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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
NASA NTRS1996

Positive selection moments identify potential functional residues in human olfactory receptors

Correlated mutation analysis and molecular models of olfactory receptors have provided evidence that residues in the transmembrane domains form a binding pocket for odor ligands. As an independent test of these results, we have calculated positive selection moments for the alpha-helical sixth transmembrane domain (TM6) of human olfactory receptors. The moments can be used to identify residues that have been preferentially affected by positive selection and are thus likely to interact with odor ligands. The results suggest that residue 622, which is commonly a serine or threonine, could form critical H-bonds. In some receptors a dual-serine subsite, formed by residues 622 and 625, could bind hydroxyl determinants on odor ligands. The potential importance of these residues is further supported by site-directed mutagenesis in the beta-adrenergic receptor. The findings should be of practical value for future physiological studies, binding assays, and site-directed mutagenesis.

Non-NASA Center↗
NASA NTRS2011

The Importance of Water for High Fidelity Information Processing and for Life

Is water an absolute prerequisite for life? Life depends on a variety of non-covalent interactions among molecules, the nature of which is determined as much by the solvent in which they occur as by the molecules themselves. Catalysis and information processing, two essential functions of life, require non-covalent molecular recognition with very high specificity. For example, to correctly reproduce a string consisting of 600,000 units of information (e.g ., 600 kilobases, equivalent to the genome of the smallest free living terrestrial organisms) with a 90% success rate requires specificity > 107 : 1 for the target molecule vs. incorrect alternatives. Such specificity requires (i) that the correct molecular association is energetically stabilized by at least 40 kJ/mol relative to alternatives, and (ii) that the system is able to sample among possible states (alternative molecular associations) rapidly enough to allow the system to fall under thermodynamic control and express the energetic stabilization. We argue that electrostatic interactions are required to confer the necessary energetic stabilization vs. a large library of molecular alternatives, and that a solvent with polarity and dielectric properties comparable to water is required for the system to sample among possible states and express thermodynamic control. Electrostatic associations can be made in non-polar solvents, but the resulting complexes are too stable to be "unmade" with sufficient frequency to confer thermodynamic control on the system. An electrostatic molecular complex representing 3 units of information (e.g., 3 base pairs) with specificity > 107 per unit has a stability in non-polar solvent comparable to that of a carbon-carbon bond at room temperature. These considerations suggest that water, or a solvent with properties very like water, is necessary to support high-fidelity information processing, and can therefore be considered a critical prerequisite for life.

Hoehler, Tori M.↗
NASA NTRS2005

Reliable Spectroscopic Constants for CCH-, NH2- and Their Isotopomers from an Accurate Potential Energy Function

Accurate quartic force fields have been determined for the CCH- and NH2- molecular anions using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). Very large one-particle basis sets have been used including diffuse functions and up through g-type functions. Correlation of the nitrogen and carbon core electrons has been included, as well as other "small" effects, such as the diagonal Born-Oppenheimer correction, and basis set extrapolation, and corrections for higher-order correlation effects and scalar relativistic effects. Fundamental vibrational frequencies have been computed using standard second-order perturbation theory as well as variational methods. Comparison with the available experimental data is presented and discussed. The implications of our research for the astronomical observation of molecular anions will be discussed.

Lee, Timothy J.↗
NASA NTRS2015

The Effect of Surface Chemical Functionality Upon Ice Adhesion

In nature, anti-freeze proteins present in fish utilize specific organic functionalities to disrupt ice crystal formation and propagation. Based on these structures, surfaces with controlled chemical functionality and chain length were evaluated both experimentally and computationally to assess the effect of both parameters in mitigating ice formation. Linear aliphatic dimethylethoxysilanes terminated with methyl or hydroxyl groups were prepared, characterized, and used to coat aluminum. The effect upon icing using a microdroplet freezing apparatus and the Adverse Environment Rotor Test Stand found hydroxyl-terminated materials exhibited a greater propensity for ice formation and adhesion. Molecular dynamics simulations of a silica substrate bearing functionalized species of similar composition were brought into contact with a pre-equilibrated ice crystal. Several parameters including chain mobility were monitored to ascertain the size of a quasi-liquid layer. The studies suggested that chain mobility affected the interface between ice and the surface more than terminal group chemical composition.

Smith, Joseph G., Jr.↗
NASA NTRS2010

Selective Functionalization of Carbon Nanotubes: Part II

An alternative method of low-temperature plasma functionalization of carbon nanotubes provides for the simultaneous attachment of molecular groups of multiple (typically two or three) different species or different mixtures of species to carbon nanotubes at different locations within the same apparatus. This method is based on similar principles, and involves the use of mostly the same basic apparatus, as those of the methods described in "Low-Temperature Plasma Functionalization of Carbon Nanotubes" (ARC-14661-1), NASA Tech Briefs, Vol. 28, No. 5 (May 2004), page 45. The figure schematically depicts the basic apparatus used in the aforementioned method, with emphasis on features that distinguish the present alternative method from the other. In this method, one exploits the fact that the composition of the deposition plasma changes as the plasma flows from its source in the precursor chamber toward the nanotubes in the target chamber. As a result, carbon nanotubes mounted in the target chamber at different flow distances (d1, d2, d3 . . .) from the precursor chamber become functionalized with different species or different mixtures of species. In one series of experiments to demonstrate this method, N2 was used as the precursor gas. After the functionalization process, the carbon nanotubes from three different positions in the target chamber were examined by Fourier-transform infrared spectroscopy to identify the molecular groups that had become attached. On carbon nanotubes from d1 = 1 cm, the attached molecular groups were found to be predominantly C-N and C=N. On carbon nanotubes from d2 = 2.5 cm, the attached molecular groups were found to be predominantly C-(NH)2 and/or C=NH2. (The H2 was believed to originate as residual hydrogen present in the nanotubes.) On carbon nanotubes from d3 = 7 cm no functionalization could be detected - perhaps, it was conjectured, because this distance is downstream of the plasma source, all of the free ions and free radicals of the plasma had recombined into molecules.

Meyyappan, Meyya↗
NASA NTRSDate not supplied

Modeling Ring-Opening Polymerization with Machine-Learned Committors

Many important industrial and biological processes depend on ring-opening polymerization (ROP), including large-scale production polymers, such as nylon 6, and a variety of biodegradable polymers and high-performance resins. Large-scale simulations (>200K atoms) of ROP were performed using a deep neural network-based method that captured the effect of the local chemical environment of the reactive sites using training data from quantum chemical methods. The utility of this method was demonstrated by modeling the cationic ROP of bis-benzoxazine, a promising resin for use in advanced high-temperature application composites (>200°C). Density functional theory calculations were used to map out the various ring opening and polymerization reaction paths that occur during the thermal processing of bis-benzoxazine. The probabilities of these reactions, as a function of local atomic configurations, were used to construct committor functions using a neural network approach. The learned committor functions were then used to determine when a particular reaction occurred within the REACTER framework for reactive molecular dynamics simulations. The experimentally observed exotherm that occurs during bis-benzoxazine ROP was captured in an effective manner in the simulations by imposing a local heating of the system that corresponds to the enthalpy of reaction for each reaction. The dependence of the final polymer morphology on the ROP reaction temperature was analyzed at the molecular scale. The results presented in this work indicate that machine-learned committor functions are a promising approach for incorporating high-fidelity reactivity criteria that capture the effect of local chemical environments into large-scale polymerization simulations.

machine learning, polymer simulations, molecular d↗
NASA NTRS1998

Study of Atmospheric Nitric Oxide

We investigated the contribution of energetic nitrogen atoms to the production of nitric oxide in the thermosphere and their influence on the infrared emission spectrum. The nitric oxide molecules are important contributors to the cooling of the atmosphere. We first pointed out that in determining the energy distribution of the nitrogen atoms, it is important to take into account the thermal motion of the atmospheric gases. It had been ignored in all earlier studies. The source spectra are broadened considerably by the center of mass motion of the reactants. We worked out the consequences for the production of nitric oxide at night, using as sources of energetic N atoms, NO(+) + e yield N + O, N(D-2) + O yield N + O. The high energy tail is enhanced by orders of magnitude. We had earlier suggested (Sharma et al. 1993) that the reaction of energetic nitrogen atoms with O2 was responsible for the rotationally enhanced NO identified in the infrared spectrum. Our calculations provided quantitative confirmation of the suggestion. We proceeded to explore the validity of another approximation used in earlier analyses, the hard sphere approximation for the energy loss in elastic collisions. We carried out precise quantum mechanical calculations of the elastic 2 differential scattering of nitrogen atoms in collisions with oxygen atoms and showed that although the hard sphere approximation was nowhere of high precision, reasonable results could be obtained with an effective cross section of 6 x 10(exp 15)sq cm. We also initiated a program to include inelastic energy loss processes in the determination of the energy distribution function. We began a calculation of the rotation and vibrational excitation cross sections of molecular nitrogen and nitrogen atoms and developed a method for including inelastic energy loss as a function of scattering angle in the Boltzmann equation. A procedure for obtaining the solution of the Boltzman equation was worked out.

Dalgarno, A.↗
NASA NTRS2005

Thermal, Radiation and Impact Protective Shields (TRIPS) for Robotic and Human Space Exploration Missions

New concepts for protective shields for NASA s Crew Exploration Vehicles (CEVs) and planetary probes offer improved mission safety and affordability. Hazards include radiation from cosmic rays and solar particle events, hypervelocity impacts from orbital debris/ micrometeorites, and the extreme heating environment experienced during entry into planetary atmospheres. The traditional approach for the design of protection systems for these hazards has been to create single-function shields, i.e. ablative and blanket-based heat shields for thermal protection systems (TPS), polymer or other low-molecular-weight materials for radiation shields, and multilayer, Whipple-type shields for protection from hypervelocity impacts. This paper introduces an approach for the development of a single, multifunctional protective shield, employing nanotechnology- based materials, to serve simultaneously as a TPS, an impact shield and as the first line of defense against radiation. The approach is first to choose low molecular weight ablative TPS materials, (existing and planned for development) and add functionalized carbon nanotubes. Together they provide both thermal and radiation (TR) shielding. Next, impact protection (IP) is furnished through a tough skin, consisting of hard, ceramic outer layers (to fracture the impactor) and sublayers of tough, nanostructured fabrics to contain the debris cloud from the impactor before it can penetrate the spacecraft s interior.

Loomis, M. P.↗
NASA NTRS2002

Insertional Mutagenesis for Genes involved in Otic/Vestibular Development and Function in Xenopus Tropicalis

Sensitivity to gravity is essential for spatial orientation. Consequently, the gravity receptor system is one of the phylogenetically oldest sensory systems, and the special adaptations that enhance sensitivity to gravity are highly conserved. The main goal of this project is to use Xenopus (frog) to identify genes expressed during vestibular and auditory development. These studies will lead a better understanding of the molecular mechanisms involved in vestibular and auditory development and function. We are using a gene-trap approach in Xenopus tropicalis with the green fluorescent protein (GFP) gene as the transgene reporter. GFP expression occurs only when the GFP gene is correctly integrated in actively transcribed genes. Using the GFP as a tag we can easily identify and clone the mutated gene. In addition, we can study the function of the mutated gene by analyzing the defects generated by insertion of the GFP transgene. To date we have tissue specific GFP expression in X. tropicalis including expression in ear, neural tube, kidney, muscle, eyes and nose. Our transgenic animals will soon reach maturity so that we can outcross them and analyze their progeny. Our next goal is to isolate RNA from our transgenics and clone the tagged genes using RACE-PCR. Currently we are optimizing the RACE-PCR method using transgenics with crystallin GFP expression.

Torrejon, Marcela↗
NASA NTRS1994

An improved quasistatic line-shape theory: The effects of molecular motion on the line wings

A theory is presented for the modification of the line-shape functions and absorption coefficient due to the breakdown of the quasistatic approximation. This breakdown arises from the effects of molecular motion and increases the absorption in the near wings. Numerical calculations for the high-frequency wing of the nu(sub 3) band of CO2 broadened by Ar are reported and it is shown that these effects are significant near the bandhead. The importance of such corrections in other spectral regions and for other systems is discussed briefly.

Ma, Q.↗
NASA NTRS1996

NanoDesign: Concepts and Software for a Nanotechnology Based on Functionalized Fullerenes

Eric Drexler has proposed a hypothetical nanotechnology based on diamond and investigated the properties of such molecular systems. While attractive, diamonoid nanotechnology is not physically accessible with straightforward extensions of current laboratory techniques. We propose a nanotechnology based on functionalized fullerenes and investigate carbon nanotube based gears with teeth added via a benzyne reaction known to occur with C60. The gears are single-walled carbon nanotubes with appended coenzyme groups for teeth. Fullerenes are in widespread laboratory use and can be functionalized in many ways. Companion papers computationally demonstrate the properties of these gears (they appear to work) and the accessibility of the benzyne/nanotube reaction. This paper describes the molecular design techniques and rationale as well as the software that implements these design techniques. The software is a set of persistent C++ objects controlled by TCL command scripts. The c++/tcl interface is automatically generated by a software system called tcl_c++ developed by the author and described here. The objects keep track of different portions of the molecular machinery to allow different simulation techniques and boundary conditions to be applied as appropriate. This capability has been required to demonstrate (computationally) our gear's feasibility. A new distributed software architecture featuring a WWW universal client, CORBA distributed objects, and agent software is under consideration. The software architecture is intended to eventually enable a widely disbursed group to develop complex simulated molecular machines.

Globus, Al↗
NASA NTRS2004

Low-Temperature Plasma Functionalization of Carbon Nanotubes

A low-temperature plasma process has been devised for attaching specified molecular groups to carbon nanotubes in order to impart desired chemical and/or physical properties to the nanotubes for specific applications. Unlike carbon-nanotube- functionalization processes reported heretofore, this process does not involve the use of wet chemicals, does not involve exposure of the nanotubes to high temperatures, and generates very little chemical residue. In addition, this process can be carried out in a relatively simple apparatus and can readily be scaled up to mass production.

Khare, Bishun↗
NASA NTRS1994

The luminosity functions of embedded stellar clusters. 1: Method of solution and analytic results

We describe a method for computing the history of the luminosity function in a young cluster still forming within a molecular cloud complex. Our method, which utilizes detailed results from stellar evolution theory, assumes that clusters arise from the continuous collapse of dense cloud cores over a protracted period of time. It is also assumed that stars reaching the main sequence are distributed in mass according to a prescribed initial mass function (IMF). We keep track separately of the contributions to the luminosity function from the populations of protostars, pre-main-sequence stars, and main-sequence stars. We derive expressions for the fractional contribution of these populations to both the total number of stars produced and the total cluster luminosity. In our model, the number of protostars rises quickly at first, but then levels off to a nearly constant value, which it maintains until the dispersal of the cloud complex. The number fraction of protostars always decreases with time. Averaged over the life of the parent cloud, this fraction is typically a few percent. The protostar mass distribution can be expressed as an integral over the IMF.

Fletcher, Andre B.↗
NASA NTRS1994

On the massive star-forming capacity of molecular clouds

Assuming that photoionization is the self-limiting process for continued star formation, we estimate the maximum number of massive (OB) stars that can form within a molecular cloud. The most efficient cloud destruction mechanism in the early stages of H II region evolution is the evaporation of the cloud by stars located near the cloud boundary. The maximum number of OB stars is of order 1 per 10(exp 4) solar mass of average molecular gas, or 10 per 10(exp 4) solar mass of dense molecular gas. The resulting star-forming efficiencies within cloud complexes range from 2% to 16% depending on both the location of the stars in the cloud and the details of the initial mass function, with an overall value of about 5% for average molecular gas.

Franco, Jose↗
NASA NTRS1972

Development of thermally stable phosphonitrile elastomers for advanced aerospace structures

Attempts to prepare low molecular weight, curable poly-(fluoroalkoxyphosphazenes) have been successful. Derivatization of /Cl2PN/n polymer with alkoxides gave functionally reactive terpolymers. These terpolymers could be crosslinked with polyisocyanates at room temperature. Attempts to control molecular weight have not been as successful. The effects of (Cl2PN)3 monomer purity, use of (Cl2PN)3,4 mixture, and early termination of the bulk polymerization of (Cl2PN)3 were studied briefly. Both low and high molecular weight polymers were obtained. Reaction of NH4Cl with PCl5 with subsequent heating to give chain extension gave either gels of oils with molecular weights of several thousand. The stabilization of poly-(fluoroalkoxyphosphazene) was investigated. The results generally were inconclusive, but acids were found to be deleterious while bases had little discernible effect. Improvements in stability by modification of end groups was inconclusive.

Reynard, K. A.↗
NASA NTRS1993

Diffusion on Cu surfaces

Understanding surface diffusion is essential in understanding surface phenomena, such as crystal growth, thin film growth, corrosion, physisorption, and chemisorption. Because of its importance, various experimental and theoretical efforts have been directed to understand this phenomena. The Field Ion Microscope (FIM) has been the major experimental tool for studying surface diffusion. FIM have been employed by various research groups to study surface diffusion of adatoms. Because of limitations of the FIM, such studies are only limited to a few surfaces: nickel, platinum, aluminum, iridium, tungsten, and rhodium. From the theoretical standpoint, various atomistic simulations are performed to study surface diffusion. In most of these calculations the Embedded Atom Method (EAM) along with the molecular static (MS) simulation are utilized. The EAM is a semi-empirical approach for modeling the interatomic interactions. The MS simulation is a technique for minimizing the total energy of a system of particles with respect to the positions of its particles. One of the objectives of this work is to develop the EAM functions for Cu and use them in conjunction with the molecular static (MS) simulation to study diffusion of a Cu atom on a perfect as well as stepped Cu(100) surfaces. This will provide a test of the validity of the EAM functions on Cu(100) surface and near the stepped environments. In particular, we construct a terrace-ledge-kink (TLK) model and calculate the migration energies of an atom on a terrace, near a ledge site, near a kink site, and going over a descending step. We have also calculated formation energies of an atom on the bare surface, a vacancy in the surface, a stepped surface, and a stepped-kink surface. Our results are compared with the available experimental and theoretical results.

Karimi, Majid↗
NASA NTRS2002

Predicting functional divergence in protein evolution by site-specific rate shifts

Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

Review↗