Ensemble Of Aggregates Research Articles

Brownian translation and rotation from the ballistic to the diffusive limit and derivation of the physical properties of dust agglomerates.

We analyzed the translational and rotational Brownian motion of aggregates of micrometer-sized silica spheres under microgravity conditions and in rarefied gas. The experimental data was collected in the form of high-speed recordings using a long-distance microscope as part of the ICAPS (Interactions in Cosmic and Atmospheric Particle Systems) experiment on board of the sounding rocket flight Texus-56. Our data analysis shows that the translational Brownian motion can be used to determine the mass and translational response time of each individual dust aggregate. The rotational Brownian motion additionally provides the moment of inertia and the rotational response time. A shallow positive correlation between mass and response time was found as predicted for aggregate structures with low fractal dimensions. Translational and rotational response times are roughly in agreement. Using the mass and the moment of inertia of each aggregate, we determined the fractal dimension of the aggregate ensemble. Slight deviations from the pure Gaussian one-dimensional displacement statistics were found in the ballistic limit for both the translational and rotational Brownian motion.

Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with arescaled RNA force field.

Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using nuclear magnetic resonance (NMR) and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using a millisecond-scale aggregate ensemble of unbiased simulations, we were able to observe a few dozen binding events. HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. SRSF1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force field modification, scaling down the intramolecular van der Waals interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens up a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes, and future perspectives of such research are discussed.

Structural Disorder as the Origin of Optical Properties and Spectral Dynamics in Squaraine Nano-Aggregates.

In contrast to regular J- and H-aggregates, thin film squaraine aggregates usually have broad absorption spectra containing both J-and H-like features, which are favorable for organic photovoltaics. Despite being successfully applied in organic photovoltaics for years, a clear interpretation of these optical properties by relating them to specific excited states and an underlying aggregate structure has not been made. In this work, by static and transient absorption spectroscopy on aggregated n-butyl anilino squaraines, we provide evidence that both the red- and blue-shifted peaks can be explained by assuming an ensemble of aggregates with intermolecular dipole-dipole resonance interactions and structural disorder deriving from the four different nearest neighbor alignments─in sharp contrast to previous association of the peaks with intermolecular charge-transfer interactions. In our model, the next-nearest neighbor dipole-dipole interactions may be negative or positive, which leads to the occurrence of J- and H-like features in the absorption spectrum. Upon femtosecond pulse excitation of the aggregated sample, a transient absorption spectrum deviating from the absorbance spectrum emerges. The deviation finds its origin in the excitation of two-exciton states by the probe pulse. The lifetime of the exciton is confirmed by the band integral dynamics, featuring a single-exponential decay with a lifetime of 205 ps. Our results disclose the aggregated structure and the origin of red- and blue-shifted peaks and explain the absence of photoluminescence in squaraine thin films. Our findings underline the important role of structural disorder of molecular aggregates for photovoltaic applications.

Percolation of rigid fractal carbon black aggregates.

We examine network formation and percolation of carbon black by means of Monte Carlo simulations and experiments. In the simulation, we model carbon black by rigid aggregates of impenetrable spheres, which we obtain by diffusion-limited aggregation. To determine the input parameters for the simulation, we experimentally characterize the micro-structure and size distribution of carbon black aggregates. We then simulate suspensions of aggregates and determine the percolation threshold as a function of the aggregate size distribution. We observe a quasi-universal relation between the percolation threshold and a weighted average radius of gyration of the aggregate ensemble. Higher order moments of the size distribution do not have an effect on the percolation threshold. We conclude further that the concentration of large carbon black aggregates has a stronger influence on the percolation threshold than the concentration of small aggregates. In the experiment, we disperse the carbon black in a polymer matrix and measure the conductivity of the composite. We successfully test the hypotheses drawn from simulation by comparing composites prepared with the same type of carbon black before and after ball milling, i.e., on changing only the distribution of aggregate sizes in the composites.

Unravelling the Complex Denaturant and Thermal-Induced Unfolding Equilibria of Human Phenylalanine Hydroxylase.

Human phenylalanine hydroxylase (PAH) is a metabolic enzyme involved in the catabolism of L-Phe in liver. Loss of conformational stability and decreased enzymatic activity in PAH variants result in the autosomal recessive disorder phenylketonuria (PKU), characterized by developmental and psychological problems if not treated early. One current therapeutic approach to treat PKU is based on pharmacological chaperones (PCs), small molecules that can displace the folding equilibrium of unstable PAH variants toward the native state, thereby rescuing the physiological function of the enzyme. Understanding the PAH folding equilibrium is essential to develop new PCs for different forms of the disease. We investigate here the urea and the thermal-induced denaturation of full-length PAH and of a truncated form lacking the regulatory and the tetramerization domains. For either protein construction, two distinct transitions are seen in chemical denaturation followed by fluorescence emission, indicating the accumulation of equilibrium unfolding intermediates where the catalytic domains are partly unfolded and dissociated from each other. According to analytical centrifugation, the chemical denaturation intermediates of either construction are not well-defined species but highly polydisperse ensembles of protein aggregates. On the other hand, each protein construction similarly shows two transitions in thermal denaturation measured by fluorescence or differential scanning calorimetry, also indicating the accumulation of equilibrium unfolding intermediates. The similar temperatures of mid denaturation of the two constructions, together with their apparent lack of response to protein concentration, indicate the catalytic domains are unfolded in the full-length PAH thermal intermediate, where they remain associated. That the catalytic domain unfolds in the first thermal transition is relevant for the choice of PCs identified in high throughput screening of chemical libraries using differential scanning fluorimetry.

Homogenization of Richards' equations in multiscale porous media with soft inclusions

The paper is devoted to the homogenization of Richards' type equations in a deterministic multiscale porous medium filled with soft inclusions. The medium consists of a deterministic ensemble of coarse aggregates embedded within a matrix containing a deterministic ensemble of fine aggregates, leading to a network in which the inclusions (of different sizes) are widely distributed. Under various settings involving the structure of the medium and the coefficients of the equation, we obtain homogenized limits of the underlying micro-model. We also provide a suitable approximation scheme for the homogenized coefficients, thereby providing a numerical method for computing these coefficients. To achieve our goal, apply tools of the multiscale sigma-convergence method.

Ensemble forecasting method

The purpose of this article is to analyze the time series based on aggregate forecasting methods. Forecasting time series comprises an important scientific and technical task which is relevant in various sectors of economy and production. The main objective of any forecasting process is to get the ability to assess trends in changes to a particular factor. To predict the behaviour of future processes, a qualitative analysis of data is required, which provides the basis for the forecast. It is also important to choose the appropriate forecasting method. The forecast obtained may not be always correct, so it is crucial to determine how accurately it is built. In the present paper, characteristics of time series are provided. The main mathematical methods of time series forecasting are analyzed and their classification is presented. Criteria for the accuracy and reliability of forecasting models are defined. The accuracy of the forecast is an important criterion for evaluating the forecasting method. The aggregate ensemble forecast has proven to be an effective method for enhancing the accuracy of forecasting. The article provides an example of constructing an aggregate ensemble forecast. The types of nonlinear models are described and several methods are selected for constructing the aggregate ensemble forecast. The practical application of exponential smoothing is considered, the MA (moving average) model and the AR (autoregressive) model are constructed.

Probing ensemble polymorphism and single aggregate structural heterogeneity in insulin amyloid self-assembly

Ensembles of protein aggregates are characterized by a nano- and micro-scale heterogeneity of the species. This diversity translates into a variety of effects that protein aggregates may have in biological systems, both in connection to neurodegenerative diseases and immunogenic risk of protein drug products. Moreover, this naturally occurring variety offers unique opportunities in the field of protein-based biomaterials. In the above-mentioned fields, the isolation and structural analysis of the different amyloid types within the same ensemble remain a priority, still representing a significant experimental challenge. Here we address such complexity in the case of insulin for its relevance as biopharmaceutical and its involvement in insulin-derived amyloidosis. By combining Fourier Transform Infrared Microscopy (micro-FTIR) and fluorescence lifetime imaging microscopy (FLIM) we show the occurrence, within the same ensemble of insulin protein aggregates, of a variable β-structure architecture and content not only dependent on the species analyzed (spherulites or fibrils), but also on the position within a single spherulite at submicron scale. We unambiguously reveal that the surface of the spherulites are characterized by β-structures with an enhanced H-bond coupling compared to the core. This information, inaccessible via bulk methods, allows us to relate the aggregate structure at molecular level to the overall morphology of the aggregates. Our findings robustly solve the problem of probing the ensemble and single particle heterogeneity of amyloid samples. Furthermore, we offer a unique, scalable and ready-to-use screening methodology for in-depth characterization of self-assembled structures, being this translatable to material sciences, drug quality control and clinical imaging of amyloid-affected tissues.

Optical Activity from the Exciton Aharonov–Bohm Effect: A Floquet Engineering Approach

Floquet engineering is a convenient strategy to induce nonequilibrium phenomena in molecular and solid-state systems, or to dramatically alter the physicochemical properties of matter, bypassing costly and time-consuming synthetic modifications. In this article, we investigate theoretically some interesting consequences of the fact that an originally achiral molecular system can exhibit nonzero circular dichroism (CD) when it is driven with elliptically polarized light. More specifically, we consider an isotropic ensemble of small cyclic molecular aggregates in solution whose local low-frequency vibrational modes are driven by an elliptically polarized continuous-wave infrared pump. We attribute the origin of a nonzero CD signal to time-reversal symmetry breaking due to an excitonic Aharonov-Bohm (AB) phase arising from a time-varying laser electric field, together with coherent interchromophoric exciton hopping. The obtained Floquet engineered excitonic AB phases are far more tunable than analogous magnetically-induced electronic AB phases in nanoscale rings, highlighting a virtually unexplored potential that Floquet engineered AB phases have in the coherent control of molecular processes and simultaneously introducing new analogues of magneto-optical effects in molecular systems which bypass the use of strong magnetic fields.

Dielectric tensor of a rectangular arrangement of Ag nanoparticles in anisotropic [formula omitted]: Analysis of the negative epsilon conditions

In the present paper we report the optical response of an ordered array of silver (Ag) nanoparticles (NPs) using the uniaxial LiNbO3 as a model case. We investigate the anisotropic effects on the effective dielectric tensor taking into account the charges interaction of particles. The Ag NPs dielectric function is described through a modified Drude model whereas the LiNbO3 dielectric functions are deduced from their experimentally established Sellmeier equations. The effective dielectric tensor components of the ensemble aggregates of Ag NPs and uniaxial LiNbO3 crystal are treated through the extended Maxwell–Garnett approximation. Following the asymmetric behaviour of uniaxial crystals, Ag NPs are sited in the ordinary plane of the crystal, giving rise to different responses in the x, y and z directions of applied electric field. Real and imaginary parts of the effective dielectric tensor components of the aggregate ensemble are investigated in terms of different structural parameters, such as the interparticle spacings, the NPs filling factor and sizes of spherically embedded nanoparticles. We demonstrate that an adequate choice of structural parameters such as NPs sizes, interparticle separation gaps or the filling factor can determine the optical properties of layered Ag–embedded uniaxial crystals such as LiNbO3. We show that the negative epsilon (NE) condition is satisfied from a critical size of Ag NPs when the filling factor and the interparticles distances (a and b) have particular values. This condition defines an interval of energies, called NE range, which clearly depend on values of structural parameters defined in the model. This NE range shows some type of bandwidth anisotropy when it is compared among the x-, y-, z- and xy-components of the effective dielectric tensor. We analyze some anisotropic features such as the bandwidth and shift resonance energies in the real and imaginary parts of the dielectric tensor when structural parameters change.

Lidar-relevant radiative properties of soot fractal aggregate ensembles

This study presents the averaged lidar-relevant radiative properties of numerically generated soot fractal aggregate ensembles. The radiative properties of these aggregates have been computed using the Superposition T-Matrix Method, with emphasis put on those that are most relevant to lidar application; the backscattering and extinction cross-sections, the Lidar Ratio and the Linear Depolarization Ratio. These lidar-relevant radiative properties have been computed over a broad spectrum, going from the ultraviolet to the near infrared, in order to address lidar instrument need for a priori knowledge in signal inversion procedures and measurement analysis. By averaging the computed radiative properties according to each set of morphological parameters, we obtain statistically representative results and we study the impacts of morphological changes on these lidar-relevant radiative properties. Our results show a strong impact of the primary particle radius on all considered radiative properties, while the number of primary particles induce significant variations on the cross-sections only. The fractal dimension, although being an essential morphological parameter, has a weak influences on the lidar-relevant radiative properties.

On the ergodic control of ensembles

Across smart-grid and smart-city application domains, there are many problems where an ensemble of agents is to be controlled such that both the aggregate behaviour and individual-level perception of the system’s performance are acceptable. In many applications, traditional PI control is used to regulate aggregate ensemble performance. Our principal contribution in this note is to demonstrate that PI control may not be always suitable for this purpose, and in some situations may lead to a loss of ergodicity for closed-loop systems. Building on this observation, a theoretical framework is proposed to both analyse and design control systems for the regulation of large scale ensembles of agents with a probabilistic intent. Examples are given to illustrate our results.

Origin of Unexpectedly Simple Oscillatory Responses in the Excited-State Dynamics of Disordered Molecular Aggregates.

Unraveling the many facets of coherent and incoherent exciton motion in an ensemble of chromophores is an inherently complex quantum mechanical problem that has triggered a vivid debate on the role of quantum effects in molecular materials and biophysical systems. Here the dynamics of a statistical ensemble of molecular aggregates consisting of identical chromophores is investigated within a new theoretical framework. Taking account of intrinsic properties of the system, the Hamiltonian of the aggregate is partitioned into two mutually commuting vibrational and vibronic operators. This representation paves the way for an analysis that reveals the role of static disorder in ensembles of aggregates. Using analytical methods, it is demonstrated that after a critical time τD ≃ 2π/σ (σ being the dispersion of the disorder) any dynamic variable of the aggregate exhibits purely vibrational dynamics. This result is confirmed by exact numerical calculations of the time-dependent site populations of the aggregate. These findings may be useful for the interpretation of recent femtosecond spectroscopic experiments on molecular aggregates.

Simulating and analysing configurational landscapes of protein-protein contact formation.

Interacting proteins can form aggregates and protein-protein interfaces with multiple patterns and different stabilities. Using molecular simulation one would like to understand the formation of these aggregates and which of the observed states are relevant for protein function and recognition. To characterize the complex configurational ensemble of protein aggregates, one needs a quantitative measure for the similarity of structures. We present well-suited descriptors that capture the essential features of non-covalent protein contact formation and domain motion. This set of collective variables is used with a nonlinear multi-dimensional scaling-based dimensionality reduction technique to obtain a low-dimensional representation of the configurational landscape of two ubiquitin proteins from coarse-grained simulations. We show that this two-dimensional representation is a powerful basis to identify meaningful states in the ensemble of aggregated structures and to calculate distributions and free energy landscapes for different sets of simulations. By using a measure to quantitatively compare free energy landscapes we can show how the introduction of a covalent bond between two ubiquitin proteins at different positions alters the configurational states of these dimers.

Supramolecular Ensemble of Perylene Bisimide Derivative and Cu2O-Ag Nanoparticles: Nano/“Dip Strip” Catalytic System for One-Pot, Three-Component Click Reaction at Room Temperature

A supramolecular ensemble of Cu2O-Ag nanoparticles (NPs) and aggregates of perylene bisimide (PBI) derivative has been developed in mixed aqueous media. The as prepared supramolecular ensemble exhi...

ESIPT‐Induced Carbazole‐Based AIEE Material for Nanomolar Detection of Cu2+ and CN– Ions: A Molecular Keypad Security Device

Herein, we have designed and synthesized a new diimino dicarbazole derivative, 3, which exhibits the phenomenon of aggregation‐induced emission enhancement (AIEE) due to the persistence of the excited‐state intramolecular proton transfer phenomenon. The aggregates of AIEE‐active material 3 selectively sense Cu2+ ions in the nanomolar range and mediate the conversion of Cu2+ ions to Cu nanorods. The ensemble of aggregates of 3 and Cu nanorods were further utilized for selective sensing of CN– ions. In addition, the fluorescence behavior of the system generates the formation of a molecular keypad security device. The keypad security device, based on AIEE material, adds to the complexity of the lock and makes it more efficient.

Supramolecular Ensemble of Tetraphenylcyclopentadienone Derivative and HgO nanoparticles: A One-Pot Approach for the Synthesis of Quinoline and Quinolone Derivatives

Electron deficient tetraphenylcyclopentadienone appended with thiophene has been designed and synthesized which exihibits aggregation induced emission enhancement (AIEE) to form fluorescent assemblies in aqueous media. These emissive aggregates exhibit mercury induced emission enhancement in aqueous media and serve as reactors for the generation of mercury oxide nanoparticles. Further, the in situ generated supramolecular ensemble of tetraphenylcyclopentadienone aggregates and HgO nanomaterial show high catalytic efficiency in the reactions for the synthesis of N-heterocyclic derivatives through ortho C−H functionalization of unprotected anilines. In addition, this catalytic system has been utilized for the kynurenic acid methyl esters (KYNA methyl ester) derivatives based non-steroidal anti-inflammatory drug through C−H functionalization strategy which is unprecedented in the literature

Growing into and out of the bouncing barrier in planetesimal formation

In recent laboratory studies the robustness of a bouncing barrier in planetesimal formation was studied with an ensemble of preformed compact mm-sized aggregates. Here we show that a bouncing barrier indeed evolves self-consistently by hit-and-stick from an ensemble of smaller dust aggregates. In addition, we feed small aggregates to an ensemble of larger bouncing aggregates. The stickiness temporarily increases, but the final number of aggregates still bouncing remains the same. However, feeding on the small particle supply, the size of the bouncing aggregates increases. This suggests that in the presence of a dust reservoir aggregates grow into but also out of a bouncing barrier at larger size.

Supramolecular Ensemble of Aggregates of Pentacenequinone Derivative and Cadmium NPs: A Potential Catalytic/Photocatalytic System for Direct C‐H Activation of Quinones and Azoles

AbstractThe present study demonstrates the utilization of in situ generated supramolecular ensemble of aggregates of pentacenequinone derivative 3 and cadmium nanoparticles (CdNPs) as an efficient catalytic system for (1) oxidant free, controlled and selective monofunctionalization and hetero/homo difunctionalization of 1,4‐benzoquinone by C−H activation at room temperature (2) photocatalytic C−H functionalization of azoles with bromoarenes and (3) C−H functionalization of benzothiazole with simple arenes in ecofriendly conditions under visible light irradiations. Thus, a range of C2‐arylated quinone and azole derivatives are synthesized from simple substrates using this newly developed catalytic/photocatalytic system under economic and ecofriendly conditions.

Discrimination of Metalloproteins by a Mini Sensor Array Based on Bispyrene Fluorophore/Surfactant Aggregate Ensembles.

Fluorescent sensor arrays with pattern recognition ability have been widely used to detect and identify multiple chemically similar analytes. In the present work, two particular bispyrene fluorophores containing hydrophilic oligo(oxyethylene) spacer, 6 and 4, were synthesized, but one is with and the other is without cholesterol unit. Their ensembles with cationic surfactant (CTAB) assemblies realize multiple fluorescence responses to different metalloproteins, including hemoglobin, myoglobin, ferritin, cytochrome c, and alcohol dehydrogenase. The combination of fluorescence variation at monomer and excimer emission of the two binary sensor ensembles enables the mini sensor array to provide a specific fingerprint pattern to each metalloprotein. Linear discriminant analysis shows that the two-ensemble-sensor-based array could well discriminate the five tested metalloproteins. The present work realizes using a mini sensor array to accomplish discrimination of complex analytes like proteins. They also display a very high sensitivity to the tested metalloproteins with detection limits in the range of picomolar concentration.