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Chesapeake Bay Water Resources: Using Earth Observations to Assess Spatial and Social Disparities in Water Quality Trends Shaping Fishing and Swimming Access in the Chesapeake Bay
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SWIM -- Sensing with Independent Micro-swimmers
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Active doping controls the mode of failure in dense colloidal gels
Mechanical properties of disordered materials are governed by their underlying free energy landscape. In contrast to external fields, embedding a small fraction of active particles within a disordered material generates nonequilibrium internal fields, which can help to circumvent kinetic barriers and modulate the free energy landscape. In this work, we investigate through computer simulations how the activity of active particles alters the mechanical response of deeply annealed polydisperse colloidal gels. We show that the “swim force” generated by the embedded active particles is responsible for determining the mode of mechanical failure, i.e., brittle vs. ductile. We find, and theoretically justify, that at a critical swim force the mechanical properties of the gel decrease abruptly, signaling a change in the mode of mechanical failure. The weakening of the elastic modulus above the critical swim force results from the change in gel porosity and distribution of attractive forces among gel particles, while below the critical swim force, the ductility enhancement is caused by an increase of gel structural disorder. Above the critical swim force, the gel develops a pronounced heterogeneous structure characterized by multiple pore spaces, and the mechanical response is controlled by dynamical heterogeneities. We contrast these results with those of a simulated monodisperse gel that exhibits a nonmonotonic trend of ductility modulation with increasing swim force, revealing a complex interplay between the gel energy landscape and embedded activity.
Information Metacatalog for a Grid
SWIM is a Software Information Metacatalog that gathers detailed information about the software components and packages installed on a grid resource. Information is currently gathered for Executable and Linking Format (ELF) executables and shared libraries, Java classes, shell scripts, and Perl and Python modules. SWIM is built on top of the POUR framework, which is described in the preceding article. SWIM consists of a set of Perl modules for extracting software information from a system, an XML schema defining the format of data that can be added by users, and a POUR XML configuration file that describes how these elements are used to generate periodic, on-demand, and user-specified information. Periodic software information is derived mainly from the package managers used on each system. SWIM collects information from native package managers in FreeBSD, Solaris, and IRX as well as the RPM, Perl, and Python package managers on multiple platforms. Because not all software is available, or installed in package form, SWIM also crawls the set of relevant paths from the File System Hierarchy Standard that defines the standard file system structure used by all major UNIX distributions. Using these two techniques, the vast majority of software installed on a system can be located. SWIM computes the same information gathered by the periodic routines for specific files on specific hosts, and locates software on a system given only its name and type.
A Semianalytical Ocean Color Inversion Algorithm with Explicit Water Column Depth and Substrate Reflectance Parameterization
A semianalytical ocean color inversion algorithm was developed for improving retrievals of inherent optical properties (IOPs) in optically shallow waters. In clear, geometrically shallow waters, light reflected off the seafloor can contribute to the water-leaving radiance signal. This can have a confounding effect on ocean color algorithms developed for optically deep waters, leading to an overestimation of IOPs. The algorithm described here, the Shallow Water Inversion Model (SWIM), uses pre-existing knowledge of bathymetry and benthic substrate brightness to account for optically shallow effects. SWIM was incorporated into the NASA Ocean Biology Processing Group's L2GEN code and tested in waters of the Great Barrier Reef, Australia, using the Moderate Resolution Imaging Spectroradiometer (MODIS) Aqua time series (2002-2013). SWIM-derived values of the total non-water absorption coefficient at 443 nm, at(443), the particulate backscattering coefficient at 443 nm, bbp(443), and the diffuse attenuation coefficient at 488 nm, Kd(488), were compared with values derived using the Generalized Inherent Optical Properties algorithm (GIOP) and the Quasi-Analytical Algorithm (QAA). The results indicated that in clear, optically shallow waters SWIM-derived values of at(443), bbp(443), and Kd(443) were realistically lower than values derived using GIOP and QAA, in agreement with radiative transfer modeling. This signified that the benthic reflectance correction was performing as expected. However, in more optically complex waters, SWIM had difficulty converging to a solution, a likely consequence of internal IOP parameterizations. Whilst a comprehensive study of the SWIM algorithm's behavior was conducted, further work is needed to validate the algorithm using in situ data.
A single oscillating proto-hypothalamic neuron gates taxis behavior in the primitive chordate Ciona
Ciona larvae display a number of behaviors, including negative phototaxis. In negative phototaxis, the larvae first perform short spontaneous rhythmic casting swims. As larvae cast in a light field, their photoreceptors are directionally shaded by an associated pigment cell, providing a phototactic cue. This then evokes an extended negative taxis swim. We report here that the larval forebrain of Ciona has a previously uncharacterized single slow-oscillating inhibitory neuron (neuron cor-assBVIN78) that projects to the midbrain, where it targets key interneurons of the phototaxis circuit known as the photoreceptor relay neurons. The anatomical location, gene expression and oscillation of cor-assBVIN78 suggest homology to oscillating neurons of the vertebrate hypothalamus. Ablation of cor-assBVIN78 results in larvae showing extended phototaxis-like swims, but which occur in the absence of phototactic cues. These results indicate that cor-assBVIN78 has a gating activity on phototaxis by projecting temporally-oscillating inhibition to the photoreceptor relay neurons. However, in intact larvae the frequency of cor-assBVIN78 oscillation does not match that of the rhythmic spontaneous swims, indicating that the troughs in oscillations do not themselves initiate swims, but rather that cor-assBVIN78 may modulate the phototaxis circuit by filtering out low level inputs while restricting them temporally to the troughs in inhibition.
Transport barriers to self-propelled particles in fluid flows
Here, we present theory and experiments demonstrating the existence of invariant manifolds that impede the motion of microswimmers in two-dimensional fluid flows. One-way barriers are apparent in a hyperbolic fluid flow that block the swimming of both smooth-swimming and run-and-tumble Bacillus subtilis bacteria. We identify key phase-space structures, called swimming invariant manifolds (SwIMs), that serve as separatrices between different regions of long-time swimmer behavior. When projected into xy space, the edges of the SwIMs act as one-way barriers, consistent with the experiments.
Mutually promoting or constraining? Disentangling the superimposed effect of velocity and illuminance on fish motion in low-velocity flows with a novel metric
Global climate change, species invasion, and human activities such as the construction of hydraulic facilities are contributing to the worldwide degradation of fish stocks. As a pivotal environmental factor that affects fish migration and population distribution, low-velocity flow has not drawn enough attention despite its extensive presence in various ecoregions. Herein, to understand the behavioural profiles of fish in low-velocity flow, we examined the motility and swimming performance of two representative cyprinids, grass carp (GC, Ctenopharyngodon idella) and silver carp (SC, Hypophthalmichthys molitrix), under the combined effect of different flow velocities and illuminance ranges. The two species were exposed to two flow velocities (0.15 and 0.25 m/s) and three illuminance ranges (100.0 – 0.9 lx, 300.0 – 2.5 lx, and 700.0 – 4.9 lx). A novel behavioural metric, composed of light preference, cruising swimming speed, rheotaxis index (RI), swimming stability (SS), and the probability of moving forwards/backwards over a certain distance (PM f -0.1 and PM b -0.1), was developed to depict the motion strategy of fish fully. By investigating the individual distribution of the fish in light gradient, we confirmed the scototaxis of GC and found the oscillating light preference in SC that changed from 84.4 – 10.2 lx to 6.0 – 2.1 lx and disappeared with increasing illuminance. At the given velocities, the RI and SS increased in both species with a faster flow, and SC was more forward-prone and stable than GC. Despite its fluctuating light preference, the higher illuminances heightened the RI and SS in SC; while in GC, higher illuminances inhibited the SS and had no impact on the RI. The results of PM f -0.1 and PM b -0.1 indicated that a higher flow velocity could facilitate temporary upstream swimming in both species, while illuminance could promote the same effect in SC only. Finally, our study proposed possible moving manoeuvres in fine-scale spatio-temporal scenarios such as attraction flow and untraditional passages and provides valuable insights into fish community dynamics, laying the groundwork for alleviating the threat from invasive species and for future fish population recovery.
A new continuum model for suspensions of gyrotactic micro-organisms
A new continuum model is formulated for dilute suspensions of swimming micro-organisms with asymmetric mass distributions. Account is taken of randomness in a cell's swimming direction, p, by postulating that the probability density function for p satisfies a Fokker-Planck equation analogous to that obtained for colloid suspensions in the presence of rotational Brownian motion. The deterministic torques on a cell, viscous and gravitational, are balanced by diffusion, represented by an isotropic rotary diffusivity Dr, which is unknown a priori, but presumably reflects stochastic influences on the cell's internal workings. When the Fokker-Planck equation is solved, macroscopic quantities such as the average cell velocity Vc, the particle diffusivity tensor D and the effective stress tensor sigma can be computed; Vc and D are required in the cell conservation equation, and sigma in the momentum equation. The Fokker-Planck equation contains two dimensionless parameters, lambda and epsilon; lambda is the ratio of the rotary diffusion time Dr-1 to the torque relaxation time B (balancing gravitational and viscous torques), while epsilon is a scale for the local vorticity or strain rate made dimensionless with B. In this paper we solve the Fokker-Planck equation exactly for epsilon = 0 (lambda arbitrary) and also obtain the first-order solution for small epsilon. Using experimental data on Vc and D obtained with the swimming alga, Chlamydomonas nivalis, in the absence of bulk flow, the epsilon = 0 results can be used to estimate the value of lambda for that species (lambda approximately 2.2; Dr approximately 0.13 s-1). The continuum model for small epsilon is then used to reanalyse the instability of a uniform suspension, previously investigated by Pedley, Hill & Kessler (1988). The only qualitatively different result is that there no longer seem to be circumstances in which disturbances with a non-zero vertical wavenumber are more unstable than purely horizontal disturbances. On the way, it is demonstrated that the only significant contribution to sigma, other than the basic Newtonian stress, is that derived from the stresslets associated with the cells' intrinsic swimming motions.
Performance Comparisons for Artificially Propagated and Wild Pacific Lamprey Juveniles and Larvae
ABSTRACT Artificially propagated Pacific lamprey ( Entosphenus tridentatus ) are produced for restoration and for use in dam passage studies to reduce the demand for wild fish. Such uses require that animals are representative of their wild counterparts. Previous work indicated that this is true for Pacific lamprey larvae and juveniles reared in the hatchery with respect to the length of sustained swimming. However, more subtle differences in behaviour and performance that lamprey need to survive have not been assessed. In this study, artificially propagated and wild fish were compared in laboratory tests under no‐flow conditions to examine light avoidance, burrowing speed, burst swim speed, volitional routine swim speed and time to come to rest. Most larvae burrowed in less than a minute, and we found highly significant differences ( p < 0.001) between artificially propagated and wild larvae burrowing times, a critical escape behaviour. This could have implications for studies of larval entrainment at irrigation diversion canals or in turbine boils at dams. Interestingly, all of the wild juveniles tested came to rest quickly after introduction to the chamber (1.5 min), while artificially propagated lamprey swam robotically near the surface and 48% did not come to rest in the first 10 min (median time to rest = 9.5 min). In contrast, wild juveniles quickly (median = 1.47 min) sought areas near the tank bottom and attached strongly with their oral disc. Such behavioural differences could have important survival consequences for artificially propagated lamprey as they approach turbine intakes, bypass screens and irrigation diversion headgates. This study highlights the need to conduct behavioural assays that examine subtleties of fish behaviour that can be missed with traditional swim tunnel comparisons.
Autonomous phototaxis of hydrogel swimmers
The design of synthetic soft matter capable of emulating the complex behaviors of living organisms, such as sensing and adapting to their environment, remains an important challenge in developing biomimetic materials. Functionalized hydrogels are ideal candidates for such materials since they are highly responsive to their environment and can be operated in water. In this work, we investigate a hybrid bonding hydrogel composed of peptide amphiphile supramolecular nanofibers covalently attached to a photoresponsive network, in which high-aspect-ratio ferromagnetic nanowires are aligned along the length of the sample, designed to swim under oscillating magnetic fields. This hybrid hydrogel swimmer can autonomously swim toward a light source by utilizing photoinduced interactions between supramolecular and covalent networks reminiscent of phototactic swimming in living systems. Using a combination of experimental techniques and a continuum model incorporating photochemistry, magnetoelasticity, and hydrodynamics, we explain the swimming mechanism and predict phototactic behavior. Our work highlights the potential role of hybrid bonding polymers, which leverage the interplay between supramolecular assemblies and covalent networks. We demonstrate how these polymers can be tailored to react dynamically to their environment, paving the way for developing intelligent and autonomous robotic systems.
Design of nematic liquid crystals to control microscale dynamics
The dynamics of small particles, both living such as swimming bacteria and inanimate, such as colloidal spheres, has fascinated scientists for centuries. If one could learn how to control and streamline their chaotic motion, that would open technological opportunities in the transformation of stored or environmental energy into systematic motion, with applications in micro-robotics, transport of matter, guided morphogenesis. This review presents an approach to command microscale dynamics by replacing an isotropic medium with a liquid crystal. Orientational order and associated properties, such as elasticity, surface anchoring, and bulk anisotropy, enable new dynamic effects, ranging from the appearance and propagation of particle-like solitary waves to self-locomotion of an active droplet. By using photoalignment, the liquid crystal can be patterned into predesigned structures. In the presence of the electric field, these patterns enable the transport of solid and fluid particles through nonlinear electrokinetics rooted in anisotropy of conductivity and permittivity. Director patterns command the dynamics of swimming bacteria, guiding their trajectories, polarity of swimming, and distribution in space. This guidance is of a higher level of complexity than a simple following of the director by rod-like microorganisms. Namely, the director gradients mediate hydrodynamic interactions of bacteria to produce an active force and collective polar modes of swimming. The patterned director could also be engraved in a liquid crystal elastomer. When an elastomer coating is activated by heat or light, these patterns produce a deterministic surface topography. The director gradients define an activation force that shapes the elastomer in a manner similar to the active stresses triggering flows in active nematics. Finally, the patterned elastomer substrates could be used to define the orientation of cells in living tissues. The liquid-crystal guidance holds a major promise in achieving the goal of commanding microscale active flows.
Genome-wide identification of novel flagellar motility genes in Pseudomonas syringae pv. tomato DC3000
Pseudomonas syringaepv.tomatoDC3000 (PstDC3000) is a plant pathogenic bacterium that possesses complicated motility regulation pathways including a typical chemotaxis system. A significant portion of our understanding about the genes functioning inPstDC3000 motility is based on comparison to other bacteria. This leaves uncertainty about whether gene functions are conserved, especially since specific regulatory modules can have opposite functions in sets ofPseudomonas. In this study, we used a competitive selection to enrich for mutants with altered swimming motility and used random barcode transposon-site sequencing (RB-TnSeq) to identify genes with significant roles in swimming motility. Besides many of the known or predicted chemotaxis and motility genes, our method identified PSPTO_0406 (dipA), PSPTO_1042 (chrR) and PSPTO_4229 (hypothetical protein) as novel motility regulators. PSPTO_0406 is a homolog ofdipA, a known cyclic di-GMP degrading enzyme inP. aeruginosa. PSPTO_1042 is part of an extracytoplasmic sensing system that controls gene expression in response to reactive oxygen species, suggesting that PSPTO_1042 may function as part of a mechanism that enablesPstDC3000 to alter motility when encountering oxidative stressors. PSPTO_4229 encodes a protein containing an HD-related output domain (HDOD), but with no previously identified functions. We found that deletion and overexpression of PSPTO_4229 both reduce swimming motility, suggesting that its function is sensitive to expression level. We used the overexpression phenotype to screen for nonsense and missense mutants of PSPTO_4229 that no longer reduce swimming motility and found a pair of conserved arginine residues that are necessary for motility suppression. Together these results provide a global perspective on regulatory and structural genes controlling flagellar motility inPstDC3000.
Dynamics of erythrocyte count, hemoglobin, and catalase activity in rat blood in hypokinesia, muscular activity and restoration
Tests were conducted to prove that muscular exertion (in this instance swimming) of different duration and intensity, as well as hypodynamia, result in an increase of hemoglobin and number of red blood cells in peripheral blood rats. Catalase activity increased with an increase in the duration of swimming, but only up to 6 hr; with 7-9 hr of swimming as well as in hypodynamia, catalase activity decreased. It was also observed that under hypodynamia as well as in 3, 5 and 6 hr exertion (swimming) the color index of blood decreased. Pressure chamber treatment (for 8 min each day for one week), alternating a 2 min negative pressure up to 35 mm Hg with 1 min positive pressure, increased the erythrocyte count and hemoglobin content.
Bioconvection in Cultures of the Calcifying Unicellular Alga Pleurochrysis Carterae
The unicellular, marine, calcifying alga P leurochiysis carterae--a model to study cell morphogenesis, cell polarity, calcification, gravitaxis, reproduction and development-- has extremely flexible culture requirements. Support studies for a flight experiment addressing cell motility suggested that cell density (cells/ml) affects cell movement in P. carterae cultures through the gradual establishment of bioconvection as the culture grows. To assess the effect of cell density on direction of the movement, without the effects of aging of the culture, swimming behavior was analyzed in aliquots from a series of dilutions obtained from a stock culture. Results showed that at low concentrations cells swim randomly. As the concentration increases, upswimming patterns overtake random swimming. Gradually, up and down movement patterns prevail, representative of bioconvection. This oriented swimming of P. carterae occurs in a wide range of concentrations, adding to the list of flexible requirements, in this case, cell concentration, to be used for spaceflight studies addressing cell motility and bioconvection in a unicellular model of biologically directed mineralization.
MESA: Message-Based System Analysis Using Runtime Verification
In this paper, we present a novel approach and framework for run-time verication of large, safety critical messaging systems. This work was motivated by verifying the System Wide Information Management (SWIM) project of the Federal Aviation Administration (FAA). SWIM provides live air traffic, site and weather data streams for the whole National Airspace System (NAS), which can easily amount to several hundred messages per second. Such safety critical systems cannot be instrumented, therefore, verification and monitoring has to happen using a nonintrusive approach, by connecting to a variety of network interfaces. Due to a large number of potential properties to check, the verification framework needs to support efficient formulation of properties with a suitable Domain Specific Language (DSL). Our approach is to utilize a distributed system that is geared towards connectivity and scalability and interface it at the message queue level to a powerful verification engine. We implemented our approach in the tool called MESA: Message-Based System Analysis, which leverages the open source projects RACE (Runtime for Airspace Concept Evaluation) and TraceContract. RACE is a platform for instantiating and running highly concurrent and distributed systems and enables connectivity to SWIM and scalability. TraceContract is a runtime verication tool that allows for checking traces against properties specified in a powerful DSL. We applied our approach to verify a SWIM service against several requirements.We found errors such as duplicate and out-of-order messages.