Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Homology modelling”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS1993

A Modeling Investigation of Thermal and Strain Induced Recovery and Nonlinear Hardening in Potential Based Viscoplasticity

Specific forms for both the Gibb's and the complementary dissipation potentials were chosen such that a complete potential based multiaxial, isothermal, viscoplastic model was obtained. This model in general possesses three internal state variables (two scalars associated with dislocation density and one tensor associated with dislocation motion) both thermal and dynamic recovery mechanisms, and nonlinear kinematic hardening. This general model, although possessing associated flow and evolutionary laws, is shown to emulate three distinct classes of theories found in the literature, by modification of the driving threshold function F. A parametric study was performed on a specialized nondimensional multiaxial form containing only a single tensorial internal state variable (i.e., internal stress). The study was conducted with the idea of examining the impact of including a strain-induced recovery mechanism and the compliance operator, derived from the Gibb's potential, on the uniaxial and multiaxial response. One important finding was that inclusion of strain recovery provided the needed flexibility in modeling stress-strain and creep response of metals at low homologous temperatures, without adversely affecting the high temperature response. Furthermore, for nonproportional loading paths, the inclusion of the compliance operator had a significant influence on the multiaxial response, but had no influence on either uniaxial or proportional load histories.

Arnold, S. M.↗
NASA NTRS1984

Energy balance of stellar coronae. III - Effect of stellar mass and radius

A homologous transformation is derived which permits the application of the numerical coronal models of Hammer from a star with solar mass and radius to other stars. This scaling requires a few approximations concerning the lower boundary conditions and the temperature dependence of the conductivity and emissivity. These approximations are discussed and found to be surprisingly mild. Therefore, the scaling of the coronal models to other stars is rather accurate; it is found to be particularly accurate for main-sequence stars. The transformation is used to derive an equation that gives the maximum temperature of open coronal regions as a function of stellar mass and radius, the coronal heating flux, and the characteristic damping length over which the corona is heated.

Hammer, R.↗
NASA NTRS2002

Genes encoding calmodulin-binding proteins in the Arabidopsis genome

Analysis of the recently completed Arabidopsis genome sequence indicates that approximately 31% of the predicted genes could not be assigned to functional categories, as they do not show any sequence similarity with proteins of known function from other organisms. Calmodulin (CaM), a ubiquitous and multifunctional Ca(2+) sensor, interacts with a wide variety of cellular proteins and modulates their activity/function in regulating diverse cellular processes. However, the primary amino acid sequence of the CaM-binding domain in different CaM-binding proteins (CBPs) is not conserved. One way to identify most of the CBPs in the Arabidopsis genome is by protein-protein interaction-based screening of expression libraries with CaM. Here, using a mixture of radiolabeled CaM isoforms from Arabidopsis, we screened several expression libraries prepared from flower meristem, seedlings, or tissues treated with hormones, an elicitor, or a pathogen. Sequence analysis of 77 positive clones that interact with CaM in a Ca(2+)-dependent manner revealed 20 CBPs, including 14 previously unknown CBPs. In addition, by searching the Arabidopsis genome sequence with the newly identified and known plant or animal CBPs, we identified a total of 27 CBPs. Among these, 16 CBPs are represented by families with 2-20 members in each family. Gene expression analysis revealed that CBPs and CBP paralogs are expressed differentially. Our data suggest that Arabidopsis has a large number of CBPs including several plant-specific ones. Although CaM is highly conserved between plants and animals, only a few CBPs are common to both plants and animals. Analysis of Arabidopsis CBPs revealed the presence of a variety of interesting domains. Our analyses identified several hypothetical proteins in the Arabidopsis genome as CaM targets, suggesting their involvement in Ca(2+)-mediated signaling networks.

NASA Discipline Plant Biology↗
NASA NTRS1981

The estimation of genetic divergence

Consideration is given to the criticism of Nei and Tateno (1978) of the REH (random evolutionary hits) theory of genetic divergence in nucleic acids and proteins, and to their proposed alternative estimator of total fixed mutations designated X2. It is argued that the assumption of nonuniform amino acid or nucleotide substitution will necessarily increase REH estimates relative to those made for a model where each locus has an equal likelihood of fixing mutations, thus the resulting value will not be an overestimation. The relative values of X2 and measures calculated on the basis of the PAM and REH theories for the number of nucleotide substitutions necessary to explain a given number of observed amino acid differences between two homologous proteins are compared, and the smaller values of X2 are attributed to (1) a mathematical model based on the incorrect assumption that an entire structural gene is free to fix mutations and (2) the assumptions of different numbers of variable codons for the X2 and REH calculations. Results of a repeat of the computer simulations of Nei and Tateno are presented which, in contrast to the original results, confirm the REH theory. It is pointed out that while a negative correlation is observed between estimations of the fixation intensity per varion and the number of varions for a given pair of sequences, the correlation between the two fixation intensities and varion numbers of two different pairs of sequences need not be negative. Finally, REH theory is used to resolve a paradox concerning the high rate of covarion turnover and the nature of general function sites as permanent covarions.

Holmquist, R.↗
NASA NTRS1989

The late behavior of supernova 1987A. I - The light curve. II - Gamma-ray transparency of the ejecta

Observations of the late (t = 20-1500 days) bolometric light curve and the gamma-lines and X-rays from supernova 1987A are compared to theoretical models. It is found that 0.073 + or - 0.015 solar masses of freshly synthesized Ni-56 must be present to fit the bolometric light curve. The results place limits on the luminosity and presumed period of the newly formed pulsar/neutron star. In the second half of the paper, the problem of computing the luminosities in gamma-ray lines and in X-rays from supernova 1987A is addressed. High-energy observations suggest the development of large-scale clumping and bubbling of radioactive material in the ejecta. A model is proposed with a hydrogen envelope mass of about 7 solar masses, homologous scale expansion velocities of about 3000 km/s, and an approximately uniform mass distribution.

Arnett, W. David↗
NASA NTRS2005

Modeling Solar Flare Hard X-ray Images and Spectra Observed with RHESSI

Observations obtained with the Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI) of a flare on February 20, 2002 indicate a hard X-ray (HXR) coronal source at or near the top of a flare loop (called a HXR looptop source). The existence of the HXR looptop source suggests that magnetic reconnection, which is believed to power flares, occurs above the loop. In order to explain this HXR looptop source, I created a steady-state particle transport model, in which high-energy electrons are continuously injected at the top of a semicircular flare loop. Based on the simulation results, I find that the model predictions are consistent with the RHESSI observations in many respects, but the spectrum of the looptop source obtained from the model is steeper than that from the RHESSI data. This suggests that, instead of being accelerated above the loop as generally believed, the particles might be accelerated in the looptop itself. RHESSI-observations of three other homologous flares that occurred between April 14 and 16, 2002, provide strong evidence for the presence of a large scale current sheet above a flare loop, which is the basis of standard flare models. The most convincing finding is the presence of the temperature distribution of a separate coronal source above the flare loops: the hotter part of the coronal source was located lower in altitude the cooler part. Together with the fact that the hotter flare loops are higher than the cooler loops, the observations support the existence of a large-scale current sheet between the top of the flare loops and the coronal source above. Blob-Like sources along a line above the loop in the decay phase of the April 15, 2002, flare, which are suggestive of magnetic islands initiated by the tearing-mode instability, and the observation of a cusp structure in microwaves, further support the presence of the current sheet. The observations of the three homologous flares reveal two other features which are beyond the predictions of the standard flare models: the downward motion of flare loops in the early impulsive phase of each flare, and an initially stationary coronal source above the loops. These features me believed to be related to the formation and development of a current sheet. In particular, the downward loop motion seem to be a common phenomenon in flares, suggesting the necessity for modifications to the existing standard flare. models. Finally, thanks to the broad energy coverage of the RHESSI spectra, a low-energy cutoff of 28 (plus or minus 2) keV in the nonthermal electron distribution was determined for the April 15, 2002, flare. As a result, the energy carried by the nonthermal electrons is found to be comparable to the thermal energy of the flare, but one order of magnitude larger than the kinetic energy of the associated coronal mass ejection. The method used to deduce the electron low-energy cutoff will be useful in the analyses of similar events.

Sui, Linhui↗
NASA NTRSDate not supplied

Investigating Biological Responses to Deep Space Radiation for Missions Beyond Low Earth Orbit (LEO) using Yeast

To enable long-term spaceflight missions and establish habitation on the Moon and Mars, we require a comprehensive understanding of the effects of chronic deep space radiation exposure on humans. BioSentinel is NASA’s first biological CubeSat to venture beyond Low Earth Orbit (LEO). It utilizes Saccharomyces cerevisiae (budding yeast) as a model organism to study biological responses to deep space radiation. Yeast share significant genetic homology with humans, including basic cellular metabolism and DNA repair mechanisms. In addition, unlike human cell cultures, yeast can survive the duration and constraints of a deep space mission. BioSentinel measures biological responses using an optical system and alamarBlue oxidation-reduction (redox) dye. Two strains of yeast are studied - a wild-type and a rad51 mutant strain that is deficient in DNA repair. Changes in metabolism and growth are monitored throughout the nominal 6-month mission. Preliminary tests indicate a significant change in the alamarBlue response to low-dose ionizing radiation (IR). Additionally, rad51 cells have shown an IR dose-dependent decrease in glucose uptake and accumulation of oxidized NADH (NAD+). These biomolecules are involved in reactions responsible for basic cell processes, including growth and development, signaling, and respiration. The current study expanded upon previous data by exposing yeast to deep space-relevant radiation. Glucose and NADH/NAD+ assays were conducted on yeast subjected to varying dosages of high-energy Fe-56 and simulated galactic cosmic rays (GCRs). The resulting data was analyzed using Excel and GraphPad Prism. A particular focus was to identify biomolecules resulting from aerobic respiration, which requires the presence of oxygen, or anaerobic processes. As long-term spaceflight missions draw near, it is increasingly important to characterize biological processes affected by the conditions of deep space. Studying biomolecular damage caused by deep space radiation may enable the development of engineering controls or biomedical therapeutics that mitigate health complications for future astronauts.

Kyra Keenan↗
NASA NTRS2020

Shedding Light on Microbial Dark Matter with A Universal Language of Life

The majority of microbial genomes have yet to be cultured, and most proteins predicted from microbial genomes or sequenced from the environment cannot be functionally annotated. As a result, current computational approaches to describe microbial systems rely on incomplete reference databases that cannot adequately capture the full functional diversity of the microbial tree of life, limiting our ability to model high-level features of biological sequences. The scientific community needs a means to capture the functionally and evolutionarily relevant features underlying biology, independent of our incomplete reference databases. Such a model can form the basis for transfer learning tasks, enabling downstream applications in environmental microbiology, medicine, and bioengineering. Here we present LookingGlass, a deep learning model capturing a “universal language of life”. LookingGlass encodes contextually-aware, functionally and evolutionarily relevant representations of short DNA reads, distinguishing reads of disparate function, homology, and environmental origin. We demonstrate the ability of LookingGlass to be fine-tuned to perform a range of diverse tasks: to identify novel oxidoreductases, to predict enzyme optimal temperature, and to recognize the reading frames of DNA sequence fragments. LookingGlass is the first contextually-aware, general purpose pre-trained “biological language” representation model for short-read DNA sequences. LookingGlass enables functionally relevant representations of otherwise unknown and unannotated sequences, shedding light on the microbial dark matter that dominates life on Earth.

A Hoarfrost↗
NASA NTRS1976

H alpha observations of the 12 August 1975 type 3-RS bursts

H alpha filtergram observations of a number of the Type III-RS (reverse slope) bursts that occurred on August 12, 1975 are presented. Solar radio emission was peculiar on that date in that a large number, and proportion, of the usually rare reverse slope bursts were observed. The radio bursts are shown to coincide in time with a homologous set of H alpha flares located at the limbward edge of spot group Mt. Wilson 19598. A model is proposed in which the reverse slope bursts are the downward branches of U bursts, whose upward branches are hidden behind the coronal density enhancement over the spot group.

Labonte, B. J.↗
NASA NTRS1994

Analysis of the early spectra and light curve of SN 1987A

Numerical modeling of supernova spectra, light curves, and hydrodynamics requires physical inputs, numerical techniques, approximations, and assumptions which must be thoroughly understood in order to study the details of supernova explosions. Here, we discuss some of these in the context of the early evolution of supernova 1987A. Gray radiation-hydrodynamics is used to calculate the bolometric light curve and the hydrodynamic evolution of the supernova. Synthetic spectra are then obtained for the resulting density and velocity structure. The spectrum calculations are performed using a special-relativistic treatment of the radiative transfer equation in the comoving frame, line blanketing by about 10(exp 5) spectral lines, and departures from local thermodynamic equilibrium (LTE) for H I, He I, Mg II, and Ca II. We find that we are able to simultaneously fit the early light curve and spectra reasonably well, using a progenitor model from Arnett (1991a), without fine-tuning the free parameters. Temperature structures and radiative equilibrium, non-LTE effects, homologous expansion, and mean opacities are discussed.

Hauschildt, Peter H.↗
NASA NTRS2002

Predicting functional divergence in protein evolution by site-specific rate shifts

Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

Review↗
NASA NTRS1976

H-alpha observations of the August 12, 1975 Type III-RS bursts

We present H-alpha filtergram observations of a number of the Type III-RS (reverse slope) bursts that occurred on August 12, 1975. Solar radio emission was peculiar on that date in that a large number, and proportion, of the usually rare reverse slope bursts were observed (Tarnstrom and Zehntner, 1975). We show that the radio bursts coincide in time with a homologous set of H-alpha flares located at the limbward edge of spot group Mt. Wilson 19598. We propose a model in which the reverse slope bursts are the downward branches of U bursts, whose upward branches are hidden behind the coronal density enhancement over the spot group.

Labonte, B. J.↗
NASA NTRSDate not supplied

Investigating Biological Responses to Space-like Radiation using the yeast Saccharomyces cerevisiae

As we plan crewed missions to the Moon, Mars, and beyond, it is essential to understand how persistent exposure to space radiation affects biology. Unlike on the International Space Station, where crew support and sample return are possible, experiments for long-duration missions require autonomous systems with no sample return. Human cells would be ideal biosensors, but limitations in culture methods, extended prelaunch storage, and long flight durations make it very difficult to keep human cells alive. Unlike other model systems, yeast can survive the constraints of long-duration spaceflight. Despite a billion years of evolution separating yeast from humans, we share homology in hundreds of genes important for basic cell function, including responses to DNA damage. Thus, yeast are excellent biosensors for detecting types/extent of damage induced by space radiation. BioSentinel is NASA’s latest biological CubeSat, and first interplanetary space bioscience mission. BioSentinel is manifested on Artemis 1, the first test flight of NASA’s Space Launch System, in the coming year. The BioSensor payload within BioSentinel contains two yeast strains. The wild type serves as a control for health and “normal” DNA damage repair (DDR). The rad51 deletion mutant is defective for DDR and will undergo alterations to growth and metabolism as it accumulates radiation damage. Changes in growth and metabolic activity will be measured using a 3-color LED detection system and the metabolic redox dye alamarBlue®. Preliminary tests indicate a significant change in alamarBlue response to space-like, low-dose ionizing radiation. We will discuss these findings in four parts – Introduction to biological CubeSats and the BioSentinel mission (presented by Sergio Santa Maria), preliminary responses to space-like ionizing radiation (presented here), a deeper dive into tracking metabolic changes after exposure to ionizing radiation (presented by Diana Gentry), and a look into methods for correcting flight optical data (presented by Abbey Kim). This work is funded by NASA’s Advanced Exploration Systems.

CubeSat↗
NASA NTRSDate not supplied

Investigating Molecular Responses to Space Radiation for Biological Missions Beyond Low Earth Orbit

As we plan crewed missions to the Moon, Mars, and beyond, it is essential to understand how persistent exposure to deep space radiation affects biology. Unlike on the International Space Station (ISS), where crew support and sample return are possible, experiments for long-duration missions require autonomous systems with no sample return. Human cells would be ideal biosensors, but limitations in culture methods, extended prelaunch storage, and long flight durations make it difficult to keep human cells alive. Unlike other model systems, yeast can survive the constraints of long-duration spaceflight. Despite a billion years of evolution separating yeast from humans, we share homology in hundreds of genes important for basic cell function, including responses to DNA damage. Thus, yeast are excellent biosensors for detecting types/extent of damage induced by space radiation. BioSentinel is NASA’s latest biological CubeSat, and first interplanetary space bioscience mission. BioSentinel is launching on Artemis 1, the first flight of NASA’s Space Launch System, in 2022. The BioSensor payload within BioSentinel contains two yeast strains. The wild type serves as a control for health and normal DNA damage repair (DDR). The rad51 deletion mutant is defective for DDR and will undergo alterations to growth and metabolism as it accumulates radiation damage. Changes in growth and metabolic activity will be measured using a 3-color LED detection system and the metabolic redox dye alamarBlue®. Preliminary tests indicate a significant change in alamarBlue responses to space-like, low-dose ionizing radiation. We will discuss these findings in five parts – Introduction to NASA’s biological CubeSats and BioSentinel (presented by Sergio Santa Maria), analysis of flight data from the ISS mission (presented by Kylie Akiyama), preliminary molecular responses to space radiation (presented here), a deeper dive into those pathways (presented by Kyra Keenan), and characterizing stress response through redox potential data (presented by Diana Gentry).

Lauren Courtney Liddell↗
NASA NTRS1983

Requirements of constitutive models for two nickel-base superalloys

The constitutive behavior of two nickel-base superalloys, Rene '80 and Inconel 718, utilized in gas turbine blade and disk components, respectively, is presented. In turbine blade applications, the high homologous temperatures result in strain-rate effects dominating behavior. In turbine disks, the temperatures are cooler so that mean stress effects become important. The impact of these two variables on the overall crack initiation lifetime and analysis methodology is discussed.

Laflen, J. H.↗
NASA NTRS2003

A Proposed Mechanism for the Thermal Denaturation of a Recombinant Bacillus Halmapalus Alpha-amylase - the Effect of Calcium Ions

The thermal stability of a recombinant alpha-amylase from Bacillus halmapalus alpha-amylase (BHA) has been investigated using circular dichroism spectroscopy (CD) and differential scanning calorimetry (DSC). This alpha-amylase is homologous to other Bacillus alpha-amylases where previous crystallographic studies have identified the existence of 3 calcium binding sites in the structure. Denaturation of BHA is irreversible with a Tm of approximately 89 C, and DSC thermograms can be described using a one-step irreversible model. A 5 C increase in T(sub m) in the presence of 10 fold excess CaCl2 was observed. However, a concomitant increase in the tendency to aggregate was also observed. The presence of 30-40 fold excess calcium chelator (EDTA or EGTA) results in a large destabilization of BHA corresponding to about 40 C lower T(sub m), as determined by both CD and DSC. Ten fold excess EGTA reveals complex DSC thermograms corresponding to both reversible and irreversible transitions, which possibly originate from different populations of BHA:calcium complexes. The observations in the present study have, in combination with structural information of homologous alpha-amylases, provided the basis for the proposal of a simple denaturation mechanism of BHA. The proposed mechanism describes the irreversible thermal denaturation of different BHA:calcium complexes and the calcium binding equilibrium involved. Furthermore, the model accounts for a temperature induced reversible structural change associated with calcium binding.

Nielsen, Anders D.↗
NASA NTRS1998

Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA

Bovine seminal ribonuclease (RNase) binds, melts, and (in the case of RNA) catalyzes the hydrolysis of double-stranded nucleic acid 30-fold better under physiological conditions than its pancreatic homologue, the well-known RNase A. Reported here are site-directed mutagenesis experiments that identify the sequence determinants of this enhanced catalytic activity. These experiments have been guided in part by experimental reconstructions of ancestral RNases from extinct organisms that were intermediates in the evolution of the RNase superfamily. It is shown that the enhanced interactions between bovine seminal RNase and double-stranded nucleic acid do not arise from the increased number of basic residues carried by the seminal enzyme. Rather, a combination of a dimeric structure and the introduction of two glycine residues at positions 38 and 111 on the periphery of the active site confers the full catalytic activity of bovine seminal RNase against duplex RNA. A structural model is presented to explain these data, the use of evolutionary reconstructions to guide protein engineering experiments is discussed, and a new variant of RNase A, A(Q28L K31C S32C D38G E111G), which contains all of the elements identified in these experiments as being important for duplex activity, is prepared. This is the most powerful catalyst within this subfamily yet observed, some 46-fold more active against duplex RNA than RNase A.

Non-NASA Center↗
NASA NTRS2000

Internal and External reconnection in a Series of Homologous Solar Flares

Using data from the Extreme Ultraviolet Telescope (EIT) on SOHO and the Soft X-ray Telescope (SXT) on Yohkoh, we examine a series of morphologically homologous solar flares occurring in NOAA AR 8210 over May 1-2, 1998. An emerging flux region (EFR) impacted against a sunspot to the west and next to a coronal hole to the east is the source of the repeated flaring. An SXT sigmoid parallels the EFR's neutral line at the site of the initial flaring in soft X-rays. In EIT, each flaring episode begins with the formation of a crinkle pattern external to the EFR. These EIT crinkles move out from, and then in toward, the EFR with velocities approximately 20 km/s. A shrinking and expansion of the width of the coronal hole coincides with the crinkle activity, and generation and evolution of a postflare loop system begins near the. time of crinkle formation. Using a schematic based on magnetograms of the region, we suggest that these observations are consistent with the standard reconnection-based model for solar eruptions, but modified by the presence of the additional magnetic fields of the sunspot and coronal hole. In the schematic, internal reconnection begins inside of the EFR-associated fields, unleashing a flare, postflare loops, and a CME. External reconnection, first occurring between the escaping CME and the coronal hole field, and second occurring between fields formed as a result of the first external reconnection, results in the EIT crinkles and changes in the coronal hole boundary. By the end of the second external reconnection, the initial setup is reinstated; thus the sequence can repeat, resulting in morphologically homologous eruptions. Our inferred magnetic topology is similar to that suggested in the "breakout model" of eruptions [Antiochos, 1998], although we cannot determine if our eruptions are released primarily by the breakout mechanism (external reconnection) or, alternatively, are released primarily by the internal reconnection.

Sterling, Alphonse C.↗