Transport of inertial particles by Lagrangian coherent structures : application to predator-prey interaction in jellyfish feeding

We use a dynamical systems approach to identify coherent structures from often chaotic motions of inertial particles in open flows. We show that particle Lagrangian coherent structures (pLCS) act as boundaries between regions in which particles have different kinematics. They provide direct geometric information about the motion of ensembles of inertial particles, which is helpful to understand their transport. As an application, we apply the methodology to a planktonic predator–prey system in which moon jellyfish Aurelia aurita uses its body motion to generate a flow that transports small plankton such as copepods to its vicinity for feeding. With the flow field generated by the jellyfish measured experimentally and the dynamics of plankton described by a modified Maxey–Riley equation, we use the pLCS to identify a capture region in which prey can be captured by the jellyfish. The properties of the pLCS and the capture region enable analysis of the effect of several physiological and mechanical parameters on the predator–prey interaction, such as prey size, escape force, predator perception, etc. The methods developed here are equally applicable to multiphase and granular flows, and can be generalized to any other particle equation of motion, e.g. equations governing the motion of reacting particles or charged particles

An overview of a Lagrangian method for analysis of animal wake dynamics

The fluid dynamic analysis of animal wakes is becoming increasingly popular in studies of animal swimming and flying, due in part to the development of quantitative flow visualization techniques such as digital particle imaging velocimetry (DPIV). In most studies, quasi-steady flow is assumed and the flow analysis is based on velocity and/or vorticity fields measured at a single time instant during the stroke cycle. The assumption of quasi-steady flow leads to neglect of unsteady (time-dependent) wake vortex added-mass effects, which can contribute significantly to the instantaneous locomotive forces. In this paper we review a Lagrangian approach recently introduced to determine unsteady wake vortex structure by tracking the trajectories of individual fluid particles in the flow, rather than by analyzing the velocity/vorticity fields at fixed locations and single instants in time as in the Eulerian perspective. Once the momentum of the wake vortex and its added mass are determined, the corresponding unsteady locomotive forces can be quantified. Unlike previous studies that estimated the time-averaged forces over the stroke cycle, this approach enables study of how instantaneous locomotive forces evolve over time. The utility of this method for analyses of DPIV velocity measurements is explored, with the goal of demonstrating its applicability to data that are typically available to investigators studying animal swimming and flying. The methods are equally applicable to computational fluid dynamics studies where velocity field calculations are available

The 'upstream wake' of swimming and flying animals and its correlation with propulsive efficiency

The interaction between swimming and flying animals and their fluid environments generates downstream wake structures such as vortices. In most studies, the upstream flow in front of the animal is neglected. In this study, we demonstrate the existence of upstream fluid structures even though the upstream flow is quiescent or possesses a uniform incoming velocity. Using a computational model, the flow generated by a swimmer (an oscillating flexible plate) is simulated and a new fluid mechanical analysis is applied to the flow to identify the upstream fluid structures. These upstream structures show the exact portion of fluid that is going to interact with the swimmer. A mass flow rate is then defined based on the upstream structures, and a metric for propulsive efficiency is established using the mass flow rate and the kinematics of the swimmer. We propose that the unsteady mass flow rate defined by the upstream fluid structures can be used as a metric to measure and objectively compare the efficiency of locomotion in water and air

Geometry of unsteady fluid transport during fluid–structure interactions

We describe the application of tools from dynamical systems to define and quantify the unsteady fluid transport that occurs during fluid–structure interactions and in unsteady recirculating flows. The properties of Lagrangian coherent structures (LCS) are used to enable analysis of flows with arbitrary time-dependence, thereby extending previous analytical results for steady and time-periodic flows. The LCS kinematics are used to formulate a unique, physically motivated definition for fluid exchange surfaces and transport lobes in the flow. The methods are applied to numerical simulations of two-dimensional flow past a circular cylinder at a Reynolds number of 200; and to measurements of a freely swimming organism, the Aurelia aurita jellyfish. The former flow provides a canonical system in which to compare the present geometrical analysis with classical, Eulerian (e.g. vortex shedding) perspectives of fluid–structure interactions. The latter flow is used to deduce the physical coupling that exists between mass and momentum transport during self-propulsion. In both cases, the present methods reveal a well-defined, unsteady recirculation zone that is not apparent in the corresponding velocity or vorticity fields. Transport rates between the ambient flow and the recirculation zone are computed for both flows. Comparison of fluid transport geometry for the cylinder crossflow and the self-propelled swimmer within the context of existing theory for two-dimensional lobe dynamics enables qualitative localization of flow three-dimensionality based on the planar measurements. Benefits and limitations of the implemented methods are discussed, and some potential applications for flow control, unsteady propulsion, and biological fluid dynamics are proposed

Assessing the Formation Scenarios for the Double Nucleus of M31 Using Two-Dimensional Image Decomposition

The double nucleus geometry of M31 is currently best explained by the eccentric disk hypothesis of Tremaine, but whether the eccentric disk resulted from the tidal disruption of an inbounding star cluster by a nuclear black hole, or by an m=1 perturbation of a native nuclear disk, remains debatable. I perform detailed 2-D decomposition of the M31 double nucleus in the Hubble Space Telescope V-band to study the bulge structure and to address competing formation scenarios of the eccentric disk. I deblend the double nucleus (P1 and P2) and the bulge simultaneously using five Sersic and one Nuker components. P1 and P2 appear to be embedded inside an intermediate component (r_e=3.2") that is nearly spherical (q=0.97+/-m0.02), while the main galaxy bulge is more elliptical (q=0.81+/-0.01). The spherical bulge mass of 2.8x10^7 M_sol is comparable to the supermassive black hole mass (3x10^7 M_sol). In the 2-D decomposition, the bulge is consistent with being centered near the UV peak of P2, but the exact position is difficult to pinpoint because of dust in the bulge. P1 and P2 are comparable in mass. Within a radius r=1\arcsec of P2, the relative mass fraction of the nuclear components is M_BH:M_bulge:P1: P2 = 4.3:1.2:1:0.7, assuming the luminous components have a common mass-to-light ratio of 5.7. The eccentric disk as a whole (P1+P2) is massive, M ~ 2.1x10^7 M_sol, comparable to the black hole and the local bulge mass. As such, the eccentric disk could not have been formed entirely out of stars that were stripped from an inbounding star cluster. Hence, the more favored scenario is that of a disk formed in situ by an m=1 perturbation, caused possibly by the passing of a giant molecular cloud, or the passing/accretion of a small globular cluster.Comment: 19 pages, 8 figures. AJ accepted. For the version of this paper with high resolution figures, go to: http://zwicky.as.arizona.edu/~cyp/work/m31.ps.g

Dimensionality Reduction in Deep Learning for Chest X-Ray Analysis of Lung Cancer

Efficiency of some dimensionality reduction techniques, like lung segmentation, bone shadow exclusion, and t-distributed stochastic neighbor embedding (t-SNE) for exclusion of outliers, is estimated for analysis of chest X-ray (CXR) 2D images by deep learning approach to help radiologists identify marks of lung cancer in CXR. Training and validation of the simple convolutional neural network (CNN) was performed on the open JSRT dataset (dataset #01), the JSRT after bone shadow exclusion - BSE-JSRT (dataset #02), JSRT after lung segmentation (dataset #03), BSE-JSRT after lung segmentation (dataset #04), and segmented BSE-JSRT after exclusion of outliers by t-SNE method (dataset #05). The results demonstrate that the pre-processed dataset obtained after lung segmentation, bone shadow exclusion, and filtering out the outliers by t-SNE (dataset #05) demonstrates the highest training rate and best accuracy in comparison to the other pre-processed datasets.Comment: 6 pages, 14 figure

Controlled generation of field squeezing with cold atomic clouds coupled to a superconducting transmission line resonator

We propose an efficient method for controlled generation of field squeezing with cold atomic clouds trapped close to a superconducting transmission line resonator. It is shown that, based on the coherent strong magnetic coupling between the collective atomic spins and microwave fields in the transmission line resonator, two-mode or single mode field squeezed states can be generated through coherent control on the dynamics of the system. The degree of squeezing and preparing time can be directly controlled through tuning the external classical fields. This protocol may offer a promising platform for implementing scalable on-chip quantum information processing with continuous variables.Comment: accepted by Phys. Rev.

Towards Quantitative Classification of Folded Proteins in Terms of Elementary Functions

A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a classification scheme that describes a protein starting from its well organized secondary structures and often involves direct human involvement, with an atomary level Physics based approach where a protein is fundamentally nothing more than an ensemble of mutually interacting carbon, hydrogen, oxygen and nitrogen atoms. In order to bridge these two complementary approaches to proteins, conceptually novel tools need to be introduced. Here we explain how the geometrical shape of entire folded proteins can be described analytically in terms of a single explicit elementary function that is familiar from nonlinear physical systems where it is known as the kink-soliton. Our approach enables the conversion of hierarchical structural information into a quantitative form that allows for a folded protein to be characterized in terms of a small number of global parameters that are in principle computable from atomary level considerations. As an example we describe in detail how the native fold of the myoglobin 1M6C emerges from a combination of kink-solitons with a very high atomary level accuracy. We also verify that our approach describes longer loops and loops connecting $\alpha$-helices with $\beta$-strands, with same overall accuracy.Comment: 3 figure

Atomistic study of electronic structure of PbSe nanowires

Lead Selenide (PbSe) is an attractive `IV-VI' semiconductor material to design optical sensors, lasers and thermoelectric devices. Improved fabrication of PbSe nanowires (NWs) enables the utilization of low dimensional quantum effects. The effect of cross-section size (W) and channel orientation on the bandstructure of PbSe NWs is studied using an 18 band $sp^3d^5$ tight-binding theory. The bandgap increases almost with the inverse of the W for all the orientations indicating a weak symmetry dependence. [111] and [110] NWs show higher ballistic conductance for the conduction and valence band compared to [100] NWs due to the significant splitting of the projected L-valleys in [100] NWs.Comment: 4 figures, Prepared for AP