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All sourcesNASA NTRSDOE OSTI
NASA NTRS2011

Environmental Signatures for Habitability: What to Measure and How to Rank the Habitability Potential of Mars

The environmental signatures for habitability are not necessarily biosignatures, even though on Earth, they are definitive proof of habitability. It is the constant overprint of the chemical signatures of life that makes it difficult to recognize the chemical and physical properties of a potentially habitable environment as distinct from an inhabited one. Mars Science Laboratory (MSL) will soon embark on a mission to Mars to assess its past or present habitability, so it is useful to examine how we measure habitability on Earth and prepare for how that approach may differ for Mars. This exercise includes: (a) articulation of fundamental assumptions about habitability, (b) an inventory of factors that affect habitability, (c) development of metrics, measurement approach and implementation, and (d) a new classification scheme for planetary habitability that goes beyond the binary "yes" or "no." There may be dozens of factors that affect habitability and they can be weighted as a function of specific environment. However a robotic, in situ investigation even on Earth has constraints that prevent the measurement of every environmental factor, so metrics must be reduced to the most relevant subset, given available time, cost, technical feasibility and scientific importance. Many of the factors could be measured with a combination of orbital data and the MSL payload. We propose that, at a minimum, a designation of high habitability potential requires the following conditions be met: (a) thermally stable with respect to extremes and frequency of fluctuation, (b) has more than one energy source, (c) sufficient chemical diversity to make compounds with covalent and hydrogen bonding, (d) can moderate ionizing radiation enough to allow a stable or evolving pool of organic molecules, (e) must have water or other high quality polar solvent, (f) must be able to renew chemical resources (e.g., plate tectonics, volcanism or something else we haven't envisioned). A measurement approach we have taken to measure habitability on Earth is : 1. Study remote sensing data, maps, etc. 2. Decide how big an area to measure. 3. Determine the spatial sampling rate. 4. Determine the temporal sampling rate. 5. Determine the order of measurements 6. Decide where to begin measurements 7. Select locations at field site and proceed While science drives each of the steps, there are additional constraints, e.g., technical, time, cost, safety (risk). This approach is also executable on Mars. Measurement of past habitability is more challenging both for Earth and Mars where access to the past means subsurface access and confrontation with unknowns about preservation of the martian past. Some environments preserve evidence of past habitability better than others, and this is where selection of the landing site to maximize the preservation potential of habitability indicators will be key. Mars presents an opportunity to discover transitional states between habitable or not, and we offer a ranking scale for planetary habitability with Mars as the second test subject: CLASS ONE Uninhabitable and likely has never been so CLASS TWO Has a high potential but no confirmed observation of life (as defined above) CLASS THREE Inhabited (we find life) 3-A Globally inhabited 3-B Primitive life; early in its evolution, but not yet globally established 3-C Exists only in refugia -- planet heading toward class four CLASS FOUR Post-habitable (there once was life, but now it's gone) MSL provides an opportunity to carefully investigate the habitability of at least one site on Mars and it will reveal much about the possible states of planetary habitability

Conrad, Pamela G.↗
NASA NTRS2011

Atomic Simulation of Complex DNA DSBs and the Interactions with the Ku70/80 Heterodimer

DNA double strand breaks (DSBs) induced by ionizing radiation (IR) usually contain modified bases such as 8-oxo-7,8-dihydroguanine (8-oxoG) and thymine glycol, apurinic/apyrimidinic (AP) sites, 2-deoxyribonolactone, or single-strand breaks (SSBs). The presence of such lesions in close proximity to the DSB terminus makes the DNA nicks more difficult to repair and rejoin than endogenously induced simple DSBs, and as such a major determinant of the biological effects of high linear energy transfer (LET) radiation as encountered in space travel. In this study we conducted molecular dynamics simulations on a series of DNA duplexes with various complex lesions of 8-oxoG and AP sites, in an effort to investigate the effects of such lesions to the structural integrity and stability of DNA after insulted by IR. We also simulated the interaction of such complex DSBs with the Ku70/80 heterodimer, the first protein in mammalian cells to embark the non-homologous end joining (NHEJ) DNA repair pathway. The results indicate, compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex, thus they present more deleterious effects to the genome integrity if not captured and repaired promptly in cells. Simulations also demonstrate the binding of Ku drastically reduces structural disruption and flexibility caused by the complex lesions, and the interactions of Ku with complex DSBs have a different potential energy landscape from the bound structure with simple DSB. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. This energy shift may help the Ku protein to secure at the DSB terminus for a longer time, so that other end processing factors or repair pathways can proceed at the lesions before NHEJ repair process starts. These atomic simulations may provide valuable new insight into the selective action of repair proteins on damaged DNA.

Hu, Shaowen↗
NASA NTRS2011

Atomistic Simulations of Complex DNA DSBs and the Interactions with Ku70/80 Heterodimer

Compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex. Binding of Ku drastically reduces the structural disruption and flexibility caused by the complex lesions. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. Binding of Ku promotes the rigidity of DNA duplexes, due to the clamp structure of the inner surface of the rings of Ku70/80.

Hu, Shaowen↗
NASA NTRS2011

Conformational Structure of Tyrosine, Tyrosyl-Glycine, and Tyrosyl-Glycyl-Glycine by Double Resonance Spectroscopy

We investigated the variation in conformation for the amino acid tyrosine (Y), alone and in the small peptides tyrosine-glycine (YC) and tyrosine-glycine-glycine (YGG), in the gas phase by using UV-UV and IR-UV double resonance spectroscopy and density functional theory calculations. For tyrosine we found seven different conformations, for YG we found four different conformations, and for YGG we found three different conformations. As the peptides get larger, we observe fewer stable conformers, despite the increasing complexity and number of degrees of freedom. We find structural trends similar to those in phenylalanine-glycine glycine (FGG) and tryptophan-glycine-glycine (WGG)j however) the effect of dispersive forces in FGG for stabilizing a folded structure is replaced by that of hydrogen bonding in YGG.

Abo-Riziq, Ali↗
NASA NTRS2014

1-Azaniumylcyclobutane-1-carboxylate monohydrate

In the title compound, C5H9NO2H2O, the amino acid is in the usual zwitterionic form involving the carboxylate group. The cyclobutane backbone of the amino acid is disordered over two conformations, with occupancies of 0.882 (7) and0.118 (7). In the crystal, NH O and OH O hydrogen bonds link the zwitterions [with the water molecule involved as both acceptor (with the NH3+) and donor (through a single carboxylate O from two different aminocyclobutane carboxylatemoities)], resulting in a two-dimensional layered structure lying parallel to (100).

Azaniumylcyclobutane↗
NASA NTRS2015

Water Distribution in the Continental and Oceanic Upper Mantle

Nominally anhydrous minerals such as olivine, pyroxene and garnet can accommodate tens to hundreds of ppm H2O in the form of hydrogen bonded to structural oxygen in lattice defects. Although in seemingly small amounts, this water can significantly alter chemical and physical properties of the minerals and rocks. Water in particular can modify their rheological properties and its distribution in the mantle derives from melting and metasomatic processes and lithology repartition (pyroxenite vs peridotite). These effects will be examined here using Fourier transform infrared spectrometry (FTIR) water analyses on minerals from mantle xenoliths from cratons, plume-influenced cratons and oceanic settings. In particular, our results on xenoliths from three different cratons will be compared. Each craton has a different water distribution and only the mantle root of Kaapvaal has evidence for dry olivine at its base. This challenges the link between olivine water content and survival of Archean cratonic mantle, and questions whether xenoliths are representative of the whole cratonic mantle. We will also present our latest data on Hawaii and Tanzanian craton xenoliths which both suggest the intriguing result that mantle lithosphere is not enriched in water when it interacts with melts from deep mantle upwellings (plumes).

Peslier, Anne H.↗
NASA NTRS2016

Water in the Cratonic Mantle Lithosphere

The fact that Archean and Proterozoic cratons are underlain by the thickest (>200 km) lithosphere on Earth has always puzzled scientists because the dynamic convection of the surrounding asthenosphere would be expected to delaminate and erode these mantle lithospheric "keels" over time. Although density and temperature of the cratonic lithosphere certainly play a role in its strength and longevity, the role of water has only been recently addressed with data on actual mantle samples. Water in mantle lithologies (primarily peridotites and pyroxenites) is mainly stored in nominally anhydrous minerals (olivine, pyroxene, garnet) where it is incorporated as hydrogen bonded to structural oxygen in lattice defects. The property of hydrolytic weakening of olivine [4] has generated the hypothesis that olivine, the main mineral of the upper mantle, may be dehydrated in cratonic mantle lithospheres, contributing to its strength. This presentation will review the distribution of water concentrations in four cratonic lithospheres. The distribution of water contents in olivine from peridotite xenoliths found in kimberlites is different in each craton (Figure 1). The range of water contents of olivine, pyroxene and garnet at each xenolith location appears linked to local metasomatic events, some of which occurred later then the Archean and Proterozoic when these peridotites initially formed via melting. Although the low olivine water contents (<10 ppm wt H2O) at > 6 GPa at the base of the Kaapvaal cratonic lithosphere may contribute to its strength, and prevent its delamination, the wide range of those from Siberian xenoliths is not compatible with providing a high enough viscosity contrast with the asthenophere. The water content in olivine inclusions from Siberian diamonds, on the other hand, have systematically low water contents (<20 ppm wt H2O). The xenoliths may represent a biased sample of the cratonic lithosphere with an over-­abundance of metasomatized peridotites with high water contents. The olivine inclusions, however, may have been protected from metasomatism by their host diamond and record the overall low olivine water content of the cratonic lithosphere. Water may thus still play a role in cratonic keel longevity.

Peslier, A. H.↗
NASA NTRS2015

Thermodynamic Derivation of the Activation Energy for Ice Nucleation

Cirrus clouds play a key role in the radiative and hydrological balance of the upper troposphere. Their correct representation in atmospheric models requires an understanding of the microscopic processes leading to ice nucleation. A key parameter in the theoretical description of ice nucleation is the activation energy, which controls the flux of water molecules from the bulk of the liquid to the solid during the early stages of ice formation. In most studies it is estimated by direct association with the bulk properties of water, typically viscosity and self-diffusivity. As the environment in the ice-liquid interface may differ from that of the bulk, this approach may introduce bias in calculated nucleation rates. In this work a theoretical model is proposed to describe the transfer of water molecules across the ice-liquid interface. Within this framework the activation energy naturally emerges from the combination of the energy required to break hydrogen bonds in the liquid, i.e., the bulk diffusion process, and the work dissipated from the molecular rearrangement of water molecules within the ice-liquid interface. The new expression is introduced into a generalized form of classical nucleation theory. Even though no nucleation rate measurements are used to fit any of the parameters of the theory the predicted nucleation rate is in good agreement with experimental results, even at temperature as low as 190 K, where it tends to be underestimated by most models. It is shown that the activation energy has a strong dependency on temperature and a weak dependency on water activity. Such dependencies are masked by thermodynamic effects at temperatures typical of homogeneous freezing of cloud droplets; however, they may affect the formation of ice in haze aerosol particles. The new model provides an independent estimation of the activation energy and the homogeneous ice nucleation rate, and it may help to improve the interpretation of experimental results and the development of parameterizations for cloud formation.

Cirrus clouds↗
NASA NTRS2016

Yield and Failure Behavior Investigated for Cross-Linked Phenolic Resins Using Molecular Dynamics

Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

Molecular dynamics↗
NASA NTRS2017

Abiotic Synthesis of Nucleic Acids: Hypochromicity and Future Research

The earliest forms of life would likely have a protocellular form, with a membrane encapsulating some form of linear charged polymer. These polymers could have enzymatic as well as genetic properties. We can simulate plausible prebiotic conditions in the laboratory to test hypotheses related to this concept. In earlier work we have shown that mononucleotides organized within a multilamellar lipid matrix can produce oligomers in the anhydrous phase of dehydration- rehydration cycles (Rajamani, 2008). If mononucleotides are in solution at millimolar concentrations, then oligomers resembling RNA are synthesized and exist in a steady state with their monomers DeGuzman, 2014). We have used conventional and novel techniques to demonstrate that secondary structures stabilized by hydrogen bonds may be present in the condensation products produced in dehydration- rehydration cycles that simulate hydrothermal fields that were present on the early Earth. Gel electrophoresis data corroborates the presence of up to 200-base pair length RNA fragments in products of Hydration-Dehydration experiments. Furthermore, hypochromicity measurements demonstrate a degree of hypochromicity found in single RNA strand of known sequence, as well as results that indicate this is true also for a sample of complementary strands of RNA. Analysis of ionic current signatures of known RNA hairpin molecule as measured using a nanopore detector indicate a significant variability in pattern, different from the signatures produced by DNA hairpin molecules. This informs how we may interpret nanopore data gathered from prebiotic simulations.

Glass, K.↗
NASA NTRS2017

Exploring the Evolutionary Accident Hypothesis: Are Extant Protein Folds the Fittest or the Luckiest?

Considering the range of functions proteins perform, it is surprising they fold into a relatively small set of structures or "folds" that facilitate such function. One explanation is that only a minority were fit enough to emerge from Darwinian selection during the early evolution of life. Alternatively, perhaps only a fraction of all possible folds were trialed. Understanding proto-catalyst selection will aid understanding of the origins and early evolution of life. To investigate which explanation is correct, we study a protein evolved in vitro to bind ATP by Jack Szostak (Fig. 1). This protein adopts a fold which is absent from nature. We are testing whether this fold would have possessed the capability to evolve that would have been essential to survive natural selection on early Earth. Folds that couldn't improve their fitness and evolve to perform new functions would have been replaced by rivals that could. To determine whether the fold is evolvable, we are attempting to change the function of the protein by rationally redesigning to bind GTP. Two design strategies in the region of the nucleobase have been implemented to provide hydrogen bonding partners for the ligand i) an insertion ii) a MET to ASN mutation. Redesigns are being studied computationally at Ames Research Center including free energy of binding calculations. Binding affinities of promising redesigns are to be validated by experimental collaborators at ForteBio using Super Streptavidin Biosensors. If the fold is found to be non-evolvable, this may suggest that many structures were trialed, but the majority were pruned on the basis of their evolvability. Alternatively, if the fold is demonstrated to be evolvable, it would be difficult to explain its absence from nature without considering the possibility that the fold simply wasn't sampled on early Earth. This would not only further our understanding of the origins of life on Earth but also suggest a common phe-nomenon of proto-catalyst evolution.

Shannon, G.↗
NASA NTRS2016

Yield and Failure Behavior Investigated for Cross-linked Phenolic Resins Using Molecular Dynamics

Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on the glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

Stress-strain curves↗
NASA NTRS2021

Physics and Chemistry of Te and HgTe-based Ternary Melts

Historically, the theoretical treatment of the liquid phases has always been more difficult and complicated than that for solid and gas phases. A liquid has no lattice structure as crystalline solids and the atoms/molecules in the liquid can migrate through it relatively rapidly. On the other hand, it is also interacting with many other atoms/molecules so that the simplifications of the kinetic theory of gases cannot be employed. For more complicated liquids, such as the liquids of high ionicity and those containing hydrogen bonds and electric dipoles, the understanding is far from complete. At the same time, accurate information on the physics and chemistry of semiconductor melts is needed for the quantitative descriptions of the process of crystal growth from melt. The pre-crystallization phenomena in the liquid phase are critical because the properties of the grown crystals depend on the state and structure of the melt as well as the thermal history of the melt during solidification process. However, the data on the liquid phase, such as thermophysical properties of semiconductor melts are scarce, especially for the HgTe-based II-VI ternary compound semiconductors because of their high vapor pressure and extreme toxicity. Analysis of the thermophysical properties of the melt can provide information about structural transitions of the melt during the solidification process. From a broader point of view, the structure of liquids is much more complicated than the crystalline solids, especially the relaxation behavior through different thermal histories. The theory of hetero-phase fluctuations of liquids is applicable to any many-body systems including condensed-matter physics, field theory, physics of nuclear-matter, cosmology, biology and even sociology. This book summarizes the physics and chemistry from the experimental measurements and theoretical analyses of phase diagram, thermodynamic properties, density, thermal conductivity, viscosity, and electrical conductivity on the binary, pseudo-binary and ternary melts of the most advanced IR-detector material systems of HgCdTe and HgZnTe as well as the analyses of these results. The main objectives of this study are: (1) to provide the phase diagrams and thermodynamic properties of Hg-Cd-Te and Hg-Zn-Te systems through quantitatively fitting the experimental data by assuming an associated solution model for the liquid phase, (2) to experimentally measure the thermophysical properties of the Hg-Cd-Te and Hg-Zn-Te melts, including density, viscosity, electrical conductivity and thermal conductivity as functions of temperature and composition and (3) to enhance the fundamental knowledge of hetero-phase fluctuations and relaxation phenomena in the melts and extend our understanding of the solidification process in order to interpret the experimental results of crystal growth so as to improve the melt growth processes of the compound semiconductor. The physics and chemistry of Te and HgTe-based ternary melts were explored through the studies of the structural transformation during melting, the supercooling during solidification, the relaxation phenomena after rapid cooling of the melts and the metal-semiconductor transition in the melts through the analyses of electrical conductivity and Lorenz number. An in-depth study on the thermophysical properties and their time-dependent structural dynamic processes taking place in the vicinity of the solid-liquid phase transition of the narrow homogeneity range HgTe-based ternary semiconductors as well as the analysis of the homogenization process in the melt will also be presented.

Thermophysical properties↗
NASA NTRS2002

Nature of the Organic Signature in Dust from the Interstellar Medium: Laboratory Analog Studies

We measured the infrared (IR) nu(sub CH) absorption bands around 3.4 microns (2800 - 3000 cm(sup -1) in large laboratory-grown magnesium oxide (MgO) and natural olivine single crystals that crystallized from CO/CO2/H2O saturated melts. These bands are very similar to those from many astronomical sources, such as from dust in the diffuse interstellar medium (ISM), from the outflow of evolved stars, etc., and they are characteristic of aliphatic -CH2- and -CH3 entities. In our laboratory single crystals the VCH bands arise from C-H entities that were introduced by a solid solution process, and that are imbedded in the mineral matrix in form of polyatomic C(sub n) entities with C atoms bonded to O and to H. Heating breaks the C-H bonds, causing hydrogen to disperse in the mineral matrix. C-H bonds are re-established rapidly during annealing. We propose that dust grains probably contain the same type of internal C(sub n)-H entities in solid matrix rather than an external organic layer covering the grain surfaces. Thermodynamical arguments show that the concentration of organics in solid solution in small grains can be comparable to that found in astronomical environments.

Freund, M. M.↗
NASA NTRS1987

Full CI benchmark calculations on N2, NO, and O2 - A comparison of methods for describing multiple bonds

Full configuration interaction (CI) calculations on the ground states of N2, NO, and O2 using a DZP Gaussian basis are compared with single-reference SDCI and coupled pair approaches (CPF), as well as with CASSCF multireference CI approaches. The CASSCF/MRCI technique is found to describe multiple bonds as well as single bonds. Although the coupled pair functional approach gave chemical accuracy (1 kcal/mol) for bonds involving hydrogen, larger errors occur in the CPF approach for the multiple bonded systems considered here. CI studies on the 1Sigma(g +) state of N2, including all single, double, triple, and quadruple excitations show that triple excitations are very important for the multiple bond case, and accounts for most of the deficiency in the coupled pair functional methods.

Bauschlicher, Charles W., Jr.↗
NASA NTRS1997

Glycolonitrile oligomerization: structure of isolated oxazolines, potential heterocycles on the early earth

A study of glycolonitrile polymerization has led to the isolation and characterization of two 2,5-dihydro-4-aminooxazoles, 4 and 5. Previous reports have misassigned these structures as s-triazines or pyrimidines. X-ray diffraction analysis of crystals of 4 and an acetylated oxazole derivative of 5 (6) confirm the proposed structures. Ab initio computations are used to assess the relative thermodynamic stability of three trimer isomers (an s-triazine, an aminohydroxypyrimidine, and an aminooxazoline), and the results indicate that 4 is a novel kinetic product. Mechanistic considerations rationalize kinetic oxazole formation over the more customary triazine or pyrimidine trimers.

Non-NASA Center↗
NASA NTRS1993

Spectroscopic ellipsometric characterization of Si/Si(1-x)Ge(x) strained-layer superlattices

Spectroscopic ellipsometry (SE) was employed to characterize Si/Si(1-x)Ge(x) strained-layer superlattices. An algorithm was developed, using the available optical constants measured at a number of fixed x values of Ge composition, to compute the dielectric function spectrum of Si(1-x)Ge(x) at an arbitrary x value in the spectral range 17 to 5.6 eV. The ellipsometrically determined superlattice thicknesses and alloy compositional fractions were in excellent agreement with results from high-resolution x ray diffraction studies. The silicon surfaces of the superlattices were subjected to a 9:1 HF cleaning prior to the SE measurements. The HF solution removed silicon oxides on the semiconductor surface, and terminated the Si surface with hydrogen-silicon bonds, which were monitored over a period of several weeks, after the HF cleaning, by SE measurements. An equivalent dielectric layer model was established to describe the hydrogen-terminated Si surface layer. The passivated Si surface remained unchanged for greater than 2 h, and very little surface oxidation took place even over 3 to 4 days.

Yao, H.↗