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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 NTRS1998

Analysis of Retrieved Hubble Space Telescope Thermal Control Materials

Townsend, Jacqueline A.↗

NASA NTRS1994

Dielectric Properties of Poly(ethylene oxide) from Molecular Dynamics Simulations

The order, conformations and dynamics of poly(oxyethylene) (POE) melts have been investigated through molecular dynamics simulations. The potential energy functions were determined from detailed ab initio electronic structure calculations of the conformational energies of the model molecules 1,2-dimethoxyethane (DME) and diethylether. The x-ray structure factor for POE from simulation will be compared to experiment. In terms of conformation, simulations reveal that chains are extended in the melt relative to isolated chains due to the presence of strong intermolecular O...H interactions, which occur at the expense of intramolecular O...H interactions. Conformational dynamics about the C-C bond were found to be significantly faster than in polymethylene, while conformational dynamics about the C-O bond even faster than the C-C dynamics. The faster local dynamics in POE relative to polymethylene is consistent with C-13 NMR spin-lattice relaxation experiments. Conformational transitions showed significant second-neighbor correlation, as was found for polymethylene. This correlation of transitions with C-C neighbors was found to be reduced relative to C-O neighbors. Dielectric relaxation from simulation will also be compared with experiment.

Smith, Grant D.↗

NASA NTRS2003

Structural Basis for "Flip-Flop" Action of Human Pyruvate Dehydrogenase

The derivative of vitamin B1, thiamin pyrophosphate is a cofactor of pyruvate dehydrogenase, a component enzyme of the mitochondrial pyruvate dehydrogenase multienzyme complex that plays a major role in directing energy metabolism in the cell. This cofactor is used to cleave the C(sup alpha)-C(=O) bond of pyruvate followed by reductive acetyl transfer to lipoyl-dihydrolipoamide acetyltransferase. In alpha(sub 2)beta(sub 2)-tetrameric human pyruvate dehydrogenase, there are two cofactor binding sites, each of them being a center of independently conducted, although highly coordinated enzymatic reactions. The dynamic nonequivalence of two, otherwise chemically equivalent, catalytic sites can now be understood based on the recently determined crystal structure of the holo-form of human pyruvate dehydrogenase at 1.95A resolution. The structure of pyruvate dehydrogenase was determined using a combination of MAD phasing and molecular replacement followed by rounds of torsion-angles molecular-dynamics simulated-annealing refinement. The final pyruvate dehydrogenase structure included coordinates for all protein amino acids two cofactor molecules, two magnesium and two potassium ions, and 742 water molecules. The structure was refined to R = 0.202 and R(sub free) = 0.244. Our structural analysis of the enzyme folding and domain assembly identified a simple mechanism of this protein motion required for the conduct of catalytic action.

Ciszak, Ewa↗

NASA NTRS2006

Modeling of Interfacial Modification Effects on Thermal Conductivity of Carbon Nanotube Composites

The effect of functionalization of carbon nanotubes on the thermal conductivity of nanocomposites has been studied using a multi-scale modeling approach. These results predict that grafting linear hydrocarbon chains to the surface of a single wall carbon nanotube with covalent chemical bonds should result in a significant increase in the thermal conductivity of these nanocomposites. This is due to the decrease in the interfacial thermal (Kapitza) resistance between the single wall carbon nanotube and the surrounding polymer matrix upon chemical functionalization. The nanocomposites studied here consist of single wall carbon nanotubes in a bulk poly(ethylene vinyl acetate) matrix. The nanotubes are functionalized by end-grafting linear hydrocarbon chains of varying length to the surface of the nanotube. The effect which this functionalization has on the interfacial thermal resistance is studied by molecular dynamics simulation. Interfacial thermal resistance values are calculated for a range of chemical grafting densities and with several chain lengths. These results are subsequently used in an analytical model to predict the resulting effect on the bulk thermal conductivity of the nanocomposite.

Clancy, Thomas C.↗

NASA NTRS2008

NASA Tech Briefs, January 2008

Topics covered include: Induction Charge Detector with Multiple Sensing Stages; Generic Helicopter-Based Testbed for Surface Terrain Imaging Sensors; Robot Electronics Architecture; Optimized Geometry for Superconducting Sensing Coils; Sensing a Changing Chemical Mixture Using an Electronic Nose; Inertial Orientation Trackers with Drift Compensation; Microstrip Yagi Antenna with Dual Aperture-Coupled Feed; Patterned Ferroelectric Films for Tunable Microwave Devices; Micron-Accurate Laser Fresnel-Diffraction Ranging System; Efficient G(sup 4)FET-Based Logic Circuits; Web-Enabled Optoelectronic Particle-Fallout Monitor; SiO2/TiO2 Composite for Removing Hg from Combustion Exhaust; Lightweight Tanks for Storing Liquefied Natural Gas; Hybrid Wound Filaments for Greater Resistance to Impacts; Making High-Tensile-Strength Amalgam Components; Bonding by Hydroxide-Catalyzed Hydration and Dehydration; Balanced Flow Meters without Moving Parts; Deflection-Compensating Beam for Use inside a Cylinder; Four-Point-Latching Microactuator; Curved Piezoelectric Actuators for Stretching Optical Fibers; Tunable Optical Assembly with Vibration Dampening; Passive Porous Treatment for Reducing Flap Side-Edge Noise; Cylindrical Piezoelectric Fiber Composite Actuators; Patterning of Indium Tin Oxide Films; Gimballed Shoulders for Friction Stir Welding; Improved Thermal Modulator for Gas Chromatography; Nuclear-Spin Gyroscope Based on an Atomic Co-Magnetometer; Utilizing Ion-Mobility Data to Estimate Molecular Masses; Optical Displacement Sensor for Sub-Hertz Applications; Polarization/Spatial Combining of Laser-Diode Pump Beams; Spatial Combining of Laser-Diode Beams for Pumping an NPRO; Algorithm Optimally Orders Forward-Chaining Inference Rules; Project Integration Architecture; High Power Amplifier and Power Supply; Estimating Mixing Heights Using Microwave Temperature Profiler; and Multiple-Cone Sunshade for a Spaceborne Telescope.

Source record↗

NASA NTRS2014

Hydrogen-Bonding Surfaces for Ice Mitigation

Ice formation on aircraft, either on the ground or in-flight, is a major safety issue. While ground icing events occur predominantly during the winter months, in-flight icing can happen anytime during the year. The latter is more problematic since it could result in increased drag and loss of lift. Under a Phase I ARMD NARI Seedling Activity, coated aluminum surfaces possessing hydrogen-bonding groups were under investigation for mitigating ice formation. Hydroxyl and methyl terminated dimethylethoxysilanes were prepared via known chemistries and characterized by spectroscopic methods. These materials were subsequently used to coat aluminum surfaces. Surface compositions were based on pure hydroxyl and methyl terminated species as well as mixtures of the two. Coated surfaces were characterized by contact angle goniometry. Receding water contact angle data suggested several potential surfaces that may exhibit reduced ice adhesion. Qualitative icing experiments performed under representative environmental temperatures using supercooled distilled water delivered via spray coating were inconclusive. Molecular modeling studies suggested that chain mobility affected the interface between ice and the surface more than terminal group chemical composition. Chain mobility resulted from the creation of "pockets" of increased free volume for longer chains to occupy.

Smith, Joseph G., Jr.↗

NASA NTRS1993

The Crystal and Molecular Structure of an Asymmetric Diacetylene Monomer, 6-(2-methyl-4-nitroanilino)-2,4-hexadiyne-1-ol

The crystal and molecular structure of an asymmetric diacetylene monomer has been determined from x-ray diffraction data. The crystals, obtained from an acetone/pentane solution, are orthorhombic, Fdd2 with Z = 16 in a unit cell having dimensions of a = 42.815(6) A, b = 22.224(5) A, c = 4.996(l) A. The structure was solved by direct methods and refined by least- squares techniques to an R(sub F) of 6.4% for 988 reflections and 171 variables. The diacetylene chains are disposed in the unit cell in a complex manner in order to satisfy the hydrogen- bonding, crystal packing, and symmetry requirements of the system. The solid state polymerization mechanism is discussed with respect to the geometric disposition of the diacetylene chains. These chains are far apart and incorrectly oriented with respect to each other to permit polymerization in the crystal by means of 1,4-addition, consistent with the Baughman mechanistic model.

Vlasse, Marcus↗

NASA NTRS1995

A Coupled-Cluster Study of the Molecular Structure, Vibrational Spectrum, and Heats of Formation of XONO2 (X=H, F, Cl)

The equilibrium structures, harmonic vibrational frequencies, dipole moments, and IR intensities of nitric acid, fluorine nitrate, and chlorine nitrate have been investigated by using the singles and doubles coupled cluster method that also includes a perturbational estimate of the effects of connected triple excitations, CCSD(T). A standard triple-zeta double-polarized basis set was utilized. The equilibrium geometries and vibrational spectra of HONO2 and ClONO2 are shown to be in excellent agreement with the available experimental data. The ab initio vibrational spectrum of FONO2 is also shown to be in excellent agreement with experiment. Unlike the FOOF and FON molecules, but similar to the cis- and trans-FONO molecules, FONO2 is shown to possess normal bond distances. The bonding in FONO2 is shown to be more similar to that in ClONO2 than that in HONO2, although there are still significant differences, especially in the partial atomic charges as deduced from Mulliken populations. This causes FONO2 to possess almost no dipole moment, which is very different to both HONO2 and ClONO2. By using large atomic natural orbital basis sets, CCSD(T) energies are computed for four isodesmic reactions in order to determine an accurate heat of formation for FONO2. Our best estimate for DELTA H(raised circle) (sub f,298) is 3.1 plus or minus 2.0 kcal/mol, indicating that the F-ONO2 bond energy is 31.3 kcal/mol.

Lee, Timothy J.↗

NASA NTRS1993

Infrared laser spectroscopy of jet-cooled carbon clusters: structure of triplet C6

We report the first structural characterization of the triplet isomer of C6. Forty-one rovibrational/fine structure transitions in the nu 4(sigma u) antisymmetric stretch fundamental of the C6 cluster have been measured by diode laser absorption spectroscopy of a supersonic carbon cluster beam. The observed spectrum is characteristic of a centrosymmetric linear triplet state with cumulene-type bonding. The measured ground state rotational constant B0 = 0.048 479 (10)cm-1 and the effective bond length r(eff) = 1.2868 (1) angstroms are in good agreement with ab initio predictions for the linear triplet (3 sigma g-) state of C6.

Non-NASA Center↗

NASA NTRS2001

Carbon Nanotubes in Water: MD Simulations of Internal and External Flow, Self Organization

We have developed computational tools, based on particle codes, for molecular dynamics (MD) simulation of carbon nanotubes (CNT) in aqueous environments. The interaction of CNTs with water is envisioned as a prototype for the design of engineering nano-devices, such as artificial sterocillia and molecular biosensors. Large scale simulations involving thousands of water molecules are possible due to our efficient parallel MD code that takes long range electrostatic interactions into account. Since CNTs can be considered as rolled up sheets of graphite, we expect the CNT-water interaction to be similar to the interaction of graphite with water. However, there are fundamental differences between considering graphite and CNTs, since the curvature of CNTs affects their chemical activity and also since capillary effects play an important role for both dynamic and static behaviour of materials inside CNTs. In recent studies Gordillo and Marti described the hydrogen bond structure as well as time dependent properties of water confined in CNTs. We are presenting results from the development of force fields describing the interaction of CNTs and water based on ab-initio quantum mechanical calculations. Furthermore, our results include both water flows external to CNTs and the behaviour of water nanodroplets inside heated CNTs. In the first case (external flows) the hydrophobic behaviour of CNTs is quantified and we analyze structural properties of water in the vicinity of CNTs with diagnostics such as hydrogen bond distribution, water dipole orientation and radial distribution functions. The presence of water leads to attractive forces between CNTs as a result of their hydrophobicity. Through extensive simulations we quantify these attractive forces in terms of the number and separation of the CNT. Results of our simulations involving arrays of CNTs indicate that these exhibit a hydrophobic behaviour that leads to self-organising structures capable of trapping water clusters. In the second case (internal flows) we study the behaviour of water droplets confined inside CNTs. Constant temperature simulations allow us to capture structural properties such as the contact angles and density profiles of the equilibrated drops. By heating and subsequently cooling of the CNT, we are able to measure the evaporation and the condensation rate of the entrapped water.

Jaffe, Richard L.↗

NASA NTRS2022

Radiation-induced D/H Exchange Rate Constants in Aliphatics Embedded in Water Ice

Gas-phase and solid-state chemistry in low-temperature interstellar clouds and cores leads to a D/H enhancement in interstellar ices, which is eventually inherited by comets, meteorites, and even planetary satellites. Hence, the D/H ratio has been widely used as a tracer for the origins of extraterrestrial chemistry. However, the D/H ratio can also be influenced by cosmic rays, which are ubiquitous and can penetrate even dense interstellar molecular cores. The effects of such high-energy radiation on deuterium fractionation have not been studied in a quantitative manner. In this study, we present rate constants for radiation-induced D-to-H exchange for fully deuterated small (1–2 C) hydrocarbons embedded in H2O ice at 20 K and H-to-D exchange for the protiated forms of these molecules in D2O ice at 20 K. We observed larger rate constants for H-to-D exchange in the D2O ice versus D-to-H exchange in H2O ice, which we have attributed to the greater bond strength of C–D versus C–H. We find that the H-to-D exchange rate constants are smaller for protiated methane than ethane, in agreement with bond energies from the literature. We are unable to obtain rate constants for the unsaturated and reactive hydrocarbons ethylene and acetylene. Interpretation of the rate constants suggest that D/H exchange products are formed in abundance alongside radiolysis products. We discuss how our quantitative and qualitative data can be used to interpret the D/H ratios of aliphatic compounds observed throughout space.

Ice destruction↗

NASA NTRS1995

A possible prebiotic synthesis of pantetheine, a precursor to coenzyme A

The involvement of coenzyme A in many enzyme reactions suggests that it acted in this capacity very early in the development of life on Earth. Particularly relevant in this regard is its role in the activation of amino acids and hydroxy acids in the biosynthesis of some peptide antibiotics--a mechanism of peptide synthesis that forms the basis for the proposal that a thioester world could have preceded the RNA world. The components of coenzyme A have been shown to be probable prebiotic compounds: beta-alanine, pantoyl lactone and cysteamine and possibly adenosine. We show here that the pantetheine moiety of coenzyme A (which also occurs in a number of enzymes) can be synthesized in yields of several per cent by heating pantoyl lactone, beta-alanine and cysteamine at temperatures as low as 40 degrees C. These components are extremely soluble and so would have been preferentially concentrated in evaporating bodies of water, for example on beaches and at lagoon margins. Our results show that amide bonds can be formed at temperatures as low as 40 degrees C, and provide circumstantial support for the suggestion that pantetheine and coenzyme A were important in the earliest metabolic systems.

NASA Discipline Number 52-20↗

NASA NTRS1998

HST Multi Layer Insulation Failure Review Board Findings

The mechanical and optical properties of the thermal control materials on the Hubble Space Telescope (HST) have degraded over the nearly seven years the telescope has been in orbit. Astronaut observations and photographs from the Second Servicing Mission (SM2) revealed large cracks in the metallized Teflon fluorinated ethylene propylene (FEP), the outer layer of the multi-layer insulation (MLI), in many locations around the telescope. Also, the absorptance of the bonded metallized Teflon FEP radiator surfaces of the telescope has increased over time. A Failure Review Board was established to determine the damage mechanism and to identify a replacement material. Samples of the top layer of the MLI and radiator material were retrieved during SM2, and a thorough investigation into the degradation followed in order to determine the primary cause of the damage. Mapping of the cracks on HST and the ground testing showed that thermal cycling with deep-layer damage from electron and proton radiation are necessary to cause the observed embrittlement. Further, strong evidence was found indicating that chain scission (reduced molecular weight) is the dominant form of damage to the metallized Teflon FEP. Given the damage to the outer layer of the multi-layer insulation (MLI) that was apparent during the second servicing mission (SM2), the decision was made to replace the outer layer during subsequent servicing missions. The replacement material had to meet the stringent thermal requirements of the spacecraft and maintain structural integrity for at least ten years. Ten candidate materials were exposed to simulated orbital environments and a replacement material was selected. This presentation will summarize the FRB results, in particular, the analysis of the retrieved specimens, the results of the simulated environmental exposures, and the selection of the replacement material. The NASA Space Environments and Effects community needs to hear these results because they reveal that Teflon (FEP) films should not be used in LEO as routinely as they are today.

Townsend, Jacqueline↗

NASA NTRS1943

A Method for Removal of Bakelite-Impregnated Wire Strain Gages

An increasing interest is being shown in the use of wire-type strain gages to measure static and dynamic stresses in aircraft-engine parts. Bakelite cement has been found satisfactory as a bonding agent for attaching the strain gages to machine parts that must operate at elevated temperatures. On many occasions, it is desired to remove Bakelite-cemented gages from the test parts for the purpose of replacing faulty gages or of returning the parts to service after strain measurements have been completed. Removal of the gages by means of scraping without prior treatment is very unsatisfactory because it is tedious and almost invariably damages the finished surface. Various solvents have been tried, but all attempts in this direction have been unsuccessful inasmuch as Bakelite cement, when properly baked, forms a polymer of very high molecular weight that resists the action of solvents. This report presents a gas-flame method of removal that is rapid and does not inure the structural part.

Kemp, Richard H.↗

NASA NTRS1992

Crystal structure of four-stranded Oxytricha telomeric DNA

The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

NASA Discipline Exobiology↗

NASA NTRS1994

Alternative bases in the RNA world: the prebiotic synthesis of urazole and its ribosides

Urazole is a five-membered heterocyclic compound which is isosteric with uracil's hydrogen-bonding segment. Urazole reacts spontaneoulsy with ribose (and other aldoses) to give a mixture of four ribosides: alpha and beta pyranosides and furanosides. This reaction occurs in aqueous solution at mild temperatures. Thermodynamic and kinetic parameters for the reaction of urazole with ribose were determined. In contrast, uracil is completely unreactive with ribose under these conditions. Urazole's unusual reactivity is ascribed to the hydrazine portion of the molecule. Urazole can be synthesized from biuret and hydrazine under prebiotic conditions. The prebiotic synthesis of guanazole, which is isosteric in part to diaminopyrimidine and cytosine, is accomplished from dicyandiamide and hydrazine. Kinetic parameters for both prebiotic reactions were measured. Urazole and guanazole are transparent in the UV, which would be a favorable property in the absence of an ozone layer on the early Earth. Urazole makes hydrogen bonds with adenine in DMSO similar to those of uracil, as established by H NMR. All of these properties make urazole an attractive potential precursor to uracil and guanazole a potential precursor to cytosine in the RNA or pre-RNA world.

Non-NASA Center↗

NASA NTRS2001

Advanced CO2 Removal Technology Development

The Advanced CO2 Removal Technical Task Agreement covers three active areas of research and development. These include a study of the economic viability of a hybrid membrane/adsorption CO2 removal system, sorbent materials development, and construction of a database of adsorption properties of important fixed gases on several adsorbent material that may be used in CO2 removal systems. The membrane/adsorption CO2 removal system was proposed as a possible way to reduce the energy consumption of the four-bed molecular sieve system now in use. Much of the energy used by the 4BMS is used to desorb water removed in the device s desiccant beds. These beds might be replaced by a desiccating membrane that moves the water from [he incoming stream directly into the outlet stream. The approach may allow the CO2 removal beds to operate at a lower temperature. A comparison between models of the 4BMS and hybrid systems is underway at Vanderbilt University. NASA Ames Research Center has been investigating a Ag-exchanged zeolites as a possible improvement over currently used Ca and Na zeolites for CO2 removal. Silver ions will complex with n:-bonds in hydrocarbons such as ethylene, giving remarkably improved selectivity for adsorption of those materials. Bonds with n: character are also present in carbon oxides. NASA Ames is also continuing to build a database for adsorption isotherms of CO2, N2, O2, CH4, and Ar on a variety of sorbents. This information is useful for analysis of existing hardware and design of new processes.

Finn, John E.↗