SEARCH · Engineering Papers

Results for “molecular evolution”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,459 records · Page 81

All sources NASA NTRS DOE OSTI

DOE OSTI2025

Interpretation of Ion Irradiation and Neutron Irradiation Damage in Additively Manufactured 316 Stainless Steel using Multiscale Modeling

The accelerated adoption of nuclear energy necessitates advanced manufacturing technologies, such as additive manufacturing, to meet heightened supply chain requirements and support innovative reactor technologies. Due to the unique microstructural characteristics of additively manufactured materials under distinct solidification conditions, comprehensive evaluation of their performance in reactor environments is essential. The Advanced Materials and Manufacturing Technologies program under the Department of Energy's Office of Nuclear Energy focuses on understanding the irradiation performance and damage evolution of laser powder bed fusion 316 stainless steel, with an emphasis on integrating ion and neutron irradiation data to accelerate the development and qualification of materials for advanced nuclear reactor applications. While ion irradiation is a cost- and time-effective method, modeling and simulation are required to interpret the data for the broader range of irradiation conditions encountered in advanced reactors. In fiscal year 2025, integrated multiscale modeling and simulations were conducted to assess irradiation damage in additively manufactured 316 stainless steel. Key outcomes include predictions of chromium enrichment at grain boundaries, nickel enrichment at dislocation cell walls and void surfaces, and heterogeneous void evolution under ion and neutron irradiation conditions. Cluster dynamics simulations revealed the coarsening of voids at high irradiation temperatures and the suppression of void growth by high network dislocation density, while also demonstrating significant growth and coarsening of voids and self-interstitial atom loops at low dose rates. Machine learning-accelerated atomistic simulations highlighted the impact of the local environment and chromium concentration on vacancy diffusivity, providing key insights on the influence of composition on void swelling and radiation-induced segregation. Additionally, molecular dynamics simulations demonstrated the presence of defect production bias and a significant effect of carbon content on defect cluster behavior. These combined efforts aim to predict the performance of additively manufactured materials under various reactor conditions, supporting their qualification for nuclear reactor applications by interpreting ion irradiation data. This report underscores the potential of integrated multiscale modeling to analyze ion irradiation data in the effort to accelerate the qualification of additively manufactured materials for nuclear reactor components.

316 stainless steel↗

NASA NTRS1987

Thermal ion complexities observed within the Spacelab 2 bay

Examples of prominent thermal ion composition variations characteristic of the Shuttle environment as observed from within the open cargo bay on the Spacelab 2 mission are discussed. Although the prominent ionization source is the inflow of the ambient plasma, water ions of Shuttle origin were present throughout the mission, and there was evidence for a local source of molecular ions NO(+) and/or O(2+) which also exist in the ionosphere. Bursts in the fluxes of these contaminant species were frequently observed coincident with thruster firings, while O(+) depletions or enhancements could occur depending on the scattering geometry. These effects bring into question whether reliable ambient thermal ion measurements can be made from the vicinity of such vehicles. The presence of significant inflows of contaminant ions into the bay within the Shuttle wake also indicates that Shuttle emissions play a significant role in the evolution of its wake structure.

Grebowsky, J. M.↗

NASA NTRS2018

Coordinated Analysis of Organic Matter in Primitive Meteorites

Carbonaceous chondrites (CC) preserve a diverse range of organic matter formed within cold interstellar environments, the solar nebula, and during subsequent parent body asteroidal processing. This organic matter maintains a unique geochemical and istopic record of organic evolution [1-4]. Bulk studies of organics within CC have revealed a complex array of organic species. However, bulk studies invariably involve solvent extraction, resulting in a loss of spatial context of the host mineral matrix [3, 5]. Correlated in situ chemical and isotopic studies suggest preservation of interstellar organics in the form of spherical, often hollow, micrometer sized organic nano-globules. Nanoglobules often exhibit significant delta 15N and delta D enrichments that imply formation through fractionation of ion-molecule reactions within cold molecular clouds and/or the outer protoplanetary disk [5]. In situ studies such as 6-8 are necessary to understand the organic evolutionary stages of nanoglobules and other components in the nebula and parent body [7]. We carried out coordinated in situ micrometer-scale chemical, mineralogical and isotopic studies of the Murchison (CM2), QUE 99177 (CR3), and Tagish Lake (C2 Ung) CC. These studies were performed using fluorescent microscopy, two-step laser mass spectrometry (microL2MS), NanoSIMS, and Scanning Electron Microscopy (SEM) with Energy Dispersive X-Ray Spectroscopy (EDX). Comparative analysis of three different meteorites will help reveal the effects of parent body processes on the chemistry and isotopic composition of organic matter.

meteorites↗

NASA NTRS2010

The Origins and Evolution of Molecules in Icy Solids

Astronomical observations of the past few decades have revealed the existence of a variety of molecules in extraterrestrial ices. These molecules include H2O, CO, and CO2, and organics such as CH4, CH30H, and C2H6. Some ices are dominated by polar molecules, while non-polar species appear to dominate others. Observations, mainly in the radio and IR regions, have allowed the inference of other solid-phase molecules whose formation remains difficult to explain by gas-phase chemistry alone. Several laboratory research groups have reported on extensive experiments on the solid-phase reaction chemistry of icy materials, generally as initiated by either ionizing radiation or vacuum-UV photons. These experiments not only permit molecular identifications to be made from astronomical observations, but also allow predictions of yet unidentified molecules. This laboratory approach has evolved over more than 30 years with much of the earliest work focusing on complex mixtures thought to represent either cometary or interstellar ices. Although those early experiments documented a rich solid-state photo- and radiation chemistry, they revealed few details of reactions for particular molecules, partly due to the multi-component nature of the samples. Since then, model systems have been examined that allow the chemistry of individual species and specific reactions to be probed. Reactions involving most of the smaller astronomical molecules have now been studied and specific processes identified. Current laboratory work suggests that a variety of reactions occur in extraterrestrial ices, including acid-base processes, radical dimerizations, proton transfers, oxidations, reductions, and isomerizations. This workshop presentation will focus on chemical reactions relevant to solar system and interstellar ices. While most of the work will be drawn from that to which the speaker has contributed, results from other laboratories also will be included. Suggestions for future studies will be made, with an emphasis on some present deficiencies. The speaker's work has been generously supported by these NASA research programs: Cassini Data Analysis, Exobiology, Mars Fundamental Research, Outer Planets Research, Planetary Atmospheres, Planetary Geology and Geophysics, and the NASA Astrobiology Institute.

Hudson, Reggie L.↗

DOE OSTI2021

Tandem synthesis of tetrahydroquinolines and identification of the reaction network by operando NMR

The study of the reaction mechanism and complex network for heterogeneously catalyzed tandem reactions is challenging but can guide reaction design and optimization. Here, we describe a case study using bifunctional metal–organic framework supported Pd nanoparticles (Pd/UiO-66(HCl)) for the one-pot tandem synthesis of substituted tetrahydroquinolines via the Claisen–Schmidt condensation and reductive intramolecular cyclization. The directly observed evolution of intermediates and products, including reactive species containing hydroxylamine group and unstable intermediate 2-phenyl-3,4-dihydroquinoline, was enabled by operando magic angle spinning nuclear magnetic resonance studies under 50 bar H 2 . The reaction network of the tandem reaction is deduced based on reaction kinetic information obtained from the operando study. The optimized procedure was applied to various acetophenone and nitrobenzaldehyde derivatives carrying different functional groups, and eight valuable substituted tetrahydroquinolines were obtained in moderate to good yields. This work provides a molecular-level understanding of the catalytic system and brings up new opportunities for efficient and sustainable synthesis of medicinally relevant building blocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Nickel(ii) complexes based on dithiolate–polyamine binary ligand systems: crystal structures, hirshfeld surface analysis, theoretical study, and catalytic activity study on photocatalytic hydrogen generation

To ascertain the influence of binary ligand systems [1,1-dicyanoethylene-2,2-dithiolate (i-mnt -2 ) and polyamine {tetraen = tris(2-aminoethyl)amine, tren = diethylene triamine and opda = o-phenylenediamine}] on the coordination modes of the Ni(II) metal center and resulting supramolecular architectures, a series of nickel(II) thiolate complexes [Ni(tetraen)(i-mnt)](DMSO) (1), [Ni 2 (tren) 2 (i-mnt) 2 ] (2), and [Ni 2 (i-mnt) 2 (opda) 2 ] n (3) have been synthesized in high yield in one step in water and structurally characterized by single crystal X-ray crystallography and spectroscopic techniques. X-ray diffraction studies disclose the diverse i-mnt -2 coordination to the Ni +2 center in the presence of active polyamine ligands, forming a slightly distorted octahedral geometry (NiN 4 S 2 ) in 1, square planar (NiS 4 ) and distorted octahedral geometries (NiN 6 ) in the bimetallic co-crystallized aggregate of cationic [Ni(tren) 2 ] +2 and anionic [Ni(i-mnt) 2 ] -2 in 2, and a one dimensional (1D) polymeric chain along the [100] axis in 3, having consecutive square planar (NiS 4 ) and octahedral (NiN 6 ) coordination kernels. The N–H···O, N–H···S, N–H···N, N–H···S, N–H···N, and N–H···O type hydrogen bonds stabilize the supramolecular assemblies in 1, 2, and 3 respectively imparting interesting graph-set-motifs. The molecular Hirshfeld surface analyses (HS) and 2D fingerprint plots were utilized for decoding all types of non-covalent contacts in the crystal networks. Atomic HS analysis of the Ni +2 centers reveals significant Ni–N metal–ligand interactions compared to Ni–S interactions. We have also studied the unorthodox interactions observed in the solid state structures of 1–3 by QTAIM and NBO analyses. Moreover, all the complexes proved to be highly active water reduction co-catalysts (WRC) in a photo-catalytic hydrogen evolution process involving iridium photosensitizers, wherein 2 and 3 having a square planar arrangement around the nickel center(s) – were found to be the most active ones, achieving 1000 and 1119 turnover numbers (TON), respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Hadronic resonance production and interaction in p-Pb collisions at LHC energies in EPOS3

Using the EPOS3 model with the Ultrarelativistic Quantum Molecular Dynamics (UrQMD) model to describe the hadronic phase, we study the production of short-lived hadronic resonances and the modification of their yields and p T spectra in p-Pb collisions at √sNN= 5.02 TeV. High-multiplicity p-Pb collisions exhibit similar behavior to midperipheral Pb-Pb collisions at LHC energies, and we find indications of a short-lived hadronic phase in p-Pb collisions that can modify resonance yields and p T spectra through scattering processes. The evolution of resonance production is investigated as a function of the system size, which is related to the lifetime of the hadronic phase in order to study the onset and evolution of scattering effects in p-Pb collisions. We also study hadron production separately in the core and corona parts of these collisions and explore how this division affects the total particle yields as the system size increases.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model

Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. Here, we report a generative model that predicts protein designs to meet complex nonlinear mechanical property-design objectives. Our model leverages deep knowledge on protein sequences from a pretrained protein language model and maps mechanical unfolding responses to create proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are de novo, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, using mechanical features as the target to enable the discovery of protein materials with superior mechanical properties.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1991

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

Rein, Robert↗

NASA NTRS1990

Toward applied behavior analysis of life aloft

This article deals with systems at multiple levels, at least from cell to organization. It also deals with learning, decision making, and other behavior at multiple levels. Technological development of a human behavioral ecosystem appropriate to space environments requires an analytic and synthetic orientation, explicitly experimental in nature, dictated by scientific and pragmatic considerations, and closely approximating procedures of established effectiveness in other areas of natural science. The conceptual basis of such an approach has its roots in environmentalism which has two main features: (1) knowledge comes from experience rather than from innate ideas, divine revelation, or other obscure sources; and (2) action is governed by consequences rather than by instinct, reason, will, beliefs, attitudes or even the currently fashionable cognitions. Without an experimentally derived data base founded upon such a functional analysis of human behavior, the overgenerality of "ecological systems" approaches render them incapable of ensuring the successful establishment of enduring space habitats. Without an experimentally derived function account of individual behavioral variability, a natural science of behavior cannot exist. And without a natural science of behavior, the social sciences will necessarily remain in their current status as disciplines of less than optimal precision or utility. Such a functional analysis of human performance should provide an operational account of behavior change in a manner similar to the way in which Darwin's approach to natural selection accounted for the evolution of phylogenetic lines (i.e., in descriptive, nonteleological terms). Similarly, as Darwin's account has subsequently been shown to be consonant with information obtained at the cellular level, so too should behavior principles ultimately prove to be in accord with an account of ontogenetic adaptation at a biochemical level. It would thus seem obvious that the most productive conceptual and methodological approaches to long-term research investments focused upon human behavior in space environments will require multidisciplinary inputs from such wide-ranging fields as molecular biology, environmental physiology, behavioral biology, architecture, sociology, and political science, among others.

Review↗

NASA NTRS2017

Organics and Ices in the Outer Solar System: Connections to the Interstellar Medium

The solar nebula, that aggregate of gas and dust that formed the birthplace of the Sun, planets and plethora of small bodies comprising the Solar System, originated in a molecular cloud that is thought to have spawned numerous additional stars, some with their own planets and attendant small bodies. The question of the chemical and physical reprocessing of the original interstellar materials in the solar nebula has challenged both theory and observations. The acquisition and analysis of samples of comet and asteroid solids, and a growing suite of in-situ and close-up analyses of relatively unaltered small Solar System bodies now adds critical new dimensions to the study of the origin and evolution of the early solar nebula. Better understanding the original composition of the material from which our solar nebula formed, and the processing that material experienced, will aid in formulations of chemistry that might occur in other solar systems. While we seek to understand the compositional history of planetary bodies in our own Solar System, we will inevitably learn more about the materials that comprise exoplanets and their surrounding systems.

SOLAR NEBULA↗

DOE OSTI2024

Pd-Ru pair on Pt surface for promoting hydrogen oxidation and evolution in alkaline media

Hydrogen oxidation reaction in alkaline media is critical for alkaline fuel cells and electrochemical ammonia compressors. The slow hydrogen oxidation reaction in alkaline electrolytes requires large amounts of scarce and expensive platinum catalysts. While transition metal decoration can enhance Pt catalysts’ activity, it often reduces the electrochemical active surface area, limiting the improvement in Pt mass activity. Here, we enhance Pt catalysts’ activity without losing surface-active sites by using a Pd-Ru pair. Utilizing a mildly catalytic thermal pyrolysis approach, Pd-Ru pairs are decorated on Pt, confirmed by extended X-ray absorption fine structure and high-angle annular dark-field scanning transmission electron microscopy. Density functional theory and ab-initio molecular dynamics simulations indicate preferred Pd and Ru dopant adsorption. The Pd-Ru decorated Pt catalyst exhibits a mass-based exchange current density of 1557 ± 85 A g –1 metal for hydrogen oxidation reaction, demonstrating superior performance in an ammonia compressor.

25 ENERGY STORAGE↗

DOE OSTI2025

Evolution of surface morphology from Stranski–Krastanov growth mode to step-flow growth mode in InSbBi thin films

The incorporation of dilute concentrations of bismuth (Bi) into traditional III–V alloys leads to a significant reduction in bandgap energy, making InSbBi a promising candidate for long-wavelength (<0.17 eV) infrared photosensors. InSbBi offers potential as a platform for exploring spin dynamics and quantum phenomena due to its strong spin–orbit coupling. Despite this promise, the material quality of InSbBi alloys remains inferior to that of conventional III–V semiconductors, primarily due to the substantial challenges associated with incorporating Bi into InSb and producing high-quality InSbBi with varying Bi compositions. In this study, we address these issues by developing a molecular beam epitaxy approach to grow smooth InSbBi thin films with tunable Bi incorporation up to 1.8% of the group V sublattice, through dynamic adjustment of Sb flux and careful control of the interplay between growth temperature and the Bi flux. In conclusion, this work paves way for the development of high-quality InSbBi thin films for applications in photodetection, spintronics, and related quantum technologies.

Edirisinghe, Chandima Kasun [Univ. of Tennessee, K↗

NASA NTRS2019

Laboratory Astrophysics Studies of the Evolution of Organic Matter with the COSmIC Facility.

Understanding the origin of organic matter in astrophysical environments ranging from circumstellar (CS) outflows to diffuse and dense interstellar (IS) clouds to protoplanetary disks and planetary bodies has become a central objective in astrophysics. Experimental facilities dedicated to the formation and characterization of laboratory analogs generated under conditions relevant to the targeted environments have been developed in the past recent years. Recent advances achieved in laboratory astrophysics using COSmIC’s laboratory data in synergy with observational data will be presented. These results include the use of laboratory spectra to search for IS organic molecules and ions in astronomical spectra, the formation of laboratory analogs of CS and IS dust grains and planetary atmospheres aerosols from molecular precursors.

Salama, Farid↗

DOE OSTI2020

Leveraging computational genomics to understand the molecular basis of metal homeostasis

Genome-based data is helping to reveal the diverse strategies plants and algae use to maintain metal homeostasis. In addition to acquisition, distribution and storage of metals, acclimating to feast or famine can involve a wealth of genes that we are just now starting to understand. The fast-paced acquisition of genome-based data, however, is far outpacing our ability to experimentally characterize protein function. Computational genomic approaches are needed to fill the gap between what is known and unknown. To avoid misconstruing bioinformatically derived data, which is the root cause of the inaccurate functional annotations that plague databases, functional inferences from diverse sources and contextualization of that evidence with a robust understanding of protein family evolution is needed. Phylogenomic- and comparative-genomic-based studies can aid in the interpretation of experimental data or provide a spark for the discovery of a new function. These analyses not only lead to novel insight into a target protein's function but can generate thought-provoking insights across protein families.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Intermetallic phase formation in Al-Si-Zr alloys during hot isostatic pressing revealed by experiments and molecular dynamics

Understanding phase transformations at alloy interfaces is critical for the design of advanced structural materials. Here, in this study, we investigate the formation mechanisms of the Al 2 SiZr intermetallic phase in the Al-Si-Zr system under hot isostatic pressing (HIP) using molecular dynamics (MD) simulations and thermodynamic analysis. A unique aspect of our approach in MD involves the replacement of a disordered Al 2 SiZr stoichiometry with an ordered phase at the Al-Zr interface once HIP results in the desired Al 2 SiZr stoichiometry, allowing us to compute the total energetic cost of transformation by accounting for both formation energies and diffusion barriers. Diffusion coefficients and activation energies, extracted across a range of temperatures, reveal that HIP substantially enhances atomic mobility, creating favorable stoichiometry for phase evolution. Our results show that Al 2 SiZr phase formation is kinetically unfavorable at lower temperatures but becomes feasible when the thermodynamic driving energy surpass a critical energy threshold.

Roy, Ankit [Pacific Northwest National Laboratory ↗

DOE OSTI2022

Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen

While most productivity on the surface of the Earth today is fueled by oxygenic photosynthesis, for much of Earth history it is thought that anoxygenic photosynthesis—using compounds like ferrous iron or sulfide as electron donors—drove most global carbon fixation. Anoxygenic photosynthesis is still performed by diverse bacteria in niche environments today. Of these, the Chlorobi (formerly green sulfur bacteria) are often interpreted as being particularly ancient and are frequently proposed to have fueled the biosphere during late Archean and early Paleoproterozoic time before the rise of oxygenic photosynthesis. Here, we perform comparative genomic, phylogenetic, and molecular clock analyses to determine the antiquity of the Chlorobi and their characteristic phenotypes. We show that contrary to common assumptions, the Chlorobi clade is relatively young, with anoxygenic phototrophy, carbon fixation via the rTCA pathway, and iron oxidation all significantly postdating the rise of oxygen ~2.3 billion years ago. The Chlorobi therefore could not have fueled the Archean biosphere, but instead represent a relatively young radiation of organisms which likely acquired the capacity for anoxygenic photosynthesis and other traits via horizontal gene transfer sometime after the evolution of oxygenic Cyanobacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Enabling Efficient Water Splitting with Advanced Materials Designed for High pH Membrane Interface

This project was focused on developing the durable, high-performance materials and interfaces for advanced water splitting, enabling a clear pathway for achieving <$2/Kg H2 (on scale) with efficiency of 43 kWh/kg H 2 via anion exchange membrane (AEM)-based electrolysis. We aimed to advance these final goals via an improved fundamental understanding of both hydrogen and oxygen evolution reactions (HER/OER) leading to novel platinum group metal (PGM)-free catalyst materials in conjunction with critical improvements in membrane and ionomers and gas evolution electrodes with corresponding characterization and testing. Northeastern University (NU) lead this effort focusing on catalyst development and characterization (both in situ and ex situ) while project partners lead improvements in ionomer and membrane materials and will aid in the development of specialized electrode and membrane electrode assemblies. In addition, close collaboration occured with the HydroGEN Energy Materials Network (EMN) National Laboratory consortium including efforts related to use of advanced ionomers, durability protocols and validation of electrolyzer materials (e.g. NREL), multiscale modeling and computation (e.g. LBNL), and molecular dynamics (MD) simulations of the membrane catalyst interface (e.g. SNL). The interactions with HydroGEN included exchange of data and materials as needed to facilitate project success.

08 HYDROGEN↗