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At least 271 records · Page 15

Light absorption and plasmon – exciton interaction in three-layer nanorods with a gold core and outer shell composed of molecular J- and H-aggregates of dyes

Optical properties of hybrid rod-like nanoparticles, consisting of a gold core, an intermediate passive organic layer (spacer) and outer layer of ordered molecular cyanine dye aggregates, are experimentally and theoretically investigated. It is shown that these dyes can form not only ordered J-aggregates but also H-aggregates (differing by the packing angle of dye molecules in an aggregate and having other spectral characteristics) in the outer shell of the hybrid nanostructure. Absorption spectra of synthesised three-layer nanorods are recorded, and their sizes are determined. The optical properties of the composite nanostructures under study are found to differ significantly, depending on the type of the molecular aggregate formed in the outer shell. The experimental data are quantitatively explained based on computer simulation using the finite-difference time-domain (FDTD) method, and characteristic features of the plasmon – exciton interaction in the systems under study are revealed. (nanophotonics)

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

De novo designed protein inhibitors of amyloid aggregation and seeding

Neurodegenerative diseases are characterized by the pathologic accumulation of aggregated proteins. Known as amyloid, these fibrillar aggregates include proteins such as tau and amyloid-β (Aβ) in Alzheimer’s disease (AD) and alpha-synuclein (αSyn) in Parkinson’s disease (PD). The development and spread of amyloid fibrils within the brain correlates with disease onset and progression, and inhibiting amyloid formation is a possible route toward therapeutic development. Recent advances have enabled the determination of amyloid fibril structures to atomic-level resolution, improving the possibility of structure-based inhibitor design. In this work, we use these amyloid structures to design inhibitors that bind to the ends of fibrils, “capping” them so as to prevent further growth. Using de novo protein design, we develop a library of miniprotein inhibitors of 35 to 48 residues that target the amyloid structures of tau, Aβ, and αSyn. Biophysical characterization of top in silico designed inhibitors shows they form stable folds, have no sequence similarity to naturally occurring proteins, and specifically prevent the aggregation of their targeted amyloid-prone proteins in vitro. The inhibitors also prevent the seeded aggregation and toxicity of fibrils in cells. In vivo evaluation reveals their ability to reduce aggregation and rescue motor deficits in Caenorhabditis elegans models of PD and AD.

59 BASIC BIOLOGICAL SCIENCES↗

CHARGING OF AGGREGATE GRAINS IN ASTROPHYSICAL ENVIRONMENTS

The charging of dust grains in astrophysical environments has been investigated with the assumption that these grains are homogeneous spheres. However, there is evidence which suggests that many grains in astrophysical environments are irregularly shaped aggregates. Recent studies have shown that aggregates acquire higher charge-to-mass ratios due to their complex structures, which in turn may alter their subsequent dynamics and evolution. In this paper, the charging of aggregates is examined including secondary electron emission and photoemission in addition to primary plasma currents. The results show that the equilibrium charge on aggregates can differ markedly from spherical grains with the same mass, but that the charge can be estimated for a given environment based on structural characteristics of the grain. The 'small particle effect' due to secondary electron emission is also important for de terming the charge of micron-sized aggregates consisting of nano-sized particles.

79 ASTRONOMY AND ASTROPHYSICS↗

Collisional disruption of gravitational aggregates in the tidal environment

The degree of disruption in collisions in free space is determined by specific impact energy, and the mass fraction of the largest remnant is a monotonically decreasing function of impact energy. However, it has not been shown whether such a relationship is applicable to collisions under the influence of a planet's tidal force, which is important in ring dynamics and satellite accretion. Here we examine the collisional disruption of gravitational aggregates in the tidal environment by using local N-body simulations. We find that outcomes of such a collision largely depend on the impact velocity, the direction of impact, and the radial distance from the planet. In the case of a strong tidal field corresponding to Saturn's F ring, collisions in the azimuthal direction are much more destructive than those in the radial direction. Numerical results of collisions sensitively depend on the impact velocity, and a complete disruption of aggregates can occur even in impacts with velocity much lower than their escape velocity. In such low-velocity collisions, the deformation of colliding aggregates plays an essential role in determining collision outcomes, because the physical size of the aggregate is comparable to its Hill radius. On the other hand, the dependence of collision outcomes on impact velocity becomes similar to the case in free space when the distance from the planet is sufficiently large. Our results are consistent with Cassini observations of the F ring, which suggest ongoing creation and disruption of aggregates within the ring.

79 ASTRONOMY AND ASTROPHYSICS↗

Identification of aggregate building thermal dynamic model and unmeasured internal heat load from data

This paper is on the problem of simultaneously identifying the parameters of an aggregate thermal dynamic model of a multi-zone building and unknown disturbances from input-output data. An aggregate model is a single-zone equivalent of a multi-zone building, and is useful for many purposes, including model based control of large heating, ventilation and air conditioning (HVAC) equipment that delivers thermal energy to the entire building. A key challenge in identification is the presence of unknown disturbance since it is not measurable but non-negligible.We first present a principled method to aggregate a multizone building model into a single zone model. We then provide a method to identify thermal parameters and the unknown disturbance for this aggregate (single-zone) model. Finally, we test our proposed identification algorithm to data generated from a virtual building. A key insight provided by the aggregation method allows us to recognize under what conditions the estimation of the disturbance signal will be necessarily poor and uncertain.

Guo, Zhong↗

A Vertically Resolved MSE Framework Highlights the Role of the Boundary Layer in Convective Self-Aggregation

Abstract Convective self-aggregation refers to a phenomenon in which random convection can self-organize into large-scale clusters over an ocean surface with uniform temperature in cloud-resolving models. Previous literature studies convective aggregation primarily by analyzing vertically integrated (VI) moist static energy (MSE) variance. That is the global MSE variance, including both the local MSE variance at a given altitude and the covariance of MSE anomalies between different altitudes. Here we present a vertically resolved (VR) MSE framework that focuses on the local MSE variance to study convective self-aggregation. Using a cloud-resolving simulation, we show that the development of self-aggregation is associated with an increase of local MSE variance, and that the diabatic and adiabatic generation of the MSE variance is mainly dominated by the boundary layer (BL; the lowest 2 km). The results agree with recent numerical simulation results and the available potential energy analyses showing that the BL plays a key role in the development of self-aggregation. Additionally, we find that the lower free troposphere (2–4 km) also generates significant MSE variance in the first 15 days. We further present a detailed comparison between the global and local MSE variance frameworks in their mathematical formulation and diagnostic results, highlighting their differences.

54 ENVIRONMENTAL SCIENCES↗

Microemulsions and Aggregation Formation in Extraction Processes for Used Nuclear Fuel: Thermodynamic and Structural Studies

Advanced nuclear fuel cycles rely on successful chemical separation of various elements in the used fuel. Numerous solvent extraction (SX) processes have been developed for the recovery and purification of metal ions from this used material. However, the predictability of process operations has been challenged by the lack of a fundamental understanding of the chemical interactions in several of these separation systems. For example, gaps in the thermodynamic description of the mechanism and the complexes formed will make predictions very challenging. Recent studies of certain extraction systems under development and a number of more established SX processes have suggested that aggregate formation in the organic phase results in a transformation of its selectivity and efficiency. Aggregation phenomena have consistently been interfering in SX process development, and have, over the years, become synonymous with an undesirable effect that must be prevented. This multiyear, multicollaborative research effort was carried out to study solvation and self-organization in non-aqueous solutions at conditions promoting aggregation phenomena. Our approach to this challenging topic was to investigate extraction systems comprising more than one extraction reagent where synergy of the metal ion could be observed. These systems were probed for the existence of stable microemulsions in the organic phase, and a number of high-end characterization tools were employed to elucidate the role of the aggregates in metal ion extraction. The ultimate goal was to find connections between synergy of metal ion extraction and reverse micellar formation. Our main accomplishment for this project was the expansion of the understanding of metal ion complexation in the extraction system combining tributyl phosphate (TBP) and dibutyl phosphoric acid (HDBP). We have found that for this system no direct correlation exists for the metal ion extraction and the formation of aggregates, meaning that the metal ion is not solubilized in a reverse micelle core. Rather we have found solid evidence that the metal ions are extracted and coordinated by the organic ligands as suggested by classic SX theories. However, we have challenged the existence of mixed complexes that have been suggested to exist in this particular extraction system. Most importantly we have generated a wealth of information and trained students on important lab techniques and strengthened the collaboration between the DOE national laboratories and US educational institution involved in this work.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Detection and Aggregation of Listeria Monocytogenes Using Polyclonal Antibody Gold-Coated Magnetic Nanoshells Surface-Enhanced Raman Spectroscopy Substrates

Magnetic nanoshells with tailored surface chemistry can enhance bacterial detection and separation technologies. This work demonstrated a simple technique to detect, capture, and aggregate bacteria with the aid of end-functionalized polyclonal antibody gold-coated magnetic nanoshells (pAb-Lis-AuMNs) as surface-enhanced Raman spectroscopy (SERS) probes. Listeria monocytogenes were used as the pathogenic bacteria and the pAb-LisAuMNs, 300 nm diameter, were used as probes allowing facile magnetic separation and aggregation. An optimized covalent bioconjugation procedure between the magnetic nanoshells and the polyclonal antibody was performed at pH six via a carbodiimide crosslinking reaction. Spectroscopic and morphological characterization techniques confirmed the fabrication of stable pAb-Lis-AuMNs. The resulting pAb-Lis-AuMNs acted as a SERS probe for L. monocytogenes based on the targeted capture via surface binding interactions and magnetically induced aggregation. Label-free SERS measurements were recorded for the minimum detectable amount of L. monocytogenes based on the SERS intensity at the 1388 cm -1 Raman shift. L. monocytogenes concentrations exhibited detection limits in the range of 10 4 –10 7 CFU ml -1 , before and after aggregation. By fitting these concentrations, the limit of detection of this method was ~10 3 CFU ml -1 . Using a low-intensity magnetic field of 35 G, pAb-LisAuMNs aggregated L. monocytogenes as demonstrated with microscopy techniques, including SEM and optical microscopy. Overall, this work presents a label-free SERS probe method comprised of a surface-modified polyclonal antibody sub-micron magnetic nanoshell structures with high sensitivity and magnetic induced separation that could lead to the fabrication of multiple single-step sensors.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Principles for problem aggregation and assignment in medium scale multiprocessors

One of the most important issues in parallel processing is the mapping of workload to processors. This paper considers a large class of problems having a high degree of potential fine grained parallelism, and execution requirements that are either not predictable, or are too costly to predict. The main issues in mapping such a problem onto medium scale multiprocessors are those of aggregation and assignment. We study a method of parameterized aggregation that makes few assumptions about the workload. The mapping of aggregate units of work onto processors is uniform, and exploits locality of workload intensity to balance the unknown workload. In general, a finer aggregate granularity leads to a better balance at the price of increased communication/synchronization costs; the aggregation parameters can be adjusted to find a reasonable granularity. The effectiveness of this scheme is demonstrated on three model problems: an adaptive one-dimensional fluid dynamics problem with message passing, a sparse triangular linear system solver on both a shared memory and a message-passing machine, and a two-dimensional time-driven battlefield simulation employing message passing. Using the model problems, the tradeoffs are studied between balanced workload and the communication/synchronization costs. Finally, an analytical model is used to explain why the method balances workload and minimizes the variance in system behavior.

Nicol, David M.↗

Size effects in models for mechanically-stressed protein crystals and aggregates

As protein aggregates increase in size, they become easier to disrupt mechanically. Using the scaling properties of models proposed to govern protein aggregation, the effect of thermal vibrations and gravity are investigated as deforming forces. For typical protein assemblies made of 30 A proteins, the assembled diameter must remain less than 100-10,000 times the molecular radius to survive in finite thermal and gravity fields. The analysis predicts the following experimental outcomes: (1) reductions in gravitational strain should favor larger protein aggregates; (2) in comparing the aggregate stability of different proteins, the addition of peptide chains should stabilize against thermal strain, but should not affect gravitational strain; (3) critical aggregate sizes should show significant (exponential) sensitivity to cluster geometry, solution preparation and growth conditions. The analysis is extended to consider qualitative size effects in crystal damage during X-ray exposure.

Noever, David A.↗

Scattering by aggregates with and without an absorbing mantle - Microwave analog experiments

We present angular scattering functions for loosely packed aggregates of 250 and 500 identical spheres near the Rayleigh size limit before and after the application of successive layers of an absorbing mantle. All measurements were obtained by using the microwave analog technique. Gross features of the scattering by aggregates without a mantle can be interpreted in terms of coherent scattering from the unit spheres acting independently of each other. The largest deviations from this approximation occur after the first minimum in forward scattering and extend to a scattering angle of 60 or 80 deg for our models. This intermediate range is also where the largest differences occur in the scattering from one aggregate to another. The angular extent of the range is largest for aggregates with the smallest dimensions. The scattering function is usually flat in the backscattering hemisphere and has little or no backscattering increase. The coherent scattering approximation breaks down when the aggregates are coated, and an equivalent spheres approximation becomes a better representation. The maximum degree of polarization near a scattering angle of 90 deg first decreases and then increases again as the mantle grows thicker.

Zerull, R. H.↗

Aspects of spatial and temporal aggregation in estimating regional carbon dioxide fluxes from temperate forest soils

We examine the influence of aggregation errors on developing estimates of regional soil-CO2 flux from temperate forests. We find daily soil-CO2 fluxes to be more sensitive to changes in soil temperatures (Q(sub 10) = 3.08) than air temperatures (Q(sub 10) = 1.99). The direct use of mean monthly air temperatures with a daily flux model underestimates regional fluxes by approximately 4%. Temporal aggregation error varies with spatial resolution. Overall, our calibrated modeling approach reduces spatial aggregation error by 9.3% and temporal aggregation error by 15.5%. After minimizing spatial and temporal aggregation errors, mature temperate forest soils are estimated to contribute 12.9 Pg C/yr to the atmosphere as carbon dioxide. Georeferenced model estimates agree well with annual soil-CO2 fluxes measured during chamber studies in mature temperate forest stands around the globe.

Kicklighter, David W.↗

The Aggregate Representation of Terrestrial Land Covers Within Global Climate Models (GCM)

This project had four initial objectives: (1) to create a realistic coupled surface-atmosphere model to investigate the aggregate description of heterogeneous surfaces; (2) to develop a simple heuristic model of surface-atmosphere interactions; (3) using the above models, to test aggregation rules for a variety of realistic cover and meteorological conditions; and (4) to reconcile biosphere-atmosphere transfer scheme (BATS) land covers with those that can be recognized from space; Our progress in meeting these objectives can be summarized as follows. Objective 1: The first objective was achieved in the first year of the project by coupling the Biosphere-Atmosphere Transfer Scheme (BATS) with a proven two-dimensional model of the atmospheric boundary layer. The resulting model, BATS-ABL, is described in detail in a Masters thesis and reported in a paper in the Journal of Hydrology Objective 2: The potential value of the heuristic model was re-evaluated early in the project and a decision was made to focus subsequent research around modeling studies with the BATS-ABL model. The value of using such coupled surface-atmosphere models in this research area was further confirmed by the success of the Tucson Aggregation Workshop. Objective 3: There was excellent progress in using the BATS-ABL model to test aggregation rules for a variety of realistic covers. The foci of attention have been the site of the First International Satellite Land Surface Climatology Project Field Experiment (FIFE) in Kansas and one of the study sites of the Anglo-Brazilian Amazonian Climate Observational Study (ABRACOS) near the city of Manaus, Amazonas, Brazil. These two sites were selected because of the ready availability of relevant field data to validate and initiate the BATS-ABL model. The results of these tests are given in a Masters thesis, and reported in two papers. Objective 4: Progress far exceeded original expectations not only in reconciling BATS land covers with those that can be recognized from space, but also in then applying remotely-sensed land cover data to map aggregate values of BATS parameters for heterogeneous covers and interpreting these parameters in terms of surface-atmosphere exchanges.

Shuttleworth, W. James↗

Mapping Surface Cover Parameters Using Aggregation Rules and Remotely Sensed Cover Classes

A coupled model, which combines the Biosphere-Atmosphere Transfer Scheme (BATS) with an advanced atmospheric boundary-layer model, was used to validate hypothetical aggregation rules for BATS-specific surface cover parameters. The model was initialized and tested with observations from the Anglo-Brazilian Amazonian Climate Observational Study and used to simulate surface fluxes for rain forest and pasture mixes at a site near Manaus in Brazil. The aggregation rules are shown to estimate parameters which give area-average surface fluxes similar to those calculated with explicit representation of forest and pasture patches for a range of meteorological and surface conditions relevant to this site, but the agreement deteriorates somewhat when there are large patch-to-patch differences in soil moisture. The aggregation rules, validated as above, were then applied to remotely sensed 1 km land cover data set to obtain grid-average values of BATS vegetation parameters for 2.8 deg x 2.8 deg and 1 deg x 1 deg grids within the conterminous United States. There are significant differences in key vegetation parameters (aerodynamic roughness length, albedo, leaf area index, and stomatal resistance) when aggregate parameters are compared to parameters for the single, dominant cover within the grid. However, the surface energy fluxes calculated by stand-alone BATS with the 2-year forcing, data from the International Satellite Land Surface Climatology Project (ISLSCP) CDROM were reasonably similar using aggregate-vegetation parameters and dominant-cover parameters, but there were some significant differences, particularly in the western USA.

Arain, Altaf M.↗

Computer Modeling of Electrostatic Aggregation of Granular Materials in Planetary and Astrophysical Settings

Electrostatic forces strongly influence the behavior of granular materials in both dispersed (cloud) systems and semi-packed systems. These forces can cause aggregation or dispersion of particles and are important in a variety of astrophysical and planetary settings. There are also many industrial and commercial settings where granular matter and electrostatics become partners for both good and bad. This partnership is important for human exploration on Mars where dust adheres to suits, machines, and habitats. Long-range Coulombic (electrostatic) forces, as opposed to contact-induced dipoles and van der Waals attractions, are generally regarded as resulting from net charge. We have proposed that in addition to net charge interactions, randomly distributed charge carriers on grains will result in a dipole moment regardless of any net charge. If grains are unconfined, or fluidized, they will rotate so that the dipole always induces attraction between grains. Aggregates are readily formed, and Coulombic polarity resulting from the dipole produces end-to-end stacking of grains to form filamentary aggregates. This has been demonstrated in USML experiments on Space Shuttle where microgravity facilitated the unmasking of static forces. It has also been demonstrated in a computer model using grains with charge carriers of both sign. Model results very closely resembled micro-g results with actual sand grains. Further computer modeling of the aggregation process has been conducted to improve our understanding of the aggregation process, and to provide a predictive tool for microgravity experiments slated for Space Station. These experiments will attempt to prove the dipole concept as outlined above. We have considerably enhanced the original computer model: refinements to the algorithm have improved the fidelity of grain behavior during grain contact, special attention has been paid to simulation time steps to enable establishment of a meaningful, quantitative time axis, and calibration of rounding accuracies have been conducted to test cumulative numerical influences in the model. The model has been run for larger grain populations, variable initial cloud densities, and we have introduced random net charging to individual grains, as well as a net charge to the cloud as a whole. The model uses 3 positive and 3 negative charges randomly distributed on each grain, with up to 160 grains contained within various size "boxes" that define the initial number densities in the clouds. Each charge represents localized charged region on a grain, but does not necessarily imply single quantized charge carriers. The Coulomb equations are then allowed to interact for each monopole: dipoles and any higher order charge coupling is a natural product of these "free" interactions over which the modeler exerts no influence. The charges are placed on surfaces of grains at random locations. A series of runs was conducted for neutral grains that had a perfect balance of negative and positive char carriers. Runs were also conducted with grains having additional fractional charges ranging between 0 and 1. By adding fractional charges of one sign, the model created grain populations in which all grains had excess charges the same sign, giving the cloud an overall net charge. This simulates clouds subjected to ionizing radiation (e. protoplanetary debris disk around a protosun), or any other process of charge biasing in a grain population (e.g., volcanic plumes). In another run series, random fractional charges of either sign were added to the grains so th some grains had a slight net positive charge while others had a slight net negative charge. This simulates triboelectrically-charged grain populations in which acquisition of an electron by one surface is at the expense creating a hole elsewhere. This dual sign charging was applied in two ways: in one case the cloud remained neutral by ensuring that all grain excess charges added to zero; in the other case, the cloud was permitted slight net char by not imposing a charge-balance condition. Additional information is contained in the original.

Marshall, J.↗

Cell and Particle Interactions and Aggregation During Electrophoretic Motion

The objectives of this research were (i) to perform experiments for observing and quantifying electrophoretic aggregation, (ii) to develop a theoretical description to appropriately analyze and compare with the experimental results, (iii) to study the combined effects of electrophoretic and gravitational aggregation of large particles, and the combined effects of electrophoretic and Brownian aggregation of small particles, and (iv) to perform a preliminary design of a potential future flight experiment involving electrophoretic aggregation. Electrophoresis refers to the motion of charged particles, droplets or molecules in response to an applied electric field. Electrophoresis is commonly used for analysis and separation of biological particles or molecules. When particles have different surface charge densities or potentials, they will migrate at different velocities in an electric field. This differential migration leads to the possibility that they will collide and aggregate, thereby preventing separation.

Davis, Robert H.↗

Optical spectroscopy of a highly fluorescent aggregate of bacteriochlorophyll c

Bacteriochlorophyll (BChl) c and a similar model compound, Mg-methyl bacteriopheophorbide d, form several types of aggregates in nonpolar solvents. One of these aggregates is highly fluorescent, with a quantum yield higher than that of the monomer. This aggregate is also unusual in that it shows a rise time in its fluorescence emission decay at certain wavelengths, which is ascribed to a change in conformation of the aggregate. An analysis of fluorescence depolarization data is consistent with either a linear aggregate of four or five monomers or preferably a cyclic arrangement of three dimers.

NASA Discipline Exobiology↗

Three-dimensional Myoblast Aggregates--Effects of Modeled Microgravity

The overall objective of these studies is to elucidate the molecular and cellular alterations that contribute to muscle atrophy in astronauts caused by exposure to microgravity conditions in space. To accomplish this, a three-dimensional model test system was developed using mouse myoblast cells (C2C12). Myoblast cells were grown as three-dimensional aggregates (without scaffolding or other solid support structures) in both modeled microgravity (Rotary Cell Culture System, Synthecon, Inc.) and at unit gravity in coated Petri dishes. Evaluation of H&E stained thin sections of the aggregates revealed the absence of any necrosis. Confocal microscopy evaluations of cells stained with the Live/Dead assay (Molecular Probes) confirmed that viable cells were present throughout the aggregates with an average of only three dead cells observed per aggregate. Preliminary results from gene array analysis (Affymetrix chip U74Av2) showed that approximately 14% of the genes were down regulated (decreased more than 3 fold) and 4% were upregulated in cells exposed to modeled microgravity for 12 hours compared to unit gravity controls. Additional studies using fluorescent phallacidin revealed a decrease in F-actin in the cells exposed to modeled microgravity compared to unit gravity. Myoblast cells grown as aggregates in modeled microgravity exhibited spontaneous differentiation into syncitia while no differentiation was seen in the unit gravity controls. These studies show that 1)the model test system developed is suitable for assessing cellular and molecular alterations in myoblasts; 2) gene expression alterations occur rapidly (within 12 hours) following exposure to modeled microgravity; and 3) modeled microgravity conditions stimulated myoblast cell differentiation. Achieving a greater understanding of the molecular alterations leading to muscle atrophy will eventually enable the development of cell-based countermeasures, which may be valuable for treatment of muscle diseases on Earth and future space explorations.

Byerly, Diane↗