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NASA NTRS2020

Interpreting Exo-Planetary Atmospheres with the Next Generation Space-Based Telescope

We will soon have the technological capability to measure the atmospheric composition of temperate Earth-sized planets orbiting nearby stars. Interpreting these atmospheric signals poses a new challenge to planetary science. In contrast to jovian-like atmospheres, whose bulk compositions consist of hydrogen and helium, terrestrial planet atmospheres are likely comprised of high mean molecular weight secondary atmospheres, which have gone through a high degree of evolution. In order to understand the processes which affect a planetary atmosphere, I use early Mars as a case study. I leverage a combination of one-dimensional climate, photochemical and energy balance models in order to create one self-consistent model that closely matches currently available climate data. However, unlike in-situ observations from our own solar system, remote sensing techniques need to be developed and understood in order to accurately characterize exo-atmospheres. I describe the models used to create synthetic transit transmission observations, which includes models of transit spectroscopy and instrumental noise. Using these, I lay the framework for an information content-based approach to optimize our observations and maximize the retrievable information from exo-atmospheres. First I test the method on observing strategies of the well-studied, low-mean-molecular weight atmospheres of warm-Neptunes and hot Jupiters. Upon verifying the methodology, I finally address optimal observing strategies for temperate, high-mean-molecular weight atmospheres (Earths/super-Earths).

Batalha, Natasha↗
NASA NTRS1991

Structure and functions of water-membrane interfaces and their role in proto-biological evolution

Among the most important developments in proto-biological evolution was the emergence of membrane-like structures. These are formed by spontaneous association of relatively simple amphiphilic molecules that would have been readily available in the primordial environment. The resulting interfacial regions between water and nonpolar interior of the membrane have several properties which made them uniquely suitable for promoting subsequent evolution. They can (1) selectively attract organic material and mediate its transport, (2) serve as simple catalysts for chemical reactions, and (3) promote the formation of trans-membrane electrical and chemical gradients which could provide energy sources for proto-cells. Understanding the structure of interfaces, their interactions with organic molecules and molecular mechanisms of their functions is an essential step to understanding proto-biological evolution. In our computer simulation studies, we showed that the structure of water at interfaces with nonpolar media is significantly different from that in the bulk. In particular, the average surface dipole density points from the vapor to the liquid. As a result, negative ions can approach the interface more easily than positive ions. Amphiphilic molecules composed of hydrocarbon conjugated rings and polar substituents (e.g., phenol) assume at the interface rigid orientations in which polar groups are buried in water while hydrocarbon parts are located in the nonpolar environment. These orientational differences are of special interest in connection with the ability of some of these molecules to efficiently absorb photons. Flexible molecules with polar substituents often adopt at interfaces conformations different from those in the bulk aquaeous solution and in the gas phase. As a result, in many instances both specificity and kinetics of chemical reactions in which these molecules can participate is modified by the presence of surfaces. Of special interest is the mechanism by which polar molecules are transferred across interface between water and a nonpolar medium. Our recent study showed that simple ionophores bind ions by the same mechanisms as ion channels and carriers from modern cells.

Pohorille, A.↗
NASA NTRS1989

Radio wavelength observations of the L134N molecular core

A detailed study of the L134N dense molecular core through radio astronomical observations of spectral lines at millimeter and centimeter wavelengths is presented. The prototypical dark cloud was chosen for the following reasons: it is a nearby cloud at a distance of 160 pc, and thus radio observations have high spatial resolution; it resides out of the galactic disk, providing unobscured viewing along the line of sight; and it is known to be a rich source of molecular emission. The absence af any embedded infrared sources leads to the assumption that L134N is either in a stage of evolution prior to star formation or is a cloud in which internal support will prohibit a star from forming. A spectral line survey of 24 molecular transitions at up to seven positions in the L134N core, and observations of molecular emission from C18O, CSm, H13CO+, SO, NH3, and C3H2 are reviewed. Results indicate different spatial distributions for each species which may be attributed to variations in the excitation conditions for each transition or chemical abundance variations within the cloud core. Observational techniques and results are presented.

Swade, Daryl A.↗
NASA NTRS2000

Fast Particle Methods for Multiscale Phenomena Simulations

We are developing particle methods oriented at improving computational modeling capabilities of multiscale physical phenomena in : (i) high Reynolds number unsteady vortical flows, (ii) particle laden and interfacial flows, (iii)molecular dynamics studies of nanoscale droplets and studies of the structure, functions, and evolution of the earliest living cell. The unifying computational approach involves particle methods implemented in parallel computer architectures. The inherent adaptivity, robustness and efficiency of particle methods makes them a multidisciplinary computational tool capable of bridging the gap of micro-scale and continuum flow simulations. Using efficient tree data structures, multipole expansion algorithms, and improved particle-grid interpolation, particle methods allow for simulations using millions of computational elements, making possible the resolution of a wide range of length and time scales of these important physical phenomena.The current challenges in these simulations are in : [i] the proper formulation of particle methods in the molecular and continuous level for the discretization of the governing equations [ii] the resolution of the wide range of time and length scales governing the phenomena under investigation. [iii] the minimization of numerical artifacts that may interfere with the physics of the systems under consideration. [iv] the parallelization of processes such as tree traversal and grid-particle interpolations We are conducting simulations using vortex methods, molecular dynamics and smooth particle hydrodynamics, exploiting their unifying concepts such as : the solution of the N-body problem in parallel computers, highly accurate particle-particle and grid-particle interpolations, parallel FFT's and the formulation of processes such as diffusion in the context of particle methods. This approach enables us to transcend among seemingly unrelated areas of research.

Koumoutsakos, P.↗
NASA NTRS1994

Circumprotostellar environments. 2: Envelopes, activity, and evolution

We have obtained 800 and 1100 micron photometric observations of a complete, flux-limited, IRAS-selected sample of cold sources in Taurus, whose infrared and molecular properties indicate them to be low-mass protostars which are younger than T Tauri stars. The goal of this study is to understand the role of the circumstellar envelope and disk during low-mass star formation and to search for signs of evolution. We find a good correlation between the submillimeter flux density (as well as of envelope mass) with both the mechanical luminosity of the molecular outflow and with the far-infrared luminosity, presumably produced by accretion onto the protostar. This suggests that the mass of the disk/envelope may be linked to the rate of accretion onto the protostar and to the generation of outflows. However, in contrast to the results of Cabrit & Andre (1991) we see no evidence for a lower limit to the disk/envelope mass which can produce outflow. We also find a significant difference between the spectral energy distributions at submillimeter wavelengths of embedded protostars compared to optically visible T Tauri stars. The more evolved (T Tuari) objects tend to have shallower spectral indices than embedded sources, suggesting (1) an evolution of dust grains, and/or (2) a more compact envelope and optically thick disk in the older objects.

Moriarty-Schieven, G. H.↗
NASA NTRS2001

Arthropod phylogeny based on eight molecular loci and morphology

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

Non-NASA Center↗
NASA NTRS2005

"The Evolution of Photosynthesis and the Transition from an Anaerobic to an Aerobic World"

This project was focused on elucidating the evolution of photosynthesis, in particular the evolutionary developments that preceded and accompanied the transition from anoxygenic to oxygenic photosynthesis. Development of this process has clearly been of central importance to evolution of life on Earth. Photosynthesis is the mechanism that ultimately provides for the energy needs of most surface-dwelling organisms. Eukaryotic organisms are absolutely dependent on the molecular oxygen that has been produced by oxygenic photosynthesis. In this project we have employed a multidisciplinary approach to understand some of the processes that took place during the evolution of photosynthesis. In this project, we made excellent progress in the overall area of understanding the origin and evolution of photosynthesis. Particular progress has been made on several more specific research questions, including the molecular evolutionary analysis of photosynthetic components and biosynthetic pathways (2,3, 5, 7, 10), as well as biochemical characterization of electron transfer proteins related to photosynthesis and active oxygen protection (4,6,9). Finally, several review and commentary papers have been published (1, 8, 1 1). A total of twelve publications arose out of this grant, references to which are given below. Some specific areas of progress are highlighted and discussed in more detail.

Blankenship, Robert E.↗
NASA NTRS1998

The origin and evolution of oxygenic photosynthesis

The evolutionary developments that led to the ability of photosynthetic organisms to oxidize water to molecular oxygen are discussed. Two major changes from a more primitive non-oxygen-evolving reaction center are required: a charge-accumulating system and a reaction center pigment with a greater oxidizing potential. Intermediate stages are proposed in which hydrogen peroxide was oxidized by the reaction center, and an intermediate pigment, similar to chlorophyll d, was present.

Review, Tutorial↗
NASA NTRS2000

Infrared Observations of Hot Gas and Cold Ice Toward the Low Mass Protostar Elias 29

We have obtained the full 1-200 micrometer spectrum of the low luminosity (36 solar luminosity Class I protostar Elias 29 in the rho Ophiuchi molecular cloud. It provides a unique opportunity to study the origin and evolution of interstellar ice and the interrelationship of interstellar ice and hot core gases around low mass protostars. We see abundant hot CO and H2O gas, as well as the absorption bands of CO, CO2, H2O and "6.85 micrometer" ices. We compare the abundances and physical conditions of the gas and ices toward Elias 29 with the conditions around several well studied luminous, high mass protostars. The high gas temperature and gas/solid ratios resemble those of relatively evolved high mass objects (e.g. GL 2591). However, none of the ice band profiles shows evidence for significant thermal processing, and in this respect Elias 29 resembles the least evolved luminous protostars, such as NGC 7538 : IRS9. Thus we conclude that the heating of the envelope of the low mass object Elias 29 is qualitatively different from that of high mass protostars. This is possibly related to a different density gradient of the envelope or shielding of the ices in a circumstellar disk. This result is important for our understanding of the evolution of interstellar ices, and their relation to cometary ices.

Boogert, A. C. A.↗
NASA NTRS2002

The Fourier-Kelvin Stellar Interferometer Mission Concept

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging interferometer for the mid-infrared spectral region (5-30 microns). FKSI is conceived as a scientific and technological precursor to TPF as well as Space Infrared Interferometric Telescope (SPIRIT), Submillimeter Probe Evolution of Cosmic Structure (SPECS), and Single Aperture for Infrared Observatory (SAFIR). It will also be a high angular resolution system complementary to Next Generation Space Telescope (NGST). The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We are in the process of studying alternative interferometer architectures and beam combination techniques, and evaluating the relevant science and technology tradeoffs. Some of the technical challenges include the development of the cryocooler systems necessary for the telescopes and focal plane array, light and stiff but well-damped truss systems to support the telescopes, and lightweight and coolable optical telescopes. The goal of the design study is to determine if a mid-infrared interferometry mission can be performed within the cost and schedule requirements of a Discovery class mission. At the present time we envision the FKSI as comprised of five one meter diameter telescopes arranged along a truss structure in a linear non-redundant array, cooled to 35 K. A maximum baseline of 20 meters gives a nominal resolution of 26 mas at 5 microns. Using a Fizeau beam combination technique, a simple focal plane camera could be used to obtain both Fourier and spectral data simultaneously for a given orientation of the array. The spacecraft will be rotated to give sufficient Fourier data to reconstruct complex images of a broad range of astrophysical sources.

Danchi, W. C.↗
NASA NTRS2003

Iterative pass optimization of sequence data

The problem of determining the minimum-cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete. This "tree alignment" problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This method, though more efficient in time and more effective in cladogram length than many alignment-based procedures, greedily optimizes nodes based on descendent information only. In their proposal of an exact multiple alignment solution, Sankoff et al. in 1976 described a heuristic procedure--the iterative improvement method--to create alignments at internal nodes by solving a series of median problems. The combination of a three-sequence direct optimization with iterative improvement and a branch-length-based cladogram cost procedure, provides an algorithm that frequently results in superior (i.e., lower) cladogram costs. This iterative pass optimization is both computation and memory intensive, but economies can be made to reduce this burden. An example in arthropod systematics is discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

NASA Discipline Evolutionary Biology↗
NASA NTRS2000

Evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus

The extension of ecological tolerance limits may be an important mechanism by which microorganisms adapt to novel environments, but it may come at the evolutionary cost of reduced performance under ancestral conditions. We combined a comparative physiological approach with phylogenetic analyses to study the evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Among the 20 laboratory clones of Synechococcus isolated from collections made along an Oregon hot spring thermal gradient, four different 16S rRNA gene sequences were identified. Phylogenies constructed by using the sequence data indicated that the clones were polyphyletic but that three of the four sequence groups formed a clade. Differences in thermotolerance were observed for clones with different 16S rRNA gene sequences, and comparison of these physiological differences within a phylogenetic framework provided evidence that more thermotolerant lineages of Synechococcus evolved from less thermotolerant ancestors. The extension of the thermal limit in these bacteria was correlated with a reduction in the breadth of the temperature range for growth, which provides evidence that enhanced thermotolerance has come at the evolutionary cost of increased thermal specialization. This study illustrates the utility of using phylogenetic comparative methods to investigate how evolutionary processes have shaped historical patterns of ecological diversification in microorganisms.

Synechococcus Group/classification/growth & develo↗
NASA NTRS2003

The Fourier-Kelvin Stellar Interferometer (FKSI): A Discovery Class TPF/DARWIN Pathfinder Mission Concept

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging and nulling interferometer for the mid-infrared spectral region (5-30 microns). FKSI is conceived as a scientific and technological pathfinder to TPF/DARWIN as well as SPIRIT, SPECS, and SAFIR. It will also be a high angular resolution system complementary to NGST. The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We have been studying alternative interferometer architectures and beam combination techniques, and evaluating the relevant science and technology tradeoffs. Some of the technical challenges include the development of the cryocooler systems necessary for the telescopes and focal plane array, light and stiff but well-damped truss systems to support the telescopes, and lightweight and coolable optical telescopes. We present results of detailed design studies of the FKSI starting with a design consisting of five one meter diameter telescopes arranged along a truss structure in a linear non-redundant array, cooled to 35 K. A maximum baseline of 20 meters gives a nominal resolution of 26 mas at 5 microns. Using a Fizeau beam combination technique, a simple focal plane camera could be used to obtain both Fourier and spectral data simultaneously for a given orientation of the array. The spacecraft will be rotated to give sufficient Fourier data to reconstruct complex images of a broad range of astrophysical sources. Alternative and simpler three and two telescope designs emphasizing nulling and spectroscopy also have been investigated and will be discussed.

Danchi, W. C.↗
NASA NTRS2005

The Fourier-Kelvin Stellar Interferometer (FKSI): A Progress Report and Preliminary Results from Our Laboratory Testbed

The Fourier-Kelvin Stellar Interferometer (FKSI) is a mission concept for an imaging and nulling interferometer for the near-infrared to mid-infrared spectral region (3-8 microns). FKSI is conceived as a scientific and technological pathfinder to TPF/DARWIN as well as SPIRIT, SPECS, and SAFIR. It will also be a high angular resolution system complementary to JWST. The scientific emphasis of the mission is on the evolution of protostellar systems, from just after the collapse of the precursor molecular cloud core, through the formation of the disk surrounding the protostar, the formation of planets in the disk, and eventual dispersal of the disk material. FKSI will also search for brown dwarfs and Jupiter mass and smaller planets, and could also play a very powerful role in the investigation of the structure of active galactic nuclei and extra-galactic star formation. We report additional studies of the imaging capabilities of the FKSI with various configurations of two to five telescopes, studies of the capabilities of FKSI assuming an increase in long wavelength response to 10 or 12 microns (depending on availability of detectors), and preliminary results from our nulling testbed.

Berry, Richard↗
NASA NTRS2003

Radioastronomical Searches for Instellar Biomolecules

Impacts of comets and asteroids could have delivered large amounts of organic matter to the early Earth. to retain a significant interstellar signature; observations of recent bright comets indicate that they have a molecular inventory consistent with their ices being largely unmodified interstellar material. Many simple organic molecules with biochemical significance observed in circumstellar envelopes and in molecular clouds, similar to that from which the Solar System formed, may have acted as the precursors of the more complex organics found in meteorites. Therefore, there is potentially a strong link between interstellar organics and prebiotic chemical evolution. Radioastronomical observations, particularly at millimeter wavelengths, allow us to determine the chemical composition and characteristics of the molecular inventory in interstellar space. Here we report some of our recent results from extensive astronomical searches for astrobiologically-important interstellar organics.

Kuan, Y.-J.↗
NASA NTRS1987

Molecular gas and star formation in HI-deficient Virgo cluster galaxies

Mapping of the CO emission line in 42 Virgo cluster galaxies reveals that the molecular gas contents and distributions are roughly normal in severaly HI-deficient Virgo spirals. The survival of the molecular component mitigates the impact of the HI-stripping on star formation and subsequent galactic evolution. For spirals which are deficient in HI by a factor of 10, far-infrared, H alpha line, and nonthermal radio continuum luminosities are lower by no more than a factor of 2. The fact that the inner galactic disks are stripped of HI, while CO is normal, suggests that the lifetime of the molecular phase is approximately one billion years in the inner regions of luminous spirals.

Kenney, Jeffrey D.↗
NASA NTRS1991

A simulation of the collapse and fragmentation of cooling molecular clouds

The application of the Smoothed Particle Hydrodynamics method to the fragmentation of rotating cloud and disk systems is described, allowing for molecular cooling due to H2 and CO. A novel approach to solving Poisson's equation for disklike structures which exploits the multigrid algorithm is also described. Numerical studies are presented which investigate the evolution of both rotating clouds and Maclaurin disks, in each case with both an isothermal equation of state and with molecular cooling. The results establish the influence of molecular cooling on the fragmentation of molecular clouds. The isothermal sequences, if they fragment at all, do so into far fewer lumps than the cooling sequences. This is not due to a cooling instability as such, but rather to the reduced thermal support. One of the sequences shows a remarkable similarity to the W49A star-forming region.

Monaghan, Joe J.↗
NASA NTRS1996

Evidence for the Evolution of Grain Properties in the NGC 2024 Star Forming Ridge

High-resolution images of the NGC 2024 molecular ridge in CS(2-1) and 3 mm continuum emission have been obtained using the Owens Valley millimeter array. The data are used to determine the temperature and dynamics of the ridge, and to ascertain the evolutionary state of the embedded protostars FIR2-7. Dust continuum emission is detected from all six FIR sources. The CS(2-1) follows the ridge closely, but does not always coincide with the FIR sources. Direct comparison of column density estimates derived from the CS and the dust emission in the ridge shows that for all FIR sources except FIR5 both methods are in agreement to within a factor of two, assuming a dust opacity k(sub 3 mm) = 0.01 cm(exp 2)/g. However, away from the FIR sources strong CS(1-0) emission is observed in several compact clumps which, with the above dust opacity, should have been detected in 3 mm dust continuum. The brightness temperature of the CS, approx. 40 K, rules out the possibility that the high line-to-continuum ratio is due to low gas temperatures; the discrepancy can be resolved if k(sub 3 mm) is a factor of 10 lower away from the FIR sources. A new high-resolution image of the 450-micron dust continuum emission obtained using the James Clerk Maxwell Telescope supports this hypothesis. These results suggest an evolution in the physical properties of the dust grains, possibly grain size, between quiescent regions in the ridge and the sites of active star formation.

Chandler, C. J.↗