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All sourcesNASA NTRSDOE OSTI
NASA NTRS2006

The 'Biologically-Inspired Computing' Column

The field of Biology changed dramatically in 1953, with the determination by Francis Crick and James Dewey Watson of the double helix structure of DNA. This discovery changed Biology for ever, allowing the sequencing of the human genome, and the emergence of a "new Biology" focused on DNA, genes, proteins, data, and search. Computational Biology and Bioinformatics heavily rely on computing to facilitate research into life and development. Simultaneously, an understanding of the biology of living organisms indicates a parallel with computing systems: molecules in living cells interact, grow, and transform according to the "program" dictated by DNA. Moreover, paradigms of Computing are emerging based on modelling and developing computer-based systems exploiting ideas that are observed in nature. This includes building into computer systems self-management and self-governance mechanisms that are inspired by the human body's autonomic nervous system, modelling evolutionary systems analogous to colonies of ants or other insects, and developing highly-efficient and highly-complex distributed systems from large numbers of (often quite simple) largely homogeneous components to reflect the behaviour of flocks of birds, swarms of bees, herds of animals, or schools of fish. This new field of "Biologically-Inspired Computing", often known in other incarnations by other names, such as: Autonomic Computing, Pervasive Computing, Organic Computing, Biomimetics, and Artificial Life, amongst others, is poised at the intersection of Computer Science, Engineering, Mathematics, and the Life Sciences. Successes have been reported in the fields of drug discovery, data communications, computer animation, control and command, exploration systems for space, undersea, and harsh environments, to name but a few, and augur much promise for future progress.

Hinchey, Mike↗
NASA NTRS2007

Two Devices for Removing Sludge From Bioreactor Wastewater

Two devices a magnetic separator and a special filter denoted a self-regenerating separator (SRS) have been developed for separating sludge from the stream of wastewater from a bioreactor. These devices were originally intended for use in microgravity, but have also been demonstrated to function in normal Earth gravity. The magnetic separator (see Figure 1) includes a thin-walled nonmagnetic, stainless-steel cylindrical drum that rotates within a cylindrical housing. The wastewater enters the separator through a recirculation inlet, and about 80 percent of the wastewater flow leaves through a recirculation outlet. Inside the drum, a magnet holder positions strong permanent magnets stationary and, except near a recirculation outlet, close to the inner drum surface. To enable magnetic separation, magnetite (a ferromagnetic and magnetically soft iron oxide) powder is mixed into the bioreactor wastewater. The magnetite becomes incorporated into the sludge by condensation, onto the powder particles, of microbe flocks that constitute the sludge. As a result, the magnets inside the drum magnetically attract the sludge onto the outer surface of the drum.

Archer, Shivaun↗
NASA NTRS2006

Controlling Herds of Cooperative Robots

A document poses, and suggests a program of research for answering, questions of how to achieve autonomous operation of herds of cooperative robots to be used in exploration and/or colonization of remote planets. In a typical scenario, a flock of mobile sensory robots would be deployed in a previously unexplored region, one of the robots would be designated the leader, and the leader would issue commands to move the robots to different locations or aim sensors at different targets to maximize scientific return. It would be necessary to provide for this hierarchical, cooperative behavior even in the face of such unpredictable factors as terrain obstacles. A potential-fields approach is proposed as a theoretical basis for developing methods of autonomous command and guidance of a herd. A survival-of-the-fittest approach is suggested as a theoretical basis for selection, mutation, and adaptation of a description of (1) the body, joints, sensors, actuators, and control computer of each robot, and (2) the connectivity of each robot with the rest of the herd, such that the herd could be regarded as consisting of a set of artificial creatures that evolve to adapt to a previously unknown environment. A distributed simulation environment has been developed to test the proposed approaches in the Titan environment. One blimp guides three surface sondes via a potential field approach. The results of the simulation demonstrate that the method used for control is feasible, even if significant uncertainty exists in the dynamics and environmental models, and that the control architecture provides the autonomy needed to enable surface science data collection.

Quadrelli, Marco B.↗
NASA NTRS2010

Particle Swarm Optimization Toolbox

The Particle Swarm Optimization Toolbox is a library of evolutionary optimization tools developed in the MATLAB environment. The algorithms contained in the library include a genetic algorithm (GA), a single-objective particle swarm optimizer (SOPSO), and a multi-objective particle swarm optimizer (MOPSO). Development focused on both the SOPSO and MOPSO. A GA was included mainly for comparison purposes, and the particle swarm optimizers appeared to perform better for a wide variety of optimization problems. All algorithms are capable of performing unconstrained and constrained optimization. The particle swarm optimizers are capable of performing single and multi-objective optimization. The SOPSO and MOPSO algorithms are based on swarming theory and bird-flocking patterns to search the trade space for the optimal solution or optimal trade in competing objectives. The MOPSO generates Pareto fronts for objectives that are in competition. A GA, based on Darwin evolutionary theory, is also included in the library. The GA consists of individuals that form a population in the design space. The population mates to form offspring at new locations in the design space. These offspring contain traits from both of the parents. The algorithm is based on this combination of traits from parents to hopefully provide an improved solution than either of the original parents. As the algorithm progresses, individuals that hold these optimal traits will emerge as the optimal solutions. Due to the generic design of all optimization algorithms, each algorithm interfaces with a user-supplied objective function. This function serves as a "black-box" to the optimizers in which the only purpose of this function is to evaluate solutions provided by the optimizers. Hence, the user-supplied function can be numerical simulations, analytical functions, etc., since the specific detail of this function is of no concern to the optimizer. These algorithms were originally developed to support entry trajectory and guidance design for the Mars Science Laboratory mission but may be applied to any optimization problem.

Grant, Michael J.↗
NASA NTRS2012

Applying Biomimetic Algorithms for Extra-Terrestrial Habitat Generation

The objective is to simulate and optimize distributed cooperation among a network of robots tasked with cooperative excavation on an extra-terrestrial surface. Additionally to examine the concept of directed Emergence among a group of limited artificially intelligent agents. Emergence is the concept of achieving complex results from very simple rules or interactions. For example, in a termite mound each individual termite does not carry a blueprint of how to make their home in a global sense, but their interactions based strictly on local desires create a complex superstructure. Leveraging this Emergence concept applied to a simulation of cooperative agents (robots) will allow an examination of the success of non-directed group strategy achieving specific results. Specifically the simulation will be a testbed to evaluate population based robotic exploration and cooperative strategies while leveraging the evolutionary teamwork approach in the face of uncertainty about the environment and partial loss of sensors. Checking against a cost function and 'social' constraints will optimize cooperation when excavating a simulated tunnel. Agents will act locally with non-local results. The rules by which the simulated robots interact will be optimized to the simplest possible for the desired result, leveraging Emergence. Sensor malfunction and line of sight issues will be incorporated into the simulation. This approach falls under Swarm Robotics, a subset of robot control concerned with finding ways to control large groups of robots. Swarm Robotics often contains biologically inspired approaches, research comes from social insect observation but also data from among groups of herding, schooling, and flocking animals. Biomimetic algorithms applied to manned space exploration is the method under consideration for further study.

Birge, Brian↗
NASA NTRS2015

Johnson Space Center's Free Range Bicycle Program.- Fall 2015 Intern Report

NASA's Johnson Space Center is a big place, encompassing 1,620 acres and more than a hundred buildings. Furthermore, there are reportedly 15 thousand employees, all of which have somewhere to be. To facilitate the movement of all these people JSC has historically relied on human power. Pedaling their way towards deep space, bicycles have been the go to method. Currently there are about 200 Free Range Bicycles at JSC. Free Range Bicycles belong to nobody, except NASA, and are available for anybody to use. They are not to be locked or hidden (although frequently are) and the intention is that there will always be a bike to hop on to get where you're going (although it may not be the bike you rode in on). Although not without its own shortcomings, the Free Range Bicycle Program has continued to provide low cost, simple transportation for NASA's JSC. In addition to the approximately 200 Free Range Bicycles, various larger divisions (like engineering) will often buy a few dozen bikes for their team members to use or individuals will bring their own personal bike to either commute or use on site. When these bicycles fall into disrepair or are abandoned (from retirees etc) they become a problem at JSC. They are an eye sore, create a safety hazard and make it harder to find a working bike in a time of need. The Free Range Program hopes to address this first problem by "tagging out" abandoned or out of service bicycles. A bright orange "DO NOT OPERATE" tag is placed on the bike and given a serial number for tracking purposes. See picture to the right. If the bike has an active owner with intentions to repair the bike the bottom of the tag has instructions for how to claim the abandoned bicycle. After being tagged the owner of the bicycle has 30 days to claim the bicycle and either haul it off site or get it repaired (and labeled) in accordance with Johnson's Bicycle Policy. If the abandoned bicycle is not claimed within 30 days it becomes the property of the Government. The bicycle is then (in short) repaired, labeled, documented and converted to a free range bicycle. Bikes beyond repair are cannibalized of useable parts and then scrapped. That was nearly the first thing I did when arriving at work. After getting settled in and coordinating the purchase of 50 new bicycles (elaboration below); I started combing the Center. Bikes are hidden and tucked away in the oddest of places and it was my priority to root all of them out. I tagged 70 bikes on the center, setting a record. I tagged so many bikes I ran out tags and had to make more. Long ago it was discovered that the same harsh elements that wreak havoc on the bikes, destroy the tags before the 30 day timeframe. The tags are labeled with instructions on how to claim the bike and numbered, then these paper labels are laminated with packing tape. It sounds like a simple process but nothing fits right, everything has to be trimmed, put on straight and is generally a pain in the neck. So I made an assembly process and knocked out a few hundred to save having to do it again for a while. I walked the center and tagged bikes at every building hiding in nearly every nook and cranny. Thus, in conclusion, I've done many things here at JSC on my first term and had a blast doing it. I've learned a lot from my multi-faceted roles and continual challenges. In short I've done my best to get folks at JSC on bikes and keep folks at JSC on bikes and tended a flock of free range bicycles. Everything from turning the rusty bolts and oiling chains to coordinating a $20,000 deal on 50 new free range bicycles. I am proud of the bicycle shop I have built and am infinitely grateful to the people who lead, help, guide and support me. I have fixed a great number of bicycles and cleaned the center of unsightly and unsafe piles of bicycles. I am immensely thankful for this opportunity to learn and serve and appreciate the privilege of coming back for a second term. A second term, in which I will continue to develop this awesome program.

Lee-Stockton, Willem↗
DOE OSTI2016

Wet scavenging of soluble gases in DC3 deep convective storms using WRF-Chem simulations and aircraft observations

In this work, we examine wet scavenging of soluble trace gases in storms observed during the Deep Convective Clouds and Chemistry (DC3) field campaign. We conduct high-resolution simulations with the Weather Research and Forecasting model with Chemistry (WRF-Chem) of a severe storm in Oklahoma. The model represents well the storm location, size, and structure as compared with Next Generation Weather Radar reflectivity, and simulated CO transport is consistent with aircraft observations. Scavenging efficiencies (SEs) between inflow and outflow of soluble species are calculated from aircraft measurements and model simulations. Using a simple wet scavenging scheme, we simulate the SE of each soluble species within the error bars of the observations. The simulated SEs of all species except nitric acid (HNO 3 ) are highly sensitive to the values specified for the fractions retained in ice when cloud water freezes. To reproduce the observations, we must assume zero ice retention for formaldehyde (CH 2 O) and hydrogen peroxide (H 2 O 2 ) and complete retention for methyl hydrogen peroxide (CH 3 OOH) and sulfur dioxide (SO 2 ), likely to compensate for the lack of aqueous chemistry in the model. We then compare scavenging efficiencies among storms that formed in Alabama and northeast Colorado and the Oklahoma storm. Significant differences in SEs are seen among storms and species. More scavenging of HNO 3 and less removal of CH 3 OOH are seen in storms with higher maximum flash rates, an indication of more graupel mass. Graupel is associated with mixed-phase scavenging and lightning production of nitrogen oxides (NOx ), processes that may explain the observed differences in HNO 3 and CH 3 OOH scavenging.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Numerical modeling of laser-driven experiments aiming to demonstrate magnetic field amplification via turbulent dynamo

The universe is permeated by magnetic fields, with strengths ranging from a femtogauss in the voids between the filaments of galaxy clusters to several teragauss in black holes and neutron stars. The standard model behind cosmological magnetic fields is the nonlinear amplification of seed fields via turbulent dynamo to the values observed. We have conceived experiments that aim to demonstrate and study the turbulent dynamo mechanism in the laboratory. Here, we describe the design of these experiments through simulation campaigns using FLASH, a highly capable radiation magnetohydrodynamics code that we have developed, and large-scale three-dimensional simulations on the Mira supercomputer at the Argonne National Laboratory. The simulation results indicate that the experimental platform may be capable of reaching a turbulent plasma state and determining the dynamo amplification. As a result, we validate and compare our numerical results with a small subset of experimental data using synthetic diagnostics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Entropy production fluctuations encode collective behavior in active matter

We derive a general lower bound on distributions of entropy production in interacting active matter systems. The bound is tight in the limit that interparticle correlations are small and short-ranged, which we explore in four canonical active matter models. In all models studied, the bound is weak where collective fluctuations result in long-ranged correlations, which subsequently links the locations of phase transitions to enhanced entropy production fluctuations. We develop a theory for the onset of enhanced fluctuations and relate it to specific phase transitions in active Brownian particles. Furthermore, we also derive optimal control forces that realize the dynamics necessary to tune dissipation and manipulate the system between phases. In so doing, we uncover a general relationship between entropy production and pattern formation in active matter, as well as ways of controlling it.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Confinement and Collective Escape of Active Particles

Active matter broadly covers the dynamics of self-propelled particles. While the onset of collective behavior in homogenous active systems is relatively well understood, the effect of inhomogeneities such as obstacles and traps lacks overall clarity. Here, we study how interacting, self-propelled particles become trapped and released from a trap. We have found that captured particles aggregate into an orbiting condensate with a crystalline structure. As more particles are added, the trapped condensates escape as a whole. Our results shed light on the effects of confinement and quenched disorder in active matter.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Generative Ensemble Regression: Learning Particle Dynamics from Observations of Ensembles with Physics-informed Deep Generative Models

Here, we propose a new method for inferring the governing stochastic ordinary differential equations (SODEs) by observing particle ensembles at discrete and sparse time instants, i.e., multiple “snapshots.” Particle coordinates at a single time instant, possibly noisy or truncated, are recorded in each snapshot but are unpaired across the snapshots. By training a physics-informed generative model that generates “fake” sample paths, we aim to fit the observed particle ensemble distributions with a curve in the probability measure space, which is induced from the inferred particle dynamics. We employ different metrics to quantify the differences between distributions, e.g., the sliced Wasserstein distances and the adversarial losses in generative adversarial networks. We refer to this method as generative “ensemble-regression” (GER), in analogy to the classic “point-regression,” where we infer the dynamics by performing regression in the Euclidean space. We illustrate the GER by learning the drift and diffusion terms of particle ensembles governed by SODEs with Brownian motions and Lévy processes up to 100 dimensions. We also discuss how to treat cases with noisy or truncated observations. Apart from systems consisting of independent particles, we also tackle nonlocal interacting particle systems with unknown interaction potential parameters by constructing a physics-informed loss function. Finally, we investigate scenarios of paired observations and discuss how to reduce the dimensionality in such cases by proving a convergence theorem that provides theoretical support.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

ON SHOCKS DRIVEN BY HIGH-MASS PLANETS IN RADIATIVELY INEFFICIENT DISKS. II. THREE-DIMENSIONAL GLOBAL DISK SIMULATIONS

Recent high-resolution, near-infrared images of protoplanetary disks have shown that these disks often present spiral features. Spiral arms are among the structures predicted by models of disk–planet interaction and thus it is tempting to suspect that planetary perturbers are responsible for these signatures. However, such interpretation is not free of problems. The observed spirals have large pitch angles, and in at least one case (HD 100546) it appears effectively unpolarized, implying thermal emission of the order of 1000 K (465 ± 40 K at closer inspection). We have recently shown in two-dimensional models that shock dissipation in the supersonic wake of high-mass planets can lead to significant heating if the disk is sufficiently adiabatic. Here we extend this analysis to three dimensions in thermodynamically evolving disks. We use the Pencil Code in spherical coordinates for our models, with a prescription for thermal cooling based on the optical depth of the local vertical gas column. We use a 5M{sub J} planet, and show that shocks in the region around the planet where the Lindblad resonances occur heat the gas to substantially higher temperatures than the ambient gas. The gas is accelerated vertically away from the midplane to form shock bores, and the gas falling back toward the midplane breaks up into a turbulent surf. This turbulence, although localized, has high α values, reaching 0.05 in the inner Lindblad resonance, and 0.1 in the outer one. We find evidence that the disk regions heated up by the shocks become superadiabatic, generating convection far from the planet’s orbit.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

RADIATION HYDRODYNAMICS MODELS OF THE INNER RIM IN PROTOPLANETARY DISKS

Many stars host planets orbiting within a few astronomical units (AU). The occurrence rate and distributions of masses and orbits vary greatly with the host star’s mass. These close planets’ origins are a mystery that motivates investigating protoplanetary disks’ central regions. A key factor governing the conditions near the star is the silicate sublimation front, which largely determines where the starlight is absorbed, and which is often called the inner rim. We present the first radiation hydrodynamical modeling of the sublimation front in the disks around the young intermediate-mass stars called Herbig Ae stars. The models are axisymmetric and include starlight heating; silicate grains sublimating and condensing to equilibrium at the local, time-dependent temperature and density; and accretion stresses parameterizing the results of MHD magnetorotational turbulence models. The results compare well with radiation hydrostatic solutions and prove to be dynamically stable. Passing the model disks into Monte Carlo radiative transfer calculations, we show that the models satisfy observational constraints on the inner rim’s location. A small optically thin halo of hot dust naturally arises between the inner rim and the star. The inner rim has a substantial radial extent, corresponding to several disk scale heights. While the front’s overall position varies with the stellar luminosity, its radial extent depends on the mass accretion rate. A pressure maximum develops near the location of thermal ionization at temperatures of about 1000 K. The pressure maximum is capable of halting solid pebbles’ radial drift and concentrating them in a zone where temperatures are sufficiently high for annealing to form crystalline silicates.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

3D Radiation Nonideal Magnetohydrodynamical Simulations of the Inner Rim in Protoplanetary Disks

Many planets orbit within 1 au of their stars, raising questions about their origins. Particularly puzzling are the planets found near the silicate sublimation front. We investigate conditions near the front in the protostellar disk around a young intermediate-mass star, using the first global 3D radiation nonideal MHD simulations in this context. We treat the starlight heating; the silicate grains’ sublimation and deposition at the local, time-varying temperature and density; temperature-dependent ohmic dissipation; and various initial magnetic fields. The results show magnetorotational turbulence around the sublimation front at 0.5 au. The disk interior to 0.8 au is turbulent, with velocities exceeding 10% of the sound speed. Beyond 0.8 au is the dead zone, cooler than 1000 K and with turbulence orders of magnitude weaker. A local pressure maximum just inside the dead zone concentrates solid particles, favoring their growth. Over many orbits, a vortex develops at the dead zone’s inner edge, increasing the disk’s thickness locally by around 10%. We synthetically observe the results using Monte Carlo transfer calculations, finding that the sublimation front is near-infrared bright. The models with net vertical magnetic fields develop extended, magnetically supported atmospheres that reprocess extra starlight, raising the near-infrared flux 20%. The vortex throws a nonaxisymmetric shadow on the outer disk. At wavelengths >2 μm, the flux varies several percent on monthly timescales. The variations are more regular when the vortex is present. The vortex is directly visible as an arc at ultraviolet through near-infrared wavelengths, given sub-au spatial resolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Analytic Expressions for the Inner-rim Structure of Passively Heated Protoplanetary Disks

We analytically derive the expressions for the structure of the inner region of protoplanetary disks based on the results from the recent hydrodynamical simulations. The inner part of a disk can be divided into four regions: a dust-free region with a gas temperature in the optically thin limit, an optically thin dust halo, an optically thick condensation front, and the classical, optically thick region, in order from the innermost to the outermost. We derive the dust-to-gas mass ratio profile in the dust halo using the fact that partial dust condensation regulates the temperature relative to the dust evaporation temperature. Beyond the dust halo, there is an optically thick condensation front where all the available silicate gas condenses out. The curvature of the condensation surface is determined by the condition that the surface temperature must be nearly equal to the characteristic temperature ∼1200 K. We derive the midplane temperature in the outer two regions using the two-layer approximation, with the additional heating by the condensation front for the outermost region. As a result, the overall temperature profile is step-like, with steep gradients at the borders between the outer three regions. The borders might act as planet traps where the inward migration of planets due to gravitational interaction with the gas disk stops. The temperature at the border between the two outermost regions coincides with the temperature needed to activate magnetorotational instability, suggesting that the inner edge of the dead zone must lie at this border. The radius of the dead zone inner edge predicted from our solution is ∼2–3 times larger than that expected from the classical optically thick temperature.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

Magnetically Induced Disk Winds and Transport in the HL Tau Disk

The mechanism of angular momentum transport in protoplanetary disks is fundamental to understanding the distributions of gas and dust in the disks. The unprecedented ALMA observations taken toward HL Tau at high spatial resolution and subsequent radiative transfer modeling reveal that a high degree of dust settling is currently achieved in the outer part of the HL Tau disk. Previous observations, however, suggest a high disk accretion rate onto the central star. This configuration is not necessarily intuitive in the framework of the conventional viscous disk model, since efficient accretion generally requires a high level of turbulence, which can suppress dust settling considerably. We develop a simplified, semi-analytical disk model to examine under what condition these two properties can be realized in a single model. Recent, non-ideal MHD simulations are utilized to realistically model the angular momentum transport both radially via MHD turbulence and vertically via magnetically induced disk winds. We find that the HL Tau disk configuration can be reproduced well when disk winds are properly taken into account. While the resulting disk properties are likely consistent with other observational results, such an ideal situation can be established only if the plasma β at the disk midplane is β {sub 0} ≃ 2 × 10{sup 4} under the assumption of steady accretion. Equivalently, the vertical magnetic flux at 100 au is about 0.2 mG. More detailed modeling is needed to fully identify the origin of the disk accretion and quantitatively examine plausible mechanisms behind the observed gap structures in the HL Tau disk.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

THE VLA VIEW OF THE HL TAU DISK: DISK MASS, GRAIN EVOLUTION, AND EARLY PLANET FORMATION

The first long-baseline ALMA campaign resolved the disk around the young star HL Tau into a number of axisymmetric bright and dark rings. Despite the very young age of HL Tau, these structures have been interpreted as signatures for the presence of (proto)planets. The ALMA images triggered numerous theoretical studies based on disk–planet interactions, magnetically driven disk structures, and grain evolution. Of special interest are the inner parts of disks, where terrestrial planets are expected to form. However, the emission from these regions in HL Tau turned out to be optically thick at all ALMA wavelengths, preventing the derivation of surface density profiles and grain-size distributions. Here, we present the most sensitive images of HL Tau obtained to date with the Karl G. Jansky Very Large Array at 7.0 mm wavelength with a spatial resolution comparable to the ALMA images. At this long wavelength, the dust emission from HL Tau is optically thin, allowing a comprehensive study of the inner disk. We obtain a total disk dust mass of (1–3) × 10{sup −3} M {sub ⊙}, depending on the assumed opacity and disk temperature. Our optically thin data also indicate fast grain growth, fragmentation, and formation of dense clumps in the inner densest parts of the disk. Our results suggest that the HL Tau disk may be actually in a very early stage of planetary formation, with planets not already formed in the gaps but in the process of future formation in the bright rings.

79 ASTRONOMY AND ASTROPHYSICS↗