Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular evolution”

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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
NASA NTRS2003

Membrane-Based Functions in the Origin of Cellular Life

How simple membrane peptides performed such essential proto-cellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we investigate how these peptides insert into membranes, self-assemble into higher-order structures and acquire functions. We have studied the insertion of an a-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)S into a model membrane. The transmembrane state is metastable, and approximately 15 kcal/mol is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)S and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self- assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to reengineering the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Wilson, Michael A.↗
NASA NTRS2003

Membrane peptides and their role in protobiological evolution

How simple membrane peptides performed such essential protocellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we explain how these peptides fold at water-membrane interfaces, insert into membranes, self-assemble into higher-order structures and acquire functions. We have investigated the interfacial behavior and folding of several peptides built of leucine and glutamine residues and have demonstrated that many of them tend to adopt ordered structures. Further, we have studied the insertion of an alpha-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)3 into a model membrane. The transmembrane state is metastable, and approximately 15 kcal mol(-1) is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)3 and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self-assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to re-engineer the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Models, Chemical↗
NASA NTRS2005

From Astrochemistry to Astrobiology

Tremendous strides have been made in our understanding of interstellar material over the past twenty five years thanks to significant developments in observational astronomy and laboratory astrophysics. Twenty years ago the composition of interstellar dust was largely guessed at, the concept of ices in dense molecular clouds ignored, and the notion of large, abundant, gas phase, carbon-rich molecules widespread throughout the interstellar medium (ISM) considered impossible. Today the composition of interstellar dust is reasonably well understood. In molecular clouds, the birthplace of stars and planets, these cold dust particles are coated with mixed molecular ices whose composition is very well constrained. Lastly, the signature of carbon-rich polycyclic aromatic hydrocarbons (PAHs), shockingly large molecules by early interstellar chemistry standards, is widespread throughout the Universe. The first part of this talk will describe how infrared spectroscopic studies of interstellar space, combined with laboratory simulations of interstellar ice chemistry, have revealed the widespread presence of interstellar PAHs and the composition of interstellar ices, the building blocks of comets. The remainder of the presentation will focus on the photochemical evolution of these materials and astrobiology. Within a molecular cloud, and especially the presolar nebula, materials frozen into the ices are photoprocessed by ultraviolet light and produce more complex molecules. As these materials are the building blocks of comets and related to carbonaceous micrometeorites, they are likely to have been important sources of complex materials delivered to the early Earth and their composition may be related to the origin of life.

Allamandola, L. J.↗
NASA NTRS1991

The nature, origin and evolution of embedded star clusters

The recent development of imaging infrared array cameras has enabled the first systematic studies of embedded protoclusters in the galaxy. Initial investigations suggest that rich embedded clusters are quite numerous and that a significant fraction of all stars formed in the galaxy may begin their lives in such stellar systems. These clusters contain extremely young stellar objects and are important laboratories for star formation research. However, observational and theoretical considerations suggest that most embedded clusters do not survive emergence from molecular clouds as bound clusters. Understanding the origin, nature, and evolution of embedded clusters requires understanding the intimate physical relation between embedded clusters and the dense molecular cloud cores from which they form.

Lada, Charles J.↗
NASA NTRSDate not supplied

Low-Temperature Production of Cosmic Grains Analogs From Gas-Phase Molecular Precursors with the NASA Ames' COSmIC Facility

Complex carbon molecules and ions are ubiquitous in space and form the building blocks of carbonaceous cosmic dust grains, ultimately contributing to the formation of planets. Here, we report the first experimental investigations of the low temperature chemical pathways leading to the production of cosmic grain analogs from gas phase molecular precursors in order to better understand the evolution of cosmic carbon. The experiments were performed using the COsmic SImulation Chamber (COSmIC) to generate and characterize grains formed from gas phase precursors under controlled conditions representative of astrophysical environments [1]. Using COSmIC, it is possible to investigate the evolution of cosmic carbon from the formation of neutral and ionized gas phase hydrocarbons and PAHs [2], to carbon grains [3, 4]. This is achieved by using a discharge nozzle to (1) produce an adiabatic jet expansion and cool down Ar-hydrocarbon/PAH gas mixtures to astrophysically relevant temperature (150 K) before inducing chemistry by generating a plasma discharge in the stream of the expansion. This plasma-induced chemistry results in the formation of complex molecules and solid particles, analogs of cosmic grains. Solid grains are produced in-situ in the plasma expansion, carried by the accelerated gas in the expansion, and collected on substrates placed a few centimeters downstream of the electrodes. The results of a preliminary solid phase ex-situ analysis of cosmic grain analogs produced at low temperature in COSmIC from gas mixtures including molecular precursors of cosmic carbon grains, i.e., such as CH4 and C2H2 found in circumstellar ejecta of late C stars [3] as well as PAHs ubiquitously detected in IR emission bands seen in galactic and extragalactic environments [4] will be discussed. Scanning Electron Microscopy imaging was used to provide insight on the morphology and growth structure of the grains produced in COSmIC, and to investigate how the precursors used to produce the grains affect these parameters [3]. Laser desorption mass spectrometry was used to identify the molecules making up the main structures within the condensed grains [4]. NIR to FIR optical properties are characterized to provide critical information (functional groups, optical constants) to the scientific community, for use in radiative transfer models in particular, and to help decipher and enhance the return data from space observations.

F. Salama↗
NASA NTRS1994

Effect Of Molecular Weight On Adhesive Properties Of The Phenylethynyl-Terminated Polyimide LARC(sup TM)-PETI-5

Future civilian aircraft will require the use of advanced adhesive systems with high temperature capabilities. One such material has been developed at the NASA Langley Research Center, a phenylethynyl-terminated polyimide given the designation LARC(sup TM)-PETI-5. Recent work has shown the advantages of similar phenylethynyl-terminated polyimides as films, moldings, adhesives, and composite matrix resins. Phenylethynyl-terminated oligomers provide greater processing windows than materials which incorporate simple ethynyl endcaps. Since these low molecular weight, low melt viscosity oligomers thermally cure without the evolution of volatile by-products, they provide an excellent means of producing polymers with high glass transition temperatures, excellent solvent resistance, and high mechanical properties. Three different versions of LARC(sup TM)-PETI-5 with theoretical number average molecular weights (M(sub n)s) of 250, 5000, and 10000 g/mol were synthesized in this work. Differential Scanning Calorimetry (DSC) measurements were performed on the dry powder form of these materials to establish cure conditions which result in high glass transition temperatures (T(sub g)s). Lap shear specimens were prepared from adhesive tape made from each material and with the thermal cure conditions determined from the DSC data. The tensile shear data established processing conditions which provided the best adhesive strengths. Further testing was performed to establish the properties of LARC(sup TM)-PETI-5 as an adhesive material and to determine its solvent resistance.

Cano, Roberto J.↗
NASA NTRS2001

The AstroBiology Explorer (ABE) MIDEX Mission Concept

The Astrobiology Explorer (ABE) is a MIDEX mission concept under study at NASA's Ames Research Center in collaboration with Ball Aerospace & Technologies, Corp. ABE will conduct IR spectroscopic observations to address important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding the distribution, identity, and evolution of ices and organic matter in dense molecular clouds, young forming stellar systems, stellar outflows, the general diffuse ISM, HII regions, Solar System bodies, and external galaxies. The ABE instrument concept includes a 0.6 m aperture Cassegrain telescope and two moderate resolution (R = 2000-3000) spectrographs covering the 2.5-16 micron spectral region. Large format (1024x 1024 pixel or larger) IR detector arrays and bandpass filters will allow each spectrograph to cover an entire octave of spectral range or more per exposure without any moving parts. The telescope will be cooled below 50K by a cryogenic dewar shielded by a sunshade. The detectors will be cooled to approximately 8K. The optimum orbital configuration for achieving the scientific objectives of the ABE mission is a low background, 1 AU Earth driftaway orbit requiring a Delta II launch vehicle. This configuration provides a low thermal background and allows adequate communications bandwidth and good access to the entire sky over the approximate 1-2 year mission lifetime.

Ennico, Kimberly↗
NASA NTRS2002

The AstroBiology Explorer (ABE) MIDEX Mission Concept: Identifying Organic Molecules in Space

The Astrobiology Explorer (ABE) is a MIDEX mission concept, currently under Concept Phase A study at NASA's Ames Research Center in collaboration with Ball Aerospace & Technologies, Corp., and managed by NASA's Jet Propulsion Laboratory. ABE will conduct infrared spectroscopic observations to address important problems in astrobiology, astrochemistry, and astrophysics. The core observational program would make fundamental scientific progress in understanding the distribution, identity, and evolution of ices and organic matter in dense molecular clouds, young forming stellar systems, stellar outflows, the general diffuse ISM, HII regions, Solar System bodies, and external galaxies. The ABE instrument concept includes a 0.6 m aperture Ritchey-Chretien telescope and three moderate resolution (R = 2000-3000) spectrometers together covering the 2.5-20 micron spectral region. Large format (1024 x 1024 pixel) IR detector arrays will allow each spectrometer to cover an entire octave of spectral range per exposure without any moving parts. The telescope will be cooled below 50 K by a cryogenic dewar shielded by a sunshade. The detectors will be cooled to approx. 7.5 K by a solid hydrogen cryostat. The optimum orbital configuration for achieving the scientific objectives of the ABE mission is a low background, 1 AU Earth driftaway orbit requiring a Delta II launch vehicle. This configuration provides a low thermal background and allows adequate communications bandwidth and good access to the entire sky over the approx. 1.5 year mission lifetime.

Ennico, Kimberly↗
NASA NTRS2005

From Astrochemistry to Astrobiology

The first part of this talk will describe how infrared spectroscopic studies of interstellar space, combined with laboratory simulations of interstellar ice chemistry, have revealed the widespread presence of interstellar PAHs and the composition of interstellar ices, the building blocks of comets. The remainder of the presentation will focus on the photochemical evolution of these materials and astrobiology. Within a molecular cloud, and especially the presolar nebula, materials frozen into the ices are photoprocessed by ultraviolet light and produce more complex molecules. As these materials are the building blocks of comets and related to carbonaceous micrometeorites, they are likely to have been important sources of complex materials delivered to the early Earth and their composition may be related to the origin of life.

Allamandola, L. J.↗
NASA NTRS2011

Post-Fragmentation Whole Genome Amplification-Based Method

This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (<400 bp) constitute a library of DNA fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

Benardini, James↗
NASA NTRS2023

Design of a Minimal di-Nickel Hydrogenase Peptide

The most ancient processes for energy production in the evolution of life involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13 amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe]-hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase (ACS), two ancient, extant proteins central to metabolism. These experimental results clearly demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth. One Sentence Summary: Small metal-binding peptides were the likely precursors of modern enzymes.

Joshua A. Mancini↗
NASA NTRS2017

Developing Model Benchtop Systems for Microbial Experimental Evolution

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA-damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO and O. Additional environmental stressor systems like temperature (extreme heat or cold), metal toxicity, and other forms of radiation will increase the scale and testing range.

Developing↗
NASA NTRS1992

The evolution of energy-transducing systems. Studies with an extremely halophilic archaebacterium

The F-type ATPases are found in remarkably similar versions in the energy-transducing membranes of eubacteria, chloroplasts, and mitochondria. Thus, it is likely that they have originated early in the evolution of life, which is consistent with their function as key enzymes of cellular metabolism. The archaebacteria are a group of microorganisms which, as shown by molecular sequencing and biochemical data, have diverged early from the main line of prokaryotic evolution. From studies of members of all three major groups of archaebacteria - the halophiles, methanogens, and thermoacidophiles - it emerged that they possess a membrane ATPase which differs from the F-ATPases. The goal of this project was a comparison of the ATPase from the halophilic archaebacterium Halobacterium saccharovorum with the well-characterized F-type ATPases on the molecular level. Amino acid sequences of critical regions of the enzyme were to be determined, as well as immunoreactions of single subunits in the search for common epitopes. The results were expected to allow a decision about the nature of archaebacterial ATPases, their classification as one of the known or, alternatively, novel enzyme complexes, and possibly deduction of events during the early evolution of energy-transducing systems.

Stan-Lotter, Helga↗
NASA NTRSDate not supplied

Molecular flow venting of a volume with an outgassing or desorbing source

A venting equation commonly used to describe the transient evolution of pressure within a volume containing an outgassing or offgassing source and a restrictive vent conductance under conditions of molecular flow has been solved analytically. Solutions are found for sources of finite thickness characterized by classical diffusion-limited behavior (proportional to inverse square root of time), as well as responses for thick material sources often observed in testing that are characterized by a more general form of power-law decay, up to inverse time behavior associated with surface desorption. Solutions involve evaluating integrals where both numerators and denominators of the integrands diverge with time, making wide-ranging transient solutions difficult to directly compute numerically. Usually, one can avoid evaluating these integrals by assuming quasistatic conditions at long time scales. A novel approach is used in this work to analytically produce solutions by generating bespoke mathematical functions, some of which solve integrals that have apparently had no previous analytical solution.

Michael Woronowicz↗
NASA NTRSDate not supplied

Molecular flow venting of a volume with an outgassing or desorbing source

"A venting equation commonly used to describe the transient evolution of pressure within a volume containing an outgassing or offgassing source and a restrictive vent conductance under conditions of molecular flow has been solved analytically. Solutions are found for sources of finite thickness characterized by classical diffusion-limited behavior (proportional to inverse square root of time), as well as responses for thick material sources often observed in testing that are characterized by a more general form of power-law decay, up to inverse time behavior associated with surface desorption. Solutions involve evaluating integrals where both numerators and denominators of the integrands diverge with time, making wide-ranging transient solutions difficult to directly compute numerically. Usually, one can avoid evaluating these integrals by assuming quasistatic conditions at long time scales. A novel approach is used in this work to analytically produce solutions by generating bespoke mathematical functions, some of which solve integrals that have apparently had no previous analytical solution."

Michael Woronowicz↗
NASA NTRS1986

Characterization of the relationship of the cure cycle chemistry to cure cycle processing properties

Dynamic Dielectric measurements made over a wide range of frequency provide a sensitive and convenient means for monitoring the cure process in thermosets and thermoplastics. The measurement of dielectric relaxation is one of only a few instrumental techniques available for studying molecular properties in both the liquid and solid states. Furthermore, it is probably the only convenient experimental technique for studying the polymerization process of going from a monomeric liquid of varying viscosity to a crosslinked, insoluble, high temperature solid. The objective of the research is to develop on-line dielectric instrumentation for quantitative nondestructive material evaluation and closed loop smart cure cycle control. The key is to relate the chemistry of the cure cycle process to the dielectric properties of the polymer system by correlating the time, temperature, and frequency dependent dielectric measurements with chemical characterization measurements. Measurement of the wide variation in magnitude of the complex permittivity with both frequency and state of cure, coupled with chemical characterization work, have been shown in the laboratory to have the potential to determine: resin quality, composition and age; cure cycle window boundaries; onset of flow and point of maximum flow; extent of and completion of reaction; evolution of volatiles; T sub g; and, crosslinking and molecular weight buildup.

Kranbuehl, D. E.↗
NASA NTRS1993

Planetary and satellite x ray spectroscopy: A new window on solid-body composition by remote sensing

The rings and most of the satellites of the outer planets orbit within the radiation belts of their parent bodies. This is an environment with intense fluxes of energetic electrons. As a result, these objects are strong emitters of X-rays. The characteristic X-ray lines from these bodies depend on atomic composition, but they are not sensitive to how the material is arranged in compounds or mixtures. X-ray fluorescence spectral analysis has demonstrated its unique value in the laboratory as a qualitative and quantitative analysis tool. This technique has yet to be fully exploited in a planetary instrument for remote sensing. The characteristic X-ray emissions provide atomic relative abundances. These results are complementary to the molecular composition information obtained from IR, visible, and UV emission spectra. The atomic relative abundances are crucial to understanding the formation and evolution of these bodies. They are also crucial to the proper interpretation of the molecular composition results from the other sensors. The intensities of the characteristic X-ray emissions are sufficiently strong to be measured with an instrument of modest size. Recent developments in X-ray detector technologies and electronic miniaturization have made possible space-flight X-ray imaging and nonimaging spectrometers of high sensitivity and excellent energy resolution that are rugged enough to survive long-duration space missions. Depending on the application, such instruments are capable of resolving elemental abundances of elements from carbon through iron. At the same time, by measuring the bremsstrahlung intensity and energy spectrum, the characteristics of the source electron flux can be determined. We will discuss these concepts, including estimated source strengths, and will describe a small instrument capable of providing this unique channel of information for future planetary missions. We propose to build this instrument using innovative electronics packaging methods to minimize size and weight.

Chenette, D. L.↗
NASA NTRS1997

The Evolution of Energy-Transducing Systems. Studies with an Extremely Halophilic Archaebacterium

The F-type ATPases are found in remarkably similar versions in the energy-transducing membranes of bacteria, chloroplasts and mitochondria (1). Thus, it is likely that they have originated early in the evolution of life, which is consistent with their function as key enzymes of cellular metabolism. The archaea (formerly called archaebacteria) are a group of microorganisms which, as shown by molecular sequencing and biochemical data, have diverged early from the main line of prokaryotic evolution (2). From studies of members of all three major groups of archaea, the halophiles, methanogens and thermoacidophiles, it emerged that they possess a membrane ATPase, which differs from the F-ATPases. The goal of this project was a comparison of the ATPase from the halophilic archaebacterium Halobacterium saccharovorum with the well-characterized F-type ATPases on the molecular level. The results were expected to allow a decision about the nature of archaebacterial ATPases, their classification as one of the known or, alternatively, novel enzyme complex, and possibly a deduction of events during the early evolution of energy-transducing systems.

Stan-Lotter, Helga↗