The collective dynamics of self-propelled particles

We propose a method for the dynamic simulation of a collection of self-propelled particles in a viscous Newtonian fluid. We restrict attention to particles whose size and velocity are small enough that the fluid motion is in the creeping flow regime. We propose a simple model for a self-propelled particle, and extended the Stokesian Dynamics method to conduct dynamic simulations of a collection of such particles. In our description, each particle is treated as a sphere with an orientation vector p, whose locomotion is driven by the action of a force dipole Sp of constant magnitude S0 at a point slightly displaced from its centre. To simplify the calculation, we place the dipole at the centre of the particle, and introduce a virtual propulsion force Fp to effect propulsion. The magnitude F0 of this force is proportional to S0. The directions of Sp and Fp are determined by p. In isolation, a self-propelled particle moves at a constant velocity u0 p, with the speed u0 determined by S0. When it coexists with many such particles, its hydrodynamic interaction with the other particles alters its velocity and, more importantly, its orientation. As a result, the motion of the particle is chaotic. Our simulations are not restricted to low particle concentration, as we implement the full hydrodynamic interactions between the particles, but we restrict the motion of particles to two dimensions to reduce computation. We have studied the statistical properties of a suspension of self-propelled particles for a range of the particle concentration, quantified by the area fraction φa. We find several interesting features in the microstructure and statistics. We find that particles tend to swim in clusters wherein they are in close proximity. Consequently, incorporating the finite size of the particles and the near-field hydrodynamic interactions is of the essence. There is a continuous process of breakage and formation of the clusters. We find that the distributions of particle velocity at low and high φa are qualitatively different; it is close to the normal distribution at high φa, in agreement with experimental measurements. The motion of the particles is diffusive at long time, and the self-diffusivity decreases with increasing φa. The pair correlation function shows a large anisotropic build-up near contact, which decays rapidly with separation. There is also an anisotropic orientation correlation near contact, which decays more slowly with separation. Movies are available with the online version of the paper.

Collective eigenstates of emission in an N-entity heterostructure and the evaluation of its Green tensors and self-energy components

Optical emission from emitters strongly interacting among themselves and also with other polarizable matter in close proximity has been approximated by emission from independent emitters. This is primarily due to our inability to evaluate the self-energy matrices and radiative properties of the collective eigenstates of emitters in heterogeneous ensembles. A method to evaluate self-energy matrices that is not limited by the geometry and material composition is presented to understand and exploit such collective excitations. Numerical evaluations using this method are used to highlight the significant differences between independent and the collective modes of emission in nanoscale heterostructures. A set of N Lorentz emitters and other polarizable entities is used to represent the coupled system of a generalized geometry in a volume integral approach. Closed form relations between the Green tensors of entity pairs in free space and their correspondents in a heterostructure are derived concisely. This is made possible for general geometries because the global matrices consisting of all free-space Green dyads are subject to conservation laws. The self-energy matrix can then be assembled using the evaluated Green tensors of the heterostructure, but a decomposition of its components into their radiative and nonradiative decay contributions is nontrivial. The relations to compute the observables of the eigenstates (such as quantum efficiency, power/energy of emission, radiative and nonradiative decay rates) are presented. A note on extension of this method to collective excitations, which also includes strong interactions with a surface in the near-field, is added. (C) 2014 Optical Society of America

Plasmon-mediated emergence of collective emission and enhanced quantum efficiency in quantum dot films

We present experimental and theoretical results on monolayer colloidal cadmium selenide quantum dot films embedded with tiny gold nanoparticles. By varying the density of the embedded gold nanoparticles, we were able to engineer a plasmon-mediated crossover from emission quenching to enhancement regime at interparticle distances for which only quenching of emission is expected. This crossover and a nonmonotonic variation of photoluminescence intensity and decay rate, in experiments, is explained in terms of a model for plasmon-mediated collective emission of quantum emitters which points to the emergence of a new regime in plasmon-exciton interactions. The presented methodology to achieve enhancement in optical quantum efficiency for optimal doping of gold nanoparticles in such ultrathin high-density quantum dot films can be beneficial for new-generation displays and photodetectors.

CREMOFAC- a database of chromatin remodeling factors

Motivation: Chromatin-remodeling is an important event in the eukaryotic nucleus rendering nucleosomal DNA accessible for various transaction processes. Remodeling Factors facilitate the dynamic nature of chromatin through participation of the collective action of (i) ATP and (ii) Non-ATP dependent factors. Considering the importance of these factors in eukaryotes, we have developed, CREMOFAC, a dedicated and frequently updated web-database for chromatin-remodeling factors.Results: The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways and phylogenetic relationships has also been covered. The development of CREMOFAC as a central repository for chromatin-remodeling factors and the absence of such a pre-existing database heighten its utility thus making its presence indispensable.

Propensity of formation of zipper architecture vs. Lincoln log arrangement in solvated molecular complexes of melamine with hydroxybenzoic acids

Molecular complexes of melamine with hydroxy and dihydroxybenzoic acids have been analyzed to assess the collective role of the hydroxyl (OH) and carboxyl (COOH) functionalities in the recognition process. In most cases, solvents of crystallization do play a major role in self-assembly and structure stabilization. Hydrated compounds generate linear chains of melamine molecules with acid molecules pendant resulting in a zipper architecture. However, anhydrous and solvated compounds generate tetrameric units consisting of melamine dimers together with acid molecules. These tetramers in turn interweave to form a Lincoln log arrangement in the crystal. The salt/co-crystal formation in these complexes cannot be predicted apriori on the basis of Delta pK(a) values as there exists a salt-to-co-crystal continuum.

A Bottom-Up Approach toward Fabrication of Ultrathin PbS Sheets

Two-dimensional (2D) sheets are currently in the spotlight of nanotechnology owing to high-performance device fabrication possibilities. Building a free-standing quantum sheet with controlled morphology is challenging when large planar geometry and ultranarrow thickness are simultaneously concerned. Coalescence of nanowires into large single-crystalline sheet is a promising approach leading to large, molecularly thick 2D sheets with controlled planar morphology. Here we report on a bottom-up approach to fabricate high-quality ultrathin 2D single crystalline sheets with well-defined rectangular morphology via collective coalescence of PbS nanowires. The ultrathin sheets are strictly rectangular with 1.8 nm thickness, 200-250 nm width, and 3-20 mu m length. The sheets show high electrical conductivity at room and cryogenic temperatures upon device fabrication. Density functional theory (DFT) calculations reveal that a single row of delocalized orbitals of a nanowire is gradually converted into several parallel conduction channels upon sheet formation, which enable superior in-plane carrier conduction.

Collective behavior with heterogeneous controllers

In this paper, we study the collective motion of individually controlled planar particles when they are coupled through heterogeneous controller gains. Two types of collective formations, synchronization and balancing, are described and analyzed under the influence of these heterogeneous controller gains. These formations are characterized by the motion of the centroid of the group of particles. In synchronized formation, the particles and their centroid move in a common direction, while in balanced formation the movement of particles possess a fixed location of the centroid. We show that, by selecting suitable controller gains, these formations can be controlled significantly to obtain not only a desired direction of motion but also a desired location of the centroid. We present the results for N-particles in synchronized formation, while in balanced formation our analysis is confined to two and three particles.

Kernelization complexity of possible winner and coalitional manipulation problems in voting

In the POSSIBLE WINNER problem in computational social choice theory, we are given a set of partial preferences and the question is whether a distinguished candidate could be made winner by extending the partial preferences to linear preferences. Previous work has provided, for many common voting rules, fixed parameter tractable algorithms for the POSSIBLE WINNER problem, with number of candidates as the parameter. However, the corresponding kernelization question is still open and in fact, has been mentioned as a key research challenge 10]. In this paper, we settle this open question for many common voting rules. We show that the POSSIBLE WINNER problem for maximin, Copeland, Bucklin, ranked pairs, and a class of scoring rules that includes the Borda voting rule does not admit a polynomial kernel with the number of candidates as the parameter. We show however that the COALITIONAL MANIPULATION problem which is an important special case of the POSSIBLE WINNER problem does admit a polynomial kernel for maximin, Copeland, ranked pairs, and a class of scoring rules that includes the Borda voting rule, when the number of manipulators is polynomial in the number of candidates. A significant conclusion of our work is that the POSSIBLE WINNER problem is harder than the COALITIONAL MANIPULATION problem since the COALITIONAL MANIPULATION problem admits a polynomial kernel whereas the POSSIBLE WINNER problem does not admit a polynomial kernel. (C) 2015 Elsevier B.V. All rights reserved.

Global lopsided instability in a purely stellar galactic disc

It is shown that pure exponential discs in spiral galaxies are capable of supporting slowly varying discrete global lopsided modes, which can explain the observed features of lopsidedness in the stellar discs. Using linearized fluid dynamical equations with the softened self-gravity and pressure of the perturbation as the collective effect, we derive self-consistently a quadratic eigenvalue equation for the lopsided perturbation in the galactic disc. On solving this, we find that the ground-state mode shows the observed characteristics of the lopsidedness in a galactic disc, namely the fractional Fourier amplitude A(1), increases smoothly with the radius. These lopsided patterns precess in the disc with a very slow pattern speed with no preferred sense of precession. We show that the lopsided modes in the stellar disc are long-lived because of a substantial reduction (approximately a factor of 10 compared to the local free precession rate) in the differential precession. The numerical solution of the equations shows that the groundstate lopsided modes are either very slowly precessing stationary normal mode oscillations of the disc or growing modes with a slow growth rate depending on the relative importance of the collective effect of the self-gravity. N-body simulations are performed to test the spontaneous growth of lopsidedness in a pure stellar disc. Both approaches are then compared and interpreted in terms of long-lived global m = 1 instabilities, with almost zero pattern speed.

Intrinsically disordered proteins and conformational noise Implications in cancer

Intrinsically disordered proteins, IDPs, are proteins that lack a rigid 3D structure under physiological conditions, at least in vitro. Despite the lack of structure, IDPs play important roles in biological processes and transition from disorder to order upon binding to their targets. With multiple conformational states and rapid conformational dynamics, they engage in myriad and often ``promiscuous'' interactions. These stochastic interactions between IDPs and their partners, defined here as conformational noise, is an inherent characteristic of IDP interactions. The collective effect of conformational noise is an ensemble of protein network configurations, from which the most suitable can be explored in response to perturbations, conferring protein networks with remarkable flexibility and resilience. Moreover, the ubiquitous presence of IDPs as transcriptional factors and, more generally, as hubs in protein networks, is indicative of their role in propagation of transcriptional (genetic) noise. As effectors of transcriptional and conformational noise, IDPs rewire protein networks and unmask latent interactions in response to perturbations. Thus, noise-driven activation of latent pathways could underlie state-switching events such as cellular transformation in cancer. To test this hypothesis, we created a model of a protein network with the topological characteristics of a cancer protein network and tested its response to a perturbation in presence of IDP hubs and conformational noise. Because numerous IDPs are found to be epigenetic modifiers and chromatin remodelers, we hypothesize that they could further channel noise into stable, heritable genotypic changes.

`Universal' recession curves and their geomorphological interpretation

The study of recession flows offers fundamental insights into basin hydrological processes and, in particular, into the collective behavior of the governing dominant subsurface flows and properties. We use here an existing geomorphological interpretation of recession dynamics, which links the exponent in the classic recession curve -dQ/dt - kQ(alpha) to the geometric properties of the time-varying drainage network to study the general properties of recession curves across a wide variety of river basins. In particular, we show how the parameter k depends on the initial soil moisture state of the basin and can be made to explicitly depend on an index discharge, representative of initial sub-subsurface storage. Through this framework we obtain a non-dimensional, event-independent, recession curve. We subsequently quantify the variability of k across different basins on the basis of their geometry, and, by rescaling, collapse curves from different events and basins to obtain a generalized, or `universal', recession curve. Finally, we analyze the resulting normalized recession curves and explain their universal characteristics, lending further support to the notion that the statistical properties of observed recession curves bear the signature of the geomorphological structure of the networks producing them. (C) 2014 Elsevier Ltd. All rights reserved.

Flocking at a distance in active granular matter

The self-organized motion of vast numbers of creatures in a single direction is a spectacular example of emergent order. Here, we recreate this phenomenon using actuated nonliving components. We report here that millimetre-sized tapered rods, rendered motile by contact with an underlying vibrated surface and interacting through a medium of spherical beads, undergo a phase transition to a state of spontaneous alignment of velocities and orientations above a threshold bead area fraction. Guided by a detailed simulation model, we construct an analytical theory of this flocking transition, with two ingredients: a moving rod drags beads; neighbouring rods reorient in the resulting flow like a weathercock in the wind. Theory and experiment agree on the structure of our phase diagram in the plane of rod and bead concentrations and power-law spatial correlations near the phase boundary. Our discovery suggests possible new mechanisms for the collective transport of particulate or cellular matter.

Crowd Flow Segmentation based on Motion Vectors in H.264 Compressed Domain

In this work, we have explored the prospect of segmenting crowd flow in H. 264 compressed videos by merely using motion vectors. The motion vectors are extracted by partially decoding the corresponding video sequence in the H. 264 compressed domain. The region of interest ie., crowd flow region is extracted and the motion vectors that spans the region of interest is preprocessed and a collective representation of the motion vectors for the entire video is obtained. The obtained motion vectors for the corresponding video is then clustered by using EM algorithm. Finally, the clusters which converges to a single flow are merged together based on the bhattacharya distance measure between the histogram of the of the orientation of the motion vectors at the boundaries of the clusters. We had implemented our proposed approach on the complex crowd flow dataset provided by 1] and compared our results by using Jaccard measure. Since we are performing crowd flow segmentation in the compressed domain using only motion vectors, our proposed approach performs much faster compared to other pixel domain counterparts still retaining better accuracy.