-01-01

Summary Hybrid graphene oxide/silver nanocubes (GO/AgNCs) arrays for surface-enhanced Raman spectroscopy (SERS) applications were prepared by means of two procedures differing for the method used in the assembly of the silver nanocubes onto the surface: Langmuir–Blodgett (LB) transfer and direct sequential physisorption of silver nanocubes (AgNCs). Adsorption of graphene oxide (GO) flakes on the AgNC assemblies obtained with both procedures was monitored by quartz crystal microbalance (QCM) technique as a function of GO bulk concentration. The experiment provided values of the adsorbed GO mass on the AgNC array and the GO saturation limit as well as the thickness and the viscoelastic properties of the GO film. Atomic force microscopy (AFM) measurements of the resulting samples revealed that a similar surface coverage was achieved with both procedures but with a different distribution of silver nanoparticles. In the GO covered LB film, the AgNC distribution is characterized by densely packed regions alternating with empty surface areas. On the other hand, AgNCs are more homogeneously dispersed over the entire sensor surface when the nanocubes spontaneously adsorb from solution. In this case, the assembly results in less-packed silver nanostructures with higher inter-cube distance. For the two assembled substrates, AFM of silver nanocubes layers fully covered with GO revealed the presence of a homogeneous, flexible and smooth GO sheet folding over the silver nanocubes and extending onto the bare surface. Preliminary SERS experiments on adenine showed a higher SERS enhancement factor for GO on Langmuir–Blodgett films of AgNCs with respect to bare AgNC systems. Conversely, poor SERS enhancement for adenine resulted for GO-covered AgNCs obtained by spontaneous adsorption. This indicated that the assembly and packing of AgNCs obtained in this way, although more homogeneous over the substrate surface, is not as effective for SERS analysis. PMID:26925348

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome

DOE PAGES

Daleo, Pedro; Alberti, Juan; Jumpponen, Ari; ...

2018-04-12

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a nullmore » model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. As a result, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization.« less

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome.

PubMed

Daleo, Pedro; Alberti, Juan; Jumpponen, Ari; Veach, Allison; Ialonardi, Florencia; Iribarne, Oscar; Silliman, Brian

2018-06-01

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a null model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. Furthermore, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization. © 2018 by the Ecological Society of America.

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome

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

Daleo, Pedro; Alberti, Juan; Jumpponen, Ari

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a nullmore » model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. As a result, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization.« less

Structurally homogeneous nanosheets from self-assembly of a collagen-mimetic peptide.

PubMed

Jiang, Tao; Xu, Chunfu; Zuo, Xiaobing; Conticello, Vincent P

2014-08-04

A collagen-mimetic peptide, NSIII, has been designed with three sequential blocks having positive, neutral, and negative charges, respectively. The non-canonical imino acid, (2S,4S)-4-aminoproline (amp), was used to specify the positive charges at the Xaa positions of (Xaa-Yaa-Gly) triads in the N-terminal domain of NSIII. Peptide NSIII underwent self-assembly from aqueous solution to form a highly homogeneous population of nanosheets. Two-dimensional crystalline sheets formed in which the length of the peptide defined the height of the sheets. These results contrasted with prior results on a similar multi-domain collagen-mimetic polypeptides in which the sheets had highly polydisperse distribution of sizes in the (x/y)- and (z)-dimensions. The structural differences between the two nanosheet assemblies were interpreted in terms of the relative stereoelectronic effects of the different aminoproline derivatives on the local triple helical conformation of the peptides. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial community assembly patterns under incipient conditions in a basaltic soil system

NASA Astrophysics Data System (ADS)

Sengupta, A.; Stegen, J.; Alves Meira Neto, A.; Wang, Y.; Chorover, J.; Troch, P. A. A.; Maier, R. M.

2017-12-01

In sub-surface environments, the biotic components are critically linked to the abiotic processes. However, there is limited understanding of community establishment, functional associations, and community assembly processes of such microbes in sub-surface environments. This study presents the first analysis of microbial signatures in an incipient terrestrial basalt soil system conducted under controlled conditions. A sub-meter scale sampling of a soil mesocosm revealed the contrasting distribution patterns of simple soil parameters such as bulk density and electrical conductivity. Phylogenetic analysis of 16S rRNA gene indicated the presence of a total 40 bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and highest abundance of Proteobacteria throughout the system. Community diversity patterns were inferred to be dependent on depth profile and average water content in the system. Predicted functional gene analysis suggested mixotrophy lifestyles with both autotrophic and heterotrophic metabolisms, likelihood of a unique salt tolerant methanogenic pathway with links to novel Euryarchea, signatures of an incomplete nitrogen cycle, and predicted enzymes of extracellular iron (II) to iron (III) conversion followed by intracellular uptake, transport and regulation. Null modeling revealed microbial community assembly was predominantly governed by variable selection, but the influence of the variable selection did not show systematic spatial structure. The presence of significant heterogeneity in predicted functions and ecologically deterministic shifts in community composition in a homogeneous incipient basalt highlights the complexity exhibited by microorganisms even in the simplest of environmental systems. This presents an opportunity to further develop our understanding of how microbial communities establish, evolve, impact, and respond in sub-surface environments.

The chromatography-free release, isolation and purification of recombinant peptide for fibril self-assembly.

PubMed

Hartmann, B M; Kaar, W; Yoo, I K; Lua, L H L; Falconer, R J; Middelberg, A P J

2009-12-01

One of the major expenses associated with recombinant peptide production is the use of chromatography in the isolation and purification stages of a bioprocess. Here we report a chromatography-free isolation and purification process for recombinant peptide expressed in Escherichia coli (E. coli). Initial peptide release is by homogenization and then by enzymatic cleavage of the peptide-containing fusion protein, directly in the E. coli homogenate. Release is followed by selective solvent precipitation (SSP) to isolate and purify the peptide away from larger cell contaminants. Specifically, we expressed in E. coli the self-assembling beta-sheet forming peptide P(11)-2 in fusion to thioredoxin. Homogenate was heat treated (55 degrees C, 15 min) and then incubated with tobacco etch virus protease (TEVp) to release P(11)-2 having a native N-terminus. SSP with ethanol at room temperature then removed contaminating proteins in an integrated isolation-purification step; it proved necessary to add 250 mM NaCl to homogenate to prevent P(11)-2 from partitioning to the precipitate. This process structure gave recombinant P(11)-2 peptide at 97% polypeptide purity and 40% overall yield, without a single chromatography step. Following buffer-exchange of the 97% pure product by bind-elute chromatography into defined chemical conditions, the resulting peptide was shown to be functionally active and able to form self-assembled fibrils. To the best of our knowledge, this manuscript reports the first published process for chromatography-free recombinant peptide release, isolation and purification. The process proved able to deliver functional recombinant peptide at high purity and potentially low cost, opening cost-sensitive materials applications for peptide-based materials.

Luminescent Carbon Dot Mimics Assembled on DNA

PubMed Central

Chan, Ke Min; Xu, Wang; Kwon, Hyukin; Kietrys, Anna M.; Kool, Eric T.

2018-01-01

Nanometer-sized fragments of carbon in the form of multilayer graphene (“carbon dots”) have been under highly active study for applications in imaging. While offering advantages of low toxicity and photostability, such nanomaterials are inhomogeneous and have limited wavelengths of emission. Here we address these issues by assembling luminescent aromatic C16–C38 hydrocarbons together on a DNA scaffold in homogeneous, soluble molecular compounds. Monomer deoxyribosides of five different aromatic hydrocarbons were synthesized and assembled into a library of 1296 different tetramer compounds on PEG-polystyrene beads. These were screened for photostability and a range of emission colors using 365 nm excitation, observing visible light (>400 nm) emission. We identified a set of six oligomers (DNA-carbon assemblies, DNA-CAs) with exceptional photostability that emit from 400 to 680 nm in water, with Stokes shifts of up to 110 nm, quantum yields ranging from 0.01 to 0.29, and fluorescence lifetimes from 3 to 42 ns. In addition, several of these DNA-CAs exhibited white emission in aqueous solution. The molecules were used in multispectral cell imaging experiments and were taken up into cells passively. The results expand the range of emission properties that can be achieved in water with all-hydrocarbon chromophores and establish the use of the DNA scaffold to arrange carbon layers in homogeneous, rapidly synthesized assemblies. PMID:28841010

A sensitive capacitive immunosensor for direct detection of human heart fatty acid-binding protein (h-FABP).

PubMed

Mihailescu, Carmen-Marinela; Stan, Dana; Iosub, Rodica; Moldovan, Carmen; Savin, Mihaela

2015-01-01

The fabrication of a capacitive interdigitated immunosensor (CID) based on a mixed self-assembled monolayer (mSAM) film for the direct detection of heart fatty-acid binding protein (h-FABP) without any labeling is described. The capacitance changes of mSAMs vs. homogenous ordered self-assembled monolayers (hSAMs) on gold work electrodes/covalently bonded antibodies/buffered medium are utilized for monitoring the specific antibody-antigen interaction. Capacitance measurements in the absence and presence of Faradaic currents were performed. The electrochemical properties of mixed monolayers were compared with those of a pure monolayer of 11-mercaptoundecanoic acid (MUA) self-assembled on gold surfaces. Taking into account the stability of the studied monolayers during the electrochemical experiments with the Faradaic process, the best SAM functionalization method was used for developing a sensitive capacitive immunosensor with a non-Faradaic process for direct immune detection of human h-FABP. Under the optimized conditions, the proposed mixed self-assembled monolayer (mSAM1) on gold electrode exhibited good insulating properties such as a capacitive behavior when detecting h-FABP from human serum in the range of 98 pg ml(-1)-100 ng ml(-1), with a detection limit of 0.836 ng ml(-1) comparative with a homogenous self-assembled monolayer (hSAM). Copyright © 2014 Elsevier B.V. All rights reserved.

Shimming Halbach magnets utilizing genetic algorithms to profit from material imperfections.

PubMed

Parker, Anna J; Zia, Wasif; Rehorn, Christian W G; Blümich, Bernhard

2016-04-01

In recent years, permanent magnet-based NMR spectrometers have resurfaced as low-cost portable alternatives to superconducting instruments. While the development of these devices as well as clever shimming methods have yielded impressive advancements, scaling the size of these magnets to miniature lengths remains a problem to be addressed. Here we present the results of a study of a discrete shimming scheme for NMR Mandhalas constructed from a set of individual magnet blocks. While our calculations predict a modest reduction in field deviation by a factor of 9.3 in the case of the shimmed ideal Mandhala, a factor of 28 is obtained in the case of the shimmed imperfect Mandhala. This indicates that imperfections of magnet blocks can lead to improved field homogeneity. We also present a new algorithm to improve the homogeneity of a permanent magnet assembly. Strategies for future magnet construction can improve the agreement between simulation and practical implementation by using data from real magnets in these assemblies as the input to such an algorithm to optimize the homogeneity of a given design. Published by Elsevier Inc.

Planning Assembly Of Large Truss Structures In Outer Space

NASA Technical Reports Server (NTRS)

De Mello, Luiz S. Homem; Desai, Rajiv S.

1992-01-01

Report dicusses developmental algorithm used in systematic planning of sequences of operations in which large truss structures assembled in outer space. Assembly sequence represented by directed graph called "assembly graph", in which each arc represents joining of two parts or subassemblies. Algorithm generates assembly graph, working backward from state of complete assembly to initial state, in which all parts disassembled. Working backward more efficient than working forward because it avoids intermediate dead ends.

Synthetic surfactant- and cross-linker-free preparation of highly stable lipid-polymer hybrid nanoparticles as potential oral delivery vehicles.

PubMed

Wang, Taoran; Xue, Jingyi; Hu, Qiaobin; Zhou, Mingyong; Chang, Chao; Luo, Yangchao

2017-06-05

The toxicity associated with concentrated synthetic surfactants and the poor stability at gastrointestinal condition are two major constraints for practical applications of solid lipid nanoparticles (SLN) as oral delivery vehicles. In this study, a synthetic surfactant-free and cross-linker-free method was developed to fabricate effective, safe, and ultra-stable lipid-polymer hybrid nanoparticles (LPN). Bovine serum albumin (BSA) and dextran varying in molecular weights were first conjugated through Maillard reaction and the conjugates were exploited to emulsify solid lipid by a solvent diffusion and sonication method. The multilayer structure was formed by self-assembly of BSA-dextran micelles to envelope solid lipid via a pH- and heating-induced facile process with simultaneous surface deposition of pectin. The efficiency of different BSA-dextran conjugates was systematically studied to prepare LPN with the smallest size, the most homogeneous distribution and the greatest stability. The molecular interactions were characterized by Fourier transform infrared and fluorescence spectroscopies. Both nano spray drying and freeze-drying methods were tested to produce spherical and uniform pectin-coated LPN powders that were able to re-assemble nanoscale structure when redispersed in water. The results demonstrated the promise of a synthetic surfactant- and cross-linker-free technique to prepare highly stable pectin-coated LPN from all natural biomaterials as potential oral delivery vehicles.

Multi-scale ordering of self-assembled InAs/GaAs(001) quantum dots

PubMed Central

Songmuang, R; Rastelli, A; Heidemeyer, H; Schmidt, OG

2006-01-01

Ordering phenomena related to the self-assembly of InAs quantum dots (QD) grown on GaAs(001) substrates are experimentally investigated on different length scales. On the shortest length-scale studied here, we examine the QD morphology and observe two types of QD shapes, i.e., pyramids and domes. Pyramids are elongated along the [1-10] directions and are bounded by {137} facets, while domes have a multi-facetted shape. By changing the growth rates, we are able to control the size and size homogeneity of freestanding QDs. QDs grown by using low growth rate are characterized by larger sizes and a narrower size distribution. The homogeneity of buried QDs is measured by photoluminescence spectroscopy and can be improved by low temperature overgrowth. The overgrowth induces the formation of nanostructures on the surface. The fabrication of self-assembled nanoholes, which are used as a template to induce short-range positioning of QDs, is also investigated. The growth of closely spaced QDs (QD molecules) containing 2–6 QDs per QD molecule is discussed. Finally, the long-range positioning of self-assembled QDs, which can be achieved by the growth on patterned substrates, is demonstrated. Lateral QD replication observed during growth of three-dimensional QD crystals is reported.

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

Sen, Ramazan Sonat; Hummel, Andrew John; Hiruta, Hikaru

The deterministic full core simulators require homogenized group constants covering the operating and transient conditions over the entire lifetime. Traditionally, the homogenized group constants are generated using lattice physics code over an assembly or block in the case of prismatic high temperature reactors (HTR). For the case of strong absorbers that causes strong local depressions on the flux profile require special techniques during homogenization over a large volume. Fuel blocks with burnable poisons or control rod blocks are example of such cases. Over past several decades, there have been a tremendous number of studies performed for improving the accuracy ofmore » full-core calculations through the homogenization procedure. However, those studies were mostly performed for light water reactor (LWR) analyses, thus, may not be directly applicable to advanced thermal reactors such as HTRs. This report presents the application of SuPer-Homogenization correction method to a hypothetical HTR core.« less

Neutronics Benchmarks for the Utilization of Mixed-Oxide Fuel: Joint U.S./ Russian Progress Report for Fiscal Year 1997, Volume 4, Part 8 - Neutron Poison Plates in Assemblies Containing Homogeneous Mixtures of Polystyrene-Moderated Plutonium and Uranium Oxides

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

Yavuz, M.

1999-05-01

In the 1970s at the Battelle Pacific Northwest Laboratory (PNL), a series of critical experiments using a remotely operated Split-Table Machine was performed with homogeneous mixtures of (Pu-U)O{sub 2}-polystyrene fuels in the form of square compacts having different heights. The experiments determined the critical geometric configurations of MOX fuel assemblies with and without neutron poison plates. With respect to PuO{sub 2} content and moderation [H/(Pu+U)atomic] ratio (MR), two different homogeneous (Pu-U) O{sub 2}-polystyrene mixtures were considered: Mixture (1) 14.62 wt% PuO{sub 2} with 30.6 MR, and Mixture (2) 30.3 wt% PuO{sub 2} with 2.8 MR. In all mixtures, the uraniummore » was depleted to about O.151 wt% U{sup 235}. Assemblies contained copper, copper-cadmium or aluminum neutron poison plates having thicknesses up to {approximately}2.5 cm. This evaluation contains 22 experiments for Mixture 1, and 10 for Mixture 2 compacts. For Mixture 1, there are 10 configurations with copper plates, 6 with aluminum, and 5 with copper-cadmium. One experiment contained no poison plate. For Mixture 2 compacts, there are 3 configurations with copper, 3 with aluminum, and 3 with copper-cadmium poison plates. One experiment contained no poison plate.« less

Estimating and mapping ecological processes influencing microbial community assembly

PubMed Central

Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

2015-01-01

Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth. PMID:25983725

Epitaxially Self-Assembled Alkane Layers for Graphene Electronics.

PubMed

Yu, Young-Jun; Lee, Gwan-Hyoung; Choi, Ji Il; Shim, Yoon Su; Lee, Chul-Ho; Kang, Seok Ju; Lee, Sunwoo; Rim, Kwang Taeg; Flynn, George W; Hone, James; Kim, Yong-Hoon; Kim, Philip; Nuckolls, Colin; Ahn, Seokhoon

2017-02-01

The epitaxially grown alkane layers on graphene are prepared by a simple drop-casting method and greatly reduce the environmentally driven doping and charge impurities in graphene. Multiscale simulation studies show that this enhancement of charge homogeneity in graphene originates from the lifting of graphene from the SiO 2 surface toward the well-ordered and rigid alkane self-assembled layers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bioenergetic Approaches and Inflammation of MPTP Toxicity

DTIC Science & Technology

2006-09-01

with 8 strokes of pestle A followed by 8 strokes of pestle B. The brain homogenate was centrifuged at 1250 g for 3 min; pellet was discarded and...legends to figures. Fluorescence of safranin O was measured with an F4500 fluorimeter (Hitachi, Japan ) equipped with a magnetic stirring assembly and...and 531 nm emission wavelengths with F4500 fluorimeter (Hitachi, Japan ) equipped with a magnetic stirring assembly and a thermostated cuvette holder

FAST TRACK COMMUNICATION Unexpected systematic degeneracy in a system of two coupled Gaudin models with homogeneous couplings

NASA Astrophysics Data System (ADS)

Erbe, B.; Schliemann, J.

2010-12-01

We report an unexpected systematic degeneracy between different multiplets in an inversion symmetric system of two coupled Gaudin models with homogeneous couplings, as occurring for example in the context of solid state quantum information processing. We construct the full degenerate subspace (being of macroscopic dimension), which turns out to lie in the kernel of the commutator between the two Gaudin models and the coupling term. Finally we investigate to what extent the degeneracy is related to the inversion symmetry of the system and find that indeed there is a large class of systems showing the same type of degeneracy.

Bottom-up assembly of metallic germanium

NASA Astrophysics Data System (ADS)

Scappucci, Giordano; Klesse, Wolfgang M.; Yeoh, Lareine A.; Carter, Damien J.; Warschkow, Oliver; Marks, Nigel A.; Jaeger, David L.; Capellini, Giovanni; Simmons, Michelle Y.; Hamilton, Alexander R.

2015-08-01

Extending chip performance beyond current limits of miniaturisation requires new materials and functionalities that integrate well with the silicon platform. Germanium fits these requirements and has been proposed as a high-mobility channel material, a light emitting medium in silicon-integrated lasers, and a plasmonic conductor for bio-sensing. Common to these diverse applications is the need for homogeneous, high electron densities in three-dimensions (3D). Here we use a bottom-up approach to demonstrate the 3D assembly of atomically sharp doping profiles in germanium by a repeated stacking of two-dimensional (2D) high-density phosphorus layers. This produces high-density (1019 to 1020 cm-3) low-resistivity (10-4Ω · cm) metallic germanium of precisely defined thickness, beyond the capabilities of diffusion-based doping technologies. We demonstrate that free electrons from distinct 2D dopant layers coalesce into a homogeneous 3D conductor using anisotropic quantum interference measurements, atom probe tomography, and density functional theory.

Looking through the Zircon Kaleidoscope: Durations, Rates, and Fluxes in Silicic Magmatic System

NASA Astrophysics Data System (ADS)

Schaltegger, U.; Wotzlaw, J. F.

2014-12-01

The crystallization rate of zircon in a cooling magma depends on the cooling rate through the saturation interval in addition to compositional and kinetic factors. Repeated influx of hot magma over 10-20 ka leads to short-amplitude temperature oscillations, which are recorded by resorption/crystallization cycles of zircon. Plotting the number of dated zircons versus their high-precision U-Pb date results in curves that qualitatively relate to the evolution of magma temperature over time [1], [2]. The trace elemental, O and Hf isotopic composition of zircon gives indications about the degree of magma homogenization and thermal evolution. Zircons from systems with small volumes and magma fluxes record non-systematic chemical and Hf isotopic heterogeneity, suggesting crystallization in non-homogenized ephemeral magma batches. Such systems typically lead to small, mid-upper crustal plutons [3]. Zircons from large-volume crystal-poor rhyolites record initial heterogeneities and rapid amalgamation of smaller magma batches over 10 ka [4], while zircons from monotonous intermediates record magma evolution over several 100 ka with coherent fractionation trends suggesting homogenization and a coherent thermal evolution [2]. In both cases, volumes and flux rates were sufficient to produce large volumes of eruptible magma on very contrasting time scales. Zircon is therefore recording cyclic crystallization-rejuvenation processes during temperature fluctuations in intermediate to upper crustal magma reservoirs but may not relate to the physical pluton emplacement or eruption. We can quantify volumes, rates of magma influx, rates of cooling and crystallization, and the degree of convective homogenization from zircon data, and infer reservoir assembly and eruption trigger mechanisms. These parameters largely control the evolution of long-lived, low-flux silicic magmatic system typical for mid-to-upper crustal plutons, monotonous intermediates are characterized by intermediate durations and fluxes while short-lived, high-flux systems preferentially produce crystal-poor rhyolites. References: [1] Caricchi et al. (2014) Nature 511, 457-461; [2] Wotzlaw et al. (2013) Geology 41, 867-870; [3] Broderick (2013) PhD thesis, Univ. of Geneva; [3] Wotzlaw et al. (2014) Geology, doi:10.1130/G35979.1

Supramolecular metal-organic frameworks that display high homogeneous and heterogeneous photocatalytic activity for H2 production

NASA Astrophysics Data System (ADS)

Tian, Jia; Xu, Zi-Yue; Zhang, Dan-Wei; Wang, Hui; Xie, Song-Hai; Xu, Da-Wen; Ren, Yuan-Hang; Wang, Hao; Liu, Yi; Li, Zhan-Ting

2016-05-01

Self-assembly has a unique presence when it comes to creating complicated, ordered supramolecular architectures from simple components under mild conditions. Here, we describe a self-assembly strategy for the generation of the first homogeneous supramolecular metal-organic framework (SMOF-1) in water at room temperature from a hexaarmed [Ru(bpy)3]2+-based precursor and cucurbit[8]uril (CB[8]). The solution-phase periodicity of this cubic transition metal-cored supramolecular organic framework (MSOF) is confirmed by small-angle X-ray scattering and diffraction experiments, which, as supported by TEM imaging, is commensurate with the periodicity in the solid state. We further demonstrate that SMOF-1 adsorbs anionic Wells-Dawson-type polyoxometalates (WD-POMs) in a one-cage-one-guest manner to give WD-POM@SMOF-1 hybrid assemblies. Upon visible-light (500 nm) irradiation, such hybrids enable fast multi-electron injection from photosensitive [Ru(bpy)3]2+ units to redox-active WD-POM units, leading to efficient hydrogen production in aqueous media and in organic media. The demonstrated strategy opens the door for the development of new classes of liquid-phase and solid-phase ordered porous materials.

A surface-confined DNA assembly amplification strategy on DNA nanostructural scaffold for electrochemiluminescence biosensing.

PubMed

Feng, Qiu-Mei; Guo, Yue-Hua; Xu, Jing-Juan; Chen, Hong-Yuan

2018-02-15

A critical challenge in surface-based DNA assembly amplification is the reduced accessibility of DNA strands arranged on a heterogeneous surface compared to that in homogeneous solution. Here, a novel in situ surface-confined DNA assembly amplification electrochemiluminescence (ECL) biosensor based on DNA nanostructural scaffold was presented. In this design, a stem-loop structural DNA segment (Hairpin 1) was constructed on the vertex of DNA nanostructural scaffold as recognition probe. In the present of target DNA, the hairpin structure changed to rod-like through complementary hybridization with target DNA, resulting in the formation of Hairpin 1:target DNA. When the obtained Hairpin 1:target DNA met Hairpin 2 labeled with glucose oxidase (GOD), the DNA cyclic amplification was activated, releasing target DNA into homogeneous solution for the next recycling. Thus, the ECL signal of Ru(bpy) 3 2+ -TPrA system was quenched by H 2 O 2 , the product of GOD catalyzing glucose. As a result, this proposed method achieved a linear range response from 50 aM to 10 pM with lower detection limit of 20 aM. Copyright © 2017 Elsevier B.V. All rights reserved.

Supramolecular metal-organic frameworks that display high homogeneous and heterogeneous photocatalytic activity for H 2 production

DOE PAGES

Tian, Jia; Xu, Zi-Yue; Zhang, Dan-Wei; ...

2016-05-10

Self-assembly has a unique presence when it comes to creating complicated, ordered supramolecular architectures from simple components under mild conditions. Here, we describe a self-assembly strategy for the generation of the first homogeneous supramolecular metal-organic framework (SMOF-1) in water at room temperature from a hexaarmed [Ru(bpy) 3 ] 2+ -based precursor and cucurbit[8] uril (CB[8]). The solution-phase periodicity of this cubic transition metal-cored supramolecular organic framework (MSOF) is confirmed by small-angle X-ray scattering and diffraction experiments, which, as supported by TEM imaging, is commensurate with the periodicity in the solid state. We further demonstrate that SMOF-1 adsorbs anionic Wells-'Dawson-type polyoxometalatesmore » (WD-POMs) in a one-cage-one-guest manner to give WD-POM@SMOF-1 hybrid assemblies. Upon visible-light (500 nm) irradiation, such hybrids enable fast multi-electron injection from photosensitive [Ru(bpy) 3 ] 2+ units to redox-active WD-POM units, leading to efficient hydrogen production in aqueous media and in organic media. The demonstrated strategy opens the door for the development of new classes of liquid-phase and solid-phase ordered porous materials.« less

Estimating and mapping ecological processes influencing microbial community assembly

DOE PAGES

Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; ...

2015-05-01

Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recentlymore » developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.« less

Distributed parameter modeling of repeated truss structures

NASA Technical Reports Server (NTRS)

Wang, Han-Ching

1994-01-01

A new approach to find homogeneous models for beam-like repeated flexible structures is proposed which conceptually involves two steps. The first step involves the approximation of 3-D non-homogeneous model by a 1-D periodic beam model. The structure is modeled as a 3-D non-homogeneous continuum. The displacement field is approximated by Taylor series expansion. Then, the cross sectional mass and stiffness matrices are obtained by energy equivalence using their additive properties. Due to the repeated nature of the flexible bodies, the mass, and stiffness matrices are also periodic. This procedure is systematic and requires less dynamics detail. The first step involves the homogenization from a 1-D periodic beam model to a 1-D homogeneous beam model. The periodic beam model is homogenized into an equivalent homogeneous beam model using the additive property of compliance along the generic axis. The major departure from previous approaches in literature is using compliance instead of stiffness in homogenization. An obvious justification is that the stiffness is additive at each cross section but not along the generic axis. The homogenized model preserves many properties of the original periodic model.

Self-assembly of [UO{sub 2}X{sub 4}]{sup 2−} (X=Cl, Br) dianions with γ substituted pyridinium cations: Structural systematics and fluorescence properties

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

Surbella, Robert G.; Andrews, Michael B.; Cahill, Christopher L., E-mail: cahill@gwu.edu

2016-04-15

Room temperature self-assembly of [UO{sub 2}X{sub 4}]{sup 2−} (X=Cl, Br) with γ substituted pyridinium cations has resulted in the formation of twelve compounds that were studied via single crystal X-ray diffraction and fluorescence spectroscopy. Systematic variation of electron donating groups on the pyridinium species is shown to influence the presence and/or strength of various supramolecular synthons, including hydrogen bonding and pi interactions. Combinations of such non-covalent interactions (NCIs) have given rise to a range of supramolecular assemblies, and are shown to influence uranyl emission by way of second sphere coordination to equatorial ligands. - Graphical abstract: Supramolecular assembly of themore » [UO{sub 2}Cl{sub 4}]{sup 2−} dianion with pyridinium cations is a viable synthetic route to the growth of uranyl containing single crystals.« less

The U.S. Media: Supermarket or Assembly Line?

ERIC Educational Resources Information Center

Bagdikian, Ben H.

1985-01-01

Considers whether the media as a whole provide a rich marketplace of ideas. Concludes that the range of ideas and information is relatively narrow due to the nature of ownership and media economics, resulting in a homogenization of content. (PD)

Covalently functionalized noble metal nanoparticles for molecular imprinted polymer biosensors: Synthesis, characterization, and SERS detection

NASA Astrophysics Data System (ADS)

Volkert, Anna Allyse

This dissertation evaluates how gold nanoparticle structure and local environment influence resulting sensor function when using these nanomaterials for complex sample analysis. Molecular imprinted polymers (MIPs), a class of plastic antibodies, are engineered and incorporated into these nanosensors thereby facilitating the quantitative detection of a variety of small molecules when Raman spectroscopy and surface enhanced Raman scattering (SERS) are used for detection. First, homogeneous seeded growth gold nanosphere synthesis is evaluated as a function of ionic double layer composition and thickness. Systematically increasing the citrate concentration during synthesis improves nanomaterial shape homogeneity; however, further elevations of citrate concentration increase the number of internal and/or external atomic defects in the nanomaterials which leads to decreasing solution-phase stability. Next, spherical gold nanoparticles are modified with self-assembled monolayer (SAM), modeled using interfacial energy calculations, and experimental characterized using transmission electron microscopy, NMR, extinction spectroscopy, zeta potential, X-ray photoelectron spectroscopy, and flocculation studies to assess the morphology, surface chemistry, optical properties, surface charge, SAM packing density, and nanoparticle stability, respectively. The number of molecules on the nanostructures increases with increasing ionic strength (by decreasing the electrostatic interfacial energy between assembled molecules) which subsequently promotes nanoparticle stability. Third, plastic antibodies that recognize three drugs commonly used to treat migraines are engineered. These methacrylate-based MIPs are synthesized, extracted, characterized, and used to quantitatively and directly detect over-the-counter drugs in complex samples using Raman microscopy. These results along with numerical approximation methods to estimate drug binding site densities and dissociation constants with the MIPs serve as a foundation for understanding how modest recognition selectivity of MIPs coupled with shifts in the vibrational energy modes from the drugs upon hydrogen binding to the polymer backbone promote sensitive and selective drug detection in complex samples. Finally, nanomaterial incorporation into MIPs for applications in SERS-based biosensors is evaluated. Importantly, gold nanorod concentration increases the detectability of the same drugs using MIPs as pre-concentration and recognition elements. This combination of materials, theory, and applications forms a solid foundation which should aid in the design and development of MIP nanobiosensors for specific and sensitive detection of small molecules in complex matrices.

Automatic Assembly of Combined Checkingfixture for Auto-Body Components Based Onfixture Elements Libraries

NASA Astrophysics Data System (ADS)

Jiang, Jingtao; Sui, Rendong; Shi, Yan; Li, Furong; Hu, Caiqi

In this paper 3-D models of combined fixture elements are designed, classified by their functions, and saved in computer as supporting elements library, jointing elements library, basic elements library, localization elements library, clamping elements library, and adjusting elements library etc. Then automatic assembly of 3-D combined checking fixture for auto-body part is presented based on modularization theory. And in virtual auto-body assembly space, Locating constraint mapping technique and assembly rule-based reasoning technique are used to calculate the position of modular elements according to localization points and clamp points of auto-body part. Auto-body part model is transformed from itself coordinate system space to virtual assembly space by homogeneous transformation matrix. Automatic assembly of different functional fixture elements and auto-body part is implemented with API function based on the second development of UG. It is proven in practice that the method in this paper is feasible and high efficiency.

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.

PubMed

Straub, Shannon C K; Parks, Matthew; Weitemier, Kevin; Fishbein, Mark; Cronn, Richard C; Liston, Aaron

2012-02-01

Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematics. Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly. We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths. We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae). Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40× and 30×, respectively. Divergence from the reference significantly affected plastome assembly, but relatively similar references are available for most seed plants. Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism. The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths. Nearly 160000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.

Observation of force-detected nuclear magnetic resonance in a homogeneous field

PubMed Central

Madsen, L. A.; Leskowitz, G. M.; Weitekamp, D. P.

2004-01-01

We report the experimental realization of BOOMERANG (better observation of magnetization, enhanced resolution, and no gradient), a sensitive and general method of magnetic resonance. The prototype millimeter-scale NMR spectrometer shows signal and noise levels in agreement with the design principles. We present 1H and 19F NMR in both solid and liquid samples, including time-domain Fourier transform NMR spectroscopy, multiple-pulse echoes, and heteronuclear J spectroscopy. By measuring a 1H-19F J coupling, this last experiment accomplishes chemically specific spectroscopy with force-detected NMR. In BOOMERANG, an assembly of permanent magnets provides a homogeneous field throughout the sample, while a harmonically suspended part of the assembly, a detector, is mechanically driven by spin-dependent forces. By placing the sample in a homogeneous field, signal dephasing by diffusion in a field gradient is made negligible, enabling application to liquids, in contrast to other force-detection methods. The design appears readily scalable to μm-scale samples where it should have sensitivity advantages over inductive detection with microcoils and where it holds great promise for application of magnetic resonance in biology, chemistry, physics, and surface science. We briefly discuss extensions of the BOOMERANG method to the μm and nm scales. PMID:15326302

Simulation numerique de l'effet du reflecteur radial sur les cellules rep en utilisant les codes DRAGON et DONJON

NASA Astrophysics Data System (ADS)

Bejaoui, Najoua

The pressurized water nuclear reactors (PWRs) is the largest fleet of nuclear reactors in operation around the world. Although these reactors have been studied extensively by designers and operators using efficient numerical methods, there are still some calculation weaknesses, given the geometric complexity of the core, still unresolved such as the analysis of the neutron flux's behavior at the core-reflector interface. The standard calculation scheme is a two steps process. In the first step, a detailed calculation at the assembly level with reflective boundary conditions, provides homogenized cross-sections for the assemblies, condensed to a reduced number of groups; this step is called the lattice calculation. The second step uses homogenized properties in each assemblies to calculate reactor properties at the core level. This step is called the full-core calculation or whole-core calculation. This decoupling of the two calculation steps is the origin of methodological bias particularly at the interface core reflector: the periodicity hypothesis used to calculate cross section librairies becomes less pertinent for assemblies that are adjacent to the reflector generally represented by these two models: thus the introduction of equivalent reflector or albedo matrices. The reflector helps to slowdown neutrons leaving the reactor and returning them to the core. This effect leads to two fission peaks in fuel assemblies localised at the core/reflector interface, the fission rate increasing due to the greater proportion of reentrant neutrons. This change in the neutron spectrum arises deep inside the fuel located on the outskirts of the core. To remedy this we simulated a peripheral assembly reflected with TMI-PWR reflector and developed an advanced calculation scheme that takes into account the environment of the peripheral assemblies and generate equivalent neutronic properties for the reflector. This scheme is tested on a core without control mechanisms and charged with fresh fuel. The results of this study showed that explicit representation of reflector and calculation of peripheral assembly with our advanced scheme allow corrections to the energy spectrum at the core interface and increase the peripheral power by up to 12% compared with that of the reference scheme.

Assembly Modulated by Particle Position and Shape: A New Concept in Self-Assembly.

PubMed

Tavacoli, Joe W; Heuvingh, Julien; Du Roure, Olivia

2017-11-10

In this communication we outline how the bespoke arrangements and design of micron-sized superparamagnetic shapes provide levers to modulate their assembly under homogeneous magnetic fields. We label this new approach, 'assembly modulated by particle position and shape' (APPS). Specifically, using rectangular lattices of superparamagnetic micron-sized cuboids, we construct distinct microstructures by adjusting lattice pitch and angle of array with respect to a magnetic field. Broadly, we find two modes of assembly: (1) immediate 2D jamming of the cuboids as they rotate to align with the applied field (rotation-induced jamming) and (2) aggregation via translation after their full alignment (dipole-dipole assembly). The boundary between these two assembly pathways is independent on field strength being solely a function of the cuboid's dimensions, lattice pitch, and array angle with respect to field-a relationship which we capture, along with other features of the assembly process, in a 'phase diagram'. In doing so, we set out initial design rules to build custom made assemblies. Moreover, these assemblies can be made flexible thanks to the hinged contacts of their particle building blocks. This flexibility, combined with the superparamagnetic nature of the architectures, renders our assembly method particularly appropriate for the construction of complex actuators at a scale hitherto not possible.

Evolving self-assembly in autonomous homogeneous robots: experiments with two physical robots.

PubMed

Ampatzis, Christos; Tuci, Elio; Trianni, Vito; Christensen, Anders Lyhne; Dorigo, Marco

2009-01-01

This research work illustrates an approach to the design of controllers for self-assembling robots in which the self-assembly is initiated and regulated by perceptual cues that are brought forth by the physical robots through their dynamical interactions. More specifically, we present a homogeneous control system that can achieve assembly between two modules (two fully autonomous robots) of a mobile self-reconfigurable system without a priori introduced behavioral or morphological heterogeneities. The controllers are dynamic neural networks evolved in simulation that directly control all the actuators of the two robots. The neurocontrollers cause the dynamic specialization of the robots by allocating roles between them based solely on their interaction. We show that the best evolved controller proves to be successful when tested on a real hardware platform, the swarm-bot. The performance achieved is similar to the one achieved by existing modular or behavior-based approaches, also due to the effect of an emergent recovery mechanism that was neither explicitly rewarded by the fitness function, nor observed during the evolutionary simulation. Our results suggest that direct access to the orientations or intentions of the other agents is not a necessary condition for robot coordination: Our robots coordinate without direct or explicit communication, contrary to what is assumed by most research works in collective robotics. This work also contributes to strengthening the evidence that evolutionary robotics is a design methodology that can tackle real-world tasks demanding fine sensory-motor coordination.

Macromolecular assemblies in reduced gravity environments

NASA Technical Reports Server (NTRS)

Moos, Philip J.; Hayes, James W.; Stodieck, Louis S.; Luttges, Marvin W.

1990-01-01

The assembly of protein macro molecules into structures commonly produced within biological systems was achieved using in vitro techniques carried out in nominal as well as reduced gravity environments. Appropriate hardware was designed and fabricated to support such studies. Experimental protocols were matched to the available reduced gravity test opportunities. In evaluations of tubulin, fibrin and collagen assembly products the influence of differing gravity test conditions are apparent. Product homogeneity and organization were characteristic enhancements documented in reduced gravity samples. These differences can be related to the fluid flow conditions that exist during in vitro product formation. Reduced gravity environments may provide a robust opportunity for directing the products formed in a variety of bioprocessing applications.

Toward a Systematic Evaluation of Vowel Target Events across Speech Tasks

ERIC Educational Resources Information Center

Kuo, Christina

2011-01-01

The core objective of this study was to examine whether acoustic variability of vowel production in American English, across speaking tasks, is systematic. Ten male speakers who spoke a relatively homogeneous Wisconsin dialect produced eight monophthong vowels (in hVd and CVC contexts) in four speaking tasks, including clear-speech, citation form,…

Alternating current dielectrophoresis of core-shell nanoparticles: Experiments and comparison with theory

NASA Astrophysics Data System (ADS)

Yang, Chungja

Nanoparticles are fascinating where physical and optical properties are related to size. Highly controllable synthesis methods and nanoparticle assembly are essential for highly innovative technological applications. Well-defined shaped and sized nanoparticles enable comparisons between experiments, theory and subsequent new models to explain experimentally observed phenomena. Among nanoparticles, nonhomogeneous core-shell nanoparticles (CSnp) have new properties that arise when varying the relative dimensions of the core and the shell. This CSnp structure enables various optical resonances, and engineered energy barriers, in addition to the high charge to surface ratio. Assembly of homogeneous nanoparticles into functional structures has become ubiquitous in biosensors (i.e. optical labeling), nanocoatings, and electrical circuits. Limited nonhomogenous nanoparticle assembly has only been explored. Many conventional nanoparticle assembly methods exist, but this work explores dielectrophoresis (DEP) as a new method. DEP is particle polarization via non-uniform electric fields while suspended in conductive fluids. Most prior DEP efforts involve microscale particles. Prior work on core-shell nanoparticle assemblies and separately, nanoparticle characterizations with dielectrophoresis and electrorotation, did not systematically explore particle size, dielectric properties (permittivity and electrical conductivity), shell thickness, particle concentration, medium conductivity, and frequency. This work is the first, to the best of our knowledge, to systematically examine these dielectrophoretic properties for core-shell nanoparticles. Further, we conduct a parametric fitting to traditional core-shell models. These biocompatible core-shell nanoparticles were studied to fill a knowledge gap in the DEP field. Experimental results (chapter 5) first examine medium conductivity, size and shell material dependencies of dielectrophoretic behaviors of spherical CSnp into 2D and 3D particle-assemblies. Chitosan (amino sugar) and poly-L-lysine (amino acid, PLL) CSnp shell materials were custom synthesized around a hollow (gas) core by utilizing a phospholipid micelle around a volatile fluid templating for the shell material; this approach proves to be novel and distinct from conventional core-shell models wherein a conductive core is coated with an insulative shell. Experiments were conducted within a 100 nl chamber housing 100 um wide Ti/Au quadrapole electrodes spaced 25 um apart. Frequencies from 100kHz to 80MHz at fixed local field of 5Vpp were tested with 10-5 and 10-3 S/m medium conductivities for 25 seconds. Dielectrophoretic responses of ~220 and 340(or ~400) nm chitosan or PLL CSnp were compiled as a function of medium conductivity, size and shell material. Experiments further examined shell thickness and particle concentration (chapter 6) dependencies on ~530 nm CSnp dielectrophoretic and electrorotational responses with ~30nm and ~80 nm shell thicknesses and at particle concentration count rates of 5000 +/- 500, 10000 +/- 500, and 15000 +/- 500 counts per second. Using similar experimental conditions, both dielectrophoretic and electrorotational CSnp responses were compiled versus frequency, shell thickness, and particle concentration. Knowledge gained from this study includes a unique resonance-like dielectrophoretic and electrorotational spectrum, which is significantly distinct from other cells and particles. CSnp dielectric properties were then calculated by parametrically fitting parameters to an existing core-shell model. The optimum conductivity and relative permittivity for the core and the shell are 1E-15 S/m, 1, 0.6 S/m, and 90, respectively. These properties can be exploited to rapidly assemble these unique core-shell particles for future structural color production in fabrics, vehicle, and wall painting.

Homogenizing and diversifying effects of intensive agricultural land-use on plant species beta diversity in Central Europe - A call to adapt our conservation measures

Treesearch

Constanze Buhk; Martin Alt; Manuel J. Steinbauer; Carl Beierkuhnlein; Steve Warren; Anke Jentsch

2017-01-01

The prevention of biodiversity loss in agricultural landscapes to protect ecosystem stability and functions is of major importance to stabilize overall diversity. Intense agriculture leads to a loss in species richness and homogenization of species pools, but the processes behind are poorly understood due to a lack of systematic case studies: The specific...

Bottom-up assembly of metallic germanium.

PubMed

Scappucci, Giordano; Klesse, Wolfgang M; Yeoh, LaReine A; Carter, Damien J; Warschkow, Oliver; Marks, Nigel A; Jaeger, David L; Capellini, Giovanni; Simmons, Michelle Y; Hamilton, Alexander R

2015-08-10

Extending chip performance beyond current limits of miniaturisation requires new materials and functionalities that integrate well with the silicon platform. Germanium fits these requirements and has been proposed as a high-mobility channel material, a light emitting medium in silicon-integrated lasers, and a plasmonic conductor for bio-sensing. Common to these diverse applications is the need for homogeneous, high electron densities in three-dimensions (3D). Here we use a bottom-up approach to demonstrate the 3D assembly of atomically sharp doping profiles in germanium by a repeated stacking of two-dimensional (2D) high-density phosphorus layers. This produces high-density (10(19) to 10(20) cm(-3)) low-resistivity (10(-4)Ω · cm) metallic germanium of precisely defined thickness, beyond the capabilities of diffusion-based doping technologies. We demonstrate that free electrons from distinct 2D dopant layers coalesce into a homogeneous 3D conductor using anisotropic quantum interference measurements, atom probe tomography, and density functional theory.

Self-assembled monolayers of alendronate on Ti6Al4V alloy surfaces enhance osteogenesis in mesenchymal stem cells

NASA Astrophysics Data System (ADS)

Rojo, Luis; Gharibi, Borzo; McLister, Robert; Meenan, Brian J.; Deb, Sanjukta

2016-07-01

Phosphonates have emerged as an alternative for functionalization of titanium surfaces by the formation of homogeneous self-assembled monolayers (SAMs) via Ti-O-P linkages. This study presents results from an investigation of the modification of Ti6Al4V alloy by chemisorption of osseoinductive alendronate using a simple, effective and clean methodology. The modified surfaces showed a tailored topography and surface chemistry as determined by SEM microscopy and RAMAN spectroscopy. X-ray photoelectron spectroscopy revealed that an effective mode of bonding is created between the metal oxide surface and the phosphate residue of alendronate, leading to formation of homogenous drug distribution along the surface. In-vitro studies showed that alendronate SAMs induce differentiation of hMSC to a bone cell phenotype and promote bone formation on modified surfaces. Here we show that this novel method for the preparation of functional coatings on titanium-based medical devices provides osseoinductive bioactive molecules to promote enhanced integration at the site of implantation.

Self-assembled monolayers of alendronate on Ti6Al4V alloy surfaces enhance osteogenesis in mesenchymal stem cells

PubMed Central

Rojo, Luis; Gharibi, Borzo; McLister, Robert; Meenan, Brian J.; Deb, Sanjukta

2016-01-01

Phosphonates have emerged as an alternative for functionalization of titanium surfaces by the formation of homogeneous self-assembled monolayers (SAMs) via Ti-O-P linkages. This study presents results from an investigation of the modification of Ti6Al4V alloy by chemisorption of osseoinductive alendronate using a simple, effective and clean methodology. The modified surfaces showed a tailored topography and surface chemistry as determined by SEM microscopy and RAMAN spectroscopy. X-ray photoelectron spectroscopy revealed that an effective mode of bonding is created between the metal oxide surface and the phosphate residue of alendronate, leading to formation of homogenous drug distribution along the surface. In-vitro studies showed that alendronate SAMs induce differentiation of hMSC to a bone cell phenotype and promote bone formation on modified surfaces. Here we show that this novel method for the preparation of functional coatings on titanium-based medical devices provides osseoinductive bioactive molecules to promote enhanced integration at the site of implantation. PMID:27468811

An Analytical Technique to Elucidate Field Impurities From Manufacturing Uncertainties of an Double Pancake Type HTS Insert for High Field LTS/HTS NMR Magnets

PubMed Central

Hahn, Seung-yong; Ahn, Min Cheol; Bobrov, Emanuel Saul; Bascuñán, Juan; Iwasa, Yukikazu

2010-01-01

This paper addresses adverse effects of dimensional uncertainties of an HTS insert assembled with double-pancake coils on spatial field homogeneity. Each DP coil was wound with Bi2223 tapes having dimensional tolerances larger than one order of magnitude of those accepted for LTS wires used in conventional NMR magnets. The paper presents: 1) dimensional variations measured in two LTS/HTS NMR magnets, 350 MHz (LH350) and 700 MHz (LH700), both built and operated at the Francis Bitter Magnet Laboratory; and 2) an analytical technique and its application to elucidate the field impurities measured with the two LTS/HTS magnets. Field impurities computed with the analytical model and those measured with the two LTS/HTS magnets agree quite well, demonstrating that this analytical technique is applicable to design a DP-assembled HTS insert with an improved field homogeneity for a high-field LTS/HTS NMR magnet. PMID:20407595

Recent developments in multidimensional transport methods for the APOLLO 2 lattice code

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

Zmijarevic, I.; Sanchez, R.

1995-12-31

A usual method of preparation of homogenized cross sections for reactor coarse-mesh calculations is based on two-dimensional multigroup transport treatment of an assembly together with an appropriate leakage model and reaction-rate-preserving homogenization technique. The actual generation of assembly spectrum codes based on collision probability methods is capable of treating complex geometries (i.e., irregular meshes of arbitrary shape), thus avoiding the modeling error that was introduced in codes with traditional tracking routines. The power and architecture of current computers allow the treatment of spatial domains comprising several mutually interacting assemblies using fine multigroup structure and retaining all geometric details of interest.more » Increasing safety requirements demand detailed two- and three-dimensional calculations for very heterogeneous problems such as control rod positioning, broken Pyrex rods, irregular compacting of mixed- oxide (MOX) pellets at an MOX-UO{sub 2} interface, and many others. An effort has been made to include accurate multi- dimensional transport methods in the APOLLO 2 lattice code. These include extension to three-dimensional axially symmetric geometries of the general-geometry collision probability module TDT and the development of new two- and three-dimensional characteristics methods for regular Cartesian meshes. In this paper we discuss the main features of recently developed multidimensional methods that are currently being tested.« less

Systematics of stretching of fluid inclusions I: fluorite and sphalerite at 1 atmosphere confining pressure.

USGS Publications Warehouse

Bodnar, R.J.; Bethke, P.M.

1984-01-01

Measured homogenization T of fluid inclusions in fluorite and sphalerite may be higher than the true homogenization T of samples that have been previously heated in the laboratory or naturally in post-entrapment events. As T and with it internal P is increased, the resulting volume increase may become inelastic. If the volume increase exceeds the precision of T measurement, the inclusion is said to have stretched. More than 1300 measurements on fluid inclusions in fluorite and sphalerite indicate that stretching is systematically related to P-V-T-X properties of the fluid, inclusion size and shape, physical properties of the host mineral, and the confining P. Experimental methods are detailed in an appendix. The mechanism of stretching is probably plastic deformation or - not observed - microfracturing. The systematic relationship between the internal P necessary to initiate stretching and the inclusion volume provides a means of recognizing previously stretched inclusions and estimating the magnitude of post-entrapment thermal events. -G.J.N.

Ionically self-assembled monolayers (ISAMs)

NASA Astrophysics Data System (ADS)

Janik, John

2001-04-01

Ionically self-assembled monolayers (ISAMs), fabricated by alternate adsorption of cationic and anionic components, yield exceptionally homogeneous thin films with sub-nanometer control of the thickness and relative special location of the component materials. Using organic electrochromic materials such as polyaniline, we report studies of electrochromic responses in ISAM films. Reversible changes in the absorption spectrum are observed with the application of voltages on the order of 1.0 V. Measurements are made using both liquid electrolytes and in all-solid state devices incorporating solid polyelectrolytes such as poly(2-acylamido 2-methyl propane sulfonic acid) (PAMPS).

Systematic Review Methodology for the Fatigue in Emergency Medical Services Project

DOT National Transportation Integrated Search

2018-01-11

Background: Guidance for managing fatigue in the Emergency Medical Services (EMS) setting is limited. The Fatigue in EMS Project sought to complete multiple systematic reviews guided by seven explicit research questions, assemble the best available e...

Enhanced cell uptake via non-covalent decollation of a single-walled carbon nanotube-DNA hybrid with polyethylene glycol-grafted poly(l-lysine) labeled with an Alexa-dye and its efficient uptake in a cancer cell

NASA Astrophysics Data System (ADS)

Fujigaya, Tsuyohiko; Yamamoto, Yuki; Kano, Arihiro; Maruyama, Atsushi; Nakashima, Naotoshi

2011-10-01

The use of single-walled carbon nanotubes (SWNTs) for biomedical applications is a promising approach due to their unique outer optical stimuli response properties, such as a photothermal response triggered by near-IR laser irradiation. The challenging task in order to realize such applications is to render the SWNTs biocompatible. For this purpose, the stable and homogeneous functionalization of the SWNTs with a molecule carrying a biocompatible group is very important. Here, we describe the design and synthesis of a polyanionic SWNT/DNA hybrid combined with a cationic poly(l-lysine) grafted by polyethylene glycol (PLL-g-PEG) to provide a supramolecular SWNT assembly. A titration experiment revealed that the assembly undergoes an approximately 1 : 1 reaction of the SWNT/DNA with PLL-g-PEG. We also found that SWNT/DNA is coated with PLL-g-PEG very homogeneously that avoids the non-specific binding of proteins on the SWNT surface. The experiment using the obtained supramolecular hybrid was carried out in vitro and a dramatic enhancement in the cell uptake efficiency compared to that of the SWNT/DNA hybrid without PLL-g-PEG was found.The use of single-walled carbon nanotubes (SWNTs) for biomedical applications is a promising approach due to their unique outer optical stimuli response properties, such as a photothermal response triggered by near-IR laser irradiation. The challenging task in order to realize such applications is to render the SWNTs biocompatible. For this purpose, the stable and homogeneous functionalization of the SWNTs with a molecule carrying a biocompatible group is very important. Here, we describe the design and synthesis of a polyanionic SWNT/DNA hybrid combined with a cationic poly(l-lysine) grafted by polyethylene glycol (PLL-g-PEG) to provide a supramolecular SWNT assembly. A titration experiment revealed that the assembly undergoes an approximately 1 : 1 reaction of the SWNT/DNA with PLL-g-PEG. We also found that SWNT/DNA is coated with PLL-g-PEG very homogeneously that avoids the non-specific binding of proteins on the SWNT surface. The experiment using the obtained supramolecular hybrid was carried out in vitro and a dramatic enhancement in the cell uptake efficiency compared to that of the SWNT/DNA hybrid without PLL-g-PEG was found. Electronic supplementary information (ESI) available: Additional absorption spectra, DLS plots and PL spectra. See DOI: 10.1039/c1nr10635j

Annealing temperature effect on self-assembled Au droplets on Si (111).

PubMed

Sui, Mao; Li, Ming-Yu; Kim, Eun-Soo; Lee, Jihoon

2013-12-13

We investigate the effect of annealing temperature on self-assembled Au droplets on Si (111). The annealing temperature is systematically varied while fixing other growth parameters such as deposition amount and annealing duration clearly to observe the annealing temperature effect. Self-assembled Au droplets are fabricated by annealing from 50°C to 850°C with 2-nm Au deposition for 30 s. With increased annealing temperatures, Au droplets show gradually increased height and diameter while the density of droplets progressively decreases. Self-assembled Au droplets with fine uniformity can be fabricated between 550°C and 800°C. While Au droplets become much larger with increased deposition amount, the extended annealing duration only mildly affects droplet size and density. The results are systematically analyzed with cross-sectional line profiles, Fourier filter transform power spectra, height histogram, surface area ratio, and size and density plots. This study can provide an aid point for the fabrication of nanowires on Si (111).

Weight of Evidence for Ecological Assessment

EPA Science Inventory

Systematic review (SR) and weight of evidence (WoE), both inform inferences based on multiple pieces of evidence, but they differ in their emphasis. Systematic reviews, such as those by Collaboration for Environmental Evidence, are assessments that emphasize the assembly of stud...

Cellular imaging by targeted assembly of hot-spot SERS and photoacoustic nanoprobes using split-fluorescent protein scaffolds.

PubMed

Köker, Tuğba; Tang, Nathalie; Tian, Chao; Zhang, Wei; Wang, Xueding; Martel, Richard; Pinaud, Fabien

2018-02-09

The in cellulo assembly of plasmonic nanomaterials into photo-responsive probes is of great interest for many bioimaging and nanophotonic applications but remains challenging with traditional nucleic acid scaffolds-based bottom-up methods. Here, we address this quandary using split-fluorescent protein (FP) fragments as molecular glue and switchable Raman reporters to assemble gold or silver plasmonic nanoparticles (NPs) into photonic clusters directly in live cells. When targeted to diffusing surface biomarkers in cancer cells, the NPs self-assemble into surface-enhanced Raman-scattering (SERS) nanoclusters having hot spots homogenously seeded by the reconstruction of full-length FPs. Within plasmonic hot spots, autocatalytic activation of the FP chromophore and near-field amplification of its Raman fingerprints enable selective and sensitive SERS imaging of targeted cells. This FP-driven assembly of metal colloids also yields enhanced photoacoustic signals, allowing the hybrid FP/NP nanoclusters to serve as contrast agents for multimodal SERS and photoacoustic microscopy with single-cell sensitivity.

Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice.

PubMed

Bhanjadeo, Madhabi M; Nayak, Ashok K; Subudhi, Umakanta

2017-04-01

DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices. Copyright © 2017 Elsevier Inc. All rights reserved.

Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ.

PubMed

Xia, Hongwei; Fu, Hailin; Zhang, Yanfeng; Shih, Kuo-Chih; Ren, Yuan; Anuganti, Murali; Nieh, Mu-Ping; Cheng, Jianjun; Lin, Yao

2017-08-16

Supramolecular polymerization or assembly of proteins or large macromolecular units by a homogeneous nucleation mechanism can be quite slow and require specific solution conditions. In nature, protein assembly is often regulated by molecules that modulate the electrostatic interactions of the protein subunits for various association strengths. The key to this regulation is the coupling of the assembly process with a reversible or irreversible chemical reaction that occurs within the constituent subunits. However, realizing this complex process by the rational design of synthetic molecules or macromolecules remains a challenge. Herein, we use a synthetic polypeptide-grafted comb macromolecule to demonstrate how the in situ modulation of interactions between the charged macromolecules affects their resulting supramolecular structures. The kinetics of structural formation was studied and can be described by a generalized model of nucleated polymerization containing secondary pathways. Basic thermodynamic analysis indicated the delicate role of the electrostatic interactions between the charged subunits in the reaction-induced assembly process. This approach may be applicable for assembling a variety of ionic soft matters that are amenable to chemical reactions in situ.

Experimental protocol for manipulating plant-induced soil heterogeneity.

PubMed

Brandt, Angela J; del Pino, Gaston A; Burns, Jean H

2014-03-13

Coexistence theory has often treated environmental heterogeneity as being independent of the community composition; however biotic feedbacks such as plant-soil feedbacks (PSF) have large effects on plant performance, and create environmental heterogeneity that depends on the community composition. Understanding the importance of PSF for plant community assembly necessitates understanding of the role of heterogeneity in PSF, in addition to mean PSF effects. Here, we describe a protocol for manipulating plant-induced soil heterogeneity. Two example experiments are presented: (1) a field experiment with a 6-patch grid of soils to measure plant population responses and (2) a greenhouse experiment with 2-patch soils to measure individual plant responses. Soils can be collected from the zone of root influence (soils from the rhizosphere and directly adjacent to the rhizosphere) of plants in the field from conspecific and heterospecific plant species. Replicate collections are used to avoid pseudoreplicating soil samples. These soils are then placed into separate patches for heterogeneous treatments or mixed for a homogenized treatment. Care should be taken to ensure that heterogeneous and homogenized treatments experience the same degree of soil disturbance. Plants can then be placed in these soil treatments to determine the effect of plant-induced soil heterogeneity on plant performance. We demonstrate that plant-induced heterogeneity results in different outcomes than predicted by traditional coexistence models, perhaps because of the dynamic nature of these feedbacks. Theory that incorporates environmental heterogeneity influenced by the assembling community and additional empirical work is needed to determine when heterogeneity intrinsic to the assembling community will result in different assembly outcomes compared with heterogeneity extrinsic to the community composition.

Self-assembly of star micelle into vesicle in solvents of variable quality: the star micelle retains its core-shell nanostructure in the vesicle.

PubMed

Liu, Nijuan; He, Qun; Bu, Weifeng

2015-03-03

Intra- and intermolecular interactions of star polymers in dilute solutions are of fundamental importance for both theoretical interest and hierarchical self-assembly into functional nanostructures. Here, star micelles with a polystyrene corona and a small ionic core bearing platinum(II) complexes have been regarded as a model of star polymers to mimic their intra- and interstar interactions and self-assembled behaviors in solvents of weakening quality. In the chloroform/methanol mixture solvents, the star micelles can self-assemble to form vesicles, in which the star micelles shrink significantly and are homogeneously distributed on the vesicle surface. Unlike the morphological evolution of conventional amphiphiles from micellar to vesicular, during which the amphiphilic molecules are commonly reorganized, the star micelles still retain their core-shell nanostructures in the vesicles and the coronal chains of the star micelle between the ionic cores are fully interpenetrated.

Controlling systematic perioperative anaerobic contamination during sinus-lift procedures by using metronidazole: an innovative approach.

PubMed

Choukroun, Joseph; Simonpieri, Alain; Del Corso, Marco; Mazor, Ziv; Sammartino, Gilberto; Dohan Ehrenfest, David M

2008-09-01

Analysis of tomodensitometric controls following sinus grafts clearly demonstrates a quite systematic lack of homogeneity. Sinus contamination by anaerobic bacteria seems almost unavoidable during bone graft surgery, and this problem may jeopardize the healing process. The aim of this study was to characterize in a systematic way the nonhomogeneities observed at 1, 2, or 3 months postsurgery within allogenous sinus grafts, and to assess the possible influence of a 0.5% sterile solution of metronidazole incorporated in the sinus bone graft. This clinical study was conducted on 72 patients treated with single or bilateral sinus-lifts: 94 sinus elevations performed with freeze-dried bone allograft (Phoenix, TBF, Mions, France), with (test group) or without (control group) metronidazole. In the test group, each bone graft was hydrated with 2 mL of a 0.5% metronidazole solution, i.e., only 10 mg of metronidazole. All the patients went through a first presurgical computerized tomography (CT)-scan followed by a second scan performed at 1, 2, or 3 months postsurgery (which was used as the preimplant reference scan). For 11 patients, 2 postsurgical CT-scans were performed respectively at 10 days and 2 months. Using an arbitrary gray scale (Arbitrary Densitometric Unit) which functions according to the Hounsfield unit principle, the degree of radiographic homogeneity of the grafts was established. Density scattering provides some information on the homogeneity or nonhomogeneity of the bone graft. The 12 grafts performed without metronidazole show significant nonhomogeneities at 1, 2, or 3 months. Moreover, when a CT-scan is performed during the first postoperative days (at 10 days), the presence of air bubbles in the graft is confirmed. The tomodensitometric aspects of all grafts treated with metronidazole in this series are absolutely identical: they show a high degree of homogeneity. Sixty-three cases (76.8%) are homogeneous, and 19 cases (23.2%) are significantly homogeneous. The time at which the control scan is performed (10 days, 1, 2, or 3 months) does not seem to influence significantly the degree of homogeneity assessed. In the control group, some inflammatory events associated with facial oedema were observed in 25% of the cases. In the test group, no such event was recorded for the 82 sinus-lifts treated with metronidazole. A possible correlation may exist between the occurrence of non homogeneities within the bone grafts and the anaerobic bacterial contamination. The local use of a very small quantity of metronidazole (equivalent to only 1/20 of a common 200 mg oral tablet) could provide more security when performing sinus-lift procedures and an improved quality of the graft. This protocol should not be considered as an antibiotherapy, but only as way to limit the initial contamination of bone graft.

Variation simulation for compliant sheet metal assemblies with applications

NASA Astrophysics Data System (ADS)

Long, Yufeng

Sheet metals are widely used in discrete products, such as automobiles, aircraft, furniture and electronics appliances, due to their good manufacturability and low cost. A typical automotive body assembly consists of more than 300 parts welded together in more than 200 assembly fixture stations. Such an assembly system is usually quite complex, and takes a long time to develop. As the automotive customer demands products of increasing quality in a shorter time, engineers in automotive industry turn to computer-aided engineering (CAE) tools for help. Computers are an invaluable resource for engineers, not only to simplify and automate the design process, but also to share design specifications with manufacturing groups so that production systems can be tooled up quickly and efficiently. Therefore, it is beneficial to develop computerized simulation and evaluation tools for development of automotive body assembly systems. It is a well-known fact that assembly architectures (joints, fixtures, and assembly lines) have a profound impact on dimensional quality of compliant sheet metal assemblies. To evaluate sheet metal assembly architectures, a special dimensional analysis tool need be developed for predicting dimensional variation of the assembly. Then, the corresponding systematic tools can be established to help engineers select the assembly architectures. In this dissertation, a unified variation model is developed to predict variation in compliant sheet metal assemblies by considering fixture-induced rigid-body motion, deformation and springback. Based on the unified variation model, variation propagation models in multiple assembly stations with various configurations are established. To evaluate the dimensional capability of assembly architectures, quantitative indices are proposed based on the sensitivity matrix, which are independent of the variation level of the process. Examples are given to demonstrate their applications in selecting robust assembly architectures, and some useful guidelines for selection of assembly architectures are summarized. In addition, to enhance the fault diagnosis, a systematic methodology is proposed for selection of measurement configurations. Specifically, principles involved in selecting measurements are generalized first; then, the corresponding quantitative indices are developed to evaluate the measurement configurations, and finally, examples are present.

Versatile and Programmable DNA Logic Gates on Universal and Label-Free Homogeneous Electrochemical Platform.

PubMed

Ge, Lei; Wang, Wenxiao; Sun, Ximei; Hou, Ting; Li, Feng

2016-10-04

Herein, a novel universal and label-free homogeneous electrochemical platform is demonstrated, on which a complete set of DNA-based two-input Boolean logic gates (OR, NAND, AND, NOR, INHIBIT, IMPLICATION, XOR, and XNOR) is constructed by simply and rationally deploying the designed DNA polymerization/nicking machines without complicated sequence modulation. Single-stranded DNA is employed as the proof-of-concept target/input to initiate or prevent the DNA polymerization/nicking cyclic reactions on these DNA machines to synthesize numerous intact G-quadruplex sequences or binary G-quadruplex subunits as the output. The generated output strands then self-assemble into G-quadruplexes that render remarkable decrease to the diffusion current response of methylene blue and, thus, provide the amplified homogeneous electrochemical readout signal not only for the logic gate operations but also for the ultrasensitive detection of the target/input. This system represents the first example of homogeneous electrochemical logic operation. Importantly, the proposed homogeneous electrochemical logic gates possess the input/output homogeneity and share a constant output threshold value. Moreover, the modular design of DNA polymerization/nicking machines enables the adaptation of these homogeneous electrochemical logic gates to various input and output sequences. The results of this study demonstrate the versatility and universality of the label-free homogeneous electrochemical platform in the design of biomolecular logic gates and provide a potential platform for the further development of large-scale DNA-based biocomputing circuits and advanced biosensors for multiple molecular targets.

Permanent magnet assembly producing a strong tilted homogeneous magnetic field: towards magic angle field spinning NMR and MRI.

PubMed

Sakellariou, Dimitris; Hugon, Cédric; Guiga, Angelo; Aubert, Guy; Cazaux, Sandrine; Hardy, Philippe

2010-12-01

We introduce a cylindrical permanent magnet design that generates a homogeneous and strong magnetic field having an arbitrary inclination with respect to the axis of the cylinder. The analytical theory of 3 D magnetostatics has been applied to this problem, and a hybrid magnet structure has been designed. This structure contains two magnets producing a longitudinal and transverse component for the magnetic field, whose amplitudes and homogeneities can be fully controlled by design. A simple prototype has been constructed using inexpensive small cube magnets, and its magnetic field has been mapped using Hall and NMR probe sensors. This magnet can, in principle, be used for magic angle field spinning NMR and MRI experiments allowing for metabolic chemical shift profiling in small living animals. Copyright © 2010 John Wiley & Sons, Ltd.

Controlled Assembly of Biocompatible Metallic Nanoaggregates Using a Small Molecule Crosslinker

PubMed Central

Van Haute, Desiree; Longmate, Julia M.; Berlin, Jacob M.

2015-01-01

By introducing a capping step and controlling reaction parameters, the assembly of metallic nanoparticle aggregates can be achieved using a small molecule crosslinker. Aggregates can be assembled from particles of varied size and composition and the size of the aggregates can be systematically adjusted. Following cell uptake of 60 nm aggregates, the aggregates are stable and non-toxic to macrophage cells up to 55mM Au. PMID:26208123

Analysis of benchmark critical experiments with ENDF/B-VI data sets

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

Hardy, J. Jr.; Kahler, A.C.

1991-12-31

Several clean critical experiments were analyzed with ENDF/B-VI data to assess the adequacy of the data for U{sup 235}, U{sup 238} and oxygen. These experiments were (1) a set of homogeneous U{sup 235}-H{sub 2}O assemblies spanning a wide range of hydrogen/uranium ratio, and (2) TRX-1, a simple, H{sub 2}O-moderated Bettis lattice of slightly-enriched uranium metal rods. The analyses used the Monte Carlo program RCP01, with explicit three-dimensional geometry and detailed representation of cross sections. For the homogeneous criticals, calculated k{sub crit} values for large, thermal assemblies show good agreement with experiment. This supports the evaluated thermal criticality parameters for U{supmore » 235}. However, for assemblies with smaller H/U ratios, k{sub crit} values increase significantly with increasing leakage and flux-spectrum hardness. These trends suggest that leakage is underpredicted and that the resonance eta of the ENDF/B-VI U{sup 235} is too large. For TRX-1, reasonably good agreement is found with measured lattice parameters (reaction-rate ratios). Of primary interest is rho28, the ratio of above-thermal to thermal U{sup 238} capture. Calculated rho28 is 2.3 ({+-} 1.7) % above measurement, suggesting that U{sup 238} resonance capture remains slightly overpredicted with ENDF/B-VI. However, agreement is better than observed with earlier versions of ENDF/B.« less

Electrochromic Behavior of Ionically Self-Assembled Thin Films

NASA Astrophysics Data System (ADS)

Janik, J. A.; Heflin, J. R.; Marciu, D.; Miller, M. B.; Davis, R. M.

2001-03-01

Ionically self-assembled monolayers (ISAMs), fabricated by alternate adsorption of cationic and anionic components, yield exceptionally homogeneous thin films with sub-nanometer control of the thickness and relative special location of the component materials. Using organic electrochromic materials such as polyaniline, we report studies of electrochromic responses in ISAM films. Reversible changes in the absorption spectrum are observed with the application of voltages on the order of 1.0 V. Measurements are made using both liquid electrolytes and in all-solid state devices incorporating solid polyelectrolytes such as poly(2-acylamido 2-methyl propane sulfonic acid) (PAMPS).

Absorbing metasurface created by diffractionless disordered arrays of nanoantennas

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

Chevalier, Paul; Minao, Laboratoire de Photonique et Nanostructures; Bouchon, Patrick, E-mail: patrick.bouchon@onera.fr

2015-12-21

We study disordered arrays of metal-insulator-metal nanoantenna in order to create a diffractionless metasurface able to absorb light in the 3–5 μm spectral range. This study is conducted with angle-resolved reflectivity measurements obtained with a Fourier transform infrared spectrometer. A first design is based on a perturbation of a periodic arrangement, leading to a significant reduction of the radiative losses. Then, a random assembly of nanoantennas is built following a Poisson-disk distribution of given density, in order to obtain a nearly perfect cluttered assembly with optical properties of a homogeneous material.

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

Altenfeld, Anika; Wohlgemuth, Sabine; Wehenkel, Annemarie

The 800 kDa complex of the human Rod, Zwilch and ZW10 proteins (the RZZ complex) was reconstituted in insect cells, purified, crystallized and subjected to preliminary X-ray diffraction analysis. The spindle-assembly checkpoint (SAC) monitors kinetochore–microtubule attachment during mitosis. In metazoans, the three-subunit Rod–Zwilch–ZW10 (RZZ) complex is a crucial SAC component that interacts with additional SAC-activating and SAC-silencing components, including the Mad1–Mad2 complex and cytoplasmic dynein. The RZZ complex contains two copies of each subunit and has a predicted molecular mass of ∼800 kDa. Given the low abundance of the RZZ complex in natural sources, its recombinant reconstitution was attempted bymore » co-expression of its subunits in insect cells. The RZZ complex was purified to homogeneity and subjected to systematic crystallization attempts. Initial crystals containing the entire RZZ complex were obtained using the sitting-drop method and were subjected to optimization to improve the diffraction resolution limit. The crystals belonged to space group P3{sub 1} (No. 144) or P3{sub 2} (No. 145), with unit-cell parameters a = b = 215.45, c = 458.7 Å, α = β = 90.0, γ = 120.0°.« less

Field Performance of an Optimized Stack of YBCO Square “Annuli” for a Compact NMR Magnet

PubMed Central

Hahn, Seungyong; Voccio, John; Bermond, Stéphane; Park, Dong-Keun; Bascuñán, Juan; Kim, Seok-Beom; Masaru, Tomita; Iwasa, Yukikazu

2011-01-01

The spatial field homogeneity and time stability of a trapped field generated by a stack of YBCO square plates with a center hole (square “annuli”) was investigated. By optimizing stacking of magnetized square annuli, we aim to construct a compact NMR magnet. The stacked magnet consists of 750 thin YBCO plates, each 40-mm square and 80- μm thick with a 25-mm bore, and has a Ø10 mm room-temperature access for NMR measurement. To improve spatial field homogeneity of the 750-plate stack (YP750) a three-step optimization was performed: 1) statistical selection of best plates from supply plates; 2) field homogeneity measurement of multi-plate modules; and 3) optimal assembly of the modules to maximize field homogeneity. In this paper, we present analytical and experimental results of field homogeneity and temporal stability at 77 K, performed on YP750 and those of a hybrid stack, YPB750, in which two YBCO bulk annuli, each Ø46 mm and 16-mm thick with a 25-mm bore, are added to YP750, one at the top and the other at the bottom. PMID:22081753

Tailored adhesion behavior of polyelectrolyte thin films deposited on plasma-treated poly(dimethylsiloxane) for functionalized membranes

NASA Astrophysics Data System (ADS)

Bassil, Joelle; Alem, Halima; Henrion, Gérard; Roizard, Denis

2016-04-01

Completely homogenous films formed via the layer-by-layer assembly of poly(diallyldimethylammonium chloride) (PDADMAC) and the poly(styrene sulfonate) were successfully obtained on plasma-treated poly(dimethylsiloxane) (PDMS) substrates. To modify the hydrophobicity of the PDMS surface, a cold plasma treatment was previously applied to the membrane, which led to the creation of hydrophilic groups on the surface of the membrane. PDMS wettability and surface morphology were successfully correlated with the plasma parameters. A combination of contact angle measurements, scanning electron microscopy (SEM) and atomic force microscopy (AFM) analysis was used to demonstrate that homogeneous and hydrophilic surfaces could be achieved on PDMS cold-plasma-treated membranes. The stability of the assembled PEL layer on the PDMS was evaluated using a combination of pull-off testing and X-ray photoelectron spectroscopy (XPS), which confirmed the relevance of a plasma pre-treatment as the adhesion of the polyelectrolyte multilayers was greatly enhanced when the deposition was completed on an activated PDMS surface at 80 W for 5 min.

A scheme to calculate higher-order homogenization as applied to micro-acoustic boundary value problems

NASA Astrophysics Data System (ADS)

Vagh, Hardik A.; Baghai-Wadji, Alireza

2008-12-01

Current technological challenges in materials science and high-tech device industry require the solution of boundary value problems (BVPs) involving regions of various scales, e.g. multiple thin layers, fibre-reinforced composites, and nano/micro pores. In most cases straightforward application of standard variational techniques to BVPs of practical relevance necessarily leads to unsatisfactorily ill-conditioned analytical and/or numerical results. To remedy the computational challenges associated with sub-sectional heterogeneities various sophisticated homogenization techniques need to be employed. Homogenization refers to the systematic process of smoothing out the sub-structural heterogeneities, leading to the determination of effective constitutive coefficients. Ordinarily, homogenization involves a sophisticated averaging and asymptotic order analysis to obtain solutions. In the majority of the cases only zero-order terms are constructed due to the complexity of the processes involved. In this paper we propose a constructive scheme for obtaining homogenized solutions involving higher order terms, and thus, guaranteeing higher accuracy and greater robustness of the numerical results. We present

Positron annihilation lifetime spectroscopy (PALS) as a characterization technique for nanostructured self-assembled amphiphile systems.

PubMed

Dong, Aurelia W; Pascual-Izarra, Carlos; Pas, Steven J; Hill, Anita J; Boyd, Ben J; Drummond, Calum J

2009-01-08

Positron annihilation lifetime spectroscopy (PALS) has potential as a novel rapid characterization method for self-assembly amphiphile systems; however, a lack of systematic correlation of PALS parameters with structural attributes has limited its more widespread application. In this study, using the well-characterized phytantriol/water and the phytantriol/vitamin E acetate/water self-assembly amphiphile systems, the impact of systematic structural changes controlled by changes in composition and temperature on PALS parameters has been studied. The PALS parameters (orthopositronium (oPs) lifetime and intensity signatures) were shown to be sensitive to the molecular packing and mobility of the self-assembled lipid molecules in various lyotropic liquid crystalline phases, enabling differentiation between liquid crystalline structures. The oPs lifetime, related to the molecular packing and mobility, is correlated with rheological properties of the individual mesophases. The oPs lifetime links the lipid chain packing and mobility in the various mesophases to resultant macroscopic properties, such as permeability, which is critical for the use of these mesophase structures as diffusion-controlled release matrices for active liposoluble compounds.

Systematic Study on the Self-Assembled Hexagonal Au Voids, Nano-Clusters and Nanoparticles on GaN (0001).

PubMed

Pandey, Puran; Sui, Mao; Li, Ming-Yu; Zhang, Quanzhen; Kim, Eun-Soo; Lee, Jihoon

2015-01-01

Au nano-clusters and nanoparticles (NPs) have been widely utilized in various electronic, optoelectronic, and bio-medical applications due to their great potentials. The size, density and configuration of Au NPs play a vital role in the performance of these devices. In this paper, we present a systematic study on the self-assembled hexagonal Au voids, nano-clusters and NPs fabricated on GaN (0001) by the variation of annealing temperature and deposition amount. At relatively low annealing temperatures between 400 and 600°C, the fabrication of hexagonal shaped Au voids and Au nano-clusters are observed and discussed based on the diffusion limited aggregation model. The size and density of voids and nano-clusters can systematically be controlled. The self-assembled Au NPs are fabricated at comparatively high temperatures from 650 to 800°C based on the Volmer-Weber growth model and also the size and density can be tuned accordingly. The results are symmetrically analyzed and discussed in conjunction with the diffusion theory and thermodynamics by utilizing AFM and SEM images, EDS maps and spectra, FFT power spectra, cross-sectional line-profiles and size and density plots.

Systematic Study on the Self-Assembled Hexagonal Au Voids, Nano-Clusters and Nanoparticles on GaN (0001)

PubMed Central

Pandey, Puran; Sui, Mao; Li, Ming-Yu; Zhang, Quanzhen; Kim, Eun-Soo; Lee, Jihoon

2015-01-01

Au nano-clusters and nanoparticles (NPs) have been widely utilized in various electronic, optoelectronic, and bio-medical applications due to their great potentials. The size, density and configuration of Au NPs play a vital role in the performance of these devices. In this paper, we present a systematic study on the self-assembled hexagonal Au voids, nano-clusters and NPs fabricated on GaN (0001) by the variation of annealing temperature and deposition amount. At relatively low annealing temperatures between 400 and 600°C, the fabrication of hexagonal shaped Au voids and Au nano-clusters are observed and discussed based on the diffusion limited aggregation model. The size and density of voids and nano-clusters can systematically be controlled. The self-assembled Au NPs are fabricated at comparatively high temperatures from 650 to 800°C based on the Volmer-Weber growth model and also the size and density can be tuned accordingly. The results are symmetrically analyzed and discussed in conjunction with the diffusion theory and thermodynamics by utilizing AFM and SEM images, EDS maps and spectra, FFT power spectra, cross-sectional line-profiles and size and density plots. PMID:26285135

High-pressure homogenization associated hydrothermal process of palygorskite for enhanced adsorption of Methylene blue

NASA Astrophysics Data System (ADS)

Zhang, Zhifang; Wang, Wenbo; Wang, Aiqin

2015-02-01

Palygorskite (PAL) was modified by a high-pressure homogenization assisted hydrothermal process. The effects of modification on the morphology, structure and physicochemical properties of PAL were systematically investigated by Field-emission scanning electron microscopy (FESEM), Transmission electron microscopy (TEM), Fourier transform infrared spectrometry (FTIR), Brunauer-Emmett-Teller (BET) analysis, X-ray diffraction (XRD) and Zeta potential analysis techniques, and the adsorption properties were systematically evaluated using Methylene blue (MB) as the model dye. The results revealed that the crystal bundles were disaggregated and the PAL nanorods became more even after treated via associated high-pressure homogenization and hydrothermal process, and the crystal bundles were dispersed as nanorods. The intrinsic crystal structure of PAL was remained after hydrothermal treatment, and the pore size calculated by the BET method was increased. The adsorption properties of PAL for MB were evidently improved (from 119 mg/g to 171 mg/g) after modification, and the dispersion of PAL before hydrothermal reaction is favorable to the adsorption. The desorption evaluation confirms that the modified PAL has stronger affinity with MB, which is benefit to fabricate a stable organic-inorganic hybrid pigment.

Classification of coordination polygons and polyhedra according to their mode of self-assembly.

PubMed

Swiegers, G F; Malefetse, T J

2001-09-03

This work extends techniques for the controlled formation of synthetic molecular containers by metal-mediated self-assembly. A new classification system based on the self-assembly of such species is proposed. The system: 1) allows a systematic identification of suitable acceptor-donor combinations, 2) widens the variety of design possibilities available, 3) allows a ready comparison of the self-assembly of different compounds, 4) reveals useful commonalities between different compounds, 5) aids in the development of novel architectures, and 6) permits identification of systems capable of being switched back-and-forth between architectures.

Self-assembly of active amphiphilic Janus particles

NASA Astrophysics Data System (ADS)

Mallory, S. A.; Alarcon, F.; Cacciuto, A.; Valeriani, C.

2017-12-01

In this article, we study the phenomenology of a two dimensional dilute suspension of active amphiphilic Janus particles. We analyze how the morphology of the aggregates emerging from their self-assembly depends on the strength and the direction of the active forces. We systematically explore and contrast the phenomenologies resulting from particles with a range of attractive patch coverages. Finally, we illustrate how the geometry of the colloids and the directionality of their interactions can be used to control the physical properties of the assembled active aggregates and suggest possible strategies to exploit self-propulsion as a tunable driving force for self-assembly.

Facile fabrication of homogeneous 3D silver nanostructures on gold-supported polyaniline membranes as promising SERS substrates.

PubMed

Xu, Ping; Mack, Nathan H; Jeon, Sea-Ho; Doorn, Stephen K; Han, Xijiang; Wang, Hsing-Lin

2010-06-01

We report a facile synthesis of large-area homogeneous three-dimensional (3D) Ag nanostructures on Au-supported polyaniline (PANI) membranes through a direct chemical reduction of metal ions by PANI. The citric acid absorbed on the Au nuclei that are prefabricated on PANI membranes directs Ag nanoaprticles (AgNPs) to self-assemble into 3D Ag nanosheet structures. The fabricated hybrid metal nanostructures display uniform surface-enhanced Raman scattering (SERS) responses throughout the whole surface area, with an average enhancement factor of 10(6)-10(7). The nanocavities formed by the stereotypical stacking of these Ag nanosheets and the junctions and gaps between two neighboring AgNPs are believed to be responsible for the strong SERS response upon plasmon absorption. These homogeneous metal nanostructure decorated PANI membranes can be used as highly efficient SERS substrates for sensitive detection of chemical and biological analytes.

Fourier-Accelerated Nodal Solvers (FANS) for homogenization problems

NASA Astrophysics Data System (ADS)

Leuschner, Matthias; Fritzen, Felix

2017-11-01

Fourier-based homogenization schemes are useful to analyze heterogeneous microstructures represented by 2D or 3D image data. These iterative schemes involve discrete periodic convolutions with global ansatz functions (mostly fundamental solutions). The convolutions are efficiently computed using the fast Fourier transform. FANS operates on nodal variables on regular grids and converges to finite element solutions. Compared to established Fourier-based methods, the number of convolutions is reduced by FANS. Additionally, fast iterations are possible by assembling the stiffness matrix. Due to the related memory requirement, the method is best suited for medium-sized problems. A comparative study involving established Fourier-based homogenization schemes is conducted for a thermal benchmark problem with a closed-form solution. Detailed technical and algorithmic descriptions are given for all methods considered in the comparison. Furthermore, many numerical examples focusing on convergence properties for both thermal and mechanical problems, including also plasticity, are presented.

A statistical image analysis framework for pore-free islands derived from heterogeneity distribution of nuclear pore complexes.

PubMed

Mimura, Yasuhiro; Takemoto, Satoko; Tachibana, Taro; Ogawa, Yutaka; Nishimura, Masaomi; Yokota, Hideo; Imamoto, Naoko

2017-11-24

Nuclear pore complexes (NPCs) maintain cellular homeostasis by mediating nucleocytoplasmic transport. Although cyclin-dependent kinases (CDKs) regulate NPC assembly in interphase, the location of NPC assembly on the nuclear envelope is not clear. CDKs also regulate the disappearance of pore-free islands, which are nuclear envelope subdomains; this subdomain gradually disappears with increase in homogeneity of the NPC in response to CDK activity. However, a causal relationship between pore-free islands and NPC assembly remains unclear. Here, we elucidated mechanisms underlying NPC assembly from a new perspective by focusing on pore-free islands. We proposed a novel framework for image-based analysis to automatically determine the detailed 'landscape' of pore-free islands from a large quantity of images, leading to the identification of NPC intermediates that appear in pore-free islands with increased frequency in response to CDK activity. Comparison of the spatial distribution between simulated and the observed NPC intermediates within pore-free islands showed that their distribution was spatially biased. These results suggested that the disappearance of pore-free islands is highly related to de novo NPC assembly and indicated the existence of specific regulatory mechanisms for the spatial arrangement of NPC assembly on nuclear envelopes.

Conformational Changes in the Hepatitis B Virus Core Protein Are Consistent with a Role for Allostery in Virus Assembly

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

Packianathan, Charles; Katen, Sarah P.; Dann, III, Charles E.

2010-01-12

In infected cells, virus components must be organized at the right place and time to ensure assembly of infectious virions. From a different perspective, assembly must be prevented until all components are available. Hypothetically, this can be achieved by allosterically controlling assembly. Consistent with this hypothesis, here we show that the structure of the hepatitis B virus (HBV) core protein dimer, which can spontaneously self-assemble, is incompatible with capsid assembly. Systematic differences between core protein dimer and capsid conformations demonstrate linkage between the intradimer interface and interdimer contact surface. These structures also provide explanations for the capsid-dimer selectivity of somemore » antibodies and the activities of assembly effectors. Solution studies suggest that the assembly-inactive state is more accurately an ensemble of conformations. Simulations show that allostery supports controlled assembly and results in capsids that are resistant to dissociation. We propose that allostery, as demonstrated in HBV, is common to most self-assembling viruses.« less

A systematic comparison of error correction enzymes by next-generation sequencing

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

Lubock, Nathan B.; Zhang, Di; Sidore, Angus M.

Gene synthesis, the process of assembling genelength fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared sixmore » different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.« less

A systematic comparison of error correction enzymes by next-generation sequencing

DOE PAGES

Lubock, Nathan B.; Zhang, Di; Sidore, Angus M.; ...

2017-08-01

Gene synthesis, the process of assembling genelength fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared sixmore » different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.« less

Self-Assembly of Octopus Nanoparticles into Pre-Programmed Finite Clusters

NASA Astrophysics Data System (ADS)

Halverson, Jonathan; Tkachenko, Alexei

2012-02-01

The precise control of the spatial arrangement of nanoparticles (NP) is often required to take full advantage of their novel optical and electronic properties. NPs have been shown to self-assemble into crystalline structures using either patchy surface regions or complementary DNA strands to direct the assembly. Due to a lack of specificity of the interactions these methods lead to only a limited number of structures. An emerging approach is to bind ssDNA at specific sites on the particle surface making so-called octopus NPs. Using octopus NPs we investigate the inverse problem of the self-assembly of finite clusters. That is, for a given target cluster (e.g., arranging the NPs on the vertices of a dodecahedron) what are the minimum number of complementary DNA strands needed for the robust self-assembly of the cluster from an initially homogeneous NP solution? Based on the results of Brownian dynamics simulations we have compiled a set of design rules for various target clusters including cubes, pyramids, dodecahedrons and truncated icosahedrons. Our approach leads to control over the kinetic pathway and has demonstrated nearly perfect yield of the target.

Rapid biotic homogenization of marine fish assemblages

PubMed Central

Magurran, Anne E.; Dornelas, Maria; Moyes, Faye; Gotelli, Nicholas J.; McGill, Brian

2015-01-01

The role human activities play in reshaping biodiversity is increasingly apparent in terrestrial ecosystems. However, the responses of entire marine assemblages are not well-understood, in part, because few monitoring programs incorporate both spatial and temporal replication. Here, we analyse an exceptionally comprehensive 29-year time series of North Atlantic groundfish assemblages monitored over 5° latitude to the west of Scotland. These fish assemblages show no systematic change in species richness through time, but steady change in species composition, leading to an increase in spatial homogenization: the species identity of colder northern localities increasingly resembles that of warmer southern localities. This biotic homogenization mirrors the spatial pattern of unevenly rising ocean temperatures over the same time period suggesting that climate change is primarily responsible for the spatial homogenization we observe. In this and other ecosystems, apparent constancy in species richness may mask major changes in species composition driven by anthropogenic change. PMID:26400102

Pyroxene Homogenization and the Isotopic Systematics of Eucrites

NASA Technical Reports Server (NTRS)

Nyquist, L. E.; Bogard, D. D.

1996-01-01

The original Mg-Fe zoning of eucritic pyroxenes has in nearly all cases been partly homogenized, an observation that has been combined with other petrographic and compositional criteria to establish a scale of thermal "metamorphism" for eucrites. To evaluate hypotheses explaining development of conditions on the HED parent body (Vesta?) leading to pyroxene homogenization against their chronological implications, it is necessary to know whether pyroxene metamorphism was recorded in the isotopic systems. However, identifying the effects of the thermal metamorphism with specific effects in the isotopic systems has been difficult, due in part to a lack of correlated isotopic and mineralogical studies of the same eucrites. Furthermore, isotopic studies often place high demands on analytical capabilities, resulting in slow growth of the isotopic database. Additionally, some isotopic systems would not respond in a direct and sensitive way to pyroxene homogenization. Nevertheless, sufficient data exist to generalize some observations, and to identify directions of potentially fruitful investigations.

Synthesis and self-assembly of Janus and patchy colloidal particles

NASA Astrophysics Data System (ADS)

Jiang, Shan

Colloidal particles are considered classically as spherical particles with homogeneous surface chemistry. When this is so, the interactions between particles are isotropic and governed only by their separations. One can take advantage of this to simulate atoms, visualizing them one-by-one in a microscope, albeit at a larger length scale and longer time scale than for true atoms. However if the particles are not homogeneous, but Janus or patchy instead, with different surface chemistry on different hemispheres or otherwise different surface sites that are addressably controlled, the interactions between these particles depend not only on their separation, but also on their orientation. Research on Janus and patchy colloidal particles has opened a new chapter in the colloid research field, allowing us to mimic the behavior of these colloidal analogues of molecules, and in this way to ask new and exciting questions of condensed matter physics. In this dissertation, I investigated the synthesis and self-assembly of Janus and patchy colloidal particles with emphasis on Janus amphiphilic particles, which are the colloidal counterpart of surfactant molecules. Improving the scale-up capability, and also the capacity to control the geometry of Janus particles, I developed a simple and versatile method to synthesize Janus particles using an approach based on Pickering emulsions with particles adsorbed at the liquid-liquid interface. I showed that this method can be scaled up to synthesize Janus particles in large quantity. Also, the Janus balance can be predictably controlled by adding surfactant molecules during emulsification. In addition, going beyond the Janus geometry, I developed another synthetic method to fabricate trivalent patchy colloidal particles using micro-contact printing. With these synthetic methods in hand, I explored the self-assembly of Janus amphiphilic particles in aqueous solutions, while controlling systematically the salt concentration, the particle concentration, and the Janus balance. Various cluster and chain structures were observed. Using in situ optical microscopy, I found these structures to be dynamic in structure, in this respect analogous to the micelles formed by small surfactant molecules. A qualitative explanation about the possible underlying mechanism was proposed, based on considering the tradeoff between enthalpy gain from hydrophobic contacts, and entropy involving rotational orientation between neighboring particles. Monolayer crystals of Janus amphiphilic particles were investigated in a system of silica-based particles. Regarding positional order, these particles adopted a conventional hexagonal packing, but their orientations formed strikingly ordered linear clusters that extended the length of tens of particles. Study of their rotational dynamics using single particle tracking showed rotation to be strongly coupled between adjacent particles, with a correlation length extending to sevearl particle diameters. This is a beautiful example of a unique physical phenomenon that simply does not exist when dealing with classical particles whose surface chemical makeup is homogeneous. At the oil-water interface, Janus amphiphilic particles adsorb strongly. With simple calculations, I showed that the adsorption energy depends not only on surface tension but also on the Janus balance. I developed a rigorous mathematical definition of "Janus balance" that may find application in emulsions stabilized by Janus particles. On the experimental side, I performed experiments to quantify the efficacy of Janus particles to stabilize emulsions for extended times.

On the Origin of GEMS

NASA Technical Reports Server (NTRS)

Keller, L. P.; Messenger, S.

2004-01-01

GEMS (glass with embedded metal and sulfides) are a major component of anhydrous interplanetary dust particles (IDPs) their physical and chemical characteristics show marked similarities to contemporary interstellar dust. Recent oxygen isotopic measurements confirm that at least a small fraction (less than 5%) of GEMS are demonstrably presolar, while the remainder have ratios that are indistinguishable from solar values. GEMS with solar oxygen isotopic compositions either (1) had their isotopic compositions homogenized through processing in the interstellar medium (ISM), or (2) formed in the early solar system. Isotopic homogenization necessarily implies chemical homogenization, so (interstellar) GEMS compositions should reflect the average composition of dust in the local ISM. We performed a systematic examination of the bulk chemistry of GEMS in primitive IDPs in order to test this hypothesis.

Airfoil lance apparatus for homogeneous humidification and sorbent dispersion in a gas stream

DOEpatents

Myers, R.B.; Yagiela, A.S.

1990-12-25

An apparatus for spraying an atomized mixture into a gas stream comprises a stream line airfoil member having a large radius leading edge and a small radius trailing edge. A nozzle assembly pierces the trailing edge of the airfoil member and is concentrically surrounded by a nacelle which directs shielding gas from the interior of the airfoil member around the nozzle assembly. Flowable medium to be atomized and atomizing gas for atomizing the medium are supplied in concentric conduits to the nozzle. A plurality of nozzles each surrounded by a nacelle are spaced along the trailing edge of the airfoil member. 3 figs.

Airfoil lance apparatus for homogeneous humidification and sorbent dispersion in a gas stream

DOEpatents

Myers, Robert B.; Yagiela, Anthony S.

1990-12-25

An apparatus for spraying an atomized mixture into a gas stream comprises a stream line airfoil member having a large radius leading edge and a small radius trailing edge. A nozzle assembly pierces the trailing edge of the airfoil member and is concentrically surrounded by a nacelle which directs shielding gas from the interior of the airfoil member around the nozzle assembly. Flowable medium to be atomized and atomizing gas for atomizing the medium are supplied in concentric conduits to the nozzle. A plurality of nozzles each surrounded by a nacelle are spaced along the trailing edge of the airfoil member.

Homogenizing Advanced Alloys: Thermodynamic and Kinetic Simulations Followed by Experimental Results

NASA Astrophysics Data System (ADS)

Jablonski, Paul D.; Hawk, Jeffrey A.

2017-01-01

Segregation of solute elements occurs in nearly all metal alloys during solidification. The resultant elemental partitioning can severely degrade as-cast material properties and lead to difficulties during post-processing (e.g., hot shorts and incipient melting). Many cast articles are subjected to a homogenization heat treatment in order to minimize segregation and improve their performance. Traditionally, homogenization heat treatments are based upon past practice or time-consuming trial and error experiments. Through the use of thermodynamic and kinetic modeling software, NETL has designed a systematic method to optimize homogenization heat treatments. Use of the method allows engineers and researchers to homogenize casting chemistries to levels appropriate for a given application. The method also allows for the adjustment of heat treatment schedules to fit limitations on in-house equipment (capability, reliability, etc.) while maintaining clear numeric targets for segregation reduction. In this approach, the Scheil module within Thermo-Calc is used to predict the as-cast segregation present within an alloy, and then diffusion controlled transformations is used to model homogenization kinetics as a function of time and temperature. Examples of computationally designed heat treatments and verification of their effects on segregation and properties of real castings are presented.

Sampling and Homogenization Strategies Significantly Influence the Detection of Foodborne Pathogens in Meat.

PubMed

Rohde, Alexander; Hammerl, Jens Andre; Appel, Bernd; Dieckmann, Ralf; Al Dahouk, Sascha

2015-01-01

Efficient preparation of food samples, comprising sampling and homogenization, for microbiological testing is an essential, yet largely neglected, component of foodstuff control. Salmonella enterica spiked chicken breasts were used as a surface contamination model whereas salami and meat paste acted as models of inner-matrix contamination. A systematic comparison of different homogenization approaches, namely, stomaching, sonication, and milling by FastPrep-24 or SpeedMill, revealed that for surface contamination a broad range of sample pretreatment steps is applicable and loss of culturability due to the homogenization procedure is marginal. In contrast, for inner-matrix contamination long treatments up to 8 min are required and only FastPrep-24 as a large-volume milling device produced consistently good recovery rates. In addition, sampling of different regions of the spiked sausages showed that pathogens are not necessarily homogenously distributed throughout the entire matrix. Instead, in meat paste the core region contained considerably more pathogens compared to the rim, whereas in the salamis the distribution was more even with an increased concentration within the intermediate region of the sausages. Our results indicate that sampling and homogenization as integral parts of food microbiology and monitoring deserve more attention to further improve food safety.

Sampling and Homogenization Strategies Significantly Influence the Detection of Foodborne Pathogens in Meat

PubMed Central

Rohde, Alexander; Hammerl, Jens Andre; Appel, Bernd; Dieckmann, Ralf; Al Dahouk, Sascha

2015-01-01

Efficient preparation of food samples, comprising sampling and homogenization, for microbiological testing is an essential, yet largely neglected, component of foodstuff control. Salmonella enterica spiked chicken breasts were used as a surface contamination model whereas salami and meat paste acted as models of inner-matrix contamination. A systematic comparison of different homogenization approaches, namely, stomaching, sonication, and milling by FastPrep-24 or SpeedMill, revealed that for surface contamination a broad range of sample pretreatment steps is applicable and loss of culturability due to the homogenization procedure is marginal. In contrast, for inner-matrix contamination long treatments up to 8 min are required and only FastPrep-24 as a large-volume milling device produced consistently good recovery rates. In addition, sampling of different regions of the spiked sausages showed that pathogens are not necessarily homogenously distributed throughout the entire matrix. Instead, in meat paste the core region contained considerably more pathogens compared to the rim, whereas in the salamis the distribution was more even with an increased concentration within the intermediate region of the sausages. Our results indicate that sampling and homogenization as integral parts of food microbiology and monitoring deserve more attention to further improve food safety. PMID:26539462

Integrating DNA strand-displacement circuitry with DNA tile self-assembly

PubMed Central

Zhang, David Yu; Hariadi, Rizal F.; Choi, Harry M.T.; Winfree, Erik

2013-01-01

DNA nanotechnology has emerged as a reliable and programmable way of controlling matter at the nanoscale through the specificity of Watson–Crick base pairing, allowing both complex self-assembled structures with nanometer precision and complex reaction networks implementing digital and analog behaviors. Here we show how two well-developed frameworks, DNA tile self-assembly and DNA strand-displacement circuits, can be systematically integrated to provide programmable kinetic control of self-assembly. We demonstrate the triggered and catalytic isothermal self-assembly of DNA nanotubes over 10 μm long from precursor DNA double-crossover tiles activated by an upstream DNA catalyst network. Integrating more sophisticated control circuits and tile systems could enable precise spatial and temporal organization of dynamic molecular structures. PMID:23756381

Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions.

PubMed

Donovan, Preston; Chehreghanianzabi, Yasaman; Rathinam, Muruhan; Zustiak, Silviya Petrova

2016-01-01

The study of diffusion in macromolecular solutions is important in many biomedical applications such as separations, drug delivery, and cell encapsulation, and key for many biological processes such as protein assembly and interstitial transport. Not surprisingly, multiple models for the a-priori prediction of diffusion in macromolecular environments have been proposed. However, most models include parameters that are not readily measurable, are specific to the polymer-solute-solvent system, or are fitted and do not have a physical meaning. Here, for the first time, we develop a homogenization theory framework for the prediction of effective solute diffusivity in macromolecular environments based on physical parameters that are easily measurable and not specific to the macromolecule-solute-solvent system. Homogenization theory is useful for situations where knowledge of fine-scale parameters is used to predict bulk system behavior. As a first approximation, we focus on a model where the solute is subjected to obstructed diffusion via stationary spherical obstacles. We find that the homogenization theory results agree well with computationally more expensive Monte Carlo simulations. Moreover, the homogenization theory agrees with effective diffusivities of a solute in dilute and semi-dilute polymer solutions measured using fluorescence correlation spectroscopy. Lastly, we provide a mathematical formula for the effective diffusivity in terms of a non-dimensional and easily measurable geometric system parameter.

Regionalized PM2.5 Community Multiscale Air Quality model performance evaluation across a continuous spatiotemporal domain.

PubMed

Reyes, Jeanette M; Xu, Yadong; Vizuete, William; Serre, Marc L

2017-01-01

The regulatory Community Multiscale Air Quality (CMAQ) model is a means to understanding the sources, concentrations and regulatory attainment of air pollutants within a model's domain. Substantial resources are allocated to the evaluation of model performance. The Regionalized Air quality Model Performance (RAMP) method introduced here explores novel ways of visualizing and evaluating CMAQ model performance and errors for daily Particulate Matter ≤ 2.5 micrometers (PM2.5) concentrations across the continental United States. The RAMP method performs a non-homogenous, non-linear, non-homoscedastic model performance evaluation at each CMAQ grid. This work demonstrates that CMAQ model performance, for a well-documented 2001 regulatory episode, is non-homogeneous across space/time. The RAMP correction of systematic errors outperforms other model evaluation methods as demonstrated by a 22.1% reduction in Mean Square Error compared to a constant domain wide correction. The RAMP method is able to accurately reproduce simulated performance with a correlation of r = 76.1%. Most of the error coming from CMAQ is random error with only a minority of error being systematic. Areas of high systematic error are collocated with areas of high random error, implying both error types originate from similar sources. Therefore, addressing underlying causes of systematic error will have the added benefit of also addressing underlying causes of random error.

Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly

PubMed Central

2012-01-01

Background In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the time course of assembly (direct assembly). In some cases, however, binding sites between the capsomers have been reported to be activated during the self-assembly process (hierarchical assembly). Results In order to study possible advantages of such hierarchical schemes for icosahedral virus capsid assembly, we use Brownian dynamics simulations of a patchy particle model that allows us to switch binding sites on and off during assembly. For T1 viruses, we implement a hierarchical assembly scheme where inter-capsomer bonds become active only if a complete pentamer has been assembled. We find direct assembly to be favorable for reversible bonds allowing for repeated structural reorganizations, while hierarchical assembly is favorable for strong bonds with small dissociation rate, as this situation is less prone to kinetic trapping. However, at the same time it is more vulnerable to monomer starvation during the final phase. Increasing the number of initial monomers does have only a weak effect on these general features. The differences between the two assembly schemes become more pronounced for more complex virus geometries, as shown here for T3 viruses, which assemble through homogeneous pentamers and heterogeneous hexamers in the hierarchical scheme. In order to complement the simulations for this more complicated case, we introduce a master equation approach that agrees well with the simulation results. Conclusions Our analysis shows for which molecular parameters hierarchical assembly schemes can outperform direct ones and suggests that viruses with high bond stability might prefer hierarchical assembly schemes. These insights increase our physical understanding of an essential biological process, with many interesting potential applications in medicine and materials science. PMID:23244740

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

Xue, Teng; Lin, Zhaoyang; Chiu, Chin-Yi

Metallic nanoparticles are emerging as an exciting class of heterogeneous catalysts with the potential advantages of exceptional activity, stability, recyclability, and easier separation than homogeneous catalysts. The traditional colloid nanoparticle syntheses usually involve strong surface binding ligands that could passivate the surface active sites and result in poor catalytic activity. The subsequent removal of surface ligands could reactivate the surface but often leads to metal ion leaching and/or severe Ostwald ripening with diminished catalytic activity or poor stability. Molecular ligand engineering represents a powerful strategy for the design of homogeneous molecular catalysts but is insufficiently explored for nanoparticle catalysts tomore » date. We report a systematic investigation on molecular ligand modulation of palladium (Pd) nanoparticle catalysts. Our studies show that β-functional groups of butyric acid ligand on Pd nanoparticles can significantly modulate the catalytic reaction process to modify the catalytic activity and stability for important aerobic reactions. With a β-hydroxybutyric acid ligand, the Pd nanoparticle catalysts exhibit exceptional catalytic activity and stability with an unsaturated turnover number (TON) >3000 for dehydrogenative oxidation of cyclohexenone to phenol, greatly exceeding that of homogeneous Pd(II) catalysts (TON, ~30). This study presents a systematic investigation of molecular ligand modulation of nanoparticle catalysts and could open up a new pathway toward the design and construction of highly efficient and robust heterogeneous catalysts through molecular ligand engineering.« less

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

PubMed Central

Schatz, Michael C.; Phillippy, Adam M.; Sommer, Daniel D.; Delcher, Arthur L.; Puiu, Daniela; Narzisi, Giuseppe; Salzberg, Steven L.; Pop, Mihai

2013-01-01

Since its launch in 2004, the open-source AMOS project has released several innovative DNA sequence analysis applications including: Hawkeye, a visual analytics tool for inspecting the structure of genome assemblies; the Assembly Forensics and FRCurve pipelines for systematically evaluating the quality of a genome assembly; and AMOScmp, the first comparative genome assembler. These applications have been used to assemble and analyze dozens of genomes ranging in complexity from simple microbial species through mammalian genomes. Recent efforts have been focused on enhancing support for new data characteristics brought on by second- and now third-generation sequencing. This review describes the major components of AMOS in light of these challenges, with an emphasis on methods for assessing assembly quality and the visual analytics capabilities of Hawkeye. These interactive graphical aspects are essential for navigating and understanding the complexities of a genome assembly, from the overall genome structure down to individual bases. Hawkeye and AMOS are available open source at http://amos.sourceforge.net. PMID:22199379

Defense Nanotechnology Research and Development Programs

DTIC Science & Technology

2005-05-17

Laser has been achieved with SBIR support. • Thermal spray ceramic nanocomposite alumina - titania has been commercialized for wear resistant...additives have been developed that, during membrane formation, self-assemble a low-fouling hydrophilic surface on all membrane surfaces (both...macroscopic and pore surfaces). • A new method for processing of ceramic nanocomposites has been demonstrated, in which a homogeneous, metastable powder is

Transport of temperature-velocity covariance in gas-solid flow and its relation to the axial dispersion coefficient

NASA Astrophysics Data System (ADS)

Subramaniam, Shankar; Sun, Bo

2015-11-01

The presence of solid particles in a steady laminar flow generates velocity fluctuations with respect to the mean fluid velocity that are termed pseudo-turbulence. The level of these pseudo-turbulent velocity fluctuations has been characterized in statistically homogeneous fixed particle assemblies and freely evolving suspensions using particle-resolved direct numerical simulation (PR-DNS) by Mehrabadi et al. (JFM, 2015), and it is found to be a significant contribution to the total kinetic energy associated with the flow. The correlation of these velocity fluctuations with temperature (or a passive scalar) generates a flux term that appears in the transport equation for the average fluid temperature (or average scalar concentration). The magnitude of this transport of temperature-velocity covariance is quantified using PR-DNS of thermally fully developed flow past a statistically homogeneous fixed assembly of particles, and the budget of the average fluid temperature equation is presented. The relation of this transport term to the axial dispersion coefficient (Brenner, Phil. Trans. Roy. Soc. A, 1980) is established. The simulation results are then interpreted in the context of our understanding of axial dispersion in gas-solid flow. NSF CBET 1336941.

His-Tag-Mediated Dimerization of Chemoreceptors Leads to Assembly of Functional Nanoarrays.

PubMed

Haglin, Elizabeth R; Yang, Wen; Briegel, Ariane; Thompson, Lynmarie K

2017-11-07

Transmembrane chemotaxis receptors are found in bacteria in extended hexagonal arrays stabilized by the membrane and by cytosolic binding partners, the kinase CheA and coupling protein CheW. Models of array architecture and assembly propose receptors cluster into trimers of dimers that associate with one CheA dimer and two CheW monomers to form the minimal "core unit" necessary for signal transduction. Reconstructing in vitro chemoreceptor ternary complexes that are homogeneous and functional and exhibit native architecture remains a challenge. Here we report that His-tag-mediated receptor dimerization with divalent metals is sufficient to drive assembly of nativelike functional arrays of a receptor cytoplasmic fragment. Our results indicate receptor dimerization initiates assembly and precedes formation of ternary complexes with partial kinase activity. Restoration of maximal kinase activity coincides with a shift to larger complexes, suggesting that kinase activity depends on interactions beyond the core unit. We hypothesize that achieving maximal activity requires building core units into hexagons and/or coalescing hexagons into the extended lattice. Overall, the minimally perturbing His-tag-mediated dimerization leads to assembly of chemoreceptor arrays with native architecture and thus serves as a powerful tool for studying the assembly and mechanism of this complex and other multiprotein complexes.

Fibrillar α-Synuclein and Huntingtin Exon 1 Assemblies Are Toxic to the Cells

PubMed Central

Pieri, Laura; Madiona, Karine; Bousset, Luc; Melki, Ronald

2012-01-01

The aggregation of alpha-synuclein (α-syn) and huntingtin (htt) into fibrillar assemblies in nerve and glial cells is a molecular hallmark of Parkinson's and Huntington's diseases. Within the aggregation process, prefibrillar and fibrillar oligomeric species form. Prefibrillar assemblies rather than fibrils are nowadays considered cytotoxic. However, recent reports describing spreading of fibrillar assemblies from one cell to another, in cell cultures, animal models, and brains of grafted patients suggest a critical role for fibrillar assemblies in pathogenesis. Here we compare the cytotoxic effect of defined and comparable particle concentrations of on-assembly pathway oligomeric and fibrillar α-syn and Htt fragment corresponding to the first exon of the protein (HttEx1). We show that homogeneous populations of α-syn and HttEx1 fibrils, rather than their precursor on-assembly pathway oligomers, are highly toxic to cultured cells and induce apoptotic cell death. We document the reasons that make fibrils toxic. We show that α-syn and HttEx1 fibrils bind and permeabilize lipid vesicles. We also show that fibrils binding to the plasma membrane in cultured cells alter Ca2+ homeostasis. Overall, our data indicate that fibrillar α-syn and HttEx1, rather than their precursor oligomers, are highly cytotoxic, the toxicity being associated to their ability to bind and permeabilize the cell membranes. PMID:22735540

Homogeneous Characterization of Transiting Exoplanet Systems

NASA Astrophysics Data System (ADS)

Gomez Maqueo Chew, Yilen; Faedi, Francesca; Hebb, Leslie; Pollacco, Don; Stassun, Keivan; Ghezzi, Luan; Cargile, Phillip; Barros, Susana; Smalley, Barry; Mack, Claude

2012-02-01

We aim to obtain a homogeneous set of high resolution, high signal- to-noise (S/N) spectra for a large and diverse sample of stars with transiting planets, using the Kitt Peak 4-m echelle spectrograph for bright Northern targets (7.7150) in combination with high precision light curves shows an improvement in the precision of the stellar parameters of 60% in Teff, 75% in FeH, 82% in mstar, and 73% in rstar, which translates into a 64% improvement in the precision of rpl, and more than 2% on mpl, relative to the discovery paper's values.

Developing chemical strategies for the assembly of nanoparticles into mesoscopic objects.

PubMed

Maneeprakorn, Weerakanya; Malik, Mohammad A; O'Brien, Paul

2010-02-17

Nanoparticles of Au, Ag, CdS, and CdSe have been linked together by a chemical reaction to form controlled assemblies of similar or different types of nanoparticles through amido or azo linkage. The capping of nanoparticles was exchanged with bifunctional groups containing active functional groups at the tails. The reaction between the tails of the capping agents resulted in the formation of amido or azo linkages. These reactions were carried out under very dilute conditions to control the assembly and avoid the polymerization. The assemblies formed included the dimers, trimers, tetramers, and hexa- or heptamers. These reactions are the first examples for the systematic approach to establish the chemical route for the controlled assembly of nanoparticles and open the way for the fabrication of nanoparticle based devices for various application.

Molecular subtypes of Alzheimer's disease.

PubMed

Di Fede, Giuseppe; Catania, Marcella; Maderna, Emanuela; Ghidoni, Roberta; Benussi, Luisa; Tonoli, Elisa; Giaccone, Giorgio; Moda, Fabio; Paterlini, Anna; Campagnani, Ilaria; Sorrentino, Stefano; Colombo, Laura; Kubis, Adriana; Bistaffa, Edoardo; Ghetti, Bernardino; Tagliavini, Fabrizio

2018-02-19

Protein misfolding and aggregation is a central feature of several neurodegenerative disorders including Alzheimer's disease (AD), in which assemblies of amyloid β (Aβ) peptides accumulate in the brain in the form of parenchymal and/or vascular amyloid. A widely accepted concept is that AD is characterized by distinct clinical and neuropathological phenotypes. Recent studies revealed that Aβ assemblies might have structural differences among AD brains and that such pleomorphic assemblies can correlate with distinct disease phenotypes. We found that in both sporadic and inherited forms of AD, amyloid aggregates differ in the biochemical composition of Aβ species. These differences affect the physicochemical properties of Aβ assemblies including aggregation kinetics, resistance to degradation by proteases and seeding ability. Aβ-amyloidosis can be induced and propagated in animal models by inoculation of brain extracts containing aggregated Aβ. We found that brain homogenates from AD patients with different molecular profiles of Aβ are able to induce distinct patterns of Aβ-amyloidosis when injected into mice. Overall these data suggest that the assembly of mixtures of Aβ peptides into different Aβ seeds leads to the formation of distinct subtypes of amyloid having distinctive physicochemical and biological properties which result in the generation of distinct AD molecular subgroups.

Self-assembling Gold Nanoparticle Monolayers in a Three-phase System - Overcoming Ligand Size Limitations

NASA Astrophysics Data System (ADS)

Yang, Guang; Nanda, Jagjit; Wang, Boya; Chen, Gang; Hallinan, Daniel T., Jr.

An effective self-assembly technique was developed to prepare centimeter-scale monolayer gold nanoparticle (Au NP) films of long-range order with hydrophobic ligands. Aqueous Au NPs were entrapped in the organic/aqueous interface where the Au NP surface was in situ modified with different types of amine ligands, including amine-terminated polystyrene. The Au NPs then spontaneously relocated to the air/water interface to form an NP monolayer. The spontaneous formation of an Au NP film at the organic/water interface was due to the minimization of the system Helmholtz free energy. Self-assembled Au NP films has a hexagonal close packed structure. The interparticle spacing was dictated by the amine ligand length. Thus-assembled Au NP monolayers exhibit tunable surface plasma resonance and excellent spacial homogeneity of surface-enhanced Raman-scattering. The ``air/water/oil'' self-assembly method developed in this study not only benefits the fundamental understanding of NP ligand conformations, but is also promising to scale up the manufacture of plasmonic nanoparticle devices with precisely designed optical properties. This study was financially supported by start-up funding supplied by the Florida State University and the FAMU-FSU College of Engineering.

The effect of Au amount on size uniformity of self-assembled Au nanoparticles

NASA Astrophysics Data System (ADS)

Chen, S.-H.; Wang, D.-C.; Chen, G.-Y.; Chen, K.-Y.

2008-03-01

The self-assembled fabrication of nanostructure, a dreaming approach in the area of fabrication engineering, is the ultimate goal of this research. A finding was proved through previous research that the size of the self-assembled gold nanoparticles could be controlled with the mole ratio between AuCl4- and thiol. In this study, the moles of Au were fixed, only the moles of thiol were adjusted. Five different mole ratios of Au/S with their effect on size uniformity were investigated. The mole ratios were 1:1/16, 1:1/8, 1:1, 1:8, 1:16, respectively. The size distributions of the gold nanoparticles were analyzed by Mac-View analysis software. HR-TEM was used to derive images of self-assembled gold nanoparticles. The result reached was also the higher the mole ratio between AuCl4- and thiol the bigger the self-assembled gold nanoparticles. Under the condition of moles of Au fixed, the most homogeneous nanoparticles in size distribution derived with the mole ratio of 1:1/8 between AuCl4- and thiol. The obtained nanoparticles could be used, for example, in uniform surface nanofabrication, leading to the fabrication of ordered array of quantum dots.

Self-Assembly through Noncovalent Preorganization of Reactants: Explaining the Formation of a Polyfluoroxometalate.

PubMed

Schreiber, Roy E; Avram, Liat; Neumann, Ronny

2018-01-09

High-order elementary reactions in homogeneous solutions involving more than two molecules are statistically improbable and very slow to proceed. They are not generally considered in classical transition-state or collision theories. Yet, rather selective, high-yield product formation is common in self-assembly processes that require many reaction steps. On the basis of recent observations of crystallization as well as reactions in dense phases, it is shown that self-assembly can occur by preorganization of reactants in a noncovalent supramolecular assembly, whereby directing forces can lead to an apparent one-step transformation of multiple reactants. A simple and general kinetic model for multiple reactant transformation in a dense phase that can account for many-bodied transformations was developed. Furthermore, the self-assembly of polyfluoroxometalate anion [H 2 F 6 NaW 18 O 56 ] 7- from simple tungstate Na 2 WO 2 F 4 was demonstrated by using 2D 19 F- 19 F NOESY, 2D 19 F- 19 F COSY NMR spectroscopy, a new 2D 19 F{ 183 W} NMR technique, as well as ESI-MS and diffusion NMR spectroscopy, and the crucial involvement of a supramolecular assembly was found. The deterministic kinetic reaction model explains the reaction in a dense phase and supports the suggested self-assembly mechanism. Reactions in dense phases may be of general importance in understanding other self-assembly reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Californium interrogation prompt neutron (CIPN) instrument for non-destructive assay of spent nuclear fuel – design concept and experimental demonstration

DOE PAGES

Henzlova, Daniela; Menlove, Howard Olsen; Rael, Carlos D.; ...

2015-10-09

Our paper presents results of the first experimental demonstration of the Californium Interrogation Prompt Neutron (CIPN) instrument developed within a multi-year effort launched by the Next Generation Safeguards Initiative Spent Fuel Project of the United States Department of Energy. The goals of this project focused on developing viable non-destructive assay techniques with capabilities to improve an independent verification of spent fuel assembly characteristics. For this purpose, the CIPN instrument combines active and passive neutron interrogation, along with passive gamma-ray measurements, to provide three independent observables. We describe the initial feasibility demonstration of the CIPN instrument, which involved measurements of fourmore » pressurized-water-reactor spent fuel assemblies with different levels of burnup and two initial enrichments. The measurements were performed at the Post-Irradiation Examination Facility at the Korea Atomic Energy Institute in the Republic of Korea. The key aim of the demonstration was to evaluate CIPN instrument performance under realistic deployment conditions, with the focus on a detailed assessment of systematic uncertainties that are best evaluated experimentally. The measurements revealed good positioning reproducibility, as well as a high degree of insensitivity of the CIPN instrument's response to irregularities in a radial burnup profile. Systematic uncertainty of individual CIPN instrument signals due to assembly rotation was found to be <4.5%, even for assemblies with fairly extreme gradients in the radial burnup profile. Lastly, these features suggest that the CIPN instrument is capable of providing a good representation of assembly average characteristics, independent of assembly orientation in the instrument.« less

Californium interrogation prompt neutron (CIPN) instrument for non-destructive assay of spent nuclear fuel – design concept and experimental demonstration

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

Henzlova, Daniela; Menlove, Howard Olsen; Rael, Carlos D.

Our paper presents results of the first experimental demonstration of the Californium Interrogation Prompt Neutron (CIPN) instrument developed within a multi-year effort launched by the Next Generation Safeguards Initiative Spent Fuel Project of the United States Department of Energy. The goals of this project focused on developing viable non-destructive assay techniques with capabilities to improve an independent verification of spent fuel assembly characteristics. For this purpose, the CIPN instrument combines active and passive neutron interrogation, along with passive gamma-ray measurements, to provide three independent observables. We describe the initial feasibility demonstration of the CIPN instrument, which involved measurements of fourmore » pressurized-water-reactor spent fuel assemblies with different levels of burnup and two initial enrichments. The measurements were performed at the Post-Irradiation Examination Facility at the Korea Atomic Energy Institute in the Republic of Korea. The key aim of the demonstration was to evaluate CIPN instrument performance under realistic deployment conditions, with the focus on a detailed assessment of systematic uncertainties that are best evaluated experimentally. The measurements revealed good positioning reproducibility, as well as a high degree of insensitivity of the CIPN instrument's response to irregularities in a radial burnup profile. Systematic uncertainty of individual CIPN instrument signals due to assembly rotation was found to be <4.5%, even for assemblies with fairly extreme gradients in the radial burnup profile. Lastly, these features suggest that the CIPN instrument is capable of providing a good representation of assembly average characteristics, independent of assembly orientation in the instrument.« less

Validation of Hansen-Roach library for highly enriched uranium metal systems

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

Wenz, T.R.; Busch, R.D.

The Hansen-Roach 16-group cross-section library has been validated for use in pure uranium metal systems by modeling the Godiva critical assembly using the neutronics transport theory code ONEDANT to perform effective multiplication factor (k{sub eff}) calculations. The cross-section library used contains data for 118 isotopes (34 unique elements), including the revised cross sections for {sup 235}U and {sup 238}U. The Godiva critical assembly is a 17.4-cm sphere composed of 93.7 wt% {sup 235}U, 1.0 wt% {sup 234}U, and 5.3 wt% {sup 238}U with an effective homogeneous density of 18.7 g/cm{sup 3}.

Carboxymethyl guar gum synthesis in homogeneous phase and macroporous 3D scaffolds design for tissue engineering.

PubMed

Kundu, Sonia; Das, Aatrayee; Basu, Aalok; Ghosh, Debjani; Datta, Pallab; Mukherjee, Arup

2018-07-01

Guar gum (GG) is a galactomannan obtained directly from the Cyamopsis tetragonoloba seeds pericarb. The biopolymer hydrates hugely in three chain associated coil formations. Chaotropic Hofmeister ion like lithium interacts at the hydrogen bonding sites and render GG homogenization in polar solvents like dimethyl sulfoxide. This phenomenon was used for the first time for galactomannan derivatisations in homogeneous phase. Higher degree of substitution (DS) that was hereto unattainable in GG was achieved due to Hofmeister ion assisted assembly deformations. Furthermore, carboxymethyl guar gum (CMGG, DS = 1.10) blends well in poly-vinyl alcohol (PVA) at 2:1 mass ratio and enabled hydrophilic porous scaffold design for cell propagation. CMGG-PVA scaffolds porosity was 70-90% and the tensile strength was 6.32 MPa. CMGG-PVA scaffolds were useful as cell factories and in tissue engineering. New generation guar gum derivative scaffolds were non cytotoxic and permitted cell propagation in growth medium. Copyright © 2018 Elsevier Ltd. All rights reserved.

A CUMULATIVE MIGRATION METHOD FOR COMPUTING RIGOROUS TRANSPORT CROSS SECTIONS AND DIFFUSION COEFFICIENTS FOR LWR LATTICES WITH MONTE CARLO

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

Zhaoyuan Liu; Kord Smith; Benoit Forget

2016-05-01

A new method for computing homogenized assembly neutron transport cross sections and dif- fusion coefficients that is both rigorous and computationally efficient is proposed in this paper. In the limit of a homogeneous hydrogen slab, the new method is equivalent to the long-used, and only-recently-published CASMO transport method. The rigorous method is used to demonstrate the sources of inaccuracy in the commonly applied “out-scatter” transport correction. It is also demonstrated that the newly developed method is directly applicable to lattice calculations per- formed by Monte Carlo and is capable of computing rigorous homogenized transport cross sections for arbitrarily heterogeneous lattices.more » Comparisons of several common transport cross section ap- proximations are presented for a simple problem of infinite medium hydrogen. The new method has also been applied in computing 2-group diffusion data for an actual PWR lattice from BEAVRS benchmark.« less

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

PubMed

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Gauge Fields in Homogeneous and Inhomogeneous Cosmologies

NASA Astrophysics Data System (ADS)

Darian, Bahman K.

Despite its formidable appearance, the study of classical Yang-Mills (YM) fields on homogeneous cosmologies is amenable to a formal treatment. This dissertation is a report on a systematic approach to the general construction of invariant YM fields on homogeneous cosmologies undertaken for the first time in this context. This construction is subsequently followed by the investigation of the behavior of YM field variables for the most simple of self-gravitating YM fields. Particularly interesting was a dynamical system analysis and the discovery of chaotic signature in the axially symmetric Bianchi I-YM cosmology. Homogeneous YM fields are well studied and are known to have chaotic properties. The chaotic behavior of YM field variables in homogeneous cosmologies might eventually lead to an invariant definition of chaos in (general) relativistic cosmological models. By choosing the gauge fields to be Abelian, the construction and the field equations presented so far reduce to that of electromagnetic field in homogeneous cosmologies. A perturbative analysis of gravitationally interacting electromagnetic and scalar fields in inhomogeneous cosmologies is performed via the Hamilton-Jacobi formulation of general relativity. An essential feature of this analysis is the spatial gradient expansion of the generating functional (Hamilton principal function) to solve the Hamiltonian constraint. Perturbations of a spatially flat Friedman-Robertson-Walker cosmology with an exponential potential for the scalar field are presented.

Homology of vanadium oxide

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

Vasyutinskii, N.A.

1987-05-01

The authors examine the homology of vanadium oxide and note that data on the existence of phases and homogeneity limits in the V-O system are very contradictory. A graphical illustration shows the homologous series of vanadium oxides. The predominant part of the discrete formations in the system V-O is characterized by integral stoichiometry and forms six homologous series. It is found that homologous series of vanadium oxides are not only a basis for systematization of such oxides, but also may serve as a means for predicting the composition of new phases, limits of homogeneity, their structure, and properties.

Chemical kinetics of homogeneous atmospheric oxidation of sulfur dioxide

NASA Technical Reports Server (NTRS)

Sander, S. P.; Seinfeld, J. H.

1976-01-01

A systematic evaluation of known homogeneous SO2 reactions which might be important in air pollution chemistry is carried out. A mechanism is developed to represent the chemistry of NOx/hydrocarbon/SO2 systems, and the mechanism is used to analyze available experimental data appropriate for quantitative analysis of SO2 oxidation kinetics. Detailed comparisons of observed and predicted concentration behavior are presented. In all cases, observed SO2 oxidation rates cannot be explained solely on the basis of those SO2 reactions for which rate constants have been measured. The role of ozone-olefin reactions in SO2 oxidation is elucidated.

Method for fabricating hafnia films

DOEpatents

Hu, Michael Z [Knoxville, TN

2007-08-21

The present invention comprises a method for fabricating hafnia film comprising the steps of providing a substrate having a surface that allows formation of a self-assembled monolayer thereon via covalent bonding; providing an aqueous solution that provides homogeneous hafnium ionic complexes and hafnium nanoclusters wherein the aqueous solution is capable of undergoing homogeneous precipitation under controlled conditions for a desired period of time at a controlled temperature and controlled solution acidity for desired nanocluster nucleation and growth kinetics, desired nanocluster size, desired growth rate of film thickness and desired film surface characteristics. The method further comprising forming the self-assembled monolayer on the surface of the substrate wherein the self-assembled monolayer comprises a plurality of hydrocarbon chains cross-linked together along the surface of the substrate, the hydrocarbon chains being uniformly spaced from one another and wherein each of the hydrocarbon chains having a functional anchoring group at a first end of the chain covalently bonded with the surface of the substrate and each of the hydrocarbon chains having a functional terminating group projected away from the surface wherein the functional terminating group provides a bonding site for the hafnium film to grow; and exposing the substrate to the aqueous solution for a desired period of time at a controlled temperature wherein the hafnium ionic complexes and the hafnium nanoclusters are deposited on the bonding site of the functional terminating group thereby forming the hafnia film wherein the hafnium bonded to the hydrocarbons and to one another provide a uniform ordered arrangement defined by the uniform arrangement of the hydrocarbons.

A Bio-Inspired Polymeric Gradient Refractive Index (GRIN) Human Eye Lens

DTIC Science & Technology

2012-11-19

confirmation of the desired aspheric surface shape. Furthermore, the wavefronts of aspheric posterior GRIN and PMMA lenses were measured and...compared a homogenous PMMA lens of an identical geometry. Finally, the anterior and posterior GRIN lenses were assembled into a bio-inspired GRIN...topography and exhibited confirmation of the desired aspheric surface shape. Furthermore, the wavefronts of aspheric posterior GRIN and PMMA lenses were

The Dependence of Galaxy Clustering on Stellar-mass Assembly History for LRGs

NASA Astrophysics Data System (ADS)

Montero-Dorta, Antonio D.; Pérez, Enrique; Prada, Francisco; Rodríguez-Torres, Sergio; Favole, Ginevra; Klypin, Anatoly; Cid Fernandes, Roberto; González Delgado, Rosa M.; Domínguez, Alberto; Bolton, Adam S.; García-Benito, Rubén; Jullo, Eric; Niemiec, Anna

2017-10-01

We analyze the spectra of 300,000 luminous red galaxies (LRGs) with stellar masses {M}* ≳ {10}11 {M}⊙ from the SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS). By studying their star formation histories, we find two main evolutionary paths converging into the same quiescent galaxy population at z˜ 0.55. Fast-growing LRGs assemble 80% of their stellar mass very early on (z˜ 5), whereas slow-growing LRGs reach the same evolutionary state at z˜ 1.5. Further investigation reveals that their clustering properties on scales of ˜1-30 Mpc are, at a high level of significance, also different. Fast-growing LRGs are found to be more strongly clustered and reside in overall denser large-scale structure environments than slow-growing systems, for a given stellar-mass threshold. Our results show a dependence of clustering on a property that is directly related to the evolution of galaxies, I.e., the stellar-mass assembly history, for a homogeneous population of similar mass and color. In a forthcoming work, we will address the halo connection in the context of galaxy assembly bias.

Novel Soluble Dietary Fiber-Tannin Self-Assembled Film: A Promising Protein Protective Material.

PubMed

Song, Guo-Bin; Xu, Juan; Zheng, Hua; Feng, Ying; Zhang, Wen-Wen; Li, Kun; Ge, Shuang-shuang; Li, Kai; Zhang, Hong

2015-06-24

In this experiment, a natural promising protein protective film was fabricated through soluble dietary fiber (SDF)-tannin nanocluster self-assembly. FT-IR, XRD, and DSC tests were employed to investigate the interaction between the SDF and tannins before and after cross-linking induced by calcium ion. On the other hand, referring to the SEM and TEM results, the self-assembly process of the protein protective film could be indicated as follows: first, calcium ion, with its cross-ability, served as the "nucleus"; SDF and tannins were combined to prepare the nanoscale SDF-tannin clusters; then, the clusters were homogeneously deposited on the surface of protein to form a protective film by self-assembling hydrogen bond between tannin component of clusters as "adhesive" and protein in aqueous solutions under very mild conditions. Film thickness could also be controlled by tannin of different concentrations ranging from 114 to 1384 μm. Antibacterial test and in vitro cytotoxicity test proved that the film had a broad spectrum of antimicrobial properties and excellent cell biocompatibility, respectively, which might open up new applications in the food preservation and biomedical fields.

Adjustable mounting device for high-volume production of beam-shaping systems for high-power diode lasers

NASA Astrophysics Data System (ADS)

Haag, Sebastian; Bernhardt, Henning; Rübenach, Olaf; Haverkamp, Tobias; Müller, Tobias; Zontar, Daniel; Brecher, Christian

2015-02-01

In many applications for high-power diode lasers, the production of beam-shaping and homogenizing optical systems experience rising volumes and dynamical market demands. The automation of assembly processes on flexible and reconfigurable machines can contribute to a more responsive and scalable production. The paper presents a flexible mounting device designed for the challenging assembly of side-tab based optical systems. It provides design elements for precisely referencing and fixating two optical elements in a well-defined geometric relation. Side tabs are presented to the machine allowing the application of glue and a rotating mechanism allows the attachment to the optical elements. The device can be adjusted to fit different form factors and it can be used in high-volume assembly machines. The paper shows the utilization of the device for a collimation module consisting of a fast-axis and a slow-axis collimation lens. Results regarding the repeatability and process capability of bonding side tab assemblies as well as estimates from 3D simulation for overall performance indicators achieved such as cycle time and throughput will be discussed.

Self-Assembled Proteins and Peptides as Scaffolds for Tissue Regeneration.

PubMed

Loo, Yihua; Goktas, Melis; Tekinay, Ayse B; Guler, Mustafa O; Hauser, Charlotte A E; Mitraki, Anna

2015-11-18

Self-assembling proteins and peptides are increasingly gaining interest for potential use as scaffolds in tissue engineering applications. They self-organize from basic building blocks under mild conditions into supramolecular structures, mimicking the native extracellular matrix. Their properties can be easily tuned through changes at the sequence level. Moreover, they can be produced in sufficient quantities with chemical synthesis or recombinant technologies to allow them to address homogeneity and standardization issues required for applications. Here. recent advances in self-assembling proteins, peptides, and peptide amphiphiles that form scaffolds suitable for tissue engineering are reviewed. The focus is on a variety of motifs, ranging from minimalistic dipeptides, simplistic ultrashort aliphatic peptides, and peptide amphiphiles to large "recombinamer" proteins. Special emphasis is placed on the rational design of self-assembling motifs and biofunctionalization strategies to influence cell behavior and modulate scaffold stability. Perspectives for combination of these "bottom-up" designer strategies with traditional "top-down" biofabrication techniques for new generations of tissue engineering scaffolds are highlighted. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions

PubMed Central

Donovan, Preston; Chehreghanianzabi, Yasaman; Rathinam, Muruhan; Zustiak, Silviya Petrova

2016-01-01

The study of diffusion in macromolecular solutions is important in many biomedical applications such as separations, drug delivery, and cell encapsulation, and key for many biological processes such as protein assembly and interstitial transport. Not surprisingly, multiple models for the a-priori prediction of diffusion in macromolecular environments have been proposed. However, most models include parameters that are not readily measurable, are specific to the polymer-solute-solvent system, or are fitted and do not have a physical meaning. Here, for the first time, we develop a homogenization theory framework for the prediction of effective solute diffusivity in macromolecular environments based on physical parameters that are easily measurable and not specific to the macromolecule-solute-solvent system. Homogenization theory is useful for situations where knowledge of fine-scale parameters is used to predict bulk system behavior. As a first approximation, we focus on a model where the solute is subjected to obstructed diffusion via stationary spherical obstacles. We find that the homogenization theory results agree well with computationally more expensive Monte Carlo simulations. Moreover, the homogenization theory agrees with effective diffusivities of a solute in dilute and semi-dilute polymer solutions measured using fluorescence correlation spectroscopy. Lastly, we provide a mathematical formula for the effective diffusivity in terms of a non-dimensional and easily measurable geometric system parameter. PMID:26731550

Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice

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

Bhanjadeo, Madhabi M.; Academy of Scientific and Innovative Research; Nayak, Ashok K.

DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Fieldmore » emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices. - Highlights: • Al foil surface-assisted self-assembly of monomeric structures into larger branched DNA lattice. • FESEM study confirms the uniform distribution of two-dimensional bDNA lattice structures across the surface of Al foil. • Enzyme-free and economic strategy to prepare higher order structures from simpler DNA nanostructures have been confirmed by recovery assay. • Use of well proven sequences for the preparation of pure Y-shaped monomeric DNA nanostructure with high yield.« less

Vertically aligned single-walled carbon nanotubes by chemical assembly--methodology, properties, and applications.

PubMed

Diao, Peng; Liu, Zhongfan

2010-04-06

Single-walled carbon nanotubes (SWNTs), as one of the most promising one-dimension nanomaterials due to its unique structure, peculiar chemical, mechanical, thermal, and electronic properties, have long been considered as an important building block to construct ordered alignments. Vertically aligned SWNTs (v-SWNTs) have been successfully prepared by using direct growth and chemical assembly strategies. In this review, we focus explicitly on the v-SWNTs fabricated via chemical assembly strategy. We provide the readers with a full and systematic summary covering the advances in all aspects of this area, including various approaches for the preparation of v-SWNTs using chemical assembly techniques, characterization, assembly kinetics, and electrochemical properties of v-SWNTs. We also review the applications of v-SWNTs in electrochemical and bioelectrochemical sensors, photoelectric conversion, and scanning probe microscopy.

Yeast Mitoribosome Large Subunit Assembly Proceeds by Hierarchical Incorporation of Protein Clusters and Modules on the Inner Membrane.

PubMed

Zeng, Rui; Smith, Erin; Barrientos, Antoni

2018-03-06

Mitoribosomes are specialized for the synthesis of hydrophobic membrane proteins encoded by mtDNA, all essential for oxidative phosphorylation. Despite their linkage to human mitochondrial diseases and the recent cryoelectron microscopy reconstruction of yeast and mammalian mitoribosomes, how they are assembled remains obscure. Here, we dissected the yeast mitoribosome large subunit (mtLSU) assembly process by systematic genomic deletion of 44 mtLSU proteins (MRPs). Analysis of the strain collection unveiled 37 proteins essential for functional mtLSU assembly, three of which are critical for mtLSU 21S rRNA stability. Hierarchical cluster analysis of mtLSU subassemblies accumulated in mutant strains revealed co-operative assembly of protein sets forming structural clusters and preassembled modules. It also indicated crucial roles for mitochondrion-specific membrane-binding MRPs in anchoring newly transcribed 21S rRNA to the inner membrane, where assembly proceeds. Our results define the yeast mtLSU assembly landscape in vivo and provide a foundation for studies of mitoribosome assembly across evolution. Copyright © 2018 Elsevier Inc. All rights reserved.

Experimental validation of depletion calculations with VESTA 2.1.5 using JEFF-3.2

NASA Astrophysics Data System (ADS)

Haeck, Wim; Ichou, Raphaëlle

2017-09-01

The removal of decay heat is a significant safety concern in nuclear engineering for the operation of a nuclear reactor both in normal and accidental conditions and for intermediate and long term waste storage facilities. The correct evaluation of the decay heat produced by an irradiated material requires first of all the calculation of the composition of the irradiated material by depletion codes such as VESTA 2.1, currently under development at IRSN in France. A set of PWR assembly decay heat measurements performed by the Swedish Central Interim Storage Facility (CLAB) located in Oskarshamm (Sweden) have been calculated using different nuclear data libraries: ENDF/B-VII.0, JEFF-3.1, JEFF-3.2 and JEFF-3.3T1. Using these nuclear data libraries, VESTA 2.1 calculates the assembly decay heat for almost all cases within 4% of the measured decay heat. On average, the ENDF/B-VII.0 calculated decay heat values appear to give a systematic underestimation of only 0.5%. When using the JEFF-3.1 library, this results a systematic underestimation of about 2%. By switching to the JEFF-3.2 library, this systematic underestimation is improved slighty (up to 1.5%). The changes made in the JEFF-3.3T1 beta library appear to be overcorrecting, as the systematic underestimation is transformed into a systematic overestimation of about 1.5%.

Systematic description of the effect of particle shape on the strength properties of granular media

NASA Astrophysics Data System (ADS)

Azéma, Emilien; Estrada, Nicolas; Preechawuttipong, Itthichai; Delenne, Jean-Yves; Radjai, Farhang

2017-06-01

In this paper, we explore numerically the effect of particle shape on the mechanical behavior of sheared granular packings. In the framework of the Contact Dynamic (CD)Method, we model angular shape as irregular polyhedral particles, non-convex shape as regular aggregates of four overlapping spheres, elongated shape as rounded cap rectangles and platy shape as square-plates. Binary granular mixture consisting of disks and elongated particles are also considered. For each above situations, the number of face of polyhedral particles, the overlap of spheres, the aspect ratio of elongated and platy particles, are systematically varied from spheres to very angular, non-convex, elongated and platy shapes. The level of homogeneity of binary mixture varies from homogenous packing to fully segregated packings. Our numerical results suggest that the effects of shape parameters are nonlinear and counterintuitive. We show that the shear strength increases as shape deviate from spherical shape. But, for angular shapes it first increases up to a maximum value and then saturates to a constant value as the particles become more angular. For mixture of two shapes, the strength increases with respect of the increase of the proportion of elongated particles, but surprisingly it is independent with the level of homogeneity of the mixture. A detailed analysis of the contact network topology, evidence that various contact types contribute differently to stress transmission at the micro-scale.

Molecular ligand modulation of palladium nanocatalysts for highly efficient and robust heterogeneous oxidation of cyclohexenone to phenol

DOE PAGES

Xue, Teng; Lin, Zhaoyang; Chiu, Chin-Yi; ...

2017-01-06

Metallic nanoparticles are emerging as an exciting class of heterogeneous catalysts with the potential advantages of exceptional activity, stability, recyclability, and easier separation than homogeneous catalysts. The traditional colloid nanoparticle syntheses usually involve strong surface binding ligands that could passivate the surface active sites and result in poor catalytic activity. The subsequent removal of surface ligands could reactivate the surface but often leads to metal ion leaching and/or severe Ostwald ripening with diminished catalytic activity or poor stability. Molecular ligand engineering represents a powerful strategy for the design of homogeneous molecular catalysts but is insufficiently explored for nanoparticle catalysts tomore » date. We report a systematic investigation on molecular ligand modulation of palladium (Pd) nanoparticle catalysts. Our studies show that β-functional groups of butyric acid ligand on Pd nanoparticles can significantly modulate the catalytic reaction process to modify the catalytic activity and stability for important aerobic reactions. With a β-hydroxybutyric acid ligand, the Pd nanoparticle catalysts exhibit exceptional catalytic activity and stability with an unsaturated turnover number (TON) >3000 for dehydrogenative oxidation of cyclohexenone to phenol, greatly exceeding that of homogeneous Pd(II) catalysts (TON, ~30). This study presents a systematic investigation of molecular ligand modulation of nanoparticle catalysts and could open up a new pathway toward the design and construction of highly efficient and robust heterogeneous catalysts through molecular ligand engineering.« less

Molecular Mechanism of Thioflavin-T Binding to the Surface of [beta]-Rich Peptide Self-Assemblies

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

Biancalana, Matthew; Makabe, Koki; Koide, Akiko

A number of small organic molecules have been developed that bind to amyloid fibrils, a subset of which also inhibit fibrillization. Among these, the benzothiol dye Thioflavin-T (ThT) has been used for decades in the diagnosis of protein-misfolding diseases and in kinetic studies of self-assembly (fibrillization). Despite its importance, efforts to characterize the ThT-binding mechanism at the atomic level have been hampered by the inherent insolubility and heterogeneity of peptide self-assemblies. To overcome these challenges, we have developed a minimalist approach to designing a ThT-binding site in a 'peptide self-assembly mimic' (PSAM) scaffold. PSAMs are engineered water-soluble proteins that mimicmore » a segment of beta-rich peptide self-assembly, and they are amenable to standard biophysical techniques and systematic mutagenesis. The PSAM beta-sheet contains rows of repetitive amino acid patterns running perpendicular to the strands (cross-strand ladders) that represent a ubiquitous structural feature of fibril-like surfaces. We successfully designed a ThT-binding site that recapitulates the hallmarks of ThT-fibril interactions by constructing a cross-strand ladder consisting of contiguous tyrosines. The X-ray crystal structures suggest that ThT interacts with the beta-sheet by docking onto surfaces formed by a single tyrosine ladder, rather than in the space between adjacent ladders. Systematic mutagenesis further demonstrated that tyrosine surfaces across four or more beta-strands formed the minimal binding site for ThT. Our work thus provides structural insights into how this widely used dye recognizes a prominent subset of peptide self-assemblies, and proposes a strategy to elucidate the mechanisms of fibril-ligand interactions.« less

Design verification test matrix development for the STME thrust chamber assembly

NASA Technical Reports Server (NTRS)

Dexter, Carol E.; Elam, Sandra K.; Sparks, David L.

1993-01-01

This report presents the results of the test matrix development for design verification at the component level for the National Launch System (NLS) space transportation main engine (STME) thrust chamber assembly (TCA) components including the following: injector, combustion chamber, and nozzle. A systematic approach was used in the development of the minimum recommended TCA matrix resulting in a minimum number of hardware units and a minimum number of hot fire tests.

Construction of Lines of Constant Density and Constant Refractive Index for Ternary Liquid Mixtures.

ERIC Educational Resources Information Center

Tasic, Aleksandar Z.; Djordjevic, Bojan D.

1983-01-01

Demonstrates construction of density constant and refractive index constant lines in triangular coordinate system on basis of systematic experimental determinations of density and refractive index for both homogeneous (single-phase) ternary liquid mixtures (of known composition) and the corresponding binary compositions. Background information,…

Native N-glycopeptide thioester synthesis through N→S acyl transfer

PubMed Central

Premdjee, Bhavesh; Adams, Anna L.; Macmillan, Derek

2011-01-01

Peptide thioesters are important tools for the total synthesis of proteins using native chemical ligation (NCL). Preparation of glycopeptide thioesters, that enable the assembly of homogeneously glycosylated proteins, is complicated by the perceived fragile nature of the sugar moiety. Herein, we demonstrate the compatibility of thioester formation via N→S acyl transfer with native N-glycopeptides and report observations that will aid in their preparation. PMID:21676613

Mesoscale studies of ionic closed membranes with polyhedral geometries

DTIC Science & Technology

2016-07-25

assembled ionic amphiphiles.4 The most commonly observed polyhedral symmetry in self-organized homogeneous structures is the icosahedron, which has the...Possible buckled structures can be obtained considering components A, B with intermediate compositions f of the B component such that the stable shape...lines aids the faceting of the shell into a polyhedral structure often with three-fold vertices. Such vertices are joined together by sharp edges

Homogeneous and single-side-operational connector mechanism for self-reconfigurable, self-assembly and self-healing systems

NASA Technical Reports Server (NTRS)

Shen, Wei-Min (Inventor); Kovac, Robert M. (Inventor)

2012-01-01

Designs of single-end-operative reconfigurable genderless connectors that include a base, a plurality of movable jaws that are formed on the base and can engage to the jaws of another connector, and an actuator that is mounted on the base and can engage and move the jaws of the reconfigurable connector to connect the reconfigurable connector with another connector.

Mn-salen@MIL101(Al): a heterogeneous, enantioselective catalyst synthesized using a 'bottle around the ship' approach.

PubMed

Bogaerts, Thomas; Van Yperen-De Deyne, Andy; Liu, Ying-Ya; Lynen, Frederic; Van Speybroeck, Veronique; Van Der Voort, Pascal

2013-09-21

An enantioselective catalyst, consisting of a chiral Mn(III)salen complex entrapped in the MIL-101 metal organic framework, is reported. For the first time, we assemble a robust MOF-cage around a chiral complex. The heterogeneous catalyst shows the same selectivity as the homogeneous complex and is fully recyclable. Theoretical calculations provide insight into this retention of selectivity.

Polymersome magneto-valves for reversible capture and release of nanoparticles

PubMed Central

van Rhee, P.G.; Rikken, R.S.M.; Abdelmohsen, L.K.E.A.; Maan, J.C.; Nolte, R.J.M.; van Hest, J.C.M.; Christianen, P.C.M.; Wilson, D.A.

2014-01-01

Stomatocytes are polymersomes with an infolded bowl-shaped architecture. This internal cavity is connected to the outside environment via a small ‘mouth’ region. Stomatocytes are assembled from diamagnetic amphiphilic block-copolymers with a highly anisotropic magnetic susceptibility, which permits to magnetically align and deform the polymeric self-assemblies. Here we show the reversible opening and closing of the mouth region of stomatocytes in homogeneous magnetic fields. The control over the size of the opening yields magneto-responsive supramolecular valves that are able to reversibly capture and release cargo. Furthermore, the increase in the size of the opening is gradual and starts at fields below 10 T, which opens the possibility of using these structures for delivery and nanoreactor applications. PMID:25248402

Electrochromic switching in ionically self-assembled nanostructures

NASA Astrophysics Data System (ADS)

Janik, Jerzy A.; Heflin, James R.; Marciu, Daniela; Miller, Michael B.; Wang, Hong; Gibson, Harry W.; Davis, Rick M.

2001-11-01

Ionically self-assembled monolayers (ISAMs), fabricated by alternate adsorption of cationic and anionic components, yield exceptionally homogeneous thin films with sub- nanometer control of the thickness and relative special location of the component materials. Using organic electrochromic materials such as polyaniline, we report studies of electrochromic responses in ISAM films. Reversible changes in the absorption spectrum are observed with the application of voltages on the order of 1.0 V. Measurements are made using both liquid electrolytes and in all-solid state devices incorporating solid polyelectrolytes such as poly(2-acylamido 2-methyl propane sulfonic acid) (PAMPS). Due to the precise nanometer scale control of thickness and composition of the electrochromic composite system, switching times faster than 50 ms have been demonstrated.

Radial elasticity of self-assembled lipid tubules.

PubMed

Zhao, Yue; Tamhane, Karan; Zhang, Xuejun; An, Linan; Fang, Jiyu

2008-07-01

Self-assembled lipid tubules with crystalline bilayer walls represent useful supramolecular architectures which hold promise as vehicles for the controlled release of preloaded drugs and templates for the synthesis of one-dimensional inorganic materials. We study the local elasticity of lipid tubules of 1,2-bis(tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine by radial atomic force microscope indentation, coupled with finite element analysis. A reduced stiffness is found to extend a distance of approximately 600 nm from the ends of lipid tubules. The middle section of lipid tubules is homogeneous in terms of their radial elasticity with a Young's modulus of approximately 703 MPa. The inhomogeneous radial elasticity likely arises from the variation of lipid packing density near the tubule ends.

A virtual maintenance-based approach for satellite assembling and troubleshooting assessment

NASA Astrophysics Data System (ADS)

Geng, Jie; Li, Ying; Wang, Ranran; Wang, Zili; Lv, Chuan; Zhou, Dong

2017-09-01

In this study, a Virtual Maintenance (VM)-based approach for satellite troubleshooting assessment is proposed. By focusing on various elements in satellite assemble troubleshooting, such as accessibility, ergonomics, wiring, and extent of damage, a systematic, quantitative, and objective assessment model is established to decrease subjectivity in satellite assembling and troubleshooting assessment. Afterwards, based on the established assessment model and satellite virtual prototype, an application process of this model suitable for a virtual environment is presented. Finally, according to the application process, all the elements in satellite troubleshooting are analyzed and assessed. The corresponding improvements, which realize the transformation from a conventional way to a virtual simulation and assessment, are suggested, and the flaws in assembling and troubleshooting are revealed. Assembling or troubleshooting schemes can be improved in the early stage of satellite design with the help of a virtual prototype. Repetition in the practical operation is beneficial to companies as risk and cost are effectively reduced.

Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle.

PubMed

Hartman, Emily C; Jakobson, Christopher M; Favor, Andrew H; Lobba, Marco J; Álvarez-Benedicto, Ester; Francis, Matthew B; Tullman-Ercek, Danielle

2018-04-11

Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report a technique, termed SyMAPS (Systematic Mutation and Assembled Particle Selection), that can be used to characterize the assembly competency of all single amino acid variants of a self-assembling viral structural protein. SyMAPS studies on the MS2 bacteriophage coat protein revealed a high-resolution fitness landscape that challenges some conventional assumptions of protein engineering. An additional round of selection identified a previously unknown variant (CP[T71H]) that is stable at neutral pH but less tolerant to acidic conditions than the wild-type coat protein. The capsids formed by this variant could be more amenable to disassembly in late endosomes or early lysosomes-a feature that is advantageous for delivery applications. In addition to providing a mutability blueprint for virus-like particles, SyMAPS can be readily applied to other self-assembling proteins.

Thorium Fuel Options for Sustained Transuranic Burning in Pressurized Water Reactors - 12381

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

Rahman, Fariz Abdul; Lee, John C.; Franceschini, Fausto

2012-07-01

As described in companion papers, Westinghouse is proposing the adoption of a thorium-based fuel cycle to burn the transuranics (TRU) contained in the current Used Nuclear Fuel (UNF) and transition towards a less radio-toxic high level waste. A combination of both light water reactors (LWR) and fast reactors (FR) is envisaged for the task, with the emphasis initially posed on their TRU burning capability and eventually to their self-sufficiency. Given the many technical challenges and development times related to the deployment of TRU burners fast reactors, an interim solution making best use of the current resources to initiate burning themore » legacy TRU inventory while developing and testing some technologies of later use is desirable. In this perspective, a portion of the LWR fleet can be used to start burning the legacy TRUs using Th-based fuels compatible with the current plants and operational features. This analysis focuses on a typical 4-loop PWR, with 17x17 fuel assembly design and TRUs (or Pu) admixed with Th (similar to U-MOX fuel, but with Th instead of U). Global calculations of the core were represented with unit assembly simulations using the Linear Reactivity Model (LRM). Several assembly configurations have been developed to offer two options that can be attractive during the TRU transmutation campaign: maximization of the TRU transmutation rate and capability for TRU multi-recycling, to extend the option of TRU recycling in LWR until the FR is available. Homogeneous as well as heterogeneous assembly configurations have been developed with various recycling schemes (Pu recycle, TRU recycle, TRU and in-bred U recycle etc.). Oxide as well as nitride fuels have been examined. This enabled an assessment of the potential for burning and multi-recycling TRU in a Th-based fuel PWR to compare against other more typical alternatives (U-MOX and variations thereof). Results will be shown indicating that Th-based PWR fuel is a promising option to multi-recycle and burn TRU in a thermal spectrum, while satisfying top-level operational and safety constraints. Various assembly designs have been proposed to assess the TRU burning potential of Th-based fuel in PWRs. In addition to typical homogeneous loading patterns, heterogeneous configurations exploiting the breeding potential of thorium to enable multiple cycles of TRU irradiation and burning have been devised. The homogeneous assembly design, with all pins featuring TRU in Th, has the benefit of a simple loading pattern and the highest rate of TRU transmutation, but it can be used only for a few cycles due to the rapid rise in the TRU content of the recycled fuel, which challenges reactivity control, safety coefficients and fuel handling. Due to its simple loading pattern, such assembly design can be used as the first step of Th implementation, achieving up to 3 times larger TRU transmutation rate than conventional U-MOX, assuming same fraction of MOX assemblies in the core. As the next step in thorium implementation, heterogeneous assemblies featuring a mixed array of Th-U and Th-U-TRU pins, where the U is in-bred from Th, have been proposed. These designs have the potential to enable burning an external supply of TRU through multiple cycles of irradiation, recovery (via reprocessing) and recycling of the residual actinides at the end of each irradiation cycle. This is achieved thanks to a larger breeding of U from Th in the heterogeneous assemblies, which reduces the TRU supply and thus mitigates the increase in the TRU core inventory for the multi-recycled fuel. While on an individual cycle basis the amount of TRU burned in the heterogeneous assembly is reduced with respect to the homogeneous design, TRU burning rates higher than single-pass U-MOX fuel can still be achieved, with the additional benefits of a multi-cycle transmutation campaign recycling all TRU isotopes. Nitride fuel, due its higher density and U breeding potential, together with its better thermal properties, ideally suits the objectives and constraints of the heterogeneous assemblies. However, significant technological advancements must be made before nitride fuels can be employed in an LWR: its water resistance needs to be improved and a viable technology to enrich N in N-15 must be devised. Moreover, for the nitride heterogeneous configurations examined in this study, the enhancement in TRU burning performance is achieved not only by replacing oxide with nitride fuel, but also by increasing the fuel rod size. This latter modification, allowed by the high thermal conductivity of nitride fuel, leads however to a very tight lattice, which may challenge reactor coolant pumps and assembly hold-down mechanisms, the former through an increase in core pressure drop and the latter through an increase in assembly lift-off forces. To alleviate these issues, while still achieving the large fuel-to-moderator ratios resulting from using tight lattices, wire wraps could be used in place of grid spacers. For tight lattices, typical grid spacers are hard to manufacture and their replacement with wire wraps is known to allow for a pressure drop reduction by at least 2 times. The studies, while certainly very preliminary, provide a starting point to devise an optimum strategy for TRU transmutation in Th-based PWR fuel. The viability of the scheme proposed depends on the timely phasing in of the associated technologies, with proper lead time and to solve the many challenges. These challenges are certainly substantial, and make the current once-through U-based scheme pursued in the US by far a more practical (and cheaper) option. However, when compared to other transmutation schemes, the proposed one has arguably similar challenges and unknowns with potentially bigger rewards. (authors)« less

A reduction for spiking integrate-and-fire network dynamics ranging from homogeneity to synchrony.

PubMed

Zhang, J W; Rangan, A V

2015-04-01

In this paper we provide a general methodology for systematically reducing the dynamics of a class of integrate-and-fire networks down to an augmented 4-dimensional system of ordinary-differential-equations. The class of integrate-and-fire networks we focus on are homogeneously-structured, strongly coupled, and fluctuation-driven. Our reduction succeeds where most current firing-rate and population-dynamics models fail because we account for the emergence of 'multiple-firing-events' involving the semi-synchronous firing of many neurons. These multiple-firing-events are largely responsible for the fluctuations generated by the network and, as a result, our reduction faithfully describes many dynamic regimes ranging from homogeneous to synchronous. Our reduction is based on first principles, and provides an analyzable link between the integrate-and-fire network parameters and the relatively low-dimensional dynamics underlying the 4-dimensional augmented ODE.

An environment-dependent semi-empirical tight binding model suitable for electron transport in bulk metals, metal alloys, metallic interfaces, and metallic nanostructures. II. Application—Effect of quantum confinement and homogeneous strain on Cu conductance

NASA Astrophysics Data System (ADS)

Hegde, Ganesh; Povolotskyi, Michael; Kubis, Tillmann; Charles, James; Klimeck, Gerhard

2014-03-01

The Semi-Empirical tight binding model developed in Part I Hegde et al. [J. Appl. Phys. 115, 123703 (2014)] is applied to metal transport problems of current relevance in Part II. A systematic study of the effect of quantum confinement, transport orientation, and homogeneous strain on electronic transport properties of Cu is carried out. It is found that quantum confinement from bulk to nanowire boundary conditions leads to significant anisotropy in conductance of Cu along different transport orientations. Compressive homogeneous strain is found to reduce resistivity by increasing the density of conducting modes in Cu. The [110] transport orientation in Cu nanowires is found to be the most favorable for mitigating conductivity degradation since it shows least reduction in conductance with confinement and responds most favorably to compressive strain.

Non-homogeneous flow profiles in sheared bacterial suspensions

NASA Astrophysics Data System (ADS)

Samanta, Devranjan; Cheng, Xiang

Bacterial suspensions under shear exhibit interesting rheological behaviors including the remarkable ``superfluidic'' state with vanishing viscosity at low shear rates. Theoretical studies have shown that such ``superfluidic'' state is linked with non-homogeneous shear flows, which are induced by coupling between nematic order of active fluids and hydrodynamics of shear flows. However, although bulk rheology of bacterial suspensions has been experimentally studied, shear profiles within bacterial suspensions have not been explored so far. Here, we experimentally investigate the flow behaviors of E. coli suspensions under planar oscillatory shear. Using confocal microscopy and PIV, we measure velocity profiles across gap between two shear plates. We find that with increasing shear rates, high-concentration bacterial suspensions exhibit an array of non-homogeneous flow behaviors like yield-stress flows and shear banding. We show that these non-homogeneous flows are due to collective motion of bacterial suspensions. The phase diagram of sheared bacterial suspensions is systematically mapped as functions of shear rates an bacterial concentrations. Our experiments provide new insights into rheology of bacterial suspensions and shed light on shear induced dynamics of active fluids. Chemical Engineering and Material Science department.

The mechanisms for nanoparticle surface diffusion and chain self-assembly determined from real-time nanoscale kinetics in liquid

DOE PAGES

Woehl, Taylor J.; Prozorov, Tanya

2015-08-20

The mechanisms for nanoparticle self-assembly are often inferred from the morphology of the final nanostructures in terms of attractive and repulsive interparticle interactions. Understanding how nanoparticle building blocks are pieced together during self-assembly is a key missing component needed to unlock new strategies and mechanistic understanding of this process. Here we use real-time nanoscale kinetics derived from liquid cell transmission electron microscopy investigation of nanoparticle self-assembly to show that nanoparticle mobility dictates the pathway for self-assembly and final nanostructure morphology. We describe a new method for modulating nanoparticle diffusion in a liquid cell, which we employ to systematically investigate themore » effect of mobility on self-assembly of nanoparticles. We interpret the observed diffusion in terms of electrostatically induced surface diffusion resulting from nanoparticle hopping on the liquid cell window surface. Slow-moving nanoparticles self-assemble predominantly into linear 1D chains by sequential attachment of nanoparticles to existing chains, while highly mobile nanoparticles self-assemble into chains and branched structures by chain–chain attachments. Self-assembly kinetics are consistent with a diffusion-driven mechanism; we attribute the change in self-assembly pathway to the increased self-assembly rate of highly mobile nanoparticles. Furthermore, these results indicate that nanoparticle mobility can dictate the self-assembly mechanism and final nanostructure morphology in a manner similar to interparticle interactions.« less

Biomimetic Layer-by-Layer Self-Assembly of Nanofilms, Nanocoatings, and 3D Scaffolds for Tissue Engineering.

PubMed

Zhang, Shichao; Xing, Malcolm; Li, Bingyun

2018-06-01

Achieving surface design and control of biomaterial scaffolds with nanometer- or micrometer-scaled functional films is critical to mimic the unique features of native extracellular matrices, which has significant technological implications for tissue engineering including cell-seeded scaffolds, microbioreactors, cell assembly, tissue regeneration, etc. Compared with other techniques available for surface design, layer-by-layer (LbL) self-assembly technology has attracted extensive attention because of its integrated features of simplicity, versatility, and nanoscale control. Here we present a brief overview of current state-of-the-art research related to the LbL self-assembly technique and its assembled biomaterials as scaffolds for tissue engineering. An overview of the LbL self-assembly technique, with a focus on issues associated with distinct routes and driving forces of self-assembly, is described briefly. Then, we highlight the controllable fabrication, properties, and applications of LbL self-assembly biomaterials in the forms of multilayer nanofilms, scaffold nanocoatings, and three-dimensional scaffolds to systematically demonstrate advances in LbL self-assembly in the field of tissue engineering. LbL self-assembly not only provides advances for molecular deposition but also opens avenues for the design and development of innovative biomaterials for tissue engineering.

Building superlattices from individual nanoparticles via template-confined DNA-mediated assembly

NASA Astrophysics Data System (ADS)

Lin, Qing-Yuan; Mason, Jarad A.; Li, Zhongyang; Zhou, Wenjie; O’Brien, Matthew N.; Brown, Keith A.; Jones, Matthew R.; Butun, Serkan; Lee, Byeongdu; Dravid, Vinayak P.; Aydin, Koray; Mirkin, Chad A.

2018-02-01

DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. Specifically, the assembly of individual colloidal plasmonic nanoparticles with different shapes and sizes is controlled by oligonucleotides containing “locked” nucleic acids and confined environments provided by polymer pores to yield oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer- and micrometer-length scales. These structures, which would be difficult to construct by other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach are explored by identifying a broadband absorber with a solvent polarity response that allows dynamic tuning of visible light absorption.

Building superlattices from individual nanoparticles via template-confined DNA-mediated assembly

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

Lin, Qing-Yuan; Mason, Jarad A.; Li, Zhongyang

DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. Specifically, individual colloidal plasmonic nanoparticles with different shapes and sizes are assembled with ‘locked” nucleic acids in polymer pores into oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer and micrometer length scales. These structures, which would be difficult to construct via other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach is explored by identifying amore » broadband absorber with a solvent polarity response that allows dynamic tuning of the wavelength response and amplitude of visible light absorption.« less

Design of Bioinorganic Materials at the Interface of Coordination and Biosupramolecular Chemistry.

PubMed

Maity, Basudev; Ueno, Takafumi

2017-04-01

Protein assemblies have recently become known as potential molecular scaffolds for applications in materials science and bio-nanotechnology. Efforts to design protein assemblies for construction of protein-based hybrid materials with metal ions, metal complexes, nanomaterials and proteins now represent a growing field with a common aim of providing novel functions and mimicking natural functions. However, the important roles of protein assemblies in coordination and biosupramolecular chemistry have not been systematically investigated and characterized. In this personal account, we focus on our recent progress in rational design of protein assemblies using bioinorganic chemistry for (1) exploration of unnatural reactions, (2) construction of functional protein architectures, and (3) in vivo applications. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein.

PubMed

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-11-30

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson's disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young's modulus).

Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein

NASA Astrophysics Data System (ADS)

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-11-01

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson’s disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young’s modulus).

Elucidating the role of methyl viologen as a scavenger of photoactivated electrons from photosystem I under aerobic and anaerobic conditions.

PubMed

Bennett, Tyler; Niroomand, Hanieh; Pamu, Ravi; Ivanov, Ilia; Mukherjee, Dibyendu; Khomami, Bamin

2016-03-28

We present detailed electrochemical investigations into the role of dissolved O2 in electrolyte solutions in scavenging photoactivated electrons from a uniform photosystem I (PS I) monolayer assembled on alkanethiolate SAM (self-assembled monolayer)/Au surfaces while using methyl viologen (MV(2+)) as the redox mediator. To this end, we report results for direct measurements of light induced photocurrent from uniform monolayer assemblies of PS I on C9 alkanethiolate SAM/Au surfaces. These measurements, apart from demonstrating the ability of dissolved O2 in the electrolyte medium to act as an electron scavenger, also reveal its essential role in driving the solution-phase methyl viologen to initiate light-induced directional electron transfer from an electron donor surface (Au) via surface assembled PS I trimers. Specifically, our systematic electrochemical measurements have revealed that the dissolved O2 in aqueous electrolyte solutions form a complex intermediate species with MV that plays the essential role in mediating redox pathways for unidirectional electron transfer processes. This critical insight into the redox-mediated electron transfer pathways allows for rational design of electron scavengers through systematic tuning of mediator combinations that promote such intermediate formation. Our current findings facilitate the incorporation of PS I-based bio-hybrid constructs as photo-anodes in future photoelectrochemical cells and bio-electronic devices.

Homogeneous coating of ionomer on electrocatalyst assisted by polybenzimidazole as an adhesive layer and its effect on fuel cell performance

NASA Astrophysics Data System (ADS)

Yang, Zehui; Fujigaya, Tsuyohiko; Nakashima, Naotoshi

2015-12-01

The fabrication of homogeneous ionomer distribution in fuel cell catalyst layers is necessary and important to improve the platinum utilization as well as the power density. Here, we focus on the effect of poly[2,2‧-(2,6-pyridine)-5,5‧-bibenzimidazole] (PyPBI) wrapped on multi-walled carbon nanotubes (MWNTs) for anchoring Nafion ionomer to the electrocatalyst, in which PyPBI functions as the binding sites for platinum nanoparticles (Pt-NPs) used as a catalyst. Based on the result using a control composite without having PyPBI, a strong interaction of the Nafion onto the PyPBI layer is recognized. Importantly, we find that the membrane-electrode assembly (MEA) shows a much higher maximum power density than that of the MEA without PyPBI. A homogeneous coating of Nafion on the electrocatalyst using the PyPBI forms a long-range network of the ionomer, leading to an improved Pt-NP utilization efficiency as well as an enhanced power density of the MEA.

Elongational Flow Assists with the Assembly of Protein Nanofibrils

NASA Astrophysics Data System (ADS)

Mittal, Nitesh; Kamada, Ayaka; Lendel, Christofer; Lundell, Fredrik; Soderberg, Daniel

2016-11-01

Controlling the aggregation process of protein-based macromolecular structures in a confined environment using small-scale flow devices and understanding their assembly mechanisms is essential to develop bio-based materials. Whey protein, a protein mixture with β-lactoglobulin as main component, is able to self-assemble into amyloid-like protein nanofibers which are stabilized by hydrogen bonds. The conditions at which the fibrillation process occurs can affect the properties and morphology of the fibrils. Here, we show that the morphology of protein nanofibers greatly affects their assembly. We used elongational flow based double flow-focusing device for this study. In-situ behavior of the straight and flexible fibrils in the flow channel is determined using small-angle X-ray scattering (SAXS) technique. Our process combines hydrodynamic alignment with dispersion to gel-transition that produces homogeneous and smooth fibers. Moreover, successful alignment before gelation demands a proper separation of the time-scales involved, which we tried to identify in the current study. The presented approach combining small scale flow devices with in-situ synchrotron X-ray studies and protein engineering is a promising route to design high performance protein-based materials with controlled physical and chemical properties. We acknowledge the support from Wallenberg Wood Science Center.

Synthetic ion channels via self-assembly: a route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes.

PubMed

Carr, Rogan; Weinstock, Ira A; Sivaprasadarao, Asipu; Müller, Achim; Aksimentiev, Aleksei

2008-11-01

Porous polyoxometalate nanocapsules of Keplerate type are known to exhibit the functionality of biological ion channels; however, their use as an artificial ion channel is tempered by the high negative charge of the capsules, which renders their spontaneous incorporation into a lipid bilayer membrane unlikely. In this Letter we report coarse-grained molecular dynamics simulations that demonstrate a route for embedding negatively charged nanocapsules into lipid bilayer membranes via self-assembly. A homogeneous mixture of water, cationic detergent, and phospholipid was observed to spontaneously self-assemble around the nanocapsule into a layered, liposome-like structure, where the nanocapsule was enveloped by a layer of cationic detergent followed by a layer of phospholipid. Fusion of such a layered liposome with a lipid bilayer membrane was observed to embed the nanocapsule into the lipid bilayer. The resulting assembly was found to remain stable even after the surface of the capsule was exposed to electrolyte. In the latter conformation, water was observed to flow into and out of the capsule as Na(+) cations entered, suggesting that a polyoxometalate nanocapsule can form a functional synthetic ion channel in a lipid bilayer membrane.

Synthetic Ion Channels via Self-Assembly: a Route for Embedding Porous Polyoxometalate Nanocapsules in Lipid Bilayer Membranes

PubMed Central

Carr, Rogan; Weinstock, Ira A.; Sivaprasadarao, Asipu; Müller, Achim; Aksimentiev, Aleksei

2010-01-01

Porous polyoxometalate nanocapsules of Keplerate type are known to exhibit the functionality of biological ion channels, however, their use as artificial ion channel is tempered by the high negative charge of the capsules, which renders their spontaneous incorporation into a lipid bilayer membrane unlikely. In this letter we report coarse-grained molecular dynamics simulations that demonstrate a route for embedding negatively charged nanocapsules into lipid bilayer membranes via self-assembly. A homogeneous mixture of water, cationic detergent, and phospholipid was observed to spontaneously self-assemble around the nanocapsule into a layered, liposome-like structure, where the nanocapsule was enveloped by a layer of cationic detergent followed by a layer of phospholipid. Fusion of such a layered liposome with a lipid bilayer membrane was observed to embed the nanocapsule into the lipid bilayer. The resulting assembly was found to remain stable even after the surface of the capsule was exposed to electrolyte. In the latter conformation, water was observed to flow into and out of the capsule as Na+ cations entered, suggesting that a polyoxometalate nanocapsule can form a functional synthetic ion channel in a lipid bilayer membrane. PMID:18844424

Microscale Mechanics of Actin Networks During Dynamic Assembly and Dissociation

NASA Astrophysics Data System (ADS)

Gurmessa, Bekele; Robertson-Anderson, Rae; Ross, Jennifer; Nguyen, Dan; Saleh, Omar

Actin is one of the key components of the cytoskeleton, enabling cells to move and divide while maintaining shape by dynamic polymerization, dissociation and crosslinking. Actin polymerization and network formation is driven by ATP hydrolysis and varies depending on the concentrations of actin monomers and crosslinking proteins. The viscoelastic properties of steady-state actin networks have been well-characterized, yet the mechanical properties of these non-equilibrium systems during dynamic assembly and disassembly remain to be understood. We use semipermeable microfluidic devices to induce in situ dissolution and re-polymerization of entangled and crosslinked actin networks, by varying ATP concentrations in real-time, while measuring the mechanical properties during disassembly and re-assembly. We use optical tweezers to sinusoidally oscillate embedded microspheres and measure the resulting force at set time-intervals and in different regions of the network during cyclic assembly/disassembly. We determine the time-dependent viscoelastic properties of non-equilibrium network intermediates and the reproducibility and homogeneity of network formation and dissolution. Results inform the role that cytoskeleton reorganization plays in the dynamic multifunctional mechanics of cells. NSF CAREER Award (DMR-1255446) and a Scialog Collaborative Innovation Award funded by Research Corporation for Scientific Advancement (Grant No. 24192).

Neutron Diffusion in a Space Lattice of Fissionable and Absorbing Materials

DOE R&D Accomplishments Database

Feynman, R. P.; Welton, T. A.

1946-08-27

Methods are developed for estimating the effect on a critical assembly of fabricating it as a lattice rather than in the more simply interpreted homogeneous manner. An idealized case is discussed supposing an infinite medium in which fission, elastic scattering and absorption can occur, neutrons of only one velocity present, and the neutron m.f.p. independent of position and equal to unity with the unit of length used.

Test Item Analysis: An Educator Professionalism Approach

ERIC Educational Resources Information Center

Hamzah, Mohd Sahandri Gani; Abdullah, Saifuddin Kumar

2011-01-01

The evaluation of learning is a systematic process involving testing, measuring and evaluation. In the testing step, a teacher needs to choose the best instrument that can test the minds of students. Testing will produce scores or marks with many variations either in homogeneous or heterogeneous forms that will be used to categorize the scores…

The Homogenization of Planetary Life: The Inner Logic of Global Market Competition. The Iconoclast.

ERIC Educational Resources Information Center

McMurtry, John

1997-01-01

Notes that the law of competitive advantage, quoted so frequently in support of the global economy, mandates a uniformity of agricultural and economic products. Argues that this systematically selects against the biodiversity of life and reduces nature's capacities to adapt and reproduce in changing biological conditions. (MJP)

Publication Bias in Meta-Analyses of the Efficacy of Psychotherapeutic Interventions for Depression

ERIC Educational Resources Information Center

Niemeyer, Helen; Musch, Jochen; Pietrowsky, Reinhard

2013-01-01

Objective: The aim of this study was to assess whether systematic reviews investigating psychotherapeutic interventions for depression are affected by publication bias. Only homogeneous data sets were included, as heterogeneous data sets can distort statistical tests of publication bias. Method: We applied Begg and Mazumdar's adjusted rank…

Effect of Exercise on Depressive Symptoms and Body Balance in the Elderly

ERIC Educational Resources Information Center

Lee, Pai-Lin; Yang, Yu-Chi; Huang, Chih-Kun; Hsiao, Ching-Hsiang; Liu, Ting-Yang; Wang, Cheng-Yen

2017-01-01

Exercise systematically improves physical and psychological performances on a wide range of measures, but the links between them are rarely examined for the high homogeneous group of institutionalized veterans. This study aims to investigate the exercise intervention effects on both depressive symptoms and body-balance. Samples were divided into…

Chemical weathering indices applied to weathering profiles developed on heterogeneous felsic metamorphic parent rocks

Treesearch

Jason R. Price; Michael A. Velbel

2003-01-01

Chemical weathering indices are commonly used for characterizing weathering profiles by incorporating bulk major element oxide chemistry into a single metric for each sample. Generally, on homogeneous parent rocks, weathering indices change systematically with depth. However, the weathering of heterogeneous metamorphic rocks confounds the relationship between...

ANALYTICAL SOLUTIONS OF THE ATMOSPHERIC DIFFUSION EQUATION WITH MULTIPLE SOURCES AND HEIGHT-DEPENDENT WIND SPEED AND EDDY DIFFUSIVITIES. (R825689C072)

EPA Science Inventory

Abstract

Three-dimensional analytical solutions of the atmospheric diffusion equation with multiple sources and height-dependent wind speed and eddy diffusivities are derived in a systematic fashion. For homogeneous Neumann (total reflection), Dirichlet (total adsorpti...

ANALYTICAL SOLUTIONS OF THE ATMOSPHERIC DIFFUSION EQUATION WITH MULTIPLE SOURCES AND HEIGHT-DEPENDENT WIND SPEED AND EDDY DIFFUSIVITIES. (R825689C048)

EPA Science Inventory

Abstract

Three-dimensional analytical solutions of the atmospheric diffusion equation with multiple sources and height-dependent wind speed and eddy diffusivities are derived in a systematic fashion. For homogeneous Neumann (total reflection), Dirichlet (total adsorpti...

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development

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

Hansen, Ryan H.; Timm, Andrea C.; Timm, Collin M.

The structure, function and evolving composition of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment. The complexity of this parameter space in naturally occurring systems has made a clear understanding of the key drivers of community development elusive. Here, we examine the role of spatial confinement on community development using a microwell platform that allows for assembly and monitoring of unique microbial communities en masse. This platform was designed to contain microwells with varied size features in order to mimic various levels of spatial confinement found in natural systems. Microbial populations assembled inmore » wells with incrementally smaller size features showed increasingly larger variations in inoculum levels. By exploiting this size dependence, large wells were used to assemble homogenous initial populations of Pseudomonas aeruginosa, allowing for reproducible, directed growth trajectories. In contrast, smaller wells were used to assemble a heterogeneous range of initial populations, resulting in a variety of growth and decay trajectories. This allowed for parallel screening of single member communities across different levels of confinement to identify initial conditions in which P. aeruginosa colonies have dramatically higher probabilities of survival. These results demonstrate a unique approach for manipulating the distribution of initial microbial populations assembled into controlled microenvironments to rapidly identify population and environmental parameters conducive or inhibitive to growth. Additionally, multi-member community assembly was characterized to demonstrate the power of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.« less

Regulation of Corneal Stroma Extracellular Matrix Assembly

PubMed Central

Chen, Shoujun; Mienaltowski, Michael J.; Birk, David E.

2014-01-01

The transparent cornea is the major refractive element of the eye. A finely controlled assembly of the stromal extracellular matrix is critical to corneal function, as well as in establishing the appropriate mechanical stability required to maintain corneal shape and curvature. In the stroma, homogeneous, small diameter collagen fibrils, regularly packed with a highly ordered hierarchical organization, are essential for function. This review focuses on corneal stroma assembly and the regulation of collagen fibrillogenesis. Corneal collagen fibrillogenesis involves multiple molecules interacting in sequential steps, as well as interactions between keratocytes and stroma matrix components. The stroma has the highest collagen V:I ratio in the body. Collagen V regulates the nucleation of protofibril assembly, thus controlling the number of fibrils and assembly of smaller diameter fibrils in the stroma. The corneal stroma is also enriched in small leucine-rich proteoglycans (SLRPs) that cooperate in a temporal and spatial manner to regulate linear and lateral collagen fibril growth. In addition, the fibril-associated collagens (FACITs) such as collagen XII and collagen XIV have roles in the regulation of fibril packing and inter-lamellar interactions. A communicating keratocyte network contributes to the overall and long-range regulation of stromal extracellular matrix assembly, by creating micro-domains where the sequential steps in stromal matrix assembly are controlled. Keratocytes control the synthesis of extracellular matrix components, which interact with the keratocytes dynamically to coordinate the regulatory steps into a cohesive process. Mutations or deficiencies in stromal regulatory molecules result in altered interactions and deficiencies in both transparency and refraction, leading to corneal stroma pathobiology such as stromal dystrophies, cornea plana and keratoconus. PMID:25819456

Self-assembly of pi-conjugated peptides in aqueous environments leading to energy-transporting bioelectronic nanostructures

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

Tavor, John

The realization of new supramolecular pi-conjugated organic structures inspired and driven by peptide-based self-assembly will offer a new approach to interface with the biotic environment in a way that will help to meet many DOE-recognized grand challenges. Previously, we developed pi-conjugated peptides that undergo supramolecular self-assembly into one-dimensional (1-D) organic electronic nanomaterials under benign aqueous conditions. The intermolecular interactions among the pi-conjugated organic segments within these nanomaterials lead to defined perturbations of their optoelectronic properties and yield nanoscale conduits that support energy transport within individual nanostructures and throughout bulk macroscopic collections of nanomaterials. Our objectives for future research are tomore » construct and study biomimetic electronic materials for energy-related technology optimized for harsher non-biological environments where peptide-driven self-assembly enhances pi-stacking within nanostructured biomaterials, as detailed in the following specific tasks: (1) synthesis and detailed optoelectronic characterization of new pi-electron units to embed within homogeneous self assembling peptides, (2) molecular and data-driven modeling of the nanomaterial aggregates and their higher-order assemblies, and (3) development of new hierarchical assembly paradigms to organize multiple electronic subunits within the nanomaterials leading to heterogeneous electronic properties (i.e. gradients and localized electric fields). These intertwined research tasks will lead to the continued development and fundamental mechanistic understanding of a powerful bioinspired materials set capable of making connections between nanoscale electronic materials and macroscopic bulk interfaces, be they those of a cell, a protein or a device.« less

Thermodynamics of phase-separating nanoalloys: Single particles and particle assemblies

NASA Astrophysics Data System (ADS)

Fèvre, Mathieu; Le Bouar, Yann; Finel, Alphonse

2018-05-01

The aim of this paper is to investigate the consequences of finite-size effects on the thermodynamics of nanoparticle assemblies and isolated particles. We consider a binary phase-separating alloy with a negligible atomic size mismatch, and equilibrium states are computed using off-lattice Monte Carlo simulations in several thermodynamic ensembles. First, a semi-grand-canonical ensemble is used to describe infinite assemblies of particles with the same size. When decreasing the particle size, we obtain a significant decrease of the solid/liquid transition temperatures as well as a growing asymmetry of the solid-state miscibility gap related to surface segregation effects. Second, a canonical ensemble is used to analyze the thermodynamic equilibrium of finite monodisperse particle assemblies. Using a general thermodynamic formulation, we show that a particle assembly may split into two subassemblies of identical particles. Moreover, if the overall average canonical concentration belongs to a discrete spectrum, the subassembly concentrations are equal to the semi-grand-canonical equilibrium ones. We also show that the equilibrium of a particle assembly with a prescribed size distribution combines a size effect and the fact that a given particle size assembly can adopt two configurations. Finally, we have considered the thermodynamics of an isolated particle to analyze whether a phase separation can be defined within a particle. When studying rather large nanoparticles, we found that the region in which a two-phase domain can be identified inside a particle is well below the bulk phase diagram, but the concentration of the homogeneous core remains very close to the bulk solubility limit.

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development

DOE PAGES

Hansen, Ryan H.; Timm, Andrea C.; Timm, Collin M.; ...

2016-05-06

The structure, function and evolving composition of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment. The complexity of this parameter space in naturally occurring systems has made a clear understanding of the key drivers of community development elusive. Here, we examine the role of spatial confinement on community development using a microwell platform that allows for assembly and monitoring of unique microbial communities en masse. This platform was designed to contain microwells with varied size features in order to mimic various levels of spatial confinement found in natural systems. Microbial populations assembled inmore » wells with incrementally smaller size features showed increasingly larger variations in inoculum levels. By exploiting this size dependence, large wells were used to assemble homogenous initial populations of Pseudomonas aeruginosa, allowing for reproducible, directed growth trajectories. In contrast, smaller wells were used to assemble a heterogeneous range of initial populations, resulting in a variety of growth and decay trajectories. This allowed for parallel screening of single member communities across different levels of confinement to identify initial conditions in which P. aeruginosa colonies have dramatically higher probabilities of survival. These results demonstrate a unique approach for manipulating the distribution of initial microbial populations assembled into controlled microenvironments to rapidly identify population and environmental parameters conducive or inhibitive to growth. Additionally, multi-member community assembly was characterized to demonstrate the power of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.« less

Assembly of the epithelial Na+ channel evaluated using sucrose gradient sedimentation analysis.

PubMed

Cheng, C; Prince, L S; Snyder, P M; Welsh, M J

1998-08-28

Three subunits, alpha, beta, and gamma, contribute to the formation of the epithelial Na+ channel. To investigate the oligomeric assembly of the channel complex, we used sucrose gradient sedimentation analysis to determine the sedimentation properties of individual subunits and heteromultimers comprised of multiple subunits. When the alpha subunit was expressed alone, it first formed an oligomeric complex with a sedimentation coefficient of 11 S, and then generated a higher order multimer of 25 S. In contrast, individual beta and gamma subunits predominately assembled into 11 S complexes. We obtained similar results with expression in cells and in vitro. When we co-expressed beta with alpha or with alpha plus gamma, the beta subunit assembled into a 25 S complex. Glycosylation of the alpha subunit was not required for assembly into a 25 S complex. We found that the alpha subunit formed intra-chain disulfide bonds. Although such bonds were not required to generate an oligomeric complex, under nonreducing conditions the alpha subunit formed a complex that migrated more homogeneously at 25 S. This suggests that intra-chain disulfide bonds may stabilize the complex. These data suggest that the epithelial Na+ channel subunits form high order oligomeric complexes and that the alpha subunit contains the information that facilitates such formation. Interestingly, the ability of the alpha, but not the beta or gamma, subunit to assemble into a 25 S homomeric complex correlates with the ability of these subunits to generate functional channels when expressed alone.

Physical therapy in the postoperative of proximal femur fracture in elderly. Literature review

PubMed Central

Carneiro, Mariana Barquet; Alves, Débora Pinheiro Lédio; Mercadante, Marcelo Tomanik

2013-01-01

The proximal femoral fracture in the elderly is a serious public health problem. Surgical treatment of this fracture is used to reduce morbidity, together with postoperative physical therapy. The objective was to conduct a systematic review of physical therapy protocols in postoperative for fractures of the proximal femur in elderly. We selected randomized controlled trials in elderly in the past 10 years, in Portuguese and English. There were 14 articles in the literature. Physical therapy has an important role in functional recovery of the elderly. Level of Evidence I, Systematic Review RCTs (Study results were homogenous). PMID:24453665

Solid oxide membrane-assisted controllable electrolytic fabrication of metal carbides in molten salt.

PubMed

Zou, Xingli; Zheng, Kai; Lu, Xionggang; Xu, Qian; Zhou, Zhongfu

2016-08-15

Silicon carbide (SiC), titanium carbide (TiC), zirconium carbide (ZrC), and tantalum carbide (TaC) have been electrochemically produced directly from their corresponding stoichiometric metal oxides/carbon (MOx/C) precursors by electrodeoxidation in molten calcium chloride (CaCl2). An assembled yttria stabilized zirconia solid oxide membrane (SOM)-based anode was employed to control the electrodeoxidation process. The SOM-assisted controllable electrochemical process was carried out in molten CaCl2 at 1000 °C with a potential of 3.5 to 4.0 V. The reaction mechanism of the electrochemical production process and the characteristics of these produced metal carbides (MCs) were systematically investigated. X-ray diffraction, scanning electron microscopy, and transmission electron microscopy analyses clearly identify that SiC, TiC, ZrC, and TaC carbides can be facilely fabricated. SiC carbide can be controlled to form a homogeneous nanowire structure, while the morphologies of TiC, ZrC, and TaC carbides exhibit porous nodular structures with micro/nanoscale particles. The complex chemical/electrochemical reaction processes including the compounding, electrodeoxidation, dissolution-electrodeposition, and in situ carbonization processes in molten CaCl2 are also discussed. The present results preliminarily demonstrate that the molten salt-based SOM-assisted electrodeoxidation process has the potential to be used for the facile and controllable electrodeoxidation of MOx/C precursors to micro/nanostructured MCs, which can potentially be used for various applications.

THE ALFALFA H α SURVEY. I. PROJECT DESCRIPTION AND THE LOCAL STAR FORMATION RATE DENSITY FROM THE FALL SAMPLE

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

Sistine, Angela Van; Salzer, John J.; Janowiecki, Steven

2016-06-10

The ALFALFA H α survey utilizes a large sample of H i-selected galaxies from the ALFALFA survey to study star formation (SF) in the local universe. ALFALFA H α contains 1555 galaxies with distances between ∼20 and ∼100 Mpc. We have obtained continuum-subtracted narrowband H α images and broadband R images for each galaxy, creating one of the largest homogeneous sets of H α images ever assembled. Our procedures were designed to minimize the uncertainties related to the calculation of the local SF rate density (SFRD). The galaxy sample we constructed is as close to volume-limited as possible, is amore » robust statistical sample, and spans a wide range of galaxy environments. In this paper, we discuss the properties of our Fall sample of 565 galaxies, our procedure for deriving individual galaxy SF rates, and our method for calculating the local SFRD. We present a preliminary value of log(SFRD[ M {sub ⊙} yr{sup −1} Mpc{sup −3}]) = −1.747 ± 0.018 (random) ±0.05 (systematic) based on the 565 galaxies in our Fall sub-sample. Compared to the weighted average of SFRD values around z ≈ 2, our local value indicates a drop in the global SFRD of a factor of 10.2 over that lookback time.« less

Design of arbitrarily homogeneous permanent magnet systems for NMR and MRI: theory and experimental developments of a simple portable magnet.

PubMed

Hugon, Cedric; D'Amico, Francesca; Aubert, Guy; Sakellariou, Dimitris

2010-07-01

Starting from general results of magnetostatics, we give fundamental considerations on the design and characterization of permanent magnets for NMR based on harmonic analysis and symmetry. We then propose a simple geometry that takes advantage of some of these considerations and discuss the practical aspects of the assembly of a real magnet based on this geometry, involving the characterization of its elements, the optimization of the layout and the correction of residual inhomogeneities due to material and geometry imperfections. We report with this low-cost, light-weight magnet (100 euros and 1.8 kg including the aluminum frame) a field of 120 mT (5.1 MHz proton) with a 10 ppm natural homogeneity over a sphere of 1.5 mm in diameter. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Electron Microscopy Structural Insights into CPAP Oligomeric Behavior: A Plausible Assembly Process of a Supramolecular Scaffold of the Centrosome

PubMed Central

Alvarez-Cabrera, Ana L.; Delgado, Sandra; Gil-Carton, David; Mortuza, Gulnahar B.; Montoya, Guillermo; Sorzano, Carlos O. S.; Tang, Tang K.; Carazo, Jose M.

2017-01-01

Centrosomal P4.1-associated protein (CPAP) is a cell cycle regulated protein fundamental for centrosome assembly and centriole elongation. In humans, the region between residues 897–1338 of CPAP mediates interactions with other proteins and includes a homodimerization domain. CPAP mutations cause primary autosomal recessive microcephaly and Seckel syndrome. Despite of the biological/clinical relevance of CPAP, its mechanistic behavior remains unclear and its C-terminus (the G-box/TCP domain) is the only part whose structure has been solved. This situation is perhaps due in part to the challenges that represent obtaining the protein in a soluble, homogeneous state for structural studies. Our work constitutes a systematic structural analysis on multiple oligomers of HsCPAP897−1338, using single-particle electron microscopy (EM) of negatively stained (NS) samples. Based on image classification into clearly different regular 3D maps (putatively corresponding to dimers and tetramers) and direct observation of individual images representing other complexes of HsCPAP897−1338 (i.e., putative flexible monomers and higher-order multimers), we report a dynamic oligomeric behavior of this protein, where different homo-oligomers coexist in variable proportions. We propose that dimerization of the putative homodimer forms a putative tetramer which could be the structural unit for the scaffold that either tethers the pericentriolar material to centrioles or promotes procentriole elongation. A coarse fitting of atomic models into the NS 3D maps at resolutions around 20 Å is performed only to complement our experimental data, allowing us to hypothesize on the oligomeric composition of the different complexes. In this way, the current EM work represents an initial step toward the structural characterization of different oligomers of CPAP, suggesting further insights to understand how this protein works, contributing to the elucidation of control mechanisms for centriole biogenesis. PMID:28396859

Structural Determination of Biomolecules in Microfluidic Systems

NASA Astrophysics Data System (ADS)

Butler, John C.; Menard, Etienne; Rogers, John A.; Wong, Gerard C. L.

2004-03-01

Supramolecular biological complexes are often too large to be crystallized for structural studies. Here, we explore the use of microfluidic arrays to order a model self-assembled cytoskeletal system. Filamentous actin (F-actin) is a negatively charged protein rod and is a key structural component in the eukaryotic cytoskeleton. In this context, F-actin can self-assemble with actin binding proteins (ABP) in a highly regulated manner to dynamically form structures for a wide range of biomechanical functions. In this work, we will systematically study the action of 3 types of actin binding proteins (a-actinin, fimbrin, cofilin) on the self-assembled structures of F-actin that have been aligned in microfluidic arrays.

Charring Rate for Fire Exposed X-Lam

NASA Astrophysics Data System (ADS)

Wong, Bernice VY; Fah Tee, Kong

2017-06-01

Design of timber structures has been outlined in Eurocode 5. Notional charring rate for softwood and hardwood timber is given. For the performance of X-LAM panels in fire, only little information on charring is available and whether the fire behaviour of X-LAM is similar to homogenous timber panels has not yet been systematically analysed. This paper presents an overview of fire performance of X-LAM and evaluation of its resistance to elevated temperature as an element of structure in comparison to homogeneous timber panels. Numerical study has been carried out based on available experimental results. Charring rates for X-LAM panels obtained from experimental results are compared with those obtained from Eurocode 5 and proposed simplified model.

Phantom Preparation and Optical Property Determination

NASA Astrophysics Data System (ADS)

He, Di; He, Jie; Mao, Heng

2018-12-01

Tissue-like optical phantoms are important in testing new imaging algorithms. Homogeneous optical phantoms with determined optical properties are the first step of making a proper heterogeneous phantom for multi-modality imaging. Typical recipes for such phantoms consist of epoxy resin, hardener, India ink and titanium oxide. By altering the concentration of India ink and titanium oxide, we are able to get multiple homogeneous phantoms with different absorption and scattering coefficients by carefully mixing all the ingredients. After fabricating the phantoms, we need to find their individual optical properties including the absorption and scattering coefficients. This is achieved by solving diffusion equation of each phantom as a homogeneous slab under canonical illumination. We solve the diffusion equation of homogeneous slab in frequency domain and get the formula for theoretical measurements. Under our steady-state diffused optical tomography (DOT) imaging system, we are able to obtain the real distribution of the incident light produced by a laser. With this source distribution we got and the formula we derived, numerical experiments show how measurements change while varying the value of absorption and scattering coefficients. Then we notice that the measurements alone will not be enough for us to get unique optical properties for steady-state DOT problem. Thus in order to determine the optical properties of a homogeneous slab we want to fix one of the coefficients first and use optimization methods to find another one. Then by assemble multiple homogeneous slab phantoms with different optical properties, we are able to obtain a heterogeneous phantom suitable for testing multi-modality imaging algorithms. In this paper, we describe how to make phantoms, derive a formula to solve the diffusion equation, demonstrate the non-uniqueness of steady-state DOT problem by analysing some numerical results of our formula, and finally propose a possible way to determine optical properties for homogeneous slab for our future work.

Packaging signals in single-stranded RNA viruses: nature's alternative to a purely electrostatic assembly mechanism.

PubMed

Stockley, Peter G; Twarock, Reidun; Bakker, Saskia E; Barker, Amy M; Borodavka, Alexander; Dykeman, Eric; Ford, Robert J; Pearson, Arwen R; Phillips, Simon E V; Ranson, Neil A; Tuma, Roman

2013-03-01

The formation of a protective protein container is an essential step in the life-cycle of most viruses. In the case of single-stranded (ss)RNA viruses, this step occurs in parallel with genome packaging in a co-assembly process. Previously, it had been thought that this process can be explained entirely by electrostatics. Inspired by recent single-molecule fluorescence experiments that recapitulate the RNA packaging specificity seen in vivo for two model viruses, we present an alternative theory, which recognizes the important cooperative roles played by RNA-coat protein interactions, at sites we have termed packaging signals. The hypothesis is that multiple copies of packaging signals, repeated according to capsid symmetry, aid formation of the required capsid protein conformers at defined positions, resulting in significantly enhanced assembly efficiency. The precise mechanistic roles of packaging signal interactions may vary between viruses, as we have demonstrated for MS2 and STNV. We quantify the impact of packaging signals on capsid assembly efficiency using a dodecahedral model system, showing that heterogeneous affinity distributions of packaging signals for capsid protein out-compete those of homogeneous affinities. These insights pave the way to a new anti-viral therapy, reducing capsid assembly efficiency by targeting of the vital roles of the packaging signals, and opens up new avenues for the efficient construction of protein nanocontainers in bionanotechnology.

Voxel-wise meta-analyses of brain blood flow and local synchrony abnormalities in medication-free patients with major depressive disorder

PubMed Central

Chen, Zi-Qi; Du, Ming-Ying; Zhao, You-Jin; Huang, Xiao-Qi; Li, Jing; Lui, Su; Hu, Jun-Mei; Sun, Huai-Qiang; Liu, Jia; Kemp, Graham J.; Gong, Qi-Yong

2015-01-01

Background Published meta-analyses of resting-state regional cerebral blood flow (rCBF) studies of major depressive disorder (MDD) have included patients receiving antidepressants, which might affect brain activity and thus bias the results. To our knowledge, no meta-analysis has investigated regional homogeneity changes in medication-free patients with MDD. Moreover, an association between regional homogeneity and rCBF has been demonstrated in some brain regions in healthy controls. We sought to explore to what extent resting-state rCBF and regional homogeneity changes co-occur in the depressed brain without the potential confound of medication. Methods Using the effect-size signed differential mapping method, we conducted 2 meta-analyses of rCBF and regional homogeneity studies of medication-free patients with MDD. Results Our systematic search identified 14 rCBF studies and 9 regional homogeneity studies. We identified conjoint decreases in resting-state rCBF and regional homogeneity in the insula and superior temporal gyrus in medication-free patients with MDD compared with controls. Other changes included altered resting-state rCBF in the precuneus and in the frontal–limbic–thalamic–striatal neural circuit as well as altered regional homogeneity in the uncus and parahippocampal gyrus. Meta-regression revealed that the percentage of female patients with MDD was negatively associated with resting-state rCBF in the right anterior cingulate cortex and that the age of patients with MDD was negatively associated with rCBF in the left insula and with regional homogeneity in the left uncus. Limitations The analysis techniques, patient characteristics and clinical variables of the included studies were heterogeneous. Conclusion The conjoint alterations of rCBF and regional homogeneity in the insula and superior temporal gyrus may be core neuropathological changes in medication-free patients with MDD and serve as a specific region of interest for further studies on MDD. PMID:25853283

Voxel-wise meta-analyses of brain blood flow and local synchrony abnormalities in medication-free patients with major depressive disorder.

PubMed

Chen, Zi-Qi; Du, Ming-Ying; Zhao, You-Jin; Huang, Xiao-Qi; Li, Jing; Lui, Su; Hu, Jun-Mei; Sun, Huai-Qiang; Liu, Jia; Kemp, Graham J; Gong, Qi-Yong

2015-11-01

Published meta-analyses of resting-state regional cerebral blood flow (rCBF) studies of major depressive disorder (MDD) have included patients receiving antidepressants, which might affect brain activity and thus bias the results. To our knowledge, no meta-analysis has investigated regional homogeneity changes in medication-free patients with MDD. Moreover, an association between regional homogeneity and rCBF has been demonstrated in some brain regions in healthy controls. We sought to explore to what extent resting-state rCBF and regional homogeneity changes co-occur in the depressed brain without the potential confound of medication. Using the effect-size signed differential mapping method, we conducted 2 meta-analyses of rCBF and regional homogeneity studies of medication-free patients with MDD. Our systematic search identified 14 rCBF studies and 9 regional homogeneity studies. We identified conjoint decreases in resting-state rCBF and regional homogeneity in the insula and superior temporal gyrus in medication-free patients with MDD compared with controls. Other changes included altered resting-state rCBF in the precuneus and in the frontal-limbic-thalamic-striatal neural circuit as well as altered regional homogeneity in the uncus and parahippocampal gyrus. Meta-regression revealed that the percentage of female patients with MDD was negatively associated with resting-state rCBF in the right anterior cingulate cortex and that the age of patients with MDD was negatively associated with rCBF in the left insula and with regional homogeneity in the left uncus. The analysis techniques, patient characteristics and clinical variables of the included studies were heterogeneous. The conjoint alterations of rCBF and regional homogeneity in the insula and superior temporal gyrus may be core neuropathological changes in medication-free patients with MDD and serve as a specific region of interest for further studies on MDD.

A new view for nanoparticle assemblies: from crystalline to binary cooperative complementarity.

PubMed

Yan, Cong; Wang, Tie

2017-03-06

Studies on nanoparticle assemblies and their applications have been research frontiers in nanoscience in the past few decades and remarkable progress has been made in the synthetic strategies and techniques. Recently, the design and fabrication of the nanoparticle-based nanomaterials or nanodevices with integrated and enhanced properties compared to those of the individual components have gradually become the mainstream. However, a systematic solution to provide a big picture for future development and guide the investigation of different aspects of the study of nanoparticle assemblies remains a challenge. The binary cooperative complementary principle could be an answer. The binary cooperative complementary principle is a universal discipline and can describe the fundamental properties of matter from the subatomic particles to the universe. According to its definition, a variety of nanoparticle assemblies, which represent the cutting-edge work in the nanoparticle studies, are naturally binary cooperative complementary materials. Therefore, the introduction of the binary cooperative complementary principle in the studies of nanoparticle assemblies could provide a unique perspective for reviewing this field and help in the design and fabrication of novel functional nanoparticle assemblies.

Molecular self-assembly using peptide nucleic acids.

PubMed

Berger, Or; Gazit, Ehud

2017-01-01

Peptide nucleic acids (PNAs) are extensively studied for the control of genetic expression since their design in the 1990s. However, the application of PNAs in nanotechnology is much more recent. PNAs share the specific base-pair recognition characteristic of DNA together with material-like properties of polyamides, both proteins and synthetic polymers, such as Kevlar and Nylon. The first application of PNA was in the form of PNA-amphiphiles, resulting in the formation of either lipid integrated structures, hydrogels or fibrillary assemblies. Heteroduplex DNA-PNA assemblies allow the formation of hybrid structures with higher stability as compared with pure DNA. A systematic screen for minimal PNA building blocks resulted in the identification of guanine-containing di-PNA assemblies and protected guanine-PNA monomer spheres showing unique optical properties. Finally, the co-assembly of PNA with thymine-like three-faced cyanuric acid allowed the assembly of poly-adenine PNA into fibers. In summary, we believe that PNAs represent a new and important family of building blocks which converges the advantages of both DNA- and peptide-nanotechnologies. © 2016 Wiley Periodicals, Inc.

Building a Systematic Data Base for the Future. Commentary on: "Bullying, Romantic Rejection, and Conflicts with Teachers: The Crucial Role of Social Dynamics in the Development of School Shootings--A Systematic Review"

ERIC Educational Resources Information Center

Smith, Peter K.

2014-01-01

In this commentary, Peter Smith questions how well we follow up after school shootings in order to diagnose causes and enhance future prevention. Sommer, Leuschner, and Scheithauer (2014) have assembled data from 126 cases available in the English and German research literature and suggested important risk categories. Notably, there are a large…

Enhanced Bioactivity of α-Tocopheryl Succinate Based Block Copolymer Nanoparticles by Reduced Hydrophobicity.

PubMed

Palao-Suay, Raquel; Aguilar, María Rosa; Parra-Ruiz, Francisco J; Maji, Samarendra; Hoogenboom, Richard; Rohner, Nathan A; Thomas, Susan N; Román, Julio San

2016-12-01

Well-structured amphiphilic copolymers are necessary to obtain self-assembled nanoparticles (NPs) based on synthetic polymers. Highly homogeneous and monodispersed macromolecules obtained by controlled polymerization have successfully been used for this purpose. However, disaggregation of the organized macromolecules is desired when a bioactive element, such as α-tocopheryl succinate, is introduced in self-assembled NPs and this element must be exposed or released to exert its action. The aim of this work is to demonstrate that the bioactivity of synthetic NPs based on defined reversible addition-fragmentation chain transfer polymerization copolymers can be enhanced by the introduction of hydrophilic comonomers in the hydrophobic segment. The amphiphilic terpolymers are based on poly(ethylene glycol) (PEG) as hydrophilic block, and a hydrophobic block based on a methacrylic derivative of α-tocopheryl succinate (MTOS) and small amounts of 2-hydroxyethyl methacrylate (HEMA) (PEG-b-poly(MTOS-co-HEMA)). The introduction of HEMA reduces hydrophobicity and introduces "disorder" both in the homogeneous blocks and the compact core of the corresponding NPs. These NPs are able to encapsulate additional α-tocopheryl succinate (α-TOS) with high efficiency and their biological activity is much higher than that described for the unmodified copolymers, proposedly due to more efficient degradation and release of α-TOS, demonstrating the importance of the hydrophilic-hydrophobic balance. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly stable and finely tuned magnetic fields generated by permanent magnet assemblies.

PubMed

Danieli, E; Perlo, J; Blümich, B; Casanova, F

2013-05-03

Permanent magnetic materials are the only magnetic source that can be used to generate magnetic fields without power consumption or maintenance. Such stand-alone magnets are very attractive for many scientific and engineering areas, but they suffer from poor temporal field stability, which arises from the strong sensitivity of the magnetic materials and mechanical support to temperature variation. In this work, we describe a highly efficient method useful to cancel the temperature coefficient of permanent magnet assemblies in a passive and accurate way. It is based on the combination of at least two units made of magnetic materials with different temperature coefficients arranged in such a way that the ratio of the fields generated by each unit matches the ratio of their effective temperature coefficients defined by both the magnetic and mechanical contributions. Although typically available magnetic materials have negative temperature coefficients, the cancellation is achieved by aligning the fields generated by each unit in the opposite direction. We demonstrate the performance of this approach by stabilizing the field generated by a dipolar Halbach magnet, recently proposed to achieve high field homogeneity. Both the field drift and the homogeneity are monitored via nuclear magnetic resonance spectroscopy experiments. The results demonstrate the compatibility of the thermal compensation approach with existing strategies useful to fine-tune the spatial dependence of the field generated by permanent magnet arrays.

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

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

Torella, JP; Boehm, CR; Lienert, F

2013-12-28

In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminatormore » parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.« less

Consistent criticality and radiation studies of Swiss spent nuclear fuel: The CS2M approach.

PubMed

Rochman, D; Vasiliev, A; Ferroukhi, H; Pecchia, M

2018-06-15

In this paper, a new method is proposed to systematically calculate at the same time canister loading curves and radiation sources, based on the inventory information from an in-core fuel management system. As a demonstration, the isotopic contents of the assemblies come from a Swiss PWR, considering more than 6000 cases from 34 reactor cycles. The CS 2 M approach consists in combining four codes: CASMO and SIMULATE to extract the assembly characteristics (based on validated models), the SNF code for source emission and MCNP for criticality calculations for specific canister loadings. The considered cases cover enrichments from 1.9 to 5.0% for the UO 2 assemblies and 4.8% for the MOX, with assembly burnup values from 7 to 74 MWd/kgU. Because such a study is based on the individual fuel assembly history, it opens the possibility to optimize canister loadings from the point-of-view of criticality, decay heat and emission sources. Copyright © 2018 Elsevier B.V. All rights reserved.

Linking rapid magma reservoir assembly and eruption trigger mechanisms at evolved Yellowstone-type supervolcanoes

USGS Publications Warehouse

Wotzlaw, J.F.; Bindeman, I.N.; Watts, Kathryn E.; Schmitt, A.K.; Caricchi, L.; Schaltegger, U.

2014-01-01

The geological record contains evidence of volcanic eruptions that were as much as two orders of magnitude larger than the most voluminous eruption experienced by modern civilizations, the A.D. 1815 Tambora (Indonesia) eruption. Perhaps nowhere on Earth are deposits of such supereruptions more prominent than in the Snake River Plain–Yellowstone Plateau (SRP-YP) volcanic province (northwest United States). While magmatic activity at Yellowstone is still ongoing, the Heise volcanic field in eastern Idaho represents the youngest complete caldera cycle in the SRP-YP, and thus is particularly instructive for current and future volcanic activity at Yellowstone. The Heise caldera cycle culminated 4.5 Ma ago in the eruption of the ∼1800 km3 Kilgore Tuff. Accessory zircons in the Kilgore Tuff display significant intercrystalline and intracrystalline oxygen isotopic heterogeneity, and the vast majority are 18O depleted. This suggests that zircons crystallized from isotopically distinct magma batches that were generated by remelting of subcaldera silicic rocks previously altered by low-δ18O meteoric-hydrothermal fluids. Prior to eruption these magma batches were assembled and homogenized into a single voluminous reservoir. U-Pb geochronology of isotopically diverse zircons using chemical abrasion–isotope dilution–thermal ionization mass spectrometry yielded indistinguishable crystallization ages with a weighted mean 206Pb/238U date of 4.4876 ± 0.0023 Ma (MSWD = 1.5; n = 24). These zircon crystallization ages are also indistinguishable from the sanidine 40Ar/39Ar dates, and thus zircons crystallized close to eruption. This requires that shallow crustal melting, assembly of isolated batches into a supervolcanic magma reservoir, homogenization, and eruption occurred extremely rapidly, within the resolution of our geochronology (103–104 yr). The crystal-scale image of the reservoir configuration, with several isolated magma batches, is very similar to the reservoir configurations inferred from seismic data at active supervolcanoes. The connection of magma batches vertically distributed over several kilometers in the upper crust would cause a substantial increase of buoyancy overpressure, providing an eruption trigger mechanism that is the direct consequence of the reservoir assembly process.

NATpipe: an integrative pipeline for systematical discovery of natural antisense transcripts (NATs) and phase-distributed nat-siRNAs from de novo assembled transcriptomes

PubMed Central

Yu, Dongliang; Meng, Yijun; Zuo, Ziwei; Xue, Jie; Wang, Huizhong

2016-01-01

Nat-siRNAs (small interfering RNAs originated from natural antisense transcripts) are a class of functional small RNA (sRNA) species discovered in both plants and animals. These siRNAs are highly enriched within the annealed regions of the NAT (natural antisense transcript) pairs. To date, great research efforts have been taken for systematical identification of the NATs in various organisms. However, developing a freely available and easy-to-use program for NAT prediction is strongly demanded by researchers. Here, we proposed an integrative pipeline named NATpipe for systematical discovery of NATs from de novo assembled transcriptomes. By utilizing sRNA sequencing data, the pipeline also allowed users to search for phase-distributed nat-siRNAs within the perfectly annealed regions of the NAT pairs. Additionally, more reliable nat-siRNA loci could be identified based on degradome sequencing data. A case study on the non-model plant Dendrobium officinale was performed to illustrate the utility of NATpipe. Finally, we hope that NATpipe would be a useful tool for NAT prediction, nat-siRNA discovery, and related functional studies. NATpipe is available at www.bioinfolab.cn/NATpipe/NATpipe.zip. PMID:26858106

A double perturbation method of postbuckling analysis in 2D curved beams for assembly of 3D ribbon-shaped structures

NASA Astrophysics Data System (ADS)

Fan, Zhichao; Hwang, Keh-Chih; Rogers, John A.; Huang, Yonggang; Zhang, Yihui

2018-02-01

Mechanically-guided 3D assembly based on controlled, compressive buckling represents a promising, emerging approach for forming complex 3D mesostructures in advanced materials. Due to the versatile applicability to a broad set of material types (including device-grade single-crystal silicon) over length scales from nanometers to centimeters, a wide range of novel applications have been demonstrated in soft electronic systems, interactive bio-interfaces as well as tunable electromagnetic devices. Previously reported 3D designs relied mainly on finite element analyses (FEA) as a guide, but the massive numerical simulations and computational efforts necessary to obtain the assembly parameters for a targeted 3D geometry prevent rapid exploration of engineering options. A systematic understanding of the relationship between a 3D shape and the associated parameters for assembly requires the development of a general theory for the postbuckling process. In this paper, a double perturbation method is established for the postbuckling analyses of planar curved beams, of direct relevance to the assembly of ribbon-shaped 3D mesostructures. By introducing two perturbation parameters related to the initial configuration and the deformation, the highly nonlinear governing equations can be transformed into a series of solvable, linear equations that give analytic solutions to the displacements and curvatures during postbuckling. Systematic analyses of postbuckling in three representative ribbon shapes (sinusoidal, polynomial and arc configurations) illustrate the validity of theoretical method, through comparisons to the results of experiment and FEA. These results shed light on the relationship between the important deformation quantities (e.g., mode ratio and maximum strain) and the assembly parameters (e.g., initial configuration and the applied strain). This double perturbation method provides an attractive route to the inverse design of ribbon-shaped 3D geometries, as demonstrated in a class of helical mesostructures.

Two sides of the coin. Part 1. Lipid and surfactant self-assembly revisited.

PubMed

Ninham, Barry W; Larsson, Kåre; Lo Nostro, Pierandrea

2017-04-01

Hofmeister, specific ion effects, hydration and van der Waals forces at and between interfaces are factors that determine curvature and microstructure in self assembled aggregates of surfactants and lipids; and in microemulsions. Lipid and surfactant head group interactions and between aggregates vary enormously and are highly specific. They act on the hydrophilic side of a bilayer, micelle or other self assembled aggregate. It is only over the last three decades that the origin of Hofmeister effects has become generally understood. Knowledge of their systematics now provides much flexibility in designing nanostructured fluids. The other side of the coin involves equally specific forces. These (opposing) forces work on the hydrophobic side of amphiphilic interfaces. They are due to the interaction of hydrocarbons and other "oils" with hydrophobic tails of surfactants and lipids. The specificity of oleophilic solutes in microemulsions and lipid membranes provides a counterpoint to Hofmeister effects and hydration. Together with global packing constraints these effects determine microstructure. Another factor that has hardly been recognised is the role of dissolved gas. This introduces further, qualitative changes in forces that prescribe microstructure. The systematics of these effects and their interplay are elucidated. Awareness of these competing factors facilitates formulation of self assembled nanostructured fluids. New and predictable geometries that emerge naturally provide insights into a variety of biological phenomena like anaesthetic and pheromone action and transmission of the nervous impulse (see Part 2). Copyright © 2017 Elsevier B.V. All rights reserved.

pH-modulated self-assembly of colloidal nanoparticles in a dual-droplet inkjet printing process.

PubMed

Al-Milaji, Karam Nashwan; Radhakrishnan, Vinod; Kamerkar, Prajakta; Zhao, Hong

2018-06-05

Interfacial self-assembly has been demonstrated as a powerful driving mechanism for creating various nanostructured assemblies. In this work, we employed a dual-droplet printing process and interfacial self-assembly mechanism to produce deposits with controlled assembly structures of colloidal nanoparticles. We hypothesize that pH modulation of the droplet will influence the interfacial self-assembly through the multibody interactions, e.g. particle-particle, particle-interface, and particle-substrate interactions, correspondingly affecting the deposition morphology of the colloidal nanoparticles. During the dual-droplet printing, a wetting droplet, containing colloidal nanoparticles, was jetted over a supporting droplet that contains water only. pH modulation was carried out to the supporting droplet. The self-assembly of two kinds of functionalized polystyrene (PS) nanoparticles (carboxyl-PS and sulfate-PS) was systematically investigated under various pH conditions. Depending on the pH level of the supporting droplet, deposits of carboxyl-PS particles ranging from clear ring-like patterns to nearly uniform monolayer depositions have been obtained. On the other hand, the sulfate-PS particles, even at extreme basic and acidic environments, successfully assemble into nearly monolayer depositions. The multibody interactions are discussed. Such findings can be harnessed in manufacturing high-performance optical and electronic devices. Copyright © 2018 Elsevier Inc. All rights reserved.

Fat suppression in magnetic resonance imaging of the head and neck region: is the two-point DIXON technique superior to spectral fat suppression?

PubMed

Wendl, Christina M; Eiglsperger, Johannes; Dendl, Lena-Marie; Brodoefel, Harald; Schebesch, Karl-Michael; Stroszczynski, Christian; Fellner, Claudia

2018-05-01

The aim of our study was to systematically compare two-point Dixon fat suppression (FS) and spectral FS techniques in contrast enhanced imaging of the head and neck region. Three independent readers analysed coronal T 1 weighted images recorded after contrast medium injection with Dixon and spectral FS techniques with regard to FS homogeneity, motion artefacts, lesion contrast, image sharpness and overall image quality. 85 patients were prospectively enrolled in the study. Images generated with Dixon-FS technique were of higher overall image quality and had a more homogenous FS over the whole field of view compared with the standard spectral fat-suppressed images (p < 0.001). Concerning motion artefacts, flow artefacts, lesion contrast and image sharpness no statistically significant difference was observed. The Dixon-FS technique is superior to the spectral technique due to improved homogeneity of FS and overall image quality while maintaining lesion contrast. Advances in knowledge: T 1 with Dixon FS technique offers, compared to spectral FS, significantly improved FS homogeneity and over all image quality in imaging of the head and neck region.

Comparing de novo assemblers for 454 transcriptome data

PubMed Central

2010-01-01

Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible final product, and this strategy is recommended. PMID:20950480

Regulation of corneal stroma extracellular matrix assembly.

PubMed

Chen, Shoujun; Mienaltowski, Michael J; Birk, David E

2015-04-01

The transparent cornea is the major refractive element of the eye. A finely controlled assembly of the stromal extracellular matrix is critical to corneal function, as well as in establishing the appropriate mechanical stability required to maintain corneal shape and curvature. In the stroma, homogeneous, small diameter collagen fibrils, regularly packed with a highly ordered hierarchical organization, are essential for function. This review focuses on corneal stroma assembly and the regulation of collagen fibrillogenesis. Corneal collagen fibrillogenesis involves multiple molecules interacting in sequential steps, as well as interactions between keratocytes and stroma matrix components. The stroma has the highest collagen V:I ratio in the body. Collagen V regulates the nucleation of protofibril assembly, thus controlling the number of fibrils and assembly of smaller diameter fibrils in the stroma. The corneal stroma is also enriched in small leucine-rich proteoglycans (SLRPs) that cooperate in a temporal and spatial manner to regulate linear and lateral collagen fibril growth. In addition, the fibril-associated collagens (FACITs) such as collagen XII and collagen XIV have roles in the regulation of fibril packing and inter-lamellar interactions. A communicating keratocyte network contributes to the overall and long-range regulation of stromal extracellular matrix assembly, by creating micro-domains where the sequential steps in stromal matrix assembly are controlled. Keratocytes control the synthesis of extracellular matrix components, which interact with the keratocytes dynamically to coordinate the regulatory steps into a cohesive process. Mutations or deficiencies in stromal regulatory molecules result in altered interactions and deficiencies in both transparency and refraction, leading to corneal stroma pathobiology such as stromal dystrophies, cornea plana and keratoconus. Copyright © 2014 Elsevier Ltd. All rights reserved.

BAC sequencing using pooled methods.

PubMed

Saski, Christopher A; Feltus, F Alex; Parida, Laxmi; Haiminen, Niina

2015-01-01

Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.

Structural Integrity Evaluation of the Lear Fan 2100 Aircraft

NASA Technical Reports Server (NTRS)

Kan, H. P.; Dyer, T. A.

1996-01-01

An in-situ nondestructive inspection was conducted to detect manufacturing and assembly induced defects in the upper two wing surfaces (skin s) and upper fuselage skin of the Lear Fan 2100 aircraft E009. The effects of the defects, detected during the inspection, on the integrity of the structure was analytically evaluated. A systematic evaluation was also conducted to determine the damage tolerance capability of the upper wing skin against impact threats and assembly induced damage. The upper wing skin was divided into small regions for damage tolerance evaluations. Structural reliability, margin of safety, allowable strains, and allowable damage size were computed. The results indicated that the impact damage threat imposed on composite military aircraft structures is too severe for the Lear Fan 2100 upper wing skin. However, the structural integrity is not significantly degraded by the assembly induced damage for properly assembled structures, such as the E009 aircraft.

Soft-template mediated synthesis of GaOOH nanorod-shelled microspheres and thermal conversion to beta-Ga2O3.

PubMed

Wang, Jian; Li, Qi; Qiu, Xiaohui; He, Yujian; Liu, Wei

2010-07-01

Micrometer-scale hollow spheres self-assembled by GaOOH nanorods were synthesized under hydrothermal conditions using gallium nitrate and sodium hydroxide as starting materials. The structures and morphologies of the products were studied by X-ray diffraction and scanning electron microscopy. Time-dependent experiments revealed three stages involved in the process of reaction including the initial stage of formation of surfactant vesicles which can be considered as soft templates, followed by the nucleation of GaOOH nanoclusters, and the assembling and growth of nanorods under the modulation of the spherical vesicles. The growth kinetics of the GaOOH nanorods was systematically investigated. Based on the experimental observation, a template-mediated assembling mechanism was proposed. We further demonstrated that the GaOOH nanorods could be converted to gallium oxide (beta-Ga2O3) nanorods by calcination without changing the spherical morphology of the assemblies.

Classification of self-assembling protein nanoparticle architectures for applications in vaccine design

NASA Astrophysics Data System (ADS)

Indelicato, G.; Burkhard, P.; Twarock, R.

2017-04-01

We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response.

Elucidating dominant pathways of the nano-particle self-assembly process.

PubMed

Zeng, Xiangze; Li, Bin; Qiao, Qin; Zhu, Lizhe; Lu, Zhong-Yuan; Huang, Xuhui

2016-09-14

Self-assembly processes play a key role in the fabrication of functional nano-structures with widespread application in drug delivery and micro-reactors. In addition to the thermodynamics, the kinetics of the self-assembled nano-structures also play an important role in determining the formed structures. However, as the self-assembly process is often highly heterogeneous, systematic elucidation of the dominant kinetic pathways of self-assembly is challenging. Here, based on mass flow, we developed a new method for the construction of kinetic network models and applied it to identify the dominant kinetic pathways for the self-assembly of star-like block copolymers. We found that the dominant pathways are controlled by two competing kinetic parameters: the encounter time Te, characterizing the frequency of collision and the transition time Tt for the aggregate morphology change from rod to sphere. Interestingly, two distinct self-assembly mechanisms, diffusion of an individual copolymer into the aggregate core and membrane closure, both appear at different stages (with different values of Tt) of a single self-assembly process. In particular, the diffusion mechanism dominates the middle-sized semi-vesicle formation stage (with large Tt), while the membrane closure mechanism dominates the large-sized vesicle formation stage (with small Tt). Through the rational design of the hydrophibicity of the copolymer, we successfully tuned the transition time Tt and altered the dominant self-assembly pathways.

DECHADE: DEtecting slight Changes with HArd DEcisions in Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Ciuonzo, D.; Salvo Rossi, P.

2018-07-01

This paper focuses on the problem of change detection through a Wireless Sensor Network (WSN) whose nodes report only binary decisions (on the presence/absence of a certain event to be monitored), due to bandwidth/energy constraints. The resulting problem can be modelled as testing the equality of samples drawn from independent Bernoulli probability mass functions, when the bit probabilities under both hypotheses are not known. Both One-Sided (OS) and Two-Sided (TS) tests are considered, with reference to: (i) identical bit probability (a homogeneous scenario), (ii) different per-sensor bit probabilities (a non-homogeneous scenario) and (iii) regions with identical bit probability (a block-homogeneous scenario) for the observed samples. The goal is to provide a systematic framework collecting a plethora of viable detectors (designed via theoretically founded criteria) which can be used for each instance of the problem. Finally, verification of the derived detectors in two relevant WSN-related problems is provided to show the appeal of the proposed framework.

Systematic analysis of EOS data system for operations

NASA Technical Reports Server (NTRS)

Moe, K. L.; Dasgupta, R.

1985-01-01

A data management analysis methodology is being proposed. The objective of the methodology is to assist mission managers by identifying a series of ordered activities to be systematically followed in order to arrive at an effective ground system design. Existing system engineering tools and concepts have been assembled into a structured framework to facilitate the work of a mission planner. It is intended that this methodology can be gainfully applied (with probable modifications and/or changes) to the EOS payloads and their associated data systems.

Assembling photoluminescent tri(8-quinolinolato)aluminum into periodic mesoporous organosilicas.

PubMed

Yang, Ying; Zhang, Xin; Kan, Qiubin

2013-12-01

Mesostructured and mesoporous materials are emerging as a new class of optical materials. However, their synthesis is nontrivial. In this work, periodic mesostructured metal complex-containing silicas of MCM- and SBA-type bearing homogeneously distributed photoluminescent tri(8-quinolinolato)aluminum inside the channel walls (denoted as Alq3@PMO-MCM and Alq3@PMO-SBA, respectively) have been achieved via one-pot co-assembling of inorganic/surfactant/optically active species. A comprehensive multianalytical characterization of the structural and optical properties demonstrates that both Alq3@PMO-MCM and Alq3@PMO-SBA series gainfully combine the photoluminescent properties of Alq3 with the porous features of PMOs. Regularly arranged pores provide high surface area to disperse optically active components well and render Alq3-containing PMOs promising materials for optoelectronic applications. Copyright © 2013. Published by Elsevier Inc.

RAFT-Polymerization-Induced Self-Assembly and Reorganizations: Ultrahigh-Molecular-Weight Polymer and Morphology-Tunable Micro-/Nanoparticles in One Pot.

PubMed

Zhang, Xiao-Yun; Liu, Dong-Ming; Lv, Xin-Hu; Sun, Miao; Sun, Xiao-Li; Wan, Wen-Ming

2016-11-01

A one-pot method is introduced for the successful synthesis of narrow-distributed (Đ = 1.22) vinyl polymer with both ultrahigh molecular weight (UHMW) (M w = 1.31 × 10 6 g mol -1 ) and micro-/nanomorphology under mild conditions. The method involves the following four stages: homogeneous polymerization, polymerization-induced self-assembly (PISA), PISA and reorganization, and PISA and multiple reorganizations. The key points to the production of UHMW polystyrene are to minimize radical termination by segregating radicals in different nanoreactors and to ensure sufficient chain propagation by promoting further reorganizations of these reactors in situ. This method therefore endows polymeric materials with the outstanding properties of both UHMW and tunable micro-/nanoparticles under mild conditions in one pot. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Convergent solid-phase synthesis of hirudin.

PubMed

Goulas, Spyros; Gatos, Dimitrios; Barlos, Kleomenis

2006-02-01

Hirudin variant 1 (HV1), a small protein consisting of 65 amino acids and three disulfide bonds, was synthesized by using Fmoc-based convergent methods on 2-chlorotrityl resin (CLTR). The linear sequence was assembled by the sequential condensation of 7 protected fragments, on the resin-bound 55-65 fragment. The conditions of fragment assembly were carefully studied to determine the most efficient synthetic protocol. Crude reduced [Cys(16, 28)(Acm)]-HV1 thus obtained was easily purified to homogeneity by RP-HPLC. Disulfide bridges were successfully formed by a two-step procedure, involving an oxidative folding step to form Cys(6)-Cys(14) and Cys(22)-Cys(39) linkages, followed by iodine oxidation to form the Cys(16)-Cys(28) bond. The correct disulfide bond alignment was established by peptide mapping using Staphylococcus aureus V8 protease at pH 4.5.

Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein

PubMed Central

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-01-01

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson’s disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young’s modulus). PMID:27901068

Canine Parvovirus VP2 Protein Expressed in Silkworm Pupae Self-Assembles into Virus-Like Particles with High Immunogenicity

PubMed Central

Wang, Hua-lei; Liang, Meng; Liang, Hongru; Guo, He; Zhao, Pingsen; Yang, Yu-jiao; Zheng, Xue-xing; Zhang, Zhi-fang; Zhao, Yong-kun; Gao, Yu-wei; Yang, Song-tao; Xia, Xian-zhu

2014-01-01

The VP2 structural protein of parvovirus can produce virus-like particles (VLPs) by a self-assembly process in vitro, making VLPs attractive vaccine candidates. In this study, the VP2 protein of canine parvovirus (CPV) was expressed using a baculovirus expression system and assembled into parvovirus-like particles in insect cells and pupae. Electron micrographs of VLPs showed that they were very similar in size and morphology when compared to the wild-type parvovirus. The immunogenicity of the VLPs was investigated in mice and dogs. Mice immunized intramuscularly with purified VLPs, in the absence of an adjuvant, elicited CD4+ and CD8+ T cell responses and were able to elicit a neutralizing antibody response against CPV, while the oral administration of raw homogenates containing VLPs to the dogs resulted in a systemic immune response and long-lasting immunity. These results demonstrate that the CPV-VLPs stimulate both cellular and humoral immune responses, and so CPV-VLPs may be a promising candidate vaccine for the prevention of CPV-associated disease. PMID:24465364

Canine parvovirus VP2 protein expressed in silkworm pupae self-assembles into virus-like particles with high immunogenicity.

PubMed

Feng, Hao; Hu, Gui-qiu; Wang, Hua-lei; Liang, Meng; Liang, Hongru; Guo, He; Zhao, Pingsen; Yang, Yu-jiao; Zheng, Xue-xing; Zhang, Zhi-fang; Zhao, Yong-kun; Gao, Yu-wei; Yang, Song-tao; Xia, Xian-zhu

2014-01-01

The VP2 structural protein of parvovirus can produce virus-like particles (VLPs) by a self-assembly process in vitro, making VLPs attractive vaccine candidates. In this study, the VP2 protein of canine parvovirus (CPV) was expressed using a baculovirus expression system and assembled into parvovirus-like particles in insect cells and pupae. Electron micrographs of VLPs showed that they were very similar in size and morphology when compared to the wild-type parvovirus. The immunogenicity of the VLPs was investigated in mice and dogs. Mice immunized intramuscularly with purified VLPs, in the absence of an adjuvant, elicited CD4(+) and CD8(+) T cell responses and were able to elicit a neutralizing antibody response against CPV, while the oral administration of raw homogenates containing VLPs to the dogs resulted in a systemic immune response and long-lasting immunity. These results demonstrate that the CPV-VLPs stimulate both cellular and humoral immune responses, and so CPV-VLPs may be a promising candidate vaccine for the prevention of CPV-associated disease.

Iron-based ferritin nanocore as a contrast agent.

PubMed

Sana, Barindra; Johnson, Eric; Sheah, Kenneth; Poh, Chueh Loo; Lim, Sierin

2010-09-01

Self-assembling protein cages have been exploited as templates for nanoparticle synthesis. The ferritin molecule, a protein cage present in most living systems, stores excess soluble ferrous iron in the form of an insoluble ferric complex within its cavity. Magnetic nanocores formed by loading excess iron within an engineered ferritin from Archaeoglobus fulgidus (AfFtn-AA) were studied as a potential magnetic resonance (MR) imaging contrast agent. The self-assembly characteristics of the AfFtn-AA were investigated using dynamic light scattering technique and size exclusion chromatography. Homogeneous size distribution of the assembled nanoparticles was observed using transmission electron microscopy. The magnetic properties of iron-loaded AfFtn-AA were studied using vibrating sample magnetometry. Images obtained from a 3.0 T whole-body MRI scanner showed significant brightening of T(1) images and signal loss of T(2) images with increased concentrations of iron-loaded AfFtn-AA. The analysis of the MR image intensities showed extremely high R(2) values (5300 mM(-1) s(-1)) for the iron-loaded AfFtn-AA confirming its potential as a T(2) contrast agent.

Self-assembly of colloids with magnetic caps

NASA Astrophysics Data System (ADS)

Novak, E. V.; Kantorovich, S. S.

2017-06-01

In our earlier work (Steinbach et al., 2016 [1]) we investigated a homogeneous system of magnetically capped colloidal particles that self-assembled via two structural patterns of different symmetry. The particles could form a compact, equilateral triangle with a three-fold rotational symmetry and zero dipole moment and a staggered chain with mirror symmetry with a net magnetisation perpendicular to the chain. The system exhibited a bistability already in clusters of three particles. Based on observations of a real magnetic particles system, analytical calculations and molecular dynamics simulations, it has been shown that the bistability is a result of an anisotropic magnetisation distribution with rotational symmetry inside the particles. The present study is a logical extension of the above research and forms a preparatory stage for the study of a self-assembly of such magnetic particles under the influence of an external magnetic field. Since the magnetic field is only an additive contribution to the total ground state energy, we can study the interparticle interaction energies of candidate ground state structures based on the field-free terms.

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

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

Graham, Emily B.; Stegen, James C.

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

DOE PAGES

Graham, Emily B.; Stegen, James C.

2017-11-01

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Investigating the thermal dissociation of viral capsid by lattice model

NASA Astrophysics Data System (ADS)

Chen, Jingzhi; Chevreuil, Maelenn; Combet, Sophie; Lansac, Yves; Tresset, Guillaume

2017-11-01

The dissociation of icosahedral viral capsids was investigated by a homogeneous and a heterogeneous lattice model. In thermal dissociation experiments with cowpea chlorotic mottle virus and probed by small-angle neutron scattering, we observed a slight shrinkage of viral capsids, which can be related to the strengthening of the hydrophobic interaction between subunits at increasing temperature. By considering the temperature dependence of hydrophobic interaction in the homogeneous lattice model, we were able to give a better estimate of the effective charge. In the heterogeneous lattice model, two sets of lattice sites represented different capsid subunits with asymmetric interaction strengths. In that case, the dissociation of capsids was found to shift from a sharp one-step transition to a gradual two-step transition by weakening the hydrophobic interaction between AB and CC subunits. We anticipate that such lattice models will shed further light on the statistical mechanics underlying virus assembly and disassembly.

Coating and Patterning Functional Materials for Large Area Electrofluidic Arrays

PubMed Central

Wu, Hao; Tang, Biao; Hayes, Robert A.; Dou, Yingying; Guo, Yuanyuan; Jiang, Hongwei; Zhou, Guofu

2016-01-01

Industrialization of electrofluidic devices requires both high performance coating laminates and efficient material utilization on large area substrates. Here we show that screen printing can be effectively used to provide homogeneous pin-hole free patterned amorphous fluoropolymer dielectric layers to provide both the insulating and fluidic reversibility required for devices. Subsequently, we over-coat photoresist using slit coating on this normally extremely hydrophobic layer. In this way, we are able to pattern the photoresist by conventional lithography to provide the chemical contrast required for liquids dosing by self-assembly and highly-reversible electrofluidic switching. Materials, interfacial chemistry, and processing all contribute to the provision of the required engineered substrate properties. Coating homogeneity as characterized by metrology and device performance data are used to validate the methodology, which is well-suited for transfer to high volume production in existing LCD cell-making facilities. PMID:28773826

Coating and Patterning Functional Materials for Large Area Electrofluidic Arrays.

PubMed

Wu, Hao; Tang, Biao; Hayes, Robert A; Dou, Yingying; Guo, Yuanyuan; Jiang, Hongwei; Zhou, Guofu

2016-08-19

Industrialization of electrofluidic devices requires both high performance coating laminates and efficient material utilization on large area substrates. Here we show that screen printing can be effectively used to provide homogeneous pin-hole free patterned amorphous fluoropolymer dielectric layers to provide both the insulating and fluidic reversibility required for devices. Subsequently, we over-coat photoresist using slit coating on this normally extremely hydrophobic layer. In this way, we are able to pattern the photoresist by conventional lithography to provide the chemical contrast required for liquids dosing by self-assembly and highly-reversible electrofluidic switching. Materials, interfacial chemistry, and processing all contribute to the provision of the required engineered substrate properties. Coating homogeneity as characterized by metrology and device performance data are used to validate the methodology, which is well-suited for transfer to high volume production in existing LCD cell-making facilities.

Solvothermal-induced self-assembly of Fe2O3/GS aerogels for high Li-storage and excellent stability.

PubMed

Wang, Ronghua; Xu, Chaohe; Du, Meng; Sun, Jing; Gao, Lian; Zhang, Peng; Yao, Heliang; Lin, Chucheng

2014-06-12

A novel solvothermal-induced self-assembly approach, using colloid sol as precursor, is developed to construct monolithic 3D metal oxide/GS (graphene sheets) aerogels. During the solvothermal process, graphene oxide (GO) is highly reduced to GS and self-assembles into 3D macroscopic hydrogels, accompanying with in situ transformation of colloid sol to metal oxides. As a proof of concept, Fe2 O3 /GS aerogels are synthesized based on Fe(OH)3 sol, in which GS self-assemble into an interconnected macroporous framework and Fe2 O3 nanocrystals (20-50 nm) uniformly deposit on GS. Benefitting from the integration of macroporous structures, large surface area, high electrical conductivity, and good electrode homogeneity, the hybrid electrode manifests a superior rate capability (930, 660 and 520 mAh g(-1) at 500, 2000 and 4000 mA g(-1), respectively) and excellent prolonged cycling stability at high rates (733 mAh g(-1) during 1000 charge/discharge cycles at 2000 mA g(-1)), demonstrating its great potential for application in high performance lithium ion batteries. The work described here provides a versatile pathway to construct various graphene-based hybrid aerogels. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments

PubMed Central

Berg, Maureen; Stenuit, Ben; Ho, Joshua; Wang, Andrew; Parke, Caitlin; Knight, Matthew; Alvarez-Cohen, Lisa; Shapira, Michael

2016-01-01

It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota. PMID:26800234

Assembly of tissue engineered blood vessels with spatially-controlled heterogeneities.

PubMed

Strobel, Hannah A; Hookway, Tracy; Piola, Marco; Fiore, Gianfranco Beniamino; Soncini, Monica; Alsberg, Eben; Rolle, Marsha

2018-05-04

Tissue-engineered human blood vessels may enable in vitro disease modeling and drug screening to accelerate advances in vascular medicine. Existing methods for tissue engineered blood vessel (TEBV) fabrication create homogenous tubes not conducive to modeling the focal pathologies characteristic of vascular disease. We developed a system for generating self-assembled human smooth muscle cell ring-units, which were fused together into TEBVs. The goal of this study was to assess the feasibility of modular assembly and fusion of ring building units to fabricate spatially-controlled, heterogeneous tissue tubes. We first aimed to enhance fusion and reduce total culture time, and determined that reducing ring pre-culture duration improved tube fusion. Next, we incorporated electrospun polymer ring units onto tube ends as reinforced extensions, which allowed us to cannulate tubes after only 7 days of fusion, and culture tubes with luminal flow in a custom bioreactor. To create focal heterogeneities, we incorporated gelatin microspheres into select ring units during self-assembly, and fused these rings between ring units without microspheres. Cells within rings maintained their spatial position within tissue tubes after fusion. This work describes a platform approach for creating modular TEBVs with spatially-defined structural heterogeneities, which may ultimately be applied to mimic focal diseases such as intimal hyperplasia or aneurysm.

Benchmarking of calculation schemes in APOLLO2 and COBAYA3 for WER lattices

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

Zheleva, N.; Ivanov, P.; Todorova, G.

This paper presents solutions of the NURISP WER lattice benchmark using APOLLO2, TRIPOLI4 and COBAYA3 pin-by-pin. The main objective is to validate MOC based calculation schemes for pin-by-pin cross-section generation with APOLLO2 against TRIPOLI4 reference results. A specific objective is to test the APOLLO2 generated cross-sections and interface discontinuity factors in COBAYA3 pin-by-pin calculations with unstructured mesh. The VVER-1000 core consists of large hexagonal assemblies with 2 mm inter-assembly water gaps which require the use of unstructured meshes in the pin-by-pin core simulators. The considered 2D benchmark problems include 19-pin clusters, fuel assemblies and 7-assembly clusters. APOLLO2 calculation schemes withmore » the step characteristic method (MOC) and the higher-order Linear Surface MOC have been tested. The comparison of APOLLO2 vs. TRIPOLI4 results shows a very close agreement. The 3D lattice solver in COBAYA3 uses transport corrected multi-group diffusion approximation with interface discontinuity factors of Generalized Equivalence Theory (GET) or Black Box Homogenization (BBH) type. The COBAYA3 pin-by-pin results in 2, 4 and 8 energy groups are close to the reference solutions when using side-dependent interface discontinuity factors. (authors)« less

Electrostatic Self-Assembly of Sandwich-Like CoAl-LDH/Polypyrrole/Graphene Nanocomposites with Enhanced Capacitive Performance.

PubMed

Zhang, Yu; Du, Dongfeng; Li, Xuejin; Sun, Hongman; Li, Li; Bai, Peng; Xing, Wei; Xue, Qingzhong; Yan, Zifeng

2017-09-20

A novel sandwich-like composite with ultrathin CoAl-layered double hydroxide (LDH) nanoplates electrostatically assembled on both sides of two-dimensional polypyrrole/graphene (PG) substrate has been successfully fabricated using facile hydrothermal techniques. The PG not only serves as an excellent conductive and structural scaffold to enhance the transmission of electrons and prevent aggregation of CoAl-LDH nanoplates but also contributes to the enhancement of the specific capacitance. Owing to the homogeneous dispersion of CoAl-LDH nanoplates and its intimate interaction with PG substrate, the resulting CoAl-LDH/PG nanocomposite material exhibits excellent capacitive performance, for example, enhanced gravimetric specific capacitance (864 F g -1 at 1 A g -1 ), high rate performance (75% retention at 20 A g -1 ), and excellent cycle life (almost no degradation in supercapacitor performance after 5000 cycles) in aqueous KOH solution. Furthermore, the assembled asymmetric capacitor is able to deliver a superhigh energy density of 46.8 Wh kg -1 at 1.2 kW kg -1 and maintain 90.1% of its initial capacitance after 10 000 cycles. These results indicate a rational assembly strategy toward a high-performance pseudocapacitive electrode material with excellent rate performance, high specific capacitance, and outstanding cycle stability.

Optimizing homogenization by chaotic unmixing?

NASA Astrophysics Data System (ADS)

Weijs, Joost; Bartolo, Denis

2016-11-01

A number of industrial processes rely on the homogeneous dispersion of non-brownian particles in a viscous fluid. An ideal mixing would yield a so-called hyperuniform particle distribution. Such configurations are characterized by density fluctuations that grow slower than the standard √{ N}-fluctuations. Even though such distributions have been found in several natural structures, e.g. retina receptors in birds, they have remained out of experimental reach until very recently. Over the last 5 years independent experiments and numerical simulations have shown that periodically driven suspensions can self-assemble hyperuniformally. Simple as the recipe may be, it has one important disadvantage. The emergence of hyperuniform states co-occurs with a critical phase transition from reversible to non reversible particle dynamics. As a consequence the homogenization dynamics occurs over a time that diverges with the system size (critical slowing down). Here, we discuss how this process can be sped up by exploiting the stirring properties of chaotic advection. Among the questions that we answer are: What are the physical mechanisms in a chaotic flow that are relevant for hyperuniformity? How can we tune the flow parameters such to obtain optimal hyperuniformity in the fastest way? JW acknowledges funding by NWO (Netherlands Organisation for Scientific Research) through a Rubicon Grant.

Advanced optical system for scanning-spot photorefractive keratectomy (PRK)

NASA Astrophysics Data System (ADS)

Mrochen, Michael; Wullner, Christian; Semchishen, Vladimir A.; Seiler, Theo

1999-06-01

Purpose: The goal of this presentation is to discuss the use of the Light Shaping Beam Homogenizer in an optical system for scanning-spot PRK. Methods: The basic principle of the LSBH is the transformation of any incident intensity distribution by light scattering on an irregular microlens structure z = f(x,y). The relief of this microlens structure is determined by a defined statistical function, i.e. it is defined by the mean root-squared tilt σ of the surface relief. Therefore, the beam evolution after the LSBH and in the focal plane of an imaging lens was measured for various root-squared tilts. Beside this, an optical setup for scanning-spot PRK was assembled according to the theoretical and experimental results. Results: The divergence, homogeneity and the Gaussian radius of the intensity distribution in the treatment plane of the scanning-spot PRK laser system is mainly characterized by dependent on root-mean-square tilt σ of the LSBH, as it will be explained by the theoretical description of the LSBH. Conclusions: The LSBH represents a simple, low cost beam homogenizer with low energy losses, for scanning-spot excimer laser systems.

Optimal lattice-structured materials

DOE PAGES

Messner, Mark C.

2016-07-09

This paper describes a method for optimizing the mesostructure of lattice-structured materials. These materials are periodic arrays of slender members resembling efficient, lightweight macroscale structures like bridges and frame buildings. Current additive manufacturing technologies can assemble lattice structures with length scales ranging from nanometers to millimeters. Previous work demonstrates that lattice materials have excellent stiffness- and strength-to-weight scaling, outperforming natural materials. However, there are currently no methods for producing optimal mesostructures that consider the full space of possible 3D lattice topologies. The inverse homogenization approach for optimizing the periodic structure of lattice materials requires a parameterized, homogenized material model describingmore » the response of an arbitrary structure. This work develops such a model, starting with a method for describing the long-wavelength, macroscale deformation of an arbitrary lattice. The work combines the homogenized model with a parameterized description of the total design space to generate a parameterized model. Finally, the work describes an optimization method capable of producing optimal mesostructures. Several examples demonstrate the optimization method. One of these examples produces an elastically isotropic, maximally stiff structure, here called the isotruss, that arguably outperforms the anisotropic octet truss topology.« less

High Current Ionic Diode Using Homogeneously Charged Asymmetric Nanochannel Network Membrane.

PubMed

Choi, Eunpyo; Wang, Cong; Chang, Gyu Tae; Park, Jungyul

2016-04-13

A high current ionic diode is achieved using an asymmetric nanochannel network membrane (NCNM) constructed by soft lithography and in situ self-assembly of nanoparticles with uniform surface charge. The asymmetric NCNM exhibits high rectified currents without losing a rectification ratio because of its ionic selectivity gradient and differentiated electrical conductance. Asymmetric ionic transport is analyzed with diode-like I-V curves and visualized via fluorescent dyes, which is closely correlated with ionic selectivity and ion distribution according to variation of NCNM geometries.

Use of protein cages as a template for confined synthesis of inorganic and organic nanoparticles.

PubMed

Uchida, Masaki; Qazi, Shefah; Edwards, Ethan; Douglas, Trevor

2015-01-01

Protein cages are hollow spherical proteins assembled from a defined number of subunits. Because they are extremely homogeneous in size and structure, their interior cavities can serve as ideal templates to encapsulate and synthesize well-defined nanoparticles. Here, we describe the exemplary synthesis of a hard and a soft material in two representative protein cages, i.e., magnetite nanoparticles in ferritin and a poly(2-aminoethyl)methacrylate inside a viral capsid derived from the bacteriophage P22.

Curie temperatures of titanomagnetite in ignimbrites: Effects of emplacement temperatures, cooling rates, exsolution, and cation ordering

NASA Astrophysics Data System (ADS)

Jackson, Mike; Bowles, Julie A.

2014-11-01

Pumices, ashes, and tuffs from Mt. St. Helens and from Novarupta contain two principal forms of titanomagnetite: homogeneous grains with Curie temperatures in the range 350-500°C and oxyexsolved grains with similar bulk composition, containing ilmenite lamellae and having Curie temperatures above 500°C. Thermomagnetic analyses and isothermal annealing experiments in combination with stratigraphic settings and thermal models show that emplacement temperatures and cooling history may have affected the relative proportions of homogeneous and exsolved grains and have clearly had a strong influence on the Curie temperature of the homogeneous phase. The exsolved grains are most common where emplacement temperatures exceeded 600°C, and in laboratory experiments, heating to over 600°C in air causes the homogeneous titanomagnetites to oxyexsolve rapidly. Where emplacement temperatures were lower, Curie temperatures of the homogeneous grains are systematically related to overburden thickness and cooling timescales, and thermomagnetic curves are generally irreversible, with lower Curie temperatures measured during cooling, but little or no change is observed in room temperature susceptibility. We interpret this irreversible behavior as reflecting variations in the degree of cation ordering in the titanomagnetites, although we cannot conclusively rule out an alternative interpretation involving fine-scale subsolvus unmixing. Short-range ordering within the octahedral sites may play a key role in the observed phenomena. Changes in the Curie temperature have important implications for the acquisition, stabilization, and retention of natural remanence and may in some cases enable quantification of the emplacement temperatures or cooling rates of volcanic units containing homogeneous titanomagnetites.

Finding order in heterogeneity: types of quality-improvement intervention publications.

PubMed

Rubenstein, L V; Hempel, S; Farmer, M M; Asch, S M; Yano, E M; Dougherty, D; Shekelle, P W

2008-12-01

Stakeholders in quality improvement agree on the need for augmenting and synthesising the scientific literature supporting it. The diversity of perspectives, approaches, and contexts critical to advancing quality improvement science, however, creates challenges. The paper explores the heterogeneity in clinical quality improvement intervention (QII) publications. A preliminary classification framework was developed for QII articles, aiming for categories homogeneous enough to support coherent scientific discussion on QII reporting standards and facilitate systematic review. QII experts were asked to identify articles important to QII science. The framework was tested and revised by applying it to the article set. The final framework screened articles into (1) empirical literature on development and testing of QIIs; (2) QII stories, theories, and frameworks; (3) QII literature syntheses and meta-analyses; or (4) development and testing of QII-related tools. To achieve homogeneity, category (1) required division into (1a) development of QIIs; 1(b) history, documentation, or description of QIIs; or (1c) success, effectiveness or impact of QIIs. By discussing unique issues and established standards relevant to each category, QII stakeholders can advance QII practice and science, including the scope and conduct of systematic literature reviews.

A modified homogeneous relaxation model for CO2 two-phase flow in vapour ejector

NASA Astrophysics Data System (ADS)

Haida, M.; Palacz, M.; Smolka, J.; Nowak, A. J.; Hafner, A.; Banasiak, K.

2016-09-01

In this study, the homogenous relaxation model (HRM) for CO2 flow in a two-phase ejector was modified in order to increase the accuracy of the numerical simulations The two- phase flow model was implemented on the effective computational tool called ejectorPL for fully automated and systematic computations of various ejector shapes and operating conditions. The modification of the HRM was performed by a change of the relaxation time and the constants included in the relaxation time equation based on the experimental result under the operating conditions typical for the supermarket refrigeration system. The modified HRM was compared to the HEM results, which were performed based on the comparison of motive nozzle and suction nozzle mass flow rates.

TMV nanorods with programmed longitudinal domains of differently addressable coat proteins

NASA Astrophysics Data System (ADS)

Geiger, Fania C.; Eber, Fabian J.; Eiben, Sabine; Mueller, Anna; Jeske, Holger; Spatz, Joachim P.; Wege, Christina

2013-04-01

The spacing of functional nanoscopic elements may play a fundamental role in nanotechnological and biomedical applications, but is so far rarely achieved on this scale. In this study we show that tobacco mosaic virus (TMV) and the RNA-guided self-assembly process of its coat protein (CP) can be used to establish new nanorod scaffolds that can be loaded not only with homogeneously distributed functionalities, but with distinct molecule species grouped and ordered along the longitudinal axis. The arrangement of the resulting domains and final carrier rod length both were governed by RNA-templated two-step in vitro assembly. Two selectively addressable TMV CP mutants carrying either thiol (TMVCys) or amino (TMVLys) groups on the exposed surface were engineered and shown to retain reactivity towards maleimides or NHS esters, respectively, after acetic acid-based purification and re-assembly to novel carrier rod types. Stepwise combination of CPCys and CPLys with RNA allowed fabrication of TMV-like nanorods with a controlled total length of 300 or 330 nm, respectively, consisting of adjacent longitudinal 100-to-200 nm domains of differently addressable CP species. This technology paves the way towards rod-shaped scaffolds with pre-defined, selectively reactive barcode patterns on the nanometer scale.The spacing of functional nanoscopic elements may play a fundamental role in nanotechnological and biomedical applications, but is so far rarely achieved on this scale. In this study we show that tobacco mosaic virus (TMV) and the RNA-guided self-assembly process of its coat protein (CP) can be used to establish new nanorod scaffolds that can be loaded not only with homogeneously distributed functionalities, but with distinct molecule species grouped and ordered along the longitudinal axis. The arrangement of the resulting domains and final carrier rod length both were governed by RNA-templated two-step in vitro assembly. Two selectively addressable TMV CP mutants carrying either thiol (TMVCys) or amino (TMVLys) groups on the exposed surface were engineered and shown to retain reactivity towards maleimides or NHS esters, respectively, after acetic acid-based purification and re-assembly to novel carrier rod types. Stepwise combination of CPCys and CPLys with RNA allowed fabrication of TMV-like nanorods with a controlled total length of 300 or 330 nm, respectively, consisting of adjacent longitudinal 100-to-200 nm domains of differently addressable CP species. This technology paves the way towards rod-shaped scaffolds with pre-defined, selectively reactive barcode patterns on the nanometer scale. Electronic supplementary information (ESI) available: Two supplementary figures, showing (a) the phenotype of different Nicotiana plant species systemically infected with TMVwt, TMVCys, or TMVLys at 9 and 15 days post-inoculation, and (b) the length distribution of partially and completely assembled VLPs with a second type of RNA template (TMVwt RNA); and one supplementary table listing the sequences of primers used for site-specific mutagenesis of the TMV CP ORF and for sequencing. See DOI: 10.1039/c3nr33724c

Cultivating Discontinuity: Pentecostal Pedagogies of Yielding and Control

ERIC Educational Resources Information Center

Brahinsky, Josh

2013-01-01

Exploring missionary study at an Assemblies of God Bible college through ethnography and training manuals demonstrates systematic pedagogies that cultivate sensory capabilities encouraging yielding, opening to rupture, and constraint. Ritual theory and the Anthropology of Christianity shift analytic scales to include "cultivation," a…

Influence of Geometries on the Assembly of Snowman-Shaped Janus Nanoparticles.

PubMed

Kang, Chengjun; Honciuc, Andrei

2018-04-24

The self-assembly of micro/nanoparticles into suprastructures is a promising way to develop reconfigurable materials and to gain insights into the fundamental question of how matter organizes itself. The geometry of particles, especially those deviating from perfectly spherical shapes, is of significant importance in colloidal assembly because it influences the particle "recognition", determines the particle packing, and ultimately dictates the formation of assembled suprastructures. In order to organize particles into desired structures, it is of vital importance to understand the relationship between the shape of the colloidal building blocks and the assembled suprastructures. This fundamental issue is an enduring topic in the assembly of molecular surfactants, but it remained elusive in colloidal assembly. To address this issue, we use snowman-shaped Janus nanoparticles (JNPs) as a model to systematically study the effect of colloidal geometries on their assembled suprastructures. Ten types of JNPs with identical chemical compositions but with different geometries were synthesized. Specifically, the synthesized JNPs differ in their lobe size ratios, phase separation degrees, and overall sizes. We show that by altering these parameters, both finite suprastructures, such as capsules with different curvatures, and nonfinite suprastructures, including free-standing single-layered or double-layered JNPs sheets, can be obtained via self-assembly. All these different types of suprastructures are constituted by highly oriented and hexagonally packed JNPs. These findings demonstrate the significance of geometries in colloidal assembly, such that slightly changing the building block geometries could result in a large variety of very different assembled structures, without altering the chemistry of the particles.

Strong species-environment feedback shapes plant community assembly along environmental gradients.

PubMed

Jiang, Jiang; Deangelis, Donald L

2013-10-01

An aim of community ecology is to understand the patterns of competing species assembly along environmental gradients. All species interact with their environments. However, theories of community assembly have seldom taken into account the effects of species that are able to engineer the environment. In this modeling study, we integrate the species' engineering trait together with processes of immigration and local dispersal into a theory of community assembly. We quantify the species' engineering trait as the degree to which it can move the local environment away from its baseline state towards the optimum state of the species (species-environment feedback). We find that, in the presence of immigration from a regional pool, strong feedback can increase local species richness; however, in the absence of continual immigration, species richness is a declining function of the strength of species-environment feedback. This shift from a negative effect of engineering strength on species richness to a positive effect, as immigration rate increases, is clearer when there is spatial heterogeneity in the form of a gradient in environmental conditions than when the environment is homogeneous or it is randomly heterogeneous. Increasing the scale over which local dispersal occurs can facilitate species richness when there is no species-environment feedback or when the feedback is weak. However, increases in the spatial scale of dispersal can reduce species richness when the species-environment feedback is strong. These results expand the theoretical basis for understanding the effects of the strength of species-environment feedback on community assembly.

Strong species-environment feedback shapes plant community assembly along environmental gradients

USGS Publications Warehouse

Jiang, Jiang; DeAngelis, Donald L.

2013-01-01

An aim of community ecology is to understand the patterns of competing species assembly along environmental gradients. All species interact with their environments. However, theories of community assembly have seldom taken into account the effects of species that are able to engineer the environment. In this modeling study, we integrate the species' engineering trait together with processes of immigration and local dispersal into a theory of community assembly. We quantify the species' engineering trait as the degree to which it can move the local environment away from its baseline state towards the optimum state of the species (species-environment feedback). We find that, in the presence of immigration from a regional pool, strong feedback can increase local species richness; however, in the absence of continual immigration, species richness is a declining function of the strength of species-environment feedback. This shift from a negative effect of engineering strength on species richness to a positive effect, as immigration rate increases, is clearer when there is spatial heterogeneity in the form of a gradient in environmental conditions than when the environment is homogeneous or it is randomly heterogeneous. Increasing the scale over which local dispersal occurs can facilitate species richness when there is no species-environment feedback or when the feedback is weak. However, increases in the spatial scale of dispersal can reduce species richness when the species-environment feedback is strong. These results expand the theoretical basis for understanding the effects of the strength of species-environment feedback on community assembly.

Growth Mechanism of Cluster-Assembled Surfaces: From Submonolayer to Thin-Film Regime

NASA Astrophysics Data System (ADS)

Borghi, Francesca; Podestà, Alessandro; Piazzoni, Claudio; Milani, Paolo

2018-04-01

Nanostructured films obtained by assembling preformed atomic clusters are of strategic importance for a wide variety of applications. The deposition of clusters produced in the gas phase onto a substrate offers the possibility to control and engineer the structural and functional properties of the cluster-assembled films. To date, the microscopic mechanisms underlying the growth and structuring of cluster-assembled films are poorly understood, and, in particular, the transition from the submonolayer to the thin-film regime is experimentally unexplored. Here we report the systematic characterization by atomic force microscopy of the evolution of the structural properties of cluster-assembled films deposited by supersonic cluster beam deposition. As a paradigm of nanostructured systems, we focus our attention on cluster-assembled zirconia films, investigating the influence of the building block dimensions on the growth mechanisms and roughening of the thin films, following the growth process from the early stages of the submonolayer to the thin-film regime. Our results demonstrate that the growth dynamics in the submonolayer regime determines different morphological properties of the cluster-assembled thin film. The evolution of the roughness with the number of deposited clusters reproduces the growth exponent of the ballistic deposition in the 2 +1 model from the submonolayer to the thin-film regime.

Terminating DNA Tile Assembly with Nanostructured Caps.

PubMed

Agrawal, Deepak K; Jiang, Ruoyu; Reinhart, Seth; Mohammed, Abdul M; Jorgenson, Tyler D; Schulman, Rebecca

2017-10-24

Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes. We find that nanostructures that present binding interfaces for all of the binding sites on a growing facet can bind selectively to growing ends and stop growth when these interfaces are presented on either a rigid or floppy scaffold. In contrast, nucleation of nanotubes requires the presentation of binding sites in an arrangement that matches the shape of the structure's facet. As a result, it is possible to build nanostructures that can terminate the growth of existing nanotubes but cannot nucleate a new structure. The resulting design principles for constructing structures that direct nucleation and termination of the growth of one-dimensional nanostructures can also serve as a starting point for programmatically directing two- and three-dimensional crystallization processes using nanostructure design.

Role of Surface Charge Density in Nanoparticle-templated Assembly of Bromovirus Protein Cages

PubMed Central

Daniel, Marie-Christine; Tsvetkova, Irina B.; Quinkert, Zachary T.; Murali, Ayaluru; De, Mrinmoy; Rotello, Vincent M.; Kao, C. Cheng; Dragnea, Bogdan

2010-01-01

Self-assembling icosahedral protein cages have potencially useful physical and chemical characteristics for a variety of nanotechnology applications, ranging from therapeutic or diagnostic vectors to building blocks for hierarchical materials. For application-specific functional control of protein cage assemblies, a deeper understanding of the interaction between the protein cage and its payload is necessary. Protein-cage encapsulated nanoparticles, with their well-defined surface chemistry, allow for systematic control over key parameters of encapsulation such as the surface charge, hydrophobicity, and size. Independent control over these variables allows experimental testing of different assembly mechanism models. Previous studies done with Brome mosaic virus capsids and negatively-charged gold nanoparticles indicated that the result of the self-assembly process depends on the diameter of the particle. However, in these experiments, the surface-ligand density was maintained at saturation levels, while the total charge and the radius of curvature remained coupled variables, making the interpretation of the observed dependence on the core size difficult. The current work furnishes evidence of a critical surface charge density for assembly through an analysis aimed at decoupling the surface charge the core size. PMID:20575505

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

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

Mansbach, Rachael A.; Ferguson, Andrew L.

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

DOE PAGES

Mansbach, Rachael A.; Ferguson, Andrew L.

2017-02-10

Self-assembled aggregates of peptides containing aromatic groups possess optoelectronic properties that make them attractive targets for the fabrication of biocompatible electronics. Molecular-level understanding of how the microscopic peptide chemistry influences the properties of the aggregates is vital for rational peptide design. We construct a coarse-grained model of Asp-Phe-Ala-Gly-OPV3-Gly-Ala-Phe-Asp (DFAG-OPV3-GAFD) peptides containing OPV3 (distyrylbenzene) π-conjugated cores explicitly parameterized against all-atom calculations and perform molecular dynamics simulations of the self-assembly of hundreds of molecules over hundreds of nanoseconds. We observe a hierarchical assembly mechanism wherein ~2-8 peptides assemble into stacks with aligned aromatic cores that subsequently form elliptical aggregates and ultimately amore » branched network with a fractal dimensionality of ~1.5. The assembly dynamics are well described by a Smoluchowski coagulation process for which we extract rate constants from the molecular simulations to both furnish insight into the microscopic assembly kinetics and extrapolate our aggregation predictions to time and length scales beyond the reach of molecular simulation. Lastly, this study presents new molecular-level understanding of the morphology and dynamics of the spontaneous self-assembly of DFAG-OPV3-GAFD peptides and establishes a systematic protocol to develop coarse-grained models of optoelectronic peptides for the exploration and design of π-conjugated peptides with tunable optoelectronic properties.« less

Recovering tubewise power from three-dimensional nodal kinetics calculation during material relocation in an HWR

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

Kalimullah; Morris, E.E.; Yang, W.S.

1994-12-31

To analyze severe accidents in some special-purpose heavy-water reactors made of assemblies consisting of a number of coaxial tubes of aluminum-clad U-Al fuel and aluminum-clad neutron-capturing material, a mechanistic model, MARTINS, for tube beatup, melting, and molten material relocation has been developed and integrated with the DIF3D nodal hexagonal-z reactor kinetics and other phenomenological modules. The DIF3D kinetics homogenizes all materials located and computes the total power produced in an axial segment of a fuel assembly. This paper presents an approximate method, used in MARTINS, to calculate the distribution of this total nodal power into the intact fuel and capturingmore » material tubes and the meat-cladding mixtures relocating during tube disruption. The method accounts for the change in intraassembly radial power profile due to assembly geometry change with the progress of segment-by-segment disruption of different tubes. Earlier methods to recover pinwise power from nodal calculation for liquid-metal-cooled reactors and light water reactors (X-Y and hexagonal unit cells) are not practical for a disrupting assembly having material relocation. Figure 1 shows the assembly`s end view, divided into rings for modeling and analysis. A ring is a coolant subchannel plus the outer surrounding tube. The present method for distributing the nodal power consists of two parts: (a) calculation of the relative values of ring-by-ring power per unit uranium mass and power per unit mass of neutron-capturing material in a given assembly segment, and (b) normalization of these relative values such that the total power of all rings (intact tubes and U-Al-Cp meat-cladding mixtures, where Cp implies the neutron-capturing material) equals the DIF3D-calculated nodal power for the assembly axial segment.« less

Dynamic self-assembly of charged colloidal strings and walls in simple fluid flows.

PubMed

Abe, Yu; Zhang, Bo; Gordillo, Leonardo; Karim, Alireza Mohammad; Francis, Lorraine F; Cheng, Xiang

2017-02-22

Colloidal particles can self-assemble into various ordered structures in fluid flows that have potential applications in biomedicine, materials synthesis and encryption. These dynamic processes are also of fundamental interest for probing the general principles of self-assembly under non-equilibrium conditions. Here, we report a simple microfluidic experiment, where charged colloidal particles self-assemble into flow-aligned 1D strings with regular particle spacing near a solid boundary. Using high-speed confocal microscopy, we systematically investigate the influence of flow rates, electrostatics and particle polydispersity on the observed string structures. By studying the detailed dynamics of stable flow-driven particle pairs, we quantitatively characterize interparticle interactions. Based on the results, we construct a simple model that explains the intriguing non-equilibrium self-assembly process. Our study shows that the colloidal strings arise from a delicate balance between attractive hydrodynamic coupling and repulsive electrostatic interaction between particles. Finally, we demonstrate that, with the assistance of transverse electric fields, a similar mechanism also leads to the formation of 2D colloidal walls.

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

PubMed

Utturkar, Sagar M; Klingeman, Dawn M; Hurt, Richard A; Brown, Steven D

2017-01-01

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

Optimized Assembly of a Multifunctional RNA-Protein Nanostructure in a Cell-Free Gene Expression System.

PubMed

Schwarz-Schilling, Matthaeus; Dupin, Aurore; Chizzolini, Fabio; Krishnan, Swati; Mansy, Sheref S; Simmel, Friedrich C

2018-04-11

Molecular complexes composed of RNA molecules and proteins are promising multifunctional nanostructures for a wide variety of applications in biological cells or in artificial cellular systems. In this study, we systematically address some of the challenges associated with the expression and assembly of such hybrid structures using cell-free gene expression systems. As a model structure, we investigated a pRNA-derived RNA scaffold functionalized with four distinct aptamers, three of which bind to proteins, streptavidin and two fluorescent proteins, while one binds the small molecule dye malachite green (MG). Using MG fluorescence and Förster resonance energy transfer (FRET) between the RNA-scaffolded proteins, we assess critical assembly parameters such as chemical stability, binding efficiency, and also resource sharing effects within the reaction compartment. We then optimize simultaneous expression and coassembly of the RNA-protein nanostructure within a single-compartment cell-free gene expression system. We demonstrate expression and assembly of the multicomponent nanostructures inside of emulsion droplets and their aptamer-mediated localization onto streptavidin-coated substrates, plus the successful assembly of the hybrid structures inside of bacterial cells.

Nuclear imaging of the fuel assembly in ignition experimentsa)

NASA Astrophysics Data System (ADS)

Grim, G. P.; Guler, N.; Merrill, F. E.; Morgan, G. L.; Danly, C. R.; Volegov, P. L.; Wilde, C. H.; Wilson, D. C.; Clark, D. S.; Hinkel, D. E.; Jones, O. S.; Raman, K. S.; Izumi, N.; Fittinghoff, D. N.; Drury, O. B.; Alger, E. T.; Arnold, P. A.; Ashabranner, R. C.; Atherton, L. J.; Barrios, M. A.; Batha, S.; Bell, P. M.; Benedetti, L. R.; Berger, R. L.; Bernstein, L. A.; Berzins, L. V.; Betti, R.; Bhandarkar, S. D.; Bionta, R. M.; Bleuel, D. L.; Boehly, T. R.; Bond, E. J.; Bowers, M. W.; Bradley, D. K.; Brunton, G. K.; Buckles, R. A.; Burkhart, S. C.; Burr, R. F.; Caggiano, J. A.; Callahan, D. A.; Casey, D. T.; Castro, C.; Celliers, P. M.; Cerjan, C. J.; Chandler, G. A.; Choate, C.; Cohen, S. J.; Collins, G. W.; Cooper, G. W.; Cox, J. R.; Cradick, J. R.; Datte, P. S.; Dewald, E. L.; Di Nicola, P.; Di Nicola, J. M.; Divol, L.; Dixit, S. N.; Dylla-Spears, R.; Dzenitis, E. G.; Eckart, M. J.; Eder, D. C.; Edgell, D. H.; Edwards, M. J.; Eggert, J. H.; Ehrlich, R. B.; Erbert, G. V.; Fair, J.; Farley, D. R.; Felker, B.; Fortner, R. J.; Frenje, J. A.; Frieders, G.; Friedrich, S.; Gatu-Johnson, M.; Gibson, C. R.; Giraldez, E.; Glebov, V. Y.; Glenn, S. M.; Glenzer, S. H.; Gururangan, G.; Haan, S. W.; Hahn, K. D.; Hammel, B. A.; Hamza, A. V.; Hartouni, E. P.; Hatarik, R.; Hatchett, S. P.; Haynam, C.; Hermann, M. R.; Herrmann, H. W.; Hicks, D. G.; Holder, J. P.; Holunga, D. M.; Horner, J. B.; Hsing, W. W.; Huang, H.; Jackson, M. C.; Jancaitis, K. S.; Kalantar, D. H.; Kauffman, R. L.; Kauffman, M. I.; Khan, S. F.; Kilkenny, J. D.; Kimbrough, J. R.; Kirkwood, R.; Kline, J. L.; Knauer, J. P.; Knittel, K. M.; Koch, J. A.; Kohut, T. R.; Kozioziemski, B. J.; Krauter, K.; Krauter, G. W.; Kritcher, A. L.; Kroll, J.; Kyrala, G. A.; Fortune, K. N. La; LaCaille, G.; Lagin, L. J.; Land, T. A.; Landen, O. L.; Larson, D. W.; Latray, D. A.; Leeper, R. J.; Lewis, T. L.; LePape, S.; Lindl, J. D.; Lowe-Webb, R. R.; Ma, T.; MacGowan, B. J.; MacKinnon, A. J.; MacPhee, A. G.; Malone, R. M.; Malsbury, T. N.; Mapoles, E.; Marshall, C. D.; Mathisen, D. G.; McKenty, P.; McNaney, J. M.; Meezan, N. B.; Michel, P.; Milovich, J. L.; Moody, J. D.; Moore, A. S.; Moran, M. J.; Moreno, K.; Moses, E. I.; Munro, D. H.; Nathan, B. R.; Nelson, A. J.; Nikroo, A.; Olson, R. E.; Orth, C.; Pak, A. E.; Palma, E. S.; Parham, T. G.; Patel, P. K.; Patterson, R. W.; Petrasso, R. D.; Prasad, R.; Ralph, J. E.; Regan, S. P.; Rinderknecht, H.; Robey, H. F.; Ross, G. F.; Ruiz, C. L.; Séguin, F. H.; Salmonson, J. D.; Sangster, T. C.; Sater, J. D.; Saunders, R. L.; Schneider, M. B.; Schneider, D. H.; Shaw, M. J.; Simanovskaia, N.; Spears, B. K.; Springer, P. T.; Stoeckl, C.; Stoeffl, W.; Suter, L. J.; Thomas, C. A.; Tommasini, R.; Town, R. P.; Traille, A. J.; Wonterghem, B. Van; Wallace, R. J.; Weaver, S.; Weber, S. V.; Wegner, P. J.; Whitman, P. K.; Widmann, K.; Widmayer, C. C.; Wood, R. D.; Young, B. K.; Zacharias, R. A.; Zylstra, A.

2013-05-01

First results from the analysis of neutron image data collected on implosions of cryogenically layered deuterium-tritium capsules during the 2011-2012 National Ignition Campaign are reported. The data span a variety of experimental designs aimed at increasing the stagnation pressure of the central hotspot and areal density of the surrounding fuel assembly. Images of neutrons produced by deuterium-tritium fusion reactions in the hotspot are presented, as well as images of neutrons that scatter in the surrounding dense fuel assembly. The image data are compared with 1D and 2D model predictions, and consistency checked using other diagnostic data. The results indicate that the size of the fusing hotspot is consistent with the model predictions, as well as other imaging data, while the overall size of the fuel assembly, inferred from the scattered neutron images, is systematically smaller than models' prediction. Preliminary studies indicate these differences are consistent with a significant fraction (20%-25%) of the initial deuterium-tritium fuel mass outside the compact fuel assembly, due either to low mode mass asymmetry or high mode 3D mix effects at the ablator-ice interface.

Self-assembling complexes between binary mixtures of lipids with different linkers and nucleic acids promote universal mRNA, DNA and siRNA delivery.

PubMed

Colombani, Thibault; Peuziat, Pauline; Dallet, Laurence; Haudebourg, Thomas; Mével, Mathieu; Berchel, Mathieu; Lambert, Olivier; Habrant, Damien; Pitard, Bruno

2017-03-10

Protein expression and RNA interference require efficient delivery of DNA or mRNA and small double stranded RNA into cells, respectively. Although cationic lipids are the most commonly used synthetic delivery vectors, a clear need still exists for a better delivery of various types of nucleic acids molecules to improve their biological activity. To optimize the transfection efficiency, a molecular approach consisting in modifying the chemical structure of a given cationic lipid is usually performed, but an alternative strategy could rely on modulating the supramolecular assembly of lipidic lamellar phases sandwiching the nucleic acids molecules. To validate this new concept, we synthesized on one hand two paromomycin-based cationic lipids, with either an amide or a phosphoramide linker, and on the other hand two imidazole-based neutral lipids, having as well either an amide or a phosphoramide function as linker. Combinations of cationic and helper lipids containing the same amide or phosphoramide linkers led to the formation of homogeneous lamellar phases, while hybrid lamellar phases were obtained when the linkers on the cationic and helper lipids were different. Cryo-transmission electron microscopy and fluorescence experiments showed that liposomes/nucleic acids complexes resulting from the association of nucleic acids with hybrid lamellar phases led to complexes that were more stable in the extracellular compartment compared to those obtained with homogeneous systems. In addition, we observed that the most active supramolecular assemblies for the delivery of DNA, mRNA and siRNA were obtained when the cationic and helper lipids possess linkers of different natures. The results clearly show that this supramolecular strategy modulating the property of the lipidic lamellar phase constitutes a new approach for increasing the delivery of various types of nucleic acid molecules. Copyright © 2017 Elsevier B.V. All rights reserved.

49 CFR 396.3 - Inspection, repair, and maintenance.

Code of Federal Regulations, 2010 CFR

2010-10-01

... systematically inspected, repaired, and maintained, all motor vehicles and intermodal equipment subject to its... affect safety of operation, including but not limited to, frame and frame assemblies, suspension systems... cause to be maintained, records for each motor vehicle they control for 30 consecutive days. Intermodal...

Investigating the effects of peptoid substitutions in self-assembly of Fmoc-diphenylalanine derivatives.

PubMed

Rajbhandary, Annada; Nilsson, Bradley L

2017-03-01

Low molecular weight agents that undergo self-assembly into fibril networks with hydrogel properties are promising biomaterials. Most low molecular weight hydrogelators are discovered empirically or serendipitously due to imperfect understanding of the mechanisms of self-assembly, the packing structure of self-assembled materials, and how the self-assembly process corresponds to emergent hydrogelation. Herein, the mechanisms of self-assembly and hydrogelation of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-PhePhe), a well-studied low molecular weight hydrogelator, is probed by systematic comparison with derivatives in which Phe residues are replaced by corresponding N-benzyl glycine peptoid (Nphe) analogs. Peptoids are peptidomimetics that shift display of side chain functionality from the α-carbon to the terminal nitrogen. This alters the hydrogen bonding capacity, the side chain presentation geometry, amide cis/trans isomerization equilibrium, and β-sheet potential of the peptoid relative to the corresponding amino acid in the context of peptidic polymers. It was found that amino acid/peptoid hybrids Fmoc-Phe-Nphe and Fmoc-Nphe-Phe have altered fibril self-assembly propensity and reduced hydrogelation capacity relative to the parent dipeptide, and that fibril self-assembly of the dipeptoid, Fmoc-Nphe-Nphe, is completely curtailed. These findings provide insight into the potential of low molecular weight peptoids and peptide/peptoid hybrids as hydrogelation agents and illuminate the importance of hydrogen bonding and π-π interaction geometry in facilitating self-assembly of Fmoc-Phe-Phe. © 2016 Wiley Periodicals, Inc.

A systematic intercomparison of regional flood frequency analysis models in a simulation framework

NASA Astrophysics Data System (ADS)

Ganora, Daniele; Laio, Francesco; Claps, Pierluigi

2015-04-01

Regional frequency analysis (RFA) is a well-established methodology to provide an estimate of the flood frequency curve (or other discharge-related variables), based on the fundamental concept of substituting temporal information at a site (no data or short time series) by exploiting observations at other sites (spatial information). Different RFA paradigms exist, depending on the way the information is transferred to the site of interest. Despite the wide use of such methodology, a systematic comparison between these paradigms has not been performed. The aim of this study is to provide a framework wherein carrying out the intercomparison: we thus synthetically generate data through Monte Carlo simulations for a number of (virtual) stations, following a GEV parent distribution; different scenarios can be created to represent different spatial heterogeneity patterns by manipulating the parameters of the parent distribution at each station (e.g. with a linear variation in space of the shape parameter of the GEV). A special case is the homogeneous scenario where each station record is sampled from the same parent distribution. For each scenario and each simulation, different regional models are applied to evaluate the 200-year growth factor at each station. Results are than compared to the exact growth factor of each station, which is known in our virtual world. Considered regional approaches include: (i) a single growth curve for the whole region; (ii) a multiple-region model based on cluster analysis which search for an adequate number of homogeneous subregions; (iii) a Region-of-Influence model which defines a homogeneous subregion for each site; (iv) a spatially-smooth estimation procedure based on linear regressions.. A further benchmark model is the at-site estimate based on the analysis of the local record. A comprehensive analysis of the results of the simulations shows that, if the scenario is homogeneous (no spatial variability), all the regional approaches have comparable performances. Moreover, as expected, regional estimates are much more reliable than the at-site estimates. If the scenario is heterogeneous, the performances of the regional models depend on the pattern of heterogeneity; in general, however, the spatially-smooth regional approach performs better than the others, and its performances improve for increasing record lengths. For heterogeneous scenarios, the at-site estimates appear to be comparably more efficient than in the homogeneous case, and in general less biased than the regional estimates.

Scattering Studies of Hydrophobic Monomers in Liposomal Bilayers: An Expanding Shell Model of Monomer Distribution

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

Richter, Andrew; Dergunov, Sergey; Ganus, Bill

2011-01-01

Hydrophobic monomers partially phase separate from saturated lipids when loaded into lipid bilayers in amounts exceeding a 1:1 monomer/lipid molar ratio. This conclusion is based on the agreement between two independent methods of examining the structure of monomer-loaded bilayers. Complete phase separation of monomers from lipids would result in an increase in bilayer thickness and a slight increase in the diameter of liposomes. A homogeneous distribution of monomers within the bilayer would not change the bilayer thickness and would lead to an increase in the liposome diameter. The increase in bilayer thickness, measured by the combination of small-angle neutron scatteringmore » (SANS) and small-angle X-ray scattering (SAXS), was approximately half of what was predicted for complete phase separation. The increase in liposome diameter, measured by dynamic light scattering (DLS), was intermediate between values predicted for a homogeneous distribution and complete phase separation. Combined SANS, SAXS, and DLS data suggest that at a 1.2 monomer/lipid ratio approximately half of the monomers are located in an interstitial layer sandwiched between lipid sheets. These results expand our understanding of using self-assembled bilayers as scaffolds for the directed covalent assembly of organic nanomaterials. In particular, the partial phase separation of monomers from lipids corroborates the successful creation of nanothin polymer materials with uniform imprinted nanopores. Pore-forming templates do not need to span the lipid bilayer to create a pore in the bilayer-templated films.« less

Scattering Studies of Hydrophobic Monomers in Liposomal Bilayers: An Expanding Shell Model of Monomer Distribution

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

Richter, Andrew G.; Dergunov, Sergey A.; Ganus, Bill

2011-03-10

Hydrophobic monomers partially phase separate from saturated lipids when loaded into lipid bilayers in amounts exceeding a 1:1 monomer/lipid molar ratio. This conclusion is based on the agreement between two independent methods of examining the structure of monomer-loaded bilayers. Complete phase separation of monomers from lipids would result in an increase in bilayer thickness and a slight increase in the diameter of liposomes. A homogeneous distribution of monomers within the bilayer would not change the bilayer thickness and would lead to an increase in the liposome diameter. The increase in bilayer thickness, measured by the combination of small-angle neutron scatteringmore » (SANS) and small-angle X-ray scattering (SAXS), was approximately half of what was predicted for complete phase separation. The increase in liposome diameter, measured by dynamic light scattering (DLS), was intermediate between values predicted for a homogeneous distribution and complete phase separation. Combined SANS, SAXS, and DLS data suggest that at a 1.2 monomer/lipid ratio approximately half of the monomers are located in an interstitial layer sandwiched between lipid sheets. These results expand our understanding of using self-assembled bilayers as scaffolds for the directed covalent assembly of organic nanomaterials. In particular, the partial phase separation of monomers from lipids corroborates the successful creation of nanothin polymer materials with uniform imprinted nanopores. Finally, pore-forming templates do not need to span the lipid bilayer to create a pore in the bilayer-templated films.« less

Preliminary Analysis of the Transient Reactor Test Facility (TREAT) with PROTEUS

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

Connaway, H. M.; Lee, C. H.

The neutron transport code PROTEUS has been used to perform preliminary simulations of the Transient Reactor Test Facility (TREAT). TREAT is an experimental reactor designed for the testing of nuclear fuels and other materials under transient conditions. It operated from 1959 to 1994, when it was placed on non-operational standby. The restart of TREAT to support the U.S. Department of Energy’s resumption of transient testing is currently underway. Both single assembly and assembly-homogenized full core models have been evaluated. Simulations were performed using a historic set of WIMS-ANL-generated cross-sections as well as a new set of Serpent-generated cross-sections. To supportmore » this work, further analyses were also performed using additional codes in order to investigate particular aspects of TREAT modeling. DIF3D and the Monte-Carlo codes MCNP and Serpent were utilized in these studies. MCNP and Serpent were used to evaluate the effect of geometry homogenization on the simulation results and to support code-to-code comparisons. New meshes for the PROTEUS simulations were created using the CUBIT toolkit, with additional meshes generated via conversion of selected DIF3D models to support code-to-code verifications. All current analyses have focused on code-to-code verifications, with additional verification and validation studies planned. The analysis of TREAT with PROTEUS-SN is an ongoing project. This report documents the studies that have been performed thus far, and highlights key challenges to address in future work.« less

Self-assembly of Janus dendrimers into uniform dendrimersomes and other complex architectures.

PubMed

Percec, Virgil; Wilson, Daniela A; Leowanawat, Pawaret; Wilson, Christopher J; Hughes, Andrew D; Kaucher, Mark S; Hammer, Daniel A; Levine, Dalia H; Kim, Anthony J; Bates, Frank S; Davis, Kevin P; Lodge, Timothy P; Klein, Michael L; DeVane, Russell H; Aqad, Emad; Rosen, Brad M; Argintaru, Andreea O; Sienkowska, Monika J; Rissanen, Kari; Nummelin, Sami; Ropponen, Jarmo

2010-05-21

Self-assembled nanostructures obtained from natural and synthetic amphiphiles serve as mimics of biological membranes and enable the delivery of drugs, proteins, genes, and imaging agents. Yet the precise molecular arrangements demanded by these functions are difficult to achieve. Libraries of amphiphilic Janus dendrimers, prepared by facile coupling of tailored hydrophilic and hydrophobic branched segments, have been screened by cryogenic transmission electron microscopy, revealing a rich palette of morphologies in water, including vesicles, denoted dendrimersomes, cubosomes, disks, tubular vesicles, and helical ribbons. Dendrimersomes marry the stability and mechanical strength obtainable from polymersomes with the biological function of stabilized phospholipid liposomes, plus superior uniformity of size, ease of formation, and chemical functionalization. This modular synthesis strategy provides access to systematic tuning of molecular structure and of self-assembled architecture.

Sample preparation methods for scanning electron microscopy of homogenized Al-Mg-Si billets: A comparative study

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

Österreicher, Johannes Albert; Kumar, Manoj

Characterization of Mg-Si precipitates is crucial for optimizing the homogenization heat treatment of Al-Mg-Si alloys. Although sample preparation is key for high quality scanning electron microscopy imaging, most common methods lead to dealloying of Mg-Si precipitates. In this article we systematically evaluate different sample preparation methods: mechanical polishing, etching with various reagents, and electropolishing using different electrolytes. We demonstrate that the use of a nitric acid and methanol electrolyte for electropolishing a homogenized Al-Mg-Si alloy prevents the dissolution of Mg-Si precipitates, resulting in micrographs of higher quality. This preparation method is investigated in depth and the obtained scanning electron microscopymore » images are compared with transmission electron micrographs: the shape and size of Mg-Si precipitates appear very similar in either method. The scanning electron micrographs allow proper identification and measurement of the Mg-Si phases including needles with lengths of roughly 200 nm. These needles are β″ precipitates as confirmed by high resolution transmission electron microscopy. - Highlights: •Secondary precipitation in homogenized 6xxx Al alloys is crucial for extrudability. •Existing sample preparation methods for SEM are improvable. •Electropolishing with nitric acid/methanol yields superior quality in SEM. •The obtained micrographs are compared to TEM micrographs.« less

Hyperbranched Hybridization Chain Reaction for Triggered Signal Amplification and Concatenated Logic Circuits.

PubMed

Bi, Sai; Chen, Min; Jia, Xiaoqiang; Dong, Ying; Wang, Zonghua

2015-07-06

A hyper-branched hybridization chain reaction (HB-HCR) is presented herein, which consists of only six species that can metastably coexist until the introduction of an initiator DNA to trigger a cascade of hybridization events, leading to the self-sustained assembly of hyper-branched and nicked double-stranded DNA structures. The system can readily achieve ultrasensitive detection of target DNA. Moreover, the HB-HCR principle is successfully applied to construct three-input concatenated logic circuits with excellent specificity and extended to design a security-mimicking keypad lock system. Significantly, the HB-HCR-based keypad lock can alarm immediately if the "password" is incorrect. Overall, the proposed HB-HCR with high amplification efficiency is simple, homogeneous, fast, robust, and low-cost, and holds great promise in the development of biosensing, in the programmable assembly of DNA architectures, and in molecular logic operations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-dimensionally bonded spongy graphene material with super compressive elasticity and near-zero Poisson’s ratio

NASA Astrophysics Data System (ADS)

Wu, Yingpeng; Yi, Ningbo; Huang, Lu; Zhang, Tengfei; Fang, Shaoli; Chang, Huicong; Li, Na; Oh, Jiyoung; Lee, Jae Ah; Kozlov, Mikhail; Chipara, Alin C.; Terrones, Humberto; Xiao, Peishuang; Long, Guankui; Huang, Yi; Zhang, Fan; Zhang, Long; Lepró, Xavier; Haines, Carter; Lima, Márcio Dias; Lopez, Nestor Perea; Rajukumar, Lakshmy P.; Elias, Ana L.; Feng, Simin; Kim, Seon Jeong; Narayanan, N. T.; Ajayan, Pulickel M.; Terrones, Mauricio; Aliev, Ali; Chu, Pengfei; Zhang, Zhong; Baughman, Ray H.; Chen, Yongsheng

2015-01-01

It is a challenge to fabricate graphene bulk materials with properties arising from the nature of individual graphene sheets, and which assemble into monolithic three-dimensional structures. Here we report the scalable self-assembly of randomly oriented graphene sheets into additive-free, essentially homogenous graphene sponge materials that provide a combination of both cork-like and rubber-like properties. These graphene sponges, with densities similar to air, display Poisson’s ratios in all directions that are near-zero and largely strain-independent during reversible compression to giant strains. And at the same time, they function as enthalpic rubbers, which can recover up to 98% compression in air and 90% in liquids, and operate between -196 and 900 °C. Furthermore, these sponges provide reversible liquid absorption for hundreds of cycles and then discharge it within seconds, while still providing an effective near-zero Poisson’s ratio.

Three-dimensionally bonded spongy graphene material with super compressive elasticity and near-zero Poisson's ratio.

PubMed

Wu, Yingpeng; Yi, Ningbo; Huang, Lu; Zhang, Tengfei; Fang, Shaoli; Chang, Huicong; Li, Na; Oh, Jiyoung; Lee, Jae Ah; Kozlov, Mikhail; Chipara, Alin C; Terrones, Humberto; Xiao, Peishuang; Long, Guankui; Huang, Yi; Zhang, Fan; Zhang, Long; Lepró, Xavier; Haines, Carter; Lima, Márcio Dias; Lopez, Nestor Perea; Rajukumar, Lakshmy P; Elias, Ana L; Feng, Simin; Kim, Seon Jeong; Narayanan, N T; Ajayan, Pulickel M; Terrones, Mauricio; Aliev, Ali; Chu, Pengfei; Zhang, Zhong; Baughman, Ray H; Chen, Yongsheng

2015-01-20

It is a challenge to fabricate graphene bulk materials with properties arising from the nature of individual graphene sheets, and which assemble into monolithic three-dimensional structures. Here we report the scalable self-assembly of randomly oriented graphene sheets into additive-free, essentially homogenous graphene sponge materials that provide a combination of both cork-like and rubber-like properties. These graphene sponges, with densities similar to air, display Poisson's ratios in all directions that are near-zero and largely strain-independent during reversible compression to giant strains. And at the same time, they function as enthalpic rubbers, which can recover up to 98% compression in air and 90% in liquids, and operate between -196 and 900 °C. Furthermore, these sponges provide reversible liquid absorption for hundreds of cycles and then discharge it within seconds, while still providing an effective near-zero Poisson's ratio.

Transparent and flexible electrodes and supercapacitors using polyaniline/single-walled carbon nanotube composite thin films

NASA Astrophysics Data System (ADS)

Ge, Jun; Cheng, Guanghui; Chen, Liwei

2011-08-01

Large-scale transparent and flexible electronic devices have been pursued for potential applications such as those in touch sensors and display technologies. These applications require that the power source of these devices must also comply with transparent and flexible features. Here we present transparent and flexible supercapacitors assembled from polyaniline (PANI)/single-walled carbon nanotube (SWNT) composite thin film electrodes. The ultrathin, optically homogeneous and transparent, electrically conducting films of the PANI/SWNT composite show a large specific capacitance due to combined double-layer capacitance and pseudo-capacitance mechanisms. A supercapacitor assembled using electrodes with a SWNT density of 10.0 µg cm-2 and 59 wt% PANI gives a specific capacitance of 55.0 F g-1 at a current density of 2.6 A g-1, showing its possibility for transparent and flexible energy storage.

Self-assembly of three-dimensional interconnected graphene-based aerogels and its application in supercapacitors.

PubMed

Ji, Chen-Chen; Xu, Mao-Wen; Bao, Shu-Juan; Cai, Chang-Jun; Lu, Zheng-Jiang; Chai, Hui; Yang, Fan; Wei, Hua

2013-10-01

Homogeneously distributed self-assembling hybrid graphene-based aerogels with 3D interconnected pores, employing three types of carbohydrates (glucose, β-cyclodextrin, and chitosan), have been fabricated by a simple hydrothermal route. Using three types of carbohydrates as morphology oriented agents and reductants can effectively tailor the microstructures, physical properties, and electrochemical performances of the products. The effects of different carbohydrates on graphene oxide reduction to form graphene-based aerogels with different microcosmic morphologies and physical properties were also systemically discussed. The electrochemical behaviors of all graphene-based aerogel samples showed remarkably strong and stable performances, which indicated that all the 3D interpenetrating microstructure graphene-based aerogel samples with well-developed porous nanostructures and interconnected conductive networks could provide fast ionic channels for electrochemical energy storage. These results demonstrate that this strategy would offer an easy and effective way to fabricate graphene-based materials. Copyright © 2013 Elsevier Inc. All rights reserved.

Colloid electrostatic self-assembly synthesis of SnO2/graphene nanocomposite for supercapacitors

NASA Astrophysics Data System (ADS)

Wang, Yankun; Liu, Yushan; Zhang, Jianmin

2015-10-01

In this paper, a simple and fast colloid electrostatic self-assembly method was adopted to prepare the SnO2/graphene nanocomposite (SGNC). The crystal structure, chemical composition, and porous property of composite were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, Raman microscopy, X-ray photoelectron spectroscopy (XPS), and N2 adsorption-desorption experiments. The morphology analyses showed that the SnO2 nanoparticles about 5 nm were distributed homogenously on the reduced graphene oxide (rGO) sheets surface. The electrochemical performance measurements exhibited that SGNC possessed the specific capacitance of 347.3 F g-1 at a scan rate of 5 mV s-1 in 1 M Na2SO4 electrolyte solution. Furthermore, this material also showed excellent cycling stability, and the specific capacitance still retained 90 % after 3000 cycles. These results indicate that the SGNC is a promising electrode material for high-performance supercapacitors.

Perspectives: Nanofibers and nanowires for disordered photonics

NASA Astrophysics Data System (ADS)

Pisignano, Dario; Persano, Luana; Camposeo, Andrea

2017-03-01

As building blocks of microscopically non-homogeneous materials, semiconductor nanowires and polymer nanofibers are emerging component materials for disordered photonics, with unique properties of light emission and scattering. Effects found in assemblies of nanowires and nanofibers include broadband reflection, significant localization of light, strong and collective multiple scattering, enhanced absorption of incident photons, synergistic effects with plasmonic particles, and random lasing. We highlight recent related discoveries, with a focus on material aspects. The control of spatial correlations in complex assemblies during deposition, the coupling of modes with efficient transmission channels provided by nanofiber waveguides, and the embedment of random architectures into individually coded nanowires will allow the potential of these photonic materials to be fully exploited, unconventional physics to be highlighted, and next-generation optical devices to be achieved. The prospects opened by this technology include enhanced random lasing and mode-locking, multi-directionally guided coupling to sensors and receivers, and low-cost encrypting miniatures for encoders and labels.

Transparent and flexible electrodes and supercapacitors using polyaniline/single-walled carbon nanotube composite thin films.

PubMed

Ge, Jun; Cheng, Guanghui; Chen, Liwei

2011-08-01

Large-scale transparent and flexible electronic devices have been pursued for potential applications such as those in touch sensors and display technologies. These applications require that the power source of these devices must also comply with transparent and flexible features. Here we present transparent and flexible supercapacitors assembled from polyaniline (PANI)/single-walled carbon nanotube (SWNT) composite thin film electrodes. The ultrathin, optically homogeneous and transparent, electrically conducting films of the PANI/SWNT composite show a large specific capacitance due to combined double-layer capacitance and pseudo-capacitance mechanisms. A supercapacitor assembled using electrodes with a SWNT density of 10.0 µg cm(-2) and 59 wt% PANI gives a specific capacitance of 55.0 F g(-1) at a current density of 2.6 A g(-1), showing its possibility for transparent and flexible energy storage. This journal is © The Royal Society of Chemistry 2011

One-step synthesis of titania nanoparticles from PS-P4VP diblock copolymer solution

NASA Astrophysics Data System (ADS)

Song, Lixin; Lam, Yeng Ming; Boothroyd, Chris; Teo, Puat Wen

2007-04-01

Polymeric films containing titania nanoparticles have potential as dielectric films for flexible electronic applications. For this purpose, the nanoparticles must be homogeneously distributed. Self-assembly is emerging as a neat, elegant method for fabricating such nanostructured hybrid materials with well-distributed nanoparticles. In this work, we report a micellar solution approach for the assembly of copolymer-titanium precursor nanostructures in which titania nanoparticles were synthesized. The ratio of the amount of titanium precursor, titanium isopropoxide, to the blocks forming the micellar core, poly(4-vinylpyridine), was found to play a key role in controlling film morphology. A sphere-to-ribbon transition was observed when the amount of titanium isopropoxide was increased. The thin film morphology can be tuned using the precursor-copolymer interaction rather than just the polymer-polymer interaction or the polymer-solution interaction. This method provides yet another way to control the morphology of nanostructures.

Fringing-field dielectrophoretic assembly of ultrahigh-density semiconducting nanotube arrays with a self-limited pitch

NASA Astrophysics Data System (ADS)

Cao, Qing; Han, Shu-Jen; Tulevski, George S.

2014-09-01

One key challenge of realizing practical high-performance electronic devices based on single-walled carbon nanotubes is to produce electronically pure nanotube arrays with both a minuscule and uniform inter-tube pitch for sufficient device-packing density and homogeneity. Here we develop a method in which the alternating voltage-fringing electric field formed between surface microelectrodes and the substrate is utilized to assemble semiconducting nanotubes into well-aligned, ultrahigh-density and submonolayered arrays, with a consistent pitch as small as 21±6 nm determined by a self-limiting mechanism, based on the unique field focusing and screening effects of the fringing field. Field-effect transistors based on such nanotube arrays exhibit record high device transconductance (>50 μS μm-1) and decent on current per nanotube (~1 μA per tube) together with high on/off ratios at a drain bias of -1 V.

Measurements of the thickness compressibility of an n-octadecyltriethoxysilane monolayer self-assembled on mica.

PubMed

Kim, Sungsoo; Cho, Kilwon; Curry, Joan E

2005-08-30

The surface forces apparatus technique and the Johnson-Kendall-Roberts theory were used to study the elastic properties of an n-octadecyltriethoxysilane self-assembled monolayer (OTE-SAM) on both untreated and plasma-treated mica. Our aim was to measure the thickness compressibilities of OTE monolayers on untreated and plasma-treated mica and to estimate their surface densities and phase-states from the film compressibility. The compressibility moduli of OTE are (0.96 +/- 0.02) x 10(8) N/m(2) on untreated mica and (1.24 +/- 0.06) x 10(8) N/m(2) on plasma-treated mica. This work suggests that the OTE phase-state is pseudocrystalline. In addition, the results from the compressibility measurements in water vapor suggest that the OTE-SAM on both untreated and plasma-treated mica is not homogeneous but rather contains both crystalline polymerized OTE domains and somewhat hydrophilic gaseous regions.

Stability of anti-reflection coatings via the self-assembly encapsulation of silica nanoparticles by diazo-resins

NASA Astrophysics Data System (ADS)

Metzman, Jonathan S.; Ridley, Jason I.; Khalifa, Moataz B.; Heflin, James R.

2015-12-01

A modified silica nanoparticle (MSNP) solution was formed by the encapsulation of negatively charged silica nanoparticles by the UV-crosslinkable polycation oligomer diazo-resin (DAR). Appropriate DAR encapsulation concentrations were determined by use of zeta-potential and dynamic light scattering measurements. The MSNPs were used in conjunction with poly(styrene sulfonate) (PSS) to grow homogenous ionic self-assembled multilayer anti-reflection coatings. Stability was induced within the films by the exposure of UV-irradiation that allowed for crosslinking of the DAR and PSS. The films were characterized by UV/vis/IR spectroscopy and field emission scanning electron microscopy. The transmission and reflection levels were >98.5% and <0.05%, respectively. The refractive indices resided in the 1.25-1.26 range. The solvent stability was tested by sonication of the films in a ternary solvent (H2O/DMF/ZnCl2 3:5:2 w/w/w).

A self-assembling lanthanide molecular nanoparticle for optical imaging†

PubMed Central

Brown, Katherine A.; Yang, Xiaoping; Schipper, Desmond; Hall, Justin W.; DePue, Lauren J.; Gnanam, Annie J.; Arambula, Jonathan F.; Jones, Jessica N.; Swaminathan, Jagannath; Dieye, Yakhya; Vadivelu, Jamuna; Chandler, Don J.; Marcotte, Edward M.; Sessler, Jonathan L.; Ehrlich, Lauren I. R.; Jones, Richard A.

2015-01-01

Chromophores that incorporate f-block elements have considerable potential for use in bioimaging applications because of their advantageous photophysical properties compared to organic dye, which are currently widely used. We are developing new classes of lanthanide-based self-assembling molecular nanoparticles as reporters for imaging and as multi-functional nanoprobes or nanosensors for use with biological samples. One class of these materials, which we call lanthanide “nano-drums”, are homogeneous 4d–4f clusters approximately 25 to 30 Å in diameter. These are capable of emitting from the visible to near-infrared wavelengths. Here, we present the synthesis, crystal structure, photophysical properties and comparative cytotoxicity data for a 32 metal Eu-Cd nano-drum [Eu8Cd24L12(OAc)48] (1). We also explored the imaging capabilities of this nano-drum using epifluorescence, TIRF, and two-photon microscopy platforms. PMID:25512085

Oligo(ethylene glycol)-sidechain microgels prepared in absence of cross-linking agent: Polymerization, characterization and variation of particle deformability.

PubMed

Welsch, Nicole; Lyon, L Andrew

2017-01-01

We present a systematic study of self-cross-linked microgels formed by precipitation polymerization of oligo ethylene glycol methacrylates. The cross-linking density of these microgels and, thus, the network flexibility can be easily tuned through the modulation of the reaction temperature during polymerization. Microgels prepared in absence of any difunctional monomer, i.e. cross-linker, show enhanced deformability and particle spreading on solid surfaces as compared to microgels cross-linked with varying amounts of poly(ethylene glycol diacrylate) (PEG-DA) in addition to self-crosslinking. Particles prepared at low reaction temperatures exhibit the highest degree of spreading due to the lightly cross-linked and flexible polymer network. Moreover, AFM force spectroscopy studies suggest that cross-linker-free microgels constitute of a more homogeneous polymer network than PEG-DA cross-linked particles and have elastic moduli at the particle apex that are ~5 times smaller than the moduli of 5 mol-% PEG-DA cross-linked microgels. Resistive pulse sensing experiments demonstrate that microgels prepared at 75 and 80°C without PEG-DA are able to deform significantly to pass through nanopores that are smaller than the microgel size. Additionally, we found that polymer network flexibility of microgels is a useful tool to control the formation of particle dewetting patterns. This offers a promising new avenue for build-up of 2D self-assembled particle structures with patterned chemical and mechanical properties.

Oligo(ethylene glycol)-sidechain microgels prepared in absence of cross-linking agent: Polymerization, characterization and variation of particle deformability

PubMed Central

Lyon, L. Andrew

2017-01-01

We present a systematic study of self-cross-linked microgels formed by precipitation polymerization of oligo ethylene glycol methacrylates. The cross-linking density of these microgels and, thus, the network flexibility can be easily tuned through the modulation of the reaction temperature during polymerization. Microgels prepared in absence of any difunctional monomer, i.e. cross-linker, show enhanced deformability and particle spreading on solid surfaces as compared to microgels cross-linked with varying amounts of poly(ethylene glycol diacrylate) (PEG-DA) in addition to self-crosslinking. Particles prepared at low reaction temperatures exhibit the highest degree of spreading due to the lightly cross-linked and flexible polymer network. Moreover, AFM force spectroscopy studies suggest that cross-linker-free microgels constitute of a more homogeneous polymer network than PEG-DA cross-linked particles and have elastic moduli at the particle apex that are ~5 times smaller than the moduli of 5 mol-% PEG-DA cross-linked microgels. Resistive pulse sensing experiments demonstrate that microgels prepared at 75 and 80°C without PEG-DA are able to deform significantly to pass through nanopores that are smaller than the microgel size. Additionally, we found that polymer network flexibility of microgels is a useful tool to control the formation of particle dewetting patterns. This offers a promising new avenue for build-up of 2D self-assembled particle structures with patterned chemical and mechanical properties. PMID:28719648

Diclofenac Loaded Lipid Nanovesicles Prepared by Double Solvent Displacement for Skin Drug Delivery.

PubMed

Sala, M; Locher, F; Bonvallet, M; Agusti, G; Elaissari, A; Fessi, H

2017-09-01

Herein, we detail a promising strategy of nanovesicle preparation based on control of phospholipid self-assembly: the Double Solvent Displacement. A systematic study was conducted and diclofenac as drug model encapsulated. In vitro skin studies were carried out to identify better formulation for dermal/transdermal delivery. This method consists in two solvent displacements. The first one, made in a free water environment, has allowed triggering a phospholipid pre-organization. The second one, based on the diffusion into an aqueous phase has led to liposome formation. Homogeneous liposomes were obtained with a size close to 100 nm and a negative zeta potential around -40 mV. After incorporation of acid diclofenac, we obtained nanoliposomes with a size between 101 ± 45 and 133 ± 66 nm, a zeta potential between 34 ± 2 and 49 ± 3 mV, and the encapsulation efficiency (EE%) was between 58 ± 3 and 87 ± 5%. In vitro permeation studies showed that formulation with higher EE% dispayed the higher transdermal passage (18,4% of the applied dose) especially targeting dermis and beyond. Our results suggest that our diclofenac loaded lipid vesicles have significant potential as transdermal skin drug delivery system. Here, we produced cost effective lipid nanovesicles in a merely manner according to a process easily transposable to industrial scale. Graphical Abstract ᅟ.

Development and use of a content search strategy for retrieving studies on patients' views and preferences.

PubMed

Selva, Anna; Solà, Ivan; Zhang, Yuan; Pardo-Hernandez, Hector; Haynes, R Brian; Martínez García, Laura; Navarro, Tamara; Schünemann, Holger; Alonso-Coello, Pablo

2017-08-30

Identifying scientific literature addressing patients' views and preferences is complex due to the wide range of studies that can be informative and the poor indexing of this evidence. Given the lack of guidance we developed a search strategy to retrieve this type of evidence. We assembled an initial list of terms from several sources, including the revision of the terms and indexing of topic-related studies and, methods research literature, and other relevant projects and systematic reviews. We used the relative recall approach, evaluating the capacity of the designed search strategy for retrieving studies included in relevant systematic reviews for the topic. We implemented in practice the final version of the search strategy for conducting systematic reviews and guidelines, and calculated search's precision and the number of references needed to read (NNR). We assembled an initial version of the search strategy, which had a relative recall of 87.4% (yield of 132/out of 151 studies). We then added some additional terms from the studies not initially identified, and re-tested this improved version against the studies included in a new set of systematic reviews, reaching a relative recall of 85.8% (151/out of 176 studies, 95% CI 79.9 to 90.2). This final version of the strategy includes two sets of terms related with two domains: "Patient Preferences and Decision Making" and "Health State Utilities Values". When we used the search strategy for the development of systematic reviews and clinical guidelines we obtained low precision values (ranging from 2% to 5%), and the NNR from 20 to 50. This search strategy fills an important research gap in this field. It will help systematic reviewers, clinical guideline developers, and policy-makers to retrieve published research on patients' views and preferences. In turn, this will facilitate the inclusion of this critical aspect when formulating heath care decisions, including recommendations.

WASTE MINIZATION OPPORTUNITY ASSESSMENT: A CLASS 8 TRUCK ASSEMBLY PLANT

EPA Science Inventory

EPA has developed a systematic approach to identify and implement options to reduce or eliminate hazardous waste. he approach is presented in a report entitled, "Waste Minimization Opportunity Assessment Manual" (EPA/625/7-88/O03). his report describes the application of the wast...

Metallicity and the level of the ultraviolet rising branch in elliptical galaxies

NASA Technical Reports Server (NTRS)

Faber, S. M.

1986-01-01

This final report concerns a project to study the systematics of the ultraviolet flux level in elliptical galaxies. Prior to the inception of this work, the systematic behavior of the ultraviolet flux level was basically unknown and ultraviolet fluxes were observed to vary greatly from galaxy to galaxy. There was a suggestion, however, that there might be a dependence of ultraviolet flux on galaxy metallicity, but the correlation was based on just six galaxies. IUE spectra of elliptical galaxies have been reanalyzed and placed on a consistent, homogenous flux system. The major conclusion is a confirmation of the original hypothesis: galaxies with stronger Mg2 lines show enhanced ultraviolet flux.

"Bed Side" Human Milk Analysis in the Neonatal Intensive Care Unit: A Systematic Review.

PubMed

Fusch, Gerhard; Kwan, Celia; Kotrri, Gynter; Fusch, Christoph

2017-03-01

Human milk analyzers can measure macronutrient content in native breast milk to tailor adequate supplementation with fortifiers. This article reviews all studies using milk analyzers, including (i) evaluation of devices, (ii) the impact of different conditions on the macronutrient analysis of human milk, and (iii) clinical trials to improve growth. Results lack consistency, potentially due to systematic errors in the validation of the device, or pre-analytical sample preparation errors like homogenization. It is crucial to introduce good laboratory and clinical practice when using these devices; otherwise a non-validated clinical usage can severely affect growth outcomes of infants. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantum Chemical Modeling of Enzymatic Reactions: The Case of Decarboxylation.

PubMed

Liao, Rong-Zhen; Yu, Jian-Guo; Himo, Fahmi

2011-05-10

We present a systematic study of the decarboxylation step of the enzyme aspartate decarboxylase with the purpose of assessing the quantum chemical cluster approach for modeling this important class of decarboxylase enzymes. Active site models ranging in size from 27 to 220 atoms are designed, and the barrier and reaction energy of this step are evaluated. To model the enzyme surrounding, homogeneous polarizable medium techniques are used with several dielectric constants. The main conclusion is that when the active site model reaches a certain size, the solvation effects from the surroundings saturate. Similar results have previously been obtained from systematic studies of other classes of enzymes, suggesting that they are of a quite general nature.

Hepatitis Virus Capsid Polymorphs Respond Differently to Changes in Encapsulated Cargo Size

PubMed Central

He, Li; Porterfield, J. Zachary; van der Schoot, Paul; Zlotnick, Adam; Dragnea, Bogdan

2017-01-01

A templated assembly approach for Hepatitis B virus-like particles was employed to determine how the T = 3 and T = 4 polymorphs of the Hepatitis B virus (HBV) icosahedral cores respond to a systematic, gradual change in the encapsulated cargo size. It was found that assembly into complete virus-like particles occurs cooperatively around a variety of core diameters, albeit the degree of cooperativity varies. Among these virus-like particles, it was found that those of an outer diameter similar to T = 4 are able to accommodate the widest range of cargo sizes. PMID:24010404

Comparative performance tests on the Mod-2, 2.5-mW wind turbine with and without vortex generators

NASA Technical Reports Server (NTRS)

Miller, G. E.

1995-01-01

A test program was conducted on the third Mod-2 unit at Goldendale, Washington, to systematically study the effect of vortex generators (VG's) on power performance. The subject unit was first tested without VG's to obtain baseline data. Vortex generators were then installed on the mid-blade assemblies, and the resulting 70% VG configuration was tested. Finally, vortex generators were mounted on the tip assemblies, and data was recorded for the 100% VG configuration. This test program and its results are discussed in this paper. The development of vortex generators is also presented.

Design and analysis of a sub-aperture scanning machine for the transmittance measurements of large-aperture optical system

NASA Astrophysics Data System (ADS)

He, Yingwei; Li, Ping; Feng, Guojin; Cheng, Li; Wang, Yu; Wu, Houping; Liu, Zilong; Zheng, Chundi; Sha, Dingguo

2010-11-01

For measuring large-aperture optical system transmittance, a novel sub-aperture scanning machine with double-rotating arms (SSMDA) was designed to obtain sub-aperture beam spot. Optical system full-aperture transmittance measurements can be achieved by applying sub-aperture beam spot scanning technology. The mathematical model of the SSMDA based on a homogeneous coordinate transformation matrix is established to develop a detailed methodology for analyzing the beam spot scanning errors. The error analysis methodology considers two fundamental sources of scanning errors, namely (1) the length systematic errors and (2) the rotational systematic errors. As the systematic errors of the parameters are given beforehand, computational results of scanning errors are between -0.007~0.028mm while scanning radius is not lager than 400.000mm. The results offer theoretical and data basis to the research on transmission characteristics of large optical system.

Effects of advanced life support versus basic life support on the mortality rates of patients with trauma in prehospital settings: a study protocol for a systematic review and meta-analysis

PubMed Central

Kondo, Yutaka; Fukuda, Tatsuma; Uchimido, Ryo; Hifumi, Toru; Hayashida, Kei

2017-01-01

Introduction Advanced life support (ALS) is thought to be associated with improved survival in prehospital trauma care when compared with basic life support (BLS). However, evidence on the benefits of prehospital ALS for patients with trauma is controversial. Therefore, we aim to clarify if ALS improves mortality in patients with trauma when compared with BLS by conducting a systematic review and meta-analysis of the recent literature. Methods and analysis We will perform searches in PubMed, Embase and the Cochrane Central Register of Controlled Trials for published observational studies, controlled before-and-after studies, randomised controlled trials and other controlled trials conducted in humans and published until March 2017. We will screen search results, assess study selection, extract data and assess the risk of bias in duplicate; disagreements will be resolved through discussions. Data from clinically homogeneous studies will be pooled using a random-effects meta-analysis, heterogeneity of effects will be assessed using the χ2 test of homogeneity, and any observed heterogeneity will be quantified using the I2 statistic. Last, the Grading of Recommendations Assessment, Development and Evaluation approach will be used to rate the quality of the evidence. Ethics and dissemination Our study does not require ethical approval as it is based on findings of previously published articles. Results will be disseminated through publication in a peer-reviewed journal, presentations at relevant conferences and publications for patient information. Trial registration number PROSPERO (International Prospective Register of Systematic Reviews) registration number CRD42017054389. PMID:29061611

Modelling of DNA-Mediated of Two- and -Three dimensional Protein-Protein and Protein-Nanoparticle Self-Assembly

NASA Astrophysics Data System (ADS)

Millan, Jaime; McMillan, Janet; Brodin, Jeff; Lee, Byeongdu; Mirkin, Chad; Olvera de La Cruz, Monica

Programmable DNA interactions represent a robust scheme to self-assemble a rich variety of tunable superlattices, where intrinsic and in some cases non-desirable nano-scale building blocks interactions are substituted for DNA hybridization events. Recent advances in synthesis has allowed the extension of this successful scheme to proteins, where DNA distribution can be tuned independently of protein shape by selectively addressing surface residues, giving rise to assembly properties in three dimensional protein-nanoparticle superlattices dependent on DNA distribution. In parallel to this advances, we introduced a scalable coarse-grained model that faithfully reproduces the previously observed co-assemblies from nanoparticles and proteins conjugates. Herein, we implement this numerical model to explain the stability of complex protein-nanoparticle binary superlattices and to elucidate experimentally inaccessible features such as protein orientation. Also, we will discuss systematic studies that highlight the role of DNA distribution and sequence on two-dimensional protein-protein and protein-nanoparticle superlattices.

Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics1

PubMed Central

Weitemier, Kevin; Straub, Shannon C. K.; Cronn, Richard C.; Fishbein, Mark; Schmickl, Roswitha; McDonnell, Angela; Liston, Aaron

2014-01-01

• Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. • Methods and Results: Genome and transcriptome assemblies for milkweed (Asclepias syriaca) were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nuclear ribosomal DNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. • Conclusions: The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics. PMID:25225629

Is it feasible to estimate radiosonde biases from interlaced measurements?

NASA Astrophysics Data System (ADS)

Kremser, Stefanie; Tradowsky, Jordis S.; Rust, Henning W.; Bodeker, Greg E.

2018-05-01

Upper-air measurements of essential climate variables (ECVs), such as temperature, are crucial for climate monitoring and climate change detection. Because of the internal variability of the climate system, many decades of measurements are typically required to robustly detect any trend in the climate data record. It is imperative for the records to be temporally homogeneous over many decades to confidently estimate any trend. Historically, records of upper-air measurements were primarily made for short-term weather forecasts and as such are seldom suitable for studying long-term climate change as they lack the required continuity and homogeneity. Recognizing this, the Global Climate Observing System (GCOS) Reference Upper-Air Network (GRUAN) has been established to provide reference-quality measurements of climate variables, such as temperature, pressure, and humidity, together with well-characterized and traceable estimates of the measurement uncertainty. To ensure that GRUAN data products are suitable to detect climate change, a scientifically robust instrument replacement strategy must always be adopted whenever there is a change in instrumentation. By fully characterizing any systematic differences between the old and new measurement system a temporally homogeneous data series can be created. One strategy is to operate both the old and new instruments in tandem for some overlap period to characterize any inter-instrument biases. However, this strategy can be prohibitively expensive at measurement sites operated by national weather services or research institutes. An alternative strategy that has been proposed is to alternate between the old and new instruments, so-called interlacing, and then statistically derive the systematic biases between the two instruments. Here we investigate the feasibility of such an approach specifically for radiosondes, i.e. flying the old and new instruments on alternating days. Synthetic data sets are used to explore the applicability of this statistical approach to radiosonde change management.

Computational studies on self-assembled paclitaxel structures: templates for hierarchical block copolymer assemblies and sustained drug release.

PubMed

Guo, Xin D; Tan, Jeremy P K; Kim, Sung H; Zhang, Li J; Zhang, Ying; Hedrick, James L; Yang, Yi Y; Qian, Yu

2009-11-01

Paclitaxel-loaded poly(ethylene oxide)-b-poly(lactide) (PEO-b-PLA) systems have been observed to assemble into fiber structures with remarkably different properties using different chirality and molecular weight of PLA segments. In this study, dissipative particle dynamics (DPD) simulations were carried out to elaborate the microstructures and properties of pure paclitaxel and paclitaxel-loaded PEO-b-PLA systems. Paclitaxel molecules formed ribbon or fiber like structures in water. With the addition of PEO-b-PDLA, PEO-b-PLLA and their stereocomplex, paclitaxel acted as a template and polymer molecules assembled around the paclitaxel structure to form core/shell structured fibers having a PEO shell. For PEO19-b-PDLA27 and PEO19-b-PLLA27 systems, PLA segments and paclitaxel molecules were distributed homogeneously in the core of fibers based on the hydrophobic interactions. In the stereocomplex formulation, paclitaxel molecules were more concentrated in the inner PLA stereocomplex core, which led to slower release of paclitaxel. By increasing the length of PLA segments (e.g. 8,16,22 and 27), the crystalline structure of paclitaxel was gradually weakened and destroyed, which was further proved by X-ray diffraction studies. All the simulation results agreed well with experimental data, suggesting that the DPD simulations may provide a powerful tool for designing drug delivery systems.

Terbium to Quantum Dot FRET Bioconjugates for Clinical Diagnostics: Influence of Human Plasma on Optical and Assembly Properties

PubMed Central

Morgner, Frank; Stufler, Stefan; Geißler, Daniel; Medintz, Igor L.; Algar, W. Russ; Susumu, Kimihiro; Stewart, Michael H.; Blanco-Canosa, Juan B.; Dawson, Philip E.; Hildebrandt, Niko

2011-01-01

Förster resonance energy transfer (FRET) from luminescent terbium complexes (LTC) as donors to semiconductor quantum dots (QDs) as acceptors allows extraordinary large FRET efficiencies due to the long Förster distances afforded. Moreover, time-gated detection permits an efficient suppression of autofluorescent background leading to sub-picomolar detection limits even within multiplexed detection formats. These characteristics make FRET-systems with LTC and QDs excellent candidates for clinical diagnostics. So far, such proofs of principle for highly sensitive multiplexed biosensing have only been performed under optimized buffer conditions and interactions between real-life clinical media such as human serum or plasma and LTC-QD-FRET-systems have not yet been taken into account. Here we present an extensive spectroscopic analysis of absorption, excitation and emission spectra along with the luminescence decay times of both the single components as well as the assembled FRET-systems in TRIS-buffer, TRIS-buffer with 2% bovine serum albumin, and fresh human plasma. Moreover, we evaluated homogeneous LTC-QD FRET assays in QD conjugates assembled with either the well-known, specific biotin-streptavidin biological interaction or, alternatively, the metal-affinity coordination of histidine to zinc. In the case of conjugates assembled with biotin-streptavidin no significant interference with the optical and binding properties occurs whereas the histidine-zinc system appears to be affected by human plasma. PMID:22163719

Lipid self-assembly and lectin-induced reorganization of the plasma membrane.

PubMed

Sych, Taras; Mély, Yves; Römer, Winfried

2018-05-26

The plasma membrane represents an outstanding example of self-organization in biology. It plays a vital role in protecting the integrity of the cell interior and regulates meticulously the import and export of diverse substances. Its major building blocks are proteins and lipids, which self-assemble to a fluid lipid bilayer driven mainly by hydrophobic forces. Even if the plasma membrane appears-globally speaking-homogeneous at physiological temperatures, the existence of specialized nano- to micrometre-sized domains of raft-type character within cellular and synthetic membrane systems has been reported. It is hypothesized that these domains are the origin of a plethora of cellular processes, such as signalling or vesicular trafficking. This review intends to highlight the driving forces of lipid self-assembly into a bilayer membrane and the formation of small, transient domains within the plasma membrane. The mechanisms of self-assembly depend on several factors, such as the lipid composition of the membrane and the geometry of lipids. Moreover, the dynamics and organization of glycosphingolipids into nanometre-sized clusters will be discussed, also in the context of multivalent lectins, which cluster several glycosphingolipid receptor molecules and thus create an asymmetric stress between the two membrane leaflets, leading to tubular plasma membrane invaginations.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Folding DNA into a Lipid-Conjugated Nanobarrel for Controlled Reconstitution of Membrane Proteins.

PubMed

Dong, Yuanchen; Chen, Shuobing; Zhang, Shijian; Sodroski, Joseph; Yang, Zhongqiang; Liu, Dongsheng; Mao, Youdong

2018-02-19

Building upon DNA origami technology, we introduce a method to reconstitute a single membrane protein into a self-assembled DNA nanobarrel that scaffolds a nanodisc-like lipid environment. Compared with the membrane-scaffolding-protein nanodisc technique, our approach gives rise to defined stoichiometry, controlled sizes, as well as enhanced stability and homogeneity in membrane protein reconstitution. We further demonstrate potential applications of the DNA nanobarrels in the structural analysis of membrane proteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

One-step hydrothermal synthesis of hexangular starfruit-like vanadium oxide for high power aqueous supercapacitors

NASA Astrophysics Data System (ADS)

Shao, Jie; Li, Xinyong; Qu, Qunting; Zheng, Honghe

2012-12-01

Homogenous hexangular starfruit-like vanadium oxide was prepared for the first time by a one-step hydrothermal method. The assembly process of hexangular starfruit-like structure was observed from TEM images. The electrochemical performance of starfruit-like vanadium oxide was examined by cyclic voltammetry and galvanostatic charge/discharge. The obtained starfruit-like vanadium oxide exhibits a high power capability (19 Wh kg-1 at the specific power of 3.4 kW kg-1) and good cycling stability for supercapacitors application.

A new configuration of membrane stack for retrieval of nickel absorbed in resins*

PubMed Central

Chen, Xue-fen; Wu, Zu-cheng

2005-01-01

A new configuration integrated ion exchange effect with both electro-migration and electrochemical reaction in a single cell was developed to effectively retrieve metal ions from simulated wastewater using ion exchange resins without additive chemicals. By simply assembling cation exchange resins and anion exchange resins separated by homogeneous membranes, we found that the system will always be acidic in the concentrate compartment so that ion exchange resins could be in-situ regenerated without hydroxide precipitation. Such a realizable design will be really suitable for wastewater purification. PMID:15909341

A novel strategy towards designing a CdSe quantum dot-metallohydrogel composite material.

PubMed

Chatterjee, Sayantan; Maitra, Uday

2016-08-11

We have described here an efficient method to disperse hydrophobic CdSe quantum dots (QDs) in an aqueous phase using cetyltrimethylammonium bromide (CTAB) micelles without any surface ligand exchange. The water soluble QDs were then embedded in 3D self assembled fibrillar networks (SAFINs) of a hydrogel showing homogeneous dispersibility as evidenced from optical and electron microscopic techniques. The photophysical studies of the hydrogel-QD composite are reported for the first time. These composite materials may have potential applications in biology, optoelectronics, sensors, non-linear optics and materials science.

How to Assess the External Validity and Model Validity of Therapeutic Trials: A Conceptual Approach to Systematic Review Methodology

PubMed Central

2014-01-01

Background. Evidence rankings do not consider equally internal (IV), external (EV), and model validity (MV) for clinical studies including complementary and alternative medicine/integrative medicine (CAM/IM) research. This paper describe this model and offers an EV assessment tool (EVAT©) for weighing studies according to EV and MV in addition to IV. Methods. An abbreviated systematic review methodology was employed to search, assemble, and evaluate the literature that has been published on EV/MV criteria. Standard databases were searched for keywords relating to EV, MV, and bias-scoring from inception to Jan 2013. Tools identified and concepts described were pooled to assemble a robust tool for evaluating these quality criteria. Results. This study assembled a streamlined, objective tool to incorporate for the evaluation of quality of EV/MV research that is more sensitive to CAM/IM research. Conclusion. Improved reporting on EV can help produce and provide information that will help guide policy makers, public health researchers, and other scientists in their selection, development, and improvement in their research-tested intervention. Overall, clinical studies with high EV have the potential to provide the most useful information about “real-world” consequences of health interventions. It is hoped that this novel tool which considers IV, EV, and MV on equal footing will better guide clinical decision making. PMID:24734111

In vivo particle polymorphism results from deletion of a N-terminal peptide molecular switch in brome mosaic virus capsid protein

PubMed Central

Calhoun, Shauni L; Speir, Jeffrey A; Rao, A.L.N.

2009-01-01

The interaction between brome mosaic virus (BMV) coat protein (CP) and viral RNA is a carefully orchestrated process resulting in the formation of homogeneous population of infectious virions with T=3 symmetry. Expression in vivo of either wild type or mutant BMV CP through homologous replication never results in the assembly of aberrant particles. In this study, we report that deletion of amino acid residues 41–47 from the N-proximal region of BMV CP resulted in the assembly of polymorphic virions in vivo. Purified virions from symptomatic leaves remain non-infectious and Northern blot analysis of virion RNA displayed packaging defects. Biochemical of variant CP by circular dichroism and MALDI-TOF, respectively, revealed that the engineered deletion affected the protein structure and capsid dynamics. Most significantly, CP subunits dissociated from polymorphic virions are incompetent for in vitro reassembly. Based on these observations, we propose a chaperon mediated mechanism for the assembly of variant CP in vivo and also hypothesize that 41KAIKAIA47 N-proximal peptide functions as a molecular switch in regulating T= 3 virion symmetry. PMID:17449079

Self-assembly of the yeast actomyosin contractile ring as an aggregation process: kinetics of formation and instability regimes

NASA Astrophysics Data System (ADS)

Ojkic, Nikola; Vavylonis, Dimitrios

2009-03-01

Fission yeast cells assemble an equatorial contractile ring for cytokinesis, the last step of mitosis. The ring assembles from ˜ 65 membrane-bound ``nodes''' containing myosin motors and other proteins. Actin filaments that grow out from the nodes establish transient connections among the nodes and aid in pulling them together in a process that appears as pair-wise attraction (Vavylonis et al. Science 97:319, 2008). We used scaling arguments, coarse grained stability analysis of homogeneous states, and Monte Carlo simulations of simple models, to explore the conditions that yield fast and efficient ring formation, as opposed to formation of isolated clumps. We described our results as a function of: number of nodes, rate of establishing connections, range of node interaction, distance traveled per node interaction and broad band width, w. Uniform cortical 2d distributions of nodes are stable over short times due to randomness of connections among nodes, but become unstable over long times due to fluctuations in the initial node distribution. Successful condensation of nodes into a ring requires sufficiently small w such that lateral contraction occurs faster then clump formation.

Multibuilding Block Janus Synthesized by Seed-Mediated Self-Assembly for Enhanced Photothermal Effects and Colored Brownian Motion in an Optical Trap.

PubMed

Sansanaphongpricha, Kanokwan; DeSantis, Michael C; Chen, Hongwei; Cheng, Wei; Sun, Kai; Wen, Bo; Sun, Duxin

2017-02-01

The asymmetrical features and unique properties of multibuilding block Janus nanostructures (JNSs) provide superior functions for biomedical applications. However, their production process is very challenging. This problem has hampered the progress of JNS research and the exploration of their applications. In this study, an asymmetrical multibuilding block gold/iron oxide JNS has been generated to enhance photothermal effects and display colored Brownian motion in an optical trap. JNS is formed by seed-mediated self-assembly of nanoparticle-loaded thermocleavable micelles, where the hydrophobic backbones of the polymer are disrupted at high temperatures, resulting in secondary self-assembly and structural rearrangement. The JNS significantly enhances photothermal effects compared to their homogeneous counterpart after near-infrared (NIR) light irradiation. The asymmetrical distribution of gold and iron oxide within JNS also generates uneven thermophoretic force to display active colored Brownian rotational motion in a single-beam gradient optical trap. These properties indicate that the asymmetrical JNS could be employed as a strong photothermal therapy mediator and a fuel-free nanoscale Janus motor under NIR light. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Initial condition of stochastic self-assembly

NASA Astrophysics Data System (ADS)

Davis, Jason K.; Sindi, Suzanne S.

2016-02-01

The formation of a stable protein aggregate is regarded as the rate limiting step in the establishment of prion diseases. In these systems, once aggregates reach a critical size the growth process accelerates and thus the waiting time until the appearance of the first critically sized aggregate is a key determinant of disease onset. In addition to prion diseases, aggregation and nucleation is a central step of many physical, chemical, and biological process. Previous studies have examined the first-arrival time at a critical nucleus size during homogeneous self-assembly under the assumption that at time t =0 the system was in the all-monomer state. However, in order to compare to in vivo biological experiments where protein constituents inherited by a newly born cell likely contain intermediate aggregates, other possibilities must be considered. We consider one such possibility by conditioning the unique ergodic size distribution on subcritical aggregate sizes; this least-informed distribution is then used as an initial condition. We make the claim that this initial condition carries fewer assumptions than an all-monomer one and verify that it can yield significantly different averaged waiting times relative to the all-monomer condition under various models of assembly.

Chemical Functionalization, Self-Assembly, and Applications of Nanomaterials and Nanocomposites

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

Jiao, Tifeng; Yan, Xingbin; Balan, Lavinia

2014-01-01

This special issue addresses the research studies on chemical functionalization, self-assembly, and applications of nanomaterials and nanocomposites. It contains twentyfour articles including two reviews and twenty-two research articles. It is used to create new functional nanomaterials and nanocomposites with a variety of sizes and morphologies such as Zn/Al layered double hydroxide, tin oxide nanowires, FeOOH-modified anion resin, Au nanoclusters silica composite nanospheres, Ti-doped ZnO sol-composite films, TiO2/ZnO composite, graphene oxide nanocomposites, LiFePO4/C nanocomposites, and chitosan nanoparticles. These nanomaterials and nanocomposites have widespread applications in tissue engineering, antitumor, sensors, photoluminescence, electrochemical, and catalytic properties. In addition, this themed issue includes somemore » research articles about self-assembly systems covering organogels and Langmuir films. Furthermore, B. Blasiak et al. performed a literature survey on the recent advances in production, functionalization, toxicity reduction, and application of nanoparticles in cancer diagnosis, treatment, and treatment monitoring. P. Colson et al. performed a literature survey on the recent advances in nanosphere lithography due to its compatibility with wafer-scale processes as well as its potential to manufacture a wide variety of homogeneous one-, two-, or three-dimensional nanostructures.« less

GDP-tubulin incorporation into growing microtubules modulates polymer stability.

PubMed

Valiron, Odile; Arnal, Isabelle; Caudron, Nicolas; Job, Didier

2010-06-04

Microtubule growth proceeds through the endwise addition of nucleotide-bound tubulin dimers. The microtubule wall is composed of GDP-tubulin subunits, which are thought to come exclusively from the incorporation of GTP-tubulin complexes at microtubule ends followed by GTP hydrolysis within the polymer. The possibility of a direct GDP-tubulin incorporation into growing polymers is regarded as hardly compatible with recent structural data. Here, we have examined GTP-tubulin and GDP-tubulin incorporation into polymerizing microtubules using a minimal assembly system comprised of nucleotide-bound tubulin dimers, in the absence of free nucleotide. We find that GDP-tubulin complexes can efficiently co-polymerize with GTP-tubulin complexes during microtubule assembly. GDP-tubulin incorporation into microtubules occurs with similar efficiency during bulk microtubule assembly as during microtubule growth from seeds or centrosomes. Microtubules formed from GTP-tubulin/GDP-tubulin mixtures display altered microtubule dynamics, in particular a decreased shrinkage rate, apparently due to intrinsic modifications of the polymer disassembly properties. Thus, although microtubules polymerized from GTP-tubulin/GDP-tubulin mixtures or from homogeneous GTP-tubulin solutions are both composed of GDP-tubulin subunits, they have different dynamic properties, and this may reveal a novel form of microtubule "structural plasticity."

Effect of internal flow and evaporation on hydrogel assembly process at droplet interface

NASA Astrophysics Data System (ADS)

Kang, Giho; Seong, Baekhoon; Gim, Yeonghyeon; Ko, Han Seo; Byun, Doyoung

2017-11-01

Recently, controlling the behavior of nanoparticles inside liquid droplet has been widely studied. There have been many reports about the mechanism of the nanoparticles assembly and fabrication of a thin film on a substrate. However, the assembly mechanism at a liquid-air interface has not been clearly understood to form polymer chains into films. Herein, we investigated the role of internal flow on the thin film assembly process at the interface of the hydrogel droplet. The internal fluid flow during the formation of the hydrogel film was visualized systematically using micro-PIV (Particle image velocimetry) technique at various temperatures. We show that the buoyancy effect and convection flow induced by heat can affect the film morphology and its mechanical characteristics. Due to the accelerated fluid flow inside the droplet and evaporation flux, densely assembled hydrogel film was able to be formed. Film strength was increased 24% with temperature increase from 40 to 80 degrees Celsius. We expect our investigations could be applied to many applications such as self-assembly of planar structures at the interface in coating and printing process. The support from the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (NRF-2015R1A2A1A05001829) is acknowledged.

Filtration-guided assembly for patterning one-dimensional nanostructures

NASA Astrophysics Data System (ADS)

Zhang, Yaozhong; Wang, Chuan; Yeom, Junghoon

2017-04-01

Tremendous progress has been made in synthesizing various types of one-dimensional (1D) nanostructures (NSs), such as nanotubes and nanowires, but some technical challenges still remain in the deterministic assembly of the solution-processed 1D NSs for device integration. In this work we investigate a scalable yet inexpensive nanomaterial assembly method, namely filtration-guided assembly (FGA), to place nanomaterials into desired locations as either an individual entity or ensembles, and form functional devices. FGA not only addresses the assembly challenges but also encompasses the notion of green nanomanufacturing, maximally utilizing nanomaterials and eliminating a waste stream of nanomaterials into the environment. FGA utilizes selective filtration of 1D NSs through the open windows on the nanoporous filter membrane whose surface is patterned by a polymer mask for guiding the 1D NS deposition. The modified soft-lithographic technique called blanket transfer (BT) is employed to create the various photoresist patterns of sub-10-micron resolution on the nanoporous filter membrane like mixed cellulose acetate. We use single-walled carbon nanotubes (SWCNTs) as a model 1D NS and demonstrate the fabrication of an array pattern of homogeneous 1D NS network films over an area of 20 cm2 within 10 min. The FGA-patterned SWCNT network films are transferred onto the substrate using the adhesive-based transfer technique, and show the highly uniform film thickness and resistance measurements across the entire substrate. Finally, the electrical performance of the back-gated transistors made from the FGA and transfer method of 95% pure SWCNTs is demonstrated.

Filtration-guided assembly for patterning one-dimensional nanostructures.

PubMed

Zhang, Yaozhong; Wang, Chuan; Yeom, Junghoon

2017-04-07

Tremendous progress has been made in synthesizing various types of one-dimensional (1D) nanostructures (NSs), such as nanotubes and nanowires, but some technical challenges still remain in the deterministic assembly of the solution-processed 1D NSs for device integration. In this work we investigate a scalable yet inexpensive nanomaterial assembly method, namely filtration-guided assembly (FGA), to place nanomaterials into desired locations as either an individual entity or ensembles, and form functional devices. FGA not only addresses the assembly challenges but also encompasses the notion of green nanomanufacturing, maximally utilizing nanomaterials and eliminating a waste stream of nanomaterials into the environment. FGA utilizes selective filtration of 1D NSs through the open windows on the nanoporous filter membrane whose surface is patterned by a polymer mask for guiding the 1D NS deposition. The modified soft-lithographic technique called blanket transfer (BT) is employed to create the various photoresist patterns of sub-10-micron resolution on the nanoporous filter membrane like mixed cellulose acetate. We use single-walled carbon nanotubes (SWCNTs) as a model 1D NS and demonstrate the fabrication of an array pattern of homogeneous 1D NS network films over an area of 20 cm 2 within 10 min. The FGA-patterned SWCNT network films are transferred onto the substrate using the adhesive-based transfer technique, and show the highly uniform film thickness and resistance measurements across the entire substrate. Finally, the electrical performance of the back-gated transistors made from the FGA and transfer method of 95% pure SWCNTs is demonstrated.

Emitter and absorber assembly for multiple self-dual operation and directional transparency

NASA Astrophysics Data System (ADS)

Kalozoumis, P. A.; Morfonios, C. V.; Kodaxis, G.; Diakonos, F. K.; Schmelcher, P.

2017-03-01

We demonstrate how to systematically design wave scattering systems with simultaneous coherent perfect absorbing and lasing operation at multiple and prescribed frequencies. The approach is based on the recursive assembly of non-Hermitian emitter and absorber units into self-dual emitter-absorber trimers at different composition levels, exploiting the simple structure of the corresponding transfer matrices. In particular, lifting the restriction to parity-time-symmetric setups enables the realization of emitter and absorber action at distinct frequencies and provides flexibility with respect to the choice of realistic parameters. We further show how the same assembled scatterers can be rearranged to produce unidirectional and bidirectional transparency at the selected frequencies. With the design procedure being generically applicable to wave scattering in single-channel settings, we demonstrate it with concrete examples of photonic multilayer setups.

Opportunities for improving legislative public health policy in Rhode Island through evidence-based education.

PubMed

Bourdeau, Moise; Winter, Ronald; Marshall, Robert

2013-10-01

The Rhode Island General Assembly considers nearly 3000 bills yearly--spanning the entire range of issues related to state government and legislative policy. This review analyzes the modest number of 40 "health-related" bills introduced during the 2009 session. It is often not clear to what extent these proposals consistently received analysis by both informed and independent organizations or experts regarding their "evidence-based" foundations. Only 25 of these bills received a committee hearing, and eventually become law. Hence, there may be a reasonable opportunity for expert, non-partisan organizations to provide the General Assembly with information related to proposed legislation on a routine or "as requested" basis. This study provides a systematic analysis of this degree of effort based on data regarding health- related legislation proposed during the 2009 session of the RI General Assembly.

The ESA GOME-Evolution "Climate" water vapor product: a homogenized time series of H2O columns from GOME, SCIAMACHY, and GOME-2

NASA Astrophysics Data System (ADS)

Beirle, Steffen; Lampel, Johannes; Wang, Yang; Mies, Kornelia; Dörner, Steffen; Grossi, Margherita; Loyola, Diego; Dehn, Angelika; Danielczok, Anja; Schröder, Marc; Wagner, Thomas

2018-03-01

We present time series of the global distribution of water vapor columns over more than 2 decades based on measurements from the satellite instruments GOME, SCIAMACHY, and GOME-2 in the red spectral range. A particular focus is the consistency amongst the different sensors to avoid jumps from one instrument to another. This is reached by applying robust and simple retrieval settings consistently. Potentially systematic effects due to differences in ground pixel size are avoided by merging SCIAMACHY and GOME-2 observations to GOME spatial resolution, which also allows for a consistent treatment of cloud effects. In addition, the GOME-2 swath is reduced to that of GOME and SCIAMACHY to have consistent viewing geometries.Remaining systematic differences between the different sensors are investigated during overlap periods and are corrected for in the homogenized time series. The resulting Climate product v2.2 (https://doi.org/10.1594/WDCC/GOME-EVL_water_vapor_clim_v2.2) allows the study of the temporal evolution of water vapor over the last 20 years on a global scale.

Effects of foot reflexology on fatigue, sleep and pain: a systematic review and meta-analysis.

PubMed

Lee, Jeongsoon; Han, Misook; Chung, Younghae; Kim, Jinsun; Choi, Jungsook

2011-12-01

The purpose of this study was to evaluate the effectiveness of foot reflexology on fatigue, sleep and pain. A systematic review and meta-analysis were conducted. Electronic database and manual searches were conducted on all published studies reporting the effects of foot reflexology on fatigue, sleep, and pain. Forty four studies were eligible including 15 studies associated with fatigue, 18 with sleep, and 11 with pain. The effects of foot reflexology were analyzed using Comprehensive Meta-Analysis Version 2.0. The homogeneity and the fail-safe N were calculated. Moreover, a funnel plot was used to assess publication bias. The effects on fatigue, sleep, and pain were not homogeneous and ranged from 0.63 to 5.29, 0.01 to 3.22, and 0.43 to 2.67, respectively. The weighted averages for fatigue, sleep, and pain were 1.43, 1.19, and 1.35, respectively. No publication bias was detected as evaluated by fail-safe N. Foot reflexology had a larger effect on fatigue and sleep and a smaller effect on pain. This meta-analysis indicates that foot reflexology is a useful nursing intervention to relieve fatigue and to promote sleep. Further studies are needed to evaluate the effects of foot reflexology on outcome variables other than fatigue, sleep and pain.

Systematic Approach for the Formulation and Optimization of Solid Lipid Nanoparticles of Efavirenz by High Pressure Homogenization Using Design of Experiments for Brain Targeting and Enhanced Bioavailability

PubMed Central

Gupta, Shweta; Kesarla, Rajesh; Chotai, Narendra; Misra, Ambikanandan

2017-01-01

The nonnucleoside reverse transcriptase inhibitors, used for the treatment of HIV infections, are reported to have low bioavailability pertaining to high first-pass metabolism, high protein binding, and enzymatic metabolism. They also show low permeability across blood brain barrier. The CNS is reported to be the most important HIV reservoir site. In the present study, solid lipid nanoparticles of efavirenz were prepared with the objective of providing increased permeability and protection of drug due to biocompatible lipidic content and nanoscale size and thus developing formulation having potential for enhanced bioavailability and brain targeting. Solid lipid nanoparticles were prepared by high pressure homogenization technique using a systematic approach of design of experiments (DoE) and evaluated for particle size, polydispersity index, zeta potential, and entrapment efficiency. Particles of average size 108.5 nm having PDI of 0.172 with 64.9% entrapment efficiency were produced. Zeta potential was found to be −21.2 mV and the formulation was found stable. The in-vivo pharmacokinetic studies revealed increased concentration of the drug in brain, as desired, when administered through intranasal route indicating its potential for an attempt towards complete eradication of HIV and cure of HIV-infected patients. PMID:28243600

Apparent cosmic acceleration from Type Ia supernovae

NASA Astrophysics Data System (ADS)

Dam, Lawrence H.; Heinesen, Asta; Wiltshire, David L.

2017-11-01

Parameters that quantify the acceleration of cosmic expansion are conventionally determined within the standard Friedmann-Lemaître-Robertson-Walker (FLRW) model, which fixes spatial curvature to be homogeneous. Generic averages of Einstein's equations in inhomogeneous cosmology lead to models with non-rigidly evolving average spatial curvature, and different parametrizations of apparent cosmic acceleration. The timescape cosmology is a viable example of such a model without dark energy. Using the largest available supernova data set, the JLA catalogue, we find that the timescape model fits the luminosity distance-redshift data with a likelihood that is statistically indistinguishable from the standard spatially flat Λ cold dark matter cosmology by Bayesian comparison. In the timescape case cosmic acceleration is non-zero but has a marginal amplitude, with best-fitting apparent deceleration parameter, q_{0}=-0.043^{+0.004}_{-0.000}. Systematic issues regarding standardization of supernova light curves are analysed. Cuts of data at the statistical homogeneity scale affect light-curve parameter fits independent of cosmology. A cosmological model dependence of empirical changes to the mean colour parameter is also found. Irrespective of which model ultimately fits better, we argue that as a competitive model with a non-FLRW expansion history, the timescape model may prove a useful diagnostic tool for disentangling selection effects and astrophysical systematics from the underlying expansion history.

Rational Design of Si@SiO2/C Composites Using Sustainable Cellulose as a Carbon Resource for Anodes in Lithium-Ion Batteries.

PubMed

Shen, Dazhi; Huang, Chaofan; Gan, Lihui; Liu, Jian; Gong, Zhengliang; Long, Minnan

2018-03-07

In this work, we propose a novel and facile route for the rational design of Si@SiO 2 /C anode materials by using sustainable and environment-friendly cellulose as a carbon resource. To simultaneously obtain a SiO 2 layer and a carbon scaffold, a specially designed homogeneous cellulose solution and commercial Si nanopowder are used as the starting materials, and the cellulose/Si composite is directly assembled by an in situ regenerating method. Subsequently, Si@SiO 2 /C composite is obtained after carbonization. As expected, Si@SiO 2 is homogeneously encapsulated in the cellulose-derived carbon network. The obtained Si@SiO 2 /C composite shows a high reversible capacity of 1071 mA h g -1 at a current density of 420 mA g -1 and 70% capacity retention after 200 cycles. This novel, sustainable, and effective design is a promising approach to obtain high-performance and cost-effective composite anodes for practical applications.

Advanced nodal neutron diffusion method with space-dependent cross sections: ILLICO-VX

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

Rajic, H.L.; Ougouag, A.M.

1987-01-01

Advanced transverse integrated nodal methods for neutron diffusion developed since the 1970s require that node- or assembly-homogenized cross sections be known. The underlying structural heterogeneity can be accurately accounted for in homogenization procedures by the use of heterogeneity or discontinuity factors. Other (milder) types of heterogeneity, burnup-induced or due to thermal-hydraulic feedback, can be resolved by explicitly accounting for the spatial variations of material properties. This can be done during the nodal computations via nonlinear iterations. The new method has been implemented in the code ILLICO-VX (ILLICO variable cross-section method). Numerous numerical tests were performed. As expected, the convergence ratemore » of ILLICO-VX is lower than that of ILLICO, requiring approx. 30% more outer iterations per k/sub eff/ computation. The methodology has also been implemented as the NOMAD-VX option of the NOMAD, multicycle, multigroup, two- and three-dimensional nodal diffusion depletion code. The burnup-induced heterogeneities (space dependence of cross sections) are calculated during the burnup steps.« less

Composite solid-state scintillators for neutron detection

DOEpatents

Dai, Sheng; Im, Hee-Jung; Pawel, Michelle D.

2006-09-12

Applicant's present invention is a composite scintillator for neutron detection comprising a matrix material fabricated from an inorganic sol-gel precursor solution homogeneously doped with a liquid scintillating material and a neutron absorbing material. The neutron absorbing material yields at least one of an electron, a proton, a triton, an alpha particle or a fission fragment when the neutron absorbing material absorbs a neutron. The composite scintillator further comprises a liquid scintillating material in a self-assembled micelle formation homogeneously doped in the matrix material through the formation of surfactant-silica composites. The scintillating material is provided to scintillate when traversed by at least one of an electron, a proton, a triton, an alpha particle or a fission fragment. The scintillating material is configured such that the matrix material surrounds the micelle formation of the scintillating material. The composite scintillator is fabricated and applied as a thin film on substrate surfaces, a coating on optical fibers or as a glass material.

Novel stable dendrimersome formulation for safe bioimaging applications

NASA Astrophysics Data System (ADS)

Filippi, M.; Patrucco, D.; Martinelli, J.; Botta, M.; Castro-Hartmann, P.; Tei, L.; Terreno, E.

2015-07-01

Dendrimersomes are nanosized vesicles constituted by amphiphilic Janus dendrimers (JDs), which have been recently proposed as innovative nanocarriers for biomedical applications. Recently, we have demonstrated that dendrimersomes self-assembled from (3,5)12G1-PE-BMPA-G2-(OH)8 dendrimers can be successfully loaded with hydrophilic and amphiphilic imaging contrast agents. Here, we present two newly synthesized low generation isomeric JDs: JDG0G1(3,5) and JDG0G1(3,4). Though less branched than the above-cited dendrimers, they retain the ability to form self-assembled, almost monodisperse vesicular nanoparticles. This contribution reports on the characterization of such nanovesicles loaded with the clinically approved MRI probe Gadoteridol and the comparison with the related nanoparticles assembled from more branched dendrimers. Special emphasis was given to the in vitro stability test of the systems in biologically relevant media, complemented by preliminary in vivo data about blood circulation lifetime collected from healthy mice. The results point to very promising safety and stability profiles of the nanovesicles, in particular for those made of JDG0G1(3,5), whose spontaneous self-organization in water gives rise to a homogeneous suspension. Importantly, the blood lifetimes of these systems are comparable to those of standard liposomes. By virtue of the reported results, the herein presented nanovesicles augur well for future use in a variety of biomedical applications.Dendrimersomes are nanosized vesicles constituted by amphiphilic Janus dendrimers (JDs), which have been recently proposed as innovative nanocarriers for biomedical applications. Recently, we have demonstrated that dendrimersomes self-assembled from (3,5)12G1-PE-BMPA-G2-(OH)8 dendrimers can be successfully loaded with hydrophilic and amphiphilic imaging contrast agents. Here, we present two newly synthesized low generation isomeric JDs: JDG0G1(3,5) and JDG0G1(3,4). Though less branched than the above-cited dendrimers, they retain the ability to form self-assembled, almost monodisperse vesicular nanoparticles. This contribution reports on the characterization of such nanovesicles loaded with the clinically approved MRI probe Gadoteridol and the comparison with the related nanoparticles assembled from more branched dendrimers. Special emphasis was given to the in vitro stability test of the systems in biologically relevant media, complemented by preliminary in vivo data about blood circulation lifetime collected from healthy mice. The results point to very promising safety and stability profiles of the nanovesicles, in particular for those made of JDG0G1(3,5), whose spontaneous self-organization in water gives rise to a homogeneous suspension. Importantly, the blood lifetimes of these systems are comparable to those of standard liposomes. By virtue of the reported results, the herein presented nanovesicles augur well for future use in a variety of biomedical applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr02695d

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

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

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

DOE PAGES

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.; ...

2017-07-18

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

PubMed Central

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Richard A.; Brown, Steven D.

2017-01-01

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences. PMID:28769883

Distinct roles for Arp2/3 regulators in actin assembly and endocytosis.

PubMed

Galletta, Brian J; Chuang, Dennis Y; Cooper, John A

2008-01-01

The Arp2/3 complex is essential for actin assembly and motility in many cell processes, and a large number of proteins have been found to bind and regulate it in vitro. A critical challenge is to understand the actions of these proteins in cells, especially in settings where multiple regulators are present. In a systematic study of the sequential multicomponent actin assembly processes that accompany endocytosis in yeast, we examined and compared the roles of WASp, two type-I myosins, and two other Arp2/3 activators, along with that of coronin, which is a proposed inhibitor of Arp2/3. Quantitative analysis of high-speed fluorescence imaging revealed individual functions for the regulators, manifested in part by novel phenotypes. We conclude that Arp2/3 regulators have distinct and overlapping roles in the processes of actin assembly that drive endocytosis in yeast. The formation of the endocytic actin patch, the creation of the endocytic vesicle, and the movement of the vesicle into the cytoplasm display distinct dependencies on different Arp2/3 regulators. Knowledge of these roles provides insight into the in vivo relevance of the dendritic nucleation model for actin assembly.

Nuclear imaging of the fuel assembly in ignition experiments

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

Grim, G. P.; Guler, N.; Merrill, F. E.

First results from the analysis of neutron image data collected on implosions of cryogenically layered deuterium-tritium capsules during the 2011-2012 National Ignition Campaign are reported. The data span a variety of experimental designs aimed at increasing the stagnation pressure of the central hotspot and areal density of the surrounding fuel assembly. Images of neutrons produced by deuterium–tritium fusion reactions in the hotspot are presented, as well as images of neutrons that scatter in the surrounding dense fuel assembly. The image data are compared with 1D and 2D model predictions, and consistency checked using other diagnostic data. The results indicate thatmore » the size of the fusing hotspot is consistent with the model predictions, as well as other imaging data, while the overall size of the fuel assembly, inferred from the scattered neutron images, is systematically smaller than models’ prediction. Preliminary studies indicate these differences are consistent with a significant fraction (20%–25%) of the initial deuterium-tritium fuel mass outside the compact fuel assembly, due either to low mode mass asymmetry or high mode 3D mix effects at the ablator-ice interface.« less

Effects of Different Manufacturing Processes on TEMPO-Oxidized Carboxylated Cellulose Nanofiber Performance as Binder for Flexible Lithium-Ion Batteries.

PubMed

Lu, Huiran; Guccini, Valentina; Kim, Hyeyun; Salazar-Alvarez, German; Lindbergh, Göran; Cornell, Ann

2017-11-01

Carboxylated cellulose nanofibers (CNF) prepared using the TEMPO-route are good binders of electrode components in flexible lithium-ion batteries (LIB). However, the different parameters employed for the defibrillation of CNF such as charge density and degree of homogenization affect its properties when used as binder. This work presents a systematic study of CNF prepared with different surface charge densities and varying degrees of homogenization and their performance as binder for flexible LiFePO 4 electrodes. The results show that the CNF with high charge density had shorter fiber lengths compared with those of CNF with low charge density, as observed with atomic force microscopy. Also, CNF processed with a large number of passes in the homogenizer showed a better fiber dispersibility, as observed from rheological measurements. The electrodes fabricated with highly charged CNF exhibited the best mechanical and electrochemical properties. The CNF at the highest charge density (1550 μmol g -1 ) and lowest degree of homogenization (3 + 3 passes in the homogenizer) achieved the overall best performance, including a high Young's modulus of approximately 311 MPa and a good rate capability with a stable specific capacity of 116 mAh g -1 even up to 1 C. This work allows a better understanding of the influence of the processing parameters of CNF on their performance as binder for flexible electrodes. The results also contribute to the understanding of the optimal processing parameters of CNF to fabricate other materials, e.g., membranes or separators.

Toward reliable characterization of functional homogeneity in the human brain: Preprocessing, scan duration, imaging resolution and computational space

PubMed Central

Zuo, Xi-Nian; Xu, Ting; Jiang, Lili; Yang, Zhi; Cao, Xiao-Yan; He, Yong; Zang, Yu-Feng; Castellanos, F. Xavier; Milham, Michael P.

2013-01-01

While researchers have extensively characterized functional connectivity between brain regions, the characterization of functional homogeneity within a region of the brain connectome is in early stages of development. Several functional homogeneity measures were proposed previously, among which regional homogeneity (ReHo) was most widely used as a measure to characterize functional homogeneity of resting state fMRI (R-fMRI) signals within a small region (Zang et al., 2004). Despite a burgeoning literature on ReHo in the field of neuroimaging brain disorders, its test–retest (TRT) reliability remains unestablished. Using two sets of public R-fMRI TRT data, we systematically evaluated the ReHo’s TRT reliability and further investigated the various factors influencing its reliability and found: 1) nuisance (head motion, white matter, and cerebrospinal fluid) correction of R-fMRI time series can significantly improve the TRT reliability of ReHo while additional removal of global brain signal reduces its reliability, 2) spatial smoothing of R-fMRI time series artificially enhances ReHo intensity and influences its reliability, 3) surface-based R-fMRI computation largely improves the TRT reliability of ReHo, 4) a scan duration of 5 min can achieve reliable estimates of ReHo, and 5) fast sampling rates of R-fMRI dramatically increase the reliability of ReHo. Inspired by these findings and seeking a highly reliable approach to exploratory analysis of the human functional connectome, we established an R-fMRI pipeline to conduct ReHo computations in both 3-dimensions (volume) and 2-dimensions (surface). PMID:23085497

From bioseparation to artificial micro-organs: microfluidic chip based particle manipulation techniques

NASA Astrophysics Data System (ADS)

Stelzle, Martin

2010-02-01

Microfluidic device technology provides unique physical phenomena which are not available in the macroscopic world. These may be exploited towards a diverse array of applications in biotechnology and biomedicine ranging from bioseparation of particulate samples to the assembly of cells into structures that resemble the smallest functional unit of an organ. In this paper a general overview of chip-based particle manipulation and separation is given. In the state of the art electric, magnetic, optical and gravitational field effects are utilized. Also, mechanical obstacles often in combination with force fields and laminar flow are employed to achieve separation of particles or molecules. In addition, three applications based on dielectrophoretic forces for particle manipulation in microfluidic systems are discussed in more detail. Firstly, a virus assay is demonstrated. There, antibody-loaded microbeads are used to bind virus particles from a sample and subsequently are accumulated to form a pico-liter sized aggregate located at a predefined position in the chip thus enabling highly sensitive fluorescence detection. Secondly, subcellular fractionation of mitochondria from cell homogenate yields pure samples as was demonstrated by Western Blot and 2D PAGE analysis. Robust long-term operation with complex cell homogenate samples while avoiding electrode fouling is achieved by a set of dedicated technical means. Finally, a chip intended for the dielectrophoretic assembly of hepatocytes and endothelial cells into a structure resembling a liver sinusoid is presented. Such "artificial micro organs" are envisioned as substance screening test systems providing significantly higher predictability with respect to the in vivo response towards a substance under test.

A chiral self-assembled monolayer derived from a resolving agent and its performance as a crystallization template for an organic compound from organic solvents.

PubMed

Bejarano-Villafuerte, Ángela; van der Meijden, Maarten W; Lingenfelder, Magalí; Wurst, Klaus; Kellogg, Richard M; Amabilino, David B

2012-12-07

A new chiral nonracemic thiol derived from a popular acidic resolving agent that incorporates a cyclic disubstituted phosphate group (phencyphos) has been prepared in enantiomerically pure form. The stereochemistry and absolute configuration were established by performing a single-crystal X-ray structural analysis of a synthetic intermediate. The thiol compound was used for the preparation of self-assembled monolayers (SAMs) on both monocrystalline and polycrystalline metallic gold, which have very different surface roughness. The monolayers were used to promote the nucleation and growth of crystals from nonaqueous solutions of an organic molecule (the parent phencyphos) of similar structure to the compound present in the monolayer. The template layers influence the nucleation and growth of the phencyphos crystals despite the lack of two-dimensional order in the surfaces. Heterogeneous nucleation of phencyphos takes place upon evaporation of either CHCl(3) or isopropanol solutions of the compound on the SAM surfaces, where the evaporation rate merely influences the size and homogeneity of the crystals. The roughness of the surface also plays an important role; the polycrystalline gold produces more homogeneous samples because of the greater number of nucleation sites. Clear evidence for nucleation and growth on the surfaces is shown by scanning electron microscopy. The variation in crystal form achieved by using different surfaces and solvents suggests that the layers are applicable for the preparation of organic crystals from organic solutions. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PubMed

Ruhlman, Tracey A; Zhang, Jin; Blazier, John C; Sabir, Jamal S M; Jansen, Robert K

2017-04-01

There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats. © 2017 Botanical Society of America.

Cobinamide production of hydrogen in a homogeneous aqueous photochemical system, and assembly and photoreduction in a (βα)8 protein

PubMed Central

Robertson, Wesley D.; Bovell, Adonis M.; Warncke, Kurt

2013-01-01

Components of a protein-integrated, earth-abundant metal-macrocycle catalyst, purposed for hydrogen (H2) production from aqueous protons under green conditions, are characterized. The cobalt (Co) -corrin complex, cobinamide, is demonstrated to produce H2 (4.4±1.8×10−3 turnover number per hour) in a homogeneous, photosensitizer/sacrificial electron donor system, in pure water at neutral pH. Turnover is proposed to be limited by the relatively low population of the gateway Co(III) hydride species. A heterolytic mechanism for H2 production from the Co(II) hydride is proposed. Two essential requirements for assembly of a functional protein catalyst complex are demonstrated, for interaction of cobinamide with the (βα)8, TIM-barrel protein, EutB, from the adenosylcobalamin-dependent ethanolamine ammonia-lyase from Salmonella typhimurium: (1) High affinity equilibrium binding of the cobinamide (dissociation constant, 2.1×10−7 M), and (2) in situ photoreduction of the cobinamide-protein complex to the Co(I) state. Molecular modeling of the cobinamide-EutB interaction shows that these features arise from specific hydrogen bond and apolar interactions of the protein with the alkylamide substituents and ring of the corrin, and accessibility of the binding site to solution. The results establish cobinamide-EutB as a platform for design and engineering of a robust H2 production metallo-catalyst, that operates under green conditions, and utilizes advantages of protein as a tunable medium and material support. PMID:23807763

Leith diffusion model for homogeneous anisotropic turbulence

DOE PAGES

Rubinstein, Robert; Clark, Timothy T.; Kurien, Susan

2017-06-01

Here, a proposal for a spectral closure model for homogeneous anisotropic turbulence. The systematic development begins by closing the third-order correlation describing nonlinear interactions by an anisotropic generalization of the Leith diffusion model for isotropic turbulence. The correlation tensor is then decomposed into a tensorially isotropic part, or directional anisotropy, and a trace-free remainder, or polarization anisotropy. The directional and polarization components are then decomposed using irreducible representations of the SO(3) symmetry group. Under the ansatz that the decomposition is truncated at quadratic order, evolution equations are derived for the directional and polarization pieces of the correlation tensor. Here, numericalmore » simulation of the model equations for a freely decaying anisotropic flow illustrate the non-trivial effects of spectral dependencies on the different return-to-isotropy rates of the directional and polarization contributions.« less

How Good Are Trainers' Personal Methods Compared to Two Structured Training Strategies?

ERIC Educational Resources Information Center

Walls, Richard T.; And Others

Training methods naturally employed by trainers were analyzed and compared to systematic structured training procedures. Trainers were observed teaching retarded subjects how to assemble a bicycle brake, roller skate, carburetor, and lawn mower engine. Trainers first taught using their own (personal) method, which was recorded in terms of types of…

Multidimensional analysis of fast-spectrum material replacement measurements for systematic estimation of cross section uncertainties

NASA Technical Reports Server (NTRS)

Klann, P. G.; Lantz, E.; Mayo, W. T.

1973-01-01

A series of central core and core-reflector interface sample replacement experiments for 16 materials performed in the NASA heavy-metal-reflected, fast spectrum critical assembly (NCA) were analyzed in four and 13 groups using the GAM 2 cross-section set. The individual worths obtained by TDSN and DOT multidimensional transport theory calculations showed significant differences from the experimental results. These were attributed to cross-section uncertainties in the GAM 2 cross sections. Simultaneous analysis of the measured and calculated sample worths permitted separation of the worths into capture and scattering components which systematically provided fast spectrum averaged correction factors to the magnitudes of the GAM 2 absorption and scattering cross sections. Several Los Alamos clean critical assemblies containing Oy, Ta, and Mo as well as one of the NCA compositions were reanalyzed using the corrected cross sections. In all cases the eigenvalues were significantly improved and were recomputed to within 1 percent of the experimental eigenvalue. A comparable procedure may be used for ENDF cross sections when these are available.

Organic crystal-binding peptides: morphology control and one-pot formation of protein-displaying organic crystals

NASA Astrophysics Data System (ADS)

Niide, Teppei; Ozawa, Kyohei; Nakazawa, Hikaru; Oliveira, Daniel; Kasai, Hitoshi; Onodera, Mari; Asano, Ryutaro; Kumagai, Izumi; Umetsu, Mitsuo

2015-11-01

Crystalline assemblies of fluorescent molecules have different functional properties than the constituent monomers, as well as unique optical characteristics that depend on the structure, size, and morphological homogeneity of the crystal particles. In this study, we selected peptides with affinity for the surface of perylene crystal particles by exposing a peptide-displaying phage library in aqueous solution to perylene crystals, eluting the surface-bound phages by means of acidic desorption or liquid-liquid extraction, and amplifying the obtained phages in Escherichia coli. One of the perylene-binding peptides, PeryBPb1: VQHNTKYSVVIR, selected by this biopanning procedure induced perylene molecules to form homogenous planar crystal nanoparticles by means of a poor solvent method, and fusion of the peptide to a fluorescent protein enabled one-pot formation of protein-immobilized crystalline nanoparticles. The nanoparticles were well-dispersed in aqueous solution, and Förster resonance energy transfer from the perylene crystals to the fluorescent protein was observed. Our results show that the crystal-binding peptide could be used for simultaneous control of perylene crystal morphology and dispersion and protein immobilization on the crystals.Crystalline assemblies of fluorescent molecules have different functional properties than the constituent monomers, as well as unique optical characteristics that depend on the structure, size, and morphological homogeneity of the crystal particles. In this study, we selected peptides with affinity for the surface of perylene crystal particles by exposing a peptide-displaying phage library in aqueous solution to perylene crystals, eluting the surface-bound phages by means of acidic desorption or liquid-liquid extraction, and amplifying the obtained phages in Escherichia coli. One of the perylene-binding peptides, PeryBPb1: VQHNTKYSVVIR, selected by this biopanning procedure induced perylene molecules to form homogenous planar crystal nanoparticles by means of a poor solvent method, and fusion of the peptide to a fluorescent protein enabled one-pot formation of protein-immobilized crystalline nanoparticles. The nanoparticles were well-dispersed in aqueous solution, and Förster resonance energy transfer from the perylene crystals to the fluorescent protein was observed. Our results show that the crystal-binding peptide could be used for simultaneous control of perylene crystal morphology and dispersion and protein immobilization on the crystals. Electronic supplementary information (ESI) available: Schematic representation of PeryBPb1-fused DsRed-Monomer, fluorescence spectra of perylene crystals and DsRed-Monomer, and emission spectra of DsRed-Monomer at various excitation wavelengths. See DOI: 10.1039/c5nr06471f

Plutons: Simmer between 350° and 500°C for 10 million years, then serve cold (Invited)

NASA Astrophysics Data System (ADS)

Coleman, D. S.; Davis, J.

2009-12-01

The growing recognition that continental plutons are assembled incrementally over millions of years requires reexamination of the thermal histories of intrusive rocks. With the exception of the suggestion that pluton magma chambers can be revitalized by mafic input at their deepest structural levels, most aspects of modern pluton petrology are built on the underlying assumption that silicic plutons intrude as discrete thermal packages that undergo subsequent monotonic decay back to a steady-state geothermal gradient. The recognition that homogeneous silicic plutons are constructed over timescales too great to be single events necessitates rethinking pluton intrusion mechanisms, textures, thermochronology, chemical evolution and links to volcanic rocks. Three-dimensional thermal modeling of sheeted (horizontal and vertical) incremental pluton assembly (using HEAT3D by Wohletz, 2007) yields several results that are largely independent of intrusive geometry and may help understand bothersome field and laboratory results from plutonic rocks. 1) All increments cool quickly below hornblende closure temperature. However, late increments are emplaced into walls warmed by earlier increments, and they cycle between hornblende and biotite closure temperatures, a range in which fluid-rich melts are likely to be present. These conditions persist until the increments are far from the region of new magma flux, or the addition of increments stops. These observations are supported by Ar thermochronology and may explain why heterogeneous early marginal intrusive phases often grade into younger homogeneous interior map units. 2) Early increments become the contact metamorphic wall rocks of later increments. This observation suggests that much of the contact metamorphism associated with a given volume of plutonic rock is “lost” via textural modification of early increments during intrusion of later increments. Johnson and Glazner (CMP, in press) argue that mappable variations in pluton texture can result from textural modification during thermal cycling associated with incremental assembly. 3) The thermal structure of the model pluton evolves toward roughly spheroidal isotherms even though the pluton is assembled from thin tabular sheets. The zone of melt-bearing rock and the shape of intrapluton contact metamorphic isograds bear little resemblance to the increments from which the pluton was built. Consequently, pluton contacts mapped by variations in texture that reflect the thermal cycling inherent to incremental assembly will inevitably be “blob” or diapir-like, but will yield little insight into magma intrusion geometry. 4) Although models yield large regions of melt-bearing rock, the melt fraction is low and the melt-bearing volume at any time is small compared to the total volume of the pluton. This observation raises doubts about the connections between zoned silicic plutons and large ignimbrite eruptions.

Effects of advanced life support versus basic life support on the mortality rates of patients with trauma in prehospital settings: a study protocol for a systematic review and meta-analysis.

PubMed

Kondo, Yutaka; Fukuda, Tatsuma; Uchimido, Ryo; Hifumi, Toru; Hayashida, Kei

2017-10-22

Advanced life support (ALS) is thought to be associated with improved survival in prehospital trauma care when compared with basic life support (BLS). However, evidence on the benefits of prehospital ALS for patients with trauma is controversial. Therefore, we aim to clarify if ALS improves mortality in patients with trauma when compared with BLS by conducting a systematic review and meta-analysis of the recent literature. We will perform searches in PubMed, Embase and the Cochrane Central Register of Controlled Trials for published observational studies, controlled before-and-after studies, randomised controlled trials and other controlled trials conducted in humans and published until March 2017. We will screen search results, assess study selection, extract data and assess the risk of bias in duplicate; disagreements will be resolved through discussions. Data from clinically homogeneous studies will be pooled using a random-effects meta-analysis, heterogeneity of effects will be assessed using the χ 2 test of homogeneity, and any observed heterogeneity will be quantified using the I 2 statistic. Last, the Grading of Recommendations Assessment, Development and Evaluation approach will be used to rate the quality of the evidence. Our study does not require ethical approval as it is based on findings of previously published articles. Results will be disseminated through publication in a peer-reviewed journal, presentations at relevant conferences and publications for patient information. PROSPERO (International Prospective Register of Systematic Reviews) registration number CRD42017054389. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The prevalence of musculoskeletal symptoms in the construction industry: a systematic review and meta-analysis.

PubMed

Umer, Waleed; Antwi-Afari, Maxwell F; Li, Heng; Szeto, Grace P Y; Wong, Arnold Y L

2018-02-01

Although individual studies have reported high prevalence of musculoskeletal symptoms (MSS) among construction workers, no systematic review has summarized their prevalence rates. Accordingly, this systematic review/meta-analysis aimed to synthesize MSS prevalence in different construction trades, gender and age groups, which may help develop specific ergonomic interventions. Nine databases were searched for articles related to the research objective. Two reviewers independently screened citations, extracted information and conducted quality assessment of the included studies. Meta-analyses were conducted on clinical and statistical homogenous data. Thirty-five out of 1130 potential citations were included reporting diverse types of period prevalence and case definitions. Only the 1-year prevalence rates of MSS (defined as at least one episode of pain/MSS in the last year) at nine anatomical regions had sufficient homogeneous data for meta-analysis. Specifically, the 1-year prevalence of MSS was 51.1% for lower back, 37.2% for knee, 32.4% for shoulder, 30.4% for wrist, 24.4% for neck, 24.0% for ankle/foot, 20.3% for elbow, 19.8% for upper back, and 15.1% for hip/thigh. Female workers demonstrated a higher prevalence of MSS while there was insufficient information on the prevalence of trade-specific or age-related MSS. The quality assessments revealed that many included studies estimated prevalence solely based on self-reported data, and did not report non-respondents' characteristics. Lumbar, knee, shoulder, and wrist MSS are the most common symptoms among construction workers. Future studies should standardize the reporting of period prevalence of MSS in different construction trades to allow meta-analyses and to develop relevant MSS prevention program.

Ion-Specific Control of the Self-Assembly Dynamics of a Nanostructured Protein Lattice

DOE PAGES

Rad, Behzad; Haxton, Thomas K.; Shon, Albert; ...

2014-12-10

Self-assembling proteins offer a potential means of creating nanostructures with complex structure and function. However, using self-assembly to create nanostructures with long-range order whose size is tunable is challenging, because the kinetics and thermodynamics of protein interactions depend sensitively on solution conditions. Here we systematically investigate the impact of varying solution conditions on the self-assembly of SbpA, a surface-layer protein from Lysinibacillus sphaericus that forms two-dimensional nanosheets. Using high-throughput light scattering measurements, we mapped out diagrams that reveal the relative yield of self-assembly of nanosheets over a wide range of concentrations of SbpA and Ca 2+. These diagrams revealed amore » localized region of optimum yield of nanosheets at intermediate Ca 2+ concentration. Replacement of Mg 2+ or Ba 2+ for Ca 2+ indicates that Ca 2+ acts both as a specific ion that is required to induce self-assembly and as a general divalent cation. In addition, we use competitive titration experiments to find that 5 Ca 2+ bind to SbpA with an affinity of 67.1 ± 0.3 μM. Finally, we show via modeling that nanosheet assembly occurs by growth from a negligibly small critical nucleus. We also chart the dynamics of nanosheet size over a variety of conditions. In conclusion, our results demonstrate control of the dynamics and size of the self-assembly of a nanostructured lattice, the constituents of which are one of a class of building blocks able to form novel hybrid nanomaterials.« less

Peptide assemblies: from cell scaffolds to immune adjuvants

NASA Astrophysics Data System (ADS)

Collier, Joel

2011-03-01

This talk will discuss two interrelated aspects of peptide self-assemblies in biological applications: their use as matrices for regenerative medicine, and their use as chemically defined adjuvants for directing immune responses against engineered antigens. In the first half of the presentation, the design of peptide self-assemblies as analogues for the extracellular matrix will be described, with a focus on self-assemblies displaying multiple different cell-binding peptides. We conducted multi-factorial investigations of peptide co-assemblies containing several different ligand-bearing peptides using statistical ``design of experiments'' (DoE). Using the DoE techniques of factorial experimentation and response surface modeling, we systematically explored how precise combinations of ligand-bearing peptides modulated endothelial cell growth, in the process finding interactions between ligands not previously appreciated. By investigating immune responses against the materials intended for tissue engineering applications, we discovered that the basic self-assembling peptides were minimally immunogenic or non-immunogenic, even when delivered in strong adjuvants. -But when they were appended to an appropriately restricted epitope peptide, these materials raised strong and persistent antibody responses. These responses were dependent on covalent conjugation between the epitope and self-assembling domains of the peptides, were mediated by T cells, and could be directed towards both peptide epitopes and conjugated protein antigens. In addition to their demonstrated utility as scaffolds for regenerative medicine, peptide self-assemblies may also be useful as chemically defined adjuvants for vaccines and immunotherapies. This work was funded by NIH/NIDCR (1 R21 DE017703-03), NIH/NIBIB (1 R01 EB009701-01), and NSF (CHE-0802286).

Can an attribution assessment be made for Yellow Rain? Systematic reanalysis in a chemical-and-biological-weapons use investigation.

PubMed

Katz, Rebecca; Singer, Burton

2007-03-01

In intelligence investigations, such as those into reports of chemical- or biological-weapons (CBW) use, evidence may be difficult to assemble and, once assembled, to weigh. We propose a methodology for such investigations and then apply it to a large body of recently declassified evidence to determine the extent to which an attribution can now be made in the Yellow Rain case. Our analysis strongly supports the hypothesis that CBW were used in Southeast Asia and Afghanistan in the late 1970s and early 1980s, although a definitive judgment cannot be made. The proposed methodology, while resource-intensive, allows evidence to be assembled and analyzed in a transparent manner so that assumptions and rationale for decisions can be challenged by external critics. We conclude with a discussion of future research directions, emphasizing the use of evolving information-extraction (IE) technologies, a sub-field of artificial intelligence (AI).

Preferential assembly of heteromeric kainate and AMPA receptor amino terminal domains

PubMed Central

Lomash, Suvendu; Chittori, Sagar; Glasser, Carla

2017-01-01

Ion conductivity and the gating characteristics of tetrameric glutamate receptor ion channels are determined by their subunit composition. Competitive homo- and hetero-dimerization of their amino-terminal domains (ATDs) is a key step controlling assembly. Here we measured systematically the thermodynamic stabilities of homodimers and heterodimers of kainate and AMPA receptors using fluorescence-detected sedimentation velocity analytical ultracentrifugation. Measured affinities span many orders of magnitude, and complexes show large differences in kinetic stabilities. The association of kainate receptor ATD dimers is generally weaker than the association of AMPA receptor ATD dimers, but both show a general pattern of increased heterodimer stability as compared to the homodimers of their constituents, matching well physiologically observed receptor combinations. The free energy maps of AMPA and kainate receptor ATD dimers provide a framework for the interpretation of observed receptor subtype combinations and possible assembly pathways. PMID:29058671

Preferential assembly of heteromeric kainate and AMPA receptor amino terminal domains.

PubMed

Zhao, Huaying; Lomash, Suvendu; Chittori, Sagar; Glasser, Carla; Mayer, Mark L; Schuck, Peter

2017-10-23

Ion conductivity and the gating characteristics of tetrameric glutamate receptor ion channels are determined by their subunit composition. Competitive homo- and hetero-dimerization of their amino-terminal domains (ATDs) is a key step controlling assembly. Here we measured systematically the thermodynamic stabilities of homodimers and heterodimers of kainate and AMPA receptors using fluorescence-detected sedimentation velocity analytical ultracentrifugation. Measured affinities span many orders of magnitude, and complexes show large differences in kinetic stabilities. The association of kainate receptor ATD dimers is generally weaker than the association of AMPA receptor ATD dimers, but both show a general pattern of increased heterodimer stability as compared to the homodimers of their constituents, matching well physiologically observed receptor combinations. The free energy maps of AMPA and kainate receptor ATD dimers provide a framework for the interpretation of observed receptor subtype combinations and possible assembly pathways.

Block copolymer self-assembly-directed synthesis of mesoporous gyroidal superconductors.

PubMed

Robbins, Spencer W; Beaucage, Peter A; Sai, Hiroaki; Tan, Kwan Wee; Werner, Jörg G; Sethna, James P; DiSalvo, Francis J; Gruner, Sol M; Van Dover, Robert B; Wiesner, Ulrich

2016-01-01

Superconductors with periodically ordered mesoporous structures are expected to have properties very different from those of their bulk counterparts. Systematic studies of such phenomena to date are sparse, however, because of a lack of versatile synthetic approaches to such materials. We demonstrate the formation of three-dimensionally continuous gyroidal mesoporous niobium nitride (NbN) superconductors from chiral ABC triblock terpolymer self-assembly-directed sol-gel-derived niobium oxide with subsequent thermal processing in air and ammonia gas. Superconducting materials exhibit a critical temperature (T c) of about 7 to 8 K, a flux exclusion of about 5% compared to a dense NbN solid, and an estimated critical current density (J c) of 440 A cm(-2) at 100 Oe and 2.5 K. We expect block copolymer self-assembly-directed mesoporous superconductors to provide interesting subjects for mesostructure-superconductivity correlation studies.

Improving the biopharmaceutical attributes of mangiferin using vitamin E-TPGS co-loaded self-assembled phosholipidic nano-mixed micellar systems.

PubMed

Khurana, Rajneet Kaur; Gaspar, Balan Louis; Welsby, Gail; Katare, O P; Singh, Kamalinder K; Singh, Bhupinder

2018-06-01

The current research work encompasses the development, characterization, and evaluation of self-assembled phospholipidic nano-mixed miceller system (SPNMS) of a poorly soluble BCS Class IV xanthone bioactive, mangiferin (Mgf) functionalized with co-delivery of vitamin E TPGS. Systematic optimization using I-optimal design yielded self-assembled phospholipidic nano-micelles with a particle size of < 60 nm and > 80% of drug release in 15 min. The cytotoxicity and cellular uptake studies performed using MCF-7 and MDA-MB-231 cell lines demonstrated greater kill and faster cellular uptake. The ex vivo intestinal permeability revealed higher lymphatic uptake, while in situ perfusion and in vivo pharmacokinetic studies indicated nearly 6.6- and 3.0-folds augmentation in permeability and bioavailability of Mgf. In a nutshell, vitamin E functionalized SPNMS of Mgf improved the biopharmaceutical performance of Mgf in rats for enhanced anticancer potency.

Two distinct sets of NS2A molecules are responsible for dengue virus RNA synthesis and virion assembly.

PubMed

Xie, Xuping; Zou, Jing; Puttikhunt, Chunya; Yuan, Zhiming; Shi, Pei-Yong

2015-01-15

Flavivirus nonstructural protein 2A (NS2A) plays important roles in both viral RNA synthesis and virion assembly. The molecular details of how the NS2A protein modulates the two distinct events have not been defined. To address this question, we have performed a systematic mutagenesis of NS2A using dengue virus (DENV) serotype 2 (DENV-2) as a model. We identified two sets of NS2A mutations with distinct defects during a viral infection cycle. One set of NS2A mutations (D125A and G200A) selectively abolished viral RNA synthesis. Mechanistically, the D125A mutation abolished viral RNA synthesis through blocking the N-terminal cleavage of the NS2A protein, leading to an unprocessed NS1-NS2A protein; this result suggests that amino acid D125 (far downstream of the N terminus of NS2A) may contribute to the recognition of host protease at the NS1-NS2A junction. The other set of NS2A mutations (G11A, E20A, E100A, Q187A, and K188A) specifically impaired virion assembly without significantly affecting viral RNA synthesis. Remarkably, mutants defective in virion assembly could be rescued by supplying in trans wild-type NS2A molecules expressed from a replicative replicon, by wild-type NS2A protein expressed alone, by a mutant NS2A (G200A) that is lethal for viral RNA synthesis, or by a different mutant NS2A that is defective in virion assembly. In contrast, none of the mutants defective in viral RNA synthesis could be rescued by trans-complementation. Collectively, the results indicate that two distinct sets of NS2A molecules are responsible for DENV RNA synthesis and virion assembly. Dengue virus (DENV) represents the most prevalent mosquito-borne human pathogen. Understanding the replication of DENV is essential for development of vaccines and therapeutics. Here we characterized the function of DENV-2 NS2A using a systematic mutagenesis approach. The mutagenesis results revealed two distinct sets of NS2A mutations: one set of mutations that result in defects in viral RNA synthesis and another set of mutations that result in defects in virion assembly. trans-Complementation analysis showed that mutants defective in viral RNA synthesis could not be rescued by wild-type NS2A; in contrast, mutants defective in virion assembly could be successfully rescued by wild-type NS2A or even by a mutant NS2A that is incompetent to support viral RNA synthesis. These results support a model in which two distinct sets of NS2A molecules are responsible for DENV RNA synthesis (located in the viral replication complex) and virion assembly (located in the virion assembly/budding site). The study confirms and extends our understanding of the two critical roles of flavivirus NS2A in viral RNA synthesis and virion assembly. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

One-dimensional Confinement Effect on the Self-assembly of Symmetric H-shaped Copolymers in a Thin Film.

PubMed

Mu, Dan; Li, Jian-Quan; Feng, Sheng-Yu

2017-10-19

The self-assembly of a reformed symmetric H-shaped copolymer with four hydrophilic branches and one hydrophobic stem was systematically investigated. The existence of vacancies is vital to regulate the sizes of self-assembled cylinders to be able to form a hexagonal arrangement. With the introduction of horizontal-orientated confinement, a micellar structure is formed through a coalescence mechanism. The short acting distance and large influencing area of the confinement produces numerous small-sized micelles. Additionally, the cycled "contraction-expansion" change helps achieve hexagonal arrangement. In contrast, the introduction of lateral-oriented confinement with long acting distance and small influencing area cannot change the cylindrical structure. Under the fission mechanism, in which the larger cylinder splits into smaller ones, it is quite efficient to generate hierarchical-sized cylinders from larger-sized cylinders in the middle region and smaller-sized cylinders near both walls. The results indicate the possibility of regulating the characteristics of a nanomaterial by tuning the molecular structure of the copolymer and the parameters of the introduced confinement, which are closely related to the self-assembly structure.

Can clays ensure nuclear waste repositories?

NASA Astrophysics Data System (ADS)

Zaoui, A.; Sekkal, W.

2015-03-01

Research on argillite as a possible host rock for nuclear waste disposal is still an open subject since many issues need to be clarified. In the Underground Research Laboratories constructed for this purpose, a damaged zone around the excavation has been systematically observed and characterized by the appearance of micro-fissures. We analyse here -at nanoscale level- the calcite/clay assembly, the main constituents of argillite, under storage conditions and show the fragility of the montmorillonite with respect to calcite. Under anisotropic stress, we have observed a shear deformation of the assembly with the presence of broken bonds in the clay mineral, localised in the octahedral rather than the tetrahedral layers. The stress/strain curve leads to a failure strength point at 18.5 MPa. The obtained in-plane response of the assembly to perpendicular deformation is characterized by smaller perpendicular moduli Ez = 48.28 GPa compared to larger in-plane moduli Ex = 141.39 GPa and Ey = 134.02 GPa. Our calculations indicate the instability of the assembly without water molecules at the interface in addition to an important shear deformation.

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation.

PubMed

Yamazaki, Tomohiro; Souquere, Sylvie; Chujo, Takeshi; Kobelke, Simon; Chong, Yee Seng; Fox, Archa H; Bond, Charles S; Nakagawa, Shinichi; Pierron, Gerard; Hirose, Tetsuro

2018-06-21

A class of long noncoding RNAs (lncRNAs) has architectural functions in nuclear body construction; however, specific RNA domains dictating their architectural functions remain uninvestigated. Here, we identified the domains of the architectural NEAT1 lncRNA that construct paraspeckles. Systematic deletion of NEAT1 portions using CRISPR/Cas9 in haploid cells revealed modular domains of NEAT1 important for RNA stability, isoform switching, and paraspeckle assembly. The middle domain, containing functionally redundant subdomains, was responsible for paraspeckle assembly. Artificial tethering of the NONO protein to a NEAT1_2 mutant lacking the functional subdomains rescued paraspeckle assembly, and this required the NOPS dimerization domain of NONO. Paraspeckles exhibit phase-separated properties including susceptibility to 1,6-hexanediol treatment. RNA fragments of the NEAT1_2 subdomains preferentially bound NONO/SFPQ, leading to phase-separated aggregates in vitro. Thus, we demonstrate that the enrichment of NONO dimers on the redundant NEAT1_2 subdomains initiates construction of phase-separated paraspeckles, providing mechanistic insights into lncRNA-based nuclear body formation. Copyright © 2018 Elsevier Inc. All rights reserved.

Controlling the Surface Chemistry of Graphite by Engineered Self-Assembled Peptides

PubMed Central

Khatayevich, Dmitriy; So, Christopher R.; Hayamizu, Yuhei; Gresswell, Carolyn; Sarikaya, Mehmet

2012-01-01

The systematic control over surface chemistry is a long-standing challenge in biomedical and nanotechnological applications for graphitic materials. As a novel approach, we utilize graphite-binding dodecapeptides that self-assemble into dense domains to form monolayer thick long-range ordered films on graphite. Specifically, the peptides are rationally designed through their amino acid sequences to predictably display hydrophilic and hydrophobic characteristics while maintaining their self-assembly capabilities on the solid substrate. The peptides are observed to maintain a high tolerance for sequence modification, allowing the control over surface chemistry via their amino acid sequence. Furthermore, through a single step co-assembly of two different designed peptides, we predictably and precisely tune the wettability of the resulting functionalized graphite surfaces from 44 to 83 degrees. The modular molecular structures and predictable behavior of short peptides demonstrated here give rise to a novel platform for functionalizing graphitic materials that offers numerous advantages, including non-invasive modification of the substrate, bio-compatible processing in an aqueous environment, and simple fusion with other functional biological molecules. PMID:22428620

Liposomes self-assembled from electrosprayed composite microparticles

NASA Astrophysics Data System (ADS)

Yu, Deng-Guang; Yang, Jun-He; Wang, Xia; Tian, Feng

2012-03-01

Composite microparticles, consisting of polyvinylpyrrolidone (PVP), naproxen (NAP) and lecithin (PC), have been successfully prepared using an electrospraying process and exploited as templates to manipulate molecular self-assembly for the synthesis of liposomes in situ. Field emission scanning electron microscope (FESEM) and transmission electron microscope (TEM) observations demonstrate that the microparticles have an average diameter of 960 ± 140 nm and a homogeneous structure. X-ray diffraction (XRD) patterns, differential scanning calorimetry (DSC) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) results verify that the building blocks NAP and PC are scattered in the polymer matrix in a molecular way owing to the very fast drying of the electrospraying process and the favorable secondary interactions among the components. FESEM, scanning probe microscope (SPM) and TEM observations demonstrate that the liposomes can be achieved through molecular self-assembly in situ when the microparticles contact water thanks to ‘like prefers like’ and by means of the confinement effect of the microparticles. The liposomes have an encapsulation rate of 91.3%, and 80.7% of the drug in the liposomes can be freed into the dissolution medium in a sustained way and by a diffusion mechanism over a period of 24 h. The developed strategy not only provides a new, facile, and effective method to assemble and organize molecules of multiple components into liposomes with electrosprayed microparticles as templates, but also opens a new avenue for nanofabrication in a step-by-step and controllable way.

Microrheological Characterization of Collagen Systems: From Molecular Solutions to Fibrillar Gels

PubMed Central

Shayegan, Marjan; Forde, Nancy R.

2013-01-01

Collagen is the most abundant protein in the extracellular matrix (ECM), where its structural organization conveys mechanical information to cells. Using optical-tweezers-based microrheology, we investigated mechanical properties both of collagen molecules at a range of concentrations in acidic solution where fibrils cannot form and of gels of collagen fibrils formed at neutral pH, as well as the development of microscale mechanical heterogeneity during the self-assembly process. The frequency scaling of the complex shear modulus even at frequencies of ∼10 kHz was not able to resolve the flexibility of collagen molecules in acidic solution. In these solutions, molecular interactions cause significant transient elasticity, as we observed for 5 mg/ml solutions at frequencies above ∼200 Hz. We found the viscoelasticity of solutions of collagen molecules to be spatially homogeneous, in sharp contrast to the heterogeneity of self-assembled fibrillar collagen systems, whose elasticity varied by more than an order of magnitude and in power-law behavior at different locations within the sample. By probing changes in the complex shear modulus over 100-minute timescales as collagen self-assembled into fibrils, we conclude that microscale heterogeneity appears during early phases of fibrillar growth and continues to develop further during this growth phase. Experiments in which growing fibrils dislodge microspheres from an optical trap suggest that fibril growth is a force-generating process. These data contribute to understanding how heterogeneities develop during self-assembly, which in turn can help synthesis of new materials for cellular engineering. PMID:23936454

Numerical Generation of Dense Plume Fingers in Unsaturated Homogeneous Porous Media

NASA Astrophysics Data System (ADS)

Cremer, C.; Graf, T.

2012-04-01

In nature, the migration of dense plumes typically results in the formation of vertical plume fingers. Flow direction in fingers is downwards, which is counterbalanced by upwards flow of less dense fluid between fingers. In heterogeneous media, heterogeneity itself is known to trigger the formation of fingers. In homogeneous media, however, fingers are also created even if all grains had the same diameter. The reason is that pore-scale heterogeneity leading to different flow velocities also exists in homogeneous media due to two effects: (i) Grains of identical size may randomly arrange differently, e.g. forming tetrahedrons, hexahedrons or octahedrons. Each arrangement creates pores of varying diameter, thus resulting in different average flow velocities. (ii) Random variations of solute concentration lead to varying buoyancy effects, thus also resulting in different velocities. As a continuation of previously made efforts to incorporate pore-scale heterogeneity into fully saturated soil such that dense fingers are realistically generated (Cremer and Graf, EGU Assembly, 2011), the current paper extends the research scope from saturated to unsaturated soil. Perturbation methods are evaluated by numerically re-simulating a laboratory-scale experiment of plume transport in homogeneous unsaturated sand (Simmons et al., Transp. Porous Media, 2002). The following 5 methods are being discussed: (i) homogeneous sand, (ii) initial perturbation of solute concentration, (iii) spatially random, time-constant perturbation of solute source, (iv) spatially and temporally random noise of simulated solute concentration, and (v) random K-field that introduces physically insignificant but numerically significant heterogeneity. Results demonstrate that, as opposed to saturated flow, perturbing the solute source will not result in plume fingering. This is because the location of the perturbed source (domain top) and the location of finger generation (groundwater surface) do not coincide. Alternatively, similar to saturated flow, applying either a random concentration noise (iv) or a random K-field (v) generates realistic plume fingering. Future work will focus on the generation mechanisms of plume finger splitting.

Occupational Exposure to Chromium of Assembly Workers in Aviation Industries.

PubMed

Genovese, G; Castiglia, L; Pieri, M; Novi, C; d'Angelo, R; Sannolo, N; Lamberti, M; Miraglia, N

2015-01-01

Aircraft are constructed by modules that are covered by a "primer" layer, which can often contain hexavalent chromium [Cr(VI)], known carcinogen to humans. While the occupational exposure to Cr(VI) during aircraft painting is ascertained, the exposure assessment of assembly workers (assemblers) requires investigations. Three biological monitoring campaigns (BM-I,II,III) were performed in an aviation industry, on homogeneous groups of assemblers (N = 43) and controls (N = 23), by measuring chromium concentrations in end-shift urine collected at the end of the working week and the chromium concentration difference between end- and before-shift urines. BM-I was conducted on full-time workers, BM-II was performed on workers after a 3-4 day absence from work, BM-III on workers using ecoprimers with lower Cr(VI) content. Samples were analyzed by atomic absorption spectroscopy and mean values were compared by T-test. Even if Cr concentrations measured during BM-I were lower than Biological Exposure Indices by ACGIH, statistically significant differences were found between urinary Cr concentrations of workers and controls. Despite 3-4 days of absence from work, urinary chromium concentrations measured during BM-II were still higher than references from nonoccupationally exposed populations. In the BM-III campaign, the obtained preliminary results suggested the efficacy of using ecoprimers. The healthcare of workers exposed to carcinogenic agents follows the principle of limiting the exposure to "the minimum technically possible". The obtained results evidence that assemblers of aviation industries, whose task does not involve the direct use of primers containing Cr(VI), show an albeit slight occupational exposure to Cr(VI), that must be carefully taken into consideration in planning suitable prevention measures during risk assessment and management processes.

Method for making nanoporous hydrophobic coatings

DOEpatents

Fan, Hongyou; Sun, Zaicheng

2013-04-23

A simple coating method is used to form nanoporous hydrophobic films that can be used as optical coatings. The method uses evaporation-induced self-assembly of materials. The coating method starts with a homogeneous solution comprising a hydrophobic polymer and a surfactant polymer in a selective solvent. The solution is coated onto a substrate. The surfactant polymer forms micelles with the hydrophobic polymer residing in the particle core when the coating is dried. The surfactant polymer can be dissolved and selectively removed from the separated phases by washing with a polar solvent to form the nanoporous hydrophobic film.

CONVECTION REACTOR

DOEpatents

Hammond, R.P.; King, L.D.P.

1960-03-22

An homogeneous nuclear power reactor utilizing convection circulation of the liquid fuel is proposed. The reactor has an internal heat exchanger looated in the same pressure vessel as the critical assembly, thereby eliminating necessity for handling the hot liquid fuel outside the reactor pressure vessel during normal operation. The liquid fuel used in this reactor eliminates the necessity for extensive radiolytic gas rocombination apparatus, and the reactor is resiliently pressurized and, without any movable mechanical apparatus, automatically regulates itself to the condition of criticality during moderate variations in temperature snd pressure and shuts itself down as the pressure exceeds a predetermined safe operating value.

Protease-catalyzed peptide bond formation: application to synthesis of the COOH-terminal octapeptide of cholecystokinin.

PubMed

Kullmann, W

1982-05-01

This study of protease-catalyzed peptide synthesis reports the preparation of the COOH-terminal octapeptide amide of cholecystokinin. The octapeptide was assembled by chemical condensation of two tetrapeptide segments that had been synthesized through the concerted catalytic reactions of several proteases of different specificities. The resulting octapeptide derivative was subjected to catalytic transfer hydrogenation, followed by sulfation of its tyrosine residue and removal of the N alpha-protecting group. The homogeneous target peptide was obtained after purification via partition chromatography, gel filtration, and ion-exchange chromatography. The synthetic octapeptide stimulated amylase release from pancreatic acinar cells.

Development of a Sono-Assembled, Bifunctional Soy Peptide Nanoparticle for Cellular Delivery of Hydrophobic Active Cargoes.

PubMed

Zhang, Yuanhong; Zhao, Mouming; Ning, Zhengxiang; Yu, Shujuan; Tang, Ning; Zhou, Feibai

2018-04-25

Soy proteins are prone to aggregate upon proteolysis, hindering their sustainable development in food processing. Here, a continuous work on the large insoluble peptide aggregates was carried out, aiming to develop a new type of soy peptide-based nanoparticle (SPN) for active cargo delivery. Sono-assembled SPN in spherical appearance and core-shell structure maintained by noncovalent interactions was successfully fabricated, exhibiting small particle size (103.95 nm) in a homogeneous distribution state (PDI = 0.18). Curcumin as a model cargo was efficiently encapsulated into SPN upon sonication, showing high water dispersity (129.6 mg/L, 10 4 higher than its water solubility) and storage stability. Additionally, the pepsin-resistant SPN contributed to the controlled release of curcumin at the intestinal phase and thus significantly improved the bioaccessibility. Encapsulated curcumin was effective in protecting glutamate-induced toxicity in PC12 cells, where the matrix SPN can simultaneously reduce lipid peroxidation and elevate antioxidant enzymes levels, innovatively demonstrating its bifunctionality during cellular delivery.

Self-assembled three-dimensional hierarchical graphene/polypyrrole nanotube hybrid aerogel and its application for supercapacitors.

PubMed

Ye, Shibing; Feng, Jiachun

2014-06-25

A three-dimensional hierarchical graphene/polypyrrole aerogel (GPA) has been fabricated using graphene oxide (GO) and already synthesized one-dimensional hollow polypyrrole nanotubes (PNTs) as the feedstock. The amphiphilic GO is helpful in effectively promoting the dispersion of well-defined PNTs to result in a stable, homogeneous GO/PNT complex solution, while the PNTs not only provide a large accessible surface area for fast transport of hydrate ions but also act as spacers to prevent the restacking of graphene sheets. By a simple one-step reduction self-assembly process, hierarchically structured, low-density, highly compressible GPAs are easily obtained, which favorably combine the advantages of graphene and PNTs. The supercapacitor electrodes based on such materials exhibit excellent electrochemical performance, including a high specific capacitance up to 253 F g(-1), good rate performance, and outstanding cycle stability. Moreover, this method may be feasible to prepare other graphene-based hybrid aerogels with structure-controllable nanostructures in large scale, thereby holding enormous potential in many application fields.

Rheological transition in simple shear of moderately dense assemblies of dry cohesive granules

NASA Astrophysics Data System (ADS)

Murphy, Eric; Sundararajan, Sriram; Subramaniam, Shankar

2018-06-01

The rheology of homogeneous cohesive granular assemblies under shear at moderate volume fractions is investigated using the discrete element method for both frictionless and frictional granules. A transition in rheology from inertial to quasistatic scaling is observed at volume fractions below the jamming point of noncohesive systems, which is a function of the granular temperature, energy dissipation, and cohesive potential. The transition is found to be the result of growing clusters, which eventually percolate the domain, and change the mode of momentum transport in the system. Differences in the behavior of the shear stress normalized by the pressure are observed when frictionless and frictional cases are compared. These differences are explained through contact anisotropy after percolation occurs. Both frictionless and frictional systems are found to be vulnerable to instabilities after full system percolation has occurred, where the former becomes thermodynamically unstable and the latter may form shear bands. Finally, implications for constitutive modeling are discussed.

Synthesis of anatase TiO2 nanoparticles with beta-cyclodextrin as a supramolecular shell.

PubMed

Li, Landong; Sun, Xiaohong; Yang, Yali; Guan, Naijia; Zhang, Fuxiang

2006-11-20

We report a novel, green hydrothermal-synthesis route to well-dispersed anatase TiO2 nanoparticles with particle sizes of 9-16 nm in the presence of beta-CD (beta-cyclodextrin). During the synthesis process, the CD-containing synthesis mixture assembled in both longitudinal and latitudinal directions. Driven by the interaction between molecules, the beta-CDs assembled in the longitudinal direction to form long-chain compounds, whereas in the latitudinal direction, they tended to form regular aggregates through coordination with the Ti species from the hydrolysis of tetrabutyl titanate. In view of the effect of the coordination and the steric hindrance of beta-CDs as a supramolecular shell, homogeneous nuclei and slow growth of TiO2 crystals during the synthesis process was observed, which was responsible for the formation of uniform TiO2 nanoparticles. The low beta-CD dosage and the high product yield (>90%) demonstrated well the potential of this synthesis route in the large-scale industrial production of anatase nanoparticles.

Direct organocatalytic enantioselective functionalization of SiOx surfaces.

PubMed

Parkin, John David; Chisholm, Ross; Frost, Aileen B; Bailey, Richard G; Smith, Andrew David; Hähner, Georg

2018-06-05

Traditional methods to prepare chiral surfaces involve either the adsorption of a chiral molecule onto an achiral surface, or adsorption of a species that forms a chiral template creating lattices with long range order. To date only limited alternative strategies to prepare chiral surfaces have been studied. In this manuscript a "bottom up" approach is developed that allows the preparation of chiral surfaces by direct enantioselective organocatalysis on a functionalized Si-oxide supported self-assembled monolayer (SAM). The efficient catalytic generation of enantiomerically enriched organic surfaces is achieved using a commercially available homogeneous isothiourea catalyst (HyperBTM) that promotes an enantioselective Michael-lactonization process upon a Si-oxide supported self-assembled monolayer functionalized with a reactive trifluoroenone group. Chiral atomic force microscopy (chi-AFM) is used to probe the enantiomeric enrichment of the organic films by measurement of the force distributions arising from interaction of D- or L-cysteine modified AFM tips and the organic films. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Self-assembly formation of palm-based esters nano-emulsion: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Abdul Rahman, Mohd. Basyaruddin; Huan, Qiu-Yi; Tejo, Bimo A.; Basri, Mahiran; Salleh, Abu Bakar; Rahman, Raja Noor Zaliha Abdul

2009-10-01

Palm-oil esters (POEs) are unsaturated and non-ionic esters that can be prepared by enzymatic synthesis from palm oil. Their nano-emulsion properties possess great potential to act as drug carrier for transdermal drug delivery system. A ratio of 75:5:20 (water/POEs/Span20) was chosen from homogenous region in the phase diagram of our previous experimental work to undergo molecular dynamics simulation. A 15 ns molecular dynamics simulation of nano-emulsion system (water/POEs/Span20) was carried out using OPLS-AA force field. The aggregations of the oil and surfactant molecules are observed throughout the simulation. After 8 ns of simulation, the molecules start to aggregate to form one spherical micelle where the POEs molecules are surrounded by the non-ionic surfactant (Span20) molecules with an average size of 4.2 ± 0.05 nm. The size of the micelle and the ability of palm-based nano-emulsion to self-assemble suggest that this nano-emulsion can potentially use in transdermal drug delivery system.

Adsorption and self-assembly of M13 phage into directionally organized structures on C and SiO2 films.

PubMed

Moghimian, Pouya; Srot, Vesna; Rothenstein, Dirk; Facey, Sandra J; Harnau, Ludger; Hauer, Bernhard; Bill, Joachim; van Aken, Peter A

2014-09-30

A versatile method for the directional assembly of M13 phage using amorphous carbon and SiO2 thin films was demonstrated. A high affinity of the M13 phage macromolecules for incorporation into aligned structures on an amorphous carbon surface was observed at the concentration range, in which the viral nanofibers tend to disorder. In contrast, the viral particles showed less freedom to adopt an aligned orientation on SiO2 films when deposited in close vicinity. Here an interpretation of the role of the carbon surface in significant enhancement of adsorption and generation of viral arrays with a high orientational order was proposed in terms of surface chemistry and competitive electrostatic interactions. This study suggests the use of amorphous carbon substrates as a template for directional organization of a closely-packed and two-dimensional M13 viral film, which can be a promising route to mineralize a variety of smooth and homogeneous inorganic nanostructure layers.

Preparation and Exceptional Mechanical Properties of Bone-Mimicking Size-Tuned Graphene Oxide@Carbon Nanotube Hybrid Paper.

PubMed

Oh, Jun Young; Kim, Yern Seung; Jung, Yeonsu; Yang, Seung Jae; Park, Chong Rae

2016-02-23

The self-assembled nanostructures of carbon nanomaterials possess a damage-tolerable architecture crucial for the inherent mechanical properties at both micro- and macroscopic levels. Bone, or "natural composite," has been known to have superior energy dissipation and fracture resistance abilities due to its unique load-bearing hybrid structure. However, few approaches have emulated the desirable structure using carbon nanomaterials. In this paper, we present an approach in fabricating a hybrid composite paper based on graphene oxide (GO) and carbon nanotube (CNT) that mimicks the natural bone structure. The size-tuning strategy enables smaller GO sheets to have more cross-linking reactions with CNTs and be homogeneously incorporated into CNT-assembled paper, which is advantageous for effective stress transfer. The resultant hybrid composite film has enhanced mechanical strength, modulus, toughness, and even electrical conductivity compared to previously reported CNT-GO based composites. We further demonstrate the usefulness of the size-tuned GOs as the "stress transfer medium" by performing in situ Raman spectroscopy during the tensile test.

Cholesterol is required for stability and infectivity of influenza A and respiratory syncytial viruses.

PubMed

Bajimaya, Shringkhala; Frankl, Tünde; Hayashi, Tsuyoshi; Takimoto, Toru

2017-10-01

Cholesterol-rich lipid raft microdomains in the plasma membrane are considered to play a major role in the enveloped virus lifecycle. However, the functional role of cholesterol in assembly, infectivity and stability of respiratory RNA viruses is not fully understood. We previously reported that depletion of cellular cholesterol by cholesterol-reducing agents decreased production of human parainfluenza virus type 1 (hPIV1) particles by inhibiting virus assembly. In this study, we analyzed the role of cholesterol on influenza A virus (IAV) and respiratory syncytial virus (RSV) production. Unlike hPIV1, treatment of human airway cells with the agents did not decrease virus particle production. However, the released virions were less homogeneous in density and unstable. Addition of exogenous cholesterol to the released virions restored virus stability and infectivity. Collectively, these data indicate a critical role of cholesterol in maintaining IAV and RSV membrane structure that is essential for sustaining viral stability and infectivity. Copyright © 2017 Elsevier Inc. All rights reserved.

Thermal transport in binary colloidal glasses: Composition dependence and percolation assessment

NASA Astrophysics Data System (ADS)

Ruckdeschel, Pia; Philipp, Alexandra; Kopera, Bernd A. F.; Bitterlich, Flora; Dulle, Martin; Pech-May, Nelson W.; Retsch, Markus

2018-02-01

The combination of various types of materials is often used to create superior composites that outperform the pure phase components. For any rational design, the thermal conductivity of the composite as a function of the volume fraction of the filler component needs to be known. When approaching the nanoscale, the homogeneous mixture of various components poses an additional challenge. Here, we investigate binary nanocomposite materials based on polymer latex beads and hollow silica nanoparticles. These form randomly mixed colloidal glasses on a sub-μ m scale. We focus on the heat transport properties through such binary assembly structures. The thermal conductivity can be well described by the effective medium theory. However, film formation of the soft polymer component leads to phase segregation and a mismatch between existing mixing models. We confirm our experimental data by finite element modeling. This additionally allowed us to assess the onset of thermal transport percolation in such random particulate structures. Our study contributes to a better understanding of thermal transport through heterostructured particulate assemblies.

Direct Assembly of Modified Proteins on Carbon Nanotubes in an Aqueous Solution

NASA Technical Reports Server (NTRS)

Kim, Jae-Woo; Lillehei, Peter T.; Park, Cheol; Harrison, Joycelyn S.

2007-01-01

Carbon nanotubes (CNTs) have superior mechanical and electrical properties that have opened up many potential applications. However, poor dispersibility and solubility, due to the substantial van der Waals attraction between tubes, have prevented the use of CNTs in practical applications, especially biotechnology applications. Effective dispersion of CNTs into small bundles or individual tubes in solvents is crucial to ensure homogeneous properties and enable practical applications. In addition to dispersion of CNTs into a solvent, the selection of appropriate solvent, which is compatible with a desired matrix, is an important factor to improve the mechanical, thermal, optical, and electrical properties of CNT-based fibers and composites. In particular, dispersion of CNTs into an aqueous system has been a challenge due to the hydrophobic nature of CNTs. Here we show an effective method for dispersion of both single wall CNTs (SWCNTs) and few wall CNTs (FWCNTs) in an aqueous buffer solution. We also show an assembly of cationized Pt-cored ferritins on the well dispersed CNTs in an aqueous buffer solution.

Natural selection in the colloid world: active chiral spirals.

PubMed

Zhang, Jie; Granick, Steve

2016-10-06

We present a model system in which to study natural selection in the colloid world. In the assembly of active Janus particles into rotating pinwheels when mixed with trace amounts of homogeneous colloids in the presence of an AC electric field, broken symmetry in the rotation direction produces spiral, chiral shapes. Locked into a central rotation point by the centre particle, the spiral arms are found to trail rotation of the overall cluster. To achieve a steady state, the spiral arms undergo an evolutionary process to coordinate their motion. Because all the particles as segments of the pinwheel arms are self-propelled, asymmetric arm lengths are tolerated. Reconfiguration of these structures can happen in various ways and various mechanisms of this directed structural change are analyzed in detail. We introduce the concept of VIP (very important particles) to express that sustainability of active structures is most sensitive to only a few particles at strategic locations in the moving self-assembled structures.

Specific Uptake of Lipid-Antibody-Functionalized LbL Microcarriers by Cells.

PubMed

Göse, Martin; Scheffler, Kira; Reibetanz, Uta

2016-11-14

The modular construction of Layer-by-Layer biopolymer microcarriers facilitates a highly specific design of drug delivery systems. A supported lipid bilayer (SLB) contributes to biocompatibility and protection of sensitive active agents. The addition of a lipid anchor equipped with PEG (shielding from opsonins) and biotin (attachment of exchangeable outer functional molecules) enhances the microcarrier functionality even more. However, a homogeneously assembled supported lipid bilayer is a prerequisite for a specific binding of functional components. Our investigations show that a tightly packed SLB improves the efficiency of functional components attached to the microcarrier's surface, as illustrated with specific antibodies in cellular application. Only a low quantity of antibodies is needed to obtain improved cellular uptake rates independent from cell type as compared to an antibody-functionalized loosely packed lipid bilayer or directly assembled antibody onto the multilayer. A fast disassembly of the lipid bilayer within endolysosomes exposing the underlying drug delivering multilayer structure demonstrates the suitability of LbL-microcarriers as a multifunctional drug delivery system.

Design of a homogeneous multifunctional supported lipid membrane on layer-by-layer coated microcarriers.

PubMed

Göse, Martin; Pescador, Paula; Reibetanz, Uta

2015-03-09

Key challenges in the development of drug delivery systems are the prevention of serum compartment interaction and the targeted delivery of the cargo. Layer-by-Layer microcarriers offer many advantages due to various options in drug assembly and multifunctional design. Surface modification with a supported lipid membrane enhances biocompatibility, drug protection ability, and specific functionality. However, the integration of functionalized lipids strongly influences the membrane formation and is often accompanied by submicrometer irregularities: The accessibility of underlying polymers to serum components may change the carrier's properties and enhances the susceptibility to opsonization. Therefore, the formation of a tightly assembled multifunctional lipid membrane has been emphasized. A phosphatidylserine/phosphatidylcholine (POPS/POPC) bilayer equipped with phosphatidylethanolamine-polyethylene glycol-biotin (PE-PEG-Biotin) was used to facilitate a biotin/streptavidin binding site for a variable attachment of an additional function, such as antibodies for specific targeting. Thus, a prefunctionalized carrier where only the outer functionality needs to be replaced without disturbing the underlying structure could be created.

A constitutive relation for the viscous flow of an oriented fiber assembly

NASA Technical Reports Server (NTRS)

Pipes, R. B.; Hearle, J. W. S.; Beaussart, A. J.; Sastry, A. M.; Okine, R. K.

1991-01-01

A constitutive relation for an equivalent, homogeneous fluid is developed for the anisotropic viscous flow of an oriented assembly of discontinuous fibers suspended in a viscous fluid. The anisotropic viscous compliance matrix can be expressed in terms of three constants by assuming the equivalent fluid to be incompressible and the microstructure to have axial symmetry (transversely isotropic). By means of a micromechanics analysis, the three terms of the constitutive relation are expressed in terms of the viscosity of the matrix fluid, the fiber aspect ratio, and the fiber volume fraction. A comparison of the viscosity terms reveals that the elongational viscosity in the fiber direction varies as the square of the fiber aspect ratio and a complex function of the fiber volume fraction. Furthermore, the ratio of the axial elongational viscosity to the transverse elongational viscosity and both axial and transverse shear viscosities was shown to be 10 exp 4 - 10 exp 6 for fiber aspect ratio of 100-1000, except at extreme values of the fiber volume fraction.

Characterisation of minimalist co-assembled fluorenylmethyloxycarbonyl self-assembling peptide systems for presentation of multiple bioactive peptides.

PubMed

Horgan, Conor C; Rodriguez, Alexandra L; Li, Rui; Bruggeman, Kiara F; Stupka, Nicole; Raynes, Jared K; Day, Li; White, John W; Williams, Richard J; Nisbet, David R

2016-07-01

The nanofibrillar structures that underpin self-assembling peptide (SAP) hydrogels offer great potential for the development of finely tuned cellular microenvironments suitable for tissue engineering. However, biofunctionalisation without disruption of the assembly remains a key issue. SAPS present the peptide sequence within their structure, and studies to date have typically focused on including a single biological motif, resulting in chemically and biologically homogenous scaffolds. This limits the utility of these systems, as they cannot effectively mimic the complexity of the multicomponent extracellular matrix (ECM). In this work, we demonstrate the first successful co-assembly of two biologically active SAPs to form a coassembled scaffold of distinct two-component nanofibrils, and demonstrate that this approach is more bioactive than either of the individual systems alone. Here, we use two bioinspired SAPs from two key ECM proteins: Fmoc-FRGDF containing the RGD sequence from fibronectin and Fmoc-DIKVAV containing the IKVAV sequence from laminin. Our results demonstrate that these SAPs are able to co-assemble to form stable hybrid nanofibres containing dual epitopes. Comparison of the co-assembled SAP system to the individual SAP hydrogels and to a mixed system (composed of the two hydrogels mixed together post-assembly) demonstrates its superior stable, transparent, shear-thinning hydrogels at biological pH, ideal characteristics for tissue engineering applications. Importantly, we show that only the coassembled hydrogel is able to induce in vitro multinucleate myotube formation with C2C12 cells. This work illustrates the importance of tissue engineering scaffold functionalisation and the need to develop increasingly advanced multicomponent systems for effective ECM mimicry. Successful control of stem cell fate in tissue engineering applications requires the use of sophisticated scaffolds that deliver biological signals to guide growth and differentiation. The complexity of such processes necessitates the presentation of multiple signals in order to effectively mimic the native extracellular matrix (ECM). Here, we establish the use of two biofunctional, minimalist self-assembling peptides (SAPs) to construct the first co-assembled SAP scaffold. Our work characterises this construct, demonstrating that the physical, chemical, and biological properties of the peptides are maintained during the co-assembly process. Importantly, the coassembled system demonstrates superior biological performance relative to the individual SAPs, highlighting the importance of complex ECM mimicry. This work has important implications for future tissue engineering studies. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Shell-binary nanoparticle materials with variable electrical and electro-mechanical properties.

PubMed

Zhang, P; Bousack, H; Dai, Y; Offenhäusser, A; Mayer, D

2018-01-18

Nanoparticle (NP) materials with the capability to adjust their electrical and electro-mechanical properties facilitate applications in strain sensing technology. Traditional NP materials based on single component NPs lack a systematic and effective means of tuning their electrical and electro-mechanical properties. Here, we report on a new type of shell-binary NP material fabricated by self-assembly with either homogeneous or heterogeneous arrangements of NPs. Variable electrical and electro-mechanical properties were obtained for both materials. We show that the electrical and electro-mechanical properties of these shell-binary NP materials are highly tunable and strongly affected by the NP species as well as their corresponding volume fraction ratio. The conductivity and the gauge factor of these shell-binary NP materials can be altered by about five and two orders of magnitude, respectively. These shell-binary NP materials with different arrangements of NPs also demonstrate different volume fraction dependent electro-mechanical properties. The shell-binary NP materials with a heterogeneous arrangement of NPs exhibit a peaking of the sensitivity at medium mixing ratios, which arises from the aggregation induced local strain enhancement. Studies on the electron transport regimes and micro-morphologies of these shell-binary NP materials revealed the different mechanisms accounting for the variable electrical and electro-mechanical properties. A model based on effective medium theory is used to describe the electrical and electro-mechanical properties of such shell-binary nanomaterials and shows an excellent match with experiment data. These shell-binary NP materials possess great potential applications in high-performance strain sensing technology due to their variable electrical and electro-mechanical properties.

Opening the Window on Galaxy Assembly: Ages and Structural Parameters of Globular Clusters Towards the Galactic Bulge

NASA Astrophysics Data System (ADS)

Cohen, Roger

2015-10-01

The primary aim of this program is to undertake a systematic investigation of highly reddened Galactic globular clusters (GGCs) located towards the Galactic bulge. These clusters have been excluded from deep space-based photometric surveys due to their severe total and differential extinction. We will exploit the photometric depth and homogeneity of two existing Treasury programs (the ACS GGC Treasury Survey and the WFC3 Bulge Treasury Program) along with the unique optical+IR parallel imaging capabilities of HST to finally place the bulge GGCs in the context of their optically well-studied counterparts. Specifically, by leveraging ACS/WFC together with WFC3/IR, we first exploit the reddening sensitivity at optical wavelengths to map severe, small-scale differential reddening in the cluster cores. Corrected two-color WFC3/IR photometry will then be used to measure cluster ages to better than 1 Gyr relative precision, finally completing the age-metallicity relation of the Milky Way GGC system. Ages are obtained using a demonstrated procedure which is strictly differential, and therefore insensitive to total distance, reddening, reddening law, or photometric calibration uncertainties. At the same time, deep archival Treasury survey imaging of the Galactic bulge will be used to decontaminate cluster luminosity functions, yielding measurements of bulge GGC mass functions and mass segregation on par with results from the ACS GGC Treasury survey. Finally, the imaging which we propose will be combined with existing wide-field near-IR PSF photometry, yielding complete radial number density profiles, structural and morphological parameters.

USAXS analysis of concentration-dependent self-assembling of polymer-brush-modified nanoparticles in ionic liquid: [I] concentrated-brush regime

NASA Astrophysics Data System (ADS)

Nakanishi, Yohei; Ishige, Ryohei; Ogawa, Hiroki; Sakakibara, Keita; Ohno, Kohji; Morinaga, Takashi; Sato, Takaya; Kanaya, Toshiji; Tsujii, Yoshinobu

2018-03-01

Using ultra-small angle X-ray scattering (USAXS), we analyzed the higher-order structures of nanoparticles with a concentrated brush of an ionic liquid (IL)-type polymer (concentrated-polymer-brush-modified silica particle; PSiP) in an IL and the structure of the swollen shell layer of PSiP. Homogeneous mixtures of PSiP and IL were successfully prepared by the solvent-casting method involving the slow evaporation of a volatile solvent, which enabled a systematic study over an exceptionally wide range of compositions. Different diffraction patterns as a function of PSiP concentration were observed in the USAXS images of the mixtures. At suitably low PSiP concentrations, the USAXS intensity profile was analyzed using the Percus-Yevick model by matching the contrast between the shell layer and IL, and the swollen structure of the shell and "effective diameter" of the PSiP were evaluated. This result confirms that under sufficiently low pressures below and near the liquid/crystal-threshold concentration, the studied PSiP can be well described using the "hard sphere" model in colloidal science. Above the threshold concentration, the PSiP forms higher-order structures. The analysis of diffraction patterns revealed structural changes from disorder to random hexagonal-closed-packing and then face-centered-cubic as the PSiP concentration increased. These results are discussed in terms of thermodynamically stable "hard" and/or "semi-soft" colloidal crystals, wherein the swollen layer of the concentrated polymer brush and its structure play an important role.

Linking Comparisons of Absolute Gravimeters: A Proof of Concept for a new Global Absolute Gravity Reference System.

NASA Astrophysics Data System (ADS)

Wziontek, H.; Palinkas, V.; Falk, R.; Vaľko, M.

2016-12-01

Since decades, absolute gravimeters are compared on a regular basis on an international level, starting at the International Bureau for Weights and Measures (BIPM) in 1981. Usually, these comparisons are based on constant reference values deduced from all accepted measurements acquired during the comparison period. Temporal changes between comparison epochs are usually not considered. Resolution No. 2, adopted by IAG during the IUGG General Assembly in Prague 2015, initiates the establishment of a Global Absolute Gravity Reference System based on key comparisons of absolute gravimeters (AG) under the International Committee for Weights and Measures (CIPM) in order to establish a common level in the microGal range. A stable and unique reference frame can only be achieved, if different AG are taking part in different kind of comparisons. Systematic deviations between the respective comparison reference values can be detected, if the AG can be considered stable over time. The continuous operation of superconducting gravimeters (SG) on selected stations further supports the temporal link of comparison reference values by establishing a reference function over time. By a homogenous reprocessing of different comparison epochs and including AG and SG time series at selected stations, links between several comparisons will be established and temporal comparison reference functions will be derived. By this, comparisons on a regional level can be traced to back to the level of key comparisons, providing a reference for other absolute gravimeters. It will be proved and discussed, how such a concept can be used to support the future absolute gravity reference system.

SKATE: a docking program that decouples systematic sampling from scoring.

PubMed

Feng, Jianwen A; Marshall, Garland R

2010-11-15

SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in-house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 A RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross-docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin-dependent kinase. 2010 Wiley Periodicals, Inc.

Forest Inventory and Analysis and Forest Health Monitoring: Piecing the Quilt

Treesearch

Joseph M. McCollum; Jamie K. Cochran

2005-01-01

Against the backdrop of a discussion about patchwork quilt assembly, the authors present background information on global grids. They show how to compose hexagons, an important task in systematically developing a subset of Forest Health Monitoring (FHM) Program plots from Forest Inventory and Analysis (FIA) plots. Finally, they outline the FHM and FIA grids, along with...

Measuring Anxiety as a Treatment Endpoint in Youth with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Lecavalier, Luc; Wood, Jeffrey J.; Halladay, Alycia K.; Jones, Nancy E.; Aman, Michael G.; Cook, Edwin H.; Handen, Benjamin L.; King, Bryan H.; Pearson, Deborah A.; Hallett, Victoria; Sullivan, Katherine Anne; Grondhuis, Sabrina; Bishop, Somer L.; Horrigan, Joseph P.; Dawson, Geraldine; Scahill, Lawrence

2014-01-01

Despite the high rate of anxiety in individuals with autism spectrum disorder (ASD), measuring anxiety in ASD is fraught with uncertainty. This is due, in part, to incomplete consensus on the manifestations of anxiety in this population. Autism Speaks assembled a panel of experts to conduct a systematic review of available measures for anxiety in…

Draft Genome Sequence of “Cohnella kolymensis” B-2846

PubMed Central

Kudryashova, Ekaterina B.; Ariskina, Elena V.

2016-01-01

A draft genome sequence of “Cohnella kolymensis” strain B-2846 was derived using IonTorrent sequencing technology. The size of the assembly and G+C content were in agreement with those of other species of this genus. Characterization of the genome of a novel species of Cohnella will assist in bacterial systematics. PMID:26769947

Who starts forest fires in Maine - and how?

Treesearch

Wayne G. Banks; Fred E. Holt

1966-01-01

In 1964 the Maine Forest Service, in cooperation with the Northeastern Forest Experiment Station, conducted intensive investigations of a systematically selected sample of the fires that occurred in the State that year. The immediate purpose was to determine precisely how the fires started and who or what started them, and to assemble relevant information about the...

On domain symmetry and its use in homogenization

DOE PAGES

Barbarosie, Cristian A.; Tortorelli, Daniel A.; Watts, Seth E.

2017-03-08

The present study focuses on solving partial differential equations in domains exhibiting symmetries and periodic boundary conditions for the purpose of homogenization. We show in a systematic manner how the symmetry can be exploited to significantly reduce the complexity of the problem and the computational burden. This is especially relevant in inverse problems, when one needs to solve the partial differential equation (the primal problem) many times in an optimization algorithm. The main motivation of our study is inverse homogenization used to design architected composite materials with novel properties which are being fabricated at ever increasing rates thanks to recentmore » advances in additive manufacturing. For example, one may optimize the morphology of a two-phase composite unit cell to achieve isotropic homogenized properties with maximal bulk modulus and minimal Poisson ratio. Typically, the isotropy is enforced by applying constraints to the optimization problem. However, in two dimensions, one can alternatively optimize the morphology of an equilateral triangle and then rotate and reflect the triangle to form a space filling D 3 symmetric hexagonal unit cell that necessarily exhibits isotropic homogenized properties. One can further use this D 3 symmetry to reduce the computational expense by performing the “unit strain” periodic boundary condition simulations on the single triangle symmetry sector rather than the six fold larger hexagon. In this paper we use group representation theory to derive the necessary periodic boundary conditions on the symmetry sectors of unit cells. The developments are done in a general setting, and specialized to the two-dimensional dihedral symmetries of the abelian D 2, i.e. orthotropic, square unit cell and nonabelian D 3, i.e. trigonal, hexagon unit cell. We then demonstrate how this theory can be applied by evaluating the homogenized properties of a two-phase planar composite over the triangle symmetry sector of a D 3 symmetric hexagonal unit cell.« less

Toward reliable characterization of functional homogeneity in the human brain: preprocessing, scan duration, imaging resolution and computational space.

PubMed

Zuo, Xi-Nian; Xu, Ting; Jiang, Lili; Yang, Zhi; Cao, Xiao-Yan; He, Yong; Zang, Yu-Feng; Castellanos, F Xavier; Milham, Michael P

2013-01-15

While researchers have extensively characterized functional connectivity between brain regions, the characterization of functional homogeneity within a region of the brain connectome is in early stages of development. Several functional homogeneity measures were proposed previously, among which regional homogeneity (ReHo) was most widely used as a measure to characterize functional homogeneity of resting state fMRI (R-fMRI) signals within a small region (Zang et al., 2004). Despite a burgeoning literature on ReHo in the field of neuroimaging brain disorders, its test-retest (TRT) reliability remains unestablished. Using two sets of public R-fMRI TRT data, we systematically evaluated the ReHo's TRT reliability and further investigated the various factors influencing its reliability and found: 1) nuisance (head motion, white matter, and cerebrospinal fluid) correction of R-fMRI time series can significantly improve the TRT reliability of ReHo while additional removal of global brain signal reduces its reliability, 2) spatial smoothing of R-fMRI time series artificially enhances ReHo intensity and influences its reliability, 3) surface-based R-fMRI computation largely improves the TRT reliability of ReHo, 4) a scan duration of 5 min can achieve reliable estimates of ReHo, and 5) fast sampling rates of R-fMRI dramatically increase the reliability of ReHo. Inspired by these findings and seeking a highly reliable approach to exploratory analysis of the human functional connectome, we established an R-fMRI pipeline to conduct ReHo computations in both 3-dimensions (volume) and 2-dimensions (surface). Copyright © 2012 Elsevier Inc. All rights reserved.

Palisade is required in the Drosophila ovary for assembly and function of the protective vitelline membrane.

PubMed

Elalayli, Maggie; Hall, Jacklyn D; Fakhouri, Mazen; Neiswender, Hannah; Ellison, Tambrea T; Han, Zhe; Roon, Penny; LeMosy, Ellen K

2008-07-15

The innermost layer of the Drosophila eggshell, the vitelline membrane, provides structural support and positional information to the embryo. It is assembled in an incompletely understood manner from four major proteins to form a homogeneous, transparent extracellular matrix. Here we show that RNAi knockdown or genetic deletion of a minor constituent of this matrix, Palisade, results in structural disruptions during the initial synthesis of the vitelline membrane by somatic follicle cells surrounding the oocyte, including wide size variation among the precursor vitelline bodies and disorganization of follicle cell microvilli. Loss of Palisade or the microvillar protein Cad99C results in abnormal uptake into the oocyte of sV17, a major vitelline membrane protein, and defects in non-disulfide cross-linking of sV17 and sV23, while loss of Palisade has additional effects on processing and disulfide cross-linking of these proteins. Embryos surrounded by the abnormal vitelline membranes synthesized when Palisade is reduced are fertilized but undergo developmental arrest, usually during the first 13 nuclear divisions, with a nuclear phenotype of chromatin margination similar to that described for wild-type embryos subjected to anoxia. Our results demonstrate that Palisade is involved in coordinating assembly of the vitelline membrane and is required for functional properties of the eggshell.

Palisade is required in the Drosophila ovary for assembly and function of the protective vitelline membrane

PubMed Central

Elalayli, Maggie; Hall, Jacklyn D.; Fakhouri, Mazen; Neiswender, Hannah; Ellison, Tambrea T.; Han, Zhe; Roon, Penny; LeMosy, Ellen K.

2008-01-01

The innermost layer of the Drosophila eggshell, the vitelline membrane, provides structural support and positional information to the embryo. It is assembled in an incompletely understood manner from four major proteins to form a homogeneous, transparent extracellular matrix. Here we show that RNAi knockdown or genetic deletion of a minor constituent of this matrix, Palisade, results in structural disruptions during the initial synthesis of the vitelline membrane by somatic follicle cells surrounding the oocyte, including wide size variation among the precursor vitelline bodies and disorganization of follicle cell microvilli. Loss of Palisade or the microvillar protein Cad99C results in abnormal uptake into the oocyte of sV17, a major vitelline membrane protein, and defects in non-disulfide cross-linking of sV17 and sV23, while loss of Palisade has additional effects on processing and disulfide cross-linking of these proteins. Embryos surrounded by the abnormal vitelline membranes synthesized when Palisade is reduced are fertilized but undergo developmental arrest, usually during the first 13 nuclear divisions, with a nuclear phenotype of chromatin margination similar to that described for wild-type embryos subjected to anoxia. Our results demonstrate that Palisade is involved in coordinating assembly of the vitelline membrane and is required for functional properties of the eggshell. PMID:18514182

Creation of a type IIS restriction endonuclease with a long recognition sequence

PubMed Central

Lippow, Shaun M.; Aha, Patti M.; Parker, Matthew H.; Blake, William J.; Baynes, Brian M.; Lipovšek, Daša

2009-01-01

Type IIS restriction endonucleases cleave DNA outside their recognition sequences, and are therefore particularly useful in the assembly of DNA from smaller fragments. A limitation of type IIS restriction endonucleases in assembly of long DNA sequences is the relative abundance of their target sites. To facilitate ligation-based assembly of extremely long pieces of DNA, we have engineered a new type IIS restriction endonuclease that combines the specificity of the homing endonuclease I-SceI with the type IIS cleavage pattern of FokI. We linked a non-cleaving mutant of I-SceI, which conveys to the chimeric enzyme its specificity for an 18-bp DNA sequence, to the catalytic domain of FokI, which cuts DNA at a defined site outside the target site. Whereas previously described chimeric endonucleases do not produce type IIS-like precise DNA overhangs suitable for ligation, our chimeric endonuclease cleaves double-stranded DNA exactly 2 and 6 nt from the target site to generate homogeneous, 5′, four-base overhangs, which can be ligated with 90% fidelity. We anticipate that these enzymes will be particularly useful in manipulation of DNA fragments larger than a thousand bases, which are very likely to contain target sites for all natural type IIS restriction endonucleases. PMID:19304757

Double-hydrophobic elastin-like polypeptides with added functional motifs: Self-assembly and cytocompatibility.

PubMed

Le, Duc H T; Tsutsui, Yoko; Sugawara-Narutaki, Ayae; Yukawa, Hiroshi; Baba, Yoshinobu; Ohtsuki, Chikara

2017-09-01

We have recently developed a novel double-hydrophobic elastin-like triblock polypeptide called GPG, designed after the uneven distribution of two different hydrophobic domains found in elastin, an extracellular matrix protein providing elasticity and resilience to tissues. Upon temperature trigger, GPG undergoes a sequential self-assembling process to form flexible beaded nanofibers with high homogeneity and excellent dispersibility in water. Given that GPG might be a potential elastin-mimetic material, we sought to explore the biological activities of this block polypeptide. Besides GPG, several functionalized derivatives were also constructed by fusing functional motifs such as KAAK or KAAKGRGDS at the C-terminal of GPG. Although the added motifs affected the kinetics of fiber formation and β-sheet contents, all three GPGs assembled into beaded nanofibers at the physiological temperature. The resulting GPG nanofibers preserved their beaded structures in cell culture medium; therefore, they were coated on polystyrene substrates to study their cytocompatibility toward mouse embryonic fibroblasts, NIH-3T3. Among the three polypeptides, GPG having the cell-binding motif GRGDS derived from fibronectin showed excellent cell adhesion and cell proliferation properties compared to other conventional materials, suggesting its promising applications as extracellular matrices for mammalian cells. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 2475-2484, 2017. © 2017 Wiley Periodicals, Inc.

RELATIONSHIP BETWEEN RIGIDITY OF EXTERNAL FIXATOR AND NUMBER OF PINS: COMPUTER ANALYSIS USING FINITE ELEMENTS

PubMed Central

Sternick, Marcelo Back; Dallacosta, Darlan; Bento, Daniela Águida; do Reis, Marcelo Lemos

2015-01-01

Objective: To analyze the rigidity of a platform-type external fixator assembly, according to different numbers of pins on each clamp. Methods: Computer simulation on a large-sized Cromus dynamic external fixator (Baumer SA) was performed using a finite element method, in accordance with the standard ASTM F1541. The models were generated with approximately 450,000 quadratic tetrahedral elements. Assemblies with two, three and four Schanz pins of 5.5 mm in diameter in each clamp were compared. Every model was subjected to a maximum force of 200 N, divided into 10 sub-steps. For the components, the behavior of the material was assumed to be linear, elastic, isotropic and homogeneous. For each model, the rigidity of the assembly and the Von Mises stress distribution were evaluated. Results: The rigidity of the system was 307.6 N/mm for two pins, 369.0 N/mm for three and 437.9 N/mm for four. Conclusion: The results showed that four Schanz pins in each clamp promoted rigidity that was 19% greater than in the configuration with three pins and 42% greater than with two pins. Higher tension occurred in configurations with fewer pins. In the models analyzed, the maximum tension occurred on the surface of the pin, close to the fixation area. PMID:27047879

Comparison of Extruded and Sonicated Vesicles for Planar Bilayer Self-Assembly

PubMed Central

Cho, Nam-Joon; Hwang, Lisa Y.; Solandt, Johan J.R.; Frank, Curtis W.

2013-01-01

Lipid vesicles are an important class of biomaterials that have a wide range of applications, including drug delivery, cosmetic formulations and model membrane platforms on solid supports. Depending on the application, properties of a vesicle population such as size distribution, charge and permeability need to be optimized. Preparation methods such as mechanical extrusion and sonication play a key role in controlling these properties, and yet the effects of vesicle preparation method on vesicular properties and integrity (e.g., shape, size, distribution and tension) remain incompletely understood. In this study, we prepared vesicles composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid by either extrusion or sonication, and investigated the effects on vesicle size distribution over time as well as the concomitant effects on the self-assembly of solid-supported planar lipid bilayers. Dynamic light scattering (DLS), quartz crystal microbalance with dissipation (QCM-D) monitoring, fluorescence recovery after photobleaching (FRAP) and atomic force microscopy (AFM) experiments were performed to characterize vesicles in solution as well as their interactions with silicon oxide substrates. Collectively, the data support that sonicated vesicles offer more robust control over the self-assembly of homogenous planar lipid bilayers, whereas extruded vesicles are vulnerable to aging and must be used soon after preparation. PMID:28811437

Control of hydroxyapatite coating by self-assembled monolayers on titanium and improvement of osteoblast adhesion.

PubMed

Shen, Juan; Qi, Yongcheng; Jin, Bo; Wang, Xiaoyan; Hu, Yamin; Jiang, Qiying

2017-01-01

Self-assembly technique was applied to introduce functional groups and form hydroxyl-, amine-, and carboxyl-terminal self-assembled monolayers (SAMs). The SAMs were grafted onto titanium substrates to obtain a molecularly smooth functional surface. Subsequent hydrothermal crystal growth formed homogeneous and crack-free crystalline hydroxyapatite (HA) coatings on these substrates. AFM and XPS were used to characterize the SAM surfaces, and XRD, SEM, and TEM were used to characterize the HA coatings. Results show that highly crystalline, dense, and oriented HA coatings can be formed on the OH-, NH 2 -, and COOH-SAM surfaces. The SAM surface with -COOH exhibited stronger nucleating ability than that with -OH and -NH 2 . The nucleation and growth processes of HA coatings were effectively controlled by varying reaction time, pH, and temperature. By using this method, highly crystalline, dense, and adherent HA coatings were obtained. In addition, in vitro cell evaluation demonstrated that HA coatings improved cell adhesion as compared with pristine titanium substrate. The proposed method is considerably effective in introducing the HA coatings on titanium surfaces for various biomedical applications and further usage in other industries. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 124-135, 2017. © 2015 Wiley Periodicals, Inc.

Exploring the application of latent class cluster analysis for investigating pedestrian crash injury severities in Switzerland.

PubMed

Sasidharan, Lekshmi; Wu, Kun-Feng; Menendez, Monica

2015-12-01

One of the major challenges in traffic safety analyses is the heterogeneous nature of safety data, due to the sundry factors involved in it. This heterogeneity often leads to difficulties in interpreting results and conclusions due to unrevealed relationships. Understanding the underlying relationship between injury severities and influential factors is critical for the selection of appropriate safety countermeasures. A method commonly employed to address systematic heterogeneity is to focus on any subgroup of data based on the research purpose. However, this need not ensure homogeneity in the data. In this paper, latent class cluster analysis is applied to identify homogenous subgroups for a specific crash type-pedestrian crashes. The manuscript employs data from police reported pedestrian (2009-2012) crashes in Switzerland. The analyses demonstrate that dividing pedestrian severity data into seven clusters helps in reducing the systematic heterogeneity of the data and to understand the hidden relationships between crash severity levels and socio-demographic, environmental, vehicle, temporal, traffic factors, and main reason for the crash. The pedestrian crash injury severity models were developed for the whole data and individual clusters, and were compared using receiver operating characteristics curve, for which results favored clustering. Overall, the study suggests that latent class clustered regression approach is suitable for reducing heterogeneity and revealing important hidden relationships in traffic safety analyses. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimization of Sinter Plant Operating Conditions Using Advanced Multivariate Statistics: Intelligent Data Processing

NASA Astrophysics Data System (ADS)

Fernández-González, Daniel; Martín-Duarte, Ramón; Ruiz-Bustinza, Íñigo; Mochón, Javier; González-Gasca, Carmen; Verdeja, Luis Felipe

2016-08-01

Blast furnace operators expect to get sinter with homogenous and regular properties (chemical and mechanical), necessary to ensure regular blast furnace operation. Blends for sintering also include several iron by-products and other wastes that are obtained in different processes inside the steelworks. Due to their source, the availability of such materials is not always consistent, but their total production should be consumed in the sintering process, to both save money and recycle wastes. The main scope of this paper is to obtain the least expensive iron ore blend for the sintering process, which will provide suitable chemical and mechanical features for the homogeneous and regular operation of the blast furnace. The systematic use of statistical tools was employed to analyze historical data, including linear and partial correlations applied to the data and fuzzy clustering based on the Sugeno Fuzzy Inference System to establish relationships among the available variables.

Self-similar assemblies of globular whey proteins at the air-water interface: effect of the structure.

PubMed

Mahmoudi, Najet; Gaillard, Cédric; Boué, François; Axelos, Monique A V; Riaublanc, Alain

2010-05-01

We investigated the structure of heat-induced assemblies of whey globular proteins using small angle neutron scattering (SANS), static and dynamic light scattering (SLS and DLS), and cryogenic transmission electron microscopy (Cryo-TEM). Whey protein molecules self-assemble in fractal aggregates with a structure density depending on the electrostatic interactions. We determined the static and dynamic properties of interfacial layer formed by the protein assemblies, upon adsorption and spreading at the air-water interface using surface film balance and interfacial dilatational rheology. Upon spreading, all whey protein systems show a power-law scaling behavior of the surface pressure versus concentration in the semi-dilute surface concentration regime, with an exponent ranging from 5.5 to 9 depending on the electrostatic interactions and the aggregation state. The dilatational modulus derived from surface pressure isotherms shows a main peak at 6-8 mN/m, generally considered to be the onset of a conformational change in the monolayer, and a second peak or a shoulder at 15 mN/m. Long-time adsorption kinetics give similar results for both the native whey proteins and the corresponding self-similar assemblies, with a systematic effect of the ionic strength. Copyright 2010 Elsevier Inc. All rights reserved.

Halogen-Adatom Mediated Phase Transition of Two-Dimensional Molecular Self-Assembly on a Metal Surface.

PubMed

Niu, Tianchao; Wu, Jinge; Ling, Faling; Jin, Shuo; Lu, Guanghong; Zhou, Miao

2018-01-09

Construction of tunable and robust two-dimensional (2D) molecular arrays with desirable lattices and functionalities over a macroscopic scale relies on spontaneous and reversible noncovalent interactions between suitable molecules as building blocks. Halogen bonding, with active tunability of direction, strength, and length, is ideal for tailoring supramolecular structures. Herein, by combining low-temperature scanning tunneling microscopy and systematic first-principles calculations, we demonstrate novel halogen bonding involving single halogen atoms and phase engineering in 2D molecular self-assembly. On the Au(111) surface, we observed catalyzed dehalogenation of hexabromobenzene (HBB) molecules, during which negatively charged bromine adatoms (Br δ- ) were generated and participated in assembly via unique C-Br δ+ ···Br δ- interaction, drastically different from HBB assembly on a chemically inert graphene substrate. We successfully mapped out different phases of the assembled superstructure, including densely packed hexagonal, tetragonal, dimer chain, and expanded hexagonal lattices at room temperature, 60 °C, 90 °C, and 110 °C, respectively, and the critical role of Br δ- in regulating lattice characteristics was highlighted. Our results show promise for manipulating the interplay between noncovalent interactions and catalytic reactions for future development of molecular nanoelectronics and 2D crystal engineering.

A rapid mechanism to remobilize and homogenize highly crystalline magma bodies.

PubMed

Burgisser, Alain; Bergantz, George W

2011-03-10

The largest products of magmatic activity on Earth, the great bodies of granite and their corresponding large eruptions, have a dual nature: homogeneity at the large scale and spatial and temporal heterogeneity at the small scale. This duality calls for a mechanism that selectively removes the large-scale heterogeneities associated with the incremental assembly of these magmatic systems and yet occurs rapidly despite crystal-rich, viscous conditions seemingly resistant to mixing. Here we show that a simple dynamic template can unify a wide range of apparently contradictory observations from both large plutonic bodies and volcanic systems by a mechanism of rapid remobilization (unzipping) of highly viscous crystal-rich mushes. We demonstrate that this remobilization can lead to rapid overturn and produce the observed juxtaposition of magmatic materials with very disparate ages and complex chemical zoning. What distinguishes our model is the recognition that the process has two stages. Initially, a stiff mushy magma is reheated from below, producing a reduction in crystallinity that leads to the growth of a subjacent buoyant mobile layer. When the thickening mobile layer becomes sufficiently buoyant, it penetrates the overlying viscous mushy magma. This second stage rapidly exports homogenized material from the lower mobile layer to the top of the system, and leads to partial overturn within the viscous mush itself as an additional mechanism of mixing. Model outputs illustrate that unzipping can rapidly produce large amounts of mobile magma available for eruption. The agreement between calculated and observed unzipping rates for historical eruptions at Pinatubo and at Montserrat demonstrates the general applicability of the model. This mechanism furthers our understanding of both the formation of periodically homogenized plutons (crust building) and of ignimbrites by large eruptions.

Optimization of synthesis process of thermally-responsive poly-n-isopropylacrylamide nanoparticles for controlled release of antimicrobial hydrophobic compounds

NASA Astrophysics Data System (ADS)

Hill, Laura E.; Gomes, Carmen L.

2014-12-01

The goal of this study was to develop an effective method to synthesize poly-n-isopropylacrylamide (PNIPAAM) nanoparticles with entrapped cinnamon bark extract (CBE) to improve its delivery to foodborne pathogens and control its release with temperature stimuli. CBE was used as a model for hydrophobic natural antimicrobials. A top-down procedure using crosslinked PNIPAAM was compared to a bottom-up procedure using NIPAAM monomer. Both processes relied on self-assembly of the molecules into micelles around the CBE at 40 °C. Processing conditions were compared including homogenization time of the polymer, hydration time prior to homogenization, lyophilization, and the effect of particle ultrafiltration. The top-down versus bottom-up synthesis methods yielded particles with significantly different characteristics, especially their release profiles and antimicrobial activities. The synthesis methods affected particle size, with the bottom-up procedure resulting in smaller (P < 0.05) diameters than the top-down procedure. The controlled release profile of CBE from nanoparticles was dependent on the release media temperature. A faster, burst release was observed at 40 °C and a slower, more sustained release was observed at lower temperatures. PNIPAAM particles containing CBE were analyzed for their antimicrobial activity against Salmonella enterica serovar Typhimurium LT2 and Listeria monocytogenes Scott A. The PNIPAAM particles synthesized via the top-down procedure had a much faster release, which led to a greater (P < 0.05) antimicrobial activity. Both of the top-down nanoparticles performed similarly, therefore the 7 min homogenization time nanoparticles would be the best for this application, as the process time is shorter and little improvement was seen by using a slightly longer homogenization.

Environment-Dependent Guest Exchange in Supramolecular Hosts

PubMed Central

2015-01-01

Dynamic exchange of guest molecules, encapsulated in host assemblies, is a phenomenon in supramolecular chemistry that has important implications in several applications. While the mechanism of exchange in micellar assemblies has been previously investigated, the effect of host and guest environment upon the guest-exchange dynamics has received little attention, if any. In this paper, we study the guest-exchange mechanism in pH-sensitive nanogels along with pH-insensitive nanogels as a control. By systematically comparing the behavior of these nanogels, we show that size, concentration, and hydrophobicity can all play a critical role in guest-exchange dynamics. More importantly, these studies reveal that the dominant mechanism of guest exchange can intimately depend on environmental factors. PMID:25244305

Extension of lattice cluster theory to strongly interacting, self-assembling polymeric systems.

PubMed

Freed, Karl F

2009-02-14

A new extension of the lattice cluster theory is developed to describe the influence of monomer structure and local correlations on the free energy of strongly interacting and self-assembling polymer systems. This extension combines a systematic high dimension (1/d) and high temperature expansion (that is appropriate for weakly interacting systems) with a direct treatment of strong interactions. The general theory is illustrated for a binary polymer blend whose two components contain "sticky" donor and acceptor groups, respectively. The free energy is determined as an explicit function of the donor-acceptor contact probabilities that depend, in turn, on the local structure and both the strong and weak interactions.

The complete mitochondrial genome of the sandbar shark Carcharhinus plumbeus.

PubMed

Blower, Dean C; Ovenden, Jennifer R

2016-01-01

The sandbar shark, Carcharhinus plumbeus, a major representative species in shark fisheries worldwide is now considered vulnerable to overfishing. A pool of 774,234 Roche 454 shotgun sequences from one individual were assembled into a 16,706 bp mitogenome with 33× average coverage depth. It comprised 13 protein coding genes, 22 transfer RNA's, 2 ribosomal genes and 2 non-coding regions, typical of a vertebrate mitogenome. As expected for sharks, an A-T nucleotide bias was evident. This adds to rapidly growing number of mitogenome assemblies for the economically important Carcharhinidae family. The C. plumbeus mitogenome will assist researchers, fisheries and conservation managers interested in shark molecular systematics, phylogeography, conservation genetics, population and stock structure.

Adaptive attitude control and momentum management for large-angle spacecraft maneuvers

NASA Technical Reports Server (NTRS)

Parlos, Alexander G.; Sunkel, John W.

1992-01-01

The fully coupled equations of motion are systematically linearized around an equilibrium point of a gravity gradient stabilized spacecraft, controlled by momentum exchange devices. These equations are then used for attitude control system design of an early Space Station Freedom flight configuration, demonstrating the errors caused by the improper approximation of the spacecraft dynamics. A full state feedback controller, incorporating gain-scheduled adaptation of the attitude gains, is developed for use during spacecraft on-orbit assembly or operations characterized by significant mass properties variations. The feasibility of the gain adaptation is demonstrated via a Space Station Freedom assembly sequence case study. The attitude controller stability robustness and transient performance during gain adaptation appear satisfactory.

Paramaterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution

NASA Astrophysics Data System (ADS)

He, Xibing; Shinoda, Wataru; DeVane, Russell; Anderson, Kelly L.; Klein, Michael L.

2010-02-01

A coarse-grained (CG) forcefield for linear alkylbenzene sulfonates (LAS) was systematically parameterized. Thermodynamic data from experiments and structural data obtained from all-atom molecular dynamics were used as targets to parameterize CG potentials for the bonded and non-bonded interactions. The added computational efficiency permits one to employ computer simulation to probe the self-assembly of LAS aqueous solutions into different morphologies starting from a random configuration. The present CG model is shown to accurately reproduce the phase behavior of solutions of pure isomers of sodium dodecylbenzene sulfonate, despite the fact that phase behavior was not directly taken into account in the forcefield parameterization.

Design of self-assembling beta-hairpin pepide-based hydrogels for tissue engineering applications

NASA Astrophysics Data System (ADS)

Butterick, Lisa Ann

The field of tissue engineering aims to repair damaged tissues and organs with diminished function. One approach used in tissue engineering is to introduce cells and/or growth factors to the damaged tissue in either one of two ways. The first method is an invasive procedure where cells are introduced to a preformed scaffold and cultured in vitro. The scaffold is then inserted into the host by making an incision at the site of interest, which must be as large as the preformed scaffold. The second method is a minimally invasive procedure where cells are suspended in a polymeric solution and injected via syringe. After leaving the syringe, the material undergoes a phase transition to form a hydrogel at the site of introduction. Regardless of the delivery mechanism employed, development of an appropriate scaffold conducive to cellular proliferation and extracellular matrix production is critical to the success of the implanted material in persuading the body to repair itself. In working toward this goal, we have developed a family of beta-hairpin peptides, based on the design MAX1, that undergoes intramolecular folding and self-assembly to form rigid hydrogels in response to changes in pH, ionic strength, and temperature. From a molecular design standpoint of view, site specific N-methylation of MAX1 was performed to determine the importance of forming hydrogen bonds during the self-assembly event and its effect on hydrogelation. The remainder of this thesis is dedicated to the development of materials and minimally methodologies to deliver gel/cell constructs via syringe to target sites to aid in tissue repair. A peptide, MAX7CNB was designed that undergoes folding and assembly in response to ultraviolet light to form hydrogel material. In addition, MAX8 was rationally designed to display the appropriate hydrogelation kinetics to achieve homogenous cellular encapsulation throughout the gel matrix. MAX8 gel/cell scaffolds can be easily delivered via syringe to secondary target sites while maintaining cellular homogeneity, viability and remain fixed at the site of introduction. Additionally, preliminary in vitro based studies employing mouse peritoneal macrophages suggest the MAX8 gels are non-inflammatory in nature and may not elicit an in vivo immune response upon implantation. It has been demonstrated throughout this thesis that by employing amino acids as fundamental building blocks, peptide sequences can be designed to undergo molecular recognition, resulting in hydrogel material for use in tissue engineering applications.

Systematic reviews on child welfare services: identifying and disseminating the evidence.

PubMed

Kornør, Hege; Bergman, Hanna; Maayan, Nicola; Soares-Weiser, Karla; Bjørndal, Arild

2015-10-01

Evidence-based practice is at an early stage of uptake within child welfare services. To facilitate well-informed decisions, we disseminated evidence from systematic reviews (SR) to local child welfare stakeholders in Norway through plain language summaries on a website (http://www.r-bup.no). We developed and implemented our dissemination strategy through seven steps: (1) systematic literature search; (2) selection of relevant SRs; (3) assembly of an advisory board; (4) selection of child welfare SRs relevant to Norway; (5) prioritization of the included SRs; (6) development of a plain language summary (PLS) after feedback from the advisory board; and (7) implementation of website. A total of 9266 potentially relevant records were screened and 120 SRs were included. The advisory board was assembled from local policymakers, practitioners, researchers, carers and consumers. The advisory board members independently ranked the 120 SRs according to relevance and prioritized 20 SRs that were written up into the PLS. The format of the PLS was tested and agreed with the board members. A website was developed and the PLSs were published starting September 2014. We think that the PLSs will be valuable resources to practitioners and it will be easily accessible to caregivers and consumers. This knowledge will inform research priorities and practice in Norway, leading the way to the use of evidence-based decisions in local child welfare services. © 2015 The Authors. Journal of Evaluation in Clinical Practice published by John Wiley & Sons, Ltd.

Electrical transport properties in Fe-Cr nanocluster-assembled granular films

NASA Astrophysics Data System (ADS)

Wang, Xiong-Zhi; Wang, Lai-Sen; Zhang, Qin-Fu; Liu, Xiang; Xie, Jia; Su, A.-Mei; Zheng, Hong-Fei; Peng, Dong-Liang

2017-09-01

The Fe100-xCrx nanocluster-assembled granular films with Cr atomic fraction (x) ranging from 0 to 100 were fabricated by using a plasma-gas-condensation cluster deposition system. The TEM characterization revealed that the uniform Fe clusters were coated with a Cr layer to form a Fe-Cr core-shell structure. Then, the as-prepared Fe100-xCrx nanoclusters were randomly assembled into a granular film in vacuum environments with increasing the deposition time. Because of the competition between interfacial resistance and shunting effect of Cr layer, the room temperature resistivity of the Fe100-xCrx nanocluster-assembled granular films first increased and then decreased with increasing the Cr atomic fraction (x), and revealed a maximum of 2 × 104 μΩ cm at x = 26 at.%. The temperature-dependent longitudinal resistivity (ρxx), magnetoresistance (MR) effect and anomalous Hall effect (AHE) of these Fe100-xCrx nanocluster-assembled granular films were also studied systematically. As the x increased from 0 to 100, the ρxx of all samples firstly decreased and then increased with increasing the measuring temperature. The dependence of ρxx on temperature could be well addressed by a mechanism incorporated for the fluctuation-induced-tunneling (FIT) conduction process and temperature-dependent scattering effect. It was found that the anomalous Hall effect (AHE) had no legible scaling relation in Fe100-xCrx nanocluster-assembled granular films. However, after deducting the contribution of tunneling effect, the scaling relation was unambiguous. Additionally, the Fe100-xCrx nanocluster-assembled granular films revealed a small negative magnetoresistance (MR), which decreased with the increase of x. The detailed physical mechanism of the electrical transport properties in these Fe100-xCrx nanocluster-assembled granular films was also studied.

Substituent Effects on the Self-Assembly/Coassembly and Hydrogelation of Phenylalanine Derivatives.

PubMed

Liyanage, Wathsala; Nilsson, Bradley L

2016-01-26

Supramolecular hydrogels derived from the self-assembly of organic molecules have been exploited for applications ranging from drug delivery to tissue engineering. The relationship between the structure of the assembly motif and the emergent properties of the resulting materials is often poorly understood, impeding rational approaches for the creation of next-generation materials. Aromatic π-π interactions play a significant role in the self-assembly of many supramolecular hydrogelators, but the exact nature of these interactions lacks definition. Conventional models that describe π-π interactions rely on quadrupolar electrostatic interactions between neighboring aryl groups in the π-system. However, recent experimental and computational studies reveal the potential importance of local dipolar interactions between elements of neighboring aromatic rings in stabilizing π-π interactions. Herein, we examine the nature of π-π interactions in the self- and coassembly of Fmoc-Phe-derived hydrogelators by systematically varying the electron-donating or electron-withdrawing nature of the side chain benzyl substituents and correlating these effects to the emergent assembly and gelation properties of the systems. These studies indicate a significant role for stabilizing dipolar interactions between neighboring benzyl groups in the assembled materials. Additional evidence for specific dipolar interactions is provided by high-resolution crystal structures obtained from dynamic transition of gel fibrils to crystals for several of the self-assembled/coassembled Fmoc-Phe derivatives. In addition to electronic effects, steric properties also have a significant effect on the interaction between neighboring benzyl groups in these assembled systems. These findings provide significant insight into the structure-function relationship for Fmoc-Phe-derived hydrogelators and give cues for the design of next-generation materials with desired emergent properties.

Homogeneous Studies of Transiting Extrasolar Planets: Current Status and Future Plans

NASA Astrophysics Data System (ADS)

Taylor, John

2011-09-01

We now know of over 500 planets orbiting stars other than our Sun. The jewels in the crown are the transiting planets, for these are the only ones whose masses and radii are measurable. They are fundamental for our understanding of the formation, evolution, structure and atmospheric properties of extrasolar planets. However, their characterization is not straightforward, requiring extremely high-precision photometry and spectroscopy as well as input from theoretical stellar models. I summarize the motivation and current status of a project to measure the physical properties of all known transiting planetary systems using homogeneous techniques (Southworth 2008, 2009, 2010, 2011 in preparation). Careful attention is paid to the treatment of limb darkening, contaminating light, correlated noise, numerical integration, orbital eccentricity and orientation, systematic errors from theoretical stellar models, and empirical constraints. Complete error budgets are calculated for each system and can be used to determine which type of observation would be most useful for improving the parameter measurements. Known correlations between the orbital periods, masses, surface gravities, and equilibrium temperatures of transiting planets can be explored more safely due to the homogeneity of the properties. I give a sneak preview of Homogeneous Studies Paper 4, which includes the properties of thirty transiting planetary systems observed by the CoRoT, Kepler and Deep Impact space missions. Future opportunities are discussed, plus remaining problems with our understanding of transiting planets. I acknowledge funding from the UK STFC in the form of an Advanced Fellowship.

Thermodynamic and structural insights into nanocomposites engineering by comparing two materials assembly techniques for graphene.

PubMed

Zhu, Jian; Zhang, Huanan; Kotov, Nicholas A

2013-06-25

Materials assembled by layer-by-layer (LBL) assembly and vacuum-assisted flocculation (VAF) have similarities, but a systematic study of their comparative advantages and disadvantages is missing. Such a study is needed from both practical and fundamental perspectives aiming at a better understanding of structure-property relationships of nanocomposites and purposeful engineering of materials with unique properties. Layered composites from polyvinyl alcohol (PVA) and reduced graphene (RG) are made by both techniques. We comparatively evaluate their structure, mechanical, and electrical properties. LBL and VAF composites demonstrate clear differences at atomic and nanoscale structural levels but reveal similarities in micrometer and submicrometer organization. Epitaxial crystallization and suppression of phase transition temperatures are more pronounced for PVA in LBL than for VAF composites. Mechanical properties are virtually identical for both assemblies at high RG contents. We conclude that mechanical properties in layered RG assemblies are largely determined by the thermodynamic state of PVA at the polymer/nanosheet interface rather than the nanometer scale differences in RG packing. High and nearly identical values of toughness for LBL and VAF composites reaching 6.1 MJ/m(3) observed for thermodynamically optimal composition confirm this conclusion. Their toughness is the highest among all other layered assemblies from RG, cellulose, clay, etc. Electrical conductivity, however, is more than 10× higher for LBL than for VAF composites for the same RG contents. Electrical properties are largely determined by the tunneling barrier between RG sheets and therefore strongly dependent on atomic/nanoscale organization. These findings open the door for application-oriented methods of materials engineering using both types of layered assemblies.

Aliphatic peptides show similar self-assembly to amyloid core sequences, challenging the importance of aromatic interactions in amyloidosis.

PubMed

Lakshmanan, Anupama; Cheong, Daniel W; Accardo, Angelo; Di Fabrizio, Enzo; Riekel, Christian; Hauser, Charlotte A E

2013-01-08

The self-assembly of abnormally folded proteins into amyloid fibrils is a hallmark of many debilitating diseases, from Alzheimer's and Parkinson diseases to prion-related disorders and diabetes type II. However, the fundamental mechanism of amyloid aggregation remains poorly understood. Core sequences of four to seven amino acids within natural amyloid proteins that form toxic fibrils have been used to study amyloidogenesis. We recently reported a class of systematically designed ultrasmall peptides that self-assemble in water into cross-β-type fibers. Here we compare the self-assembly of these peptides with natural core sequences. These include core segments from Alzheimer's amyloid-β, human amylin, and calcitonin. We analyzed the self-assembly process using circular dichroism, electron microscopy, X-ray diffraction, rheology, and molecular dynamics simulations. We found that the designed aliphatic peptides exhibited a similar self-assembly mechanism to several natural sequences, with formation of α-helical intermediates being a common feature. Interestingly, the self-assembly of a second core sequence from amyloid-β, containing the diphenylalanine motif, was distinctly different from all other examined sequences. The diphenylalanine-containing sequence formed β-sheet aggregates without going through the α-helical intermediate step, giving a unique fiber-diffraction pattern and simulation structure. Based on these results, we propose a simplified aliphatic model system to study amyloidosis. Our results provide vital insight into the nature of early intermediates formed and suggest that aromatic interactions are not as important in amyloid formation as previously postulated. This information is necessary for developing therapeutic drugs that inhibit and control amyloid formation.

Self-assembly of gelator molecules in liquid crystals studied by ESR

NASA Astrophysics Data System (ADS)

Andreis, Mladen; Carić, Dejana; Vujičić, Nataša Šijaković; Jokić, Milan; Žinić, Mladen; Kveder, Marina

2012-07-01

Thermotropic liquid crystal trans-4-heptylcyclohexanecarboxylic acid (HCCA) doped with 4-oxo-2,2,6,6,-tetramethyl-1-piperidinyloxy spin probe (Tempone) is investigated by electron spin resonance (ESR) spectroscopy in the presence of chiral bisoxalamide gelator 1 during both cooling and heating cycles. In the temperature range 295-383 K, where HCCA displays isotropic, nematic, smectic B and crystalline phases, the impact of 1 self-organization was detected via (non) homogeneous partitioning of the spin probe in the environments varying in the polarity, an effect dependent on the gelator concentration. In particular, the evidence of the onset of the gelator network self-assembly in the nematic phase was detected by ESR at higher temperatures than the ones reported so far by other experimental techniques. Additionally, the spectral analysis points to the switching of the polarity in the vicinity of the spin probe when the transfer of chirality from 1 to HCCA upon cooling of the sample from isotropic to chiral nematic phase appears and when the event of LC gelation results in the achiral nematic phase during chiral gel fibers formation. When the gelation proceeds in the smectic phase, the melting of the gelator network is studied in the nematic phase during the heating cycle. Furthermore, the event of HCCA crystallization is shown to be strongly affected by the presence of 1 as well. The experimental evidence is provided that gelator network confines the HCCA into the domains within the bulk crystalline matrix where the local molecular dynamics are still not frozen. Therefore, we propose that non-homogeneous polarity profile of molecular organization/packing within LC gels could be determinable for the physical properties of various LC gel phases.

SHARP Multiphysics Tutorials

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

Yu, Y. Q.; Shemon, E. R.; Mahadevan, Vijay S.

SHARP, developed under the NEAMS Reactor Product Line, is an advanced modeling and simulation toolkit for the analysis of advanced nuclear reactors. SHARP is comprised of three physics modules currently including neutronics, thermal hydraulics, and structural mechanics. SHARP empowers designers to produce accurate results for modeling physical phenomena that have been identified as important for nuclear reactor analysis. SHARP can use existing physics codes and take advantage of existing infrastructure capabilities in the MOAB framework and the coupling driver/solver library, the Coupled Physics Environment (CouPE), which utilizes the widely used, scalable PETSc library. This report aims at identifying the coupled-physicsmore » simulation capability of SHARP by introducing the demonstration example called sahex in advance of the SHARP release expected by Mar 2016. sahex consists of 6 fuel pins with cladding, 1 control rod, sodium coolant and an outer duct wall that encloses all the other components. This example is carefully chosen to demonstrate the proof of concept for solving more complex demonstration examples such as EBR II assembly and ABTR full core. The workflow of preparing the input files, running the case and analyzing the results is demonstrated in this report. Moreover, an extension of the sahex model called sahex_core, which adds six homogenized neighboring assemblies to the full heterogeneous sahex model, is presented to test homogenization capabilities in both Nek5000 and PROTEUS. Some primary information on the configuration and build aspects for the SHARP toolkit, which includes capability to auto-download dependencies and configure/install with optimal flags in an architecture-aware fashion, is also covered by this report. A step-by-step instruction is provided to help users to create their cases. Details on these processes will be provided in the SHARP user manual that will accompany the first release.« less

Constitutive modeling of the rheological behavior of platelet suspensions

NASA Astrophysics Data System (ADS)

Sommer, Drew E.

Compression molding of chopped fiber composites is used to manufacture complex 3D geometries with high fiber volume fractions of 50-60% and long, discontinuous fibers and thermoplastic matrices. When prepreg, chopped into platelets, is used as a charge material, the individual platelets remain intact during the molding process and flow relative to one another, as experimental observations show. Heterogeneity of the platelet/resin suspension cannot be considered at the structural scale of molding simulation. Instead, the suspension should be idealized into the homogenized anisotropic and viscous system which obeys the prescribed anisotropic stress-strain rate constitutive relation. The viscosity tensor of the aforementioned constitutive law was analytically evaluated in this work through the representative volume element (RVE) based analysis. An idealized microstructure of platelets was developed to perform such an analysis. The platelets were aligned and arranged in a planar configuration with periodic boundary conditions. Analytic expressions for the effective, anisotropic viscosities were derived by micromechanical analysis for the idealized microstructure of rigid platelets. In this analysis, the load transfer mechanisms and their contribution to the viscosity of the platelet assembly were investigated. The kinematic assumption of linear velocity distributions consistent with the mechanism of shearing rate was adopted. While the platelets were assumed to be rigid, the resin was taken as an incompressible, isotropic fluid which provided for the platelet-to-platelet load transfer. Strain rate and temperature dependence were included by modeling the polymer matrix as a Carreau fluid. Shear strain in the resin was developed due to the relative motion of adjacent platelets. The resin shear strain rate was expressed in terms of the corresponding platelet velocities. Equilibrium of the platelet was used to relate the applied far-field stress to the average strain rate through the viscosity of neat resin and geometric parameters of the RVE constituents. When combined, these parameters defined the effective homogenized viscosities of an anisotropic system equivalent to the platelet/resin suspension. The expressions for the effective viscosities were found to be dependent on the platelet geometry, stack geometry, the platelet volume fraction and the viscosity of neat resin. In this study, the platelet volume fraction was defined as the volume of platelets within the RVE divided by the RVE volume and discriminated from the fiber volume fraction within a platelet. An approach using the "viscous solid analogy'' was developed to leverage structural finite element methods to predict homogenized viscosities of the platelet assembly. A finite element model was constructed to develop a comparison to the analytic expressions for rigid platelets and include the effect of deformation within the platelets. To compare with the analytic expressions, large viscosities were prescribed for the platelet to approximate rigidity. The properties of the deformable platelets were determined by an approach proposed by Pipes and co-workers. The assumption of rigidity was found to be approximate except in the case of elongation along the fiber direction. A laminate analogy was implemented as a homogenization tool to include the effect of orientation on the apparent viscosities of a multi-axial platelet assembly. The aligned platelet suspension was used to predict the `pseudo-ply' properties. Pseudo-laminates, which were assumed to approximate the microstructure, were developed. The effective `pseudo-laminate' viscosities were predicted with classical lamination theory.

Search for subgrid scale parameterization by projection pursuit regression

NASA Technical Reports Server (NTRS)

Meneveau, C.; Lund, T. S.; Moin, Parviz

1992-01-01

The dependence of subgrid-scale stresses on variables of the resolved field is studied using direct numerical simulations of isotropic turbulence, homogeneous shear flow, and channel flow. The projection pursuit algorithm, a promising new regression tool for high-dimensional data, is used to systematically search through a large collection of resolved variables, such as components of the strain rate, vorticity, velocity gradients at neighboring grid points, etc. For the case of isotropic turbulence, the search algorithm recovers the linear dependence on the rate of strain (which is necessary to transfer energy to subgrid scales) but is unable to determine any other more complex relationship. For shear flows, however, new systematic relations beyond eddy viscosity are found. For the homogeneous shear flow, the results suggest that products of the mean rotation rate tensor with both the fluctuating strain rate and fluctuating rotation rate tensors are important quantities in parameterizing the subgrid-scale stresses. A model incorporating these terms is proposed. When evaluated with direct numerical simulation data, this model significantly increases the correlation between the modeled and exact stresses, as compared with the Smagorinsky model. In the case of channel flow, the stresses are found to correlate with products of the fluctuating strain and rotation rate tensors. The mean rates of rotation or strain do not appear to be important in this case, and the model determined for homogeneous shear flow does not perform well when tested with channel flow data. Many questions remain about the physical mechanisms underlying these findings, about possible Reynolds number dependence, and, given the low level of correlations, about their impact on modeling. Nevertheless, demonstration of the existence of causal relations between sgs stresses and large-scale characteristics of turbulent shear flows, in addition to those necessary for energy transfer, provides important insight into the relation between scales in turbulent flows.

Using Hierarchical Cluster Models to Systematically Identify Groups of Jobs With Similar Occupational Questionnaire Response Patterns to Assist Rule-Based Expert Exposure Assessment in Population-Based Studies

PubMed Central

Friesen, Melissa C.; Shortreed, Susan M.; Wheeler, David C.; Burstyn, Igor; Vermeulen, Roel; Pronk, Anjoeka; Colt, Joanne S.; Baris, Dalsu; Karagas, Margaret R.; Schwenn, Molly; Johnson, Alison; Armenti, Karla R.; Silverman, Debra T.; Yu, Kai

2015-01-01

Objectives: Rule-based expert exposure assessment based on questionnaire response patterns in population-based studies improves the transparency of the decisions. The number of unique response patterns, however, can be nearly equal to the number of jobs. An expert may reduce the number of patterns that need assessment using expert opinion, but each expert may identify different patterns of responses that identify an exposure scenario. Here, hierarchical clustering methods are proposed as a systematic data reduction step to reproducibly identify similar questionnaire response patterns prior to obtaining expert estimates. As a proof-of-concept, we used hierarchical clustering methods to identify groups of jobs (clusters) with similar responses to diesel exhaust-related questions and then evaluated whether the jobs within a cluster had similar (previously assessed) estimates of occupational diesel exhaust exposure. Methods: Using the New England Bladder Cancer Study as a case study, we applied hierarchical cluster models to the diesel-related variables extracted from the occupational history and job- and industry-specific questionnaires (modules). Cluster models were separately developed for two subsets: (i) 5395 jobs with ≥1 variable extracted from the occupational history indicating a potential diesel exposure scenario, but without a module with diesel-related questions; and (ii) 5929 jobs with both occupational history and module responses to diesel-relevant questions. For each subset, we varied the numbers of clusters extracted from the cluster tree developed for each model from 100 to 1000 groups of jobs. Using previously made estimates of the probability (ordinal), intensity (µg m−3 respirable elemental carbon), and frequency (hours per week) of occupational exposure to diesel exhaust, we examined the similarity of the exposure estimates for jobs within the same cluster in two ways. First, the clusters’ homogeneity (defined as >75% with the same estimate) was examined compared to a dichotomized probability estimate (<5 versus ≥5%; <50 versus ≥50%). Second, for the ordinal probability metric and continuous intensity and frequency metrics, we calculated the intraclass correlation coefficients (ICCs) between each job’s estimate and the mean estimate for all jobs within the cluster. Results: Within-cluster homogeneity increased when more clusters were used. For example, ≥80% of the clusters were homogeneous when 500 clusters were used. Similarly, ICCs were generally above 0.7 when ≥200 clusters were used, indicating minimal within-cluster variability. The most within-cluster variability was observed for the frequency metric (ICCs from 0.4 to 0.8). We estimated that using an expert to assign exposure at the cluster-level assignment and then to review each job in non-homogeneous clusters would require ~2000 decisions per expert, in contrast to evaluating 4255 unique questionnaire patterns or 14983 individual jobs. Conclusions: This proof-of-concept shows that using cluster models as a data reduction step to identify jobs with similar response patterns prior to obtaining expert ratings has the potential to aid rule-based assessment by systematically reducing the number of exposure decisions needed. While promising, additional research is needed to quantify the actual reduction in exposure decisions and the resulting homogeneity of exposure estimates within clusters for an exposure assessment effort that obtains cluster-level expert assessments as part of the assessment process. PMID:25477475

Using hierarchical cluster models to systematically identify groups of jobs with similar occupational questionnaire response patterns to assist rule-based expert exposure assessment in population-based studies.

PubMed

Friesen, Melissa C; Shortreed, Susan M; Wheeler, David C; Burstyn, Igor; Vermeulen, Roel; Pronk, Anjoeka; Colt, Joanne S; Baris, Dalsu; Karagas, Margaret R; Schwenn, Molly; Johnson, Alison; Armenti, Karla R; Silverman, Debra T; Yu, Kai

2015-05-01

Rule-based expert exposure assessment based on questionnaire response patterns in population-based studies improves the transparency of the decisions. The number of unique response patterns, however, can be nearly equal to the number of jobs. An expert may reduce the number of patterns that need assessment using expert opinion, but each expert may identify different patterns of responses that identify an exposure scenario. Here, hierarchical clustering methods are proposed as a systematic data reduction step to reproducibly identify similar questionnaire response patterns prior to obtaining expert estimates. As a proof-of-concept, we used hierarchical clustering methods to identify groups of jobs (clusters) with similar responses to diesel exhaust-related questions and then evaluated whether the jobs within a cluster had similar (previously assessed) estimates of occupational diesel exhaust exposure. Using the New England Bladder Cancer Study as a case study, we applied hierarchical cluster models to the diesel-related variables extracted from the occupational history and job- and industry-specific questionnaires (modules). Cluster models were separately developed for two subsets: (i) 5395 jobs with ≥1 variable extracted from the occupational history indicating a potential diesel exposure scenario, but without a module with diesel-related questions; and (ii) 5929 jobs with both occupational history and module responses to diesel-relevant questions. For each subset, we varied the numbers of clusters extracted from the cluster tree developed for each model from 100 to 1000 groups of jobs. Using previously made estimates of the probability (ordinal), intensity (µg m(-3) respirable elemental carbon), and frequency (hours per week) of occupational exposure to diesel exhaust, we examined the similarity of the exposure estimates for jobs within the same cluster in two ways. First, the clusters' homogeneity (defined as >75% with the same estimate) was examined compared to a dichotomized probability estimate (<5 versus ≥5%; <50 versus ≥50%). Second, for the ordinal probability metric and continuous intensity and frequency metrics, we calculated the intraclass correlation coefficients (ICCs) between each job's estimate and the mean estimate for all jobs within the cluster. Within-cluster homogeneity increased when more clusters were used. For example, ≥80% of the clusters were homogeneous when 500 clusters were used. Similarly, ICCs were generally above 0.7 when ≥200 clusters were used, indicating minimal within-cluster variability. The most within-cluster variability was observed for the frequency metric (ICCs from 0.4 to 0.8). We estimated that using an expert to assign exposure at the cluster-level assignment and then to review each job in non-homogeneous clusters would require ~2000 decisions per expert, in contrast to evaluating 4255 unique questionnaire patterns or 14983 individual jobs. This proof-of-concept shows that using cluster models as a data reduction step to identify jobs with similar response patterns prior to obtaining expert ratings has the potential to aid rule-based assessment by systematically reducing the number of exposure decisions needed. While promising, additional research is needed to quantify the actual reduction in exposure decisions and the resulting homogeneity of exposure estimates within clusters for an exposure assessment effort that obtains cluster-level expert assessments as part of the assessment process. Published by Oxford University Press on behalf of the British Occupational Hygiene Society 2014.

Exciton antennas and concentrators from core-shell and corrugated carbon nanotube filaments of homogeneous composition.

PubMed

Han, Jae-Hee; Paulus, Geraldine L C; Maruyama, Ryuichiro; Heller, Daniel A; Kim, Woo-Jae; Barone, Paul W; Lee, Chang Young; Choi, Jong Hyun; Ham, Moon-Ho; Song, Changsik; Fantini, C; Strano, Michael S

2010-10-01

There has been renewed interest in solar concentrators and optical antennas for improvements in photovoltaic energy harvesting and new optoelectronic devices. In this work, we dielectrophoretically assemble single-walled carbon nanotubes (SWNTs) of homogeneous composition into aligned filaments that can exchange excitation energy, concentrating it to the centre of core-shell structures with radial gradients in the optical bandgap. We find an unusually sharp, reversible decay in photoemission that occurs as such filaments are cycled from ambient temperature to only 357 K, attributed to the strongly temperature-dependent second-order Auger process. Core-shell structures consisting of annular shells of mostly (6,5) SWNTs (E(g)=1.21 eV) and cores with bandgaps smaller than those of the shell (E(g)=1.17 eV (7,5)-0.98 eV (8,7)) demonstrate the concentration concept: broadband absorption in the ultraviolet-near-infrared wavelength regime provides quasi-singular photoemission at the (8,7) SWNTs. This approach demonstrates the potential of specifically designed collections of nanotubes to manipulate and concentrate excitons in unique ways.

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

Semkova, Valentina; Otuka, Naohiko; Mikhailiukova, Marina

Members of the International Network of Nuclear Reaction Data Centres (NRDC) have collaborated since the 1960s on the worldwide collection, compilation and dissemination of experimental nuclear reaction data. New publications are systematically complied, and all agreed data assembled and incorporated within the EXFOR database. Here, recent upgrades to achieve greater completeness of the contents are described, along with reviews and adjustments of the compilation rules for specific types of data.

Hyb-Seq: combining target enrichment and genome skimming for plant phylogenomics

Treesearch

Kevin Weitemier; Shannon C.K. Straub; Richard C. Cronn; Mark Fishbein; Roswitha Schmickl; Angela McDonnell; Aaron Liston

2014-01-01

• Premise of the study: Hyb-Seq, the combination of target enrichment and genome skimming, allows simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. • Methods and Results: Genome and transcriptome assemblies for milkweed ( Asclepias syriaca ) were used to design enrichment probes for 3385...

The Linear Imperative: An Inventory and Conceptual Analysis of Students Overuse of Linearity

ERIC Educational Resources Information Center

Van Dooren, Wim; De Bock, Dirk; Janssens, Dirk; Verschaffel, Lieven

2008-01-01

The overreliance on linear methods in students' reasoning and problem solving has been documented and discussed by several scholars in the field. So far, however, there have been no attempts to assemble the evidence and to analyze it is a systematic way. This article provides an overview and a conceptual analysis of students' tendency to use…

MHD Turbulence Sheared in Fixed and Rotating Frames

NASA Technical Reports Server (NTRS)

Kassinos, S. C.; Knaepen, B.; Wray, A.

2004-01-01

We consider homogeneous turbulence in a conducting fluid that is exposed to a uniform external magnetic field while being sheared in fixed and rotating frames. We take both the frame-rotation axis and the applied magnetic field to be aligned in the direction normal to the plane of the mean shear. Here a systematic parametric study is carried out in a series of Direct Numerical Simulations (DNS) in order to clarify the main effects determining the structural anisotropy and stability of the flow.

Internal energy fluctuations of a granular gas under steady uniform shear flow.

PubMed

Brey, J Javier; García de Soria, M I; Maynar, P

2012-09-01

The stochastic properties of the total internal energy of a dilute granular gas in the steady uniform shear flow state are investigated. A recent theory formulated for fluctuations about the homogeneous cooling state is extended by analogy with molecular systems. The theoretical predictions are compared with molecular dynamics simulation results. Good agreement is found in the limit of weak inelasticity, while systematic and relevant discrepancies are observed when the inelasticity increases. The origin of this behavior is discussed.

Synthesis and liquid crystalline properties of mono-, di- and tri-O-alkyl pentaerythritol derivatives bearing tri-, di- or monogalactosyl heads: the effects of curvature of molecular packing on mesophase formation.

PubMed

Dumoulin, Fabienne; Lafont, Dominique; Huynh, Thai-Lê; Boullanger, Paul; Mackenzie, Grahame; West, Jon J; Goodby, John W

2007-01-01

Self-organisation and self-assembly are critical to the stability of synthetic and biological membranes. Of particular importance is consideration of the packing arrangements of the various molecular species. Both phospho- and glycolipids can pack in ways in which curvature can be introduced into self-organised or self-assembled systems. For instance, it is known that the degree of curvature can affect the structures of any condensed phases that are formed. In this article we report on a systematic study in which we have varied the shapes of glycolipids and examined the condensed phases that they form. In doing so, we have also unified the shape dependency of lyotropic liquid crystals with those of thermotropic liquid crystals. In order to undertake this systematic study a range of different pentaerythritol derivatives was synthesized, which covers combinations of one to three alkyl chains of different lengths (6,7,9,10,11,12,14,16 carbon atoms) and three to one galactosyl heads. Mono- and di-O-galactosyl derivatives were prepared directly by glycosylation of the corresponding alcohols using 2,3,4,6-tetra-O-benzoyl or acetyl-alpha-D-galactopyranosyl trichloroacetimidate or bromide as the donors; the tri-O-galactosyl derivatives were synthesized from O-alkyl-O-benzyl di-O-galactosyl pentaerythritol intermediates, followed by de-O-benzylation and glycosylation steps. All of the fully deprotected products were obtained by standard methods, and their self-organising and self-assembling properties examined.

Supramolecular organic frameworks: engineering periodicity in water through host-guest chemistry.

PubMed

Tian, Jia; Chen, Lan; Zhang, Dan-Wei; Liu, Yi; Li, Zhan-Ting

2016-05-11

The development of homogeneous, water-soluble periodic self-assembled structures comprise repeating units that produce porosity in two-dimensional (2D) or three-dimensional (3D) spaces has become a topic of growing interest in the field of supramolecular chemistry. Such novel self-assembled entities, known as supramolecular organic frameworks (SOFs), are the result of programmed host-guest interactions, which allows for the thermodynamically controlled generation of monolayer sheets or a diamondoid architecture with regular internal cavities or pores under mild conditions. This feature article aims at propagating the conceptually novel SOFs as a new entry into conventional supramolecular polymers. In the first section, we will describe the background of porous solid frameworks and supramolecular polymers. We then introduce the self-assembling behaviour of several multitopic flexible molecules, which is closely related to the design of periodic SOFs from rigid multitopic building blocks. This is followed by a brief discussion of cucurbit[8]uril (CB[8])-encapsulation-enhanced aromatic stacking in water. The three-component host-guest pattern based on this stacking motif has been utilized to drive the formation of most of the new SOFs. In the following two sections, we will highlight the main advances in the construction of 2D and 3D SOFs and the related functional aspects. Finally, we will offer our opinions on future directions for both structures and functions. We hope that this article will trigger the interest of researchers in the field of chemistry, physics, biology and materials science, which should help accelerate the applications of this new family of soft self-assembled organic frameworks.

Two global conformation states of a novel NAD(P) reductase like protein of the thermogenic appendix of the Sauromatum guttatum inflorescence.

PubMed

Skubatz, Hanna; Howald, William N

2013-06-01

A novel NAD(P) reductase like protein (RL) belonging to a class of reductases involved in phenylpropanoid synthesis was previously purified to homogeneity from the Sauromatum guttatum appendix. The Sauromatum appendix raises its temperature above ambient temperature to ~30 °C on the day of inflorescence opening (D-day). Changes in the charge state distribution of the protein in electrospray ionization-mass spectrometry spectra were observed during the development of the appendix. RL adopted two conformations, state A (an extended state) that appeared before heat-production (D - 4 to D - 2), and state B (a compact state) that began appearing on D - 1 and reached a maximum on D-day. RL in healthy leaves of Arabidopsis is present in state A, whereas in thermogenic sporophylls of male cones of Encephalartos ferox is present in state B. These conformational changes strongly suggest an involvement of RL in heat-production. The biophysical properties of this protein are remarkable. It is self-assembled in aqueous solutions into micrometer sizes of organized morphologies. The assembly produces a broad range of cyclic and linear morphologies that resemble micelles, rods, lamellar micelles, as well as vesicles. The assemblies could also form network structures. RL molecules entangle with each other and formed branched, interconnected networks. These unusual assemblies suggest that RL is an oligomer, and its oligomerization can provide additional information needed for thermoregulation. We hypothesize that state A controls the plant basal temperature and state B allows a shift in the temperature set point to above ambient temperature.

Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells

PubMed Central

Shu, Yi; Shu, Dan; Haque, Farzin; Guo, Peixuan

2013-01-01

RNA nanotechnology is a term that refers to the design, fabrication, and utilization of nanoparticles mainly composed of ribonucleic acids via bottom-up self-assembly. The packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor has been developed into a nano-delivery platform. This protocol describes the synthesis, assembly, and functionalization of pRNA nanoparticles based on three ‘toolkits’ derived from pRNA structural features: interlocking loops for hand-in-hand interactions, palindrome sequences for foot-to-foot interactions, and an RNA three-way junction for branch-extension. siRNAs, ribozymes, aptamers, chemical ligands, fluorophores, and other functionalities can also be fused to the pRNA prior to the assembly of the nanoparticles, so as to ensure the production of homogeneous nanoparticles and the retention of appropriate folding and function of the incorporated modules. The resulting self-assembled multivalent pRNA nanoparticles are thermodynamically and chemically stable, and they remain intact at ultra-low concentrations. Gene silencing effects are progressively enhanced with increasing number of siRNA in each pRNA nanoparticle. Systemic injection of the pRNA nanoparticles into xenograft-bearing mice has revealed strong binding to tumors without accumulation in vital organs or tissues. The pRNA-based nano-delivery scaffold paves a new way towards nanotechnological application of pRNA-based nanoparticles for disease detection and treatment. The time required for completing one round of this protocol is 3–4 weeks, including in vitro functional assays, or 2–3 months including in vivo studies. PMID:23928498

Self-assembled organic-inorganic magnetic hybrid adsorbent ferrite based on cyclodextrin nanoparticles.

PubMed

Denadai, Angelo M L; De Sousa, Frederico B; Passos, Joel J; Guatimosim, Fernando C; Barbosa, Kirla D; Burgos, Ana E; de Oliveira, Fernando Castro; da Silva, Jeann C; Neves, Bernardo R A; Mohallem, Nelcy D S; Sinisterra, Rubén D

2012-01-01

Organic-inorganic magnetic hybrid materials (MHMs) combine a nonmagnetic and a magnetic component by means of electrostatic interactions or covalent bonds, and notable features can be achieved. Herein, we describe an application of a self-assembled material based on ferrite associated with β-cyclodextrin (Fe-Ni/Zn/βCD) at the nanoscale level. This MHM and pure ferrite (Fe-Ni/Zn) were used as an adsorbent system for Cr(3+) and Cr(2)O(7) (2-) ions in aqueous solutions. Prior to the adsorption studies, both ferrites were characterized in order to determine the particle size distribution, morphology and available binding sites on the surface of the materials. Microscopy analysis demonstrated that both ferrites present two different size domains, at the micro- and nanoscale level, with the latter being able to self-assemble into larger particles. Fe-Ni/Zn/βCD presented smaller particles and a more homogeneous particle size distribution. Higher porosity for this MHM compared to Fe-Ni/Zn was observed by Brunauer-Emmett-Teller isotherms and positron-annihilation-lifetime spectroscopy. Based on the pKa values, potentiometric titrations demonstrated the presence of βCD in the inorganic matrix, indicating that the lamellar structures verified by transmission electronic microscopy can be associated with βCD assembled structures. Colloidal stability was inferred as a function of time at different pH values, indicating the sedimentation rate as a function of pH. Zeta potential measurements identified an amphoteric behavior for the Fe-Ni/Zn/βCD, suggesting its better capability to remove ions (cations and anions) from aqueous solutions compared to that of Fe-Ni/Zn.

ZPR-3 Assembly 11 : A cylindrical sssembly of highly enriched uranium and depleted uranium with an average {sup 235}U enrichment of 12 atom % and a depleted uranium reflector.

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

Lell, R. M.; McKnight, R. D.; Tsiboulia, A.

2010-09-30

Over a period of 30 years, more than a hundred Zero Power Reactor (ZPR) critical assemblies were constructed at Argonne National Laboratory. The ZPR facilities, ZPR-3, ZPR-6, ZPR-9 and ZPPR, were all fast critical assembly facilities. The ZPR critical assemblies were constructed to support fast reactor development, but data from some of these assemblies are also well suited for nuclear data validation and to form the basis for criticality safety benchmarks. A number of the Argonne ZPR/ZPPR critical assemblies have been evaluated as ICSBEP and IRPhEP benchmarks. Of the three classes of ZPR assemblies, engineering mockups, engineering benchmarks and physicsmore » benchmarks, the last group tends to be most useful for criticality safety. Because physics benchmarks were designed to test fast reactor physics data and methods, they were as simple as possible in geometry and composition. The principal fissile species was {sup 235}U or {sup 239}Pu. Fuel enrichments ranged from 9% to 95%. Often there were only one or two main core diluent materials, such as aluminum, graphite, iron, sodium or stainless steel. The cores were reflected (and insulated from room return effects) by one or two layers of materials such as depleted uranium, lead or stainless steel. Despite their more complex nature, a small number of assemblies from the other two classes would make useful criticality safety benchmarks because they have features related to criticality safety issues, such as reflection by soil-like material. ZPR-3 Assembly 11 (ZPR-3/11) was designed as a fast reactor physics benchmark experiment with an average core {sup 235}U enrichment of approximately 12 at.% and a depleted uranium reflector. Approximately 79.7% of the total fissions in this assembly occur above 100 keV, approximately 20.3% occur below 100 keV, and essentially none below 0.625 eV - thus the classification as a 'fast' assembly. This assembly is Fast Reactor Benchmark No. 8 in the Cross Section Evaluation Working Group (CSEWG) Benchmark Specificationsa and has historically been used as a data validation benchmark assembly. Loading of ZPR-3 Assembly 11 began in early January 1958, and the Assembly 11 program ended in late January 1958. The core consisted of highly enriched uranium (HEU) plates and depleted uranium plates loaded into stainless steel drawers, which were inserted into the central square stainless steel tubes of a 31 x 31 matrix on a split table machine. The core unit cell consisted of two columns of 0.125 in.-wide (3.175 mm) HEU plates, six columns of 0.125 in.-wide (3.175 mm) depleted uranium plates and one column of 1.0 in.-wide (25.4 mm) depleted uranium plates. The length of each column was 10 in. (254.0 mm) in each half of the core. The axial blanket consisted of 12 in. (304.8 mm) of depleted uranium behind the core. The thickness of the depleted uranium radial blanket was approximately 14 in. (355.6 mm), and the length of the radial blanket in each half of the matrix was 22 in. (558.8 mm). The assembly geometry approximated a right circular cylinder as closely as the square matrix tubes allowed. According to the logbook and loading records for ZPR-3/11, the reference critical configuration was loading 10 which was critical on January 21, 1958. Subsequent loadings were very similar but less clean for criticality because there were modifications made to accommodate reactor physics measurements other than criticality. Accordingly, ZPR-3/11 loading 10 was selected as the only configuration for this benchmark. As documented below, it was determined to be acceptable as a criticality safety benchmark experiment. A very accurate transformation to a simplified model is needed to make any ZPR assembly a practical criticality-safety benchmark. There is simply too much geometric detail in an exact (as-built) model of a ZPR assembly, even a clean core such as ZPR-3/11 loading 10. The transformation must reduce the detail to a practical level without masking any of the important features of the critical experiment. And it must do this without increasing the total uncertainty far beyond that of the original experiment. Such a transformation is described in Section 3. It was obtained using a pair of continuous-energy Monte Carlo calculations. First, the critical configuration was modeled in full detail - every plate, drawer, matrix tube, and air gap was modeled explicitly. Then the regionwise compositions and volumes from the detailed as-built model were used to construct a homogeneous, two-dimensional (RZ) model of ZPR-3/11 that conserved the mass of each nuclide and volume of each region. The simple cylindrical model is the criticality-safety benchmark model. The difference in the calculated k{sub eff} values between the as-built three-dimensional model and the homogeneous two-dimensional benchmark model was used to adjust the measured excess reactivity of ZPR-3/11 loading 10 to obtain the k{sub eff} for the benchmark model.« less

Ex vivo mammalian prions are formed of paired double helical prion protein fibrils.

PubMed

Terry, Cassandra; Wenborn, Adam; Gros, Nathalie; Sells, Jessica; Joiner, Susan; Hosszu, Laszlo L P; Tattum, M Howard; Panico, Silvia; Clare, Daniel K; Collinge, John; Saibil, Helen R; Wadsworth, Jonathan D F

2016-05-01

Mammalian prions are hypothesized to be fibrillar or amyloid forms of prion protein (PrP), but structures observed to date have not been definitively correlated with infectivity and the three-dimensional structure of infectious prions has remained obscure. Recently, we developed novel methods to obtain exceptionally pure preparations of prions from mouse brain and showed that pathogenic PrP in these high-titre preparations is assembled into rod-like assemblies. Here, we have used precise cell culture-based prion infectivity assays to define the physical relationship between the PrP rods and prion infectivity and have used electron tomography to define their architecture. We show that infectious PrP rods isolated from multiple prion strains have a common hierarchical assembly comprising twisted pairs of short fibres with repeating substructure. The architecture of the PrP rods provides a new structural basis for understanding prion infectivity and can explain the inability to systematically generate high-titre synthetic prions from recombinant PrP. © 2016 The Authors.

High flux nanofiltration membranes based on layer-by-layer assembly modified electrospun nanofibrous substrate

NASA Astrophysics Data System (ADS)

Xu, Guo-Rong; Liu, Xiao-Yu; Xu, Jian-Mei; Li, Lu; Su, Hui-Chao; Zhao, He-Li; Feng, Hou-Jun

2018-03-01

Herein, high flux nanofiltration (NF) membranes were fabricated by combined procedures of electrospinning, layer-by-layer (LBL) assembly, and phase inversion. The membranes displayed three-dual structure constituted polyether sulfone (PES) coating layer, LBL assembly modified electrospun polyester (PET) nanofibrous mats, and non-woven supports. High flux NF membranes thus prepared are characterized by ultrathin phase inversion layer (∼10 μm) while that of conventional membranes are 100-150 μm, implying that very high flux could be expected. Various factors including electrospinning conditions, chitosan (CHI)/alginate (ALG) concentration, PES concentration, exposed time, coagulating temperature, thermal treatment, and sulfonated poly ether ketone (SPEEK) content were systematically investigated. Structures of the membranes were characterized by field emission scanning electron microscopy (FESEM), mechanical properties test, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR) and static contact angle measurements. The separation experiments indicated that thus prepared membranes exhibited high flux of as high as ∼75 L m-2 h-1 with Mg SO4 rejection of ∼80%.

Computational Design of Self-Assembling Cyclic Protein Homo-oligomers

PubMed Central

Fallas, Jorge A.; Ueda, George; Sheffler, William; Nguyen, Vanessa; McNamara, Dan E.; Sankaran, Banumathi; Pereira, Jose Henrique; Parmeggiani, Fabio; Brunette, TJ; Cascio, Duilio; Yeates, Todd R.; Zwart, Peter; Baker, David

2016-01-01

Self-assembling cyclic protein homo-oligomers play important roles in biology and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue pair transform method for assessing the design ability of a protein-protein interface. This method is sufficiently rapid to enable systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were experimentally characterized, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (4 homodimers, 6 homotrimers, 6 homotetramers and 1 homopentamer) had solution small angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each of these were shown to be very close to their design model. PMID:28338692

Interface electronic structures of reversible double-docking self-assembled monolayers on an Au(111) surface

PubMed Central

Zhang, Tian; Ma, Zhongyun; Wang, Linjun; Xi, Jinyang; Shuai, Zhigang

2014-01-01

Double-docking self-assembled monolayers (DDSAMs), namely self-assembled monolayers (SAMs) formed by molecules possessing two docking groups, provide great flexibility to tune the work function of metal electrodes and the tunnelling barrier between metal electrodes and the SAMs, and thus offer promising applications in both organic and molecular electronics. Based on the dispersion-corrected density functional theory (DFT) in comparison with conventional DFT, we carry out a systematic investigation on the dual configurations of a series of DDSAMs on an Au(111) surface. Through analysing the interface electronic structures, we obtain the relationship between single molecular properties and the SAM-induced work-function modification as well as the level alignment between the metal Fermi level and molecular frontier states. The two possible conformations of one type of DDSAM on a metal surface reveal a strong difference in the work-function modification and the electron/hole tunnelling barriers. Fermi-level pinning is found to be a key factor to understand the interface electronic properties. PMID:24615153

Nanoparticle Assemblies at Fluid Interfaces

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

Russell, Thomas P.

2015-03-10

A systematic study of the structure and dynamics of nanoparticles (NP) and NP-surfactants was performed. The ligands attached to both the NPs and NP-surfactants dictate the manner in which the nanoscopic materials assemble at fluid interfaces. Studies have shown that a single layer of the nanoscpic materials form at the interface to reduce the interactions between the two immiscible fluids. The shape of the NP is, also, important, where for spherical particles, a disordered, liquid-like monolayer forms, and, for nanorods, ordered domains at the interface is found and, if the monolayers are compressed, the orientation of the nanorods with respectmore » to the interface can change. By associating end-functionalized polymers to the NPs assembled at the interface, NP-surfactants are formed that increase the energetic gain in segregating each NP at the interface which allows the NP-surfactants to jam at the interface when compressed. This has opened the possibility of structuring the two liquids by freezing in shape changes of the liquids.« less

Dielectric Properties of Reduced Graphene Oxide/Copper Phthalocyanine Nanocomposites Fabricated Through π- π Interaction

NASA Astrophysics Data System (ADS)

Wang, Zicheng; Wei, Renbo; Liu, Xiaobo

2017-01-01

Reduced graphene oxide/copper phthalocyanine nanocomposites are successfully prepared through a simple and effective two-step method, involving preferential reduction of graphene oxide and followed by self-assembly with copper phthalocyanine. The results of photographs, ultraviolet visible, x-ray diffraction, x-ray photoelectron spectroscopy, and scanning electron microscopy show that the in situ blending method can effectively facilitate graphene sheets to disperse homogenously in the copper phthalocyanine matrix through π- π interactions. As a result, the reduction of graphene oxide and restoration of the sp 2 carbon sites in graphene can enhance the dielectric properties and alternating current conductivity of copper phthalocyanine effectively.

Performances of a HGCDTE APD Based Detector with Electric Cooling for 2-μm DIAL/IPDA Applications

NASA Astrophysics Data System (ADS)

Dumas, A.; Rothman, J.; Gibert, F.; Lasfargues, G.; Zanatta, J.-P.; Edouart, D.

2016-06-01

In this work we report on design and testing of an HgCdTe Avalanche Photodiode (APD) detector assembly for lidar applications in the Short Wavelength Infrared Region (SWIR : 1,5 - 2 μm). This detector consists in a set of diodes set in parallel -making a 200 μm large sensitive area- and connected to a custom high gain TransImpedance Amplifier (TIA). A commercial four stages Peltier cooler is used to reach an operating temperature of 185K. Crucial performances for lidar use are investigated : linearity, dynamic range, spatial homogeneity, noise and resistance to intense illumination.

Geometrical Optics of Dense Aerosols

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

Hay, Michael J.; Valeo, Ernest J.; Fisch, Nathaniel J.

2013-04-24

Assembling a free-standing, sharp-edged slab of homogeneous material that is much denser than gas, but much more rare ed than a solid, is an outstanding technological challenge. The solution may lie in focusing a dense aerosol to assume this geometry. However, whereas the geometrical optics of dilute aerosols is a well-developed fi eld, the dense aerosol limit is mostly unexplored. Yet controlling the geometrical optics of dense aerosols is necessary in preparing such a material slab. Focusing dense aerosols is shown here to be possible, but the nite particle density reduces the eff ective Stokes number of the flow, amore » critical result for controlled focusing. __________________________________________________« less

Geometrical optics of dense aerosols: forming dense plasma slabs.

PubMed

Hay, Michael J; Valeo, Ernest J; Fisch, Nathaniel J

2013-11-01

Assembling a freestanding, sharp-edged slab of homogeneous material that is much denser than gas, but much more rarefied than a solid, is an outstanding technological challenge. The solution may lie in focusing a dense aerosol to assume this geometry. However, whereas the geometrical optics of dilute aerosols is a well-developed field, the dense aerosol limit is mostly unexplored. Yet controlling the geometrical optics of dense aerosols is necessary in preparing such a material slab. Focusing dense aerosols is shown here to be possible, but the finite particle density reduces the effective Stokes number of the flow, a critical result for controlled focusing.

The production of multiprotein complexes in insect cells using the baculovirus expression system.

PubMed

Abdulrahman, Wassim; Radu, Laura; Garzoni, Frederic; Kolesnikova, Olga; Gupta, Kapil; Osz-Papai, Judit; Berger, Imre; Poterszman, Arnaud

2015-01-01

The production of a homogeneous protein sample in sufficient quantities is an essential prerequisite not only for structural investigations but represents also a rate-limiting step for many functional studies. In the cell, a large fraction of eukaryotic proteins exists as large multicomponent assemblies with many subunits, which act in concert to catalyze specific activities. Many of these complexes cannot be obtained from endogenous source material, so recombinant expression and reconstitution are then required to overcome this bottleneck. This chapter describes current strategies and protocols for the efficient production of multiprotein complexes in large quantities and of high quality, using the baculovirus/insect cell expression system.

Chemisorbed monolayers of corannulene penta-thioethers on gold.

PubMed

Angelova, Polina; Solel, Ephrath; Parvari, Galit; Turchanin, Andrey; Botoshansky, Mark; Gölzhäuser, Armin; Keinan, Ehud

2013-02-19

Penta(tert-butylthio)corannulene and penta(4-dimethylaminophenylthio)corannulene form highly stable monolayers on gold surfaces, as indicated by X-ray photoelectron spectroscopy (XPS). Formation of these homogeneous monolayers involves multivalent coordination of the five sulfur atoms to gold with the peripheral alkyl or aryl substituents pointing away from the surface. No dissociation of C-S bonds upon binding could be observed at room temperature. Yet, the XPS experiments reveal strong chemical bonding between the thioether groups and gold. Temperature-dependent XPS study shows that the thermal stability of the monolayers is higher than the typical stability of self-assembled monolayers (SAMs) of thiolates on gold.

Molten salt-supported polycondensation of optically active diacid monomers with an aromatic thiazole-bearing diamine using microwave irradiation.

PubMed

Mallakpour, Shadpour; Zadehnazari, Amin

2014-05-01

Microwave heating was used to prepare optically active thiazole-bearing poly(amide-imide)s. Polymerization reactions were carried out in the molten tetrabutylammonium bromide as a green molten salt medium and triphenyl phosphite as the homogenizer. Structural elucidation of the compounds was performed by Fourier transform infrared and NMR spectroscopic data and elemental analysis results. The polymeric samples were readily soluble in various organic solvents, forming low-colored and flexible thin films via solution casting. They showed high thermal stability with decomposition temperature being above 360 °C. They were assembled randomly in a nanoscale size.

Active mixing of complex fluids at the microscale

DOE PAGES

Ober, Thomas J.; Foresti, Daniele; Lewis, Jennifer A.

2015-09-22

Mixing of complex fluids at low Reynolds number is fundamental for a broad range of applications, including materials assembly, microfluidics, and biomedical devices. Of these materials, yield stress fluids (and gels) pose the most significant challenges, especially when they must be mixed in low volumes over short timescales. New scaling relationships between mixer dimensions and operating conditions are derived and experimentally verified to create a framework for designing active microfluidic mixers that can efficiently homogenize a wide range of complex fluids. As a result, active mixing printheads are then designed and implemented for multimaterial 3D printing of viscoelastic inks withmore » programmable control of local composition.« less

Protease-catalyzed peptide bond formation: application to synthesis of the COOH-terminal octapeptide of cholecystokinin.

PubMed Central

Kullmann, W

1982-01-01

This study of protease-catalyzed peptide synthesis reports the preparation of the COOH-terminal octapeptide amide of cholecystokinin. The octapeptide was assembled by chemical condensation of two tetrapeptide segments that had been synthesized through the concerted catalytic reactions of several proteases of different specificities. The resulting octapeptide derivative was subjected to catalytic transfer hydrogenation, followed by sulfation of its tyrosine residue and removal of the N alpha-protecting group. The homogeneous target peptide was obtained after purification via partition chromatography, gel filtration, and ion-exchange chromatography. The synthetic octapeptide stimulated amylase release from pancreatic acinar cells. Images PMID:6283547

Molten salt-supported polycondensation of optically active diacid monomers with an aromatic thiazole-bearing diamine using microwave irradiation

PubMed Central

Mallakpour, Shadpour; Zadehnazari, Amin

2013-01-01

Microwave heating was used to prepare optically active thiazole-bearing poly(amide-imide)s. Polymerization reactions were carried out in the molten tetrabutylammonium bromide as a green molten salt medium and triphenyl phosphite as the homogenizer. Structural elucidation of the compounds was performed by Fourier transform infrared and NMR spectroscopic data and elemental analysis results. The polymeric samples were readily soluble in various organic solvents, forming low-colored and flexible thin films via solution casting. They showed high thermal stability with decomposition temperature being above 360 °C. They were assembled randomly in a nanoscale size. PMID:25685498

Active mixing of complex fluids at the microscale

PubMed Central

Ober, Thomas J.; Foresti, Daniele; Lewis, Jennifer A.

2015-01-01

Mixing of complex fluids at low Reynolds number is fundamental for a broad range of applications, including materials assembly, microfluidics, and biomedical devices. Of these materials, yield stress fluids (and gels) pose the most significant challenges, especially when they must be mixed in low volumes over short timescales. New scaling relationships between mixer dimensions and operating conditions are derived and experimentally verified to create a framework for designing active microfluidic mixers that can efficiently homogenize a wide range of complex fluids. Active mixing printheads are then designed and implemented for multimaterial 3D printing of viscoelastic inks with programmable control of local composition. PMID:26396254

Verification and Validation of Requirements on the CEV Parachute Assembly System Using Design of Experiments

NASA Technical Reports Server (NTRS)

Schulte, Peter Z.; Moore, James W.

2011-01-01

The Crew Exploration Vehicle Parachute Assembly System (CPAS) project conducts computer simulations to verify that flight performance requirements on parachute loads and terminal rate of descent are met. Design of Experiments (DoE) provides a systematic method for variation of simulation input parameters. When implemented and interpreted correctly, a DoE study of parachute simulation tools indicates values and combinations of parameters that may cause requirement limits to be violated. This paper describes one implementation of DoE that is currently being developed by CPAS, explains how DoE results can be interpreted, and presents the results of several preliminary studies. The potential uses of DoE to validate parachute simulation models and verify requirements are also explored.

An effective model for ergonomic optimization applied to a new automotive assembly line

NASA Astrophysics Data System (ADS)

Duraccio, Vincenzo; Elia, Valerio; Forcina, Antonio

2016-06-01

An efficient ergonomic optimization can lead to a significant improvement in production performance and a considerable reduction of costs. In the present paper new model for ergonomic optimization is proposed. The new approach is based on the criteria defined by National Institute of Occupational Safety and Health and, adapted to Italian legislation. The proposed model provides an ergonomic optimization, by analyzing ergonomic relations between manual work in correct conditions. The model includes a schematic and systematic analysis method of the operations, and identifies all possible ergonomic aspects to be evaluated. The proposed approach has been applied to an automotive assembly line, where the operation repeatability makes the optimization fundamental. The proposed application clearly demonstrates the effectiveness of the new approach.

A proteome-scale map of the human interactome network

PubMed Central

Rolland, Thomas; Taşan, Murat; Charloteaux, Benoit; Pevzner, Samuel J.; Zhong, Quan; Sahni, Nidhi; Yi, Song; Lemmens, Irma; Fontanillo, Celia; Mosca, Roberto; Kamburov, Atanas; Ghiassian, Susan D.; Yang, Xinping; Ghamsari, Lila; Balcha, Dawit; Begg, Bridget E.; Braun, Pascal; Brehme, Marc; Broly, Martin P.; Carvunis, Anne-Ruxandra; Convery-Zupan, Dan; Corominas, Roser; Coulombe-Huntington, Jasmin; Dann, Elizabeth; Dreze, Matija; Dricot, Amélie; Fan, Changyu; Franzosa, Eric; Gebreab, Fana; Gutierrez, Bryan J.; Hardy, Madeleine F.; Jin, Mike; Kang, Shuli; Kiros, Ruth; Lin, Guan Ning; Luck, Katja; MacWilliams, Andrew; Menche, Jörg; Murray, Ryan R.; Palagi, Alexandre; Poulin, Matthew M.; Rambout, Xavier; Rasla, John; Reichert, Patrick; Romero, Viviana; Ruyssinck, Elien; Sahalie, Julie M.; Scholz, Annemarie; Shah, Akash A.; Sharma, Amitabh; Shen, Yun; Spirohn, Kerstin; Tam, Stanley; Tejeda, Alexander O.; Trigg, Shelly A.; Twizere, Jean-Claude; Vega, Kerwin; Walsh, Jennifer; Cusick, Michael E.; Xia, Yu; Barabási, Albert-László; Iakoucheva, Lilia M.; Aloy, Patrick; De Las Rivas, Javier; Tavernier, Jan; Calderwood, Michael A.; Hill, David E.; Hao, Tong; Roth, Frederick P.; Vidal, Marc

2014-01-01

SUMMARY Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ~14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ~30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a “broader” human interactome network than currently appreciated. The map also uncovers significant inter-connectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high quality interactome models will help “connect the dots” of the genomic revolution. PMID:25416956

Argon: Systematic Review on Neuro- and Organoprotective Properties of an “Inert” Gas

PubMed Central

Höllig, Anke; Schug, Anita; Fahlenkamp, Astrid V.; Rossaint, Rolf; Coburn, Mark

2014-01-01

Argon belongs to the group of noble gases, which are regarded as chemically inert. Astonishingly some of these gases exert biological properties and during the last decades more and more reports demonstrated neuroprotective and organoprotective effects. Recent studies predominately use in vivo or in vitro models for ischemic pathologies to investigate the effect of argon treatment. Promising data has been published concerning pathologies like cerebral ischemia, traumatic brain injury and hypoxic ischemic encephalopathy. However, models applied and administration of the therapeutic gas vary. Here we provide a systematic review to summarize the available data on argon’s neuro- and organoprotective effects and discuss its possible mechanism of action. We aim to provide a summary to allow further studies with a more homogeneous setting to investigate possible clinical applications of argon. PMID:25310646

Centroid stabilization for laser alignment to corner cubes: designing a matched filter

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

Awwal, Abdul A. S.; Bliss, Erlan; Brunton, Gordon

2016-11-08

Automation of image-based alignment of National Ignition Facility high energy laser beams is providing the capability of executing multiple target shots per day. One important alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retroreflecting corner cubes as centering references for each beam. Beam-to-beam variations and systematic beam changes over time in the FOA corner cube images can lead to a reduction in accuracy as well as increased convergence durations for the template-based position detector. A systematic approach is described that maintains FOA corner cube templates and guaranteesmore » stable position estimation.« less

Centroid stabilization for laser alignment to corner cubes: designing a matched filter

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

Awwal, Abdul A. S.; Bliss, Erlan; Brunton, Gordon

2016-11-08

Automation of image-based alignment of NIF high energy laser beams is providing the capability of executing multiple target shots per day. One important alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retro-reflecting corner cubes as centering references for each beam. Beam-to-beam variations and systematic beam changes over time in the FOA corner cube images can lead to a reduction in accuracy as well as increased convergence durations for the template-based position detector. A systematic approach is described that maintains FOA corner cube templates and guarantees stable positionmore » estimation.« less

[Dentists and National Socialism. Systematic Literature Review and Research Questions].

PubMed

Schwanke, Enno; Krischel, Matthis; Gross, Dominik

2016-01-01

Compared to the rich literature on Nazi medicine in general, the connection between dentists and National Socialism is less well documented. Neither the elites of the field from this era nor those excluded from the profession are catalogued in a systematic manner. The aims of this contribution are to assemble and review the relevant literature and show how German dentistry organizations have handled this chapter of their professional history. Trends in the literature since the 1980s are examined and it is pointed out, which areas have received some attention and which have not yet been addressed. Thus, this contribution will serve as both the basis and the starting point for new research into the field.

Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

PubMed Central

Li, Runsheng; Hsieh, Chia-Ling; Young, Amanda; Zhang, Zhihong; Ren, Xiaoliang; Zhao, Zhongying

2015-01-01

Most next-generation sequencing platforms permit acquisition of high-throughput DNA sequences, but the relatively short read length limits their use in genome assembly or finishing. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking. We evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans genome with no gap. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences prevents pre-assembly of long reads in the relevant genomic region. Second, the reads are able to reliably detect missing but not extra sequences in the C. elegans genome. Third, the reads of smaller size are more capable of recovering repetitive sequences than those of bigger size. Fourth, at least 40 Kbp missing genomic sequences are recovered in the C. elegans genome using the long reads. Finally, an N50 contig size of at least 86 Kbp can be achieved with 24×reads but with substantial mis-assembly errors, highlighting a need for novel assembly algorithm for the long reads. PMID:26039588

Regional Homogeneity

PubMed Central

Jiang, Lili; Zuo, Xi-Nian

2015-01-01

Much effort has been made to understand the organizational principles of human brain function using functional magnetic resonance imaging (fMRI) methods, among which resting-state fMRI (rfMRI) is an increasingly recognized technique for measuring the intrinsic dynamics of the human brain. Functional connectivity (FC) with rfMRI is the most widely used method to describe remote or long-distance relationships in studies of cerebral cortex parcellation, interindividual variability, and brain disorders. In contrast, local or short-distance functional interactions, especially at a scale of millimeters, have rarely been investigated or systematically reviewed like remote FC, although some local FC algorithms have been developed and applied to the discovery of brain-based changes under neuropsychiatric conditions. To fill this gap between remote and local FC studies, this review will (1) briefly survey the history of studies on organizational principles of human brain function; (2) propose local functional homogeneity as a network centrality to characterize multimodal local features of the brain connectome; (3) render a neurobiological perspective on local functional homogeneity by linking its temporal, spatial, and individual variability to information processing, anatomical morphology, and brain development; and (4) discuss its role in performing connectome-wide association studies and identify relevant challenges, and recommend its use in future brain connectomics studies. PMID:26170004

LES on unstructured deforming meshes: Towards reciprocating IC engines

NASA Technical Reports Server (NTRS)

Haworth, D. C.; Jansen, K.

1996-01-01

A variable explicit/implicit characteristics-based advection scheme that is second-order accurate in space and time has been developed recently for unstructured deforming meshes (O'Rourke & Sahota 1996a). To explore the suitability of this methodology for Large-Eddy Simulation (LES), three subgrid-scale turbulence models have been implemented in the CHAD CFD code (O'Rourke & Sahota 1996b): a constant-coefficient Smagorinsky model, a dynamic Smagorinsky model for flows having one or more directions of statistical homogeneity, and a Lagrangian dynamic Smagorinsky model for flows having no spatial or temporal homogeneity (Meneveau et al. 1996). Computations have been made for three canonical flows, progressing towards the intended application of in-cylinder flow in a reciprocating engine. Grid sizes were selected to be comparable to the coarsest meshes used in earlier spectral LES studies. Quantitative results are reported for decaying homogeneous isotropic turbulence, and for a planar channel flow. Computations are compared to experimental measurements, to Direct-Numerical Simulation (DNS) data, and to Rapid-Distortion Theory (RDT) where appropriate. Generally satisfactory evolution of first and second moments is found on these coarse meshes; deviations are attributed to insufficient mesh resolution. Issues include mesh resolution and computational requirements for a specified level of accuracy, analytic characterization of the filtering implied by the numerical method, wall treatment, and inflow boundary conditions. To resolve these issues, finer-mesh simulations and computations of a simplified axisymmetric reciprocating piston-cylinder assembly are in progress.

Technical Note: A new zeolite PET phantom to test segmentation algorithms on heterogeneous activity distributions featured with ground-truth contours.

PubMed

Soffientini, Chiara D; De Bernardi, Elisabetta; Casati, Rosangela; Baselli, Giuseppe; Zito, Felicia

2017-01-01

Design, realization, scan, and characterization of a phantom for PET Automatic Segmentation (PET-AS) assessment are presented. Radioactive zeolites immersed in a radioactive heterogeneous background simulate realistic wall-less lesions with known irregular shape and known homogeneous or heterogeneous internal activity. Three different zeolite families were evaluated in terms of radioactive uptake homogeneity, necessary to define activity and contour ground truth. Heterogeneous lesions were simulated by the perfect matching of two portions of a broken zeolite, soaked in two different 18 F-FDG radioactive solutions. Heterogeneous backgrounds were obtained with tissue paper balls and sponge pieces immersed into radioactive solutions. Natural clinoptilolite proved to be the most suitable zeolite for the construction of artificial objects mimicking homogeneous and heterogeneous uptakes in 18 F-FDG PET lesions. Heterogeneous backgrounds showed a coefficient of variation equal to 269% and 443% of a uniform radioactive solution. Assembled phantom included eight lesions with volumes ranging from 1.86 to 7.24 ml and lesion to background contrasts ranging from 4.8:1 to 21.7:1. A novel phantom for the evaluation of PET-AS algorithms was developed. It is provided with both reference contours and activity ground truth, and it covers a wide range of volumes and lesion to background contrasts. The dataset is open to the community of PET-AS developers and utilizers. © 2016 American Association of Physicists in Medicine.

Systematic investigation of the SERS efficiency and SERS hotspots in gas-phase deposited Ag nanoparticle assemblies.

PubMed

He, L B; Wang, Y L; Xie, X; Han, M; Song, F Q; Wang, B J; Cheng, W L; Xu, H X; Sun, L T

2017-02-15

Gas-phase deposited Ag nanoparticle assemblies are one of the most commonly used plasmonic substrates benefiting from their remarkable advantages such as clean particle surface, tunable particle density, available inter-particle gaps, low-cost and scalable fabrication, and excellent industry compatibility. However, their performance efficiencies are difficult to optimize due to the lack of knowledge of the hotspots inside their structures. We here report a design of delicate rainbow-like Ag nanoparticle assemblies, based on which the hotspots can be revealed through a combinatorial approach. The findings show that the hotspots in gas-phase deposited Ag nanoparticle assemblies are uniquely entangled by the excitation energy and specific inter-particle gaps, differing from the matching conditions in periodic arrays. For Ag nanoparticle assemblies deposited on Formvar-filmed substrates, the mean particle size is maintained around 10 nm, while the particle density can be widely tuned. The one possessing the highest SERS efficiency (under 473 nm excitation) have a particle number density of around 7100 μm -2 . Gaps with an inter-particle spacing of around 3 nm are found to serve as SERS hotspots, and these hotspots contribute to 68% of the overall SERS intensity. For Ag nanoparticle assemblies fabricated on carbon-filmed substrates, the mean particle size can be feasibly tuned. The one possessing the highest SERS efficiency under 473 nm excitation has a particle number density of around 460 μm -2 and a mean particle size of around 42.1 nm. The construction of Ag-analyte-Ag sandwich-like nanoparticle assemblies by a two-step-deposition method slightly improves the SERS efficiency when the particle number density is low, but suppresses the SERS efficiency when the particle number density is high.

Micro-photoluminescence of GaAs/AlGaAs triple concentric quantum rings.

PubMed

Abbarchi, Marco; Cavigli, Lucia; Somaschini, Claudio; Bietti, Sergio; Gurioli, Massimo; Vinattieri, Anna; Sanguinetti, Stefano

2011-10-31

A systematic optical study, including micro, ensemble and time resolved photoluminescence of GaAs/AlGaAs triple concentric quantum rings, self-assembled via droplet epitaxy, is presented. Clear emission from localized states belonging to the ring structures is reported. The triple rings show a fast decay dynamics, around 40 ps, which is expected to be useful for ultrafast optical switching applications.

Ferritin-Polymer Conjugates: Grafting Chemistry and Self-Assembly

DTIC Science & Technology

2009-10-26

a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. a...Chemoselective modification of M13 bacteriophage and cell imaging We systematically investigated the chemical modification of three kinds of reactive...tyrosine residues, on M13 surface. The reactivity for each group was identified by conjugation with small fluorescent molecules. Furthermore, the

Incidence, prevalence and genetic determinants of neonatal diabetes mellitus: a systematic review and meta-analysis protocol.

PubMed

Nansseu, Jobert Richie N; Ngo-Um, Suzanne S; Balti, Eric V

2016-11-10

In the absence of existing data, the present review intends to determine the incidence, prevalence and/or genetic determinants of neonatal diabetes mellitus (NDM), with expected contribution to disease characterization. We will include cross-sectional, cohort or case-control studies which have reported the incidence, prevalence and/or genetic determinants of NDM between January 01, 2000 and May 31, 2016, published in English or French languages and without any geographical limitation. PubMed and EMBASE will be extensively screened to identify potentially eligible studies, completed by manual search. Two authors will independently screen, select studies, extract data, and assess the risk of bias; disagreements will be resolved by consensus. Clinical heterogeneity will be investigated by examining the design and setting (including geographic region), procedure used for genetic testing, calculation of incidence or prevalence, and outcomes in each study. Studies found to be clinically homogeneous will be pooled together through a random effects meta-analysis. Statistical heterogeneity will be assessed using the chi-square test of homogeneity and quantified using the I 2 statistic. In case of substantial heterogeneity, subgroup analyses will be undertaken. Publication bias will be assessed with funnel plots, complemented with the use of Egger's test of bias. This systematic review and meta-analysis is expected to draw a clear picture of phenotypic and genotypic presentations of NDM in order to better understand the condition and adequately address challenges in respect with its management. PROSPERO CRD42016039765.

In quest of a systematic framework for unifying and defining nanoscience

PubMed Central

2009-01-01

This article proposes a systematic framework for unifying and defining nanoscience based on historic first principles and step logic that led to a “central paradigm” (i.e., unifying framework) for traditional elemental/small-molecule chemistry. As such, a Nanomaterials classification roadmap is proposed, which divides all nanomatter into Category I: discrete, well-defined and Category II: statistical, undefined nanoparticles. We consider only Category I, well-defined nanoparticles which are >90% monodisperse as a function of Critical Nanoscale Design Parameters (CNDPs) defined according to: (a) size, (b) shape, (c) surface chemistry, (d) flexibility, and (e) elemental composition. Classified as either hard (H) (i.e., inorganic-based) or soft (S) (i.e., organic-based) categories, these nanoparticles were found to manifest pervasive atom mimicry features that included: (1) a dominance of zero-dimensional (0D) core–shell nanoarchitectures, (2) the ability to self-assemble or chemically bond as discrete, quantized nanounits, and (3) exhibited well-defined nanoscale valencies and stoichiometries reminiscent of atom-based elements. These discrete nanoparticle categories are referred to as hard or soft particle nanoelements. Many examples describing chemical bonding/assembly of these nanoelements have been reported in the literature. We refer to these hard:hard (H-n:H-n), soft:soft (S-n:S-n), or hard:soft (H-n:S-n) nanoelement combinations as nanocompounds. Due to their quantized features, many nanoelement and nanocompound categories are reported to exhibit well-defined nanoperiodic property patterns. These periodic property patterns are dependent on their quantized nanofeatures (CNDPs) and dramatically influence intrinsic physicochemical properties (i.e., melting points, reactivity/self-assembly, sterics, and nanoencapsulation), as well as important functional/performance properties (i.e., magnetic, photonic, electronic, and toxicologic properties). We propose this perspective as a modest first step toward more clearly defining synthetic nanochemistry as well as providing a systematic framework for unifying nanoscience. With further progress, one should anticipate the evolution of future nanoperiodic table(s) suitable for predicting important risk/benefit boundaries in the field of nanoscience. Electronic supplementary material The online version of this article (doi:10.1007/s11051-009-9632-z) contains supplementary material, which is available to authorized users. PMID:21170133

Thin film assembly of nano-sized Zn(II)-8-hydroxy-5,7-dinitroquinolate by using successive ion layer adsorption and reaction (SILAR) technique: characterization and optical-electrical-photovoltaic properties.

PubMed

Farag, A A M; Haggag, Sawsan M S; Mahmoud, Mohamed E

2012-07-01

A method is described for thin film assembly of nano-sized Zn(II)-8-hydroxy-5,7-dinitroquinolate complex, Zn[((NO(2))(2)-8HQ)(2)] by using successive ion layer adsorption and reaction (SILAR) technique. Highly homogeneous assembled nano-sized metal complex thin films with particle size distribution in the range 27-47nm was identified by using scanning electron microscopy (SEM). Zn[((NO(2))(2)-8HQ)(2)] and [(NO(2))(2)-8HQ] ligand were studied by thermal gravimetric analysis (TGA). Graphical representation of temperature dependence of the dark electrical conductivity produced two distinct linear parts for two activation energies at 0.377eV and 1.11eV. The analysis of the spectral behavior of the absorption coefficient in the intrinsic absorption region reveals a direct allowed transition with a fundamental band gap of 2.74eV. The dark current density-voltage (J-V) characteristics showed the rectification effect due to the formation of junction barrier of Zn[((NO(2))(2)-8HQ)(2)] complex film/n-Si interface. The photocurrent in the reverse direction is strongly increased by photo-illumination and the photovoltaic characteristics were also determined and evaluated. Copyright © 2012 Elsevier B.V. All rights reserved.

Visual Perception-Based Statistical Modeling of Complex Grain Image for Product Quality Monitoring and Supervision on Assembly Production Line

PubMed Central

Chen, Qing; Xu, Pengfei; Liu, Wenzhong

2016-01-01

Computer vision as a fast, low-cost, noncontact, and online monitoring technology has been an important tool to inspect product quality, particularly on a large-scale assembly production line. However, the current industrial vision system is far from satisfactory in the intelligent perception of complex grain images, comprising a large number of local homogeneous fragmentations or patches without distinct foreground and background. We attempt to solve this problem based on the statistical modeling of spatial structures of grain images. We present a physical explanation in advance to indicate that the spatial structures of the complex grain images are subject to a representative Weibull distribution according to the theory of sequential fragmentation, which is well known in the continued comminution of ore grinding. To delineate the spatial structure of the grain image, we present a method of multiscale and omnidirectional Gaussian derivative filtering. Then, a product quality classifier based on sparse multikernel–least squares support vector machine is proposed to solve the low-confidence classification problem of imbalanced data distribution. The proposed method is applied on the assembly line of a food-processing enterprise to classify (or identify) automatically the production quality of rice. The experiments on the real application case, compared with the commonly used methods, illustrate the validity of our method. PMID:26986726

Biodegradable self-assembled PEG-PCL-PEG micelles for hydrophobic honokiol delivery: I. Preparation and characterization

NASA Astrophysics Data System (ADS)

Gong, ChangYang; Wei, XiaWei; Wang, XiuHong; Wang, YuJun; Guo, Gang; Mao, YongQiu; Luo, Feng; Qian, ZhiYong

2010-05-01

This study aims to develop self-assembled poly(ethylene glycol)-poly(ɛ-caprolactone)-poly(ethylene glycol) (PEG-PCL-PEG, PECE) micelles to encapsulate hydrophobic honokiol (HK) in order to overcome its poor water solubility and to meet the requirement of intravenous administration. Honokiol loaded micelles (HK-micelles) were prepared by self-assembly of PECE copolymer in aqueous solution, triggered by its amphiphilic characteristic assisted by ultrasonication without any organic solvents, surfactants and vigorous stirring. The particle size of the prepared HK-micelles measured by Malvern laser particle size analyzer were 58 nm, which is small enough to be a candidate for an intravenous drug delivery system. Furthermore, the HK-micelles could be lyophilized into powder without any adjuvant, and the re-dissolved HK-micelles are stable and homogeneous with particle size about 61 nm. Furthermore, the in vitro release profile showed a significant difference between the rapid release of free HK and the much slower and sustained release of HK-micelles. Moreover, the cytotoxicity results of blank micelles and HK-micelles showed that the PECE micelle was a safe carrier and the encapsulated HK retained its potent antitumor effect. In short, the HK-micelles were successfully prepared by an improved method and might be promising carriers for intravenous delivery of HK in cancer chemotherapy, being effective, stable, safe (organic solvent and surfactant free), and easy to produce and scale up.

Gold Nanoparticle Monolayers from Sequential Interfacial Ligand Exchange and Migration in a Three-Phase System

PubMed Central

Yang, Guang; Hallinan, Daniel T.

2016-01-01

Using a three-phase system, centimeter-scale monolayer gold nanoparticle (Au NP) films have been prepared that have long-range order and hydrophobic ligands. The system contains an interface between an aqueous phase containing Au NPs and an oil phase containing one of various types of amine ligands, and a water/air interface. As the Au NPs diffuse to the water/oil interface, ligand exchange takes place which temporarily traps them at the water/oil interface. The ligand-exchanged particles then spontaneously migrate to the air/water interface, where they self-assemble, forming a monolayer under certain conditions. The spontaneous formation of the NP film at the air/water interface was due to the minimization of the system Helmholtz free energy. However, the extent of surface functionalization was dictated by kinetics. This decouples interfacial ligand exchange from interfacial self-assembly, while maintaining the simplicity of a single system. The interparticle center-to-center distance was dictated by the amine ligand length. The Au NP monolayers exhibit tunable surface plasma resonance and excellent spatial homogeneity, which is useful for surface-enhanced Raman scattering. The “air/water/oil” self-assembly method developed here not only benefits the fundamental understanding of NP ligand conformations, but is also applicable to the manufacture of plasmonic nanoparticle devices with precisely designed optical properties. PMID:27762394

Design and assembly of an 8 tesla whole-body MR scanner.

PubMed

Robitaille, P M; Warner, R; Jagadeesh, J; Abduljalil, A M; Kangarlu, A; Burgess, R E; Yu, Y; Yang, L; Zhu, H; Jiang, Z; Bailey, R E; Chung, W; Somawiharja, Y; Feynan, P; Rayner, D L

1999-01-01

The purpose of this report is to describe the design and construction of an 8 T/80 cm whole-body MRI system operating at 340 MHz. The 8 T/80 cm magnet was constructed from 414 km of niobium titanium superconducting wire. The winding of this wire on four aluminum formers resulted in a total inductance of 4,155 H. Gradient subsystems included either a body gradient or a head gradient along with a removable shim insert. The magnet and gradient subsystems were interfaced to two spectrometers. These provided the control of the gradient amplifiers and the two sets of four RF power amplifiers. The latter provide in excess of 8 kW of RF power from 10 to 140 MHz and 10 kW of RF power from 245 to 345 MHz. A dedicated computer-controlled patient table was designed and assembled. The entire system is located in a clinical setting, facilitating patient-based studies. The 8 T/80 cm magnet was energized without complication and achieved persistent operation using 198.9 A of current, thereby storing 81.5 MJ of magnetic energy. Exceptional performance was observed for nearly all components both in isolation and when combined within the complete system. An 8 T/80 cm MRI system has been assembled. The magnet subsystem is extremely stable and is characterized by good homogeneity and acceptable boil-off rates.

Facile self-assembly and stabilization of metal oxide nanoparticles.

PubMed

Charbonneau, Cecile; Holliman, Peter J; Davies, Matthew L; Watson, Trystan M; Worsley, David A

2015-03-15

This paper describes a facile method of self-assembling different metal oxide nanoparticles into nanostructured materials via di-carboxylate linkers (oxalic acid) using TiO2 as an example. In this method, the di-carboxylate linkers react with surface hydroxyls on metal oxide nanoparticles forming covalent, ester-like bonds, which enable the binding of two metal oxide particles, one at either end of the linker and facilitates efficient self-assembly of one group of metal oxide nanoparticles homogeneously distributed onto the surface of another group. The oxalate linkers can then be removed by thermal decomposition. This approach is shown to be effective using differently-sized TiO2 nanoparticles, namely in-house synthesized 3-5nm anatase nanocrystals and Degussa P25 titania particles (mean 21nm particle size). Our data show that the application of a high temperature heat treatment (450°C for 30min), conventionally applied to achieve a stable porous structure by thermal decomposition of the linker molecules and by inducing inter-particle necking, damages the surface area of the nanostructured material. However, here we show that sintering at 300°C for 30min or by flash near infrared radiation sintering for 12s efficiently decomposes the oxalate linkers and stabilizes the nanostructure of the material whilst maintaining its high surface area. Copyright © 2013 Elsevier Inc. All rights reserved.

Fabrication of dopamine-modified hyaluronic acid/chitosan multilayers on titanium alloy by layer-by-layer self-assembly for promoting osteoblast growth

NASA Astrophysics Data System (ADS)

Zhang, Xinming; Li, Zhaoyang; Yuan, Xubo; Cui, Zhenduo; Yang, Xianjin

2013-11-01

The bare inert surface of titanium (Ti) alloy typically causes early failures in implants. Layer-by-layer self-assembly is one of the simple methods for fabricating bioactive multilayer coatings on titanium implants. In this study, a dopamine-modified hyaluronic acid/chitosan (DHA/CHI) bioactive multilayer was built on the surface of Ti-24Nb-2Zr (TNZ) alloy. Zeta potential oscillated between -2 and 17 mV for DHA- and CHI-ending layers during the assembly process, respectively. The DHA/CHI multilayer considerably decreased the contact angle and dramatically improved the wettability of TNZ alloy. Atomic force microscopy results revealed a rough surface on the original TNZ alloy, while the surface became smoother and more homogeneous after the deposition of approximately 5 bilayers (TNZ/(DHA/CHI)5). X-ray photoelectron spectroscopy analysis indicated that the TNZ/(DHA/CHI)5 sample was completely covered by polyelectrolytes. Pre-osteoblast MC3T3-E1 cells were cultured on the original TNZ alloy and TNZ/(DHA/CHI)5 to evaluate the effects of DHA/CHI multilayer on osteoblast proliferation in vitro. The proliferation of osteoblasts on TNZ/(DHA/CHI)5 was significantly higher than that on the original TNZ alloy. The results of this study indicate that the proposed technique improves the biocompatibility of TNZ alloy and can serve as a potential modification method in orthopedic applications.

Minimal-effort planning of active alignment processes for beam-shaping optics

NASA Astrophysics Data System (ADS)

Haag, Sebastian; Schranner, Matthias; Müller, Tobias; Zontar, Daniel; Schlette, Christian; Losch, Daniel; Brecher, Christian; Roßmann, Jürgen

2015-03-01

In science and industry, the alignment of beam-shaping optics is usually a manual procedure. Many industrial applications utilizing beam-shaping optical systems require more scalable production solutions and therefore effort has been invested in research regarding the automation of optics assembly. In previous works, the authors and other researchers have proven the feasibility of automated alignment of beam-shaping optics such as collimation lenses or homogenization optics. Nevertheless, the planning efforts as well as additional knowledge from the fields of automation and control required for such alignment processes are immense. This paper presents a novel approach of planning active alignment processes of beam-shaping optics with the focus of minimizing the planning efforts for active alignment. The approach utilizes optical simulation and the genetic programming paradigm from computer science for automatically extracting features from a simulated data basis with a high correlation coefficient regarding the individual degrees of freedom of alignment. The strategy is capable of finding active alignment strategies that can be executed by an automated assembly system. The paper presents a tool making the algorithm available to end-users and it discusses the results of planning the active alignment of the well-known assembly of a fast-axis collimator. The paper concludes with an outlook on the transferability to other use cases such as application specific intensity distributions which will benefit from reduced planning efforts.

Investigation of methods for hydroclimatic data homogenization

NASA Astrophysics Data System (ADS)

Steirou, E.; Koutsoyiannis, D.

2012-04-01

We investigate the methods used for the adjustment of inhomogeneities of temperature time series covering the last 100 years. Based on a systematic study of scientific literature, we classify and evaluate the observed inhomogeneities in historical and modern time series, as well as their adjustment methods. It turns out that these methods are mainly statistical, not well justified by experiments and are rarely supported by metadata. In many of the cases studied the proposed corrections are not even statistically significant. From the global database GHCN-Monthly Version 2, we examine all stations containing both raw and adjusted data that satisfy certain criteria of continuity and distribution over the globe. In the United States of America, because of the large number of available stations, stations were chosen after a suitable sampling. In total we analyzed 181 stations globally. For these stations we calculated the differences between the adjusted and non-adjusted linear 100-year trends. It was found that in the two thirds of the cases, the homogenization procedure increased the positive or decreased the negative temperature trends. One of the most common homogenization methods, 'SNHT for single shifts', was applied to synthetic time series with selected statistical characteristics, occasionally with offsets. The method was satisfactory when applied to independent data normally distributed, but not in data with long-term persistence. The above results cast some doubts in the use of homogenization procedures and tend to indicate that the global temperature increase during the last century is between 0.4°C and 0.7°C, where these two values are the estimates derived from raw and adjusted data, respectively.

Diurnal Variations of the Flux Imbalance Over Homogeneous and Heterogeneous Landscapes

NASA Astrophysics Data System (ADS)

Zhou, Yanzhao; Li, Dan; Liu, Heping; Li, Xin

2018-05-01

It is well known that the sum of the turbulent sensible and latent heat fluxes as measured by the eddy-covariance method is systematically lower than the available energy (i.e., the net radiation minus the ground heat flux). We examine the separate and joint effects of diurnal and spatial variations of surface temperature on this flux imbalance in a dry convective boundary layer using the Weather Research and Forecasting model. Results show that, over homogeneous surfaces, the flux due to turbulent-organized structures is responsible for the imbalance, whereas over heterogeneous surfaces, the flux due to mesoscale or secondary circulations is the main contributor to the imbalance. Over homogeneous surfaces, the flux imbalance in free convective conditions exhibits a clear diurnal cycle, showing that the flux-imbalance magnitude slowly decreases during the morning period and rapidly increases during the afternoon period. However, in shear convective conditions, the flux-imbalance magnitude is much smaller, but slightly increases with time. The flux imbalance over heterogeneous surfaces exhibits a diurnal cycle under both free and shear convective conditions, which is similar to that over homogeneous surfaces in free convective conditions, and is also consistent with the general trend in the global observations. The rapid increase in the flux-imbalance magnitude during the afternoon period is mainly caused by the afternoon decay of the turbulent kinetic energy (TKE). Interestingly, over heterogeneous surfaces, the flux imbalance is linearly related to the TKE and the difference between the potential temperature and surface temperature, ΔT; the larger the TKE and ΔT values, the smaller the flux-imbalance magnitude.

Dietitians and Nutritionists: Stigma in the Context of Obesity. A Systematic Review

PubMed Central

Jung, Franziska U. C. E.; Luck-Sikorski, Claudia; Wiemers, Nina; Riedel-Heller, Steffi G.

2015-01-01

Aim Negative attitudes towards people with obesity are common even in health care settings. So far, the attitudes and causal beliefs of dietitians and nutritionists have not been investigated systematically. The aim of this article was to review the current state of quantitative research on weight-related stigma by dietitians and nutritionists. Method A systematic literature review was conducted in 2014 using PubMed, PsycINFO, Web of Science and Cochrane Library. Results Eight studies were found that differ in regard to study characteristics, instruments and the origin of the sample. Six out of eight studies reported weight stigma expressed by dietitians and nutritionists. Their believed causes of obesity indicated a defined preference for internal factors rather than genetics or biology. Discussion Results of studies were not homogenous. The degree of negative attitudes by dietitians and nutritionists towards people with obesity appeared to be slightly less pronounced compared to the general public and other health care professionals. Stigma and its consequences should be included into educational programs to optimally prepare dietitians and nutritionists. PMID:26466329

Mn-53-Cr-53 Systematics of R-Chondrite NWA 753

NASA Technical Reports Server (NTRS)

Jogo, K.; Shih, C-Y.; Reese, Y. D.; Nyquist, L. E.

2006-01-01

Chondrules and chondrites are interpreted as objects formed in the early solar system, and it is important to study them in order to elucidate its evolution. Here, we report the study of the Mn-Cr systematics of the R-Chondrite NWA753 and compare the results to other chondrite data. The goal was to determine Cr isotopic and age variations among chondrite groups with different O-isotope signatures. The Mn-53-Cr-53 method as applied to individual chondrules [1] or bulk chondrites [2] is based on the assumption that 53Mn was initially homogeneously distributed in that portion the solar nebula where the chondrules and/or chondrites formed. However, different groups of chondrites formed from regions of different O-isotope compositions. So, different types of chondrites also may have had different initial Mn-53 abundances and/or Cr isotopic compositions. Thus, it is important to determine the Cr isotopic systematics among chondrites from various chondrite groups. We are studying CO-chondrite ALH83108 and Tagish Lake in addition to R-Chondrite NWA753. These meteorites have very distinct O-isotope compositions (Figure 1).

GCSS Cirrus Parcel Model Comparison Project

NASA Technical Reports Server (NTRS)

Lin, Ruei-Fong; Starr, David OC.; DeMott, Paul J.; Cotton, Richard; Jensen, Eric; Sassen, Kenneth; Einaudi, Franco (Technical Monitor)

2000-01-01

The Cirrus Parcel Model Comparison Project, a project of GCSS Working Group on Cirrus Cloud Systems (WG2), involves the systematic comparison of current models of ice crystal nucleation and growth for specified, typical, cirrus cloud environments. The goal of this project is to document and understand the factors resulting in significant inter-model differences. The intent is to foment research leading to model improvement and validation. In Phase 1 of the project reported here, simulated cirrus cloud microphysical properties are compared for situations of "warm" (-40 C) and "cold" (-60 C) cirrus subject to updrafts of 4, 20 and 100 cm/s, respectively. Five models participated. These models employ explicit microphysical schemes wherein the size distribution of each class of particles (aerosols and ice crystals) is resolved into bins. Simulations are made including both homogeneous and heterogeneous ice nucleation mechanisms. A single initial aerosol population of sulfuric acid particles is prescribed for all simulations. To isolate the treatment of the homogeneous freezing (of haze drops) nucleation process, the heterogeneous nucleation mechanism is disabled for a second parallel set of simulations. Qualitative agreement is found for the homogeneous-nucleation-only simulations, e.g., the number density of nucleated ice crystals increases with the strength of the prescribed updraft. However, non-negligible quantitative differences are found. Detailed analysis reveals that the homogeneous nucleation formulation, aerosol size, ice crystal growth rate (particularly the deposition coefficient), and water vapor uptake rate are critical components that lead to differences in predicted microphysics. Systematic bias exists between results based on a modified classical theory approach and models using an effective freezing temperature approach to the treatment of nucleation. Each approach is constrained by critical freezing data from laboratory studies, but each includes assumptions that can only be justified by further laboratory data. Consequently, it is not yet clear if the two approaches can be made consistent. Large haze particles may deviate considerably from equilibrium size in moderate to strong updrafts (20-100 cm/s) at -60 C when the commonly invoked equilibrium assumption is lifted. The resulting difference in particle-size-dependent solution concentration of haze particles may significantly affect the ice nucleation rate during the initial nucleation interval. The uptake rate for water vapor excess by ice crystals is another key component regulating the total number of nucleated ice crystals. This rate, the product of ice number concentration and ice crystal diffusional growth rate, which is sensitive to the deposition coefficient when ice particles are small, partially controls the peak nucleation rate achieved in an air parcel and the duration of the active nucleation time period. The effects of heterogeneous nucleation are most pronounced in weak updraft situations. Vapor competition by the nucleated (heterogeneous) ice crystals limits the achieved ice supersaturation and thus suppresses the contribution of homogeneous nucleation. Correspondingly, ice crystal number density is markedly reduced. Definitive laboratory and atmospheric benchmark data are needed for the heterogeneous nucleation process. Inter-model differences are correspondingly greater than in the case of the homogeneous nucleation process acting alone.

Cirrus Parcel Model Comparison Project. Phase 1; The Critical Components to Simulate Cirrus Initiation Explicitly

NASA Technical Reports Server (NTRS)

Lin, Ruei-Fong; Starr, David OC; DeMott, Paul J.; Cotton, Richard; Sassen, Kenneth; Jensen, Eric; Einaudi, Franco (Technical Monitor)

2001-01-01

The Cirrus Parcel Model Comparison Project, a project of the GCSS (GEWEX Cloud System Studies) Working Group on Cirrus Cloud Systems, involves the systematic comparison of current models of ice crystal nucleation and growth for specified, typical, cirrus cloud environments. In Phase I of the project reported here, simulated cirrus cloud microphysical properties are compared for situations of "warm" (40 C) and "cold" (-60 C) cirrus, both subject to updrafts of 4, 20 and 100 centimeters per second. Five models participated. The various models employ explicit microphysical schemes wherein the size distribution of each class of particles (aerosols and ice crystals) is resolved into bins or treated separately. Simulations are made including both the homogeneous and heterogeneous ice nucleation mechanisms. A single initial aerosol population of sulfuric acid particles is prescribed for all simulations. To isolate the treatment of the homogeneous freezing (of haze droplets) nucleation process, the heterogeneous nucleation mechanism is disabled for a second parallel set of simulations. Qualitative agreement is found for the homogeneous-nucleation- only simulations, e.g., the number density of nucleated ice crystals increases with the strength of the prescribed updraft. However, significant quantitative differences are found. Detailed analysis reveals that the homogeneous nucleation rate, haze particle solution concentration, and water vapor uptake rate by ice crystal growth (particularly as controlled by the deposition coefficient) are critical components that lead to differences in predicted microphysics. Systematic bias exists between results based on a modified classical theory approach and models using an effective freezing temperature approach to the treatment of nucleation. Each approach is constrained by critical freezing data from laboratory studies, but each includes assumptions that can only be justified by further laboratory research. Consequently, it is not yet clear if the two approaches can be made consistent. Large haze particles may deviate considerably from equilibrium size in moderate to strong updrafts (20-100 centimeters per second) at -60 C when the commonly invoked equilibrium assumption is lifted. The resulting difference in particle-size- dependent solution concentration of haze particles may significantly affect the ice particle formation rate during the initial nucleation interval. The uptake rate for water vapor excess by ice crystals is another key component regulating the total number of nucleated ice crystals. This rate, the product of particle number concentration and ice crystal diffusional growth rate, which is particularly sensitive to the deposition coefficient when ice particles are small, modulates the peak particle formation rate achieved in an air parcel and the duration of the active nucleation time period. The effects of heterogeneous nucleation are most pronounced in weak updraft situations. Vapor competition by the heterogeneously nucleated ice crystals may limit the achieved ice supersaturation and thus suppresses the contribution of homogeneous nucleation. Correspondingly, ice crystal number density is markedly reduced. Definitive laboratory and atmospheric benchmark data are needed for the heterogeneous nucleation process. Inter-model differences are correspondingly greater than in the case of the homogeneous nucleation process acting alone.

A Three-State System Based on Branched DNA Hybrids.

PubMed

He, Shiliang; Richert, Clemens

2018-03-26

There is a need for materials that respond to chemical or physical stimuli through a change in their structure. While a transition between water-soluble form and solid is not uncommon for DNA-based structures, systems that transition between three different states at room temperature and ambient pressure are rare. Here we report the preparation of branched DNA hybrids with eight oligodeoxycytidylate arms via solution-phase, H-phosphonate-based synthesis. Some hybrids assemble into hydrogels upon lowering the pH, acting as efficient gelators at pH 4-6, but can also transition into a more condensed solid state form upon exposure to divalent cations. Together with the homogeneous solutions that the i-motif-forming compounds give at neutral pH, three-state systems result. Each state has its own color, if chromophores are included in the system. The assembly and gelation properties can be tuned by choosing the chain length of the arms. Their responsive properties make the dC-rich DNA hybrids candidates for smart material applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microfluidic assisted one-step fabrication of porous silicon@acetalated dextran nanocomposites for precisely controlled combination chemotherapy.

PubMed

Liu, Dongfei; Zhang, Hongbo; Mäkilä, Ermei; Fan, Jin; Herranz-Blanco, Bárbara; Wang, Chang-Fang; Rosa, Ricardo; Ribeiro, António J; Salonen, Jarno; Hirvonen, Jouni; Santos, Hélder A

2015-01-01

An advanced nanocomposite consisting of an encapsulated porous silicon (PSi) nanoparticle and an acid-degradable acetalated dextran (AcDX) matrix (nano-in-nano), was efficiently fabricated by a one-step microfluidic self-assembly approach. The obtained nano-in-nano PSi@AcDX composites showed improved surface smoothness, homogeneous size distribution, and considerably enhanced cytocompatibility. Furthermore, multiple drugs with different physicochemical properties have been simultaneously loaded into the nanocomposites with a ratiometric control. The release kinetics of all the payloads was predominantly controlled by the decomposition rate of the outer AcDX matrix. To facilitate the intracellular drug delivery, a nona-arginine cell-penetrating peptide (CPP) was chemically conjugated onto the surface of the nanocomposites by oxime click chemistry. Taking advantage of the significantly improved cell uptake, the proliferation of two breast cancer cell lines was markedly inhibited by the CPP-functionalized multidrug-loaded nanocomposites. Overall, this nano-in-nano PSi@polymer composite prepared by the microfluidic self-assembly approach is a universal platform for nanoparticles encapsulation and precisely controlled combination chemotherapy. Copyright © 2014 Elsevier Ltd. All rights reserved.

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

PubMed Central

Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole K.; Jakobsen, Kjetill S.; Jentoft, Sissel

2017-01-01

Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts. PMID:28094797

Galaxy And Mass Assembly (GAMA): AUTOZ spectral redshift measurements, confidence and errors

NASA Astrophysics Data System (ADS)

Baldry, I. K.; Alpaslan, M.; Bauer, A. E.; Bland-Hawthorn, J.; Brough, S.; Cluver, M. E.; Croom, S. M.; Davies, L. J. M.; Driver, S. P.; Gunawardhana, M. L. P.; Holwerda, B. W.; Hopkins, A. M.; Kelvin, L. S.; Liske, J.; López-Sánchez, Á. R.; Loveday, J.; Norberg, P.; Peacock, J.; Robotham, A. S. G.; Taylor, E. N.

2014-07-01

The Galaxy And Mass Assembly (GAMA) survey has obtained spectra of over 230 000 targets using the Anglo-Australian Telescope. To homogenize the redshift measurements and improve the reliability, a fully automatic redshift code was developed (AUTOZ). The measurements were made using a cross-correlation method for both the absorption- and the emission-line spectra. Large deviations in the high-pass-filtered spectra are partially clipped in order to be robust against uncorrected artefacts and to reduce the weight given to single-line matches. A single figure of merit (FOM) was developed that puts all template matches on to a similar confidence scale. The redshift confidence as a function of the FOM was fitted with a tanh function using a maximum likelihood method applied to repeat observations of targets. The method could be adapted to provide robust automatic redshifts for other large galaxy redshift surveys. For the GAMA survey, there was a substantial improvement in the reliability of assigned redshifts and in the lowering of redshift uncertainties with a median velocity uncertainty of 33 km s-1.

Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically disordered proteins in C. elegans

PubMed Central

Wang, Jennifer T; Smith, Jarrett; Chen, Bi-Chang; Schmidt, Helen; Rasoloson, Dominique; Paix, Alexandre; Lambrus, Bramwell G; Calidas, Deepika; Betzig, Eric; Seydoux, Geraldine

2014-01-01

RNA granules have been likened to liquid droplets whose dynamics depend on the controlled dissolution and condensation of internal components. The molecules and reactions that drive these dynamics in vivo are not well understood. In this study, we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos. The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility. We demonstrate that MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2APPTR−½. Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly. Using lattice light sheet microscopy on live embryos, we show that GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule. We conclude that, despite their liquid-like behavior, P granules are non-homogeneous structures whose assembly in embryos is regulated by phosphorylation. DOI: http://dx.doi.org/10.7554/eLife.04591.001 PMID:25535836

UV-LIGA microfabrication process for sub-terahertz waveguides utilizing multiple layered SU-8 photoresist

NASA Astrophysics Data System (ADS)

Malekabadi, Ali; Paoloni, Claudio

2016-09-01

A microfabrication process based on UV LIGA (German acronym of lithography, electroplating and molding) is proposed for the fabrication of relatively high aspect ratio sub-terahertz (100-1000 GHz) metal waveguides, to be used as a slow wave structure in sub-THz vacuum electron devices. The high accuracy and tight tolerances required to properly support frequencies in the sub-THz range can be only achieved by a stable process with full parameter control. The proposed process, based on SU-8 photoresist, has been developed to satisfy high planar surface requirements for metal sub-THz waveguides. It will be demonstrated that, for a given thickness, it is more effective to stack a number of layers of SU-8 with lower thickness rather than using a single thick layer obtained at lower spin rate. The multiple layer approach provides the planarity and the surface quality required for electroforming of ground planes or assembly surfaces and for assuring low ohmic losses of waveguides. A systematic procedure is provided to calculate soft and post-bake times to produce high homogeneity SU-8 multiple layer coating as a mold for very high quality metal waveguides. A double corrugated waveguide designed for 0.3 THz operating frequency, to be used in vacuum electronic devices, was fabricated as test structure. The proposed process based on UV LIGA will enable low cost production of high accuracy sub-THz 3D waveguides. This is fundamental for producing a new generation of affordable sub-THz vacuum electron devices, to fill the technological gap that still prevents a wide diffusion of numerous applications based on THz radiation.

Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation.

PubMed

Ozgur, Beytullah; Sayar, Mehmet

2016-10-06

Peptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. A triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: β-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with ≤1% by weight peptide concentration. In this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall β-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, alternative structures such as zero-dimensional aggregates with two β-sheets oriented orthogonally (which we refer to as a cross-packed structure) and β-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.

Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly.

PubMed

Bakou, Maria; Hille, Kathleen; Kracklauer, Michael; Spanopoulou, Anna; Frost, Christina V; Malideli, Eleni; Yan, Li-Mei; Caporale, Andrea; Zacharias, Martin; Kapurniotu, Aphrodite

2017-09-01

The interaction of the intrinsically disordered polypeptide islet amyloid polypeptide (IAPP), which is associated with type 2 diabetes (T2D), with the Alzheimer's disease amyloid-β (Aβ) peptide modulates their self-assembly into amyloid fibrils and may link the pathogeneses of these two cell-degenerative diseases. However, the molecular determinants of this interaction remain elusive. Using a systematic alanine scan approach, fluorescence spectroscopy, and other biophysical methods, including heterocomplex pulldown assays, far-UV CD spectroscopy, the thioflavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified single aromatic/hydrophobic residues within the amyloid core IAPP region as hot spots or key residues of its cross-interaction with Aβ40(42) peptide. Importantly, we also find that none of these residues in isolation plays a key role in IAPP self-assembly, whereas simultaneous substitution of four aromatic/hydrophobic residues with Ala dramatically impairs both IAPP self-assembly and hetero-assembly with Aβ40(42). Furthermore, our experiments yielded several novel IAPP analogs, whose sequences are highly similar to that of IAPP but have distinct amyloid self- or cross-interaction potentials. The identified similarities and major differences controlling IAPP cross-peptide interaction with Aβ40(42) versus its amyloid self-assembly offer a molecular basis for understanding the underlying mechanisms. We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Experimental evaluation of models for predicting Cherenkov light intensities from short-cooled nuclear fuel assemblies

NASA Astrophysics Data System (ADS)

Branger, E.; Grape, S.; Jansson, P.; Jacobsson Svärd, S.

2018-02-01

The Digital Cherenkov Viewing Device (DCVD) is a tool used by nuclear safeguards inspectors to verify irradiated nuclear fuel assemblies in wet storage based on the recording of Cherenkov light produced by the assemblies. One type of verification involves comparing the measured light intensity from an assembly with a predicted intensity, based on assembly declarations. Crucial for such analyses is the performance of the prediction model used, and recently new modelling methods have been introduced to allow for enhanced prediction capabilities by taking the irradiation history into account, and by including the cross-talk radiation from neighbouring assemblies in the predictions. In this work, the performance of three models for Cherenkov-light intensity prediction is evaluated by applying them to a set of short-cooled PWR 17x17 assemblies for which experimental DCVD measurements and operator-declared irradiation data was available; (1) a two-parameter model, based on total burnup and cooling time, previously used by the safeguards inspectors, (2) a newly introduced gamma-spectrum-based model, which incorporates cycle-wise burnup histories, and (3) the latter gamma-spectrum-based model with the addition to account for contributions from neighbouring assemblies. The results show that the two gamma-spectrum-based models provide significantly higher precision for the measured inventory compared to the two-parameter model, lowering the standard deviation between relative measured and predicted intensities from 15.2 % to 8.1 % respectively 7.8 %. The results show some systematic differences between assemblies of different designs (produced by different manufacturers) in spite of their similar PWR 17x17 geometries, and possible ways are discussed to address such differences, which may allow for even higher prediction capabilities. Still, it is concluded that the gamma-spectrum-based models enable confident verification of the fuel assembly inventory at the currently used detection limit for partial defects, being a 30 % discrepancy between measured and predicted intensities, while some false detection occurs with the two-parameter model. The results also indicate that the gamma-spectrum-based prediction methods are accurate enough that the 30 % discrepancy limit could potentially be lowered.

Jack Rabbit Pretest Shadowplate Drawings For TATB IHE Model Development

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

Hart, M M; McDaniel, D W

The Jack Rabbit Pretest (PT) series consisted of 5 focused hydrodynamic experiments 2021E PT3, PT4, PT5, PT6, and PT7. They were fired in March and April of 2008 at the Contained Firing Facility, Site 300, Lawrence Livermore National Laboratory, Livermore, California. These experiments measured deadzone formation and impulse gradients created during the detonation of TATB based insensitive high explosive. When setting up computer simulations of the Jack Rabbit Pretest series, the modeler or code developer can execute simulations with increasing degrees of refinement using detail found in the shadowplate design. The easiest way to get started is by treating themore » shadowplate in each experiment as a monolithic homogeneous piece of stainless steel. The simulation of detonation would begin as a point initiation below the center, bottom surface of the shadowplate. The detonation running through the ultrafine TATB booster can be simulated using program burn and then switched over to a reactive flow detonation model as the detonation front crosses the boundary into the main charge LX-17 IHE. A modeler wanting to further refine the simulation and progression of shock through the shadowplate can use the more detailed shadowplate design information presented in this document. The source drawings are included in Appendix A of this document. Their titles and drawing numbers are listed. Each experiment's shadowplate consists of two major components. A 303 stainless steel shape that defines the outer dimensions of shadowplate and a cylindrical 303 stainless steel detonator housing that is located in a closely machined pocket in the shape. The SIMPLE ASSY drawing accurately represents the dimensions of the outer shape, it's machined cylindrical pocket, and detonator body which is treated as a monolithic, homogeneous piece of stainless steel. The detonator body cross section shows an accurately dimensioned void where the slapper flyer barrel, LX-16 (pressed PETN) pellet, and pellet can flyer barrel are located. The FULL ASSY drawing accurately represents the dimensions of the outer shadowplate shape and it's machined pocket. The detonator dimensions and materials are detailed in cross section and exploded view. All diameters, thicknesses, and materials are called out in the drawing. You will notice that the detonator includes a multilayer slapper assembly with two layers of electrically insulating Kapton sandwiching the copper foil bridge circuit. The Kapton insulated circuit is sandwiched between two thin stainless steel sheets. This slapper assembly is secured to the detonator body with two screws. There is a 0.25 mm gap between the slapper assembly and the outer shadowplate shape. The stainless steel detonator body contains an off-center titanium wheel. This titanium wheel is secured to the detonator body with one screw and two pins to maintain position and orientation of the pellet can assembly in the center of the detonator body. The titanium wheel contains a tantalum/tungsten washer and pellet can assembly. The pellet can assembly consists of a pressed LX-16 initiator pellet contained in an extruded aluminum foil can. It may be useful for the modeler to include some of the details of the shadowplate and detonator design to further refine simulations of the Jack Rabbit Pretest experiments. These details may be relevant to the progression of shock originating from the PETN initiation pellet and ultrafine TATB booster that propagates through the shadowplate.« less

Physical-geometric optics method for large size faceted particles.

PubMed

Sun, Bingqiang; Yang, Ping; Kattawar, George W; Zhang, Xiaodong

2017-10-02

A new physical-geometric optics method is developed to compute the single-scattering properties of faceted particles. It incorporates a general absorption vector to accurately account for inhomogeneous wave effects, and subsequently yields the relevant analytical formulas effective and computationally efficient for absorptive scattering particles. A bundle of rays incident on a certain facet can be traced as a single beam. For a beam incident on multiple facets, a systematic beam-splitting technique based on computer graphics is used to split the original beam into several sub-beams so that each sub-beam is incident only on an individual facet. The new beam-splitting technique significantly reduces the computational burden. The present physical-geometric optics method can be generalized to arbitrary faceted particles with either convex or concave shapes and with a homogeneous or an inhomogeneous (e.g., a particle with a core) composition. The single-scattering properties of irregular convex homogeneous and inhomogeneous hexahedra are simulated and compared to their counterparts from two other methods including a numerically rigorous method.

Self-assembly of hierarchically ordered structures in DNA nanotube systems

NASA Astrophysics Data System (ADS)

Glaser, Martin; Schnauß, Jörg; Tschirner, Teresa; Schmidt, B. U. Sebastian; Moebius-Winkler, Maximilian; Käs, Josef A.; Smith, David M.

2016-05-01

The self-assembly of molecular and macromolecular building blocks into organized patterns is a complex process found in diverse systems over a wide range of size and time scales. The formation of star- or aster-like configurations, for example, is a common characteristic in solutions of polymers or other molecules containing multi-scaled, hierarchical assembly processes. This is a recurring phenomenon in numerous pattern-forming systems ranging from cellular constructs to solutions of ferromagnetic colloids or synthetic plastics. To date, however, it has not been possible to systematically parameterize structural properties of the constituent components in order to study their influence on assembled states. Here, we circumvent this limitation by using DNA nanotubes with programmable mechanical properties as our basic building blocks. A small set of DNA oligonucleotides can be chosen to hybridize into micron-length DNA nanotubes with a well-defined circumference and stiffness. The self-assembly of these nanotubes to hierarchically ordered structures is driven by depletion forces caused by the presence of polyethylene glycol. This trait allowed us to investigate self-assembly effects while maintaining a complete decoupling of density, self-association or bundling strength, and stiffness of the nanotubes. Our findings show diverse ranges of emerging structures including heterogeneous networks, aster-like structures, and densely bundled needle-like structures, which compare to configurations found in many other systems. These show a strong dependence not only on concentration and bundling strength, but also on the underlying mechanical properties of the nanotubes. Similar network architectures to those caused by depletion forces in the low-density regime are obtained when an alternative hybridization-based bundling mechanism is employed to induce self-assembly in an isotropic network of pre-formed DNA nanotubes. This emphasizes the universal effect inevitable attractive forces in crowded environments have on systems of self-assembling soft matter, which should be considered for macromolecular structures applied in crowded systems such as cells.

ECLAIRs detection plane: current state of development

NASA Astrophysics Data System (ADS)

Lacombe, K.; Pons, R.; Amoros, C.; Atteia, J.-L.; Barret, D.; Billot, M.; Bordon, S.; Cordier, B.; Gevin, O.; Godet, O.; Gonzalez, F.; Houret, B.; Mercier, K.; Mandrou, P.; Marty, W.; Nasser, G.; Rambaud, D.; Ramon, P.; Rouaix, G.; Waegebaert, V.

2014-07-01

ECLAIRs, a 2-D coded-mask imaging camera on-board the Sino-French SVOM space mission, will detect and locate Gamma-ray bursts (GRBs) in near real time in the 4-150 keV energy band. The design of ECLAIRs has been mainly driven by the objective of achieving a low-energy threshold of 4 keV, unprecedented for this type of instrument. The detection plane is an assembly of 6400 Schottky CdTe semiconductor detectors of size 4x4x1 mm3 organized on elementary hybrid matrices of 4x8 detectors. The detectors will be polarized from -300V to -500V and operated at -20°C to reduce both the leakage current and the polarization effect induced by the Schottky contact. The remarkable low-energy threshold homogeneity required for the detection plane has been achieved thanks to: i) an extensive characterization and selection of the detectors, ii) the development of a specific low-noise 32-channel ASIC, iii) the realization of an innovative hybrid module composed of a thick film ceramic (holding 32 CdTe detectors with their high voltage grid), associated to an HTCC ceramic (housing the ASIC chip within an hermetic enclosure). In this paper, we start describing a complete hybrid matrix, and then the manufacturing of a first set of 50 matrices (representing 1600 detectors, i.e. a quarter of ECLAIRs detector's array). We show how this manufacturing allowed to validate the different technologies used for this hybridization, as well as the industrialization processes. During this phase, we systematically measured the leakage current on Detector Ceramics after an outgassing, and the Equivalent Noise Charge (ENC) for each of the 32 channels on ASIC Ceramics, in order to optimize the coupling of the two ceramics. Finally, we performed on each hybrid module, spectral measurements at -20°C in our vacuum chamber, using several calibrated radioactive sources (241Am and 55Fe), to check the performance homogeneity of the 50 modules. The results demonstrated that the 32-detector hybrid matrices presented homogeneous spectral properties and that a lowenergy threshold of 4 keV for each detector could be reached. In conclusion, our hybrid module has obtained the performance required at the SVOM mission level and successfully withstood the space environment tests (TRL 6/7). This development phase has given us the opportunity to build a detector's array prototype (Engineering Model) equipped with 50 hybrid modules. Thanks to this prototype we are in the process of validating a complete detection chain (from the detectors to the backend electronics) and checking the performance. In addition it enables us to consolidate the instrument's mechanical and thermal design, and to write preliminary versions of the quality procedures required for integration, functional tests and calibration steps. At the end of this prototype development and testing, we will be ready to start the detailed design of the detection plane Flight Model.

Heparin-mimicking multilayer coating on polymeric membrane via LbL assembly of cyclodextrin-based supramolecules.

PubMed

Deng, Jie; Liu, Xinyue; Ma, Lang; Cheng, Chong; Shi, Wenbin; Nie, Chuanxiong; Zhao, Changsheng

2014-12-10

In this study, multifunctional and heparin-mimicking star-shaped supramolecules-deposited 3D porous multilayer films with improved biocompatibility were fabricated via a layer-by-layer (LbL) self-assembly method on polymeric membrane substrates. Star-shaped heparin-mimicking polyanions (including poly(styrenesulfonate-co-sodium acrylate; Star-PSS-AANa) and poly(styrenesulfonate-co-poly(ethylene glycol)methyl ether methacrylate; Star-PSS-EGMA)) and polycations (poly(methyl chloride-quaternized 2-(dimethylamino)ethyl methacrylate; Star-PMeDMA) were first synthesized by atom transfer radical polymerization (ATRP) from β-cyclodextrin (β-CD) based cores. Then assembly of 3D porous multilayers onto polymeric membrane surfaces was carried out by alternating deposition of the polyanions and polycations via electrostatic interaction. The surface morphology and composition, water contact angle, blood activation, and thrombotic potential as well as cell viability for the coated heparin-mimicking films were systematically investigated. The results of surface ATR-FTIR spectra and XPS spectra verified successful deposition of the star-shaped supramolecules onto the biomedical membrane surfaces; scanning electron microscopy (SEM) and atomic force microscopy (AFM) observations revealed that the modified substrate had 3D porous surface morphology, which might have a great biological influence on the biointerface. Furthermore, systematic in vitro investigation of protein adsorption, platelet adhesion, human platelet factor 4 (PF4, indicates platelet activation), activate partial thromboplastin time (APTT), thrombin time (TT), coagulation activation (thrombin-antithrombin III complex (TAT, indicates blood coagulant)), and blood-related complement activation (C3a and C5a, indicates inflammation potential) confirmed that the heparin-mimicking multilayer coated membranes exhibited ultralow blood component activations and excellent hemocompatibility. Meanwhile, after surface coating, endothelial cell viability was also promoted, which indicated that the heparin-mimicking multilayer coating might extend the application fields of polymeric membranes in biomedical fields.