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All sourcesNASA NTRSDOE OSTI
NASA NTRS2000

Theoretical Modeling and Computer Simulations for the Origins and Evolution of Reproducing Molecular Systems and Complex Systems with Many Interactive Parts

Our research effort has produced nine publications in peer-reviewed journals listed at the end of this report. The work reported here are in the following areas: (1) genetic network modeling; (2) autocatalytic model of pre-biotic evolution; (3) theoretical and computational studies of strongly correlated electron systems; (4) reducing thermal oscillations in atomic force microscope; (5) transcription termination mechanism in prokaryotic cells; and (6) the low glutamine usage in thennophiles obtained by studying completely sequenced genomes. We discuss the main accomplishments of these publications.

Liang, Shoudan↗
NASA NTRS1986

Second Symposium on Chemical Evolution and the Origin of Life

Recent findings by NASA Exobiology investigators are reported. Scientific papers are presented in the following areas: cosmic evolution of biogenic compounds, prebiotic evolution (planetary and molecular), early evolution of life (biological and geochemical), evolution of advanced life, solar system exploration, and the Search for Extraterrestrial Intelligence (SETI).

Donald L Devincenzi↗
NASA NTRS1991

Fourth Symposium on Chemical Evolution and the Origin and Evolution of Life

This symposium was held at the NASA Ames Research Center, Moffett Field, California, July 24-27, 1990. The NASA exobiology investigators reported their recent research findings. Scientific papers were presented in the following areas: cosmic evolution of biogenic compounds, prebiotic evolution (planetary and molecular), early evolution of life (biological and geochemical), evolution of advanced life, solar system exploration, and the Search for Extraterrestrial Intelligence (SETI).

Wharton, Robert A., Jr.↗
NASA NTRS1994

Chemistry of Star-Forming Cores

Chemical effects arising from the exchange of molecules between dust and gas in dense clumps are described. Selective desorption of CO and N2 from grains in cool cores can account for the presence of ammonia in several cores in the NGC 2024 cloud. Evaporation of ices containing methanol and ethanol can lead to detectable abundances of (C2H5)(sub 2)O and CH3OC2H5. Results are presented for the hot core chemistries of sulphur and phosphorus which are initiated by evaporated hydrogen sulphide and phosphine. The implications of these studies for understanding the nature of molecular mantles, the evolution of molecular complexity in the gas phase, and the presence of small-scale abundance gradients in star-forming regions, are briefly discussed.

Charnley, S. B.↗
NASA NTRS1999

Autonomous Agents: The Origins and Co-Evolution of Reproducing Molecular Systems

The central aim of this award concerned an investigation into, and adequate formulation of, the concept of an "autonomous agent." If we consider a bacterium swimming upstream in a glucose gradient, we are willing to say of the bacterium that it is going to get food. That is, we are willing, and do, describe the bacterium as acting on its own behalf in an environment. All free living cells are, in this sense, autonomous agents. But the bacterium is "just" a set of molecules. We define an autonomous agent as a physical system able to act on its own behalf in an environment, then ask, "What must a physical system be to be an autonomous agent?" The tentative definition for a molecular autonomous agent is that it must be self-reproducing and carry out at least one thermodynamic work cycle. The work carried out in this grant involved, among other features, the development of a detailed model of a molecular autonomous agent, and study of the kinetics of this system. In particular, a molecular autonomous agent must, by the above tentative definition, not only reproduce, but must carry out at least one work cycle. I took, as a simple example of a self-reproducing molecular system, the single-stranded DNA hexamer 3'CCGCGG5' which can line up and ligate its two complementary trimers, 5'CCG3' and 5'CGG3'. But the two ligated trimers constitute the same molecular sequence in the 3' to 5' direction as the initial hexamer, hence this system is autocatalytic. On the other hand the above system is not yet an autonomous agent. At the minimum, autonomous agents, as I have defined them, are a new class of chemical reaction network. At a maximum, they may constitute a proper definition of life itself.

Kauffman, Stuart↗
NASA NTRS2026

The Evolution in Coma Molecular Composition of Comet C/2017 K2 (PanSTARRS) Across the H 2 O Sublimation Zone: ALMA Imaging of an H 2 O-Dominated Coma

We report a survey of molecular emission from cometary volatiles using the Atacama Large Millimeter/Submillimeter Array (ALMA) toward comet C/2017 K2 (PanSTARRS) carried out on UT 2022 September 21, 22, and 23 at a heliocentric distance r H 3 OH, and H 2 CO (along with continuum emission from dust) sampled molecular chemistry in C/2017 K2 at the inner edge of the H 2 O sublimation zone, the region from r H 2 O begins vigorously subliming and increasingly dominating comet activity, discerning parent from daughter or extended source species. This work presents spectrally integrated flux maps, production rates, and parent scale lengths for each molecule. CH 3 OH, CO, and HCN were produced within ~250 km of the nucleus, potentially including contributions from sublimation of icy grains. CS was consistent with production from CS 2 photolysis, and H 2 CO required production from extended sources in the coma. An ortho-to-para ratio of 2.9 ± 0.4 for H 2 CO was derived from simultaneously measured transitions of each spin species. The continuum was extended and spatially resolved, consistent with thermal emission from dust in the coma. Analysis of the continuum visibilities provided an upper limit on the nucleus diameter d <6.6 km and coma dust masses of (1.2-2.4) times10 11 kg.

Nathan X Roth↗
NASA NTRS2004

A molecular timescale of eukaryote evolution and the rise of complex multicellular life

BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.

Evolution, Molecular↗
NASA NTRS1992

Nonenzymatic template-directed synthesis on oligodeoxycytidylate sequences in hairpin oligonucleotides

We have developed a novel method for studying template-directed synthesis in hairpin oligonucleotides. An unpaired segment at the 5'-terminus of the hairpin acts as an intramolecular template for the extension of the paired 3'-terminus. Products are analyzed by denaturing gel electrophoresis of [32P]-labeled hairpins. Using this system, we have studied the synthesis of oligoguanylates on an oligodeoxycytidylate template. We find that guanosine 5'-phosphoro(2-methyl)imidazolide adds efficiently to a terminal riboguanylate residue at temperatures in the range 0-37 degrees C but not at 50 degrees C. At 0 degree C, the half-time for addition of the first G residue is about 3 h, and the reaction rate is independent of pH in the range 6.5-8.0. The first addition reaction results in the formation of a predominantly 3'-5'-internucleotide bond. When the 3'-terminal riboguanylate residue is placed by a deoxyguanylate residue, the half-time for the first addition increases from about 3 to about 30 h.

NASA Discipline Exobiology↗
NASA NTRS1995

Faster rates with less catalyst in template-directed reactions

We have recently shown that the polycytidylic acid-directed polymerization of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) is amenable to kinetic study and that rate determinations as a function of 2-MeImpG concentration can reveal much mechanistic detail (Kanavarioti et al. 1993). Here we report kinetic data which show that, once the reaction has been initiated by the formation of dimers, the elongation of dimers to form longer oligomers is accelerated by decreasing polycytidylate (poly(C)) concentration from 0.05 to 0.002 M. This result is consistent with the previously proposed mechanism. The increase in the observed pseudo-first order rate constant for formation of the trimer, k3', and the corresponding constant for formation of oligomers longer than the trimer, ki' (ki' is independent of oligomer length for i > or = 4), with decreasing template concentration for a given monomer concentration is attributed to an increase in template occupancy as template concentration is reduced.

NASA Discipline Exobiology↗
NASA NTRS1994

A C(18)O survey of dense cores in the Taurus molecular cloud: Signatures of evolution and protostellar collapse

We have mapped 11 dense cores in the Taurus molecular cloud in the C(18)O J = 2 goes to 1 line at a linear resolution of 0.02 pc. The core masses derived from C(18)O range from 0.06 to 5 solar mass. Five of them have embedded infrared sources, and six do not. Dense cores without infrared sources show multiple emission peaks. In contrast, dense cores with infrared sources have a single peak and smaller sizes. The cores with infrared sources have line widths that are 2-3 times the value expected from correlations found in previous surveys. This enhancement may be accounted for by models of gravitational collapse. The data are consistent with the idea that dense cores evolve first toward smaller sizes and smaller line width along the line width-size relation, and then toward larger line width and constant or smaller sizes as an infrared source becomes observable. A good collapse candidate, L1527, is identified based on the shapes of C(18)O and H2CO lines.

Zhou, Shudong↗
DOE OSTI2025

Breaking the mold: Overcoming the time constraints of molecular dynamics on general-purpose hardware

The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of accuracy, atom count (spatial scale), and duration (temporal scale). Since the mid-2000s, computer platforms have, however, failed to provide strong scaling for MD, as scale-out central processing unit (CPU) and graphics processing unit (GPU) platforms that provide substantial increases to spatial scale do not lead to proportional increases in temporal scale. Important scientific problems therefore remained inaccessible to direct simulation, prompting the development of increasingly sophisticated algorithms that present significant complexity, accuracy, and efficiency challenges. While bespoke MD-only hardware solutions have provided a path to longer timescales for specific physical systems, their impact on the broader community has been mitigated by their limited adaptability to new methods and potentials. In this work, we show that a novel computing architecture, the Cerebras wafer scale engine, completely alters the scaling path by delivering unprecedentedly high simulation rates up to 1.144 M steps/s for 200 000 atoms whose interactions are described by an embedded atom method potential. This enables direct simulations of the evolution of materials using general-purpose programmable hardware over millisecond timescales, dramatically increasing the space of direct MD simulations that can be carried out. In this paper, we provide an overview of advances in MD over the last 60 years and present our recent result in the context of historical MD performance trends.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Iron and molecular opacities and the evolution of Population I stars

Effects of recent opacity revisions on the evolution of Population I stars are explored over the range 1.5-60 solar masses. Opacity parameters considered include the angular momentum coupling scheme for iron, the relative iron abundance, the total metal abundance, and diatomic and triatomic molecular sources. Only the total metal abundance exerts an important control over the evolutionary tracks. Blue loops on the H-R diagram during core helium burning can be very sensitive to opacity, but only insofar as the simple formation or suppression of a blue loop is concerned. The blue loops are most robust for stellar masses around 10 solar masses. We confirm, from a comparison of stellar models with observational data, that the total metal abundance is close to solar and that convective core overshooting is likely to be very slight. The new models predict the existence of an iron convection zone in the envelope and a great widening of the main-sequence band in the H-R diagram at luminosities brighter than 100,000 solar luminosities.

Stothers, Richard B.↗
NASA NTRS2003

Giant Molecular Cloud Structure and Evolution

Bodenheimer and Burkert extended earlier calculations of cloud core models to study collapse and fragmentation. The initial condition for an SPH collapse calculation is the density distribution of a Bonnor-Ebert sphere, with near balance between turbulent plus thermal energy and gravitational energy. The main parameter is the turbulent Mach number. For each Mach number several runs are made, each with a different random realization of the initial turbulent velocity field. The turbulence decays on a dynamical time scale, leading the cloud into collapse. The collapse proceeds isothermally until the density has increased to about 10(exp 13) g cm(exp -3). Then heating is included in the dense regions. The nature of the fragmentation is investigated. About 15 different runs have been performed with Mach numbers ranging from 0.3 to 3.5 (the typical value observed in molecular cloud cores is 0.7). The results show a definite trend of increasing multiplicity with increasing Mach number (M), with the number of fragments approximately proportional to (1 + M). In general, this result agrees with that of Fisher, Klein, and McKee who published three cases with an AMR grid code. However our results show that there is a large spread about this curve. For example, for M=0.3 one case resulted in no fragmentation while a second produced three fragments. Thus it is not only the value of M but also the details of the superposition of the various velocity modes that play a critical role in the formation of binaries. Also, the simulations produce a wide range of separations (10-1000 AU) for the multiple systems, in rough agreement with observations. These results are discussed in two conference proceedings.

Hollenbach, David↗
DOE OSTI2025

Time evolution of a pumped molecular magnet—A time-resolved inelastic neutron scattering study

Introducing an experimental technique of time-resolved inelastic neutron scattering (TRINS), we explore the time-dependent effects of resonant pulsed microwaves on the molecular magnet Cr 8 F 8 Piv 16 . The octagonal rings of magnetic Cr 3+ atoms with antiferromagnetic interactions form a singlet ground state with a weakly split triplet of excitations at 0.8 meV. A 4.6 tesla field was applied to tune the splitting between two members of the triplet excited level |1$\rangle$ ↔ |2$\rangle$ to resonance with 105 GHz (0.434 meV) microwaves. The time-dependent occupations of the ground state |0$\rangle$, lower lying levels |1$\rangle$ and |2$\rangle$, and higher energy states |λ ≥ 3$\rangle$ were extracted during and after 20 s long microwave pulses incident along the (101) direction of a Cr 8 F 8 Piv 16 crystal held at 1.9 K. At significantly elevated spin temperatures, we found underpopulation relative to thermal equilibrium of |2$\rangle$ and spin-lattice thermalization time scales ranging from 1.6(2) s to 5.7(2) s depending on the power level. This contrasts with the relaxation time τ 1 (T → 0) = 27(5) 𝛍 s inferred for |2$\rangle$ from in situ Electron Spin Resonance measurements. By probing a broad range of excited states during intense microwave pumping, TRINS thus provides a first view of long lived excited states in a molecular antiferromagnet.

Science & Technology - Other Topics↗
DOE OSTI2025

Using Ultrafast Entangled Photon Correlations to Measure the Temporal Evolution of Optically Excited Molecular Entanglement (Final Technical Report)

The goal of this project is to build an ultrafast entangled photon spectrometer and use it to measure theoretical predictions that photoexcited states are enhanced by spin-photon interactions. Entanglement of two states describes a specific type of quantum superposition in which measuring one state gives information about a second state. While entanglement is well explored for quantum information and computing systems, its effects on photoexcited states are less understood, especially in the ultrafast domains of molecular vibronic coupling. The grant designs a frequency and temporally resolved entangled photon spectrometer and uses it to test theoretical predictions like enhanced two photon absorption, non-reciprocal Fourier relations, and coupling of photons to spin systems. The end goal of the project is an understanding of how, when, and where entanglement is useful for spectroscopy.

47 OTHER INSTRUMENTATION↗