Rarefied Gas and Free Molecular Flow Modeling Applications in Spacecraft Contamination Control at JPL
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Alred, John↗
SEARCH · Engineering Papers
Results for “molecular modelling”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Molecular column densities in selected model atmospheres
Molecular column densities are presented for 35 molecules in a variety of cool stellar model atmospheres. From an examination of the predicted column densities, we draw the following conclusions: (1) OH might be visible in carbon stars which have been generated from triplet-alpha burning, but will be absent from carbon stars generated from the CNO bi-cycle; (2) the TiO/ZrO ratio shows small but interesting variations as C/O is changed and as the effective temperature is changed; (3) the column density of silicon dicarbide (SiC2) is sensitive to abundance, temperature, and gravity; hence, all relationships between the strength of SiC2 and other stellar parameters will show appreciable scatter. There is, however, a substantial luminosity effect present in the SiC2 column densities; (4) unexpectedly, SiC2 is anticorrelated with C2; (5) the presence of SiC2 in a carbon star allows us to eliminate the possibility that these stars are both 'hot' (T sub eff greater than or equal to 3000 K) and have been produced through the CNO bi-cycle (so that C/H is less than solar).
Johnson, H. R.↗
A generalized hard-sphere model for Monte Carlo simulation
A new molecular model, called the generalized hard-sphere, or GHS model, is introduced. This model contains, as a special case, the variable hard-sphere model of Bird (1981) and is capable of reproducing all of the analytic viscosity coefficients available in the literature that are derived for a variety of interaction potentials incorporating attraction and repulsion. In addition, a new procedure for determining interaction potentials in a gas mixture is outlined. Expressions needed for implementing the new model in the direct simulation Monte Carlo methods are derived. This development makes it possible to employ interaction models that have the same level of complexity as used in Navier-Stokes calculations.
Hassan, H. A.↗
A Monte Carlo technique for determining sphere drag in near free molecular flow
First collision Monte Carlo method for calculating aerodynamic drag on hard sphere and Maxwell molecular models in near-free molecular flow
Robertson, S. J.↗
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↗
A proposal for the proper use of pseudopotentials in molecular orbital cluster model studies of chemisorption
The interaction of CO with Cu5, Ni5, and Al4 are treated as model systems for molecular adsorption on metal surfaces. The effect of the use of pseudopotentials for the metal atoms is studied by considering three types of clusters. In the first case, all of the metal electrons are explicitly included in the wave function; an all electron (AE) treatment. In the second case, the metal atom which directly interacts with the CO is described by AE but the remaining metal atoms include a pseudopotential for their core electrons. Finally, in the third case, all of the metal atoms in the cluster have a pseudopotential treatment for the core electrons. The AE cluster results are taken as reference values for the two pseudopotential treatments. The mixed cluster results are in excellent agreement with those of the all AE clusters; however, the results for the all pseudopotential cluster of Ni5CO or of Cu5CO are qualitatively different. The pseudopotential treatment for all of the metal atoms often leads to results that contain serious errors and it is not a reliable approach.
Bagus, P. S.↗
Preparation, Fabrication, and Evaluation of Advanced Polymeric and Composite Materials
The thesis titles are given below: physical and mechanical behavior of amorphous poly(arylene ether-co-imidasole)s and poly(arylene ether-co-imidasole) modification epoxies; the requirements of patentability as applied to the chemical arts; fabrication of thermoplastic polymer composite ribbon; blend of reactive diluents with phenylethynyl-terminated arylene ether oligomers; the synthesis, characterization, and application of ether-containing polyimides; the synthesis of reflective and electrically conductive polyimide films via an in-situ self-metalization procedure using silver (I) complexes; the thermal cure of phenylethynyl terminated polyimides and selected model compounds; and the synthesis, characterization, and molecular modeling of cyclic arylene ether oligomers.
Orwoll, Robert A.↗
A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate
We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.
Non-NASA Center↗
On the coalescence-dispersion modeling of turbulent molecular mixing
The general coalescence-dispersion (C/D) closure provides phenomenological modeling of turbulent molecular mixing. The models of Curl and Dopazo and O'Brien appear as two limiting C/D models that bracket the range of results one can obtain by various models. This finding is used to investigate the sensitivtiy of the results to the choice of the model. Inert scalar mixing is found to be less model-sensitive than mixing accompanied by chemical reaction. Infinitely fast chemistry approximation is used to relate the C/D approach to Toor's earlier results. Pure mixing and infinite rate chemistry calculations are compared to study further a recent result of Hsieh and O'Brien who found that higher concentration moments are not sensitive to chemistry.
Givi, Peyman↗
Computer display and manipulation of biological molecules
This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.
Coeckelenbergh, Y.↗
Thermodynamics of a solar mixture of molecular hydrogen and helium at high pressure
The thermodynamic properties of a model molecular hydrogen and helium mixture are calculated in the strongly interacting region of 0.005 to 0.3 per cu cm for a range of temperatures that are of interest for the envelopes of the Jovian planets. Computed adiabats fit the gravity data and boundary conditions from model atmospheres of Jupiter.
Slattery, W. L.↗
Investigation on the Origins of Comets as Revealed through IR High Resolution Spectroscopy: I. Molecular Abundances
We report and analyze molecular abundances updatedin twenty comets by employingmodern data reduction procedures and molecular models. Using boxplots and scatterplots, we examine how the different molecular species are distributed among the comet population, while by means of pie charts we investigate the relative proportions of these molecular species in each comet. We compare these results with the orbital parametersof the selected targets in order to identify trends related to the dynamical history of each comet. In this way, we identify at least three chemical classes based mainly on relative abundances of CO, CH3OH, CH4, C2H6, HCN and NH3. The combination of relative abundances and orbital parameters is then compared with chemical models of planetary system formation and may offer an alternative approach to investigate the origin and evolution of the material in cometary nuclei.Our study also confirms the need to add more objects to our sample in order to improve the statistics, especially for hyper-volatiles (i.e. CH4and CO) in Jupiter Family comets.
M Lippi↗
The Earliest Ion Channels in Protocellular Membranes
Cellular membranes with their hydrophobic interior are virtually impermeable to ions. Bulk of ion transport through them is enabled through ion channels. Ion channels of contemporary cells are complex protein molecules which span the membrane creating a cylindrical pore filled with water. Protocells, which are widely regarded as precursors to modern cells, had similarly impermeable membranes, but the set of proteins in their disposal was much simpler and more limited. We have been, therefore, exploring an idea that the first ion channels in protocellular membranes were formed by much smaller peptide molecules that could spontaneously selfassemble into short-lived cylindrical bundles in a membrane. Earlier studies have shown that a group of peptides known as peptaibols is capable of forming ion channels in lipid bilayers when they are exposed to an electric field. Peptaibols are small, non-genetically encoded peptides produced by some fungi as a part of their system of defense against bacteria. They are usually only 14-20 residues long, which is just enough to span the membrane. Their sequence is characterized by the presence of non-standard amino acids which, interestingly, are also expected to have existed on the early earth. In particular, the presence of 2-aminoisobutyric acid (AIB) gives peptaibols strong helix forming propensities. Association of the helices inside membranes leads to the formation of cylindrical bundles, typically containing 4 to 10 monomers. Although peptaibols are excellent candidates for models of the earliest ion channels their structures, which are stabilized only by van der Waals forces and occasional hydrogen bonds between neighboring helices, are not very stable. Although it might properly reflect protobiological reality, it is also a major obstacle in studying channel behavior. For this reason we focused on two members of the peptaibol family, trichotoxin and antiamoebin, which are characterized by a single conductance level. This indicates that their structures are unique and stable. In addition, it is also believed that the trichotoxin channel displays some selectivity between potassium and chloride ions. This makes trichotoxin and antiamoebin ideal models of the earliest ion channels that could provide insight into the origins of ion conductance and selectivity. In the absence of crystal structure of the trichotoxin and antiamoebin channels, we propose their molecular models based on experimentally determined number of monomers forming the bundles. We use molecular dynamics simulations to validate the models in terms of their conductance and selectivity. On the basis of our simulations we show that the emergence of channels built of small, alpha-helical peptides was protobiologically plausible and did not require highly specific amino acid sequences, which is a convenient evolutionary trait. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. To this end, we will discuss how the amino acid sequence and structure of primitive channels give rise to the phenomena of ionic conductance and selectivity across the earliest cell walls, which were essential functions for the emergence and early evolution of protocells. Furthermore, we will argue that even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.
Mijajlovic, Milan↗
Computer-aided design of polymers and composites
This book on computer-aided design of polymers and composites introduces and discusses the subject from the viewpoint of atomic and molecular models. Thus, the origins of stiffness, strength, extensibility, and fracture toughness in composite materials can be analyzed directly in terms of chemical composition and molecular structure. Aspects of polymer composite reliability are considered along with characterization techniques for composite reliability, relations between atomic and molecular properties, computer aided design and manufacture, polymer CAD/CAM models, and composite CAD/CAM models. Attention is given to multiphase structural adhesives, fibrous composite reliability, metal joint reliability, polymer physical states and transitions, chemical quality assurance, processability testing, cure monitoring and management, nondestructive evaluation (NDE), surface NDE, elementary properties, ionic-covalent bonding, molecular analysis, acid-base interactions, the manufacturing science, and peel mechanics.
Kaelble, D. H.↗
Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations
Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.
Hinkley, J.A.↗
Progress toward an explicit mechanistic model for the light-driven pump, bacteriorhodopsin
Recent crystallographic information about the structure of bacteriorhodopsin and some of its photointermediates, together with a large amount of spectroscopic and mutational data, suggest a mechanistic model for how this protein couples light energy to the translocation of protons across the membrane. Now nearing completion, this detailed molecular model will describe the nature of the steric and electrostatic conflicts at the photoisomerized retinal, as well as the means by which it induces proton transfers in the two half-channels leading to the two membrane surfaces, thereby causing unidirectional, uphill transport.
Review, Tutorial↗
Optical models of the molecular atmosphere
The use of optical and laser methods for performing atmospheric investigations has stimulated the development of the optical models of the atmosphere. The principles of constructing the optical models of molecular atmosphere for radiation with different spectral composition (wideband, narrowband, and monochromatic) are considered in the case of linear and nonlinear absorptions. The example of the development of a system which provides for the modeling of the processes of optical-wave energy transfer in the atmosphere is presented. Its physical foundations, structure, programming software, and functioning were considered.
Zuev, V. E.↗
Model For Dense Molecular Cloud Cores
We present a detailed theoretical model for the thermal balance, chemistry, and radiative transfer within quiescent dense molecular cloud cores that contain a central protostar. In the interior of such cores, we expect the dust and gas temperatures to be well coupled, while in the outer regions CO rotational emissions dominate the gas cooling and the predicted gas temperature lies significantly below the dust temperature. Large spatial variations in the gas temperature are expected to affect the gas phase chemistry dramatically; in particular, the predicted water abundance varies by more than a factor of 1000 within cloud cores that contain luminous protostars. Based upon our predictions for the thermal and chemical structure of cloud cores, we have constructed self-consistent radiative transfer models to compute the line strengths and line profiles for transitions of (12)CO, (13)CO, C(18)O, ortho- and para-H2(16)O, ortho- and para-H2(18)O, and O I. We carried out a general parameter study to determine the dependence of the model predictions upon the parameters assumed for the source. We expect many of the far-infrared and submillimeter rotational transitions of water to be detectable either in emission or absorption with the use of the Infrared Space Observatory (ISO) and the Submillimeter Wave Astronomy Satellite. Quiescent, radiatively heated hot cores are expected to show low-gain maser emission in the 183 GHz 3(sub 13)-2(sub 20) water line, such as has been observed toward several hot core regions using ground-based telescopes. We predict the (3)P(sub l) - (3)P(sub 2) fine-structure transition of atomic oxygen near 63 micron to be in strong absorption against the continuum for many sources. Our model can also account successfully for recent ISO observations of absorption in rovibrational transitions of water toward the source AFGL 2591.
Doty, Steven D.↗