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NASA NTRS2011

Origins of Protein Functions in Cells

In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis and in vitro evolution of very large libraries of random amino acid sequences. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions yet, important clues have been uncovered. In one example (Keefe and Szostak, 2001), novel ATP binding proteins were identified that appear to be unrelated in both sequence and structure to any known ATP binding proteins. One of these proteins was subsequently redesigned computationally to bind GTP through introducing several mutations that introduce targeted structural changes to the protein, improve its binding to guanine and prevent water from accessing the active center. This study facilitates further investigations of individual evolutionary steps that lead to a change of function in primordial proteins. In a second study (Seelig and Szostak, 2007), novel enzymes were generated that can join two pieces of RNA in a reaction for which no natural enzymes are known. Recently it was found that, as in the previous case, the proteins have a structure unknown among modern enzymes. In this case, in vitro evolution started from a small, non-enzymatic protein. A similar selection process initiated from a library of random polypeptides is in progress. These results not only allow for estimating the occurrence of function in random protein assemblies but also provide evidence for the possibility of alternative protein worlds. Extant proteins might simply represent a frozen accident in the world of possible proteins. Alternative collections of proteins, even with similar functions, could originate alternative evolutionary paths.

Seelig, Burchard↗

NASA NTRS2012

Recursive Branching Simulated Annealing Algorithm

This innovation is a variation of a simulated-annealing optimization algorithm that uses a recursive-branching structure to parallelize the search of a parameter space for the globally optimal solution to an objective. The algorithm has been demonstrated to be more effective at searching a parameter space than traditional simulated-annealing methods for a particular problem of interest, and it can readily be applied to a wide variety of optimization problems, including those with a parameter space having both discrete-value parameters (combinatorial) and continuous-variable parameters. It can take the place of a conventional simulated- annealing, Monte-Carlo, or random- walk algorithm. In a conventional simulated-annealing (SA) algorithm, a starting configuration is randomly selected within the parameter space. The algorithm randomly selects another configuration from the parameter space and evaluates the objective function for that configuration. If the objective function value is better than the previous value, the new configuration is adopted as the new point of interest in the parameter space. If the objective function value is worse than the previous value, the new configuration may be adopted, with a probability determined by a temperature parameter, used in analogy to annealing in metals. As the optimization continues, the region of the parameter space from which new configurations can be selected shrinks, and in conjunction with lowering the annealing temperature (and thus lowering the probability for adopting configurations in parameter space with worse objective functions), the algorithm can converge on the globally optimal configuration. The Recursive Branching Simulated Annealing (RBSA) algorithm shares some features with the SA algorithm, notably including the basic principles that a starting configuration is randomly selected from within the parameter space, the algorithm tests other configurations with the goal of finding the globally optimal solution, and the region from which new configurations can be selected shrinks as the search continues. The key difference between these algorithms is that in the SA algorithm, a single path, or trajectory, is taken in parameter space, from the starting point to the globally optimal solution, while in the RBSA algorithm, many trajectories are taken; by exploring multiple regions of the parameter space simultaneously, the algorithm has been shown to converge on the globally optimal solution about an order of magnitude faster than when using conventional algorithms. Novel features of the RBSA algorithm include: 1. More efficient searching of the parameter space due to the branching structure, in which multiple random configurations are generated and multiple promising regions of the parameter space are explored; 2. The implementation of a trust region for each parameter in the parameter space, which provides a natural way of enforcing upper- and lower-bound constraints on the parameters; and 3. The optional use of a constrained gradient- search optimization, performed on the continuous variables around each branch s configuration in parameter space to improve search efficiency by allowing for fast fine-tuning of the continuous variables within the trust region at that configuration point.

Bolcar, Matthew↗

NASA NTRS2014

Tuning Monotonic Basin Hopping: Improving the Efficiency of Stochastic Search as Applied to Low-Thrust Trajectory Optimization

Trajectory optimization methods using monotonic basin hopping (MBH) have become well developed during the past decade [1, 2, 3, 4, 5, 6]. An essential component of MBH is a controlled random search through the multi-dimensional space of possible solutions. Historically, the randomness has been generated by drawing random variable (RV)s from a uniform probability distribution. Here, we investigate the generating the randomness by drawing the RVs from Cauchy and Pareto distributions, chosen because of their characteristic long tails. We demonstrate that using Cauchy distributions (as first suggested by J. Englander [3, 6]) significantly improves monotonic basin hopping (MBH) performance, and that Pareto distributions provide even greater improvements. Improved performance is defined in terms of efficiency and robustness. Efficiency is finding better solutions in less time. Robustness is efficiency that is undiminished by (a) the boundary conditions and internal constraints of the optimization problem being solved, and (b) by variations in the parameters of the probability distribution. Robustness is important for achieving performance improvements that are not problem specific. In this work we show that the performance improvements are the result of how these long-tailed distributions enable MBH to search the solution space faster and more thoroughly. In developing this explanation, we use the concepts of sub-diffusive, normally-diffusive, and super-diffusive random walks (RWs) originally developed in the field of statistical physics.

autonomous↗

NASA NTRS2015

Calibration of Predictor Models Using Multiple Validation Experiments

This paper presents a framework for calibrating computational models using data from several and possibly dissimilar validation experiments. The offset between model predictions and observations, which might be caused by measurement noise, model-form uncertainty, and numerical error, drives the process by which uncertainty in the models parameters is characterized. The resulting description of uncertainty along with the computational model constitute a predictor model. Two types of predictor models are studied: Interval Predictor Models (IPMs) and Random Predictor Models (RPMs). IPMs use sets to characterize uncertainty, whereas RPMs use random vectors. The propagation of a set through a model makes the response an interval valued function of the state, whereas the propagation of a random vector yields a random process. Optimization-based strategies for calculating both types of predictor models are proposed. Whereas the formulations used to calculate IPMs target solutions leading to the interval value function of minimal spread containing all observations, those for RPMs seek to maximize the models' ability to reproduce the distribution of observations. Regarding RPMs, we choose a structure for the random vector (i.e., the assignment of probability to points in the parameter space) solely dependent on the prediction error. As such, the probabilistic description of uncertainty is not a subjective assignment of belief, nor is it expected to asymptotically converge to a fixed value, but instead it casts the model's ability to reproduce the experimental data. This framework enables evaluating the spread and distribution of the predicted response of target applications depending on the same parameters beyond the validation domain.

Crespo, Luis G.↗

NASA NTRS2016

The Viability of Trajectory Analysis for Diagnosing Dynamical and Chemical Influences on Ozone Concentrations in the UTLS

The viability of trajectory analysis for diagnosing the interplay between chemistry and dynamics is investigated by comparing ozone mixing ratios modelled using air-parcel pathways to values observed along flight tracks during ATTREX (Airborne Tropical TRopopause EXperiment). Trajectories are initiated at the locations of ozone observations and tracked backward in time to their sources at termini of backward trajectories. The modelled values of ozone utilize 3-dimensional analysis fields from WACCM (Whole Atmosphere Community Climate Model) (a chemical-climate model with dynamical fields nudged towards MERRA (Modern-Era Retrospective Analysis and Research Applications) reanalysis) and ERA-interim (product of ECMWF - the European Centre for Medium-Range Weather Forecasts) to determine source mixing ratios with chemical production and loss terms derived from the ozone chemistry used in WACCM. A statistical base of modelled ozone is constructed with 6 trajectory platforms (adiabatic, diabatic, and kinematic forced by ERA-interim and MERRA), two chemical models (WACCM chemistry and no chemistry), and 4 trajectory lengths (5, 10, 20, and 30 days). Linear regression is employed to separate systematic errors from random errors and to characterize the impact of source mixing ratios, path length, vertical motion, and chemistry on modelled ozone errors. Errors in the analysis ozone fields are large, if not dominant, contributors to model error. Random errors are particularly large for point-by-point comparisons, however averaging over 800 km (75 minutes) flight segments substantially reduces random error and exposes systematic errors. Of the two analysis ozone data sets, WACCM, which incorporates detailed chemistry, provides the smaller systematic errors while ERA-interim, which has crude chemistry but assimilates observational data, has the smaller random errors. Of the different trajectory platforms, adiabatic calculations produce the smaller random errors (irrespective of the use of chemistry) but both vertical motion and chemistry are required to optimally reduce systematic errors. These results suggest that meaningful analysis of dynamical and chemical interactions that control ozone mixing ratios are viable on spatial scales larger than a few reanalysis grid spaces, that errors in the analyzed ozone data sets are large but not prohibitively so, and that vertical velocities and heating rates from reanalysis data, while problematic, contain useful information [on the ozone concentrations in the UTLS (Upper Troposphere/Lower Stratosphere)].

ozone↗

NASA NTRS2018

Environmental Testing of the HERMeS TDU-2 Hall Thruster

The Hall Effect Rocket with Magnetic Shielding (HERMeS) is a 12.5 kW magnetically shielded Hall thruster presently under development for deep-space missions. A development model HERMeS thruster, TDU-2, with borosilicate channel walls, has successfully undergone proto-qualification testing including random vibration and thermal-vacuum, demonstrating the thruster can survive critical launch and operational environmental requirements. The three-axis random vibrational tests were performed with the thruster body mounted directly to the shaker table using a modified loading schedule to compensate for the vibration isolation dampers under design for the flight thruster. Initial random vibration testing revealed issues with fragmentation of magnetic coil potting material and thruster spool mount fabrication weaknesses that were addressed with an alternate potting material and fabrication revisions that were then successfully retested with an additional round of random vibration tests. Thermal-vacuum testing involved three cycles of full-power 600 V 12.5 kW thruster operation from -121°C to +373°C which included eight hours at peak temperature as well as a hot restart. A thermal model of the test configuration was developed and validated with the experiment results within an average difference of 5°C. Before and after the random vibrational and thermal-vacuum tests, the thruster performance, plasma plume, thrust vector angle, discharge characteristics, and magnetic field profile were measured. The thruster performance, magnetic field, and most other parameters remained invariant throughout the environmental testing campaign. During the thermal testing, an increase in the discharge oscillation amplitude of 11% was observed as well as subtle thrust vector changes of ±0.2° as the thruster warmed from -121°C to +373°C.

Sorenson, Ryan↗

NASA NTRS2000

Constructing high complexity synthetic libraries of long ORFs using in vitro selection

We present a method that can significantly increase the complexity of protein libraries used for in vitro or in vivo protein selection experiments. Protein libraries are often encoded by chemically synthesized DNA, in which part of the open reading frame is randomized. There are, however, major obstacles associated with the chemical synthesis of long open reading frames, especially those containing random segments. Insertions and deletions that occur during chemical synthesis cause frameshifts, and stop codons in the random region will cause premature termination. These problems can together greatly reduce the number of full-length synthetic genes in the library. We describe a strategy in which smaller segments of the synthetic open reading frame are selected in vitro using mRNA display for the absence of frameshifts and stop codons. These smaller segments are then ligated together to form combinatorial libraries of long uninterrupted open reading frames. This process can increase the number of full-length open reading frames in libraries by up to two orders of magnitude, resulting in protein libraries with complexities of greater than 10(13). We have used this methodology to generate three types of displayed protein library: a completely random sequence library, a library of concatemerized oligopeptide cassettes with a propensity for forming amphipathic alpha-helical or beta-strand structures, and a library based on one of the most common enzymatic scaffolds, the alpha/beta (TIM) barrel. Copyright 2000 Academic Press.

Non-NASA Center↗

NASA NTRSDate not supplied

Variational Coupled Loads Analysis using the Hybrid Parametric Variation Method

Time-domain coupled loads analysis (CLA)is used to determine the response of a launch vehicle and payload system to transient forces, such as liftoff, engine ignitions and shutdowns, jettison events, and atmospheric flight loads, such as buffet. CLA, using Hurty/Craig-Bampton (HCB)component models, is the accepted method for the establishment of design-level loads for launch systems. However, uncertainty in the component models flows into uncertainty in predicted system results. Uncertainty in the structural responses during launch is a significant concern because small variations in launch vehicle and payload mode shapes and their interactions can result in significant variations in system loads. Uncertainty quantification (UQ)is used to determine statistical bounds on prediction accuracy based on model uncertainty. In this paper uncertainty is treated at the HCB component-model level. In an effort to account for model uncertainties and statistically bound their effect on CLA predictions, this work combines CLA with UQ in a process termed variational coupled loads analysis (VCLA). The modeling of uncertainty using a parametric approach, in which input parameters are represented by random variables, is common, but its major drawback is the resulting uncertainty is limited to the form of the nominal model. Uncertainty in model form is one of the biggest contributors to uncertainty in complex built-up structures. Model-form uncertainty can be represented using a nonparametric approach based on random matrix theory (RMT). In this work, UQ is performed using the hybrid parametric variation (HPV)method, which combines parametric with nonparametric uncertainty at the HCB component model level. The HPV method requires the selection of dispersion values for the HCB fixed-interface (FI)eigenvalues, and the HCB mass and stiffness matrices. The dispersions are based upon component test-analysis modal correlation results. During VCLA, random component models are assembled into an ensemble of random systems using a Monte Carlo (MC)approach. CLA is applied to each of the ensemble members to produce an ensemble of system-level responses for statistical analysis. The proposed methodology is demonstrated through its application to a buffet loads analysis of NASA’s Space Launch System (SLS)during the transonic regime fifty seconds after liftoff. Core stage (CS)section shears and moments are recovered, and statistics are computed.

Uncertainty Quantification↗

NASA NTRS1973

Exact intervals and tests for median when one sample value possibly an outliner

Available are independent observations (continuous data) that are believed to be a random sample. Desired are distribution-free confidence intervals and significance tests for the population median. However, there is the possibility that either the smallest or the largest observation is an outlier. Then, use of a procedure for rejection of an outlying observation might seem appropriate. Such a procedure would consider that two alternative situations are possible and would select one of them. Either (1) the n observations are truly a random sample, or (2) an outlier exists and its removal leaves a random sample of size n-1. For either situation, confidence intervals and tests are desired for the median of the population yielding the random sample. Unfortunately, satisfactory rejection procedures of a distribution-free nature do not seem to be available. Moreover, all rejection procedures impose undesirable conditional effects on the observations, and also, can select the wrong one of the two above situations. It is found that two-sided intervals and tests based on two symmetrically located order statistics (not the largest and smallest) of the n observations have this property.

Keller, G. J.↗

NASA NTRS1975

Crack growth under spectrum loading: A crack closure model

A concept based on the crack-closure phenomenon was developed to replace random load spectra with constant amplitude loading in both analysis and tests. The maximum load and the crack opening load in the constant amplitude loading are chosen to be equal to those for the spectrum, so that both crack growth mode and the crack length at failure are equivalent to those under random load spectra. The number of cycles of constant- amplitude loading is chosen so that the amount of crack growth is equal to that due to a given sequence or block of the random spectrum loading. The concept was tested experimentally after predicting the equivalent number of constant-amplitude cycles for six different random load sequences. The agreement between predictions and test results was good.

Elber, W.↗

NASA NTRS1975

Simulator studies and psychophysical ride comfort models

An elementary psychophysical model to predict ride comfort was developed using flight and simulator data where subjects were exposed to six degrees of freedom. The model presumes that the comfort response is proportional to the logarithm of the stimulus above some threshold stimulus. In order to verify this concept of comfort modeling, it was necessary to obtain ride comfort data for single degree of freedom random motions and for combinations of random motions. Accordingly, a simulator program was performed at the NASA Langley Research Center to measure subjective comfort response ratings using one degree of freedom, two degrees of freedom, three degrees of freedom, and six degrees of freedom. An analysis of the single degree of freedom and two degrees of freedom data is presented. Preliminary models of ride comfort response for single degree of freedom random motions and for certain combinations of two degrees of freedom random motions were developed.

Stone, R. W., Jr.↗

NASA NTRS1976

Autocorrelation peaks in congruential pseudorandom number generators

The complete correlation structure of several congruential pseudorandom number generators (PRNG) of the same type and small cycle length was studied to deal with the problem of congruential PRNG almost repeating themselves at intervals smaller than their cycle lengths, during simulation of bandpass filtered normal random noise. Maximum period multiplicative and mixed congruential generators were studied, with inferences drawn from examination of several tractable members of a class of random number generators, and moduli from 2 to the 5th power to 2 to the 9th power. High correlation is shown to exist in mixed and multiplicative congruential random number generators and prime moduli Lehmer generators for shifts a fraction of their cycle length. The random noise sequences in question are required when simulating electrical noise, air turbulence, or time variation of wind parameters.

Neuman, F.↗

NASA NTRS1976

Reliability analysis of structures under periodic proof tests in service

A reliability analysis of structures subjected to random service loads and periodic proof tests treats gust loads and maneuver loads as random processes. Crack initiation, crack propagation, and strength degradation are treated as the fatigue process. The time to fatigue crack initiation and ultimate strength are random variables. Residual strength decreases during crack propagation, so that failure rate increases with time. When a structure fails under periodic proof testing, a new structure is built and proof-tested. The probability of structural failure in service is derived from treatment of all the random variables, strength degradations, service loads, proof tests, and the renewal of failed structures. Some numerical examples are worked out.

Yang, J.-N.↗

NASA NTRS1976

A technique for generating correlated X-band weather degradation statistics

It is, known that the X-band noise temperature of DSN receivers can go up from 20 K to over 100 K or more, if the air is heavily laden with water vapor, although that is an uncommon occurrence. It is proposed that the DSN furnish flight projects relying on X-band degradation models, one for each DSN Complex. Such models would be in the form of a random process generator, say in an MBASIC program, that would permit the project to generate X-band degradation data with the right autocorrelations for periods of interest to the Projects. The autocorrelation modeling is especially important because bursts of degradation lasting several days can affect data storage and mission sequence design strategy. One approach which works if the degradation statistics obey a half-gaussian law. That is, the random variables are formed by taking the absolute values of another set of random variables, themselves having a Gaussian distribution. The technique then permits the half-gaussian random variables to have given one and two-step correlation coefficients.

Posner, E. C.↗

NASA NTRS1975

Seminar on Understanding Digital Control and Analysis in Vibration Test Systems, part 2

A number of techniques for dealing with important technical aspects of the random vibration control problem are described. These include the generation of pseudo-random and true random noise, the control spectrum estimation problem, the accuracy/speed tradeoff, and control correction strategies. System hardware, the operator-system interface, safety features, and operational capabilities of sophisticated digital random vibration control systems are also discussed.

Source record↗

NASA NTRS1977

Optimal spatial sampling techniques for ground truth data in microwave remote sensing of soil moisture

The paper examines optimal sampling techniques for obtaining accurate spatial averages of soil moisture, at various depths and for cell sizes in the range 2.5-40 acres, with a minimum number of samples. Both simple random sampling and stratified sampling procedures are used to reach a set of recommended sample sizes for each depth and for each cell size. Major conclusions from statistical sampling test results are that (1) the number of samples required decreases with increasing depth; (2) when the total number of samples cannot be prespecified or the moisture in only one single layer is of interest, then a simple random sample procedure should be used which is based on the observed mean and SD for data from a single field; (3) when the total number of samples can be prespecified and the objective is to measure the soil moisture profile with depth, then stratified random sampling based on optimal allocation should be used; and (4) decreasing the sensor resolution cell size leads to fairly large decreases in samples sizes with stratified sampling procedures, whereas only a moderate decrease is obtained in simple random sampling procedures.

Rao, R. G. S.↗

NASA NTRS1982

The noise of BL Lacertae

Results are presented from an intensive optical and IR monitoring program of the flux and polarization characteristics of BL Lac. It is found that the polarization variations increase in amplitude with increasing time interval, and that the path traced out by the polarization vector in the Q-U plane is a random walk. In view of earlier measurements of BL Lac, the polarization fluctuations can be represented at low frequencies by the flat power spectrum of white noise, up to a frequency of 0.05 cycles/day. Above this frequency, the spectrum steepens to that of a random walk. A model for BL Lac suggested by the polarimetric noise can be constructed from independent sources of light with randomly oriented, strong polarization. Small random differences in spectral index from source to source could also explain the variable wavelength dependence of polarization.

Moore, R. L.↗

NASA NTRS1983

A procedure for combining acoustically induced and mechanically induced loads (first passage failure design criterion)

The combined load statistics are developed by taking the acoustically induced load to be a random population, assumed to be stationary. Each element of this ensemble of acoustically induced loads is assumed to have the same power spectral density (PSD), obtained previously from a random response analysis employing the given acoustic field in the STS cargo bay as a stationary random excitation. The mechanically induced load is treated as either (1) a known deterministic transient, or (2) a nonstationary random variable of known first and second statistical moments which vary with time. A method is then shown for determining the probability that the combined load would, at any time, have a value equal to or less than a certain level. Having obtained a statistical representation of how the acoustic and mechanical loads are expected to combine, an analytical approximation for defining design levels for these loads is presented using the First Passage failure criterion.

Crowe, D. R.↗