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Results for “Directed 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.

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

Kinetic dissection of individual steps in the poly(C)-directed oligoguanylate synthesis from guanosine 5'-monophosphate 2-methylimidazolide

A kinetic study of oligoguanylate synthesis on a polycytidylate template, poly(C), as a function of the concentration of the activated monomer, guanosine 5'-monophosphate 2-methylimidazolide, 2-MeImpG, is reported. Reactions were run with 0.005-0.045 M 2-MeImpG in the presence of 0.05 M poly(C) at 23 degrees C. The kinetic results are consistent with a reaction scheme (eq 1) that consists of a series of consecutive steps, each step representing the addition of one molecule of 2-MeImpG to the growing oligomer. This scheme allows the calculation of second-order rate constants for every step by analyzing the time-dependent growth of each oligomer. Computer simulations of the course of reaction based on the determined rate constants and eq 1 are in excellent agreement with the product distributions seen in the HPLC profiles. In accord with an earlier study (Fakhrai, H.; Inoue, T.; Orgel, L. E. Tetrahedron 1984, 40, 39), rate constants, ki, for the formation of the tetramer and longer oligomers up to the 16-mer were found to be independent of length and somewhat higher than k3 (formation of trimer), which in turn is much higher than k2 (formation of dimer). The ki (i > or = 4), k3, and k2 values are not true second-order rate constants but vary with monomer concentration. Mechanistic models for the dimerization (Scheme I) and elongation reactions (Scheme II) are proposed that are consistent with our results. These models take into account that the monomer associates with the template in a cooperative manner. Our kinetic analysis allowed the determination of rate constants for the elementary processes of covalent bond formation between two monomers (dimerization) and between an oligomer and a monomer (elongation) on the template. A major conclusion from our study is that bond formation between two monomer units or between a primer and a monomer is assisted by the presence of additional next-neighbor monomer units. This is consistent with recent findings with hairpin oligonucleotides (Wu, T.; Orgel, L. E. J. Am. Chem. Soc. 1992, 114, 317). Our study is the first of its kind that shows the feasibility of a thorough kinetic analysis of a template-directed oligomerization and provides a detailed mechanistic model of these reactions.

Non-NASA Center↗
NASA NTRS1995

Affinity of guanosine derivatives for polycytidylate revisited

Evidence is presented for complexation of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) with polycytidylate (poly(C)) at pH 8.0 and 23 degrees C in the presence of 1.0 M NaCl2 and 0.2 M MgCl2 in water. The association of 2-MeImpG with poly(C) was investigated using UV-vis spectroscopy as well as by monitoring the kinetics of the nucleophilic substitution reaction of the imidazole moiety by amines. The results of both methods are consistent with moderately strong poly(C) 2-MeImpG complexation and the spectrophotometric measurements allowed the construction of a binding isotherm with a concentration of 2-MeImpG equal to 5.55 +/- 0.15 mM at half occupancy. UV spectroscopy was employed to establish the binding of other guanosine derivatives on poly(C). These derivatives are guanosine 5'-monophosphate (5'GMP), guanosine 5'-monophosphate imidazolide (ImpG), and guanosine 5'-monophosphate morpholidate (morpG). Within experimental error these guanosine derivatives exhibit the same affinity for poly(C) as 2-MeImpG.

Non-NASA Center↗
NASA NTRS1993

Climbing Darwin's ladder

The work of Bartel and Szostak, in which RNA molecules were selected to enhance the ability to catalyze a reaction similar to a step in protein-catalyzed RNA replication, is discussed. An important aspect of this experiment was the ability to reach a high level of functional organization in ten evolutionary steps. Further steps necessary to obtain an RNA enzyme with RNA replicase activity include performing the reaction with mononucleoside 5'-triphosphates, generalizing the reaction to include a variety of sequences without loss of template-dependent specificity, and overcoming template self-structure that could prevent some regions from being copied efficiently.

NASA Discipline Exobiology↗
NASA NTRS1992

Nonenzymatic template-directed synthesis on hairpin oligonucleotides. 2. Templates containing cytidine and guanosine residues

We have prepared hairpin oligonucleotides in which a 5'-terminal single-stranded segment contains cytidylate (C) and guanylate (G) residues. When these hairpin substrates are incubated with a mixture of cytidine 5'-phosphoro(2-methly)imidazolide (2-MeImpC) and guanosine 5'-phosphoro(2-methyl)imidazolide (2-MeImpG), the 5'-terminal segment acts as a template to facilitate sequence-specific addition of G and C residues to the 3'-terminus of the hairpin. If an isolated G residue is present at the 3'-end of the template strand, it is copied regiospecifically in the presence of 2-MeImpC and 2-MeImpG to give a product containing an isolated C residue linked to its G neighbors by 3'-5'-internucleotide bonds. However, if only 2-MeImpC is present in the reaction mixture, very little reaction occurs. Thus, the presence of 2-MeImpG catalyzes the incorporation of C. If the template strand contains a short sequence of G residues, it is copied in the presence of a mixture of 2-MeImpC and 2-MeImpG. If only 2-MeImpC is present in the reaction mixture, efficient synthesis occurs to give a final product containing one fewer C residue than the number of G residues in the template.

NASA Program Exobiology↗
DOE OSTI2020

Spatially Offset Femtosecond Stimulated Raman Spectroscopy: Observing Exciton Transport through a Vibrational Lens

To design better molecular electronic devices, we need a strong understanding of how charges or excitons propagate, as many efficiency losses arise during transport. Exciton transport has been difficult to study because excitons tend to be short-lived, have short diffusion lengths, and can easily recombine. Here, we debut spatially offset femtosecond stimulated Raman spectroscopy (SO-FSRS), a three-pulse ultrafast microscopy technique. By offsetting the photoexcitation beam, we can monitor Raman spectral changes as a function of both time and position. We used SO-FSRS on 6,13-bis(triisopropylsilylethynyl) pentacene, a well-studied organic semiconductor used in photovoltaics and field-effect transistors. Furthermore, we demonstrated that the fast exciton and free charge carrier transport axes are identical and observed that exciton transport is less anisotropic by a factor of ~3. SO-FSRS is the first technique that directly tracks molecular structural evolution during exciton transport, which can provide roadmaps for tailor-making molecules for specific electronic devices.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

In-situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries

Dynamic molecular evolution at solid/liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe/observe the solid/liquid interface under reaction conditions, which in essence appears to be similarly true for all the fields involving solid/liquid phases, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization, We use in-situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid electrode/liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to deplete the salt anion and with low concentration of Li+ ions, which essentially leads to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributes to the overpotential of the cell. This unprecedented molecular level dynamic observation at the solid electrode/liquid electrolyte interface provides vital chemical information that is needed for designing of better battery chemistry for enhanced performance, and ultimately opens new avenues for using liquid SIMS to probe molecular evolution at solid/liquid interface in general.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2022

Seeing structural evolution of organic molecular nano-crystallites using 4D scanning confocal electron diffraction (4D-SCED)

Abstract Direct observation of organic molecular nanocrystals and their evolution using electron microscopy is extremely challenging, due to their radiation sensitivity and complex structure. Here, we introduce 4D-scanning confocal electron diffraction (4D-SCED), which enables direct in situ observation of bulk heterojunction (BHJ) thin films. 4D-SCED combines confocal electron optic setup with a pixelated detector to record focused spot-like diffraction patterns with high angular resolution, using an order of magnitude lower dose than previous methods. We apply it to study an active layer in organic solar cells, namely DRCN5T:PC 71 BM BHJ thin films. Structural details of DRCN5T nano-crystallites oriented both in- and out-of-plane are imaged at ~5 nm resolution and dose budget of ~5 e − /Å 2 . We use in situ annealing to observe the growth of the donor crystals, evolution of the crystal orientation, and progressive enrichment of PC 71 BM at interfaces. This highly dose-efficient method opens more possibilities for studying beam sensitive soft materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2004

Evolutionary Models of Cold, Magnetized, Interstellar Clouds

We modeled the long-term and small-scale evolution of molecular clouds using direct 2D and 3D magnetohydrodynamic (MHD) simulations. This work followed up on previous research by our group under auspices of the ATP in which we studied the energetics of turbulent, magnetized clouds and their internal structure on intermediate scales. Our new work focused on both global and smallscale aspects of the evolution of turbulent, magnetized clouds, and in particular studied the response of turbulent proto-cloud material to passage through the Galactic spiral potential, and the dynamical collapse of turbulent, magnetized (supercritical) clouds into fragments to initiate the formation of a stellar cluster. Technical advances under this program include developing an adaptive-mesh MHD code as a successor to ZEUS (ATHENA) in order to follow cloud fragmentation, developing a shearing-sheet MHD code which includes self-gravity and externally-imposed gravity to follow the evolution of clouds in the Galactic potential, and developing radiative transfer models to evaluate the internal ionization of clumpy clouds exposed to external photoionizing UV and CR radiation. Gammie's work at UIUC focused on the radiative transfer aspects of this program.

Gammie, Charles F.↗
DOE OSTI2025

Best of both worlds: Enforcing detailed balance in machine learning models of transition rates

The slow microstructural evolution of materials often plays a key role in determining material properties. When the unit steps of the evolution process are slow, direct simulation approaches such as molecular dynamics become prohibitive and Kinetic Monte-Carlo (kMC) algorithms, where the state-to-state evolution of the system is represented in terms of a continuous-time Markov chain, are instead frequently relied upon to efficiently predict long-time evolution. The accuracy of kMC simulations however relies on the complete and accurate knowledge of reaction pathways and corresponding kinetics. This requirement becomes extremely stringent in complex systems such as concentrated alloys where the astronomical number of local atomic configurations makes the a priori tabulation of all possible transitions impractical. Machine learning models of transition kinetics have been used to mitigate this problem by enabling the efficient on-the-fly prediction of kinetic parameters. While conventional KMC methods based on transition state theory naturally yield reversible dynamics that exactly obey the detailed balance criterion, providing strong guarantees on the properties of the stationary distribution, many recently-proposed ML-based approaches to barrier predictions provide no such guarantees. In this study, we derive conditions under which physics-informed ML architectures exactly enforce the detailed balance condition by construction, even when relying on non-extensive descriptions of states in terms of local environments around mobile defects. In conclusion, using the diffusion of a vacancy in a concentrated alloy as an example, we show that such ML architectures also exhibit superior performance in terms of prediction accuracy, demonstrating that the imposition of physical constraints can facilitate the accurate learning of barriers at no increase in computational cost.

36 MATERIALS SCIENCE↗
NASA NTRS2000

In vitro evolution of a ribozyme that contains 5-bromouridine

The Tetrahymena group I ribozyme was modified by replacing all 99 component uridine residues with 5-bromouridine. This resulted in a 13-fold reduction in catalytic efficiency in the RNA-catalyzed phosphoester-transfer reaction compared to the behavior of the unmodified ribozyme. A population of 10(13) variant ribozymes was constructed, each containing 5-bromouridine in place of uridine. Five successive 'generations' of in vitro evolution were carried out, selecting for improved phosphoester transferase activity. The evolved molecules exhibited a 27-fold increase in catalytic efficiency compared to the wild-type bromouridine-containing ribozyme, even exceeding that of the wild-type ribozyme in the non-brominated form. Three specific mutations were found to be responsible for this altered behavior. These mutations enhanced activity in the context of 5-bromouridine, but were detrimental in the context of unmodified uridine. The evolved RNAs not only tolerated but came to exploit the presence of the nucleotide analogue in carrying out their catalytic function.

NASA Discipline Exobiology↗
DOE OSTI2016

The formation and dynamical evolution of young star clusters

Recent observations have revealed a variety of young star clusters, including embedded systems, young massive clusters, and associations. We study the formation and dynamical evolution of these clusters using a combination of simulations and theoretical models. Our simulations start with a turbulent molecular cloud that collapses under its own gravity. The stars are assumed to form in the densest regions in the collapsing cloud after an initial free-fall time of the molecular cloud. The dynamical evolution of these stellar distributions is continued by means of direct N-body simulations. The molecular clouds typical of the Milky Way Galaxy tend to form embedded clusters that evolve to resemble open clusters. The associations were initially considerably more clumpy, but they lost their irregularity in about a dynamical timescale, due to the relaxation process. The densest molecular clouds, which are absent in the Milky Way but are typical in starburst galaxies, form massive, young star clusters. They indeed are rare in the Milky Way. Our models indicate a distinct evolutionary path from molecular clouds to open clusters and associations or to massive star clusters. The mass–radius relation for both types of evolutionary tracks excellently matches the observations. According to our calculations, the time evolution of the half-mass–radius relation for open clusters and associations follows r{sub h}/pc=2.7(t{sub age}/pc){sup 2/3}, whereas for massive star clusters r{sub h}/pc=0.34(t{sub age}/Myr){sup 2/3}. Both trends are consistent with the observed age–mass–radius relation for clusters in the Milky Way.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Time Dependent Structural Evolution of Porous Organic Cage CC3

Porous organic cage compounds are emerged with remarkable structural diversity and functionality that have applications in gas separation, catalysis and energy storage. Fundamental understanding of nucleation and growth of such materials have significant implications for understanding molecularly directed self-assembly phenomena. Herein we followed the structural evolution of a prototypical type of porous organic cage, CC3 as a function of synthesis time. Three distinctive crystal formation stages were identified: at short synthesis times, a rapid crystal growth stage in which amorphous agglomerates transformed into larger irregular particles was observed. At intermediate synthesis times, a decrease in crystal size over time was observed presumably due to crystal fragmentation, redissolution and/or homogeneous nucleation led. Finally, at longer synthesis times, a regrowth process was observed in which particles coalesced through Ostwald ripening leading to a continuous increase in crystal size. Molecular simulation studies, based on the construction of in silico CC3 models and simulation of XRD patterns and nitrogen isotherms, confirm the samples at different synthesis times to be a mixture of CC3α and CC3 amorphous phases. The CC3α phase is found to contract at different synthesis times, and the amorphous phase is found to essentially disappear at the longest synthesis time. Nitrogen and carbon dioxide adsorption properties of these CC3 phases were evaluated, and were highly dependent on synthesis time.

Growth↗
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↗
DOE OSTI2019

Direct dioxygen evolution in collisions of carbon dioxide with surfaces

The intramolecular conversion of CO 2 to molecular oxygen is an exotic reaction, rarely observed even with extreme optical or electronic excitation means. Here we show that this reaction occurs readily when CO 2 ions scatter from solid surfaces in a two-step sequential collision process at hyperthermal incidence energies. The produced O 2 is preferentially ionized by charge transfer from the surface over the predominant atomic oxygen product, leading to direct detection of both O 2 + and O 2 - . First-principles simulations of the collisional dynamics reveal that O 2 production proceeds via strongly-bent CO 2 configurations, without visiting other intermediates. Bent CO 2 provides dynamic access to the symmetric dissociation of CO2 to C+O2 with a calculated yield of 1 to 2% depending on molecular orientation. This unexpected collision-induced transformation of individual CO 2 molecules provides an accessible pathway for generating O 2 in astrophysical environments and may inspire plasmadriven electro- and photo-catalytic strategies for terrestrial CO 2 reduction.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1987

Non-enzymatic transcription of an oligodeoxynucleotide 14 residues long

Nonenzymatic synthesis of oligodeoxynucleotides up to 14 residues long from 2-MeImpG and 2-MeImpC mononucleotides was demonstrated. The synthesis is primed by 14-mer and 15-mer oligonucleotides d(C3GC3GC3GC2) and d(C3GC3GC3GC3) as templates. The predominant products are a series of 3-prime-5-prime-linked oligonucleotides, complementary to the template, ranging in length from GGC to GGCGGGCGGGCGGG. The 15-mer template directed the synthesis of the same family of products that were formed on the 14-mer template. This finding is explained by the preferential conversion of the dimer GG to GGC rather than to GGG. In the context of molecular evolution, these results suggest that the detailed kinetics of template-directed synthesis could form the basis for the selection of one replicating oligonucleotide from a family of closely related oligonucleotides.

Acevedo, Oscar L.↗
DOE OSTI2025

Crossing the Oxo‐Peroxo Wall for Selective Electrochemical Epoxidation

Electrochemical oxidation in water requires the formation of reactive oxygen species to be able to oxidize unsaturated hydrocarbons to epoxides, aldehydes, and ketones. These reactions, broadly classified as alternative oxidation reactions (AOR), directly compete with the prevalent oxygen evolution reaction (OER). In molecular catalysis, the Oxo-Wall dictates a transition from a stable oxo intermediate (OER active) to a meta-stable metal-oxo (OER inactive) generally occurs. In this work on heterogeneous catalysis, the same Oxo-Wall applies, however, a meta-stable oxo preferentially coordinates with lattice oxygen to form a more stable surface peroxo intermediate. A universal free energy onset of this process is identified at 3.39 eV under electrochemical activation in water and show that it is completely decoupled from the OER oxo species. Such decoupling gives rise to a new region of oxygen reactivity relevant for AOR where a selective oxidation of the unsaturated C-C bonds is predicted to occur instead of OER. A distinct AOR overpotential volcano is constructed and identify recently reported electrocatalysts, including palladium-platinum for propylene epoxidation and silver-nickel for ethylene epoxidation, along with others such as TiO 2 and CuO. Broader implications and limitations of electrochemical AOR are discussed, highlighting their potential to enable electrochemically enhanced thermal catalysis.

Electrocatalysis↗
DOE OSTI2015

Long Duration Directional Drives for Star Formation and Photoionization

This research will; confirm the possibility of studying the structure and evolution of star-forming regions of molecular clouds in the laboratory; test the cometary model for the formation of the pillar structures in molecular clouds; assess the effect of magnetic fields on the evolution of structures in molecular clouds; and develop and demonstrate a new, long-duration (60-100 ns), directional source of x-ray radiation that can be used for the study of deeply nonlinear hydrodynamics, hydrodynamic instabilities that occur in the presence of directional radiation, shock-driven and radiatively-driven collapse of dense cores, and photoionization. Due to the iconic status of the pillars of the Eagle Nebula, this research will bring popular attention to plasma physics, HED laboratory physics, and fundamental science at NIF and other experimental facilities. The result will be to both to bring new perspectives to the studies of hydrodynamics in inertial confinement fusion and HED scenarios in general, and to promote interest in the STEM disciplines.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗