Dynamic Cluster Formation Research Articles

Real time in vivo analysis of granulomonocytic cell migration in the collagen induced arthritis model

BackgroundGranulomonocytic cells (GMC) drive the inflammatory process at the earliest stages of rheumatoid arthritis (RA). The migratory behavior and functional properties of GMC within the synovial tissue are, however, only...

Distinguishing the monomer to cluster phase transition in concentrated lysozyme solutions by studying the temperature dependence of the short-time dynamics

Recent combined experiments by small angle neutron scattering (SANS) and neutron spin echo (NSE) have demonstrated that dynamic clusters can form in concentrated lysozyme solutions when the right combination of a short-ranged attraction and a long-ranged electrostatic repulsion exists. In this paper, we investigate the temperature effect on the dynamic cluster formation and try to pinpoint the transition concentration from a monomeric protein phase to a cluster phase. Interestingly, even at a relatively high concentration (10% mass fraction), despite the significant change in the SANS patterns that are associated with the change of the short-ranged attraction among proteins, the normalized short-time self-diffusion coefficient is not affected between 5 and 40 °C. This is interpreted as a lack of cluster formation in this condition. However, at larger concentrations such as 17.5% and 22.5% mass fraction, we show that the average hydrodynamic radius increases significantly and causes a large decrease of the normalized self-diffusion coefficient as a result of cluster formation when the temperature is changed from 25 to 5 °C.

Modeling of cluster structure-dependent drag with Eulerian approach for circulating fluidized beds

Flow behavior of gas and solids is simulated in combination the gas–solid two-fluid model with a cluster structure-dependent (CSD) drag coefficient model. The dispersed phase is modeled by a Eulerian approach based upon the kinetic theory of granular flow (KTGF) including models for describing the dispersed phase interactions with the continuous phase. The drag forces of gas–solid phases are predicted from the local structure parameters of the dense and dilute phases based on the minimization of the energy consumed by heterogeneous drag. The cluster structure-dependent (CSD) drag coefficients are incorporated into the two-fluid model to simulate flow behavior of gas and particles in a riser. Simulation results indicate that the dynamic formation and dissolution of clusters can be captured with the cluster structure-dependent drag coefficient model. Simulated solid velocity and concentration of particles profiles are in reasonable agreement with experimental results.

Selective Exocytosis and Spatiotemporal Regulation of Protein Recycling at the Plasma Membrane

The concentration of membrane proteins on the cell surface and time they spend in the plasma membrane is defined by dynamic equilibrium between exocytotic delivery and endocytic recycling processes. However, the mechanisms by which cell is able to differentially regulate recycling kinetics of its plasma membrane components is not well understood.In the current study we present new insights how selective exocytosis and spatial redistribution of proteins in the plasma membrane may regulate their recycling kinetics independent of amount of protein in the plasma membrane. We applied fluorescence photo-activation localization microscopy (FPALM) together with multi-color total-internal reflection fluorescence microscopy to track individual proteins and detect their quantum delivery and internalization via exo- and endocytosis. We showed that upon fusion of exocytic vesicle membrane cargo can be either released into the plasma membrane or retained at the site of fusion. We further provide evidence that protein-specific retention serves as a fusion-associated mechanism for formation of dynamic clusters of proteins in the plasma membrane. These clusters of proteins were found to mediate a dynamic exchange of monomers (protein molecules) with the rest of the plasma membrane and also showed transient association with clathrin. Clathrin assembly at the sites of clusters led to formation of endocytic vesicles that mediated quantum internalization of the clustered protein.Taken together, these data provide novel mechanism by which spatiotemporal retention and release of membrane proteins during selective exocytosis regulates protein-specific recycling at the plasma membrane. Different models of protein-specific retention/release will be compared and discussed.

Thermodynamic study of aqueous solutions of polyelectrolytes of low and medium charge density without added salt by direct measurement of osmotic pressure

A special block osmometer has been constructed and applied to a systematic study of poly (vinyl alcohol and vinyl sulphate ester) (PVS) sodium salts in dilute and moderately concentrated salt free aqueous solutions. In order to avoid surely ionic contamination all parts of the equipment that can contact with the polyelectrolyte solutions were made of different kinds of plastics and glass. The pressure range spans from (50 to 1.3 · 10 5) Pa. The measuring system was found to be appropriate for determination of the molar mass of water soluble polymers, too. Above a certain analytical density of dissociable groups (ADDG) an ion size dependent transition was observed on the reduced osmotic pressure vs. concentration curves. The analysis of the osmotic pressure data has clearly revealed that the dependence of the degree of dissociation on ADDG calculated at zero polyelectrolyte concentration contradicts to ‘ion condensation’ theory. With increasing polyelectrolyte concentration the degree of dissociation decreased rather steeply but at very low concentrations sharp maximums appeared due either to the change in conformation of these charged macromolecules, or formation of dynamic clusters induced by salting out of neutral parts of the macromolecules by the ionized groups. The applicability of the scaling concept as well as the many possible ways of characterization of non-ideality of polyelectrolyte solutions will be discussed in detail.

Role of Cationic Residues in Fine Tuning the Flexibility of Charged Single α-helices

A few highly charged natural peptide sequences have recently been suggested to form stable α-helical structures in aqueous solution. Here we show that these sequences represent a more widespread structural motif called 'charged single α-helix' (CSAH). We have developed two conceptually different computational methods capable of scanning large databases: SCAN4CSAH is based on sequence features characteristic for salt bridge stabilized single α-helices, while FT_CHARGE applies Fourier transformation to charges along sequences. Using the consensus of the two approaches, a remarkable number of proteins were found to contain putative CSAH domains. Recombinant fragments of 50-60 residues in length corresponding to selected hits (from myosin 6, Golgi complex associated protein-60, and mitogen-activated protein kinase M4K4) were found to adopt a highly stable α-helical structure in water. Molecular dynamic simulations of five CSAH peptides (the above three plus peptides from caldesmon and myosin 10) showed that the formation of dynamic ion-pair clusters significantly contribute to the stability of the helices. Furthermore, cationic residues were found to play a differential role in tuning the local flexibility of the CSAH domains. We conclude that sequence specific tuning of flexibility of CSAH peptides could have important role in the mechanical performance of CSAH-containing myosin motors, such as myosin 6 and 10, or in other protein functions.This work was supported by the Hungarian National Science Fund (OTKA).

Direct Observation of Nanoparticle Self-Assembly Dynamics at the Water−Air Interface Using Differential Interference Contrast Microscopy

Understanding the dynamics of the nanoparticle (NP) self-assembly process is very important for both fundamental and applied research of functional nanomaterials. In this report, high-contrast differential interference contrast microscopy was used for real time observation of evaporation-mediated self-assembly of gold nanoparticles (GNPs) at the water−air (w/a) interface. GNPs were found to be trapped at the w/a interface and gradually assembled into clusters. The dynamic cluster formation process was driven by evaporation-induced electrostatic repulsion decrease and can be divided into two stages. During the whole period, individual particles moved in random patterns that were indistinguishable from those produced by computer simulation of two-dimensional random walk, but interactions with surrounding particles and clusters caused a more directional flow motion. The observed dynamics of GNP cluster formation is more like the reaction-limited cluster formation model where the sticking probability is less ...

SecLEACH—On the security of clustered sensor networks

Clustered sensor networks have recently been shown to increase system throughput, decrease system delay, and save energy while performing data aggregation. Whereas those with rotating cluster heads, such as LEACH (low-energy adaptive clustering hierarchy), have also advantages in terms of security, the dynamic nature of their communication makes most existing security solutions inadequate for them. In this paper, we investigate the problem of adding security to hierarchical (cluster-based) sensor networks where clusters are formed dynamically and periodically, such as LEACH. For this purpose, we show how random key predistribution, widely studied in the context of flat networks, and μ TESLA , a building block from SPINS, can be both used to secure communications in this type of network. We present our solution, and provide a detailed analysis of how different values for the various parameters in such a system impact a hierarchical network in terms of security and energy efficiency. To the best of our knowledge, ours is the first that investigates security in hierarchical WSNs with dynamic cluster formation.

Evaluating EMMS Model for Simulating High Solid Flux Risers

Gas–solid flows in high solid flux risers exhibit dynamic formation of clusters of solid particles. This work attempts to understand and investigate the influence of formation of such clusters on effective drag between gas and solid phases using the energy minimization multi scale (EMMS) model. Unlike previous works on EMMS, the model is investigated outside the CFD domain and predictions were compared with the experimental data for risers and downers. The predicted drag coefficient from the EMMS approach was evaluated for its sensitivity with respect to model parameters. Though overall picture postulated in EMMS looks promising, the critical examination of EMMS for simulating gas solid flows reveal some limitations of the EMMS model. The minimum energy consumption was obtained at lowest possible of cluster voidage, arbitrarily assumed in the model simulation. The cluster voidage significantly affected the predicted drag coefficient. Possible ways to minimize or eliminate some of the limitations were also discussed. The results presented in this work will provide a useful basis for further improvements in the EMMS framework and for further work on gas–solid flows.

Dynamic structure and cluster formation in confined nanofluids under the action of an external force field

The dynamic structure and the formation of clusters in nanoparticle colloidal solutions (nanofluids) confined between two parallel walls and submitted to the action of an external force field is studied by extensive Brownian-dynamics simulations. The self-correlation of individual particles and the time correlation between distinct particles are analyzed by calculating the density-density time correlation (van Hove) function. It is shown that the self-diffusion is reduced by the external force field while the lifetime of collective modes of nanoparticles (i.e., natural phonons) is significantly enhanced by this force. We demonstrate that this result is related to disorder-order transitions in the nanoparticle spatial distribution under perturbation. Interestingly, we highlight that the interaction forces mediated by the walls act like repulsive interparticle forces. They tend to increase the structural disorder and to lower the lifetime of collective modes. Our results suggest that the heat transport properties of nanofluids could be actively controlled in nanometer-size systems.

Dynamic self-organization in particle-laden channel flow

We study dynamic flow-structuring and mean-flow properties of turbulent particle-laden riser-flow at significant particle volume fractions of about 1.5%. We include particle–particle as well as particle–fluid interactions through inelastic collisions and drag forces, in a so-called four-way coupled description. These interactions are the origin for the emergence of coherent particle swarms in a flow. The dynamic cluster-formation and cluster-disintegration are associated with the competition between turbulent dispersion and inelastic particle collisions. We establish the basic scenario of this self-organization and investigate the dominant mean-flow aspects of the resulting turbulence modulation for particles with high Stokes response-time. Large-eddy simulations of turbulent channel flow, using dynamic subgrid models and particles at a significant volume fraction and realistic mass load are presented. These simulations indicate the development of a thinner boundary layer, a flatter velocity profile, an higher effective Von Kármán constant and an accumulation of particles near the walls. Moreover, it was found that neglecting particle–particle interactions, as done in so-called two-way coupling, leads to a modulated flow which displays a strong ‘center-channel-jet’ that is not found in physical experiments.

Dynamic cluster formation using level set methods

Density-based clustering has the advantages for 1) allowing arbitrary shape of cluster and 2) not requiring the number of clusters as input. However, when clusters touch each other, both the cluster centers and cluster boundaries (as the peaks and valleys of the density distribution) become fuzzy and difficult to determine. We introduce the notion of cluster intensity function (CIF) which captures the important characteristics of clusters. When clusters are well-separated, CIFs are similar to density functions. But, when clusters become closed to each other, CIFs still clearly reveal cluster centers, cluster boundaries, and degree of membership of each data point to the cluster that it belongs. Clustering through bump hunting and valley seeking based on these functions are more robust than that based on density functions obtained by kernel density estimation, which are often oscillatory or oversmoothed. These problems of kernel density estimation are resolved using Level Set Methods and related techniques. Comparisons with two existing density-based methods, valley seeking and DBSCAN, are presented which illustrate the advantages of our approach.

Synchronization and clustering in electroencephalographic signals

Abstract Two order parameters introduced in the context of coupled chaotic systems subject to external noise are employed to measure the degrees of synchronization and dynamical cluster formation in electroencephalographic (EEG) signals. These parameters are calculated in EEG signals from a group of healthy subjects and from a group of epileptic patients, including a patient experiencing an epileptic crisis. The evolution of these parameters show the occurrence of intermittent synchronization and clustering in the brain activity during an epileptic crisis. Significantly, the existence of an instantaneous maximum of synchronization previous to the onset of a crisis is revealed by this procedure. The mean values of the order parameters and their standard deviations are compared between both groups of individuals.

CFD simulation of concurrent-up gas–solid flow in circulating fluidized beds with structure-dependent drag coefficient

Meso-scale structure existing in the form of particle clusters or strands in concurrent-up gas–solid two-phase flow has been extensively corroborated in experimental research. However, its significant effects on interfacial drag coefficient are seldom taken into account in current computational fluid dynamic (CFD) simulations by using the two-fluid models. The energy-minimization multi-scale (EMMS) approach, in which the heterogeneous structure is described by the so-called multi-scale resolution and energy-minimization method, is adapted in this study for investigating the dependence of drag coefficient on structure parameters. The structure-dependent drag coefficients calculated from the EMMS approach are then incorporated into the two-fluid model to simulate the behavior of the concurrent-up gas–solid flow in a riser. Simulation results indicate that the simulated solid concentration with the Wen and Yu/Ergun drag correlations is rather dilute, leading to a more homogenous structure; while the dynamic formation and dissolution of clusters can be captured with the drag correlations derived from the EMMS approach, and the simulated outlet solid flux and voidage profile in both radial and axial directions are in reasonable agreement with experimental results, suggesting the feasibility for the EMMS approach to be used as a sub-grid closure law for drag coefficient.

Animation of Soap Bubble Dynamics, Cluster Formation and Collision

What is happening when a soap bubble floats on the air? How do bubbles coalesce to form beautiful three-dimensional clusters? The physical-based model and animation described herein provide the answers. This paper deals with a complete computer simulation of soap bubbles from a dynamic perspective, which should prove to be of great interest to physicists and mathematicians. We discuss the dynamic formation of irregular bubble clusters and how to animate bubbles. The resulting model takes into account surface tension, film elasticity, and shape variations due to gravity and external wind forces.

Anomalous rotational dynamics of NH4 ions in the paraelectric phase of K1-x(NH4)xH2PO4 mixed crystals

A study of the rotational dynamics of NH4 ions in the paraelectric phase of mixed crystals of K1-x(NH4)xH2PO4 by quasielectric neutron scattering is reported. For high NH4 concentrations (x=0.9) no anomalous behaviour was found and the model of NH4 ion jumps between equivalent orientations in the crystal gave a good description of the experimental data. In contrast the crystal with x=0.6, which forms a protonic dipolar glass state at low temperatures, revealed an unusual temperature dependence of the elastic incoherent structure factor far above the glass formation boundary. This temperature dependence is analysed in the framework of the model of dynamical cluster formation in the paraelectric phase. The order parameter for the gradually condensing NH4 groups is obtained. The results are compared with data obtained by other methods on related compounds.

On the equilibrium vibrational renewal process: Dynamics of liquid crystal media by spectral profile analysis of probe oscillators

We discuss here the distribution of the rapid time-dependent dynamics of the intermolecular potential in the liquid of 4-n-nonyl-4′-cyanobiphenyl (9-CB) in the temperature range 328–473 K through numerical Fourier transformation of the isotropic Raman profile of the CN stretching fundamental (Linear Response Theory). We consider the stochastic fluctuations of the intermolecular potential, coupling to the oscillator coordinate, to represent an equilibrium vibrational renewal process in terms of many independent, parallel relaxation pathways in the amorphous medium. The results predict persistence of glassy characteristics even to relatively high temperatures in the macroscopically isotropic liquid: Typical ranges of the relaxation times of the potential fluctuations of the liquid crystal medium stretch over 1–11 ps at 328 K but narrow to 0.50–2 ps at 473 K, reflecting thereby the persistence of dynamical molecular cluster formation at the clarification point and their gradual dissolution at kinetic energies but far above. The values of the most probable relaxation rates in the medium correspond to frequencies of 8 (328 K) and 33 (473 K) cm −1, which puts them into the domain of hindered inter- and intramolecular segmental-skeletal motions.

On the nature of high-Tc superconductor metallic reflectivity

A novel interpretation of the distinctive features of metallic reflection in normal-state high-Tc superconducting crystals is presented. It is based on the fact that doping of the parent compounds inevitably leads to separation of the crystal bulk into dielectric and metallic phases, i.e. to bulk inhomogeneity. Since metallic clusters maybe less than 1 mu m in size, it is their low dimensionality that permits an adequate description of the optical properties of high-Tc samples. The author has assumed that inhomogeneity arises primarily from 'electronic phase separation'. In real space it manifests itself in the formation of dynamic clusters bunching up free holes. A piece of a cuprate layer containing one isolated hole may be regarded as the most extreme instance of such a cluster. Electronic excitations of dynamic clusters in the near infrared are treated as precursors of free carrier intraband transitions taking place within the metallic non-superconducting phase formed under heavy doping.

Self-diffusion of polystyrene in solution 1. Experimental results of the NMR pulsed field gradient technique

We report self-diffusion measurements for polystyrene dissolved in benzene and chloroform using the NMR pulsed field gradient technique. The observed echo attenuations point to dynamic exchange processes or cluster formation in the semidilute solution. The experimental results are compared with theoretical predictions from the reptation mechanism and the ‘blob’ theory. There is qualitative agreement, but a more comprehensive analysis of the data and results from experiments with polymer mixtures show that polymer self diffusion in semidilute solutions cannot be explained by the reptation mechanism in its simple form.

Evidence for precursor clusters associated with structural phase transitions in antifluorite crystals

Measurements of the temperature dependence of the intensities of the halogen nuclear quadrupole resonances in K2PtBr6 and K2ReCl6, in the cubic phase are reported. These results provide indirect evidence for the formation of dynamic clusters of the low symmetry phase as a precursor to the occurrence of rotative type phase transitions to tetragonal structures in these crystals.