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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.

Great Barrier Reef

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.

NASA Discipline Number 28-20

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.

Frick, Kinsey [Fish Ecology Division, Northwest Fi

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.

Science & Technology - Other Topics

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.

Microbiology

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.

Taneyeva, G. V.

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.

Montufar-Solis, Dina

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.

Message-based System

Progress on the Organic and Inorganic Modules of the Spacecraft Water Impurity Monitor, a Next Generation Complete Water Analysis System for Crewed Vehicles

The Spacecraft Water Impurity Monitor (SWIM) is a joint collaboration to develop an instrument platform that will perform in-flight measurements and deliver a more complete picture of water quality to decision makers. For exploration missions, returned water samples will not be an option, so spacecraft and habitats will need to be equipped with advanced water monitoring capabilities. Eventually, missions to the moon, Mars, and beyond should be equipped with analytical capabilities roughly analogous to those found in terrestrial labs. Based on what we know about current and future spacecraft environments, SWIM will seek to provide enhanced analytical capability that enables NASA to confidently send astronauts on distant missions without the possibility of returned water samples. The SWIM architecture can be broken down in an Organic Water Module (OWM) and an Inorganic Water Module (IWM), independent of each other but can be flown together if desired; an integrated system may share some commonality, e.g., single sample injection, sampling consumables, waste, etc. Each of these main modules can be broken down further into separation (if required) and detection modules. And, each separation module can be paired with one or more detection module depending on mission, spacecraft, customer needs, and size/mass/power constraints. This paper discusses the research and development progress toward the goal of a total water analysis system. For OWM, one of the analysis technologies that the SWIM team have been developing is a liquid-injection gas chromatograph mass spectrometer system; these systems are the workhorses of analytical chemistry laboratories world-wide. For IWM, the team is exploring a number of technologies ranging from traditional liquid chromatography technologies (e.g. ion chromatography, capillary electrophoresis) to flight-heritage technology such as ion-specific electrodes.

Stuart J Pensinger

Progress on the Organic and Inorganic Modules of the Spacecraft Water Impurity Monitor, a Next Generation Complete Water Analysis System for Crewed Vehicles

The Spacecraft Water Impurity Monitor (SWIM) is a joint collaboration to develop an instrument platform that will perform in-flight measurements and deliver a more complete picture of water quality to decision makers. For exploration missions, returned water samples will not be an option, so spacecraft and habitats will need to be equipped with advanced water monitoring capabilities. Eventually, missions to the moon, Mars, and beyond should be equipped with analytical capabilities roughly analogous to those found in terrestrial labs. Based on what we know about current and future spacecraft environments, SWIM will seek to provide enhanced analytical capability that enables NASA to confidently send astronauts on distant missions without the possibility of returned water samples. The SWIM architecture can be broken down in an Organic Water Module (OWM) and an Inorganic Water Module (IWM), independent of each other but can be flown together if desired; an integrated system may share some commonality, e.g., single sample injection, sampling consumables, waste, etc. Each of these main modules can be broken down further into separation (if required) and detection modules. And, each separation module can be paired with one or more detection module depending on mission, spacecraft, customer needs, and size/mass/power constraints. This paper discusses the research and development progress toward the goal of a total water analysis system. For OWM, one of the analysis technologies that the SWIM team have been developing is a liquid-injection gas chromatograph mass spectrometer system; these systems are the workhorses of analytical chemistry laboratories world-wide. For IWM, the team is exploring a number of technologies ranging from traditional liquid chromatography technologies (e.g. ion chromatography, capillary electrophoresis) to flight-heritage technology such as ion-specific electrodes.

Stuart J. Pensinger

Progress on the Organic and Inorganic Modules of the Spacecraft Water Impurity Monitor, a Next Generation Complete Water Analysis System for Crewed Vehicles

The Spacecraft Water Impurity Monitor (SWIM) is a joint collaboration to develop an instrument platform that will perform in-flight measurements and deliver a more complete picture of water quality to decision makers. For exploration missions, returned water samples will not be an option, so spacecraft and habitats will need to be equipped with advanced water monitoring capabilities. Eventually, missions to the moon, Mars, and beyond should be equipped with analytical capabilities roughly analogous to those found in terrestrial labs. Based on what we know about current and future spacecraft environments, SWIM will seek to provide enhanced analytical capability that enables NASA to confidently send astronauts on distant missions without the possibility of returned water samples. The SWIM architecture can be broken down in an Organic Water Module (OWM) and an Inorganic Water Module (IWM), independent of each other but can be flown together if desired; an integrated system may share some commonality, e.g., single sample injection, sampling consumables, waste, etc. Each of these main modules can be broken down further into separation (if required) and detection modules. And, each separation module can be paired with one or more detection module depending on mission, spacecraft, customer needs, and size/mass/power constraints. This paper discusses the research and development progress toward the goal of a total water analysis system. For OWM, one of the analysis technologies that the SWIM team have been developing is a liquid-injection gas chromatograph mass spectrometer system; these systems are the workhorses of analytical chemistry laboratories world-wide. For IWM, the team is exploring a number of technologies ranging from traditional liquid chromatography technologies (e.g. ion chromatography, capillary electrophoresis) to flight-heritage technology such as ion-specific electrodes.

Stuart J Pensinger

Progress on the Organic and Inorganic Modules of the Spacecraft Water Impurity Monitor, a Next Generation Complete Water Analysis System for Crewed Vehicles

The Spacecraft Water Impurity Monitor (SWIM) is a joint collaboration to develop an instrument platform that will perform in-flight measurements and deliver a more complete picture of water quality to decision makers. For exploration missions, returned water samples will not be an option, so spacecraft and habitats will need to be equipped with advanced water monitoring capabilities. Eventually, missions to the moon, Mars, and beyond should be equipped with analytical capabilities roughly analogous to those found in terrestrial labs. Based on what we know about current and future spacecraft environments, SWIM will seek to provide enhanced analytical capability that enables NASA to confidently send astronauts on distant missions without the possibility of returned water samples. The SWIM architecture can be broken down in an Organic Water Module (OWM) and an Inorganic Water Module (IWM), independent of each other but can be flown together if desired; an integrated system may share some commonality, e.g., single sample injection, sampling consumables, waste, etc. Each of these main modules can be broken down further into separation (if required) and detection modules. And, each separation module can be paired with one or more detection module depending on mission, spacecraft, customer needs, and size/mass/power constraints. This paper discusses the research and development progress toward the goal of a total water analysis system. For OWM, one of the analysis technologies that the SWIM team have been developing is a liquid-injection gas chromatograph mass spectrometer system; these systems are the workhorses of analytical chemistry laboratories world-wide. For IWM, the team is exploring a number of technologies ranging from traditional liquid chromatography technologies (e.g. ion chromatography, capillary electrophoresis) to flight-heritage technology such as ion-specific electrodes.

Stuart Pensinger

Changes in gravity influence rat postnatal motor system development: from simulation to space flight

Our research examines the role of the environment in postnatal nervous system development. Recently we have been studying the effects of changes in gravity on the motor system of rats from postnatal day (P) 2 to 31 using kinematic analysis of swimming, walking, and righting reflexes. Using the tail suspension model of weightlessness we identified sensitive and critical periods of motor system development corresponding to the time during which a motor skill is first achieved. Motor performance in suspended animals was marked by slow swimming, walking, and air-righting, all of which were characterized by hindlimb extension. (Walton et al, Neurosci. 52,763,1992). The critical periods identified in these studies contributed to determining the age of animals for a small payload, NIH.R3. This 9-day mission (STS-72) included 2 litters at P5, P7, or P15 at launch. The P7-16 and P15-24 groups were studied post-flight. On the landing day (R+0) surface righting, swimming and walking were slower in flight compared to control animals. Differences were more marked in the younger animals and the hindlimbs were more affected than the forelimbs with marked, prolonged extension of, at least, the ankle joint angle. Readaptation to 1G was slower in the P7-16 group with righting reflexes adapting first, walking last. We have shown that gravity is an important factor in postnatal nervous system development and that its affect depends on the age of the animal, duration of the perturbation, and the motor function studied.

Non-NASA Center

Killifish Hatching and Orientation experiment MA-161

The killifish Fundulus heteroclitus was used as a model system for study of embryonic development and vestibular adaptation in orbital flight. Juvenile fish in a zero gravity environment exhibited looping swimming activity similar to that observed during the Skylab 3 mission. Hatchings from a 336 hour egg stage were also observed to loop. At splashdown, both juveniles and hatchings exhibited a typical diving response suggesting relatively normal vestibular function. Juveniles exhibited swimming patterns suggestive of abnormal swim bladders. The embryos exhibited no abnormalities resulting from development in a zero gravity environment.

H W Scheld

Gravity receptors in a microcrustacean water flea - Sensitivity of antennal-socket setae in Daphnia magna

Gravity receptors of Dephnia magna were discovered on the basal segment of the swimming antennae and were shown to respond to upward water currents that pass the animal as it sinks between swimming strokes. Sensitivity of the gravity perceiving mechanism was tested by subjecting daphnids to a series of five decreasingly dense aqueous solutions (neutral density to water) in darkness (to avoid visual cues). Three-dimensional, video analysis of body position (pitch, yaw and roll) and swimming path (hop and sink, vertical and horizontal patterns) revealed a gradual threshold that occurred near a density difference between the animal and its environment of less than 0.25%. Because daphnids do not sink but continue to slide after stroking in the increased density solutions, gravity perception appears to occur during a vertical swing of the longitudinal body axis to the vertical plane, about their center of gravity, and, thereby, implies a multidirectional sensitivity for the antennal-socket setae.

Meyers, D. G.

Ring Bubbles of Dolphins

The article discusses how dolphins create and play with three types of air-filled vortices. The underlying physics is discussed. Photographs and sketches illustrating the dolphin's actions and physics are presented. The dolphins engage in this behavior on their own initiative without food reward. These behaviors are done repeatedly and with singleminded effort. The first type is the ejection of bubbles which, after some practice on the part of the dolphin, turn into toroidal vortex ring bubbles by the mechanism of baroclinic torque. These bubbles grow in radius and become thinner as they rise vertically to the surface. One dolphin would blow two in succession and guide them to fuse into one. Physicists call this a vortex reconnection. In the second type, the dolphins first create an invisible vortex ring in the water by swimming on their side and waving their tail fin (also called flukes) vigorously. This vortex ring travels horizontally in the water. The dolphin then turns around, finds the vortex and injects a stream of air into it from its blowhole. The air "fills-out" the core of the vortex ring. Often, the dolphin would knock-off a smaller ring bubble from the larger ring (this also involves vortex reconnection) and steer the smaller ring around the tank. One other dolphin employed a few other techniques for planting air into the fluke vortex. One technique included standing vertically in the water with tail-up, head-down and tail piercing the free surface. As the fluke is waved to create the vortex ring, air is entrained from above the surface. Another technique was gulping air in the mouth, diving down, releasing air bubbles from the mouth and curling them into a ring when they rose to the level of the fluke. In the third type, demonstrated by only one dolphin, the longitudinal vortex created by the dorsal fin on the back is used to produce 10-15 foot long helical bubbles. In one technique she swims in a curved path. This creates a dorsal fin vortex since centrifugal force has to be balanced by a lift-like force. She then re-traces her path and injects air into the vortex from her blowhole. She can even make a ring reconnect from the helix. In the second technique, demonstrated a few times, she again swims in a curved path, releases a cloud or group of bubbles from her blowhole and turns sharply away (Which presumably strengthens the vortex). As the bubbles encounter the vortex, they travel to the center of the vortex, merge and, in a flash, elongate along the core of the vortex. In all the three types, the air-water interface is shiny smooth and stable because the pressure gradient in the vortex flow around the bubble stabilizes it. A lot of the interesting physics still remains to be explored.

Shariff, Karim

Detection of Directions of Gravity by Organisms and Contributions to SmaggIce

Research covers the following: In the Microgravity Environment and Telescience Branch, a study wasI extended thar focused upon a flagellated alga or other swimming microbe and the effect of gravity upon its swimming direction. It has long been known that many organisms tend to swim up or down on Earth. How organisms detect the direction of gravity is a question not fully resolved. The response of such organisms to reduced gravity or the absence of gravity is also of interest, particularly because the expected modified behavior may affect the health of astronauts.

Dill, Loren H.

Consumption, supply and transport: self-organization without direct communication

Swimming bacteria of the species Bacillus subtilis require and consume oxygen. In static liquid cultures the cells' swimming behaviour leads them to accumulate up oxygen concentration gradients generated by consumption and supply. Since the density of bacterial cells exceeds that of the fluid in which they live, fluid regions where cells have accumulated are denser than depleted regions. These density variations cause convection. The fluid motion is dynamically maintained by the swimming of the cells toward regions of attraction: the air-fluid interface and the fluctuating advecting attractors, gradients of oxygen concentration that are embedded in the convecting fluid. Because of the fluid dynamical conservation laws, these complex physical and biological factors generate patterns ordered over distances > 10000 bacterial cell diameters. The convection enhances long-range transport and mixing of oxygen, cells and extracellular products by orders of magnitude. Thus, through the interplay of physical and biological factors, a population of undifferentiated selfish cells creates functional dynamic patterns. Populations of bacteria that have organised themselves into regularly patterned regions of vigorous convection and varying cell concentration interact with their environment as if they were one purposeful, coherent multicellular individual. The mathematical and experimental ingredients of these remarkable phenomena are presented here.

Non-NASA Center