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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2022

Electronic coherences in nonadiabatic molecular photophysics revealed by time-resolved photoelectron spectroscopy

Significance Time-resolved photoelectron spectroscopy (TRPES) is a promising technique for the study of ultrafast molecular processes, such as the nonadiabatic dynamics taking place at conical intersections. Directly accessing the evolution of the coherences generated at the conical intersection should provide most valuable dynamical information. However, the signals are dominated by background contributions due to state populations, and most theoretical treatments completely neglect the role of the coherences. Here we show that distinguishable signatures of molecular coherences appear in TRPES. These can be recorded using currently available ultrashort pulses and unambiguously extracted at the postprocessing stage. The technique thus provides direct access to nonadiabatic coherence dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Spatio-temporal mapping of ablated species in ultrafast laser-produced graphite plasmas

We studied the spatial and temporal distributions of ionic, neutral, and molecular species generated by femtosecond laser produced plasma under varying ambient nitrogen gas pressures. Plasmas were generated by irradiating planar graphite targets using 40 fs pulses of 800 nm radiation from a Ti:Sapphire laser. The results show that in the presence of an ambient gas, the molecular species spatial extension and lifetime are directly correlated to the evolution of excited ions. The present studies also provide valuable insights into the evolution history of various species and their excitation during ultrafast laser ablation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS1986

Protobiological informatoin, bidirectional recognition and reverse translation

Emergence of protobiological information has been suggested by experiments in which heated mixtures of alpha-amino acids order themselves into a self limited array of thermal proteins. The polymers display selective catalytic, hormonal, and other activities. Interactions of varied cationic thermal proteins with polynucleotides indicate selective recognition in both directions. Reverse translation is partly a missing link in the molecular evolution flowsheet. The self ordering of amino acids serves conceptually as a deterministic evolutionary precursor of the modern coding mechanism. The possibility for the evolution of information at an early nontemplated protein stage is supported by findings of electrical signals from proteinoid microspheres prepared with no DNA/RNA in their history. The deposition of thermal copolyamino acids on lipid membranes in the Mueller-Rudin apparatus has here been found to produce electrical behavior like that evoked by bacterial EIM polypeptide. A new procedure is to make a film of membrane on the electrode; the results provide maximal repeatability. The principle of nonrandom biomacromolecular specificity identified by these studies in molecular evolution have been extrapolated to principles of evolution of advanced organisms.

Fox, S. W.↗
DOE OSTI2021

Switchable wetting of oxygen-evolving oxide catalysts

The surface wettability of catalysts is typically controlled via surface treatments that promote catalytic performance. Here we report on potential-regulated hydrophobicity/hydrophilicity at cobalt-based oxide interfaces with an alkaline solution. The switchable wetting of single particles, directly related to their activity and stability towards the oxygen evolution reaction, was revealed by electrochemical liquid-phase transmission electron microscopy. Analysis of the movement of the liquid in real time revealed distinctive wettability behaviour associated with specific potential ranges. At low potentials, an overall reduction of the hydrophobicity of the oxides was probed. Upon reversible reconstruction towards the surface oxyhydroxide phase, electrowetting was found to cause a change in the interfacial capacitance. At high potentials, the evolution of molecular oxygen, confirmed by operando electron energy-loss spectroscopy, was accompanied by a globally thinner liquid layer. This work directly links the physical wetting with the chemical oxygen evolution reaction of single particles, providing fundamental insights into solid–liquid interfacial interactions of oxygen-evolving oxides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness

One of the long-standing holy grails of molecular evolution has been the ability to predict an organism’s fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 β-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of β-lactamase can be directly predicted by thermodynamic folding and binding free energies. We focus upon β-lactamase because of its long history as a model enzyme and its central role in antibiotic resistance. Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. Interestingly, while these techniques also yield sensible double mutant free energies, we show that they do so for the wrong physical reasons. We then go on to assess how well both experimental and computational folding free energies explain single mutant fitness. We find that folding free energies account for, at most, 24% of the variance in β-lactamase fitness values according to linear models and, somewhat surprisingly, complementing folding free energies with computationally-predicted binding free energies of residues near the active site only increases the folding-only figure by a few percent. This strongly suggests that the majority of β-lactamase’s fitness is controlled by factors other than free energies. Overall, our results shed a bright light on to what extent the community is justified in using thermodynamic measures to infer protein fitness as well as how applicable modern computational techniques for predicting free energies will be to the large data sets of multiply-mutated proteins forthcoming.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Formation and Evolution of Metallocene Single-Molecule Circuits with Direct Gold-π Links

Single molecule circuits with group 8 metallocenes are formed without additional linker groups in Scanning Tunnelling Microscope-based break junction (STMBJ) measurements at cryogenic and room temperature conditions with gold (Au) electrodes. We investigate the nature of this direct gold-π binding motif and its affect on molecular conductance and persistence characteristics during junction evolution. The measurement technique under cryogenic conditions tracks molecular plateaus through the full cycle of extension and compression. Analysis reveals that junction persistence when the metal electrodes are pushed together correlates with whether electrodes are locally sharp or blunt, suggesting distinct scenarios for metallocene junction formation and evolution. The top and bottom surfaces of the "barrel" shaped metallocenes present the electron-rich π system of cyclopentadienyl rings which interacts with the gold electrodes in two distinct ways. An undercoordinated gold atom on a sharp tip forms a donor-acceptor bond to a specific carbon atom in the ring. However, a small, flat patch on a dull tip can bind more strongly to the ring as a whole through Van der Waals interactions. Density functional theory (DFT) based calculations of model electrode structures provide an atomic-scale picture of these scenarios, demonstrating the role of these bonding motifs during junction evolution and showing that the conductance is relatively independent of tip atomic-scale structure. Furthermore, the non-specific interaction of the cyclopentadienyl rings with the electrodes enables extended conductance plateaus, a mechanism distinct from that identified for the more commonly studied, rod-shaped organic molecular wires.

25 ENERGY STORAGE↗
DOE OSTI2023

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries.

Choe, Kisurb↗
DOE OSTI2023

Unfaulting mechanisms of interstitial Frank loops in fluorite-structured ThO 2

Unfaulting of Frank loops in irradiated fluorite-structured oxides is of significance for understanding microstructural evolution. However, the mechanisms have not yet been directly observed. To this end, we utilize molecular dynamics to reveal the atomistic details related to the unfaulting process of interstitial Frank loops in ThO 2 , which involve a single pair or multiple pairs of co-propagating Shockley partials to annihilate the stacking faults. Here, we find that the unfaulting is achieved via a synchronous shear of the partial pairs to remove the extrinsic stacking fault in the cation sublattice and the intrinsic stacking fault in the anion sublattice. The high mobility of oxygen at the dislocation core may reduce the activation barriers of dislocation nucleation and migration. These findings provide a fundamental understanding of the transformation of faulted loops in irradiated ThO 2 , and could be transferable to other fluorite-structured oxides.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

In vitro continuous protein evolution empowered by machine learning and automation

Directed evolution has become one of the most successful and powerful tools for protein engineering. However, the efforts required for designing, constructing, and screening a large library of variants can be laborious, time-consuming, and costly. With the recent advent of machine learning (ML) in the directed evolution of proteins, researchers can now evaluate variants in silico and guide a more efficient directed evolution campaign. Furthermore, recent advancements in laboratory automation have enabled the rapid execution of long, complex experiments for high-throughput data acquisition in both industrial and academic settings, thus providing the means to collect a large quantity of data required to develop ML models for protein engineering. In this perspective, here we propose a closed-loop in vitro continuous protein evolution framework that leverages the best of both worlds, ML and automation, and provide a brief overview of the recent developments in the field.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Engineering Enantiocomplementary Protoglobins for Stereoconvergent Construction of N -Alkylated α-Aminoketones

The synthesis of enantiopure compounds from a mixture of E/Z alkenes represents a notable challenge in synthetic chemistry. While enzymes excel in achieving unparalleled selectivity, their inherent specificity often confines activity to a single stereoisomeric substrate, consequently restricting the overall efficiency of such transformations. Here, we demonstrate that protoglobin-derived hemoproteins can catalyze stereoconvergent intermolecular amination using simple N-alkyl hydroxylamines as nitrene precursors, a transformation which remains elusive in synthetic chemistry. These engineered enzymes process E/Z mixtures of silyl enol ethers, enabling the precise incorporation of N-alkyl amino moieties (−NHAlkyl) into diverse molecular structures (up to 79% yield and 95% ee). Two complementary protoglobin variants were engineered using directed evolution to enable enantiodivergent synthesis of both enantiomers of α-aminoketones. This enzymatic platform achieves stereoconvergent and enantiodivergent transformations, facilitating the conversion of simple chemicals into an array of valuable pharmaceutical compounds featuring aminoketone functionalities.

Alcohols↗
DOE OSTI2018

Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function

Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses seven times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2025

Establishing defect-property relationships for 2D-nanomaterials (Final technical report)

Studies of new families of two-dimensional nanomaterials (2DNMs) have established that they possess unique properties that diverge from those of their bulk counterparts. This project aimed to determine how tolerant 2DNMs are to extreme photon and particle fluxes and to identify the mechanisms governing their radiation response. Early work indicated that graphene is not as representative of other 2DNMs as previously assumed; however, the origin of this difference remained unclear. To address these knowledge gaps, this project investigated the physical processes occurring at multiple length scales in transition metal dichalcogenides (TMDs) and quantified their structural stability and property evolution under far-from-equilibrium conditions. In-situ and ex-situ ion and electron irradiations were performed to directly control and monitor defect formation in TMDs. Complementary density functional theory (DFT) and molecular dynamics (MD) simulations were employed to elucidate the mechanisms of defect generation and evolution. The outcomes of this work established mechanistic understanding of irradiation-induced defect formation in 2DNMs, quantified the radiation tolerance of TMDs, and built a fundamental knowledge base for correlating defect structures with material properties. Collectively, these results provide new insights into the stability of low-dimensional materials in extreme environments and enable the predictive design of radiation-tolerant 2DNMs.

2D materials↗
DOE OSTI2023

Dynamic Molecular Investigation of the Solid-Electrolyte Interphase of an Anode-Free Lithium Metal Battery Using In Situ Liquid SIMS and Cryo-TEM

Solid electrolyte interphase (SEI) has been widely perceived to play a critical role in the stable cycling of rechargeable batteries. However, associated with the fragile and air-sensitive nature of the SEI layer, delineation of the formation process and the nature of SEI remains a big challenge. Here, we use in situ liquid time-of-flight secondary ion mass spectroscopy (TOF-SIMS), cryo- transmission electron microscope (TEM) and density functional theory (DFT) calculation to delineate molecular process on the formation of SEI layer under the dynamic operating condition. We discover that the onset potential for SEI layer formation and the thickness of the SEI show dependence on the solvation shell structure. Using LiCoO 2 as a cathode and Cu film as an anode, the SEI is noticed to start to form at around 2.0 V and reach its final thickness (irreversible part, ~ 40-50 nm) at about 3.0 V in the 1 M LiPF 6 –EC/DMC electrolyte, while for the case of 1 M LiFSI–DME, the SEI starts to form at around 1.5 V and reaches its final thickness (~ 20 nm) at about 2.0 V. The in situ TOF-SIMS clearly indicates the outer SEI layer formation and dissipation upon charging and discharging, implying a continued evolution of electrolyte structure with extended cycling. In conclusion, the present work establishes a direct correlation between the molecular signature of SEI layer with solvation feature of electrolytes in lithium batteries, providing insights for tailoring SEI layer toward improved electrochemical properties of lithium batteries.

25 ENERGY STORAGE↗
NASA NTRS2010

Proceedings of the Astrobiology Science Conference 2010. Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond

The Program of the 2010 Astrobiology Science Conference: Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond, included sessions on: 50 Years of Exobiology and Astrobiology: Greatest Hits; Extraterrestrial Molecular Evolution and Pre-Biological Chemistry: From the Interstellar Medium to the Solar System I; Human Exploration, Astronaut Health; Diversity in Astrobiology Research and Education; Titan: Past, Present, and Future; Energy Flow in Microbial Ecosystems; Extraterrestrial Molecular Evolution and Prebiological Chemistry: From the Interstellar Medium to the Solar System II; Astrobiology in Orbit; Astrobiology and Interdisciplinary Communication; Science from Rio Tinto: An Acidic Environment; Can We Rule Out Spontaneous Generation of RNA as the Key Step in the Origin of Life?; How Hellish Was the Hadean Earth?; Results from ASTEP and Other Astrobiology Field Campaigns I; Prebiotic Evolution: From Chemistry to Life I; Adaptation of Life in Hostile Space Environments; Extrasolar Terrestrial Planets I: Formation and Composition; Collaborative Tools and Technology for Astrobiology; Results from ASTEP and Other Astrobiology Field Campaigns II; Prebiotic Evolution: From Chemistry to Life II; Survival, Growth, and Evolution of Microrganisms in Model Extraterrestrial Environments; Extrasolar Terrestrial Planets II: Habitability and Life; Planetary Science Decadal Survey Update; Astrobiology Research Funding; Bioessential Elements Through Space and Time I; State of the Art in Life Detection; Terrestrial Evolution: Implications for the Past, Present, and Future of Life on Earth; Psychrophiles and Polar Environments; Life in Volcanic Environments: On Earth and Beyond; Geochronology and Astrobiology On and Off the Earth; Bioessential Elements Through Space and Time II; Origins and Evolution of Genetic Systems; Evolution of Advanced Life; Water-rich Asteroids and Moons: Composition and Astrobiological Potential; Impact Events and Evolution; A Warm, Wet Mars?; Titan Versus Europa - Potential for Astrobiology; Habitability Potential of Mars; Biosignatures: Tools and Development I; Origins of Molecular Asymmetry, Homochirality, and Life Detection; Deserts and Evaporite Basins and Associated Microbialite Systems; Ancient Life and Synthetic Biology: Crossroad of the Past and Future; Biosignatures: Tools and Development II; Free Oxygen: Proxies, Causes, and Consequences; Life in Modern Microbialite Systems - Function and Adaptation; Hydrothermal Systems and Organosynthesis Processes: Origin and Evolution of Life; Where Should We Go on Mars to Seek Signs of Life?; Search for Intelligent Life I. Innovative SETI Observing Programs and Future Directions; Integrating Astrobiology Research Across and Beyond the Community; Education in Astrobiology in K-12; Search for Intelligent Life II. Global Engagement and Interstellar Message Construction; Poster sessions included: Extraterrestrial Molecular Evolution and Pre-Biological Chemistry; Prebiotic Evolution: From Chemistry to Life; RNA World; Terrestrial Evolution: Implications for the Past, Present, and Future of Life on Earth; Hydrothermal Systems and Organosynthesis Processes: Origin and Evolution of Life; Virology and Astrobiology; Horizontal Genetic Transfer and Properties of Ancestral Organisms; Life in Volcanic Environments: On Earth and Beyond; Impact Events and Evolution; Evolution of Advanced Life; Evolution of Intelligent Life; Education in Astrobiology in K-12; Origins of Molecular Asymmetry, Homochirality, and Life Detection; Astrobiology and Interdisciplinary Communication; Diversity in Astrobiology Research and Education; Integrating Astrobiology Research Across and Beyond the Community; Policy and Societal Issues: Dealing with Potential Bumps in the Astrobiology Road Ahead; Results from ASTEP and Other Astrobiology Field Campaigns; Energy Flow in Microbial Ecosystems; Psychrophiles and Polar Environments; Deserts and Evaporite Basins and Associated Microbialite stems; Life in Modern Microbialite Systems - Function and Adaptation; Free Oxygen: Proxies, Causes, and Consequences; Bioessential Elements Through Space and Time; Water-rich Asteroids and Moons: Composition and Astrobiological Potential; Biosignatures: Tools and Developments; Robotics and Instrumentation for Astrobiology; State of the Art in Life Detection; Astrobiology in Orbit; Survival, Growth, and Evolution of Microrganisms in Model Extraterrestrial Evolution; Search for Intelligent Life; Habitability Potential of Mars; How and Where Should We Seek Signs of Life on Mars?; Titan: Past, Present, and Future; Extrasolar Terrestrial Planets: Formation, Composition, Diversity, Habitability and Life; Human Exploration, Astronaut Health; Science from Rio Tinto: An Acidic Environment and Adaptation of Life in Hostile Space Environments;

Source record↗