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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-$α$-amino acids in vitro and in vivo

The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-L-α-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Here we report that pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants accept α-hydroxy, α-thio and N-formyl-L-α-amino acids, as well as α-carboxy acid monomers that are precursors to polyketide natural products. These monomers are accommodated and accepted by the translation apparatus in vitro; those with reactive nucleophiles are incorporated into proteins in vivo. High-resolution structural analysis of the complex formed between one PylRS enzyme and a m-substituted 2-benzylmalonic acid derivative revealed an active site that discriminates prochiral carboxylates and accommodates the large size and distinct electrostatics of an α-carboxy substituent. This work emphasizes the potential of PylRS-derived enzymes for acylating tRNA with monomers whose α-substituent diverges substantially from the α-amine of proteinogenic amino acids. These enzymes or derivatives thereof could synergize with natural or evolved ribosomes and/or translation factors to generate diverse sequence-defined non-protein heteropolymers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Clades of huge phages from across Earth’s ecosystems

Bacteriophages typically have small genomes and depend on their bacterial hosts for replication. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Smectic pair-density-wave order in EuRbFe 4 As 4

The pair density wave (PDW) is a superconducting state in which Cooper pairs carry centre-of-mass momentum in equilibrium, leading to the breaking of translational symmetry. Experimental evidence for such a state exists in high magnetic field and in some materials that feature density-wave orders that explicitly break translational symmetry. However, evidence for a zero-field PDW state that exists independent of other spatially ordered states has so far been elusive. Here we show that such a state exists in the iron pnictide superconductor EuRbFe 4 As 4 , a material that features co-existing superconductivity (superconducting transition temperature ( T c ) ≈ 37 kelvin) and magnetism (magnetic transition temperature ( T m ) ≈ 15 kelvin). Using spectroscopic imaging scanning tunnelling microscopy (SI-STM) measurements, we show that the superconducting gap at low temperature has long-range, unidirectional spatial modulations with an incommensurate period of about eight unit cells. Upon increasing the temperature above Tm, the modulated superconductor disappears, but a uniform superconducting gap survives to T c . When an external magnetic field is applied, gap modulations disappear inside the vortex halo. The SI-STM and bulk measurements show the absence of other density-wave orders, indicating that the PDW state is a primary, zero-field superconducting state in this compound. FInally, both four-fold rotational symmetry and translation symmetry are recovered above T m , indicating that the PDW is a smectic order.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Tuning commensurability in twisted van der Waals bilayers

Moiré superlattices based on van der Waals bilayers created at small twist angles lead to a long wavelength pattern with approximate translational symmetry. At large twist angles ( θ t ), moiré patterns are, in general, incommensurate except for a few discrete angles. Here we show that large-angle twisted bilayers offer distinctly different platforms. More specifically, by using twisted tungsten diselenide bilayers, we create the incommensurate dodecagon quasicrystals at θ t = 30° and the commensurate moiré crystals at θ t = 21.8° and 38.2°. Further, valley-resolved scanning tunnelling spectroscopy shows disparate behaviours between moiré crystals (with translational symmetry) and quasicrystals (with broken translational symmetry). In particular, the K valley shows rich electronic structures exemplified by the formation of mini-gaps near the valence band maximum. These discoveries demonstrate that bilayers with large twist angles offer a design platform to explore moiré physics beyond those formed with small twist angles.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Effects of pore connectivity and tortuosity on the dynamics of fluids confined in sub-nanometer pores

Dynamical behavior of fluids under nano-pore confinement is studied extensively as it has important implications for several industrial as well as geological processes. Pore network in many porous materials exhibits a varied degree of inter connections. The extent of this pore connectivity may affect the structural and dynamical behavior of the confined fluid. However, studies of fluid confinement addressing these effects systematically are lacking. In this paper we report molecular dynamics simulation studies addressing the effects of pore connectivity on the dynamics of two representative fluids – CO 2 and ethane in silicalite by systematically varying the degree of pore connectivity through selectively blocking some pore space with immobile methane molecules. By selectively turning off the pore spaces in the shape of straight, or tortuous zigzag channels, we also probe the effects of pore tortuosity. In general, pore connectivity is found to facilitate both the translational as well as rotational dynamics of both fluids, while the intermolecular modes of vibration in both fluids remain largely unaffected. The effects of providing connections between a set of straight or zigzag channel-like pores are however more nuanced. Pore tortuosity facilitates the rotational motion, but suppresses the translational motion of CO 2 , while its effects on the rotational and translational motion of ethane are less pronounced. The intermolecular vibrational modes of both fluids shift to higher energies with an increase in the number of tortuous pores. The results reported here provide a detailed molecular level understanding of the effects of pore connectivity on the dynamics of fluids and thus have implications for applications like fluid separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Intermediate scattering functions of a rigid body monoclonal antibody protein in solution studied by dissipative particle dynamic simulation

In the past decade, there was increased research interest in studying internal motions of flexible proteins in solution using Neutron Spin Echo (NSE) as NSE can simultaneously probe the dynamics at the length and time scales comparable to protein domain motions. However, the collective intermediate scattering function (ISF) measured by NSE has the contributions from translational, rotational, and internal motions, which are rather complicated to be separated. Widely used NSE theories to interpret experimental data usually assume that the translational and rotational motions of a rigid particle are decoupled and independent to each other. To evaluate the accuracy of this approximation for monoclonal antibody (mAb) proteins in solution, dissipative particle dynamic computer simulation is used here to simulate a rigid-body mAb for up to about 200 ns. The total ISF together with the ISFs due to only the translational and rotational motions as well as their corresponding effective diffusion coefficients is calculated. The aforementioned approximation introduces appreciable errors to the calculated effective diffusion coefficients and the ISFs. For the effective diffusion coefficient, the error introduced by this approximation can be as large as about 10% even though the overall agreement is considered reasonable. Thus, we need to be cautious when interpreting the data with a small signal change. In addition, the accuracy of the calculated ISFs due to the finite computer simulation time is also discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Photodissociation dynamics of the tert -butyl perthiyl radical

Here, the photodissociation dynamics of the tert-butyl perthiyl (t-BuSS) radical are investigated by fast-beam coincidence translational spectroscopy. A fast (6 keV-8 keV) beam of neutral t-BuSS radicals is produced via photodetachment of the corresponding anion, followed by photodissociation at 248 nm (5.00 eV) or 193 nm (6.42 eV) and coincident detection of the neutral products. Photofragment mass and translational energy distributions are obtained at both wavelengths. At 248 nm, the dominant product channel (90%) is found to be S loss, with a product translational energy distribution that peaks close to the maximum available energy and an anisotropic photofragment angular distribution, indicating dissociation along a repulsive excited state. A minor channel (10%) leading to the formation of S 2 + t-Bu is also observed. At 193 nm, both two- and three-body dissociation are observed. The formation of S 2 + t-Bu is the dominant two-body product channel, with multiple electronic states of the S 2 molecule produced via excited-state dissociation processes. The formation of S + t-BuS is a minor two-body channel at this dissociation energy. The three-body channels are S 2 + H + isobutene, S 2 + CH 3 + propene, and S + SH + isobutene. The first two of these channels result from a sequential dissociation process in which the loss of S 2 from t-BuSS results in ground-state t-Bu with sufficient internal energy to undergo secondary fragmentation. The third three-body channel, S + SH + isobutene, is attributed to the loss of internally excited HS 2 from t-BuSS, which then rapidly dissociates to form S + SH in an asynchronous concerted dissociation process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Voltage waveform tailoring for high aspect ratio plasma etching of SiO 2 using Ar/CF 4 /O 2 mixtures: Consequences of low fundamental frequency biases

The use of non-sinusoidal waveforms in low pressure capacitively coupled plasmas intended for microelectronics fabrication has the goal of customizing ion and electron energy and angular distributions to the wafer. One such non-sinusoidal waveform uses the sum of consecutive harmonics of a fundamental sinusoidal frequency, f 0 , having a variable phase offset between the fundamental and even harmonics. In this paper, we discuss results from a computational investigation of the relation between ion energy and DC self-bias when varying the fundamental frequency f 0 for capacitively coupled plasmas sustained in Ar/CF 4 /O 2 and how those trends translate to a high aspect ratio etching of trenches in SiO 2 . The fundamental frequency, f 0 , was varied from 1 to 10 MHz and the relative phase from 0° to 180°. Two distinct regimes were identified. Average ion energy onto the wafer is strongly correlated with the DC self-bias at high f 0 , with there being a maximum at φ = 0° and minimum at φ = 180°. In the low frequency regime, this correlation is weak. Average ion energy onto the wafer is instead dominated by dynamic transients in the applied voltage waveforms, with a maximum at φ = 180° and minimum at φ = 0°. The trends in ion energy translate to etch properties. In both, the high and low frequency regimes, higher ion energies translate to higher etch rates and generally preferable final features, though behaving differently with phase angle.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus–programmed ribosomal frameshifting element

A hallmark of retrovirus replication is the translation of two different polyproteins from one RNA through programmed –1 frameshifting. This is a mechanism in which the actively translating ribosome is induced to slip in the 5′ direction at a defined codon and then continues translating in the new reading frame. Programmed frameshifting controls the stoichiometry of viral proteins and is therefore under stringent evolutionary selection. Forty years ago, the first frameshifting stimulatory element was discovered in the Rous sarcoma virus. The ~120 nt RNA segment was predicted to contain a pseudoknot, but its 3D structure has remained elusive. Now, we have determined cryoEM and X-ray crystallographic structures of this classic retroviral element, finding that it adopts a butterfly-like double-pseudoknot fold. One “wing” contains a dynamic pyrimidine-rich helix, observed crystallographically in two conformations and in a third conformation via cryoEM. The other wing encompasses the predicted pseudoknot, which interacts with a second unexpected pseudoknot through a toggle residue, A2546. This key purine switches conformations between structural states and tunes the stability of interacting residues in the two wings. We find that its mutation can modulate frameshifting by as much as 50-fold, likely by altering the relative abundance of different structural states in the conformational ensemble of the RNA. Taken together, our structure–function analyses reveal how a dynamic double pseudoknot junction stimulates frameshifting by taking advantage of conformational heterogeneity, supporting a multistate model in which high Shannon entropy enhances frameshifting efficiency.

Science & Technology - Other Topics↗
DOE OSTI2024

Reversible to irreversible transitions for ac driven skyrmions on periodic substrates

Abstract Using atomistic simulations, we investigate the dynamical behavior of magnetic skyrmions in dimer and trimer molecular crystal arrangements, as well as bipartite lattices at 3/2 and 5/2 fillings, under ac driving over a square array of anisotropy defects. For low ac amplitudes, at all fillings reversible motion appears in which the skyrmions return to their original positions at the end of each ac drive cycle and the diffusion is zero. We also identify two distinct irreversible regimes. The first is a translating regime in which the skyrmions form channels of flow in opposing directions and translate by one substrate lattice constant per ac drive cycle. The translating state appears in the dimer and trimer arrangements, and produces pronounced peaks in the diffusivity in the direction perpendicular to the external drive. For larger ac amplitudes, we find chaotic irreversible motion in which the skyrmions can randomly exchange places with each other over time, producing long-time diffusive behavior both parallel and perpendicular to the ac driving direction.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Asymptotic reversibility of thermal operations for interacting quantum spin systems via generalized quantum Stein’s lemma

Abstract For quantum spin systems in any spatial dimension with a local, translation-invariant Hamiltonian, we prove that asymptotic state convertibility from a quantum state to another one by a thermodynamically feasible class of quantum dynamics, called thermal operations, is completely characterized by the Kullback–Leibler (KL) divergence rate, if the state is translation-invariant and spatially ergodic. Our proof consists of two parts and is phrased in terms of a branch of the quantum information theory called the resource theory. First, we prove that any states, for which the min and max Rényi divergences collapse approximately to a single value, can be approximately reversibly converted into one another by thermal operations with the aid of a small source of quantum coherence. Second, we prove that these divergences collapse asymptotically to the KL divergence rate for any translation-invariant ergodic state. We show this via a generalization of the quantum Stein’s lemma for quantum hypothesis testing beyond independent and identically distributed situations. Our result implies that the KL divergence rate serves as a thermodynamic potential that provides a complete characterization of thermodynamic convertibility of ergodic states of quantum many-body systems in the thermodynamic limit, including out-of-equilibrium and fully quantum situations.

Physics↗
DOE OSTI2023

Language Barriers in Organismal Biology: What Can Journals Do Better?

Synopsis In the field of organismal biology, as in much of academia, there is a strong incentive to publish in internationally recognized, highly regarded, English-language journals to promote career advancement. This expectation has created a linguistic hegemony in scientific publishing, whereby scholars for whom English is an additional language face additional barriers to achieving the same scientific recognition as scholars who speak English as a first language. Here, we surveyed the author guidelines of 230 journals in organismal biology with impact factors of 1.5 or greater for linguistically inclusive and equitable practices and policies. We looked for efforts that reflect first steps toward reducing barriers to publication for authors globally, including the presence of statements that encouraged submissions from authors of diverse nationalities and backgrounds, policies regarding manuscript rejection based on perceived inadequacies of the English language, the existence of bias-conscious reviewer practices, whether translation and editing resources or services are available, allowance for non-English abstracts, summaries, or translations, and whether journals offer license options that would permit authors (or other scholars) to translate their work and publish it elsewhere. We also directly contacted a subset of journals to verify whether the information on their author guidelines page accurately reflects their policies and the accommodations they would make. We reveal that journals and publishers have made little progress toward beginning to recognize or reduce language barriers. Counter to our predictions, journals associated with scientific societies did not appear to have more inclusive policies compared to non-society journals. Many policies lacked transparency and clarity, which can generate uncertainty, result in avoidable manuscript rejections, and necessitate additional time and effort from both prospective authors and journal editors. We highlight examples of equitable policies and summarize actions that journals can take to begin to alleviate barriers to scientific publishing.

Nolde-Lopez, B.↗
DOE OSTI2023

Structural basis for cloverleaf RNA-initiated viral genome replication

The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CD pro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (A•C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CD pro binding site on cloverleaf. We determined that the A•C-U base triple restricts the flexibility of the cloverleaf stem–loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the A•C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Phase diagram of twisted bilayer graphene at filling factor $v = ±3$

Here, we study the correlated insulating phases of twisted bilayer graphene (TBG) in the absence of lattice strain at integer filling $v = ±3$. Using the self-consistent Hartree-Fock method on a particle-hole symmetric model and allowing translation symmetry breaking terms, we obtain the phase diagram with respect to the ratio of AA interlayer hopping (w 0 ) and AB interlayer hopping (w 1 ). When the interlayer hopping ratio is close to the chiral limit (w 0 /w 1 ≲ 0.5), a quantum anomalous Hall state with Chern number v c = ±1 can be observed consistent with previous studies. Around the realistic value w 0 /w 1 ≈ 0.8, we find a spin and valley polarized, translation symmetry breaking, state with C 2⁢z T symmetry, a charge gap and a doubling of the moiré unit cell, dubbed theC 2⁢z T stripe phase. The real-space total charge distribution of this C 2⁢z T stripe phase in the flat band limit does not have modulation between different moiré unit cells, although the charge density in each layer is modulated, and the translation symmetry is strongly broken. Other symmetries, including C 2⁢z , C 2⁢x , particle-hole symmetry P, and the topology of the C 2⁢z T stripe phase, are also discussed in detail. We observed braiding and annihilation of the Dirac nodes by continuously turning on the order parameter to its fully self-consistent value, and provide a detailed explanation of the mechanism for the charge gap opening despite preserving C 2⁢z T and valley U⁡(1) symmetries. In the transition region between the quantum anomalous Hall phase and the C 2⁢z T stripe phase, we find an additional competing state with comparable energy corresponding to a phase with a tripling of the moiré unit cell.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Multitiered computational methodology for extracting three-dimensional rotational diffusion coefficients from x-ray photon correlation spectroscopy data without structural information

X-ray photon correlation spectroscopy (XPCS) is a powerful technique for analyzing particle systems by investigating their dynamics in suspensions across a broad range of temporal and spatial scales. This is done by illuminating samples with coherent x-ray beams and calculating the correlation function of the obtained x-ray scattering images. XPCS is uniquely suited for studying Brownian dynamics, consisting of translational and rotational diffusion. While traditional XPCS image analysis techniques can extract translational diffusion components, they are unable to estimate rotational diffusion coefficients. Here, we introduce a methodology that combines the angular-temporal cross-correlation analysis and a algorithmic framework called Multi-Tiered Estimation for Correlation Spectroscopy in 3D for estimating three-dimensional rotational diffusion coefficients from XPCS images of three-dimensional particle systems. We demonstrate our methodology for extracting rotational diffusion coefficients from XPCS data by applying it to simulated noisy x-ray images of systems of crossing nanotubes and proteins that evolve under translational and rotational Brownian motion for different diffusion rates. Furthermore, our results show that our approach determines rotational diffusion coefficients within a few percent error.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Operator dynamics in Floquet many-body systems

We study operator dynamics in many-body quantum systems, focusing on generic features of systems that are ergodic, spatially extended, and lack conserved densities. Quantum circuits of various types provide simple models for such systems. We focus on Floquet quantum circuits, comparing their behavior with what has been found previously for circuits that are random in time. Floquet circuits, which have discrete time-translation symmetry, represent an intermediate case between circuits that are random in time and lack any symmetry, and systems with a time-independent Hamiltonian and continuous time-translation invariance. By making this comparison, one of our aims is to identify signatures of time-translation symmetry in Floquet operator dynamics. To characterize behavior we examine a variety of quantities in solvable models and numerically: operator autocorrelation functions; the partial spectral form factor; the out-of-time-order correlator (OTOC); and the paths in operator space that make the dominant contributions to the ensemble-averaged autocorrelation functions. Our most striking result is that ensemble-averaged autocorrelation functions show behavior that is distinctively different in Floquet systems compared to systems in which successive time-steps are independent. Specifically, while average autocorrelation functions decay on a microscopic timescale for circuits that are random in time, in Floquet systems they have a late-time tail with a duration that grows parametrically with the size of the operator support. In the simplest models this tail is separated from the initial decay by a minimum, so that the average autocorrelation function has an intermediate-time peak. The existence of these tails provides a way to understand deviations of the spectral form factor from random matrix behavior at times shorter than the Thouless time. In contrast to this feature in autocorrelation functions, we find no new aspects to the behavior of OTOCs for Floquet models compared to random-in-time circuits. We show that this difference between averaged autocorrelation functions and OTOCs can be understood in terms of the paths in operator space that contribute to the two quantities: paths for the former retain a limited support at late times, while paths for the latter are dominated by operator spreading. Published by the American Physical Society 2025

Yoshimura, Takato (ORCID:0000000309159846)↗
DOE OSTI2023

Energy cost of localization of relational quantum information

Entanglement of spatially separated quantum states is usually defined with respect to a reference frame provided by some external observer. Thus, if one wishes to localize the quantum information within a spatially separated entangled state, one must enact an entanglement extraction protocol also defined with respect to that external frame. Entanglement extraction for Gaussian ground states in such an external frame construction has been shown to require a minimum energy and is hence an interesting process for gravitational physics, where examinations of localization vs energy cost have a long history. General covariance, however, precludes dependence on external frames. In order to enact an extraction protocol in a generally covariant theory, dependence on the external reference frame must first be removed and the states made relational. Here, we examine the implementation of an extraction protocol for Gaussian states, whose center of mass and relational degrees of freedom are entangled, in a relational toy model where translation invariance stands in for full diffeomorphism invariance. Constructing fully relational states and the corresponding extraction/localization can, in principle, be done in two ways. External frame position information can be removed through 𝐺-twirling over translations or one can spontaneously break the translation symmetry via the gradient of an auxiliary field, or 𝑍-model. We determine the energetics of quantum information localization after the states have been made fully relational via both the 𝐺-twirl and 𝑍-model. We also show one can obtain the 𝐺-twirl construction from a 𝑍-model as a limit of positive operator valued measurements.

79 ASTRONOMY AND ASTROPHYSICS↗