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All sourcesNASA NTRSDOE OSTI
NASA NTRS1991

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↗
NASA NTRS1992

Stagnation-point heat-transfer rate predictions at aeroassist flight conditions

The results are presented for the stagnation-point heat-transfer rates used in the design process of the Aeroassist Flight Experiment (AFE) vehicle over its entire aeropass trajectory. The prediction methods used in this investigation demonstrate the application of computational fluid dynamics (CFD) techniques to a wide range of flight conditions and their usefulness in a design process. The heating rates were computed by a viscous-shock-layer (VSL) code at the lower altitudes and by a Navier-Stokes (N-S) code for the higher altitude cases. For both methods, finite-rate chemically reacting gas was considered, and a temperature-dependent wall-catalysis model was used. The wall temperature for each case was assumed to be radiative equilibrium temperature, based on total heating. The radiative heating was estimated by using a correlation equation. Wall slip was included in the N-S calculation method, and this method implicitly accounts for shock slip. The N-S/VSL combination of projection methods was established by comparison with the published benchmark flow-field code LAURA results at lower altitudes, and the direct simulation Monte Carlo results at higher altitude cases. To obtain the design heating rate over the entire forward face of the vehicle, a boundary-layer method (BLIMP code) that employs reacting chemistry and surface catalysis was used. The ratio of the VSL or N-S method prediction to that obtained from the boundary-layer method code at the stagnation point is used to define an adjustment factor, which accounts for the errors involved in using the boundary-layer method.

Gupta, Roop N.↗
NASA NTRS1992

Oligomerization reactions of ribonucleotides - The reaction of the 5'-phosphorimidazolide of nucleosides on montmorillonite and other minerals

The reaction of ImpA in the presence of Na(+)-montmorillonite 22A or Na(+)-Volclay in aqueous, pH 8 solution gives a 50-60 percent yield of dimers and trimers (pA)2 and (pA)3. The ratio of 3',5'-phosphodiester bond formation is twice as great as 2',5'-bond formation. The reaction requires the presence of Mg2+ and is inhibited by 0.4 M imidazole. N-methylimidazole enhances the rate of the reaction but does not cause major changes in yield or product composition. Higher yields were obtained when Li+- or Ca2+-montmorillonites were used in place of Na+-montmorillonite. Little or no phosphodiester bond formation was observed with Mg2+- or Al3+-montmorillonite. Montmorillonites other than 22A and Volclay exhibited litle or no catalysis. In addittion, little or no catalysis was exhibited in ferrugenous smectite, nontronite, allophane, imogolite or sepiolite. Oligomers were also formed by the reaction of ImpG, 2-methylImpG, ImpC and ImpU in the presence of Na+-montmorillonite. The pyrimidine nucleotides gave significantly lower yields of oligomers.

Ferris, James P.↗
NASA NTRS1995

Self-Incorporation of Coenzymes by Ribozymes

RNA molecules that are assembled from the four standard nucleotides contain a limited number of chemical functional groups, a characteristic that is generally thought to restrict the potential for catalysis by ribozymes. Although polypeptides carry a wider range of functional groups, many contemporary protein-based enzymes employ coenzymes to augment their capabilities. The coenzymes possess additional chemical moieties that can participate directly in catalysis and thereby enhance catalytic function. In this work, we demonstrate a mechanism by which ribozymes can supplement their limited repertoire of functional groups through RNAcatalyzed incorporation of various coenzymes and coenzyme analogues. The group I ribozyme of Tetrahymena thermophila normally mediates a phosphoester transfer reaction that results in the covalent attachment of guanosine to the ribozyme. Here, a shortened version of the ribozyme is shown to catalyze the self-incorporation of coenzymes and coenzyme analogues, such as NAD+ and dephosphorylated CoA-SH. Similar ribozyme activities may have played an important role in the "RNA world," when RNA enzymes are thought to have maintained a complex metabolism in the absence of proteins and would have benefited from the inclusion of additional functional groups.

Breaker, Ronald R.↗
NASA NTRS1998

RNA Research

It is generally believed that an RNA World existed at an early stage in the history of life. During this early period, RNA molecules are seen to be potentially involved in both catalysis and the storage of genetic information. It is widely believed that this RNA World was extensive and therefore a sophisticated nucleic acid replication machinery would presumably predate the translation machinery which would not be needed until later stages in the development of life. This view of an extended RNA World is not necessarily correct. From the point of view of exobiology, the difference in these two views mainly affects the significance of studies of the extent of catalysis possible by RNA- In either case, the origin of the translation machinery and the principles of RNA evolution remain central problems in exobiology. Translation presents several interrelated themes of inquiry for exobiology. First, it is essential, for understanding the very origin of life, how peptides and eventually proteins might have come to be made on the early Earth in a template directed manner. Second, it is necessary to understand how a machinery of similar complexity to that found in the ribosomes of modem organisms came to exist by the time of the last common ancestor (as detected by 16S RRNA sequence studies). Third, the RNAs that comprise the ribosome are themselves likely of very early origin and studies of their history may be very informative about the nature of the RNA World. Moreover, studies of these RNAs will contribute to a better understanding of the potential roles of RNA in early evolution.

Source record↗
NASA NTRS2001

Aerothermal Analysis of the Project Fire II Afterbody Flow

Computational fluid dynamics (CFD) is used to simulate the wake flow and afterbody heating of the Project Fire II ballistic reentry to Earth at 11.4 km/sec. Laminar results are obtained over a portion of the trajectory between the initial heat pulse and peak afterbody heating. Although non-catalytic forebody convective heating results are in excellent agreement with previous computations, initial predictions of afterbody heating were about a factor of two below the experimental values. Further analysis suggests that significant catalysis may be occurring on the afterbody heat shield. Computations including finite-rate catalysis on the afterbody surface are in good agreement with the data over the early portion of the trajectory, but are conservative near the peak afterbody heating point, especially on the rear portion of the conical frustum. Further analysis of the flight data from Fire II shows that peak afterbody heating occurs before peak forebody heating, a result that contradicts computations and flight data from other entry vehicles. This result suggests that another mechanism, possibly pyrolysis, may be occurring during the later portion of the trajectory, resulting in less total heat transfer than the current predictions.

Wright, Michael J.↗
NASA NTRS2003

Catalyzed Combustion In Micro-Propulsion Devices: Project Status

In recent years, there has been a tendency toward shrinking the size of spacecraft. New classes of spacecraft called micro-spacecraft have been defined by their mass, power, and size ranges. Spacecraft in the range of 20 to 100 kg represent the class most likely to be utilized by most small sat users in the near future. There are also efforts to develop 10 to 20 kg class spacecraft for use in satellite constellations. More ambitious efforts will be to develop spacecraft less than 10 kg, in which MEMS fabrication technology is required. These new micro-spacecraft will require new micro-propulsion technology. Although micro-propulsion includes electric propulsion approaches, the focus of this proposed program is micro-chemical propulsion which requires the development of microcombustors. As combustors are scaled down, the surface to volume ratio increases. The heat release rate in the combustor scales with volume, while heat loss rate scales with surface area. Consequently, heat loss eventually dominates over heat release when the combustor size becomes smaller, thereby leading to flame quenching. The limitations imposed on chamber length and diameter has an immediate impact on the degree of miniaturization of a micro-combustor. Before micro-combustors can be realized, such a difficulty must be overcome. One viable combustion alternative is to take advantage of surface catalysis. Micro-chemical propulsion for small spacecraft can be used for primary thrust, orbit insertion, trajectory-control, and attitude control. Grouping micro-propulsion devices in arrays will allow their use for larger thrust applications. By using an array composed of hundreds or thousands of micro-thruster units, a particular configuration can be arranged to be best suited for a specific application. Moreover, different thruster sizes would provide for a range of thrust levels (from N s to mN s) within the same array. Several thrusters could be fired simultaneously for thrust levels higher than the basic units, or in a rapid sequence in order to provide gradual but steady low-g acceleration. These arrays of micro-propulsion systems would offer unprecedented flexibility and redundancy for satellite propulsion and reaction control for launch vehicles. A high-pressure bi-propellant micro-rocket engine is already being developed using MEMS technology. High pressure turbopumps and valves are to be incorporated onto the rocket chip . High pressure combustion of methane and O2 in a micro-combustor has been demonstrated without catalysis, but ignition was established with a spark. This combustor has rectangular dimensions of 1.5 mm by 8 mm (hydraulic diameter 3.9 mm) and a length of 4.5 mm and was operated at 1250 kPa with plans to operate it at 12.7 MPa. These high operating pressures enable the combustion process in these devices, but these pressures are not practical for pressure fed satellite propulsion systems. Note that the use of these propellants requires an ignition system and that the use of a spark would impose a size limitation to this micro-propulsion device because the spark unit cannot be shrunk proportionately with the thruster. Results presented in this paper consist of an experimental evaluation of the minimum catalyst temperature for initiating/supporting combustion in sub-millimeter diameter tubes. The tubes are resistively heated and reactive premixed gases are passed through the tubes. Tube temperature and inlet pressure are monitored for an indication of exothermic reactions and composition changes in the gases.

Sung, C. J.↗
NASA NTRS1993

Modeling study on the cleavage step of the self-splicing reaction in group I introns

A three-dimensional model of the Tetrahymena thermophila group I intron is used to further explore the catalytic mechanism of the transphosphorylation reaction of the cleavage step. Based on the coordinates of the catalytic core model proposed by Michel and Westhof (Michel, F., Westhof, E. J. Mol. Biol. 216, 585-610 (1990)), we first converted their ligation step model into a model of the cleavage step by the substitution of several bases and the removal of helix P9. Next, an attempt to place a trigonal bipyramidal transition state model in the active site revealed that this modified model for the cleavage step could not accommodate the transition state due to insufficient space. A lowering of P1 helix relative to surrounding helices provided the additional space required. Simultaneously, it provided a better starting geometry to model the molecular contacts proposed by Pyle et al. (Pyle, A. M., Murphy, F. L., Cech, T. R. Nature 358, 123-128. (1992)), based on mutational studies involving the J8/7 segment. Two hydrated Mg2+ complexes were placed in the active site of the ribozyme model, using the crystal structure of the functionally similar Klenow fragment (Beese, L.S., Steitz, T.A. EMBO J. 10, 25-33 (1991)) as a guide. The presence of two metal ions in the active site of the intron differs from previous models, which incorporate one metal ion in the catalytic site to fulfill the postulated roles of Mg2+ in catalysis. The reaction profile is simulated based on a trigonal bipyramidal transition state, and the role of the hydrated Mg2+ complexes in catalysis is further explored using molecular orbital calculations.

NASA Discipline Exobiology↗
NASA NTRS1991

Nucleotides as nucleophiles: reactions of nucleotides with phosphoimidazolide activated guanosine

An earlier study of the reaction of phosphoimidazolide activated nucleosides (ImpN) in aqueous phosphate buffers indicated two modes of reaction of the phosphate monoanion and dianion. The first mode is catalysis of the hydrolysis of the P-N bond in ImpN's which leads to imidazole and nucleoside 5'-monophosphate. The second represents a nucleophilic substitution of the imidazole to yield the nucleoside 5'-diphosphate. This earlier study thus served as a model for the reaction of ImpN with nucleoside monophosphates (pN) because the latter can be regarded as phosphate derivatives. In the present study we investigated the reaction of guanosine 5'-phosphate-2-methylimidazolide, 2-MeImpG, in the presence of pN (N = guanosine, adenosine and uridine) in the range 6.9 less than or equal to pH less than or equal to 7.7. We observed that pN's do act as nucleophiles to form NppG, and as general base to enhance the hydrolysis of the P-N bond in 2-MeImpG, i.e. pN show the same behavior as inorganic phosphate. The kinetic analysis yields the following rate constants for the dianion pN2-: knpN = 0.17 +/- 0.02 M-1 h-1 for nucleophilic attack and khpN = 0.11 +/- 0.07 M-1 h-1 for general base catalysis of the hydrolysis. These rate constants which are independent of the nucleobase compare with kp.2 = 0.415 M-1 h-1 and khp2. = 0.217 M-1 h-1 for the reactions of HPO4(2-). In addition, this study shows that under conditions where pN presumably form stacks, the reaction mechanism remains unchanged although in quantitative terms stacked pN are somewhat less reactive. Attack by the 2'-OH and 3'-OH groups of the ribose moiety in amounts greater than or equal to 1% is not observed; this is attributed to the large difference in nucleophilicity in the neutral pH range between the phosphate group and the ribose hydroxyls. This nucleophilicity rank is not altered by stacking.

NASA Discipline Exobiology↗
NASA NTRS2009

Method of Heating a Foam-Based Catalyst Bed

A method of heating a foam-based catalyst bed has been developed using silicon carbide as the catalyst support due to its readily accessible, high surface area that is oxidation-resistant and is electrically conductive. The foam support may be resistively heated by passing an electric current through it. This allows the catalyst bed to be heated directly, requiring less power to reach the desired temperature more quickly. Designed for heterogeneous catalysis, the method can be used by the petrochemical, chemical processing, and power-generating industries, as well as automotive catalytic converters. Catalyst beds must be heated to a light-off temperature before they catalyze the desired reactions. This typically is done by heating the assembly that contains the catalyst bed, which results in much of the power being wasted and/or lost to the surrounding environment. The catalyst bed is heated indirectly, thus requiring excessive power. With the electrically heated catalyst bed, virtually all of the power is used to heat the support, and only a small fraction is lost to the surroundings. Although the light-off temperature of most catalysts is only a few hundred degrees Celsius, the electrically heated foam is able to achieve temperatures of 1,200 C. Lower temperatures are achievable by supplying less electrical power to the foam. Furthermore, because of the foam s open-cell structure, the catalyst can be applied either directly to the foam ligaments or in the form of a catalyst- containing washcoat. This innovation would be very useful for heterogeneous catalysis where elevated temperatures are needed to drive the reaction.

Fortini, Arthur J.↗
NASA NTRS2000

Applications of Low Density Flow Techniques and Catalytic Recombination at the Johnson Space Center

The talk presents a brief background on defInitions of catalysis and effects associated with chemically nonequilibrium and low-density flows of aerospace interest. Applications of catalytic recombination on surfaces in dissociated flow are given, including aero heating on reentry spacecraft thermal protection surfaces and reflection of plume flow on pressure distributions associated with the space station. Examples include aero heating predictions for the X-38 test vehicle, the inlet of a proposed gas-sampling probe used in high enthalpy test facilities, and a parabolic body at angle of attack. The effect of accommodation coefficients on thruster induced pressure distributions is also included. Examples of tools used include simple aero heating formulas based on boundary layer solutions, an engineering approximation that uses axisymmetric viscous shock layer flow to simulate full three dimensional flow, full computational fluid dynamics, and direct simulation Monte-Carlo calculations. Methods of determining catalytic recombination rates in arc jet flow are discus ed. An area of catalysis not fully understood is the formation of single-wall carbon nanotubes (SWNT) with gas phase or nano-size metal particles. The Johnson Space Center is making SWNTs using both a laser ablation technique and an electric arc vaporization technique.

Scott, Carl D.↗
NASA NTRS2012

Processes that Drove the Transition from Chemistry to Biology: Concepts and Evidence

Two properties are particularly germane to the transition from chemistry to biology. One is the emergence of complex molecules (polymers) capable of performing non-trivial functions, such as catalysis, energy transduction or transport across cell walls. The other is the ability of several functions to work in concert to provide reproductive advantage to systems hosting these functions. Biological systems exhibit these properties at remarkable levels of efficiency and accuracy in a way that appears effortless. However, dissection of these properties reveals great complexities that are involved. This opens a question: how a simple, ancestral system could have acquired the required properties? Other questions follow. What are the chances that a functional polymer emerges at random? What is the minimum structural complexity of a polymer to carry out a function at a reasonable level of efficiency? Can we identify concrete, protobiologically plausible mechanisms that yield advantageous coupling between different functions? These and similar questions are at the core of the main topic of this session: how soulless chemistry became life? Clearly, we do not have complete answers to any of these questions. However, in recent years a number of new and sometimes unexpected clues have been brought to light. Of particular interest are proteins because they are the main functional polymers in contemporary cells. The emergence of protein functions is a puzzle. It is widely accepted that a well ]defined, compact structure (fold) is a prerequisite for function. It is equally widely accepted that compact folds are rare among random amino acid polymers. Then, how did protein functionality start? According to one hypothesis well folded were preceded by their poorly folded, yet still functional ancestors. Only recently, however, experimental evidence supporting this hypothesis has been presented. In particular, a small enzyme capable of ligating two RNA fragments with the rate of 106 above background was evolved in vitro. This enzyme does not look like any contemporary protein. It is very flexible and its structure is kept together just by a single salt bridge between a charged residue and a coordinating zinc. A similar picture emerges from studies of simple transmembrane channels that mimic those in ancestral cells. Again, they are extremely flexible and do not form a conventional pore. Yet, they efficiently mediate ion transport. Studies on simple proteins that are on-going in several laboratories hold promise of revealing crucial links between chemical and biological catalysis and other ubiquitous cell functions. Interaction between composition, growth and division of protobiologically relevant vesicles and metabolic reactions that they encapsulate is an example of coupling between simple functions that promotes reproduction and evolution. Recent studies have demonstrated possible mechanisms by which vesicles might have evolved their composition from fatty acids to phospholipids, thus facilitating a number of new cellular functions. Conversely, it has been also demonstrated that an encapsulated metabolism might drive vesicle division. These are, again, examples of processes that might have driven the transition from chemistry to biology.

Pohorille, Andrew↗
NASA NTRS2013

Advanced Exploration Systems Logistics Reduction and Repurposing Trash-to-Gas and Heat Melt Compactor KSC

Topics covered: 1. Project Structure 2. "Trash to Gas" 3. "Smashing Trash! The Heat Melt Compactor" 4. "Heat Melt Compaction as an Effective Treatment for Eliminating Microorganisms from Solid Waste" Thermal degradation of trash reduces volume while creating water, carbon dioxide and ash. CO2 can be fed to Sabatier reactor for CH4 production to fuel LOX/LCH4 ascent vehicle. Optimal performance: HFWS, full temperature ramp to 500-600 C. Tar challenges exist. Catalysis: Dolomag did eliminate allene byproducts from the product stream. 2nd Gen Reactor Studies. Targeting power, mass, time efficiency. Gas separation, Catalysis to reduce tar formation. Microgravity effects. Downselect in August will determine where we should spend time optimizing the technology.

Caraccio, Anne J.↗
NASA NTRS2017

Development of a Detailed Surface Chemistry Framework in DSMC

Many of the current direct simulation Monte Carlo (DSMC) codes still employ only simple surface catalysis models. These include only basic mechanisms such as dissociation, recombination, and exchange reactions, without any provision for adsorption and finite rate kinetics. Incorporating finite rate chemistry at the surface is increasingly becoming a necessity for various applications such as high speed re-entry flows over thermal protection systems (TPS), micro-electro-mechanical systems (MEMS), surface catalysis, etc. In the recent years, relatively few works have examined finite-rate surface reaction modeling using the DSMC method.In this work, a generalized finite-rate surface chemistry framework incorporating a comprehensive list of reaction mechanisms is developed and implemented into the DSMC solver SPARTA. The various mechanisms include adsorption, desorption, Langmuir-Hinshelwood (LH), Eley-Rideal (ER), Collision Induced (CI), condensation, sublimation, etc. The approach is to stochastically model the various competing reactions occurring on a set of active sites. Both gas-surface (e.g., ER, CI) and pure-surface (e.g., LH, desorption) reaction mechanisms are incorporated. The reaction mechanisms could also be catalytic or surface altering based on the participation of the bulk-phase species (e.g., bulk carbon atoms). Marschall and MacLean developed a general formulation in which multiple phases and surface sites are used and we adopt a similar convention in the current work. Microscopic parameters of reaction probabilities (for gas-surface reactions) and frequencies (for pure-surface reactions) that are require for DSMC are computed from the surface properties and macroscopic parameters such as rate constants, sticking coefficients, etc. The energy and angular distributions of the products are decided based on the reaction type and input parameters. Thus, the user has the capability to model various surface reactions via user-specified reaction rate constants, surface properties and parameters.

Gas↗
NASA NTRS2024

Aerothermal Analysis of the Rocket Lab Venus Probe Heatshield

This document provides an overview of the aerothermodynamic analyses performed by the Aerothermodynamics Branch at NASA Langley Research Center for the Rocket Lab Venus Probe (RLVP). In addition to defining the baseline heating environment to the heatshield, this document pursues the experimental validation of key physical models at RLVP-relevant conditions. This experimental validation analysis, which captures the model form uncertainty, is used as one of two primary components of the margin assessment, where the other component is the parametric uncertainty. These model form (experimental) and parametric uncertainty components are used to construct a spatial and time varying margin for the heating to the RLVP heatshield. The margin is evaluated as the sum of the parametric and model form uncertainty components. The model form uncertainty is defined as the difference between the RLVP-relevant measurements and their simulations, using the upper limit uncertainty bounds for both the measurements and simulations in the comparisons. The differences in the dominant physics in the stagnation region and flank lead to the separate RLVP-relevant measurements for assessing the model form uncertainty in these two regions. These regions are addressed as follows: Stagnation Region Heating Environment: For the high-temperature stagnation-region, both the radiative heating and impact of blowing on convective heating are significant, while the impacts of turbulence and roughness are negligible. Coupled radiation and ablation LAURA/HARA solutions with ray-tracing provide the radiative heating over the entire vehicle, including the contributions from the Venus atmosphere and ablation species. Non-ablating LAURA simulations provide the convective heating. During the material-response computation typically used for TPS sizing, this non-ablating convective heating is corrected for the impact of ablation using the blowing correction. Coupled ablation LAURA simulations that capture finite-rate sur-face processes show that this blowing correction may be non-conservative over most of the heatshield. This non-conservatism is due to hydrogen recombination in the finite-rate surface model, which tends to increase the coupled ablation convective heating to near the non-ablating values, therefore making any reduction in the non-ablating value through the blowing correction non-conservative. This non-conservatism due to H catalysis is captured in the parametric component of the margin. The best available ground-test measurements that capture the impact of blowing on stagnation region convective heating, at RLVP-relevant conditions, indicate that the current blowing reduction model is non-conservative by up to 20% at RLVP-relevant blowing rates (the coupled blowing simulations were also non-conservative). Because of the relatively low velocity of the ground tests and the non-Venus atmospheric chemistry, these measurements do not capture the chemistry and therefore do not inform the uncertainty due to H catalysis. However, they do capture the fluid mechanics of blowing. The non-conservatism of the blowing correction implied by these measurements is covered by the model form component of the margin, which leads to total margin values over 50%. For the radiative heating, the shock-tube informed bias approach suggests a model form uncertainty of roughly 20%, while the parametric uncertainty analysis suggests values over 100%. The combined stagnation-point radiation margin of over 100% leads to peak margined radiative heating values of over300 W/cm2, which remains small relative to the peak margined convective heating of nearly 2000 W/cm2. Based on this analysis, at the stagnation point, the peak margined heat rate is 2203 W/cm2 and the margined total heat load is 31.5 kJ/cm2 for the current nominal trajectory. Flank Heating Environment: The forebody flank (and near-shoulder) heating environment is dominated by the impact of turbulence, roughness augmentation, and ablation on the convective heating. An extensive collection of ground test measurements with RLVP-relevant turbulence and roughness is studied to show that the maximum difference between the simulated and measured convective heating is 5%. However, with the exception of the Holden measurements from the 1980s, these measurements do not include roughness elements extending into the supersonic region of the boundary layer, which is likely to occur for RLVP (due to the 45 degree sphere-cone geometry). The interaction between the supersonic flow and roughness could cause convective heating augmentation fundamentally different than for locally subsonic flow. Although these Holden measurements are consistent with the other measurements considered, another path was pursued to assure that the rough-ness height extending into supersonic flow does not fundamentally change the roughness augmentation. This additional path was a computational effort to resolve the roughness elements in the CFD grid, so that the interaction be-tween the roughness elements and locally supersonic flow may be simulated in detail. This roughness-resolved CFD simulation is feasible because of the RLVP forebody TPS’s patterned roughness, which may be approximated analytically, and because of the axisymmetric nominal flow field, which allows a narrow surface region to be simulated and therefore make the computational expense feasible. These grid-resolved roughness simulations, which are performed at actual RLVP flight conditions, result in heating augmentation values that are below the design approach for roughness augmentation. This provides evidence that the design approach for RLVP roughness augmentation is sufficient. Based on this analysis, at this flank or near-shoulder location, the peak margined total heat rate is 2088 W/cm2and the margined total heat load is 26.0 kJ/cm2for the current nominal trajectory. Heat flux, shear, pressure and heat transfer coefficient at the RLVP stagnation point and near shoulder location are evaluated for the entire trajectory, and curved fit to a functional form of F=AρB∞UC∞. These simplified relationships for the nominal and margined aerothermal environments are referred to as aerothermal indicators, and presented at the end of this document.

Christopher O Johnston↗
NASA NTRS1994

In vitro selection of catalytic RNAs

In vitro selection techniques are poised to allow a rapid expansion of the study of catalysis by RNA enzymes (ribozymes). This truly molecular version of genetics has already been applied to the study of the structures of known ribozymes and to the tailoring of their catalytic activity to meet specific requirements of substrate specificity or reaction conditions. During the past year, in vitro selection has been successfully used to isolate novel RNA catalysts from random sequence pools.

NASA Discipline Exobiology↗
NASA NTRS1996

Chance and necessity in the selection of nucleic acid catalysts

In Tom Stoppard's famous play [Rosencrantz and Guildenstern are Dead], the ill-fated heroes toss a coin 101 times. The first 100 times they do so the coin lands heads up. The chance of this happening is approximately 1 in 10(30), a sequence of events so rare that one might argue that it could only happen in such a delightful fiction. Similarly rare events, however, may underlie the origins of biological catalysis. What is the probability that an RNA, DNA, or protein molecule of a given random sequence will display a particular catalytic activity? The answer to this question determines whether a collection of such sequences, such as might result from prebiotic chemistry on the early earth, is extremely likely or unlikely to contain catalytically active molecules, and hence whether the origin of life itself is a virtually inevitable consequence of chemical laws or merely a bizarre fluke. The fact that a priori estimates of this probability, given by otherwise informed chemists and biologists, ranged from 10(-5) to 10(-50), inspired us to begin to address the question experimentally. As it turns out, the chance that a given random sequence RNA molecule will be able to catalyze an RNA polymerase-like phosphoryl transfer reaction is close to 1 in 10(13), rare enough, to be sure, but nevertheless in a range that is comfortably accessible by experiment. It is the purpose of this Account to describe the recent advances in combinatorial biochemistry that have made it possible for us to explore the abundance and diversity of catalysts existing in nucleic acid sequence space.

Review, Tutorial↗
NASA NTRS1996

Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation

The role of divalent cations in the mechanism of pyrophosphate-activated, template-directed oligoribonucleotide ligation has been investigated. The dependence of the reaction rate on Mg2+ concentration suggests a kinetic scheme in which a Mg2+ ion must bind before ligation can proceed. Mn2+, Ca2+, Sr2+, and Ba2+ can also catalyze the reaction. Although Pb2+ and Zn2+ do not catalyze the reaction in the absence of other divalent ions, they significantly modulate the reaction rate when added in the presence of Mg2+, with Pb2+ stimulating the reaction (up to 65-fold) and Zn2+ inhibiting the reaction. The logarithm of the ligation rate increases linearly, with slope of 0.95, as a function of pH, indicating that the reaction involves a single critical deprotonation step. The ligation rates observed with the different divalent metal ion catalysts (Mn2+ > Mg2+ > Ca2+ > Sr2+ = Ba2+) vary inversely with the pKa values of their bound water molecules. The pH profile and these relative ligation rates suggest a mechanism in which a metal-bound hydroxide ion located near the ligation junction promotes catalysis, most likely by deprotonation of the hydroxl nucleophile. The effects of changing either the leaving group or the attacking hydroxyl, together with the large delta S(++) value for oligonucleotide ligation (about -20 eu), are consistent with an associative transition state.

Non-NASA Center↗