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At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes

Abstract Cytochromes are electron transfer (ET) proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electrons outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis, and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and to elucidate the stepwise ET along the respiratory paths. However, investigating direct ET events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. Nuclear magnetic resonance (NMR) spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor ET within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of ET between c-type cytochromes, using as model a triheme periplasmic cytochrome and a membrane-associated monoheme cytochrome from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional ET within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory ET chains.

Morgado, Leonor (ORCID:0000000237605180)↗
DOE OSTI2020

Mycobacterial DNA polymerase I: activities and crystal structures of the POL domain as apoenzyme and in complex with a DNA primer-template and of the full-length FEN/EXO–POL enzyme

Mycobacterial Pol1 is a bifunctional enzyme composed of an N-terminal DNA flap endonuclease/5' exonuclease domain (FEN/EXO) and a C-terminal DNA polymerase domain (POL). Here we document additional functions of Pol1: FEN activity on the flap RNA strand of an RNA:DNA hybrid and reverse transcriptase activity on a DNA-primed RNA template. We report crystal structures of the POL domain, as apoenzyme and as ternary complex with 3'-dideoxy-terminated DNA primer-template and dNTP. The thumb, palm, and fingers subdomains of POL form an extensive interface with the primer-template and the triphosphate of the incoming dNTP. Progression from an open conformation of the apoenzyme to a nearly closed conformation of the ternary complex entails a disordered-to-ordered transition of several segments of the thumb and fingers modules and an inward motion of the fingers subdomain—especially the O helix—to engage the primer-template and dNTP triphosphate. Distinctive structural features of mycobacterial Pol1 POL include a manganese binding site in the vestigial 3' exonuclease subdomain and a non-catalytic water-bridged magnesium complex at the protein-DNA interface. We report a crystal structure of the bifunctional FEN/EXO–POL apoenzyme that reveals the positions of two active site metals in the FEN/EXO domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Pot1 promotes telomere DNA replication via the Stn1-Ten1 complex in fission yeast

Abstract Telomeres are nucleoprotein complexes that protect the chromosome-ends from eliciting DNA repair while ensuring their complete duplication. Pot1 is a subunit of telomere capping complex that binds to the G-rich overhang and inhibits the activation of DNA damage checkpoints. In this study, we explore new functions of fission yeast Pot1 by using a pot1-1 temperature sensitive mutant. We show that pot1 inactivation impairs telomere DNA replication resulting in the accumulation of ssDNA leading to the complete loss of telomeric DNA. Recruitment of Stn1 to telomeres, an auxiliary factor of DNA lagging strand synthesis, is reduced in pot1-1 mutants and overexpression of Stn1 rescues loss of telomeres and cell viability at restrictive temperature. We propose that Pot1 plays a crucial function in telomere DNA replication by recruiting Stn1-Ten1 and Polα-primase complex to telomeres via Tpz1, thus promoting lagging-strand DNA synthesis at stalled replication forks.

Carvalho Borges, Pâmela C. (ORCID:0000000244919874↗
DOE OSTI2025

Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass

Genomic prediction has accelerated breeding processes and provided mechanistic insights into the genetic bases of complex traits. To further optimize genomic prediction, we assess the impact of genome assemblies, genotyping approaches, variant types, allelic complexities, polyploidy levels, and population structures on the prediction of 20 complex traits in switchgrass (Panicum virgatum L.), a perennial biofuel feedstock. Surprisingly, short read-based genome assembly performs comparably to or even better than long read-based assembly. Due to higher gene coverage, exome capture and multi-allelic variants outperform genotyping-by-sequencing and bi-allelic variants, respectively. Tetraploid models show higher prediction accuracy than octoploid models for most traits, likely due to the greater genetic distances among tetraploids. Depending on the trait in question, different types of variants need to be integrated for optimal predictions. Furthermore, our study provides insights into the factors influencing genomic prediction outcomes, guiding best practices for future studies and for improving agronomic traits in switchgrass and other species through selective breeding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes

Abstract Accurately reconstructing the reticulate histories of polyploids remains a central challenge for understanding plant evolution. Although phylogenetic networks can provide insights into relationships among polyploid lineages, inferring networks may be hindered by the complexities of homology determination in polyploid taxa. We use simulations to show that phasing alleles from allopolyploid individuals can improve phylogenetic network inference under the multispecies coalescent by obtaining the true network with fewer loci compared with haplotype consensus sequences or sequences with heterozygous bases represented as ambiguity codes. Phased allelic data can also improve divergence time estimates for networks, which is helpful for evaluating allopolyploid speciation hypotheses and proposing mechanisms of speciation. To achieve these outcomes in empirical data, we present a novel pipeline that leverages a recently developed phasing algorithm to reliably phase alleles from polyploids. This pipeline is especially appropriate for target enrichment data, where the depth of coverage is typically high enough to phase entire loci. We provide an empirical example in the North American Dryopteris fern complex that demonstrates insights from phased data as well as the challenges of network inference. We establish that our pipeline (PATÉ: Phased Alleles from Target Enrichment data) is capable of recovering a high proportion of phased loci from both diploids and polyploids. These data may improve network estimates compared with using haplotype consensus assemblies by accurately inferring the direction of gene flow, but statistical nonidentifiability of phylogenetic networks poses a barrier to inferring the evolutionary history of reticulate complexes.

Evolutionary Biology↗
DOE OSTI2025

Krylov complexity in mixed phase space

We investigate the Krylov complexity of thermofield double states in systems with mixed phase space, uncovering a direct correlation with the Brody distribution, which interpolates between Poisson and Wigner statistics. Our analysis spans two-dimensional random matrix models featuring (I) GOE-Poisson and (II) GUE-Poisson transitions and extends to higher-dimensional cases, including a stringy matrix model (GOE-Poisson) and the mass-deformed SYK model (GUE-Poisson). Krylov complexity consistently emerges as a reliable marker of quantum chaos, displaying a characteristic peak in the chaotic regime that gradually diminishes as the Brody parameter approaches zero, signaling a shift toward integrability. These results establish Krylov complexity as a powerful diagnostic of quantum chaos and highlight its interplay with eigenvalue statistics in mixed phase systems.

chaos & nonlinear dynamics↗
DOE OSTI2021

Validity of Machine Learning in the Quantitative Analysis of Complex Scanning Near-Field Optical Microscopy Signals Using Simulated Data

Scattering-type scanning near-field optical microscope (s-SNOM) is a modern technique for subdiffractional optical imaging and spectroscopy. Over the past two decades, tremendous efforts have been devoted to modeling complex tip-sample interactions in s-SNOM, aimed at understanding the electrodynamics of materials at the nanoscale. However, due to complexities in analytical methods and the limited computation power for fully numerical simulations, compromises must be made to facilitate the modeling of tip-sample interaction, such as using quasistatic approximation or unrealistic tip geometries. Here, we apply a variety of widely utilized machine-learning methods, including k nearest neighbor and feedforward neural network etc. to study the phase-resolved spectroscopic near-field response. With only a small set of training data, which is simulated using the finite-dipole model, we demonstrate that the relation between the experimental near-field signal and sample optical constant can be one to one mapped without the need for tip modeling: for a given material with a moderate dielectric function, its complex near-field spectrum can be accurately determined within the mid-IR spectral range, and vice versa. Our preliminary study sets the stage for future exploration using real experimental data. Our method is beneficial for processing the increasing amount of data accumulated across many research groups and especially useful for user facilities such as synchrotron-based national laboratories where a large amount of data is generated on a daily basis.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Complex structure due to As bonding and interplay with electronic structure in superconducting BaNi 2 As 2

BaNi 2 As 2 is a superconductor chemically related to the Fe-based superconductors, with a complex and poorly understood structural phase transition. We show, based on first-principles calculations, that, in fact, there are two distinct competing structures. These structures are different from the electronic, transport, and bonding points of view but are close in energy. These arise due to complex As bonding patterns and drive distortions of the Ni layers. This is supported by photoemission experiments. This is very distinct from views of the distortion as being primarily driven by electrons at the Fermi surface as in a classical charge density wave, or by correlated electron physics associated with the Ni d electrons and the Ni d orbitals. The structural distortion, although connected with As does lead to an interplay of electronic and structural behavior including induced anisotropic electronic transport. Here, the local bonding nature of the instabilities and the competition between distortions is discussed in the context of the complex behavior observed in BaNi 2 As 2 samples.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Origin of spin-driven ferroelectricity and effect of external pressure on the complex magnetism of the 6⁢ H perovskite Ba 3 ⁢Ho⁢Ru 2⁢ O 9

The compound Ba 3 HoRu 2 O 9 magnetically orders at 50 K (T N1 ), followed by another complex magnetic ordering at 10.2 K (T N2 ). The second magnetic phase transition was characterized by the coexistence of two competing magnetic ground states associated with two different magnetic wave vectors (K 1 = 0.5 0 0 and K 2 = 0.25 0.25 0). The multiferroicity and magnetoelectric coupling were predicted below T N2 in these 4d-based materials. Here, in this work, we have discussed the origin of spin-driven ferroelectricity, which is not known yet, and the nature of magnetoelectric domains. We have investigated the compound through time-of-flight neutron diffraction, synchrotron x-ray diffraction (XRD), ac susceptibility, frequency-dependent complex dielectric spectroscopy, and dc magnetization under external pressure. We have demonstrated that the noncollinear structure involving two different magnetic ions, Ru (4d) and Ho (4f), breaks the spatial inversion symmetry via inverse Dzyaloshinskii-Moriya (DM) interaction through strong 4d-4f magnetic correlation, which shifts the oxygen atoms and results in nonzero polarization. Such an observation of inverse DM interaction from two different magnetic ions which cause ferroelectricity is rarely observed. The stronger spin-orbit coupling of 4d orbital might play a major role in creating DM interaction of noncollinear spins. We have systematically studied the spin and dipolar dynamics, which exhibit intriguing behavior with shorter coherence lengths of second magnetic phase associated with the k 2 wave vector. The results manifest the development of finite-size magnetoelectric domains instead of true long-range ordering, which justifies the experimentally obtained low value of ferroelectric polarization. The lattice parameters and volume show a sharp anomaly at T N2 obtained by analyzing the temperature-dependence XRD, which is consistent with the ferroelectric transition, predicting a noncentrosymmetric space group, $P\bar{6}2c$, for this compound. Furthermore, we have investigated the effect of external pressure on this complex magnetism. The result reveals an enhancement of ordering temperature by the application of external pressure (~1.6 K/GPa). The external pressure might favor stabilizing the magnetic ground state associated with second magnetic phase. Our study shows an unconventional mechanism of spin-driven ferroelectricity involving inverse DM interaction between Ru (4d) and Ho (4f) magnetic ions due to strong 4d-4f cross coupling.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Intrinsic and complex defect engineering of quasi-one-dimensional ribbons Sb 2 S 3 for photovoltaics performance

Sb 2 S 3 has attracted great attention recently as a prospective solar cell absorber material. In this work, intrinsic defects, dopants, and their complexes in Sb 2 S 3 are systematically investigated by using hybrid functional theory. V Sb and V S are dominant native defects and pin the Fermi level near the midgap, which is consistent with the high resistivity observed experimentally. Both V Sb and V S introduce deep levels inside the band gap, which can trap free carriers. Our calculated deep transition levels of V Sb and Sb S are consistent well with the results of the deep-level transient spectroscopy measurement. We further study dopants (including Cu, Ti, Zn, Br, and Cl) in Sb 2 S 3 and find that Zn and Br/Cl are shallow acceptors and donors, respectively, which may be used to control the carrier and trap densities in Sb 2 S 3 . In addition, the defect complexes, i.e., Cu(Zn) Sb +V S and Cl(Br) S +V Sb are also investigated. The interaction between the donor and acceptor defects makes the defect levels of complexes shallower and less detrimental to carrier transport.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Two transitions in complex eigenvalue statistics: Hermiticity and integrability breaking

Open quantum systems have complex energy eigenvalues which are expected to follow non-Hermitian random matrix statistics, when chaotic, or two-dimensional (2d) Poisson statistics, when integrable. We investigate the spectral properties of a many-body quantum spin chain, i.e., the Hermitian Heisenberg model with imaginary disorder. Its rich complex eigenvalue statistics is found to separately break both Hermiticity and integrability at different scales of the disorder strength. With no disorder, the system is integrable and Hermitian, with spectral statistics corresponding to the 1d Poisson point process. At very small disorder, we find a transition from 1d Poisson statistics to an effective D -dimensional Poisson point process, showing Hermiticity breaking. At intermediate disorder, we find integrability breaking, as inferred from the statistics matching that of non-Hermitian complex symmetric random matrices in class AI † . For large disorder, as the spins align, we recover the expected integrability (now in the non-Hermitian setup), indicated by 2d Poisson statistics. These conclusions are based on fitting the spin-chain data of numerically generated nearest- and next-to-nearest-neighbor spacing distributions to an effective 2d Coulomb gas description at inverse temperature β . We confirm that such an effective description of random matrices also applies in classes AI † and AII † up to next-to-nearest-neighbor spacings. Published by the American Physical Society 2025

Akemann, Gernot (ORCID:0000000217104258)↗
DOE OSTI2024

Glassy Word Problems: Ultraslow Relaxation, Hilbert Space Jamming, and Computational Complexity

We introduce a family of local models of dynamics based on “word problems” from computer science and group theory, for which we can place rigorous lower bounds on relaxation timescales. These models can be regarded either as random circuit or local Hamiltonian dynamics and include many familiar examples of constrained dynamics as special cases. The configuration space of these models splits into dynamically disconnected sectors, and for initial states to relax, they must “work out” the other states in the sector to which they belong. When this problem has a high time complexity, relaxation is slow. In some of the cases we study, this problem also has high space complexity. When the space complexity is larger than the system size, an unconventional type of jamming transition can occur, whereby a system of a fixed size is not ergodic but can be made ergodic by appending a large reservoir of sites in a trivial product state. This finding manifests itself in a new type of Hilbert space fragmentation that we call fragile fragmentation. We present explicit examples where slow relaxation and jamming strongly modify the hydrodynamics of conserved densities. In one example, density modulations of wave vector q exhibit almost no relaxation until times O ( exp ( 1 / q ) ) , at which point they abruptly collapse. We also comment on extensions of our results to higher dimensions. Published by the American Physical Society 2024

Physics↗
DOE OSTI2025

Defect Complexes in CrSBr Revealed Through Electron Microscopy and Deep Learning

Atomic defects underpin the properties of van der Waals materials, and their understanding is essential for advancing quantum and energy technologies. Scanning transmission electron microscopy is a powerful tool for defect identification in atomically thin materials, and extending it to multilayer and beam-sensitive materials would accelerate their exploration. Here, we establish a comprehensive defect library in a bilayer of the magnetic quasi-1D semiconductor CrSBr by combining atomic-resolution imaging, deep learning, and calculations. We apply a custom-developed machine learning work flow to detect, classify, and average point vacancy defects. This classification enables us to uncover several distinct Cr interstitial defect complexes, combined Cr and Br vacancy defect complexes, and lines of vacancy defects that extend over many unit cells. We show that their occurrence is in agreement with our computed structures and binding energy densities, reflecting the intriguing layer interlocked crystal structure of CrSBr. Our ab initio calculations show that the interstitial defect complexes give rise to highly localized electronic states. These states are of particular interest due to the reduced electronic dimensionality and magnetic properties of CrSBr and are, furthermore, predicted to be optically active. Our results broaden the scope of defect studies in challenging materials and reveal new defect types in bilayer CrSBr that can be extrapolated to the bulk and to over 20 materials belonging to the same FeOCl structural family.

deep learning↗
DOE OSTI2025

Sparsity dependence of Krylov state complexity in the SYK model

We study the Krylov state complexity of the Sachdev-Ye-Kitaev (SYK) model for 𝑁 ≤28 Majorana fermions with 𝑞-body fermion interaction with 𝑞 =4, 6, 8 for a range of sparse parameter 𝑘 that controls the number of remaining terms in the original SYK model after sparsification. The critical value of 𝑘 below which the model ceases to be holographic, denoted 𝑘 𝑐 , has been subject of several recent investigations. Using Krylov complexity as a probe, we find that the peak value of complexity does not change as we increase 𝑘 beyond 𝑘 ≥ 𝑘 min at large temperatures. We argue that this behavior is related to the change in the holographic nature of the Hamiltonian in the sparse SYK-type models such that the model is holographic for all 𝑘 ≥ 𝑘 min ≈ 𝑘 𝑐 . Our results provide a novel way to determine 𝑘 𝑐 in SYK-type models.

gauge-gravity dualitites↗
DOE OSTI2022

Deep Learning-Assisted Real-Time Forward Modeling of Electromagnetic Logging in Complex Formations

Higher dimensional (i.e., 2-D and 3-D) modeling is indispensable to correctly evaluate the responses of electromagnetic logging tools in complex formation environments. However, limited by the high computational cost of rigorous modeling such as finite difference method and the finite element method, the real-time applications in the well logging industry primarily rely on the 1-D forward solver, which would result in erroneous formation evaluation for complex scenarios. As a result, aiming at realizing fast modeling for electromagnetic logging tools in complex formations, this paper proposes a general framework assisted by deep neural networks (DNNs). The framework consists of three modules: earth model classification, parameter extraction, and surrogate construction. Separate DNNs are trained and tested for different modules. The accuracy and efficiency of the DNN assisted fast modeling are validated by several experiments. Here, this study finds that the fast modeling assisted by DNNs is able to calculate the tool responses and reconstruct the subsurface formations in real-time.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Plant terpene specialized metabolism: complex networks or simple linear pathways?

From the perspectives of pathway evolution, discovery and engineering of plant specialized metabolism, the nature of the biosynthetic routes represents a critical aspect. Classical models depict biosynthesis typically from an end-point angle and as linear, for example, connecting central and specialized metabolism. As the number of functionally elucidated routes increased, the enzymatic foundation of complex plant chemistries became increasingly well understood. The perception of linear pathway models has been severely challenged. With a focus on plant terpenoid specialized metabolism, we review here illustrative examples supporting that plants have evolved complex networks driving chemical diversification. The completion of several diterpene, sesquiterpene and monoterpene routes shows complex formation of scaffolds and their subsequent functionalization. These networks show that branch points, including multiple sub-routes, mean that metabolic grids are the rule rather than the exception. This concept presents significant implications for biotechnological production.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Bayesian, Multifidelity Operator Learning for Complex Engineering Systems–A Position Paper

Abstract Deep learning has significantly improved the state-of-the-art in computer vision and natural language processing, and holds great potential to design effective tools for predicting and simulating complex engineering systems. In particular, scientific machine learning seeks to apply the power of deep learning to scientific and engineering tasks, with operator learning (OL) emerging as a particularly effective tool. OL can approximate nonlinear operators arising in complex engineering systems, making it useful for simulating, designing, and controlling those systems. In this position paper, we provide a comprehensive overview of OL, including its potential applications to complex engineering domains. We cover three variations of OL approaches: deterministic OL for modeling nonautonomous systems, OL with uncertainty quantification (UQ) capabilities, and multifidelity OL. For each variation, we discuss drawbacks and potential applications to engineering, in addition to providing a detailed explanation. We also highlight how multifidelity OL approaches with UQ capabilities can be used to design, optimize, and control engineering systems. Finally, we outline some potential challenges for OL within the engineering domain.

Computer Science↗
DOE OSTI2020

Proven Technologies for the Solidification of Complex Liquid Radioactive Waste (LRW): Global Case Studies of Applications and Disposal Options - 20424

Legacy radioactive waste streams from the Cold War still exist and newly generated waste streams from nuclear power plants and research institutes go untreated and expose environmental hazards at many nuclear sites. The nature of the waste is diverse, depending upon the source or the process from which it originated. The most problematic waste streams include complex liquids such as organic (tri-butyl-phosphate TBP) solutions contaminated with Pu and U isotopes, mixed sludge types, high acid radioactive waste, H-3 contaminated organic and aqueous streams, etc. Technological, environmental and economic challenges exist for the treatment and disposal of such waste streams. A proven technology that has been applied to LRW on a global basis provides one option as a low-cost solution to legacy streams and small volume, highly complex LRW frequently found during decommissioning at nuclear power plants and weapons sites. The engineered polymer technology from Nochar, USA, is capable of solidifying standard and highly complex LLW and ILW waste streams for interim or final storage, or for incineration. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗