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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 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

On‐site surrogates for large‐scale calibration

Abstract Motivated by a computer model calibration problem from the oil and gas industry, involving the design of a honeycomb seal, we develop a new Bayesian methodology to cope with limitations in the canonical apparatus stemming from several factors. We propose a new strategy of on‐site design and surrogate modeling for a computer simulator acting on a high‐dimensional input space that, although relatively speedy, is prone to numerical instabilities, missing data, and nonstationary dynamics. Our aim is to strike a balance between data‐faithful modeling and computational tractability in a calibration framework—tailoring the computer model to a limited field experiment. Situating our on‐site surrogates within the canonical calibration apparatus requires updates to that framework. We describe a novel yet intuitive Bayesian setup that carefully decomposes otherwise prohibitively large matrices by exploiting the sparse blockwise structure. Empirical illustrations demonstrate that this approach performs well on toy data and our motivating honeycomb example.

Huang, Jiangeng↗
DOE OSTI2026

A conservative discontinuous Galerkin algorithm for particle kinetics on smooth manifolds

A novel, conservative discontinuous Galerkin algorithm is presented for particle kinetics on manifolds. The motion of particles on the manifold is represented using both canonical and non-canonical Hamiltonian formulations. Our schemes apply to both formulations, but the canonical formulation results in a particularly efficient scheme that also conserves particle density and energy exactly. The collisionless update is coupled to a Bhatnagar-Gross-Krook (BGK) collision operator that provides a simplified model for relaxation to local thermodynamic equilibrium. An iterative scheme is constructed to ensure collisional invariants (density, momentum and energy) are preserved numerically. Rotation of the manifold is incorporated by modifying the Hamiltonian while ensuring a canonical formulation. Several test problems, including a kinetic version of the classical Sod shock problem, Kelvin-Helmholtz instability on the surfaces of a sphere and a hyperboloid, with and without rotations, are presented. A prospectus for further development of this approach to simulation of kinetic theory in general relativity is presented.

Discontinuous Galerkin↗
DOE OSTI2021

Koopman wavefunctions and Clebsch variables in Vlasov–Maxwell kinetic theory

Motivated by recent discussions on the possible role of quantum computation in plasma simulations, here, we present different approaches to Koopman's Hilbert-space formulation of classical mechanics in the context of Vlasov–Maxwell kinetic theory. The celebrated Koopman–von Neumann construction is provided with two different Hamiltonian structures: one is canonical and recovers the usual Clebsch representation of the Vlasov density, the other is non-canonical and appears to overcome certain issues emerging in the canonical formalism. Furthermore, the canonical structure is restored for a variant of the Koopman–von Neumann construction that carries a different phase dynamics. Going back to van Hove's prequantum theory, the corresponding Koopman–van Hove equation provides an alternative Clebsch representation which is then coupled to the electromagnetic fields. Finally, the role of gauge transformations in the new context is discussed in detail.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Lectures on statistical mechanics

Presented here is a transcription of the lecture notes from Professor Allan N. Kaufman’s graduate statistical mechanics course Physics 212A and 212B at the University of California Berkeley from the 1972–1973 academic year. 212A addressed equilibrium statistical mechanics with topics: fundamentals (micro-canonical and sub-canonical ensembles, adiabatic law and action conservation, fluctuations, pressure, and virial theorem), classical fluids and other systems (equation of state, deviations from ideality, virial coefficients and van der Waals potential, canonical ensemble and partition function, quasistatic evolution, grand-canonical ensemble and partition function, chemical potential, simple model of a phase transition, quantum virial expansion, numerical simulation of equations of state, and phase transition), chemical equilibrium (systems with multiple species and chemical reactions, law of mass action, Saha equation, chemical equilibrium including ionization and excited states), and long-range interactions (including Coulomb, dipole, and gravitational interactions, Debye–Hückel theory, and shielding). 212B addressed nonequilibrium statistical mechanics with topics: fundamentals (definitions: realizations, moments, characteristic function, and discrete variables), Brownian motion (Langevin equation, fluctuation–dissipation theorem, spatial diffusion, Boltzmann’s H-theorem), Liouville and Klimontovich equations, Landau equation (derivation, elaboration, and H-theorem, and irreversibility), Markov processes and Fokker–Planck equation (derivations of the Fokker–Planck equation and a master equation), linear response and transport theory (linear Boltzmann equation, linear response theory of Kubo and Mori, relation of entropy production to electrical conductivity, transport relations and coefficients, normal mode solutions of the transport equations, sketch of a generalized Langevin equation method for transport theory), and an introduction to nonequilibrium quantum statistical mechanics.

plasma dynamics↗
DOE OSTI2021

An Improved Top-Down Mass Spectrometry Characterization of Chlamydomonas reinhardtii Histones and Their Post-translational Modifications

We present an updated analysis of the linker and core histone proteins and their proteoforms in the green microalga Chlamydomonas reinhardtii by top-down mass spectrometry (TDMS). The combination of high-resolution liquid chromatographic separation, robust fragmentation high, mass spectral resolution, the application of a custom search algorithm, and extensive manual analysis enabled the characterization of 86 proteoforms across all four core histones H2A, H2B, H3 and H4, and the linker histone H1. All canonical H2A paralogs, which vary in their C-termini, were identified, along with an unreported non-canonical variant that had both high levels of acetylation and C-terminal truncations. Similarly, a majority of the canonical H2B paralogs were identified, along with a smaller non-canonical variant, H2B.v, that was highly acetylated. Histone H4 exhibited a novel acetylation profile that differs significantly from that found in other organisms. A majority of H3 was monomethylated at K4, while a small fraction of H3 was trimethylated at K4 and also highly acetylated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure of the Wnt–Frizzled–LRP6 initiation complex reveals the basis for coreceptor discrimination

Wnt morphogens are critical for embryonic development and tissue regeneration. Canonical Wnts form ternary receptor complexes composed of tissue-specific Frizzled (Fzd) receptors together with the shared LRP5/6 coreceptors to initiate β-catenin signaling. The cryo-EM structure of a ternary initiation complex of an affinity-matured XWnt8–Frizzled8–LRP6 complex elucidates the basis of coreceptor discrimination by canonical Wnts by means of their N termini and linker domains that engage the LRP6 E1E2 domain funnels. Chimeric Wnts bearing modular linker “grafts” were able to transfer LRP6 domain specificity between different Wnts and enable non-canonical Wnt5a to signal through the canonical pathway. Synthetic peptides comprising the linker domain serve as Wnt-specific antagonists. The structure of the ternary complex provides a topological blueprint for the orientation and proximity of Frizzled and LRP6 within the Wnt cell surface signalosome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Nonenzymatic RNA copying with a potentially primordial genetic alphabet

Nonenzymatic RNA copying is thought to have been responsible for the replication of genetic information during the origin of life. However, chemical copying with the canonical nucleotides (A, U, G, and C) strongly favors the incorporation of G and C and disfavors the incorporation of A and especially U because of the stronger G:C vs. A:U base pair and the weaker stacking interactions of U. Recent advances in prebiotic chemistry suggest that the 2-thiopyrimidines were precursors to the canonical pyrimidines, raising the possibility that they may have played an important early role in RNA copying chemistry. Furthermore, 2-thiouridine (s 2 U) and inosine (I) form by deamination of 2-thiocytidine (s 2 C) and A, respectively. We used thermodynamic and crystallographic analyses to compare the I:s 2 C and A:s 2 U base pairs. We find that the I:s 2 C base pair is isomorphic and isoenergetic with the A:s 2 U base pair. The I:s 2 C base pair is weaker than a canonical G:C base pair, while the A:s 2 U base pair is stronger than the canonical A:U base pair, so that a genetic alphabet consisting of s 2 U, s 2 C, I, and A generates RNA duplexes with uniform base pairing energies. Consistent with these results, kinetic analysis of nonenzymatic template-directed primer extension reactions reveals that s 2 C and s 2 U substrates bind similarly to I and A in the template, and vice versa. Our work supports the plausibility of a potentially primordial genetic alphabet consisting of s 2 U, s 2 C, I, and A and offers a potential solution to the long-standing problem of biased nucleotide incorporation during nonenzymatic template copying.

Science & Technology - Other Topics↗
DOE OSTI2024

An ascomycete H4 variant with an unknown function

Histone variants leading to altered nucleosome structure, dynamics and DNA accessibility occur frequently, albeit rarely for H4. We carried out a comprehensive in silico scrutiny of fungal genomes, which revealed the presence of a novel H4 variant (H4E) in the ascomycetes, throughout the Pezizomycotina, in basal species of the Taphrinomycotina and also in the Glomeromycota. The coding cognate genes show a specific intron/exon organization, different from H4 canonical genes. H4Es diverge from canonical H4s mainly in the N- and C-terminal extensions, showing marked differences in the distribution and number of Lys and Arg residues, which may result in novel post-translational modifications. In Aspergillus nidulans (Pezizomycotina, Eurotiomycetes) the H4E variant protein level is low in mycelia. However, the encoding gene is well expressed at 37°C under nitrogen starvation. H4E localizes to the nucleus and interacts with H3, but its absence or overexpression does not result in any detectable phenotype. Deletion of only one of the of the two canonical H4 genes results in a strikingly impaired growth phenotype, which indicates that H4E cannot replace this canonical histone. Thus, an H4 variant is present throughout a whole subphylum of the ascomycetes, but with hitherto no experimentally detectable function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Quantum Joule expansion of one-dimensional systems

Here, we investigate the Joule expansion of nonintegrable quantum systems that contain bosons or spinless fermions in one-dimensional lattices. A barrier initially confines the particles to be in half of the system in a thermal state described by the canonical ensemble and is removed at time t = 0. We investigate the properties of the time-evolved density matrix, the diagonal ensemble density matrix, and the corresponding canonical ensemble density matrix with an effective temperature determined by the total energy conservation using exact diagonalization. The weights for the diagonal ensemble and the canonical ensemble match well for high initial temperatures that correspond to negative effective final temperatures after the expansion. At long times after the barrier is removed, the time-evolved Rényi entropy of subsystems bigger than half can equilibrate to the thermal entropy with exponentially small fluctuations. The time-evolved reduced density matrix at long times can be approximated by a thermal density matrix for small subsystems. Few-body observables, like the momentum distribution function, can be approximated by a thermal expectation of the canonical ensemble with strongly suppressed fluctuations. The negative effective temperatures for finite systems go to non-negative temperatures in the thermodynamic limit for bosons, but there is a true thermodynamic effect for fermions, which is confirmed by finite-temperature density matrix renormalization group calculations. We propose the Joule expansion as a way to dynamically create negative temperature states for fermion systems with repulsive interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Developing a pipeline to expand the genetic code of diverse bacteria for microbial engineering

Microbial biotechnologies are key to addressing grand challenges to promote human health, reverse carbon emissions, recycle mixed plastic waste, remediate contaminated soils, and achieve sustainable economies. Synthetic biology has enabled design of diverse microbes and their proteins for useful purposes, but the narrowness of the natural genetic code limits functional diversity (e.g., biosynthesis) of engineered microbes. The natural genetic code defines the fundamental rules of translating genetic information into proteins comprised of 22 ‘canonical’ amino acids. However, using a technique called genetic code expansion (GCE), the chemical properties and therefore functions of proteins can be transformed by incorporation of one or more of ~200 chemically diverse ‘non-canonical’ amino acids. The effective application of genetic code expansion in diverse microbes has the potential to revolutionize biotechnology. However, despite over 50 years of research and its transformative potential, the application of genetic code expansion has been limited to a handful of bacterial species. In this project, we will perform three tasks to both overcome the barriers that prevent wide spread adoption of GCE as molecular tool and demonstrate its potential for biotechnological applications. Specifically, we will (1) develop a genetic engineering methodology that will enable use of GCE in a broad range of bacterial hosts, (2) use high-throughput functional genomics methods to identify physiological responses to both genetic code expansion and exposure to non-canonical amino acids in three different bacteria, and (3) demonstrate an application of GCE by selectively incorporate non-canonical amino acids into surface displayed peptides such as those used for biomining.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

Abstract An i‐motif is a non‐canonical DNA structure implicated in gene regulation and linked to cancers. The C‐rich strand of the HRAS oncogene, 5′‐CG CCC GTG CCC TGCG CCC GCAA CCC GA‐3′ (herein referred to as iHRAS), forms an i‐motif in vitro but its exact structure was unknown. HRAS is a member of the RAS proto‐oncogene family. About 19 % of US cancer patients carry mutations in RAS genes. We solved the structure of iHRAS at 1.77 Å resolution. The structure reveals that iHRAS folds into a double hairpin. The two double hairpins associate in an antiparallel fashion, forming an i‐motif dimer capped by two loops on each end and linked by a connecting region. Six C−C + base pairs form each i‐motif core, and the core regions are extended by a G−G base pair and a cytosine stacking. Extensive canonical and non‐canonical base pairing and stacking stabilizes the connecting region and loops. The iHRAS structure is the first atomic resolution structure of an i‐motif from a human oncogene. This structure sheds light on i‐motifs folding and function in the cell.

Li, Kevin S.↗
DOE OSTI2023

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

Abstract An i‐motif is a non‐canonical DNA structure implicated in gene regulation and linked to cancers. The C‐rich strand of the HRAS oncogene, 5′‐CG CCC GTG CCC TGCG CCC GCAA CCC GA‐3′ (herein referred to as iHRAS), forms an i‐motif in vitro but its exact structure was unknown. HRAS is a member of the RAS proto‐oncogene family. About 19 % of US cancer patients carry mutations in RAS genes. We solved the structure of iHRAS at 1.77 Å resolution. The structure reveals that iHRAS folds into a double hairpin. The two double hairpins associate in an antiparallel fashion, forming an i‐motif dimer capped by two loops on each end and linked by a connecting region. Six C−C + base pairs form each i‐motif core, and the core regions are extended by a G−G base pair and a cytosine stacking. Extensive canonical and non‐canonical base pairing and stacking stabilizes the connecting region and loops. The iHRAS structure is the first atomic resolution structure of an i‐motif from a human oncogene. This structure sheds light on i‐motifs folding and function in the cell.

Li, Kevin S.↗
DOE OSTI2021

The repulsive Casimir-type forces in binary mixture of weakly interacting Bose–Einstein condensates gases

Highlights: • The equations of the state of a binary mixture weakly interacting Bose gases are established based on the Lagrangian of the system. • The formulae of the Casimir-type energy and the resulting Casimir-type force are produced from the quantum part of the grand canonical energy. • The results for the Casimir-type effect in the one-field case can be re-obtained by using the results of the two-field case. Within the framework of the quantum field theory (QFT) in the one-loop approximation, we investigate the Casimir-type effect in a mixture of two-component weakly interacting Bose-Einstein condensates (BECs) gases confined between two parallel plates at zero temperature. The Casimir-type forces in the miscible state of BECs for different boundary conditions (BCs) are discovered and compared to each other. The repulsive nature of the Casimir-type force in BECs is defined for the first time. Our calculations are finished in both grand canonical ensemble (GCE) and canonical ensemble (CE).

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Linear-Scaling Local Natural Orbital-Based Full Triples Treatment in Coupled-Cluster Theory

We present an efficient, asymptotically linear-scaling implementation of the canonically O(N 8 ) coupled-cluster method with singles, doubles, and full triples excitations (CCSDT) method. We apply the domain-based local pair natural orbital (DLPNO) approach for computing CCSDT amplitudes. Our method, called DLPNO–CCSDT, uses the converged coupled-cluster amplitudes from a preceding DLPNO–CCSD(T) computation as a starting point for the solution of the CCSDT equations in the local natural orbital basis. To simplify the working equations, we t1-dress our two-electron integrals and Fock matrices, allowing our equations to take on the form of CCDT. With appropriate parameters, our method can recover more than 99.99% of the total canonical CCSDT correlation energy. In addition, we demonstrate that our method consistently yields sub-kJ mol –1 errors in relative energies when compared to canonical CCSDT, and, likewise, when computing the difference between CCSDT and CCSD(T). Finally, to highlight the low scaling of our algorithm, we present timings on linear alkanes (up to 30 carbons and 730 basis functions) and water clusters (up to 131 water molecules and 3144 basis functions).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Python Library for Monte Carlo Simulations with Ab Initio and Machine-Learned Interatomic Potentials

There is a growing need in the simulation community for software that provides a transparent, reproducible, usable, and extensible (TRUE) Monte Carlo (MC) simulation framework employing energies from ab initio methods and machine-learning interatomic potentials (MLIPs). We introduce a Python library (ASE-MC) that adds Monte Carlo functionality to the Atomic Simulation Environment (ASE) package. Now, we can combine the powerful tools used to build systems and perform ab initio and MLIP in ASE with MC simulation algorithms to sample the configurational space with a concise Python script. After presenting the design philosophy, we demonstrate the flexibility of our approach using selected examples. These example simulations include liquid water described with a message-passing MLIP in the canonical and isothermal–isobaric ensembles, sampling the characteristic dihedral angle of biphenyl and comparing an MLIP to first-principles calculations, and a grand canonical Monte Carlo simulation of ammonia adsorption on Pt(111). These examples showcase the main features of the software, which include flexibility in the choice of ab initio or MLIP engine, ab initio or MLIP grand canonical MC with cavity bias insertions and deletions, the ability to add custom MC moves to the move set, and how users can condense complex MC workflows into a single Python script. Finally, this library serves as a framework for reproducible Monte Carlo simulations, facilitating easy reproduction of the work and application to new systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Zika virus RNA structure controls its unique neurotropism by bipartite binding to Musashi-1

Human RNA binding protein Musashi-1 (MSI1) plays a critical role in neural progenitor cells (NPCs) by binding to various host RNA transcripts. The canonical MSI1 binding site (MBS), A/GU (1-3) AG single-strand motif, is present in many RNA virus genomes, but only Zika virus (ZIKV) genome has been demonstrated to bind MSI1. Herein, we identified the AUAG motif and the AGAA tetraloop in the Xrn1-resistant RNA 2 (xrRNA2) as the canonical and non-canonical MBS, respectively, and both are crucial for ZIKV neurotropism. More importantly, the unique AGNN-type tetraloop is evolutionally conserved, and distinguishes ZIKV from other known viruses with putative MBSs. Integrated structural analysis showed that MSI1 binds to the AUAG motif and AGAA tetraloop of ZIKV in a bipartite fashion. Thus, our results not only identified an unusual viral RNA structure responsible for MSI recognition, but also revealed a role for the highly structured xrRNA in controlling viral neurotropism.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Mechanistic basis of atypical TERT promoter mutations

Non-coding mutations in the TERT promoter (TERTp), typically at one of two bases -124 and -146 bp upstream of the start codon, are among the most prevalent driver mutations in human cancer. Several additional recurrent TERTp mutations have been reported but their functions and origins remain largely unexplained. Here, we show that atypical TERTp mutations arise secondary to canonical TERTp mutations in a two-step process. Canonical TERTp mutations create de novo binding sites for ETS family transcription factors that induce favourable conditions for DNA damage formation by UV light, thus creating a hotspot effect but only after a first mutational hit. In agreement, atypical TERTp mutations co-occur with canonical driver mutations in large cancer cohorts and arise subclonally specifically on the TERTp driver mutant chromosome homolog of melanoma cells treated with UV light in vitro. Our study gives an in-depth view of TERTp mutations in cancer and provides a mechanistic explanation for atypical TERTp mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

How generic is iodide-tagging photoelectron spectroscopy: An extended investigation on the Gly· X - (Gly = glycine, X = Cl or Br) complexes

We report a joint negative ion photoelectron spectroscopy (NIPES) and quantum chemical computational study on glycine-chloride/bromide complexes (denoted Gly·X - , X = Cl/Br) in close comparison to the previously studied Gly·I - cluster ion. Combining experimental NIPE spectra and theoretical calculations, various Gly·X - complexes were found to adopt the same types of low-lying isomers, albeit with different relative energies. Despite more congested spectral profiles for Gly·Cl - and Gly·Br - , spectral assignments were accomplished with the guidance of the knowledge learned from Gly·I - , where a larger spin–orbit splitting of iodine afforded well-resolved, recognizable spectral peaks. Three canonical plus one zwitterionic isomer for Gly·Cl - and four canonical conformers for Gly·Br - were experimentally identified and characterized in contrast to the five canonical ones observed for Gly·I - under similar experimental conditions. Taken together, this study investigates both genericity and variations in binding patterns for the complexes composed of glycine and various halides, demonstrating that iodide-tagging is an effective spectroscopic means to unravel diverse ion-molecule binding motifs for cluster anions with congested spectral bands by substituting the respective ion with iodide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗