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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
NASA NTRS1990

DNA dynamics in aqueous solution: opening the double helix

The opening of a DNA base pair is a simple reaction that is a prerequisite for replication, transcription, and other vital biological functions. Understanding the molecular mechanisms of biological reactions is crucial for predicting and, ultimately, controlling them. Realistic computer simulations of the reactions can provide the needed understanding. To model even the simplest reaction in aqueous solution requires hundreds of hours of supercomputing time. We have used molecular dynamics techniques to simulate fraying of the ends of a six base pair double strand of DNA, [TCGCGA]2, where the four bases of DNA are denoted by T (thymine), C (cytosine), G (guanine), and A (adenine), and to estimate the free energy barrier to this process. The calculations, in which the DNA was surrounded by 2,594 water molecules, required 50 hours of CRAY-2 CPU time for every simulated 100 picoseconds. A free energy barrier to fraying, which is mainly characterized by the movement of adenine away from thymine into aqueous environment, was estimated to be 4 kcal/mol. Another fraying pathway, which leads to stacking between terminal adenine and thymine, was also observed. These detailed pictures of the motions and energetics of DNA base pair opening in water are a first step toward understanding how DNA will interact with any molecule.

NASA Discipline Number 52-20↗
NASA NTRS2004

Model of Mixing Layer With Multicomponent Evaporating Drops

A mathematical model of a three-dimensional mixing layer laden with evaporating fuel drops composed of many chemical species has been derived. The study is motivated by the fact that typical real petroleum fuels contain hundreds of chemical species. Previously, for the sake of computational efficiency, spray studies were performed using either models based on a single representative species or models based on surrogate fuels of at most 15 species. The present multicomponent model makes it possible to perform more realistic simulations by accounting for hundreds of chemical species in a computationally efficient manner. The model is used to perform Direct Numerical Simulations in continuing studies directed toward understanding the behavior of liquid petroleum fuel sprays. The model includes governing equations formulated in an Eulerian and a Lagrangian reference frame for the gas and the drops, respectively. This representation is consistent with the expected volumetrically small loading of the drops in gas (of the order of 10 3), although the mass loading can be substantial because of the high ratio (of the order of 103) between the densities of liquid and gas. The drops are treated as point sources of mass, momentum, and energy; this representation is consistent with the drop size being smaller than the Kolmogorov scale. Unsteady drag, added-mass effects, Basset history forces, and collisions between the drops are neglected, and the gas is assumed calorically perfect. The model incorporates the concept of continuous thermodynamics, according to which the chemical composition of a fuel is described probabilistically, by use of a distribution function. Distribution functions generally depend on many parameters. However, for mixtures of homologous species, the distribution can be approximated with acceptable accuracy as a sole function of the molecular weight. The mixing layer is initially laden with drops in its lower stream, and the drops are colder than the gas. Drop evaporation leads to a change in the gas-phase composition, which, like the composition of the drops, is described in a probabilistic manner

Bellan, Josette↗
NASA NTRS2012

Multifunctional and biologically active matrices from multicomponent polymeric solutions

A functionalized electrospun matrix for the controlled-release of biologically active agents, such as growth factors, is presented. The functionalized matrix comprises a matrix polymer, a compatibilizing polymer and a biomolecule or other small functioning molecule. In certain aspects the electrospun polymer fibers comprise at least one biologically active molecule functionalized with low molecular weight heparin.

Kiick, Kristi L.↗
NASA NTRSDate not supplied

The Search for Chiral Asymmetry as a Potential Biosignature in Samples from Mars

The search for evidence of extraterrestrial life in our solar system is currently guided by our understanding of terrestrial biology and its associated biosignatures. The observed homochirality in all life on Earth, that is, the predominance of “left-handed” or L-amino acids and “right-handed” or D-sugars, is a unique property of life that is crucial for molecular recognition, enzymatic function, information storage and structure and is thought to be a prerequisite for the origin or early evolution of life. Therefore, the detection of L- or D-enantiomeric excesses of chiral amino acids and sugars could be a powerful indicator of extant or extinct life on Mars or other habitable environments in our solar system. The exploration of habitable environments on Mars, including an assessment of the preservation potential for complex organics of either abiotic or biological origin, remains a key goal of both current and future Mars missions. Now with the unambiguous detection of indigenous organic matter in sedimentary rocks on Mars [1-3], NASA’s Curiosity rover has significantly advanced our understanding of the preservation of potential chemical biosignatures in the martian near surface. Although amino acids have not yet been identified by in situ measurements on Mars, if they were present, it is expected that amino acid hydrolysis and racemization would be very slow and any chiral or isotopic signatures from an extinct martian biota could be preserved for billions of years, given the extremely cold and dry surface conditions [4]. One of ESA’s Rosalind Franklin rover payload instruments called the Mars Organic Molecule Analyzer (MOMA) includes a wet chemistry package capable of measuring the enantiomeric ratios of any chiral amino acids present at part-per-million concentrations or higher [5]. The complexity and limited duration of spaceflight operations and the known analytical challenges associated with in situ extraction and characterization of trace reduced organic compounds in ancient rocks make it challenging to determine the origins of martian organic matter found to date. Coordinated state-of-the-art laboratory measurements of returned samples from Mars that include spatially resolved chemical, mineralogical, and isotopic studies and molecule-specific isotopic and enantiomeric measurements will be required to firmly establish whether the complex organic matter detected on Mars comes from biotic or abiotic sources. Ultimately, sample return may be our best chance of identifying chemical biosignatures from a past or present martian biota, if one ever existed on Mars. NASA’s Perseverance rover will collect dozens of surface sample cores for possible future return to Earth by NASA and ESA. Here we review our current knowledge of the distributions and enantiomeric and isotopic compositions of non-biological amino acids found in meteorites compared to terrestrial biochemistry and propose a set of measurement criteria that should be used to help establish the origin of any chiral asymmetry detected in samples from Mars [6].

Daniel P Glavin↗
NASA NTRSDate not supplied

The Search for Chiral Asymmetry as a Potential Biosignature in Samples from Mars

The search for evidence of extraterrestrial life in our solar system has been guided by our under-standing of terrestrial biology and its associated biosignatures. The observed homochirality in all life on Earth, that is, the predominance of “left-handed” or L-amino acids and “right-handed” or D-sugars, is a unique property of life that is crucial for molecular recognition, enzymatic function, information storage and structure, and is thought to be a prerequisite for the origin or early evolution of life. Therefore, the detection of L- or D-excesses of chiral amino acids or sugars could be a powerful indicator of extant or extinct life on Mars or other habitable environments in our solar system. However, studies of primitive meteorites have revealed that they contain extraterrestrial amino acids and sugar acids with large enantiomeric excesses (60% and higher) that resulted from non-biological processes [1], complicating the use of chiral asymmetry by itself as a definitive biosignature. The exploration of habitable environments on Mars, including an assessment of the preservation potential for complex organics of either abiotic or biological origin, is an objective of both current and future Mars missions. Now with the unambiguous detection of indigenous organic matter in sedimentary rocks by the Sample Analysis at Mars (SAM) instrument suite on Mars [2-5], NASA’s Curiosity rover has found evidence of the preservation of potential chemical biosignatures in the martian near surface. Although amino acids have not yet been identified by in situ measurements on Mars [5], indigenous achiral amino acids have been identified in one martian meteorite [6]. It is expected that amino acid racemization would be very slow and any chiral or isotopic signatures from an extinct martian biota could be preserved for billions of years, given the extremely cold and dry surface conditions [7]. The ESA/Roscosmos ExoMars mission scheduled for launch next year includes the Rosalind Franklin rover designed to acquire samples from a depth of ~2 m and deliver them to a suite of instruments, including the Mars Organic Molecule Analyzer (MOMA). The MOMA instrument contains a wet chemistry experiment designed specifically for the detection of amino acids and measurement of their enantiomeric compositions [8]. The complexity and limited duration of spaceflight operations, and the known analytical challenges associated with in situ extraction and characterization of trace reduced organic com-pounds in ancient rocks, make it challenging to determine the origins of martian organic matter found to date. Coordinated state-of-the-art laboratory measurements of returned samples from Mars that include spatially resolved chemical, mineralogical, bulk and molecule-specific isotopic, and enantiomeric measurements will be required to firmly establish whether the complex organic matter detected on Mars derives from bio-tic or abiotic processes. Ultimately, Mars Sample Return of rock cores collected by NASA’s Perseverance rover may be our best chance of identifying chemical biosignatures, including any chiral amino acid asymmetry resulting from a past or present martian biota, if one ever existed on Mars. Here we review our current knowledge of the distributions, and enantiomeric and isotopic com-positions of amino acids found in meteorites compared to terrestrial biochemistry. We also propose a set of measurement criteria that should be used to help establish the sources of any amino acids detected in samples returned from Mars using state-of-the-art gas and liquid chromatography mass spectrometry techniques [1].

D P Glavin↗
NASA NTRS2024

Effect of the Liquid-Vacuum Transition on the Relative Abundances of Amino and Fatty Acids Sought as Biosignatures on Icy Ocean Worlds

Interpreting measurements by robotic missions searching for signs of life in material erupted by cryovolcanic ocean worlds (e.g., Enceladus, Europa, Ceres) requires linking the composition of this material to that of its subsurface liquid source. Irrespective of the properties of –and processes along– the path of ejection, material erupted on airless worlds undergoes a transition from liquid to vacuum. Here, we investigate experimentally the effect of a direct transition from liquid to vacuum environments on the relative abundances of amino and carboxylic (fatty) acids, a metric used to distinguish between biological and abiotic sources for these compounds. Amino acids were dissolved in parent solutions prepared with 1 wt.% NaCl and pH 9–10 to match properties inferred from Enceladus plume grains. Compositional analysis of the dry solids resulting from the injection of this solution into vacuum indicates a < 50% change in amino acid abundances relative to glycine. Injection of two fatty acids, phenylacetic acid (soluble and undersaturated in the parent solution) and palmitic acid (insoluble and supersaturated) resulted in a change of less than a factor of 7 in their relative abundances. At this bulk scale (all grains aggregated together), proportions of amino and fatty acids were sufficiently conserved to allow distinction between end-member example biological and abiotic sources. We did not find strong correlations between the relative enrichment or depletion of amino or fatty acids with molecular properties such as molecular mass, hydrophobicity, functionality, or charge, other than high under-or supersaturation. Most of the organic residue was deposited along the experimental injection path, which suggests that cryovolcanic conduit walls on icy ocean worlds may be enriched in organic material relative to material having undergone the liquid-vacuum transition.

Amino acids↗
NASA NTRS1998

Molecular Static Third-Order Polarizabilities of Carbon-Cage Fullerene and Their Correlation with Three Geometric Properties: Symmetry, Aromaticity, and Size

The static third-order polarizabilities (gamma) of C60, C70, five isomers of C78 and two isomers of C84 were analyzed in terms of three properties, from a geometric point of view: symmetry, aromaticity and size. The polarizability values were based on the finite field approximation using a semiempirical Hamiltonian (AM1) and applied to molecular structures obtained from density functional theory calculations. Symmetry was characterized by the molecular group order. The selection of 6-member rings as aromatic was determined from an analysis of bond lengths. Maximum interatomic distance and surface area were the parameters considered with respect to size. Based on triple linear regression analysis, it was found that the static linear polarizability (alpha) and gamma in these molecules respond differently to geometrical properties: alpha depends almost exclusively on surface area while gamma is affected by a combination of number of aromatic rings, length and group order, in decreasing importance. In the case of alpha, valence electron contributions provide the same information as all-electron estimates. For gamma, the best correlation coefficients are obtained when all-electron estimates are used and when the dependent parameter is ln(gamma) instead of gamma.

Moore, C. E.↗
NASA NTRS2006

Biomimetic/Optical Sensors for Detecting Bacterial Species

Biomimetic/optical sensors have been proposed as means of real-time detection of bacteria in liquid samples through real-time detection of compounds secreted by the bacteria. Bacterial species of interest would be identified through detection of signaling compounds unique to those species. The best-characterized examples of quorum-signaling compounds are acyl-homoserine lactones and peptides. Each compound, secreted by each bacterium of an affected species, serves as a signal to other bacteria of the same species to engage in a collective behavior when the population density of that species reaches a threshold level analogous to a quorum. A sensor according to the proposal would include a specially formulated biomimetic film, made of a molecularly imprinted polymer (MIP), that would respond optically to the signaling compound of interest. The MIP film would be integrated directly onto an opticalwaveguide- based ring resonator for optical readout. Optically, the sensor would resemble the one described in Chemical Sensors Based on Optical Ring Resonators (NPO-40601), NASA Tech Briefs, Vol. 29, No. 10 (October 2005), page 32. MIPs have been used before as molecular- recognition compounds, though not in the manner of the present proposal. Molecular imprinting is an approach to making molecularly selective cavities in a polymer matrix. These cavities function much as enzyme receptor sites: the chemical functionality and shape of a cavity in the polymer matrix cause the cavity to bind to specific molecules. An MIP matrix is made by polymerizing monomers in the presence of the compound of interest (template molecule). The polymer forms around the template. After the polymer solidifies, the template molecules are removed from the polymer matrix by decomplexing them from their binding sites and then dissolving them, leaving cavities that are matched to the template molecules in size, shape, and chemical functionality. The cavities thus become molecular-recognition sites that bind only to molecules matched to the sites; other molecules are excluded. In a sensor according to the proposal, the MIP would feature molecular recognition sites that would bind the specific signaling molecules selectively according to their size, shape, and chemical functionality (see figure). As the film took up the signaling molecules in the molecular recognition sites, the index of refraction and thickness of the film would change, causing a wavelength shift of the peak of the resonance spectrum. It has been estimated that by measuring this wavelength shift, it should be possible to detect as little as 10 picomoles of a peptide signaling compound.

Homer, Margie↗
NASA NTRS1986

Space station molecular sieve development

An essential function of a space environmental control system is the removal of carbon dioxide (CO2) from the atmosphere to control the partial pressure of this gas at levels lower than 3 mm Hg. The use of regenerable solid adsorbents for this purpose was demonstrated effectively during the Skylab mission. Earlier sorbent systems used zeolite molecular sieves. The carbon molecular sieve is a hydrophobic adsorbent with excellent potential for space station application. Although carbon molecular sieves were synthesized and investigated, these sieves were designed to simulate the sieving properties of 5A zeolite and for O2/N2 separation. This program was designed to develop hydrophobic carbon molecular sieves for CO2 removal from a space station crew environment. It is a first phase effort involved in sorbent material development and in demonstrating the utility of such a material for CO2 removal on space stations. The sieve must incorporate the following requirements: it must be hydrophobic; it must have high dynamic capacity for carbon dioxide at the low partial pressure of the space station atmosphere; and it must be chemiclly stable and will not generate contaminants.

Chang, C.↗
NASA NTRS1992

Effects of microgravity or simulated launch on testicular function in rats

Reproductive toxicology and cellular and molecular biology approaches were used to evaluate testicular function in rats from Cosmos 2044. It is found that concentrations of testosterone in testicular tissue or peripheral blood plasma were reduced in flight rates to less than 20 percent of values for simulated-launch or vivarium controls. Spermatogenesis was essentially normal in flight rats, but production of testosterone was severely depressed.

Amann, R. P.↗
NASA NTRS2003

A lignin-specific peroxidase in tobacco whose antisense suppression leads to vascular tissue modification

A tobacco peroxidase isoenzyme (TP60) was down-regulated in tobacco using an antisense strategy, this affording transformants with lignin reductions of up to 40-50% of wild type (control) plants. Significantly, both guaiacyl and syringyl levels decreased in essentially a linear manner with the reductions in lignin amounts, as determined by both thioacidolysis and nitrobenzene oxidative analyses. These data provisionally suggest that a feedback mechanism is operative in lignifying cells, which prevents build-up of monolignols should oxidative capacity for their subsequent metabolism be reduced. Prior to this study, the only known rate-limiting processes in the monolignol/lignin pathways involved that of Phe supply and the relative activities of cinnamate-4-hydroxylase/p-coumarate-3-hydroxylase, respectively. These transformants thus provide an additional experimental means in which to further dissect and delineate the factors involved in monolignol targeting to precise regions in the cell wall, and of subsequent lignin assembly. Interestingly, the lignin down-regulated tobacco phenotypes displayed no readily observable differences in overall growth and development profiles, although the vascular apparatus was modified.

NASA Program Fundamental Space Biology↗
NASA NTRS2001

CAP: A Computer Code for Generating Tabular Thermodynamic Functions from NASA Lewis Coefficients

For several decades the NASA Glenn Research Center has been providing a file of thermodynamic data for use in several computer programs. These data are in the form of least-squares coefficients that have been calculated from tabular thermodynamic data by means of the NASA Properties and Coefficients (PAC) program. The source thermodynamic data are obtained from the literature or from standard compilations. Most gas-phase thermodynamic functions are calculated by the authors from molecular constant data using ideal gas partition functions. The Coefficients and Properties (CAP) program described in this report permits the generation of tabulated thermodynamic functions from the NASA least-squares coefficients. CAP provides considerable flexibility in the output format, the number of temperatures to be tabulated, and the energy units of the calculated properties. This report provides a detailed description of input preparation, examples of input and output for several species, and a listing of all species in the current NASA Glenn thermodynamic data file.

Zehe, Michael J.↗
NASA NTRS2002

CAP: A Computer Code for Generating Tabular Thermodynamic Functions from NASA Lewis Coefficients

For several decades the NASA Glenn Research Center has been providing a file of thermodynamic data for use in several computer programs. These data are in the form of least-squares coefficients that have been calculated from tabular thermodynamic data by means of the NASA Properties and Coefficients (PAC) program. The source thermodynamic data are obtained from the literature or from standard compilations. Most gas-phase thermodynamic functions are calculated by the authors from molecular constant data using ideal gas partition functions. The Coefficients and Properties (CAP) program described in this report permits the generation of tabulated thermodynamic functions from the NASA least-squares coefficients. CAP provides considerable flexibility in the output format, the number of temperatures to be tabulated, and the energy units of the calculated properties. This report provides a detailed description of input preparation, examples of input and output for several species, and a listing of all species in the current NASA Glenn thermodynamic data file.

Zehe, Michael J.↗
NASA NTRS2010

Reinforced Thermoplastic Polyimide with Dispersed Functionalized Single Wall Carbon Nanotubes

Molecular pi-complexes were formed from pristine HiPCO single-wall carbon nanotubes (SWCNTs) and 1-pyrene- N-(4- N'-(5-norbornene-2,3-dicarboxyimido)phenyl butanamide, 1. Polyimide films were prepared with these complexes as well as uncomplexed SWCNTs and the effects of nanoadditive addition on mechanical, thermal, and electrical properties of these films were evaluated. Although these properties were enhanced by both nanoadditives, larger increases in tensile strength and thermal and electrical conductivities were obtained when the SWCNT/1 complexes were used. At a loading level of 5.5 wt %, the Tg of the polyimide increased from 169 to 197 C and the storage modulus increased 20-fold (from 142 to 3045 MPa). The addition of 3.5 wt % SWCNT/1 complexes increased the tensile strength of the polyimide from 61.4 to 129 MPa; higher loading levels led to embrittlement and lower tensile strengths. The electrical conductivities (DC surface) of the polyimides increased to 1 x 10(exp -4) Scm(exp -1) (SWCNT/1 complexes loading level of 9 wt %). Details of the preparation of these complexes and their effects on polyimide film properties are discussed.

Lebron-Colon, Marisabel↗
NASA NTRS2003

The Chemistry and Excitation of Water in Molecular Clouds

We model the chemistry and thermal balance of opaque molecular clouds exposed to an external flux of ultraviolet photons. We include the processes of gas phase and grain surface chemical reactions; in particular we examine closely the freezing of atoms and molecules onto grain surfaces and the desorption of molecules from grain surfaces as a function of depth into a molecular cloud. We find that on the surface of a molecular cloud the gas phase water abundances are low because of photodissociation, and the grain phase water (ice) abundance is low because of photodesorption of water from the grain surfaces. Deeper into the cloud, at A(sub v) less than or approximately 2-8 depending on the strength of the external ultraviolet flux, the gas phase water abundance increases with depth as the photodissociation rates decline due to dust attenuation of the ultraviolet field. However, beyond A(sub v) less than or approximately 2-8 the gas phase water abundance declines because the water freezes as water ice on the grains, and photodesorption is no longer effective in clearing the ice. A peak water abundance of about 10(exp -6) to 10(exp -7) occurs at about A(sub v) approximately 2-8, relatively independent of the gas density and the ultraviolet field. We show that such a model matches very closely the observations of the Submillimeter Wave Astronomical Satellite (SWAS), a NASA Small Explorer Mission. The model elucidates several mechanisms that have been recently invoked to understand gas phase chemistry in clouds, including-the freeze-out of molecules onto grain surface, the desorption of these molecules from the surfaces, and the abundance gradients of molecules as functions of depth into molecular clouds.

Hollenbach, David↗
NASA NTRS1991

Effect of the rotational-vibrational excitation on molecular diameters

The kinetic molecular diameters of rotationally and vibrationally excited diatomic molecules and molecular ions are derived as functions of the rotational and vibrational quantum numbers of the molecules. Typical molecular diameters are studied in two cases: in low-temperature gas, where the molecular diameter is independent of the degree of rotational-vibrational excitation of the molecules, and in high-temperature gas, where the molecular diameter depends on the degree of rotational-vibrational excitation of the molecules. The rotational-vibrational excitation of molecules is shown to have a meaningful effect on the collisional properties of gases. The effect is stronger in gases of weakly-bound molecules.

Kang, S. H.↗