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At least 325 records · Page 18

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NASA NTRS1993

Structure and thermochemistry of ClO2 radicals

The structure of ClO2 has been calculated for the X 2A-double prime ground state using unrestricted Hartree-Fock (UHF), unrestricted second-order Moller-Plesset perturbation (UMP2), configuration interaction employing single and double excitation (CISD), and quadratic configuration interaction (QCI) ab initio molecular orbital methods. Calculations using UMP2 and CISD wave functions predict a ClO bond length of 1.728 +/- 0.01 A. The single-configuration-based QCI in the singles and doubles space with perturbation inclusion of triple substitutions, denoted QCISD(T), yield a ClO bond length of 2.205 A. The QCI results are consistent with results of Jensen (1990) who showed that the ClO bond length is 2.181 A using annihilated self-consistent methods (AUMP2). The thermochemistry of ClO2 radical has been calculated using MP2 and QCI methods employing an isodesmic scheme. Our scheme predicts the heat of formation for ClO2 at 0 K to be 24.6 +/- 2 kcal/mol.

Francisco, J. S.↗

NASA NTRS1999

Computational Study of Field Initiated Surface Reactions for Synthesis of Diamond and Silicon

This project involves using quantum chemistry to simulate surface chemical reactions in the presence of an electric field for nanofabrication of diamond and silicon. A field delivered by a scanning tunneling microscope (STM) to a nanometer scale region of a surface affects chemical reaction potential energy surfaces (PES) to direct atomic scale surface modification to fabricate sub-nanometer structures. Our original hypothesis is that the applied voltage polarizes the charge distribution of the valence electrons and that these distorted molecular orbitals can be manipulated with the STM so as to change the relative stabilities of the electronic configurations over the reaction coordinates and thus the topology of the PES and reaction kinetics. Our objective is to investigate the effect of applied bias on surface reactions and the extent to which STM delivered fields can be used to direct surface chemical reactions on an atomic scale on diamond and silicon. To analyze the fundamentals of field induced chemistry and to investigate the application of this technique for the fabrication of nanostructures, we have employed methods capable of accurately describing molecular electronic structure. The methods we employ are density functional theory (DFT) quantum chemical (QC) methods. To determine the effect of applied bias on surface reactions we have calculated the QC PESs in various applied external fields for various reaction steps for depositing or etching diamond and silicon. We have chosen reactions which are thought to play a role in etching and the chemical vapor deposition growth of Si and diamond. The PESs of the elementary reaction steps involved are then calculated under the applied fields, which we vary in magnitude and configuration. We pay special attention to the change in the reaction barriers, and transition state locations, and search for low energy reaction channels which were inaccessible without the applied bias.

Musgrave, Charles Bruce↗

NASA NTRS2001

Simulation of Peptides at Aqueous Interfaces

Behavior of peptides at water-membrane interfaces is of great interest in studies on cellular transport and signaling, membrane fusion, and the action of toxins and antibiotics. Many peptides, which exist in water only as random coils, can form sequence-dependent, ordered structures at aqueous interfaces, incorporate into membranes and self-assembly into functional units, such as simple ion channels. Multi -nanosecond molecular dynamics simulations have been carried out to study the mechanism and energetics of interfacial folding of both non-polar and amphiphilic peptides, their insertion into membranes and association into higher-order structures. The simulations indicate that peptides fold non-sequentially, often through a series of amphiphilic intermediates. They further incorporate into the membrane in a preferred direction as folded monomers, and only then aggregate into dimers and, possibly, further into "dimers of dimers".

Pohorille, Andrew↗

NASA NTRS1996

Transport proteins of the plant plasma membrane

Recently developed molecular and genetic approaches have enabled the identification and functional characterization of novel genes encoding ion channels, ion carriers, and water channels of the plant plasma membrane.

Non-NASA Center↗

NASA NTRS2005

Drosophila melanogaster--the model organism of choice for the complex biology of multi-cellular organisms

Drosophila melanogaster has been intensely studied for almost 100 years. The sophisticated array of genetic and molecular tools that have evolved for analysis of gene function in this organism are unique. Further, Drosophila is a complex multi-cellular organism in which many aspects of development and behavior parallel those in human beings. These combined advantages have permitted research in Drosophila to make seminal contributions to the understanding of fundamental biological processes and ensure that Drosophila will continue to provide unique insights in the genomic era. An overview of the genetic methodologies available in Drosophila is given here, together with examples of outstanding recent contributions of Drosophila to our understanding of cell and organismal biology. The growing contribution of Drosophila to our knowledge of gravity-related responses is addressed.

Review, Tutorial↗

NASA NTRS1987

Diatomic molecules in the solar infrared spectrum from ATMOS-SL 3 high resolution observations

The ATMOS Fourier Transform Spectrometer has observed, for the first time, the solar infrared spectrum, from 2 to 16 microns, free of any telluric absorption. A very large number of molecular lines are present on these high quality spectra: vibration-rotation lines of CO (Delta-v = 1 and 2; including the isotopic species C-13, O-18 and O-17), CH, NH, OH and pure rotation lines of OH. The analysis of these lines will allow to derive accurate values for the solar abundances of C, N and O and the isotopic ratios C-13/C-12, O-18/O-16, and O-17/O-16, to test the photospheric model from high to deep layers, to test the electric dipole moment functions of the different molecules and to derive much better molecular constants for CH.

Grevesse, Nicolas↗

NASA NTRS2004

Computational studies of Ras and PI3K

Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

Ren, Lei↗

NASA NTRS1985

Enhancement of molecular weight build up in polyimides using ether solvents

Two linear polyimides were prepared in various ether and amide solvents. The inherent viscosity was then monitored as a function of time. The polymers made in the ether solvents consistently gave higher inherent viscosities, and thus molecular weights, than the same polymers made in the amide solvents. This molecular weight buildup is attributed to the unique solvation mechanism of the ether solvents which enhances the basicity of the amines via hydrogen bonding.

Egli, Annemarie H.↗

NASA NTRS1999

A molecular description of the evolution of resistance

BACKGROUND: In vitro evolution has been used to obtain nucleic acid molecules with interesting functional properties. The evolution process usually is carried out in a stepwise manner, involving successive rounds of selection, amplification and mutation. Recently, a continuous in vitro evolution system was devised for RNAs that catalyze the ligation of oligonucleotide substrates, allowing the evolution of catalytic function to be studied in real time. RESULTS: Continuous in vitro evolution of an RNA ligase ribozyme was carried out in the presence of a DNA enzyme that was capable of cleaving, and thereby inactivating, the ribozyme. The DNA concentration was increased steadily over 33.5 hours of evolution, reaching a final concentration that would have been sufficient to inactivate the starting population in one second. The evolved population of ribozymes developed resistance to the DNA enzyme, reducing their vulnerability to cleavage by 2000-fold but retaining their own catalytic function. Based on sequencing and kinetic analysis of the ribozymes, two mechanisms are proposed for this resistance. One involves three nucleotide substitutions, together with two compensatory mutations, that alter the site at which the DNA enzyme binds the ribozyme. The other involves enhancement of the ribozyme's ability to bind its own substrate in a way that protects it from cleavage by the DNA enzyme. CONCLUSIONS: The ability to direct the evolution of an enzyme's biochemical properties in response to the behavior of another macromolecule provides insight into the evolution of resistance and may be useful in developing enzymes with novel or enhanced function.

Non-NASA Center↗

NASA NTRS1987

Computer modeling of the neurotoxin binding site of acetylcholine receptor spanning residues 185 through 196

A model of the complex between the acetylcholine receptor and the snake neurotoxin, cobratoxin, was built by molecular model building and energy optimization techniques. The experimentally identified functionally important residues of cobratoxin and the dodecapeptide corresponding to the residues 185-196 of acetylcholine receptor alpha subunit were used to build the model. Both cis and trans conformers of cyclic L-cystine portion of the dodecapeptide were examined. Binding residues independently identified on cobratoxin are shown to interact with the dodecapeptide AChR model.

NASA Discipline Exobiology↗

NASA NTRS1984

A low Earth orbit molecular beam space simulation facility

A brief synopsis of the low Earth orbit (LEO) satellite environment is presented including neutral and ionic species. Two ground based atomic and molecular beam instruments are described which are capable of simulating the interaction of spacecraft surfaces with the LEO environment and detecting the results of these interactions. The first detects mass spectrometrically low level fluxes of reactively and nonreactively surface scattered species as a function of scattering angle and velocity while the second ultrahigh velocity (UHV) molecular beam, laser induced fluorescence apparatus is capable of measuring chemiluminescence produced by either gas phase or gas-surface interactions. A number of proposed experiments are described.

Cross, J. B.↗

NASA NTRS1987

Thermal instabilities in diffuse molecular clouds - Formation of molecular cloud cores

The stability of diffuse clouds to thermal instabilities is examined using the semiempirical cooling function derived by Tarafdar et al. (1985) for these clouds. It is found that diffuse clouds which obey such a cooling function are susceptible to thermal instability at densities n of less than about 70-80/cu cm. The growth rate for instability is large and the mass contained in unstable regions ranges from about 0.001 to 1 solar mass. It is suggested that such instabilities may trigger formation of molecular cloud cores of the type found in low-mass molecular clouds (e.g., TMC-2). Criteria for thermal instability in self-gravitating systems are also derived.

Graziani, Frank R.↗

NASA NTRS2000

T Lymphocyte Activation Threshold is Increased in Reduced Gravity

There have been substantial advances in molecular and cellular biology that have provided new insight into the biochemical and genetic basis of lymphocyte recognition, activation and expression of distinct functional phenotypes. It has now become evident that for both T and B cells, stimuli delivered through their receptors can result in either clonal expansion or apoptosis. In the case of T cells, clonal expansion of helper cells is accompanied by differentiation into two major functional subsets which regulate the immune response. The pathways between the membrane and the nucleus and their molecular components are an area of very active investigation. This meeting will draw together scientists working on diverse aspects of this problem, including receptor ligand interactions, intracellular pathways that transmit receptor mediated signals and the effect of such signal transduction pathways on gene regulation. The aim of this meeting is to integrate the information from these various experimental approaches into a new synthesis and molecular explanation of T cell activation, differentiation and death.

Adams, Charley L.↗

NASA NTRS2000

The origin of cellular life

This essay presents a scenario of the origin of life that is based on analysis of biological architecture and mechanical design at the microstructural level. My thesis is that the same architectural and energetic constraints that shape cells today also guided the evolution of the first cells and that the molecular scaffolds that support solid-phase biochemistry in modern cells represent living microfossils of past life forms. This concept emerged from the discovery that cells mechanically stabilize themselves using tensegrity architecture and that these same building rules guide hierarchical self-assembly at all size scales (Sci. Amer 278:48-57;1998). When combined with other fundamental design principles (e.g., energy minimization, topological constraints, structural hierarchies, autocatalytic sets, solid-state biochemistry), tensegrity provides a physical basis to explain how atomic and molecular elements progressively self-assembled to create hierarchical structures with increasingly complex functions, including living cells that can self-reproduce.

Review, Academic↗

NASA NTRS1991

Simulation studies for surfaces and materials strength

Investigations were carried out in the following three areas. First, a simulation study was conducted to investigate the early stages of a nucleation and growth mechanism taking place on diamond surfaces. The energetically most favorable binding sites were calculated along with the binding energies for up to three carbon atoms deposited on the planes of a diamond crystal. Secondly, calculations were carried out to analyze energies and structural properties for restructured patterns of the surface of a diamond. Two different model functions, developed recently for carbon, were employed in the calculations. Lastly, a crack propagation process for the graphitic basal plane, was investigated using a molecular dynamics technique. Interactions among carbon atoms in the system were calculated using the Tersoff potential energy function.

Halicioglu, Timur↗

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 NTRS1972

Quantum statistical mechanics of dense partially ionized hydrogen

The theory of dense hydrogen plasmas beginning with the two component quantum grand partition function is reviewed. It is shown that ionization equilibrium and molecular dissociation equilibrium can be treated in the same manner with proper consideration of all two-body states. A quantum perturbation expansion is used to give an accurate calculation of the equation of state of the gas for any degree of dissociation and ionization. The statistical mechanical calculation of the plasma equation of state is intended for stellar interiors. The general approach is extended to the calculation of the equation of state of the outer layers of large planets.

Dewitt, H. E.↗

NASA NTRS1982

Some characteristics of polymers in composite materials and as electrical conductors

The characteristics of carbon fibers (CF) made from polyacrylonitrile (PAN) materials are discussed, together with research on conducting polymers. CF materials have better mechanical properties, chemical inertness, and higher stiffness than metallic materials but are subject to environmental instability, flammability, and delamination fatigue. Polymerization procedures for the monopolymer PAN are described, noting the use of SEM and X-ray diffraction techniques for studying the fiber structure. High modulus and strength of CF are caused by covalent sp(2) bonds in hexagonal carbon rings, which are stronger than the same links in diamonds. Details of the molecular chain structures and macroformations, stress-strain as a function of temperature, and thermosetting and glass transition temperatures of polymers are provided. Computational quantum chemistry techniques are being applied to studying electrical conductance in polymers, mainly to discover ways to stabilize the materials. Doped CH(x) has exhibited photovoltaic properties and other polymers have become superconductors at cryogenic temperatures.

Hansen, C. F.↗