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Results for “Complexity bounding”

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 OSTI2024

Dinickel enzyme evolved to metabolize the pharmaceutical metformin and its implications for wastewater and human microbiomes

Metformin is the first-line treatment for type II diabetes patients and a pervasive pollutant with more than 180 million kg ingested globally and entering wastewater. The drug’s direct mode of action is currently unknown but is linked to effects on gut microbiomes and may involve specific gut microbial reactions to the drug. In wastewater treatment plants, metformin is known to be transformed by microbes to guanylurea, although genes encoding this metabolism had not been elucidated. In the present study, we revealed the function of two genes responsible for metformin decomposition (mfmA and mfmB) found in isolated bacteria from activated sludge. MfmA and MfmB form an active heterocomplex (MfmAB) and are members of the ureohydrolase protein superfamily with binuclear metal-dependent activity. MfmAB is nickel-dependent and catalyzes the hydrolysis of metformin to dimethylamine and guanylurea with a catalytic efficiency (k cat /K M ) of 9.6 × 10 3 M -1 s -1 and KM for metformin of 0.82 mM. MfmAB shows preferential activity for metformin, being able to discriminate other close substrates by several orders of magnitude. Crystal structures of MfmAB show coordination of binuclear nickel bound in the active site of the MfmA subunit but not MfmB subunits, indicating that MfmA is the active site for the MfmAB complex. Mutagenesis of residues conserved in the MfmA active site revealed those critical to metformin hydrolase activity and its small substrate binding pocket allowed for modeling of bound metformin. In conclusion, this study characterizes the products of the mfmAB genes identified in wastewater treatment plants on three continents, suggesting that metformin hydrolase is widespread globally in wastewater.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations

Abstract Molecular analysis of interactions between IgE antibody and allergen allows the structural basis of IgE recognition to be defined. Human IgE (hIgE) epitopes of respiratory lipocalin allergens, including Can f 1, remain elusive due to a lack of IgE‐allergen complexes. This study aims to map the structure of allergenic epitopes on Can f 1. The fragment antigen‐binding (Fab) regions of Can f 1 specific human IgE monoclonal antibodies (hIgE mAb) were used to determine the structures of IgE epitopes. Epitope mutants were designed to target Can f 1 epitopes. Immunoassays and a human FcεRIαtransgenic mouse model of passive anaphylaxis in vivo were used to assess the functional activity of epitope mutants. Crystal structures of natural or recombinant Can f 1 complexed with two hIgE mAb 1J11 and 12F3 Fabs, respectively, were determined. The hIgE mAb bound to two partially overlapping epitopes and recognized two different Can f 1 conformations. The hIgE mAb 12F3 showed an unusual mode of binding by protruding its heavy chain CDR3 inside the Can f 1 calyx. Epitope mutants generated based on the structural analyses displayed a 64%–89% reduction in IgE antibody binding and failed to induce passive anaphylaxis in a human FcεRIαtransgenic mouse model. In summary, the structures of Can f 1‐hIgE Fab complexes revealed two unique and partially overlapping epitopes on Can f 1. The modification of the identified IgE epitopes provides a pathway for the design of hypoallergens to treat dog allergies.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Advancing Tassel Detection and Counting: Annotation and Algorithms

Tassel counts provide valuable information related to flowering and yield prediction in maize, but are expensive and time-consuming to acquire via traditional manual approaches. High-resolution RGB imagery acquired by unmanned aerial vehicles (UAVs), coupled with advanced machine learning approaches, including deep learning (DL), provides a new capability for monitoring flowering. In this article, three state-of-the-art DL techniques, CenterNet based on point annotation, task-aware spatial disentanglement (TSD), and detecting objects with recursive feature pyramids and switchable atrous convolution (DetectoRS) based on bounding box annotation, are modified to improve their performance for this application and evaluated for tassel detection relative to Tasselnetv2+. The dataset for the experiments is comprised of RGB images of maize tassels from plant breeding experiments, which vary in size, complexity, and overlap. Results show that the point annotations are more accurate and simpler to acquire than the bounding boxes, and bounding box-based approaches are more sensitive to the size of the bounding boxes and background than point-based approaches. Overall, CenterNet has high accuracy in comparison to the other techniques, but DetectoRS can better detect early-stage tassels. The results for these experiments were more robust than Tasselnetv2+, which is sensitive to the number of tassels in the image.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Quantifying the generalization error in deep learning in terms of data distribution and neural network smoothness

We report the accuracy of deep learning, i.e., deep neural networks, can be characterized by dividing the total error into three main types: approximation error, optimization error, and generalization error. Whereas there are some satisfactory answers to the problems of approximation and optimization, much less is known about the theory of generalization. Most existing theoretical works for generalization fail to explain the performance of neural networks in practice. To derive a meaningful bound, we study the generalization error of neural networks for classification problems in terms of data distribution and neural network smoothness. We introduce the cover complexity (CC) to measure the difficulty of learning a data set and the inverse of the modulus of continuity to quantify neural network smoothness. A quantitative bound for expected accuracy/error is derived by considering both the CC and neural network smoothness. Although most of the analysis is general and not specific to neural networks, we validate our theoretical assumptions and results numerically for neural networks by several data sets of images. The numerical results confirm that the expected error of trained networks scaled with the square root of the number of classes has a linear relationship with respect to the CC. We also observe a clear consistency between test loss and neural network smoothness during the training process. In addition, we demonstrate empirically that the neural network smoothness decreases when the network size increases whereas the smoothness is insensitive to training dataset size.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Bounding uncertainty in functional data: A case study

Functional data are fast becoming a preeminent source of information across a wide range of industries. A particularly challenging aspect of functional data is bounding uncertainty. In this unique case study, we present our attempts at creating bounding functions for selected applications at Sandia National Laboratories (SNL). The first attempt involved a simple extension of functional principal component analysis (fPCA) to incorporate covariates. Though this method was straightforward, the extension was plagued by poor coverage accuracy for the bounding curve. This led to a second attempt utilizing elastic methodology which yielded more accurate coverage at the cost of more complexity.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

High-order limiting methods using maximum principle bounds derived from the Boltzmann equation I: Euler equations

The use of limiting methods for high-order numerical approximations of hyperbolic conservation laws generally requires defining an admissible region/bounds for the solution. In this work, we present a novel approach for computing solution bounds and limiting for the Euler equations through the kinetic representation provided by the Boltzmann equation, which allows for extending limiters designed for linear advection directly to the Euler equations. Given an arbitrary set of solution values to compute bounds over (e.g., numerical stencil) and a desired linear advection limiter, the proposed approach yields an analytic expression for the admissible region of particle distribution function values, which may be numerically integrated to yield a set of bounds for the density, momentum, and total energy. Further, these solution bounds are shown to preserve positivity of density/pressure/internal energy and, when paired with a limiting technique, can robustly resolve strong discontinuities while recovering high-order accuracy in smooth regions without any ad hoc corrections (e.g., relaxing the bounds). This approach is demonstrated in the context of an explicit unstructured high-order discontinuous Galerkin/flux reconstruction scheme for a variety of difficult problems in gas dynamics, including cases with extreme shocks and shock-vortex interactions. Furthermore, this work presents a foundation for limiting techniques for more complex macroscopic governing equations that can be derived from an underlying kinetic representation for which admissible solution bounds are not well-understood.

42 ENGINEERING↗
DOE OSTI2023

Insights into pyrrolysine function from structures of a trimethylamine methyltransferase and its corrinoid protein complex

The 22nd genetically encoded amino acid, pyrrolysine, plays a unique role in the key step in the growth of methanogens on mono-, di-, and tri-methylamines by activating the methyl group of these substrates for transfer to a corrinoid cofactor. Previous crystal structures of the Methanosarcina barkeri monomethylamine methyltransferase elucidated the structure of pyrrolysine and provide insight into its role in monomethylamine activation. Herein, we report the second structure of a pyrrolysine-containing protein, the M. barkeri trimethylamine methyltransferase MttB, and its structure bound to sulfite, a substrate analog of trimethylamine. We also report the structure of MttB in complex with its cognate corrinoid protein MttC, which specifically receives the methyl group from the pyrrolysine-activated trimethylamine substrate during methanogenesis. Together these structures provide key insights into the role of pyrrolysine in methyl group transfer from trimethylamine to the corrinoid cofactor in MttC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Quantitative Separation of Unknown Organic–Metal Complexes by Liquid Chromatography–Inductively Coupled Plasma-Mass Spectrometry

Dissolved organic matter (DOM) is widely recognized to control the solubility and reactivity of trace metals in the environment. However, the mechanisms that govern metal-DOM complexation remain elusive, primarily due to the analytical challenge of fractionating and quantifying metal–organic species within the complex mixture of organic compounds that comprise DOM. Here, we describe a quantitative method for fractionation and element-specific detection of organic–metal complexes using liquid chromatography with online inductively coupled plasma mass spectrometry (LC–ICP-MS). The method implements a post-column compensation gradient to stabilize ICP–MS elemental response across the LC solvent gradient, thereby overcoming a major barrier to achieving quantitative accuracy with LC–ICP-MS. With external calibration and internal standard correction, the method yields concentrations of organic–metal complexes that were consistently within 6% of their true values, regardless of the complex’s elution time. We used the method to evaluate the effects of four stationary phases (C18, phenyl, amide, and pentafluoroylphenyl propyl) on the recovery and separation of environmentally relevant trace metals (Mn, Fe, Co, Ni, Cu, Zn, Cd, and Pb) in Suwannee River Fulvic Acid and Suwannee River Natural Organic Matter. The C18, amide, and phenyl phases generally yielded optimal metal recoveries (>75% for all metals except Pb), with the phenyl phase separating polar species to a greater extent than C18 or amide. We also fractionated organic-bound Fe, Cu, and Ni in oxidized and reduced soils, revealing divergent metal-DOM speciation across soil redox environments. Finally, by enabling quantitative fractionation of DOM-bound metals, our method offers a means for advancing a mechanistic understanding of metal–organic complexation throughout the environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Phosphine Ligand Binding and Catalytic Activity of Group 10–14 Heterobimetallic Complexes

We report heterobimetallic complexes have attracted much interest due to their broad range of structures and reactivities as well as unique catalytic abilities. Additionally, these complexes can be utilized as single-source precursors for the synthesis of binary intermetallic compounds. An example is the family of bis(pyridine-2-thiolato)dichloro-germanium and tin complexes of group 10 metals (Pd and Pt). The reactivity of these heterobimetallic complexes is highly tunable through substitution of the group 14 element and the neutral ligand bound to the transition metal. Here, we study the binding energies of three different phosphorous-based ligands, PR 3 (R = Bu, Ph, and OPh) by density functional theory and restricted Hartree–Fock methods. The PR 3 ligand-binding energies follow the trend of PBu 3 > PPh 3 > P(OPh) 3 , in agreement with their sigma-bonding ability. These results are confirmed by ligand exchange experiments monitored with 31 P NMR spectroscopy, in which a weaker binding PR 3 ligand is replaced with a stronger one. Furthermore, we demonstrate that the heterobimetallic complexes are active catalysts in the Negishi coupling reaction, where stronger binding PR 3 ligands inhibit access to an active site at the metal center. Similar strategies could be applied to other complexes to better understand their ligand-binding energetics and predict their reactivity as both precursors and catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Dehydration of UO 2 Cl 2 ·3H 2 O and Nd(NO 3 ) 3 ·6H 2 O with a Soft Donor Ligand and Comparison of Their Interactions through X-ray Diffraction and Theoretical Investigation [plus Supplemental Information]

Herein we investigated whether the relatively Lewis basic imidazole-2-thiones could be used to substitute water ligands bound to f-element cations and generate f-element soft donor complexes. Reactions of 1,3-diethylimidazole-2-thione (C 2 C 2 ImT) with Nd(NO 3 ) 3 ·6H 2 O and UO 2 Cl 2 ·3H 2 O led to the isolation of the anhydrous thione complexes Nd(NO 3 ) 3 (C 2 C 2 ImT) 3 and UO 2 Cl 2 (C 2 C 2 ImT) 2 , characterized by single crystal X-ray diffraction. Differences in the strength of metal–thione interactions have been examined by means of the crystal structure analysis and density functional theory (DFT) calculations. The C 2 C 2 ImT ligands were found to be affected by both coordination and noncovalent interactions, making it impossible to deconvolute the effects of one from the other. Calculated partial atomic charges indicated greater ligand-to-metal charge transfer in the [UO 2 ] 2+ complex, indicative of a stronger interaction. The reactivity of C 2 C 2 ImT demonstrates its usefulness in the preparation of f-element soft donor complexes from readily available hydrates that could be useful intermediates for promoting the coordination and studying the effects of soft donor anions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens

Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

SALSAA: a statistical approach to line shapes from an average atom

Ion-Stark line broadening is a key density diagnostic for hot dense plasmas relevant to inertial fusion and astrophysics. It is caused by interactions of a radiating ion with nearby perturbing ions, whose electric microfields lead to changes in bound-bound transition energies. Ion-Stark broadening becomes increasingly difficult to compute for complex, many-electron ions with myriad transitions. In this paper, we propose a simplified approach to ion-Stark broadening based on self-consistent ion distributions and electronic structure from an average-atom model. We find that this approach reproduces the line shape predictions of one traditional method for high-n K-shell emission lines in aluminum ions with accuracy sufficient for density diagnostics in thermal plasmas with equal ion and electron temperatures. We expect that this approach can be extended to provide a reasonable picture of ion-Stark broadening in many-electron ions, enabling rapid calculations of line profiles in complex spectra.

average-atom↗
DOE OSTI2020

Virtual-Voltage Partition-Based Approach to Optimal Transmission Switching

This article deals with optimal transmission switching (OTS) problems involving binary decisions about network topology and nonconvex power flow constraints. We adopt a semidefinite programming formulation for the optimal power flow (OPF) problem that, however, remains nonconvex due to the presence of discrete variables and bilinear products between the decision variables. To tackle the latter, we introduce a physically inspired, virtual-voltage approximation that leads to provable lower and upper bounds on the solution of the original problem. To deal with the exponential complexity caused by the discrete variables, we introduce a graph partition-based algorithm that breaks the problem into several parallel mixed-integer subproblems of smaller size. Simulations on the IEEE bus test cases demonstrate the high degree of accuracy and affordable computational requirements of our approach.

42 ENGINEERING↗
DOE OSTI2024

Charm meson and charm-meson molecule in an expanding hadron gas

We present our studies on the evolution of charm mesons after the kinetic freeze-out of the expanding hadron gas produced in a heavy-ion collision and the thermal correction to a loosely bound charm-meson molecule in a pion gas. The πD* → πD* reaction rates have t-channel singularities that give contributions inversely proportional to the thermal width of the D. The ratio of the D 0 and D + production rate can differ significantly from those predicted using the measured D* branching fractions. The thermal correction to a loosely bound charm-meson molecule in a pion gas comes primarily from the complex thermal energy shift of the charm-meson constituents.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

A synthetic cell density signal can drive proliferation in chick embryonic tendon cells and tendon cells from a full size rooster can produce high levels of procollagen in cell culture

Cell density signaling drives tendon morphogenesis by regulating both procollagen production and cell proliferation. The signal is composed of a small, highly conserved protein (SNZR P) tightly bound to a tissue-specific, unique lipid (SNZR L). This allows the complex (SNZR PL) to bind to the membrane of the cell and locally diffuse over a radius of ~1 mm. The cell produces low levels of this signal but the binding to the membrane increases with the number of tendon cells in the local environment. In this article SNZR P was produced in E.coli and SNZR L was chemically synthesized. The two bind together when heated to 60 °C in the presence of Ca ++ and Mg ++ and the synthesized SNZR PL at ng/ml levels can replace serum. Adding SNZR PL to the medium was also tested on primary tendon cells from adult roosters. The older cells were in a maintenance state in vivo and in cell culture they proliferate more slowly than embryonic cells. Nevertheless, after reaching a moderately high cell density, they produced high levels of procollagen similar to the embryonic cells. This data was not expected from older cells but suggests that adult tendon cells can regenerate the tissue after injury when given the correct signals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Compressing branch-and-bound trees

A branch-and-bound (BB) tree certifies a dual bound on the value of an integer program. In this work, we introduce the tree compression problem (TCP): Given a BB tree T that certifies a dual bound, can we obtain a smaller tree with the same (or stronger) bound by either (1) applying a different disjunction at some node in T or (2) removing leaves from T? Here we believe such post-hoc analysis of BB trees may assist in identifying helpful general disjunctions in BB algorithms. We initiate our study by considering computational complexity and limitations of TCP. We then conduct experiments to evaluate the compressibility of realistic branch-and-bound trees generated by commonly-used branching strategies, using both an exact and a heuristic compression algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism

Abstract DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A Model for the Signal Initiation Complex Between Arrestin-3 and the Src Family Kinase Fgr

Arrestins regulate a wide range of signaling events, most notably when bound to active G protein-coupled receptors (GPCRs). Among the known effectors recruited by GPCR-bound arrestins are Src family kinases, which regulate cellular growth and proliferation. Here, we focus on arrestin-3 interactions with Fgr kinase, a member of the Src family. Previous reports demonstrated that Fgr exhibits high constitutive activity, but can be further activated by both arrestin-dependent and arrestin-independent pathways. We report that arrestin-3 modulates Fgr activity with a hallmark bell-shaped concentration-dependence, consistent with a role as a signaling scaffold. Here, we further demonstrate using NMR spectroscopy that a polyproline motif within arrestin-3 interacts directly with the SH3 domain of Fgr. To provide a framework for this interaction, we determined the crystal structure of the Fgr SH3 domain at 1.9 Å resolution and developed a model for the GPCR-arrestin-3-Fgr complex that is supported by mutagenesis. This model suggests that Fgr interacts with arrestin-3 at multiple sites and is consistent with the locations of disease-associated Fgr mutations. Collectively, these studies provide a structural framework for arrestin-dependent activation of Fgr.

59 BASIC BIOLOGICAL SCIENCES↗