Ensemble Of Aggregates Research Articles

An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase.

The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils.

Why are Jupiter-family comets active and asteroids in cometary-like orbits inactive?

Context: Surveys in the visible and near-infrared spectral range have revealed the presence of low-albedo asteroids in cometary like orbits (ACOs). In contrast to Jupiter family comets (JFCs), ACOs are inactive, but possess similar orbital parameters. Aims: In this work, we discuss why ACOs are inactive, whereas JFCs show gas-driven dust activity, although both belong to the same class of primitive solar system bodies. Methods: We hypothesize that ACOs and JFCs have formed under the same physical conditions, namely by the gravitational collapse of ensembles of ice and dust aggregates. We use the memory effect of dust-aggregate layers under gravitational compression to discuss under which conditions the gas-driven dust activity of these bodies is possible. Results: Owing to their smaller sizes, JFCs can sustain gas-driven dust activity much longer than the bigger ACOs, whose sub-surface regions possess an increased tensile strength, due to gravitational compression of the material. The increased tensile strength leads to the passivation against dust activity after a relatively short time of activity. Conclusions: The gravitational-collapse model of the formation of planetesimals, together with the gravitational compression of the sub-surface material simultaneously, explains the inactivity of ACOs and the gas-driven dust activity of JFCs. Their initially larger sizes means that ACOs possess a higher tensile strength of their sub-surface material, which leads to a faster termination of gas-driven dust activity. Most objects with radii larger than $2 \, \mathrm{km}$ have already lost their activity due to former gravitational compression of their current surface material.

A supramolecular ensemble of a PBI derivative and Cu2O NPs: potential photocatalysts for the Suzuki and Suzuki type coupling reactions

The in situ generated supramolecular ensemble (2:Cu2O) of Cu2O NPs and aggregates of PBI derivative 2 exhibited excellent photocatalytic efficiency in the Suzuki–Miyaura and Suzuki type cross-coupling reactions under mild and eco-friendly conditions.

EXPERIMENTAL STUDY ON BOUNCING BARRIERS IN PROTOPLANETARY DISKS

For dust aggregates in protoplanetary discs a transition between sticking and bouncing in individual collisions at mm to cm size has been observed in the past. This lead to the notion of a bouncing barrier for which growth gets stalled. Here, we present long term laboratory experiments on the outcome of repeated aggregate collisions at the bouncing barrier. About 100 SiO$_2$ dust aggregates of 1 mm in size were observed interacting with each other. Collisions occured within a velocity range from below mm/s up to cm/s. Aggregates continuously interacted with each other over a period of 900 s. During this time more than $10^5$ collisions occured. Nearly 2000 collisions were analyzed in detail. No temporal stable net growth of larger aggregates was observed even though sticking collision occur. Larger ensembles of aggregates sticking together are formed but were disassembled again during the further collisional evolution. The concept of a bouncing barrier supports the formation of planetesimals by seeded collisional growth as well as by gravitational instability favouring a significant total mass being limited to certain size ranges. Within our parameter set the experiments confirm that bouncing barriers are one possible and likely evolutionary limit of a self consistent particle growth.

Fluorescent supramolecular metal assemblies as 'no quenching' probes for detection of threonine in the nanomolar range.

A highly sensitive detection of threonine is realized using a supramolecular ensemble of aggregates of hetero-oligophenylene derivative and Zn(2+) ions. On the basis of fluorogenic response of aggregates of toward Zn(2+) ions and threonine, we have constructed a 2-input, 3-output sequential logic circuit at the molecular level.

The suborbital particle aggregation and collision experiment (SPACE): Studying the collision behavior of submillimeter-sized dust aggregates on the suborbital rocket flight REXUS 12

The Suborbital Particle Aggregation and Collision Experiment (SPACE) is a novel approach to study the collision properties of submillimeter-sized, highly porous dust aggregates. The experiment was designed, built, and carried out to increase our knowledge about the processes dominating the first phase of planet formation. During this phase, the growth of planetary precursors occurs by agglomeration of micrometer-sized dust grains into aggregates of at least millimeters to centimeters in size. However, the formation of larger bodies from the so-formed building blocks is not yet fully understood. Recent numerical models on dust growth lack a particular support by experimental studies in the size range of submillimeters, because these particles are predicted to collide at very gentle relative velocities of below 1 cm/s that can only be achieved in a reduced-gravity environment. The SPACE experiment investigates the collision behavior of an ensemble of silicate-dust aggregates inside several evacuated glass containers which are being agitated by a shaker to induce the desired collisions at chosen velocities. The dust aggregates are being observed by a high-speed camera, allowing for the determination of the collision properties of the protoplanetary dust analog material. The data obtained from the suborbital flight with the REXUS (Rocket Experiments for University Students) 12 rocket will be directly implemented into a state-of-the-art dust growth and collision model.

Absorption and scattering of light from ensembles of randomly oriented aggregates

This paper presents one approach to the absorption and scattering of light from aggregates of primary particles. The primary particles are sphere-like and small compared to the wavelength, whereas the aggregate can be large compared to the wavelength. This situation applies to when soot particles formed in flames are measured using methods based on laser light. The method presented in this work, called generalized Rayleigh-Debye-Gans, leads to closed-form expressions for the scattered intensity and the absorbed power of an ensemble of aggregates with random positions and orientations. The expressions ensure a fast and accurate numerical evaluation of the scattering and absorption from ensembles of aggregates. The numerical results are compared with the ones obtained from the T-matrix method and the discrete dipole approximation method.

Breakup of small aggregates driven by turbulent hydrodynamical stress

The breakup of small solid aggregates in homogeneous and isotropic turbulence is studied theoretically and by using direct numerical simulations at high Reynolds number, Reλ =/~ 400. We show that turbulent fluctuations of the hydrodynamic stress along the aggregate trajectory play a key role in determining the aggregate mass distribution function. The differences between turbulent and laminar flows are discussed. A definition of the fragmentation rate is proposed in terms of the typical frequency at which the hydrodynamic stress becomes sufficiently high to cause breakup along each Lagrangian path. We also define an Eulerian proxy of the real fragmentation rate, based on the joint statistics of the stress and its time derivative, which should be easier to measure in any experimental setup. Both our Eulerian and Lagrangian formulations define a clear procedure for the computation of the mass distribution function due to fragmentation. Contrary, previous estimates based only on single point statistics of the hydrodynamic stress exhibit some deficiencies. These are discussed by investigating the evolution of an ensemble of aggregates undergoing breakup and aggregation.

Dust release and tensile strength of the non-volatile layer of cometary nuclei

We developed a thermophysical model for cometary nuclei, which is based upon the assumption that comets form by the gravitational instability of an ensemble of dust and ice aggregates. Under this condition, the tensile strength of the ice-free outer layers of a cometary nucleus can be calculated, using the dust–aggregate collision and adhesion model of Weidling et al. (Weidling, R. et al. [2012]. Icarus, 218, 688-700). Based on available laboratory data on the gas permeability and thermal conductivity of ice-free dust layers, we derived the temperature and pressure at the dust–ice interface for pure water and pure carbon dioxide ice. Comparison of the vapor pressure below the dust crust with its tensile strength allows the prediction of dust release from cometary surfaces. Our model predicts dust activity for pure CO2 ice and for heliocentric distances of ≲3AU, whereas pure H2O ice cannot explain the dust emission.

Free collisions in a microgravity many-particle experiment – II: The collision dynamics of dust-coated chondrules

The formation of planetesimals in the early Solar System is hardly understood, and in particular the growth of dust aggregates above millimeter sizes has recently turned out to be a difficult task in our understanding (Zsom, A., Ormel, C.W., Güttler, C., Blum, J., Dullemond, C.P. [2010]. Astron. Astrophys., 513, A57). Laboratory experiments have shown that dust aggregates of these sizes stick to one another only at unreasonably low velocities. However, in the protoplanetary disk, millimeter-sized particles are known to have been ubiquitous. One can find relics of them in the form of solid chondrules as the main constituent of chondrites. Most of these chondrules were found to feature a fine-grained rim, which is hypothesized to have formed from accreting dust grains in the solar nebula. To study the influence of these dust-coated chondrules on the formation of chondrites and possibly planetesimals, we conducted collision experiments between millimeter-sized, dust-coated chondrule analogs at velocities of a few cms−1. For 2 and 3mm diameter chondrule analogs covered by dusty rims of a volume filling factor of 0.18 and 0.35–0.58, we found sticking velocities of a few cms−1. This velocity is higher than the sticking velocity of dust aggregates of the same size. We therefore conclude that chondrules may be an important step towards a deeper understanding of the collisional growth of larger bodies. Moreover, we analyzed the collision behavior in an ensemble of dust aggregates and non-coated chondrule analogs. While neither the dust aggregates nor the solid chondrule analogs show sticking in collisions among their species, we found an enhanced sicking efficiency in collisions between the two constituents, which leads us to the conjecture that chondrules might act as “catalyzers” for the growth of larger bodies in the young Solar System.

The effect of particle aggregation on the absorption and emission properties of mono- and polydisperse soot aggregates

This study concerns the effect of soot-particle aggregation on the soot temperature derived from the signal ratio in two-color laser-induced incandescence measurements. The emissivity of aggregated fractal soot particles was calculated using both the commonly used Rayleigh–Debye–Gans fractal-aggregate theory and the generalized Mie-solution method in conjunction with numerically generated fractal aggregates of specified fractal parameters typical of flame-generated soot. The effect of aggregation on soot temperature was first evaluated for monodisperse aggregates of different sizes and for a lognormally distributed aggregate ensemble at given signal ratios between the two wavelengths. Numerical calculations were also conducted to account for the effect of aggregation on both laser heating and thermal emission at the two wavelengths for determining the effective soot temperature of polydisperse soot aggregates. The results show that the effect of aggregation on laser energy absorption is important at low fluences. The effect of aggregation on soot emissivity is relatively unimportant in LII applications to typical laminar diffusion flames at atmospheric pressure, but it can become more important in flames at high pressures due to larger primary particles and wider aggregate distributions associated with enhanced soot loading.

Robust ensemble learning for mining noisy data streams

In this paper, we study the problem of learning from concept drifting data streams with noise, where samples in a data stream may be mislabeled or contain erroneous values. Our essential goal is to build a robust prediction model from noisy stream data to accurately predict future samples. For noisy data sources, most existing works rely on data preprocessing techniques to cleanse noisy samples before the training of decision models. In data stream environments, these data preprocessing techniques are, unfortunately, hard to apply, mainly because the concept drifting in a data stream may make it very difficult to differentiate noise from samples of changing concepts. Accordingly, we propose an aggregate ensemble (AE) learning framework. The aim of AE is to build a robust ensemble model that can tolerate data errors. Theoretical and empirical studies on both synthetic and real-world data streams demonstrate that the proposed AE learning framework is capable of building accurate classification models from noisy data streams.

Does Shape Anisotropy Control the Fractal Dimension in Diffusion-Limited Cluster-Cluster Aggregation?

Motivated by recent experiments of soot formation in premixed flames where a minority population of the “stringy” aggregates is found to have a fractal dimension as low as 1.2 instead of the classic diffusion-limited cluster-cluster aggregation (DLCA) value of 1.8, we address this same question in our simulation study: is there a distribution of fractal dimensions in a given ensemble of aggregates and does shape anisotropy of clusters control the fractal dimension? Our results, however, clearly show classic DLCA yields aggregates of a broad range of shapes all with Df≈1.8 independent of their shape, but with a shape dependent pre-factor k0 , in the relation between radius of gyration Rg , mass N, monomer radius a, and fractal dimension . Thus the pre-factor k0 gains in status as a descriptor of aggregate morphology so that aggregates should be described by the pair of parameters Df and k 0 , i.e., (Df, k0).

Radiative Properties of Numerically Generated Fractal Soot Aggregates: The Importance of Configuration Averaging

The radiative properties of numerically generated fractal soot aggregates were studied using the numerically accurate generalized multisphere Mie-solution method. The fractal aggregates investigated in this study contain 10–600 primary particles of 30 nm in diameter. These fractal aggregates were numerically generated using a combination of the particle-cluster and cluster-cluster aggregation algorithms with fractal parameters representing flame-generated soot. Ten different realizations were obtained for a given aggregate size measured by the number of primary particles. The wavelength considered is 532 nm, and the corresponding size parameter of primary particle is 0.177. Attention is paid to the effect of different realizations of a fractal aggregate with identical fractal dimension, prefactor, primary particle diameter, and the number of primary particles on its orientation-averaged radiative properties. Most properties of practical interest exhibit relatively small variation with aggregate realization. However, other scattering properties, especially the vertical-horizontal differential scattering cross section, are very sensitive to the variation in geometrical configuration of primary particles. Orientation-averaged radiative properties of a single aggregate realization are not always sufficient to represent the properties of random-oriented ensemble of fractal aggregates.

Nonlinear susceptibility of a metal-dielectric nanocomposite caused by induced dipole-dipole forces between particles

The optical coefficients of a nonlinearity for a macroscopic ensemble of aggregates of metal nanoparticles that is caused by deformation of the spatial structure of clusters in a strong light field are calculated for the first time. For a continuous medium that consists of a nonabsorbing dielectric containing aggregated silver nanoparticles that do not possess an intrinsic optical nonlinearity, coefficients of nonlinear absorption are obtained in relation to the intensity and frequency of incident light. It is shown that, at intensities of up to a few megawatts per square centimeter, the addition to the absorption of a nanocomposite to be modeled is adequately described by a third-order nonlinearity. The magnitude and sign of the nonlinear absorption coefficient agree well with the previously obtained experimental data for aggregated silver and gold colloids under nanosecond excitation.

Self-Sustained Levitation of Dust Aggregate Ensembles by Temperature-Gradient-Induced Overpressures

In laboratory experiments we observe dust aggregates from 100 mum to 1 cm in size composed of micrometer-sized grains levitating over a hot surface. Depending on the dust sample aggregates start to levitate at a temperature of 400 K. Levitation of dust aggregates is restricted to a pressure range between 1-40 mbar. The levitating is caused by a Knudsen compressor effect. Based on thermal transpiration through the dust aggregates the pressure increases between surface and aggregates. Dust aggregates are typically balanced approximately 100 microm over the surface. On a slightly concave surface individual aggregates are trapped at the center. Ensembles of aggregates are confined in a 2D plane. Aggregates are subject to systematic and random translational and rotational motion. The levitated aggregates are well suited to study photophoretic or thermophoretic forces or the mutual interaction between dust aggregates.

Radiative characteristics of plant leaf

Existing leaf radiation models are reviewed. A new concept of the optical model of the leaf as a multiphase system containing three aggregate ensembles of particles significantly different in microphysical and optical characteristics is proposed. The proposed model is based on the reconstruction of the particle size distribution function from the experimental leaf absorption spectrum. Based on the obtained microphysical model of the plant leaf, the spectra of optical radiation reflection and transmission in the range of 400–800 nm are calculated for various relative concentrations of light-absorbing pigments (chlorophyll a, b and carotenes) and various leaf thicknesses. Optical radiation propagation was simulated using the stochastic Monte Carlo method. The simulation results are in good agreement with relevant experimental spectra.

MOS Uncertainty Estimates in an Ensemble Framework

Abstract It is being increasingly recognized that the uncertainty in weather forecasts should be quantified and furnished to users along with the single-value forecasts usually provided. Probabilistic forecasts of “events” have been made in special cases; for instance, probabilistic forecasts of the event defined as 0.01 in. or more of precipitation at a point over a specified time period [i.e., the probability of precipitation (PoP)] have been disseminated to the public by the Weather Bureau/National Weather Service since 1966. Within the past decade, ensembles of operational numerical weather prediction models have been produced and used to some degree to provide probabilistic estimates of events easily dealt with, such as the occurrence of specific amounts of precipitation. In most such applications, the number of ensembles restricts this “enumeration” method, and the ensembles are characteristically underdispersive. However, fewer attempts have been made to provide a probability density function (PDF) or cumulative distribution function (CDF) for a continuous variable. The Meteorological Development Laboratory (MDL) has used the error estimation capabilities of the linear regression framework and kernel density fitting applied to individual and aggregate ensemble members of the Global Ensemble Forecast System of the National Centers for Environmental Prediction to develop PDFs and CDFs. This paper describes the method and results for temperature, dewpoint, daytime maximum temperature, and nighttime minimum temperature. The method produces reliable forecasts with accuracy exceeding the raw ensembles. Points on the CDF for 1650 stations have been mapped to the National Digital Forecast Database 5-km grid and an example is provided.

How liquid is biological signalling?

This paper proposes an investigation of the global statistics of synthetic protein networks—a step towards a systemic understanding of their design space. We derive a liquidity index which describes the onset of the phase transition where an ensemble of agents aggregates into a giant cluster. This index captures the influence of both the domain distribution of agents and the binding strengths of their various domains in the limit of infinite populations. In simple cases it is possible to derive an explicit analytical expression of this index, which allows one to compare with simulations, and get a sense of how it transfers to the concrete finite case.

Evolution of an ensemble of fractal aggregates in a colloidal system

A theoretical study is presented of primary-minimum aggregation of colloidal particles, which generally leads to the formation of ramified fractal clusters. The focus is placed on the cooperative effects due to competition between aggregates for particles moving freely in the colloidal suspension. An analysis shows that the competition leads to aggregate density distributions and aggregation kinetics governed by more complicated laws as compared to those established in previous numerical and analytical studies of single-cluster growth.