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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 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

System, method, and computer-accessible medium for remote sensing of the electrical distribution grid with hypertemporal imaging

An exemplary system, method, and computer-accessible medium for determining a property(ies) regarding an electrical grid(s) can be provided, which can include, for example, receiving a video(s) of the electrical grid(s), determining a flicker(s) in the electrical grid(s) based on the video(s), and determining the property(ies) based on the flicker(s). The flicker(s) can be a 120 Hertz flicker. The flicker(s) can be a flicker in a light(s) recorded in the video(s). A frequency and a phase of the flicker(s) can be determined.

Bianco, Federica B.↗
DOE OSTI2023

Mechanical, Morphological, and Charge Transport Properties of NDI Polymers with Variable Built‐in Π‐Conjugation Lengths Probed by Simulation and Experiment

Abstract Mechanically deformable polymeric semiconductors are a key material for fabricating flexible organic thin‐film transistors (FOTFTs)—the building block of electronic circuits and wearable electronic devices. However, for many π‐conjugated polymers achieving mechanical deformability and efficient charge transport remains challenging. Here the effects of polymer backbone bending stiffness and film microstructure on mechanical flexibility and charge transport are investigated via experimental and computational methods for a series of electron‐transporting naphthalene diimide (NDI) polymers having differing extents of π‐conjugation. The results show that replacing increasing amounts of the π‐conjugated comonomer dithienylvinylene (TVT) with the π‐nonconjugated comonomer dithienylethane (TET) in the backbone of the fully π‐conjugated polymeric semiconductor, PNDI‐TVT 100 (yielding polymeric series PNDI‐TVT x , 100 ≥x≥ 0), lowers backbone rigidity, degree of texturing, and π–π stacking interactions between NDI moieties. Importantly, this comonomer substitution increases the mechanical robustness of PNDI‐TVT x while retaining efficient charge transport. Thus, reducing the TVT content of PNDI‐TVT x suppresses film crack formation and dramatically stabilizes the field‐effect electron mobility upon bending (e.g., 2 mm over 2000 bending cycles). This work provides a route to tune π–π stacking in π‐conjugated polymers while simultaneously promoting mechanical flexibility and retaining good carrier mobility in FOTFTs.

Chemistry↗
DOE OSTI2020

Modulating Electrostatic Interactions in Ion Pair Intermediates To Alter Site Selectivity in the C−O Deoxygenation of Sugars

Abstract Controlling which products one can access from the predefined biomass‐derived sugars is challenging. Changing from CH 2 Cl 2 to the greener alternative toluene alters which C−O bonds in a sugar are cleaved by the tris(pentafluorophenyl)borane/HSiR 3 catalyst system. This increases the diversity of high‐value products that can be obtained through one‐step, high‐yielding, catalytic transformations of the mono‐, di‐, and oligosaccharides. Computational methods helped identify this non‐intuitive outcome in low dielectric solvents to non‐isotropic electrostatic enhancements in the key ion pair intermediates, which influence the reaction coordinate in the reactivity‐/selectivity‐determining step. Molecular‐level models for these effects have far‐reaching consequences in stereoselective ion pair catalysis.

Lowe, Jared M.↗
DOE OSTI2023

Four‐Electron Oxidative Addition of an N=N Double Bond at a Chromium Metallocyclopropene**

Abstract This report describes the synthesis of a pseudo‐tetrahedral chromium alkyne complex supported by a bidentate phosphinimide ligand and its reactivity with an azobenzene derivative. Characterization of the former by structural and computational methods reveals an unprecedented extent of alkyne activation by a formal chromium(II) center, suggesting that this complex is best described as a chromium(IV)‐metallocyclopropene. Exposure of this compound to 4,4′‐difluoroazobenzene results in the formation of a chromium(VI) diimido complex, which constitutes a rare 4‐electron oxidative addition of an N=N double bond. The isolation of a chromium(IV)‐hydrazido intermediate enabled mechanistic investigations of this challenging bond cleavage process. This work substantiates the notion that terminal phosphinimide ligands can engender first‐row transition metal ions with exceptional reactivity.

Chemistry↗
DOE OSTI2020

Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus

Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene-deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild-type strain as well as in β-glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non-diauxic growth and metabolite consumptions of the wild-type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially-useful strains. Importantly, the model is able to explain the role of the different β-glucosidases and their behavior under genetic perturbations. Here, this integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers

Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. In this study, we aim to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Atomistic‐Level Effects of Noncovalent Interactions and Crystalline Packing for Organic Material Structural Integrity upon Exposure to Gamma Radiation

Developing an atomistic understanding of ionizing radiation induced changes to organic materials is necessary for intentional design of greener and more sustainable materials for radiation shielding and detection. Cocrystals are promising for these purposes, but a detailed understanding of how the specific intermolecular interactions within the lattice upon exposure to radiation affect the structural stability of the organic crystalline material is unknown. This study evaluates atomistic-level effects of γ radiation on both single- and multicomponent organic crystalline materials and how specific noncovalent interactions and packing within the crystalline lattice enhance structural stability. Dose studies were performed on all crystalline systems and evaluated via experimental and computational methods. Changes in crystallinity were evaluated by p-XRD and free radical formation was analyzed via EPR spectroscopy. Type of intermolecular interactions and packing within the crystal lattice was delineated and related to the specific free radical species formed and the structural integrity of each material. Periodic DFT and HOMO-LUMO surface mapping calculations provided atomistic-level identifications of the most probable sites for the radicals formed upon exposure to γ radiation and relate intermolecular interactions and molecular packing within the crystalline lattice to experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

Abstract Host‐associated and environmental microbiomes play central roles in human health, biogeochemical cycling, response to ecosystem change, and agriculture. Scientific approaches that can reveal the functional activities that contribute to observed phenotypes are needed in microbiome research. Broad characterization of the functional activity of microbes within microbiomes is currently hampered by approaches that rely on inference of function from metagenomes or indirect measurements. Activity‐based protein profiling is uniquely positioned to overcome these challenges and reveal the protein‐level mechanisms associated with microbiome phenotypes. In this review we describe the progress made to date using ABPP in gut microbiome, plant‐microbe interaction, and soil microbiome research, and suggest how ABPP data can be coupled with advanced computational methods to enable phenotype prediction and bioengineering of microbiomes for applied purposes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Stress field and interaction forces between dislocations and precipitate distributions

A computational method is developed for calculation of the stress field and interaction forces between dislocations and precipitates of arbitrary shape and distribution. The internal stress generated by precipitates due to coherency strain is implemented within the discrete dislocation dynamics (DDD) framework. The s-version finite element method (s-FEM), which models a precipitate of arbitrary shape using a local mesh is used to calculate coherency stress fields. The method facilitates meshing precipitate volumes of arbitrary geometry, and multiple local meshes can be superimposed at various positions of the global mesh. Accuracy and convergence conditions of the method are established. For a single precipiate, the method is shown to be 3.5 times faster than a standard FEM calculation for the same accuracy, and the gain in speed increases with the number of precipitates. The CRSS of spherical precipitates is found to be higher than disk-shaped precipitates of the same volume fraction.

42 ENGINEERING↗
DOE OSTI2023

Dissecting the structural heterogeneity of proteins by native mass spectrometry

Abstract A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Smoky Mountain Data Challenge 2021: An Open Call to Solve Scientific Data Challenges Using Advanced Data Analytics and Edge Computing

The 2021 Smoky Mountains Computational Sciences and Engineering Conference enlists scientists from across Oak Ridge National Laboratory (ORNL) and industry to be data sponsors and help create data analytics and edge computing challenges for eminent datasets in a variety of scientific domains. This work describes the significance of each of the eight datasets and their associated challenge questions. The challenge questions for each dataset were required to cover multiple difficulty levels. An international call for participation was sent to students, asking them to form teams of up to six people and apply novel data analytics and edge computing methods to solve these challenges.

Devineni, Pravallika↗
DOE OSTI2024

Stable vacua with realistic phenomenology and cosmology in heterotic M-theory satisfying Swampland conjectures

We recently described a protocol for computing the potential energy in heterotic M-theory for the dilaton, complex structure and Kähler moduli. This included the leading order non-perturbative contributions to the complex structure, gaugino condensation and worldsheet instantons assuming a hidden sector that contains an anomalous U(1) structure group embedded in E8. In this paper, we elucidate, in detail, the mathematical and computational methods required to utilize this protocol. These methods are then applied to a realistic heterotic M-theory model, the B – L MSSM, whose observable sector is consistent with all particle physics requirements. Within this context, it is shown that the dilaton and universal moduli can be completely stabilized at values compatible with every phenomenological and mathematical constraint — as well as with ΛCDM cosmology. We also show that the heterotic M-theory vacua are consistent with all well-supported Swampland conjectures based on considerations of string theory and quantum gravity, and we discuss the implications of dark energy theorems for compactified theories.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. Additionally, in geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T–A and U–A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Modeling in High Temperature Corrosion: A Review and Outlook

Realizing higher operating temperatures to increase efficiency of future applications for energy conversion and storage while minimizing cost is a challenge for development of high-temperature materials. Simultaneous optimization of mechanical properties and corrosion resistance continues to be a difficult task but is essential due to the need to significantly accelerate the transition between technology readiness levels in the future. Furthermore, oxidation-induced degradation will be a critical life-limiting mechanism at increased operating temperatures. Suitable high-temperature materials cannot be solely identified by time-consuming experiments and reliable computational methods incorporating the relevant physics of processes must be considered to complement the experimental efforts. In the present work, a review of the methods employed to model oxidation-induced material degradation described in literature will be discussed. Furthermore, their capability to predict lifetime and aid in material selection will be evaluated.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Combined Experimental and Computational Study of Molybdenum and Niobium for Nuclear Sensor Application

Due to their novel electromagnetic and thermal properties, molybdenum (Mo) and niobium (Nb) become optimal temperature sensor materials for nuclear energy applications. We leveraged voltage recorded during a heat ramp to tune a computational method to predict the Seebeck electromotive force (EMF) of Mo and Nb. Using a combined Density Functional Theory (DFT) and Boltzmann Transport Equations (BTE) method the voltage was predicted but did not include the effects of temperature on atomic structure. Combining Ab Initio Molecular Dynamics (AIMD) and BTE included temperature effects on structure optimization and yielded voltages in a good agreement with experiment. Lanthanum (La) and Phosphorus (P) additives in Mo and Nb, respectively, could increase the EMF compared to those of the pure metals. The presence of oxygen (O) in Mo increases the EMF while O in Nb slightly reduces the EMF. Furthermore, our studies suggested that heat treatment-induced structural changes that lead to a reduction in voltage occur not only at the mesoscale as previously understood but also at the atomic scale.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2020

Machine learning a molecular Hamiltonian for predicting electron dynamics

We develop a computational method to learn a molecular Hamiltonian matrix from matrix-valued time series of the electron density. As we demonstrate for three small molecules, the resulting Hamiltonians can be used for electron density evolution, producing highly accurate results even when propagating 1,000 time steps beyond the training data. As a more rigorous test, we use the learned Hamiltonians to simulate electron dynamics in the presence of an applied electric field, extrapolating to a problem that is beyond the field-free training data. We find that the resulting electron dynamics predicted by our learned Hamiltonian are in close quantitative agreement with the ground truth. Our method relies on combining a reduced-dimensional, linear statistical model of the Hamiltonian with a time-discretization of the quantum Liouville equation within time-dependent Hartree Fock theory. In conclusion, we train the model using a least-squares solver, avoiding numerous, CPU-intensive optimization steps. For both field-free and field-on problems, we quantify training and propagation errors, highlighting areas for future development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Chlorophylls as primary electron acceptors in reaction centers

Photosynthetic Reaction Centers (RCs) can be considered blueprints for highly efficient energy transfer. Embedded with an array of cofactors, including (bacterio)chlorophyll ((B)Chl) and (B)pheophytin ((B)Pheo) molecules, RCs function with a high quantum yield that spans a wide spectral range. Understanding the principles that underlie their function can influence the design of the next generation of artificial photosynthetic devices. We are particularly interested in the factors that influence the early stages of light-driven charge separation in RCs. With the recent publication of several highly anticipated RC structures and advanced computational methods available, it is possible to probe both the geometric and electronic structures of an array of RCs. In this chapter, we review the electronic and geometric structures of the (B)Chl and (B)Pheo primary electron acceptors from fiveRCs, comprising both Type I and Type II RCs and representing both heterodimeric and homodimeric systems. We showcase the dimeric A0•- state of Type I RCs, whereby the unpaired electron is delocalized, to various extents, over two (B)Chl molecules (B)Chl2 and (B)Chl3. This delocalization is controlled by several factors, including the structure of the (B)Chls, interactions with the surrounding protein matrix, and the orientation and distances of the cofactors themselves. In contrast, the primary acceptors of Type II RCs are entirely monomeric, with electron density residing solely on the (B)Pheo. We compare the natural design of the primary acceptors of the Type I and Type II RCs from both an evolutionary and application based perspective.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗