Engineering Papers⌕ Search

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5

Maxwell's second- and third-order equations of transfer for non-Maxwellian gases

Condensed algebraic forms for Maxwell's second- and third-order equations of transfer are developed for the case of molecules described by either elastic hard spheres, inverse-power potentials, or by Bird's variable hard-sphere model. These hardly reduced, yet exact, equations provide a new point of origin, when using the moment method, in seeking approximate solutions in the kinetic theory of gases for molecular models that are physically more realistic than that provided by the Maxwell model. An important by-product of the analysis when using these second- and third-order relations is that a clear mathematical connection develops between Bird's variable hard-sphere model and that for the inverse-power potential.

Baganoff, D.↗

State of the Art Assessment of Simulation in Advanced Materials Development

Advances in both the underlying theory and in the practical implementation of molecular modeling techniques have increased their value in the advanced materials development process. The objective is to accelerate the maturation of emerging materials by tightly integrating modeling with the other critical processes: synthesis, processing, and characterization. The aims of this report are to summarize the state of the art of existing modeling tools and to highlight a number of areas in which additional development is required. In an effort to maintain focus and limit length, this survey is restricted to classical simulation techniques including molecular dynamics and Monte Carlo simulations.

Wise, Kristopher E.↗

Electrostatic Properties of Polymers Subjected to Atmospheric Pressure Plasma Treatment; Correlation of Experimental Results with Atomistic Modeling

this study, PE, PTFE, PS and PMMA were exposed to a He+O2, APGD and pre and post treatment surface chemistries were analyzed by X-ray photoelectron spectroscopy and contact angle measurements. Semi-empirical and ab-initio calculations were performed to correlate the experimental results with sonic plausible molecular and electronic structure features of the oxidation process. For the PE and PS, significant surface oxidation showing C-O, C=O, and O-C=O bonding, and a decrease in the surface contact angles was observed. For the PTFE and PM MA, little change in the surface composition was observed. The molecular modeling calculations were performed on single and multiple oligomers and showed regardless of oxidation mechanism, e.g. -OH, =O or a combination thereof, experimentally observed levels of surface oxidation were unlikely to lead to a significant change in the electronic structure of PE and PS, and that the increased hydrophilic properties are the primary reason for the observed changes in its electrostatic behavior. Calculations for PTFE and PMMA argue strongly against significant oxidation of those materials, as confirmed by the XPS results.

Trigwell, S.↗

Neural network error correction for solving coupled ordinary differential equations

A neural network is presented to learn errors generated by a numerical algorithm for solving coupled nonlinear differential equations. The method is based on using a neural network to correctly learn the error generated by, for example, Runge-Kutta on a model molecular dynamics (MD) problem. The neural network programs used in this study were developed by NASA. Comparisons are made for training the neural network using backpropagation and a new method which was found to converge with fewer iterations. The neural net programs, the MD model and the calculations are discussed.

Shelton, R. O.↗

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗

Motion of Drops on Surfaces with Wettability Gradients

A liquid drop present on a solid surface can move because of a gradient in wettability along the surface, as manifested by a gradient in the contact angle. The contact angle at a given point on the contact line between a solid and a liquid in a gaseous medium is the angle between the tangent planes to the liquid and the solid surfaces at that point and is measured within the liquid side, by convention. The motion of the drop occurs in the direction of increasing wettability. The cause of the motion is the net force exerted on the drop by the solid surface because of the variation of the contact angle around the periphery. This force causes acceleration of an initially stationary drop, and leads to its motion in the direction of decreasing contact angle. The nature of the motion is determined by the balance between the motivating force and the resisting hydrodynamic force from the solid surface and the surrounding gaseous medium. A wettability gradient can be chemically induced as shown by Chaudhury and Whitesides who provided unambiguous experimental evidence that drops can move in such gradients. The phenomenon can be important in heat transfer applications in low gravity, such as when condensation occurs on a surface. Daniel et al have demonstrated that the velocity of a drop on a surface due to a wettability gradient in the presence of condensation can be more than two orders of magnitude larger than that observed in the absence of condensation. In the present research program, we have begun to study the motion of a drop in a wettability gradient systematically using a model system. Our initial efforts will be restricted to a system in which no condensation occurs. The experiments are performed as follows. First, a rectangular strip of approximate dimensions 10 x 20 mm is cut out of a silicon wafer. The strip is cleaned thoroughly and its surface is exposed to the vapor from an alkylchlorosilane for a period lasting between one and two minutes inside a desiccator. This is done using an approximate line source of the vapor in the form of a string soaked in the alkylchlorosilane. Ordinarily, many fluids, including water, wet the surface of silicon quite well. This means that the contact angle is small. But the silanized surface resists wetting, with contact angles that are as large as 100 degs. Therefore, a gradient of wettability is formed on the silicon surface. The region near the string is highly hydrophobic, and the contact angle decreases gradually toward a small value at the hydrophilic end away from this region. The change in wettability occurs over a distance of several mm. The strip is placed on a platform within a Plexiglas cell. Drops of a suitable liquid are introduced on top of the strip near the hydrophobic end. An optical system attached to a video camera is trained on the drop so that images of the moving drop can be captured on videotape for subsequent analysis. We have performed preliminary experiments with water as well as ethylene glycol drops. Results from these experiments will be presented in the poster. Future plans include the refinement of the experimental system so as to permit images to be recorded from the side as well as the top, and the conduct of a systematic study in which the drop size is varied over a good range. Experiments will be conducted with different fluids so as to obtain the largest possible range of suitably defined Reynolds and Capillary numbers. Also, an effort will be initiated on theoretical modeling of this motion. The challenges in the development of the theoretical description lie in the proper analysis of the region in the vicinity of the contact line, as well as in the free boundary nature of the problem. It is known that continuum models assuming the no slip condition all the way to the contact line fail by predicting that the stress on the solid surface becomes singular as the contact line is approached. One approach for dealing with this issue has been to relax the no-slip boundary condition using the Navier model. Molecular dynamics simulations of the contact line region show that for a non-polar liquid on a solid surface, the no-slip boundary condition is in fact incorrect near the contact line. Furthermore, the same simulations also show that the usual relationship between stress and the rate of deformation breaks down in the vicinity of the contact line. In developing continuum theoretical models of the system, we shall accommodate this knowledge to the extent possible.

Subramanian, R. Shankar↗

Biochemical Kinetics Model of DSB Repair and GammaH2AX FOCI by Non-homologous End Joining

We developed a biochemical kinetics approach to describe the repair of double strand breaks (DSB) produced by low LET radiation by modeling molecular events associated with the mechanisms of non-homologous end-joining (NHEJ). A system of coupled non-linear ordinary differential equations describes the induction of DSB and activation pathways for major NHEJ components including Ku(sub 70/80), DNA-PK(sub cs), and the Ligase IV-XRCC4 hetero-dimer. The autophosphorylation of DNA-PK(sub cs and subsequent induction of gamma-H2AX foci observed after ionizing radiation exposure were modeled. A two-step model of DNA-PK(sub cs) regulation of repair was developed with the initial step allowing access of other NHEJ components to breaks, and a second step limiting access to Ligase IV-XRCC4. Our model assumes that the transition from the first to second-step depends on DSB complexity, with a much slower-rate for complex DSB. The model faithfully reproduced several experimental data sets, including DSB rejoining as measured by pulsed-field electrophoresis (PFGE), quantification of the induction of gamma-H2AX foci, and live cell imaging of the induction of Ku(sub 70/80). Predictions are made for the behaviors of NHEJ components at low doses and dose-rates, where a steady-state is found at dose-rates of 0.1 Gy/hr or lower.

Cucinotta, Francis, A.↗

Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

NASA Discipline Neuroscience↗

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↗

Fracture Behavior in Nylon 6 Fibers

Electron paramagnetic resonance (EPR) techniques are used to determine the number of free radicals produced during deformation leading to fracture of nylon 6 fibers. A reaction rate molecular model is proposed to explain some of the deformation and bond rupture behavior leading to fracture. High-strength polymer fibers are assumed to consist of a sandwich structure of disordered and ordered regions along the fiber axis. In the disordered or critical flaw regions, tie chains connecting the ordered or crystalline block regions are assumed to have a statistical distribution in length. These chains are, therefore, subjected to different stresses. The effective length distribution was determined by EPR. The probability of bond rupture was assumed to be controlled by reaction-rate theory with a stress-aided activation energy and behavior of various loadings determined by numerical techniques. The model is successfully correlated with experimental stress, strain, and bond rupture results for creep, constant rate loadings, cyclic stress, stress relaxation and step strain tests at room temperature.

Lloyd, B. A.↗

Linear momentum transfer effects in molecular dissociation produced by electron impact.

In this study of molecular dissociation produced by electron impact, diatomic systems and polyatomic molecules are considered, and attention is given to the effects of thermal motion and of momentum transfer in the collision process. A procedure is described which makes it possible to 'construct' both the laboratory angular distribution and velocity distribution of the atomic fragments (or, alternatively, the time-of-flight distribution). The calculation assumes that s-wave electron scattering predominates, i.e., that excitation occurs near threshold. The computational procedure may also be reversed to allow construction of possible molecular models to fit given experimental angular and velocity distribution data.

Misakian, M.↗

Molecular correlations with fracture in fibers and granular-filled composites

Results are presented for an experimental electron spin resonance study of chain-scission kinetics in oriented nylon fibers and in granular-filled elastomer composites. A reaction-rate molecular model is proposed as a tool to predict failure under various loadings. The model assumes a statistical distribution in stress on the polymeric chain structure. Interfacial failure in the filled composites is examined. Failure at the interface between the filler and the matrix may be largely adhesive or cohesive, depending on the magnitude of the interactive forces. It appears that the mechanical behavior of both single-component and filled composites depends on the composite nature of the structure. The electron spin resonance technique is shown to be suitable for experimental observation of phenomena directly related to atomic occurrences.

Devries, K. L.↗

The Raman spectra of N-14O2 and N-15O2 solids at 20 K

The Raman spectra of N-14O2 and N-15O2 have been studied at 20 K. The far infrared of N-14O2 at 20 K was also measured. The data were assigned on the basis of a C-sub 2 nu molecular model. Normal coordinate calculations were performed for a variety of assignments. The assignment that yielded the best fit is presented. The solid state effects are discussed.

Durig, J. R.↗

Submillimeter, millimeter, and microwave spectral line catalogue

A computer accessible catalogue of submillimeter, millimeter, and microwave spectral lines in the frequency range between O and 3000 GHz (such as; wavelengths longer than 100 m) is discussed. The catalogue was used as a planning guide and as an aid in the identification and analysis of observed spectral lines. The information listed for each spectral line includes the frequency and its estimated error, the intensity, lower state energy, and quantum number assignment. The catalogue was constructed by using theoretical least squares fits of published spectral lines to accepted molecular models. The associated predictions and their estimated errors are based upon the resultant fitted parameters and their covariances.

Poynter, R. L.↗