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NASA NTRS1998

A Numerical Study of the Effect of Periodic Nutrient Supply on Pathways of Carbon in a Coastal Upwelling Regime

A size-based ecosystem model was modified to include periodic upwelling events and used to evaluate the effect of episodic nutrient supply on the standing stock, carbon uptake, and carbon flow into mesozooplankton grazing and sinking flux in a coastal upwelling regime. Two ecosystem configurations were compared: a single food chain made up of net phytoplankton and mesozooplankton (one autotroph and one heterotroph, A1H1), and three interconnected food chains plus bacteria (three autotrophs and four heterotrophs, A3H4). The carbon pathways in the A1H1 simulations were under stronger physical control than those of the A3H4 runs, where the small size classes are not affected by frequent upwelling events. In the more complex food web simulations, the microbial pathway determines the total carbon uptake and grazing rates, and regenerated nitrogen accounts for more than half of the total primary production for periods of 20 days or longer between events. By contrast, new production, export of carbon through sinking and mesozooplankton grazing are more important in the A1H1 simulations. In the A3H4 simulations, the turnover time scale of the autotroph biomass increases as the period between upwelling events increases, because of the larger contribution of slow-growing net phytoplankton. The upwelling period was characterized for three upwelling sites from the alongshore wind speed measured by the NASA Scatterometer (NSCAT) and the corresponding model output compared with literature data. This validation exercise for three upwelling sites and a downstream embayment suggests that standing stock, carbon uptake and size fractionation were best supported by the A3H4 simulations, while the simulated sinking fluxes are not distinguishable in the two configurations.

Carr, Mary-Elena↗

NASA NTRS1994

Conformational Characteristics of Poly(tetrafluoroethylene) (PTFE) Based Upon Ab Initio Electronic Structure Calculations on Model Molecules

Conformational energy contours of perfluoroalkanes, determined from ab initio calculations, confirm the well-known spitting of trans states into two minima at plus or minus 17 degrees but also show that the gauche states split as well, with minima at plus or minus 124 degrees and plus or minus 84 in order to relieve steric crowding. The directions of such split distortions from the perfectly staggered states are strongly coupled for adjacent pairs of bonds in a manner identical to the intradyad pair for poly (isobutylene) chains. These conformational characteristics are fully represented by a six-state rotational isomeric state (RIS) model for PTFE comprised of t(+), t(-), g(sup +)+, g(sup +)-, g(sup -) + and g(sup -)-states, located at the split energy minima. The resultant 6 x 6 statistical weight matrix is described by first-order interaction parameters for the g+(+) (ca. 0.6 kcal/mol) and g+- (ca. 2.0 kcal/mol) states, and second order parameters for the g(sup +)+g(sup +)+ (ca 0.6 kcal/mol) and g(sup +)+g(sup -)+ (ca. 1.0 kcal/mol) states. This six-state RIS model, without adjustment of the geometric or energy parameters as determined from the ab initio calculations, predicts the unperturbed chain dimensions and the fraction of gauche bonds as a function of temperature for PTFE in good agreement with available experimental values.

Smith, Grant D.↗

NASA NTRS2001

SRS Computer Animation and Drive Train System

The spinning rocket simulator (SRS) is an ongoing project at Oral Roberts University. The goal of the SRS is to gather crucial data concerning a spinning rocket under thrust for the purpose of analysis and correction of the coning motion experienced by this type of spacecraft maneuver. The computer animation simulates a virtual, scale model of the component of the SRS that represents the spacecraft itself. This component is known as the (VSM), or virtual spacecraft model. During actual physical simulation, this component of the SRS will experience a coning. The goal of the animation is to cone the VSM within that range to accurately represent the motion of the actual simulator. The drive system of the SRS is the apparatus that turns the actual simulator. It consists of a drive motor, motor mount and chain to power the simulator into motion. The motor mount is adjustable and rigid for high torque application. A digital stepper motor controller actuates the main drive motor for linear acceleration. The chain transfers power from the motor to the simulator via sprockets on both ends.

Arthun, Daniel↗

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 NTRS2001

Remobilizing the Interface of Thermocapillary Driven Bubbles Retarded By the Adsorption of a Surfactant Impurity on the Bubble Surface

Thermocapillary migration is a method for moving bubbles in space in the absence of buoyancy. A temperature gradient is the continuous phase in which a bubble is situated, and the applied gradient impressed on the bubble surface causes one pole of the drop to be cooler than the opposite pole. As the surface tension is a decreasing function of temperature, the cooler pole pulls at the warmer pole, creating a flow that propels the bubble in the direction of the warmer fluid. A major impediment to the practical use of thermocapillary to direct the movement of bubbles in space is the fact that surfactant impurities, which are unavoidably present in the continuous phase, can significantly reduce the migration velocity. A surfactant impurity adsorbed onto the bubble interface is swept to the trailing end of the bubble. When bulk concentrations are low (which is the case with an impurity), diffusion of surfactant to the front end is slow relative to convection, and surfactant collects at the back end of the bubble. Collection at the back lowers the surface tension relative to the front end setting up a reverse tension gradient. (This can also be the case if kinetic desorption of surfactant at the back end of the bubble is much slower than convection.) For buoyancy driven bubble motions in the absence of a thermocapillarity, the tension gradient opposes the surface flow, and reduces the surface and terminal velocities (the interface becomes more solid-like and bubbles translate as solid particles). When thermocapillary forces are present, the reverse tension gradient set up by the surfactant accumulation reduces the temperature-induced tension gradient, and can decrease to near zero the bubble's thermocapillary velocity. The objective of our research is to develop a method for enhancing the thermocapillary migration of bubbles which have be retarded by the adsorption onto the bubble surface of a surfactant impurity. Our remobilization theory proposes to use surfactant molecules which kinetically rapidly exchange between the bulk and the surface and are at high bulk concentrations. Because the remobilizing surfactant is present at much higher concentrations than the impurity, it adsorbs to the bubble surface much faster than the impurity when the bubble is formed, and thereby prevents the impurity from adsorbing onto the surface. In addition, the rapid kinetic exchange and high bulk concentration maintain a saturated surface with uniform surface concentrations. This prevents retarding surface tension gradients and keeps the thermocapillary velocity high. In our reports over the first 2 years, we presented numerical simulations of the bubble motion and surfactant transport which verified theoretically the concept of remobilization, and the development of an apparatus to track and measure the velocity of rising bubbles in a glycerol/water surfactant solution. This year, we detail experimental observations of remobilization. Two polyethylene oxide surfactants were studied, C12E6 (CH3(CH2)11(OCH2)6OH) and C10E8 (CH3(CH2)4(OCH2CH2)8OH). Measurements of the kinetic exchange for these surfactants show that the one with the longer hydrophobe chain C12E6 has a lower rate of kinetic exchange. In addition, this surfactant is much less soluble in the glycerol/water mixture because of the shorter ethoxylate chain. As a result, we found that C12E6 had only a very limited ability to remobilize rising bubbles because of the limited kinetic exchange and reduced solubility. However, C10E8, with its higher solubility and more rapid exchange was found to dramatically remobilize rising bubbles. We also compared our theoretical calculations to the experimental measurements of velocity for both the non-remobilizing and remobilizing surfactants and found excellent agreement. We further observed that for C10E8 at high concentrations, which exceeded the critical micelle concentrations, additional remobilization was measured. In this case the rapid exchange of monomer between micelle and surfactant provides an additional mechanism for maintaining a uniform surface concentrations.

Palaparthi, Ravi↗

NASA NTRS2001

Viscosity Relaxation in Molten HgZnTe

Rotating cup measurements of the viscosity of the pseudo-binary melt, HgZnTe have shown that the isothermal liquid with zinc mole fraction 0.16 requires tens of hours of equilibration time before a steady viscous state can be achieved. Over this relaxation period, the viscosity at 790 C increases by a factor of two, while the viscosity at 810 C increases by 40%. Noting that the Group VI elements tend to polymerize when molten, we suggest that the viscosity of the melt is enhanced by the slow formation of Te atom chains. To explain the build-up of linear Te n-mers, we propose a scheme, which contains formation reactions with second order kinetics that increase the molecular weight, and decomposition reactions with first order kinetics that inactivate the chains. The resulting rate equations can be solved for the time dependence of each molecular weight fraction. Using these molecular weight fractions, we calculate the time dependence of the average molecular weight. Using the standard semi-empirical relation between polymer average molecular weight and viscosity, we then calculate the viscosity relaxation curve. By curve fitting, we find that the data imply that the rate constant for n-mer formation is much smaller than the rate constant for n-mer deactivation, suggesting that Te atoms only weakly polymerize in molten HgZnTe. The steady state toward which the melt relaxes occurs as the rate of formation of an n-mer becomes exactly balanced by the sum of the rate for its deactivation and the rate for its polymerization to form an (n+1)-mer.

Su, Ching-Hua↗

NASA NTRS1998

Tidal Disruption of Strengthless Rubble Piles: A Dimensional Analysis

A relatively simple prescription for estimating the number of debris clumps (n) that form after a catastrophic tidal disruption event is presented. Following the breakup event, it is assumed that the individual debris particles follow keplerian orbits about the planet until the debris' gravitational contraction timescale (t(sub c)) becomes shorter than its orbital spreading timescale (t(sub s)). When the two timescales become comparable, self-gravity breaks up the debris train into n = L/D clumps, which is the debris length/diameter ratio at that instant. The clumps subsequently orbit the planet independent of each other. The predicted number of clumps n is in good agreement with more sophisticated N-body treatments of tidal breakup for parabolic encounters, and the dependence of n upon the progenitor's density as well as its orbit is also mapped out for hyperbolic encounters. These findings may be used to further constrain both the orbits and densities of the tidally disrupted bodies that struck Callisto and Ganymede. A cursory analysis shows that the Gomul and Gipul crater chains on Callisto, which have the greatest number of craters among the known chains, were formed by projectiles having comet-like densities estimated at rho(sub o) < 1 gm/cc.

Hahn, Joseph M.↗

NASA NTRS1995

Identification And Survival Of Bacteriohopanepolyol In A Hot Spring Microbial Mat

The polar lipids of a hot spring microbial mat located in Yellowstone National Park were examined for the presence of bacteriohopanepolvols (BHP). BHP are a group of molecules consisting of a hopanoid (peotacyclic triterpene) linked via a n-alkyl polyhydroxylated chain to a variety of polar end groups. BHP have been isolated in varying amounts from phylogenetically diverse eubacterial groups including cyanobacteria, methanotrophs and the Rhodospirillaceae. The hopanoids are excellent biomarkers and have been detected in sedimentary rocks as old as 1.7 bya. In order to interpret the ancient organic record, it is important to understand the abundance, source and fate of such biomarker compounds in microbial mats. A 40 sq cm mat section was taken from a 52 to 55 C site in the effluent channel of Octopus Spring and was sampled vertically over approximately 16 mm. The first 5-6 mm was sectioned into a top green layer (310 mg dry weight) and several subjacent, deep orange layers (240 and 250 mg, respectively). The lower 10 mm of the mat was sectioned into two gelatinous orange layers containing a siliceous gritty material (260 and 440 mg) which increased with depth, and a bottom layer composed almost exclusively of siliceous sinter (4.1 g). The progressive decrease in total organic carbon from 45% in the top green layer to only 4% in the bottom layer reflects the observed increase in siliceous deposition. GC-MS analysis of the phospholipid and glycolipid fatty acids yielded predominantly saturated normal chain acids, n-15 to n-18, and iso-branched acids, i-15 to i-17. Small amounts of unsaturated fatty acids (16:1, two positional isomers of 18:1, and two cyclopropyl acids, C(sub 17) and C(sub 19)) were present mainly in the top layer. Esterified fatty acid which is a good index for intact cellular membrane, i.e. viable organisms, was highest in the top two layers (203 and 231 micro g/mg total lipid, respectively) and gradually decreased to 66 micro g/mg total lipid in the bottom layer. Small amounts of BHP were present in all six layers, however in this case, BHP was lowest in the top green and subjacent deep-orange layers (118 and 172 micro g/mg total lipid, respectively) and increased with depth reaching almost 400 micro g/mg in the bottom two layers. This data suggest that BHP are survivina the initial phase of mat degradation and may be preferentially enriched in any organic record of such thermal environments. The relatively low level of BHP in the top layer also suggests that cyanobacteria may not be the major source of BHP in this mat. Since Chloroflexus a major component of the deep-orange layer has been reported to lack BHP, this material may prove a valuable biomarker for some other mat inhabitant. Further isotopic characterization of this BHP should help resolve this finding.

Janke, Linda L.↗

NASA NTRS1997

Peptide Folding and Translocation Across the Water-Membrane Interface

The ability of small peptides to organize at aqueous interfaces was examined by performing a series of large-scale, molecular dynamics computer simulations of several peptides composed of two amino acids, nonpolar leucine (L) and polar glutamine (Q). The peptides differed in size and sequence of the amino acids. Studies on dipeptides LL, LQ, QL and QQ were extended to two heptamers, LQQLLQL and LQLQLQL, designed to maximize interfacial stability of an alpha-helix and a beta-strand, respectively, by exposing polar side chains to water and nonpolar side chains to a nonpolar phase. Finally, a transition of an undecamer, composed entirely of leucine residues, from a disordered structure in water to an alpha-helix in a nonpolar phase representing the interior of the membrane was investigated. Complete folding of a peptide in solution was accomplished for the first time in computer simulations. The simulations revealed several basic principles governing the sequence-dependent organization of peptides at interfaces. Short peptides tend to accumulate at interfaces and acquire ordered structures, providing that they have a proper sequence of polar and nonpolar amino acids. The dominant factor determining the interfacial structure of peptides is the hydrophobic effect, which is manifested at aqueous interfaces as a tendency for polar and nonpolar groups of the solute to segregate into the aqueous and nonpolar phases, respectively. If peptides consist of nonpolar residue's only, they become inserted into the nonpolar phase. As demonstrated by the example of the leucine undecamer, such peptides fold into an alpha-helix as they partition into the nonpolar medium. The folding proceeds through an intermediate, called 3-10-helix, which remains in equilibrium with the alpha-helix. Once in the nonpolar environment, the peptides can readily change their orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with respect to the interface from parallel to perpendicular, especially in response to local electric fields. The ability of nonpolar peptides to modify both the structure and orientation with changing external conditions may have provided a simple mechanism of transmitting signals from the environment to the interior of a cell.

Pohorille, Andrew↗

NASA NTRS2002

The Effects of Ultra Thin Films on Dynamic Wetting

Dynamic wetting, the displacement of one fluid by another immiscible fluid on a surface, controls many natural and technological phenomena, such as coating, printing, spray painting and lubricating. Particularly in coating and spraying applications, contact lines advance across pre-existing fluid films. Most previous work has focused on contact lines advancing across films sufficiently thick that they behave as simple Newtonian fluids. Ultrathin films, where the film thickness may impinge on fundamental length scales in the fluid, have received less attention. In this talk, we will discuss the effects of ultrathin polymer films on dynamic wetting. We measure the interface shape within microns of moving contact lines advancing across preexisting films and compare the measurements to existing models of viscous bending for interfaces advancing across dry surfaces and 'thick' (in the sense that they behave as liquids) films. In the experiments, we advance a contact line of 10-poise and 1-poise polydimethylsiloxane (silicone oil) across pre-coated films of the same fluid with thickness from a single chain thickness (approx. 10 A) through a couple of radii of gyration (100-200 A) to films so thick they are likely bulk in behavior (10(exp 3) A). All films are physisorbed, i.e. they readily rinse from the surface. Thus, molecules in the film are not anchored to the surface and can move within the film if the hydrodynamics dictate such motion. For films of the thickness of a single chain (approx. 10 A), our experiments indicate that the advancing fluid behaves just as it would if it advanced over a dry surface. For the thicker films (10(exp 3) A), we find behavior indicating that the molecules in the film are acting as a fluid with the bulk properties. In this regime, results for the two different fluids are identical when the experiments are performed at the same pre-existing film thickness and advancing capillary number, Ca. For film of thickness of a few radii of gyration (approx. 100-200 A), the behavior depends on Ca of the advancing meniscus. At low Ca, the viscous bending of the interface near the contact line does not behave as it would on a dry surface. It has a lower curvature than expected. However, at higher Ca, the viscous bending is described by the model for spreading over a dry surface. These results show that the fluid flow in the film does behave differently than bulk as the film thickness becomes comparable to molecular length scale. But even more intriguing is the unusual velocity dependence of that behavior where the film behaves more solid-like at higher contact line speeds. We will discuss these results in terms of the properties of confined polymer melts.

Chen, Xia↗

NASA NTRS2002

Granular Materials Research at NASA-Glenn

This paper presents viewgraphs of granular materials research at NASA-Glenn. The topics include: 1) Impulse dispersion of a tapered granular chain; 2) High Speed Digital Images of Tapered Chain Dynamics; 3) Impulse Dispersion; 4) Three Dimensional Granular Bed Experimental Setup; 5) Magnetic Resonance Imaging of Fluid Flow in Porous Media; and 6) Net Charge on Granular Materials (NCharG).

Agui, Juan H.↗

NASA NTRS2002

IMAGE-EUV Observation of Large Scale Standing Wave Pattern in the Nightside Plasmasphere

We present analyses of a nightside plasmaspheric pattern of bifurcated, filamentary He(+) 30.4-nm emission enhancements observed by IMAGE EUV between approximately 19:40-22:13 UT on 28 June 2000 that indicate the presence of a large-scale, global ULF standing wave pattern. Analysis of coincident IMAGE magnetometer chain data reveals that these ULF waves extend across the magnetic latitude-longitude range of the chain and possess multiple spectral features between 0.6-5-mHz (3-30 minute period). Additionally, analysis of ACE SWE data reveals similarly structured spectral components in the solar wind. Collectively, these analyses lead to the conclusion that the observed large-scale ULF wave pattern is the result of solar wind pressure pulses 'ringing' the inner-magnetosphere.

Six, N. Frank↗

NASA NTRS2003

Web-based Weather Expert System (WES) for Space Shuttle Launch

The Web-based Weather Expert System (WES) is a critical module of the Virtual Test Bed development to support 'go/no go' decisions for Space Shuttle operations in the Intelligent Launch and Range Operations program of NASA. The weather rules characterize certain aspects of the environment related to the launching or landing site, the time of the day or night, the pad or runway conditions, the mission durations, the runway equipment and landing type. Expert system rules are derived from weather contingency rules, which were developed over years by NASA. Backward chaining, a goal-directed inference method is adopted, because a particular consequence or goal clause is evaluated first, and then chained backward through the rules. Once a rule is satisfied or true, then that particular rule is fired and the decision is expressed. The expert system is continuously verifying the rules against the past one-hour weather conditions and the decisions are made. The normal procedure of operations requires a formal pre-launch weather briefing held on Launch minus 1 day, which is a specific weather briefing for all areas of Space Shuttle launch operations. In this paper, the Web-based Weather Expert System of the Intelligent Launch and range Operations program is presented.

Bardina, Jorge E.↗

NASA NTRS2001

Catalysis in the 3rd Dimension: How Organic Molecules May be Formed

Catalysis is often little more than a word to phenomenologically describe the fact that a reaction follows a pat1 that leads to products of an unexpected kind or of unexpected yield. Low activation energy barriers for intermediates are recognized as the most likely cause why a system deviates from the thermodynamic pull towards minimizing its free energy and ends up in a metastable state. Seldom is the mechanism known. This i: particularly true for heterogeneous catalysis under hydrothermal conditions with minerals as catalysts. It is commonly assumed that catalytic action takes place across solid-fluid interfaces and that, on the atomic level, interfaces are just 2-dimensional contacts. This makes it difficult to understand, for instance, the assembly of long-chain carboxylic (fatty) acids. 3y studying single crystals that grew from a melt in the presence of H2O and CO2, we can show: (1) that numerals take up the fluid components into solid solution, (2) that some-thing happens converting them to -educedH and C, (3) that C atoms segregate into dislocations and tie C-C bonds. The products are medium-to-long chain Cn protomolecules, with some C-H attached, pre-assembled in the dislocations. Upon solvent extraction, these proto-molecules turn into carboxylic and dicarboxylic acids. This observation suggests that, in a very elementary step, catalysis under hydrothermal conditions leading to fatty acids involves the pre-assembly of Cn entities in the interface that is not 2-D but extends into the 3rd dimension, with dislocations as synthesis sites.

Freund, Friedemann↗

NASA NTRS2003

Electrostrictive Graft Elastomers

An electrostrictive graft elastomer has a backbone molecule which is a non-crystallizable, flexible macromolecular chain and a grafted polymer forming polar graft moieties with backbone molecules. The polar graft moieties have been rotated by an applied electric field, e.g., into substantial polar alignment. The rotation is sustained until the electric field is removed. In another embodiment, a process for producing strain in an elastomer includes: (a) providing a graft elastomer having a backbone molecule which is a non-crystallizable, flexible macromolecular chain and a grafted polymer forming polar graft moieties with backbone molecules; and (b) applying an electric field to the graft elastomer to rotate the polar graft moieties, e.g., into substantial polar alignment.

Su, Ji↗

NASA NTRS2004

Spectroscopy of the Perseus Cluster

We present preliminary results of a XMM-Newton 50 ks observation of the Perseus Cluster that provides an unprecedented view of the central 0.5 Mpc region. The projected gas temperature declines smoothly by a factor of 2 from a maximum value of approx. 7 keV in the outer regions to just above 3 keV at the cluster center. Over this same range, the heavy-element abundance rises slowly from 0.4 to 0.5 solar as the radius decreases from 14 ft. to 5 ft., and then it rises to a peak of almost 0.7 solar at 1&farcm;25 before declining to 0.4 at the center. Th global east-west asymmetry of the gas temperature and surface brightness distributions, approximately aligned with the chain of bright galaxies, suggests an ongoing merger, although the modest degree of the observed asymmetry certainly excludes a major merger interpretation. The chain of galaxies probably traces the filament along which accretion started some time ago and is continuing at the present time. A cold and dense (low-entropy) cluster core like Perseus is probably well "protected" against the penetration of the gas of infalling groups and poor clusters, whereas in non-cooling core clusters such as Coma and A1367, infalling subclusters can penetrate deeply into the core region. In Perseus, gas associated with infalling groups may be stripped completely at the outskirts of the main cluster and only compression waves (shocks) may reach the central regions. We argue, and show supporting simulations, that the passage of such a wave(s) can qualitatively explain the overall horseshoe shaped appearance of the gas temperature map (the hot horseshoe surrounds the colder, low-entropy core) as well as other features of the Perseus Cluster core. These simulations also show that as compression waves traverse the cluster core, they can induce oscillatory motion of the cluster gas that can generate multiple sharp "edges" on opposite sides of the central galaxy. Gas motions induced by mergers may be a natural way to explain the high frequency of "edges" seen in clusters with cooling cores.

Jones, Christine↗

NASA NTRS2003

Structure, Function, Self-Assembly and Origin of Simple Membrane Proteins

Integral membrane proteins perform such essential cellular functions as transport of ions, nutrients and waste products across cell walls, transduction of environmental signals, regulation of cell fusion, recognition of other cells, energy capture and its conversion into high-energy compounds. In fact, 30-40% of genes in modem organisms codes for membrane proteins. Although contemporary membrane proteins or their functional assemblies can be quite complex, their transmembrane fragments are usually remarkably simple. The most common structural motif for these fragments is a bundle of alpha-helices, but occasionally it could be a beta-barrel. In a series of molecular dynamics computer simulations we investigated self-organizing properties of simple membrane proteins based on these structural motifs. Specifically, we studied folding and insertion into membranes of short, nonpolar or amphiphatic peptides. We also investigated glycophorin A, a peptide that forms sequence-specific dimers, and a transmembrane aggregate of four identical alpha-helices that forms an efficient and selective voltage-gated proton channel was investigated. Many peptides are attracted to water-membrane interfaces. Once at the interface, nonpolar peptides spontaneously fold to a-helices. Whenever the sequence permits, peptides that contain both polar and nonpolar amino also adopt helical structures, in which polar and nonpolar amino acid side chains are immersed in water and membrane, respectively. Specific identity of side chains is less important. Helical peptides at the interface could insert into the membrane and adopt a transmembrane conformation. However, insertion of a single helix is unfavorable because polar groups in the peptide become completely dehydrated upon insertion. The unfavorable free energy of insertion can be regained by spontaneous association of peptides in the membrane. The first step in this process is the formation of dimers, although the most common are aggregates of 4-7 helices. The helices could arrange themselves such that they formed pores capable of transporting ions and small molecules across membranes. Stability of transmembrane aggregates of simple proteins is often only marginal and, therefore, it can be regulated by environmental signals or small sequence modifications in the region of interhelical interactions. A key step in the earliest evolution of membrane proteins was the emergence of selectivity for specific substrates. Many channels could become selective if one or only a few properly chosen amino acids are properly placed along the channel, acting as filters or gates. This is a convenient evolutionary solution because it does not require imposing conditions on the whole sequence.

Pohorille, Andrew↗

NASA NTRS2004

Coarse-Grained and Atomistic Modeling of Polyimides

A coarse-grained model for a set of three polyimide isomers is developed. Each polyimide is comprised of BPDA (3,3,4,4' - biphenyltetracarboxylic dianhydride) and one of three APB isomers: 1,3-bis(4-aminophenoxy)benzene, 1,4-bis(4-aminophenoxy)benzene or 1,3-bis(3-aminophenoxy)benzene. The coarse-grained model is constructed as a series of linked vectors following the contour of the polymer backbone. Beads located at the midpoint of each vector define centers for long range interaction energy between monomer subunits. A bulk simulation of each coarse-grained polyimide model is performed with a dynamic Monte Carlo procedure. These coarsegrained models are then reverse-mapped to fully atomistic models. The coarse-grained models show the expected trends in decreasing chain dimensions with increasing meta linkage in the APB section of the repeat unit, although these differences were minor due to the relatively short chains simulated here. Considerable differences are seen among the dynamic Monte Carlo properties of the three polyimide isomers. Decreasing relaxation times are seen with increasing meta linkage in the APB section of the repeat unit.

Clancy, Thomas C.↗