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At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
NASA NTRS1974

Evolution of models for evolution

The paper discusses models of evolution and their values, and some critiques of these models and the value of these critiques. A model is investigated which involves the formation of prebiotic protein from amino acids. Its formation by four theoretical critiques that suggest alternative environmental conditions is discussed. Experiments are reviewed so as to illustrate the experimental testing of the possible weaknesses of a model for a single molecular evolutionary phase and to suggest some necessary changes in the model.

Rohlfing, D. L.↗
NASA NTRS1994

An investigation of solar wind effects on the evolution of the Martian atmosphere

This investigation concentrated on the question of how atmosphere escape, related to both photochemistry and the Mars solar wind interaction, may have affected the evolution of Mars' atmosphere over time. The principal investigator and postdoctoral researcher adopted the premise that contemporary escape processes have dominated the losses to space over the past 3.5 billion years, but that the associated loss rates have been modified by solar evolution. A model was constructed for the contemporary escape scenario based on knowledge gained from both Venus in-situ measurements from Pioneer Venus Orbiter and Mars measurements from Phobos-2. Venus provided a valuable second example of a weakly magnetized planet having a similar solar wind interaction where we have more knowledge from observations. The model included photochemical losses from recombining ionospheric molecular ions, scavenging Martian upper atmosphere ('pickup') ions by the solar wind, and sputtering of the atmosphere by reentering pickup ions. The existence of the latter mechanism was realized during the course of the supported investigation, and is now thought by Jakosky and Pepin to explain some of the Martian noble gas isotope ratios.

Luhmann, Janet G.↗
NASA NTRS2000

Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous mixing. A similar difficulty may be encountered in any method relying on global modifications of phase space.

Darve, Eric↗
NASA NTRS2018

New O+CO2 Scattering Cross Sections and Their Impact on Photochemical Atmospheric Escape of Oxygen from Mars

Dissociative recombination of O2+ and CO2+ molecular ions in the upper atmosphere of Mars is a major source of suprathermal (hot) oxygen atoms. A significant fraction of hot O atoms are sufficiently fast to overcome Mars' gravitational potential and escape to space. This mechanism is known as photochemical escape (PE) and found to be one of the major escape mechanisms presently active on Mars. The Mars Atmosphere and Volatile Evolution Mission (MAVEN) can constrain the PE rate from measurements of electron temperature and density and ion temperature and density. Escape probabilities of hot O can then be constructed from in-situ neutral densities and escaping O flux loss due to collisions with atmospheric background gases. Due to CO2 abundance in the upper atmosphere, O+CO2 scattering is the most important sink of the escaping hot O flux that strongly affects estimates of total atomic oxygen escape rate obtained from MAVEN data, as outlined above. New O+CO2 elastic and inelastic cross sections were constructed from first principles for collision energies from 0.01-5 eV. O(3P)+CO2 collisions were described using new 4D electronic potential energy surfaces (PESs) for restricted geometries. Three lowest triplet states of CO2 were considered for symmetric, bending, and asymmetric vibrational modes. The cross sections were determined from close-coupling calculations performed on individual surfaces using vibrating rotor approximations for CO2 molecule. Differential and momentum transfer cross sections, of use in energy transfer atmospheric models, were also constructed. The obtained cross sections are in excellent agreement with published results. Our new elastic cross sections are significantly smaller than assumed in earlier atmospheric escape models, resulting in larger photochemical escape rate of O from Mars, as estimated from a 1D escape model. Our results agree well with estimated hot O flux (about 9 x 10(sup 25) s(sup -1)) derived from altitude profiles of 130.4 nm O emission measured up to ~4,000 km by the Imaging Ultraviolet Spectrograph on MAVEN orbiter.

Atmospheric↗
NASA NTRS2019

Measuring the D/H Ratios of Exoplanets and Brown Dwarfs

The relative abundance of deuterium and hydrogen is a potent tracer of planet formation and evolution. Jupiter and Saturn have protosolar atmospheric D/H ratios, a relic of substantial gas accretion from the nebula, while the atmospheres of Neptune and Uranus are enhanced in D by accretion of ices into their envelopes. For terrestrial planets, D/H ratios are used to determine the mechanisms of volatile delivery and subsequent atmosphere loss over the lifetime of the planet. Planets and brown dwarfs more massive than ~13 M(J) quickly fuse their initial D reservoir. Here, we simulate spectra for giant exoplanets and brown dwarfs (2 M(Neptune) to ~10 M(Jupiter)) from T(eff) = 200–1800 K including both CH3D and HDO to determine the observability of these dominant deuterium isotopologues in mid-infrared thermal emission spectra. Colder objects have stronger molecular features in their spectra, due to the temperature dependence of molecular cross sections. CH3D is easier to observe than HDO at all temperatures considered, due to the strength of its absorption bands and locations of features at wavelengths with few other strong absorption features. We predict that for nearby cool brown dwarfs, the CH3D abundance can be measured at high signal to noise with the James Webb Space Telescope (JWST); for objects from 200 to 800 K closer than 10 pc, a protosolar D/H ratio would be readily observable in 2.5 hr. Moderately young Jupiter-mass planets (100–300 Myr) and young Neptunes (10 Myr) may be discovered with JWST and provide the best targets for detecting deuterium on an exoplanet in the coming decade. Future telescope designs should consider the importance of isotopes for understanding the formation and evolution of planetary atmospheres.

Caroline V. Morley↗
DOE OSTI2020

Atomistic Characterization of Gramicidin Channel Formation

We investigated gramicidin A (gA) subunit dimerization in lipid bilayers using microsecond-long replica-exchange umbrella sampling simulations, millisecond-long unbiased molecular dynamics simulations, and machine learning. Our simulations led to a dimer structure that is indistinguishable from the experimentally determined gA channel structures, with the two gA subunits joined by six hydrogen bonds (6HB). The simulations also uncovered two additional dimer structures, with different gA–gA stacking orientations that were stabilized by four or two hydrogen bonds (4HB or 2HB). When examining the temporal evolution of the dimerization, we found that two bilayer-inserted gA subunits can form the 6HB dimer directly, with no discernible intermediate states, as well as through paths that involve the 2HB and 4HB dimers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Direct Observation of the Pressure-Induced Structural Variation in Gold Nanoclusters and the Correlated Optical Response

The ability to gradually modify the atomic structures of nanomaterials and directly identify such structural variation is important in nanoscience research. Here, we present the first example of a high-pressure single-crystal X-ray diffraction analysis of atomically precise metal nanoclusters. The pressure-dependent, subangstrom structural evolution of an ultrasmall gold nanoparticle, Au 25 S 18 , has been directly identified. We found that a 0.1 Å decrease of the Au–Au bond length could induce a blue-shift of 30 nm in the photoluminescence spectra of gold nanoclusters. From theoretical calculations, the origins of the blue-shift and enhanced photoluminescence under pressure are investigated, which are ascribed to molecular orbital symmetry and conformational locking, respectively. Here, the combination of the high-pressure in situ X-ray results with both theoretical and experimental optical spectra provides a direct and generalizable avenue to unveil the underlying structure–property relations for nanoclusters and nanoparticles which cannot be obtained through traditional physical chemistry measurements.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Modeling Functional Organic Chemistry in Arctic Rivers: An Idealized Siberian System

Rivers of the Arctic will become ever more important for the global climate, since they carry a majority of continental dissolved organic carbon flux into the rapidly changing polar ocean. Aqueous organics comprise a wide array of functional groups, several of which are likely to impact coastal and open water biophysical properties. Light attenuation, interfacial films, aerosol formation, gas release and momentum exchange can all be cited. We performed Lagrangian kinetic modeling for the evolution of riverine organic chemistry as the molecules in question make their way from the highlands to Arctic outlets. Classes as diverse as the proteins, sugars, lipids, re-condensates, humics, bio-tracers and small volatiles are all included. Our reduced framework constitutes an idealized northward flow driving a major hydrological discharge rate and primarily representing the Russian Lena. Mountainous, high solute and tundra sources are all simulated, and they meet up at several points between soil and delta process reactors. Turnover rates are parameterized beginning with extrapolated coastal values imposed along a limited tributary network, with connections between different terrestrial sub-ecologies. Temporal variation of our total dissolved matter most closely resembles the observations when we focus on the restricted removal and low initial carbon loads, suggesting relatively slow transformation along the water course. Thus, channel combinations and mixing must play a dominant role. Nevertheless, microbial and photochemical losses help determine the final concentrations for most species. Chemical evolution is distinct for the various functionalities, with special contributions from pre- and post-reactivity in soil and delta waters. Several functions are combined linearly to represent the collective chromophoric dissolved matter, characterized here by its absorption. Tributaries carry the signature of lignin phenols to segregate tundra versus taiga sources, and special attention is paid to the early then marine behaviors of low molecular weight volatiles. Heteropolycondensates comprise the largest percentage of reactive carbon in our simulations due to recombination/accumulation, and they tend to be preeminent at the mouth. Outlet concentrations of individual structures such as amino acids and absorbers lie above threshold values for biophysical influence, on the monolayer and light attenuation. The extent of coastal spreading is examined through targeted regional box modeling, relying on salinity and color for calibration. In some cases, plumes reach the scale of peripheral arctic seas, and amplification is expected during upcoming decades. Conclusions are mapped from the Lena to other boreal discharges, and future research questions are outlined regarding the bonding type versus mass release as permafrost degrades. Dynamic aqueous organic coupling is recommended for polar system models, from headwaters to coastal diluent.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1986

Intramolecular interactions in aminoacyl nucleotides: Implications regarding the origin of genetic coding and protein synthesis

Cellular organisms store information as sequences of nucleotides in double stranded DNA. This information is useless unless it can be converted into the active molecular species, protein. This is done in contemporary creatures first by transcription of one strand to give a complementary strand of mRNA. The sequence of nucleotides is then translated into a specific sequence of amino acids in a protein. Translation is made possible by a genetic coding system in which a sequence of three nucleotides codes for a specific amino acid. The origin and evolution of any chemical system can be understood through elucidation of the properties of the chemical entities which make up the system. There is an underlying logic to the coding system revealed by a correlation of the hydrophobicities of amino acids and their anticodonic nucleotides (i.e., the complement of the codon). Its importance lies in the fact that every amino acid going into protein synthesis must first be activated. This is universally accomplished with ATP. Past studies have concentrated on the chemistry of the adenylates, but more recently we have found, through the use of NMR, that we can observe intramolecular interactions even at low concentrations, between amino acid side chains and nucleotide base rings in these adenylates. The use of this type of compound thus affords a novel way of elucidating the manner in which amino acids and nucleotides interact with each other. In aqueous solution, when a hydrophobic amino acid is attached to the most hydrophobic nucleotide, AMP, a hydrophobic interaction takes place between the amino acid side chain and the adenine ring. The studies to be reported concern these hydrophobic interactions.

Lacey, J. C., Jr.↗
NASA NTRS2018

Marginal protein stability drives subcellular proteome isoelectric point

There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome—a highly acidic compartment in the cell—have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.

Kaiser Loell↗
DOE OSTI2022

Far-from-equilibrium slow modes and momentum anisotropy in expanding plasma

The momentum distribution of particle production in heavy-ion collisions encodes information about thermalization processes in the early-stage quark-gluon plasma. We use kinetic theory to study the far-from-equilibrium evolution of an expanding plasma with an anisotropic momentumspace distribution. We identify slow and fast degrees of freedom in the far-from-equilibrium plasma from the evolution of moments of this distribution. At late times, the slow modes correspond to hydrodynamic degrees of freedom and are naturally gapped from the fast modes by the inverse of the relaxation time, $τ$$^{–1}_{R}$. At early times, however, there are an infinite number of slow modes with a gap inversely proportional to time, τ –1 . From the evolution of the slow modes we generalize the paradigm of the far-from-equilibrium attractor to vector and tensor components of the energy momentum tensor, and even to higher moments of the distribution function that are not part of the hydrodynamic evolution. We predict that initial-state momentum anisotropy decays slowly in the far-from-equilibrium phase and may persist until the relaxation time.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2025

SUDA: A SUrface Dust Analyser for Compositional Mapping of the Galilean Moon Europa

Abstract The Surface Dust Analyser (SUDA) is a mass spectrometer onboard the Europa Clipper mission for investigating the surface composition of the Galilean moon Europa. Atmosphereless planetary moons such as the Galilean satellites are wrapped into a ballistic dust exosphere populated by tiny samples from the moon’s surface produced by impacts of fast micrometeoroids. SUDA will measure the composition of such surface ejecta during close flybys of Europa to obtain key chemical signatures for revealing the satellite’s composition such as organic molecules and salts, history, and geological evolution. Because of their ballistic orbits, detected ejecta can be traced back to the surface with a spatial resolution roughly equal to the instantaneous altitude of the spacecraft. SUDA is a Time-Of-Flight (TOF), reflectron-type impact mass spectrometer, optimized for a high mass resolution which only weakly depends on the impact location. The instrument will measure the mass, speed, charge, elemental, molecular, and isotopic composition of impacting grains. The instrument’s small size of$268 ~\mathrm {mm} \times 250 ~\mathrm {mm} \times 171$ 268 mm × 250 mm × 171 $~\mathrm {mm}$ mm , radiation-hard design, and rather large sensitive area of 220 cm 2 matches well the challenging demands of the Clipper mission.

Astronomy & Astrophysics↗
DOE OSTI2023

Athermal annealing of pre-existing defects in crystalline silicon

Systematic investigations of electronic energy loss (S e ) effects on pre-existing defects in crystalline silicon (Si) are crucial to provide reliance on the use of ionizing irradiation to anneal pre-existing defects, leading to successful implementation of this technology in the fabrication of Si-based devices. In this regard, the S e effects on nonequilibrium defect evolution in pre-damaged Si single crystals at 300 K has been investigated using intermediate-energy ions (12 MeV O and Si ions) that interact with the pre-damaged surface layers of Si mainly by ionization, except at the end of their range where the nuclear energy loss (S n ) is no longer negligible. Furthermore, under these irradiation conditions, experimental results and molecular dynamics simulations have revealed that pre-existing disorder in Si can be almost fully annealed by subsequent irradiation with intermediate-energy incident ions with S e values as low as 1.5–3.0 keV/nm. Selective annealing of pre-existing defect levels in Si at room temperature can be considered as an effective strategy to mediate the transient enhanced diffusion of dopants in Si. This approach is more desirable than the regular thermal annealing, which is not compatible with the processing requirements that fall below the typical thermal budget.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Comparison of the Arrhenius parameters between conventional hydrothermal and microwave-assisted synthesis methods for tin oxide nanoparticles

Microwave (MW) irradiation has emerged as a powerful tool for accelerating materials synthesis, yet the origins of its specific influence on reaction kinetics remain elusive. While multiple studies have attributed the observed enhancements in reaction rates under MW heating to reduced activation energies, other accounts have suggested modifications to the Arrhenius pre-exponential factor as the predominant cause. Distinguishing between these parameters in modern applications of MW processing in nanomaterials requires experimental approaches capable of resolving the dynamic and nuanced structural kinetics that govern MW-assisted chemistry. Here, we combine in-situ synchrotron X-ray total scattering with pair distribution function (PDF) analysis to track the structural evolution of SnO 2 nanoparticles synthesized via MW-assisted and conventional hydrothermal conditions. Avrami modeling and Arrhenius analysis suggest that although MW irradiation yields a higher apparent activation energy, the enhanced crystallization is better explained by a pre-exponential factor several orders of magnitude larger than that of conventional heating. These findings suggest that the MW field induces a higher frequency of successful molecular rearrangements rather than lowering the intrinsic activation barrier. The results contribute further insights clarifying the role of the applied MW field for materials design where MW-specific effects can be deliberately harnessed. Furthermore, this work presents a framework promoting the utility of in-situ PDF characterization coupled with kinetic analysis for developing more sophisticated descriptions of nanoscale transformations for MW-driven reaction kinetics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Isotopic fractionation as in-situ sensor of subsurface reactive flow and precursor for rock failure

Greater utilization of subsurface reservoirs perturbs in-situ chemical-mechanical conditions with wide ranging consequences from decreased performance to project failure. Understanding the chemical precursors to rock deformation is critical to reducing the risks of these activities. To address this need, we investigated the coupled flow-dissolution- precipitation-adsorption reactions involving calcite and environmentally-relevant solid phases. Experimentally, we quantified (1) stable isotope fractionation processes for strontium during calcite nucleation and growth, and during reactive fluid flow; (2) consolidation behavior of calcite assemblages in the common brines. Numerically, we quantified water weakening of calcite using molecular dynamics simulations; and quantified the impact of calcite dissolution rate on macroscopic fracturing using finite element models. With microfluidic experiments and modeling, we show the effect of local flow fields on the dissolution kinetics of calcite. Taken together across a wide range of scales and methods, our studies allow us to separate the effects of reaction, flow, and transport, on calcite fracturing and the evolution of strontium isotopic signatures in the reactive fluids.

42 ENGINEERING↗
NASA NTRS1984

Mass loss from red giants - A simple evolutionary model for NGC 7027

NGC 7027 is a young planetary nebula with the remnants of a red giant circumstellar envelope surrounding the central, ionized region. By comparing the outer molecular envelope with the inner ionized material, it is argued that the mass loss rate has decreased by at least a factor of 3, and more probably by about a factor of 10, during the past 1000 years. From this result, it is argued that the luminosity of the central star has also decreased substantially during the same time, consistent with models for the rapid evolution of stars just after they evolve off the asymptotic giant branch. In this picture, the distance to NGC 7027 is less than 1300 pc. NGC 7027 was the last (and best) example of a star where apparently the momentum in the outflowing mass /M(dot)v/ is considerably greater than the momentum in the radiation field (L/c). With the above description of this object, the evidence is now strong that quite often the mass lost from late-type giants is ultimately driven to infinity by radiation pressure on grains. If M(dot)v is as large as L/c for asymptotic branch stars, then it is expected that the total amount of mass lost during this stage of evolution is of the same magnitude as the initial mass of the star, and therefore this mass loss can profoundly affect the star's ultimate fate.

Jura, M.↗
NASA NTRS1988

The formation of interstellar jets

The formation of interstellar jets by convergence of supersonic conical flows and the further dynamical evolution of these jets are investigated theoretically by means of numerical simulations. The results are presented in extensive graphs and characterized in detail. Strong radiative cooling is shown to result in jets with Mach numbers 2.5-29 propagating to lengths 50-100 times their original widths, with condensation of swept-up interstellar matter at Mach 5 or greater. The characteristics of so-called molecular outflows are well reproduced by the simulations of low-Mach-number and quasi-adiabatic jets.

Tenorio-Tagle, G.↗