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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Micro Reactor Simulation Using the PROTEUS Suite in FY19

Two micro reactor cores were simulated using the MOC solver of PROTEUS: MegaPower for a heat pipe micro reactor and Holos-Quad for a high-temperature gas-cooled micro reactor. Verification of PROTEUS standalone was performed by simulating 2D and 3D core benchmark problems developed based on MegaPower and Holos-Quad. Simulation results indicated that PROTEUS successfully modelled 2D and 3D cores of the MegaPower and Holos-Quad micro reactors and PROTEUS eigenvalues agreed well with the SERPENT Monte Carlo solutions. For a heat pipe cooled micro reactor, multiphysics simulations were performed using PROTEUS / FLUENT / ANLHTP. The coupling system of the three codes were developed using Python-based drivers, which exchange the data (power, temperature, and heat rate) required for the coupling and control the boundary conditions of FLUENT and ANLHTP. The coupled system was qualitatively verified using a 3D unit assembly problem composed of six fuel rods and seven heat pipes, which was developed based on the MegaPower compositions. The steady-state problem was solved using FLUENT / ANLHTP with given asymmetric fuel powers, demonstrating the reasonable convergence of temperatures of 7 heat pipes. Transient simulations were also performed by making one out of 7 heat pipes fail. For the transient, the coupled system of PROTEUS / FLUENT / ANLHTP demonstrated reasonable changes of total power and heat pipe temperatures with time, accounting for temperature feedback effects. In this simulation, no effect of structural change was accounted for, which will be performed using ANSYS-mechanical in future along with further verification with larger or whole-core 3D problems.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2018

A High-Order Low-Order Algorithm with Exponentially Convergent Monte Carlo for Thermal Radiative Transfer

In this paper, we have implemented a new high-order low-order (HOLO) algorithm for solving thermal radiative transfer problems. The low-order (LO) system is based on the spatial and angular moments of the transport equation and a linear-discontinuous finite-element spatial representation, producing equations similar to the standard S 2 equations. The LO solver is fully implicit in time and efficiently resolves the nonlinear temperature dependence at each time step. The high-order (HO) solver utilizes exponentially convergent Monte Carlo (ECMC) to give a globally accurate solution for the angular intensity to a fixed-source pure-absorber transport problem. This global solution is used to compute consistency terms, which require the HO and LO solutions to converge toward the same solution. The use of ECMC allows for the efficient reduction of statistical noise in the Monte Carlo solution, reducing inaccuracies introduced through the LO consistency terms. Finally, we compare results with an implicit Monte Carlo code for one-dimensional gray test problems and demonstrate the efficiency of ECMC over standard Monte Carlo in this HOLO algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

A comparison of acceleration methods for solving the neutron transport k-eigenvalue problem

Over the past several years a number of papers have been written describing modern techniques for numerically computing the dominant eigenvalue of the neutron transport criticality problem. These methods fall into two distinct categories. The first category of methods rewrite the multi-group k-eigenvalue problem as a nonlinear system of equations and solve the resulting system using either a Jacobian-Free Newton–Krylov (JFNK) method or Nonlinear Krylov Acceleration (NKA), a variant of Anderson Acceleration. These methods are generally successful in significantly reducing the number of transport sweeps required to compute the dominant eigenvalue. The second category of methods utilize Moment-Based Acceleration (or High-Order/Low-Order (HOLO) Acceleration). These methods solve a sequence of modified diffusion eigenvalue problems whose solutions converge to the solution of the original transport eigenvalue problem. This second class of methods is, in our experience, always superior to the first, as most of the computational work is eliminated by the acceleration from the LO diffusion system. In this paper, we review each of these methods. Our computational results support our claim that the choice of which nonlinear solver to use, JFNK or NKA, should be secondary. The primary computational savings result from the implementation of a HOLO algorithm. We display computational results for a series of challenging multi-dimensional test problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2013

DBSI: DNA-binding site identifier

In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound (APO-29) and 30 bound (HOLO-30) protein structures distinct from the training data. We computed 480 candidate features for identifying protein residues that bind DNA, including new features that capture the electrostatic microenvironment within shells near the protein surface. Our iterative feature selection process identified features important in other models, as well as features unique to the DBSI model, such as a banded electrostatic feature with spatial separation comparable with the canonical width of the DNA minor groove. Validations and comparisons with established methods using a range of performance metrics clearly demonstrate the predictive advantage of DBSI, and its comparable performance on unbound (APO-29) and bound (HOLO-30) conformations demonstrates robustness to binding-induced protein conformational changes. Finally, we offer our feature data table to others for integration into their own models or for testing improved feature selection and model training strategies based on DBSI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor

A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 107 variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection (~2 μM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work.

Jha, Ramesh K.↗
DOE OSTI2015

Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH

Clostridium histolyticum collagenases ColG and ColH are segmental enzymes that are thought to be activated by Ca 2+ -triggered domain reorientation to cause extensive tissue destruction. The collagenases consist of a collagenase module (s1), a variable number of polycystic kidney disease-like (PKD-like) domains (s2a and s2b in ColH and s2 in ColG) and a variable number of collagen-binding domains (s3 in ColH and s3a and s3b in ColG). The X-ray crystal structures of Ca 2+ -bound holo s2b (1.4 Å resolution, R = 15.0%, R free = 19.1%) and holo s2a (1.9 Å resolution, R = 16.3%, R free = 20.7%), as well as of Ca 2+ -free apo s2a (1.8 Å resolution, R = 20.7%, R free = 27.2%) and two new forms of N-terminally truncated apo s2 (1.4 Å resolution, R = 16.9%, R free = 21.2%; 1.6 Å resolution, R = 16.2%, R free = 19.2%), are reported. The structurally similar PKD-like domains resemble the V-set Ig fold. In addition to a conserved β-bulge, the PKD-like domains feature a second bulge that also changes the allegiance of the subsequent β-strand. This β-bulge and the genesis of a Ca 2+ pocket in the archaeal PKD-like domain suggest a close kinship between bacterial and archaeal PKD-like domains. Different surface properties and indications of different dynamics suggest unique roles for the PKD-like domains in ColG and in ColH. Surface aromatic residues found on ColH s2a-s2b, but not on ColG s2, may provide the weak interaction in the biphasic collagen-binding mode previously found in s2b-s3. B -factor analyses suggest that in the presence of Ca 2+ the midsection of s2 becomes more flexible but the midsections of s2a and s2b stay rigid. The different surface properties and dynamics of the domains suggest that the PKD-like domains of M9B bacterial collagenase can be grouped into either a ColG subset or a ColH subset. The conserved properties of PKD-like domains in ColG and in ColH include Ca 2+ binding. Conserved residues not only interact with Ca 2+ , but also position the Ca 2+ -interacting water molecule. Ca 2+ aligns the N-terminal linker approximately parallel to the major axis of the domain. Ca 2+ binding also increases stability against heat and guanidine hydrochloride, and may improve the longevity in the extracellular matrix. The results of this study will further assist in developing collagen-targeting vehicles for various signal molecules.

Bauer, Ryan↗
DOE OSTI2015

X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O 2 -reduction states

During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O 2 to 2H 2 O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase ( Tth -MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth -MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O 2 reduction was found in a double conformation: Glu451a (~7 Å from the TNC) and Glu451b (~4.5 Å from the TNC). A positive peak of electron density above 3.5σ in an F o - F c map for Glu451a O ε2 indicates the presence of a carboxyl functional group at the side chain, while its significant absence in Glu451b strongly suggests a carboxylate functional group. In contrast, for apo Tth -MCO and in Hg-bound structures neither the positive peak nor double conformations were observed. Together, these observations provide the first structural evidence for a proton-relay mechanism in the MCO family and also support previous studies indicating that Asp106 does not provide protons for this mechanism. In addition, eight composite structures ( Tth -MCO-C1–8) with different X-ray-absorbed doses allowed the observation of different O 2 -reduction states, and a total depletion of T2Cu at doses higher than 0.2 MGy showed the high susceptibility of this Cu atom to radiation damage, highlighting the importance of taking radiation effects into account in biochemical interpretations of an MCO structure.

copper depletion↗
DOE OSTI2014

Integration of Apo-α-Phycocyanin into Phycobilisomes and Its Association with FNR L in the Absence of the Phycocyanin α-Subunit Lyase (CpcF) in Synechocystis sp. PCC 6803

Phycocyanin is an important component of the phycobilisome, which is the principal light-harvesting complex in cyanobacteria. The covalent attachment of the phycocyanobilin chromophore to phycocyanin is catalyzed by the enzyme phycocyanin lyase. The photosynthetic properties and phycobilisome assembly state were characterized in wild type and two mutants which lack holo-a-phycocyanin. Insertional inactivation of the phycocyanin a-subunit lyase (DcpcF mutant) prevents the ligation of phycocyanobilin to a-phycocyanin (CpcA), while disruption of the cpcB/A/C2/C1 operon in the CK mutant prevents synthesis of both apo-a-phycocyanin (apo-CpcA) and apo-b-phycocyanin (apo-CpcB). Both mutants exhibited similar light saturation curves under white actinic light illumination conditions, indicating the phycobilisomes in the DcpcF mutant are not fully functional in excitation energy transfer. Under red actinic light illumination, wild type and both phycocyanin mutant strains exhibited similar light saturation characteristics. This indicates that all three strains contain functional allophycocyanin cores associated with their phycobilisomes. Analysis of the phycobilisome content of these strains indicated that, as expected, wild type exhibited normal phycobilisome assembly and the CK mutant assembled only the allophycocyanin core. However, the DcpcF mutant assembled phycobilisomes which, while much larger than the allophycocyanin core observed in the CK mutant, were significantly smaller than phycobilisomes observed in wild type. Interestingly, the phycobilisomes from the DcpcF mutant contained holo-CpcB and apo-CpcA. Additionally, we found that the large form of FNR (FNR L ) accumulated to normal levels in wild type and the DcpcF mutant. In the CK mutant, however, significantly less FNR L accumulated. FNR L has been reported to associate with the phycocyanin rods in phycobilisomes via its N-terminal domain, which shares sequence homology with a phycocyanin linker polypeptide. We suggest that the assembly of apo-CpcA in the phycobilisomes of DcpcF can stabilize FNR L and modulate its function. These phycobilisomes, however, inefficiently transfer excitation energy to Photosystem II.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ANL Design Team Analysis: Transportable Modular Reactor by Balance of Plant Elimination

HolosGen LLC is developing “Holos-Quad” a transportable gas-cooled reactor, with integral load following power conversion systems equipping subcritical power modules (SPMs), fully comprised within standard transport containers. The design eliminates the Balance of Plant (BoP) and greatly simplifies the design layout. A closed-loop full Brayton gas thermodynamic cycle converts the fuel cartridges thermal energy into electricity. This ARPA-E project utilizes advanced reactor modeling tools and manufacturing-testing of a scaled SPM equipped with a surrogate fuel cartridge to eliminate the most significant technology gaps to accelerate commercialization. The Argonne Design Team contributes to the research by demonstrating feasibility of various aspects of the Holos-Quad design by performing high-fidelity neutronic modeling, and investigating various reactivity control systems. This work consists of two main tasks: evaluation of HolosGen’s design features and alternative options study for reactivity control.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2021

Structural insight into the dual function of LbpB in mediating Neisserial pathogenesis

Lactoferrin-binding protein B (LbpB) is a lipoprotein present on the surface of Neisseria that has been postulated to serve dual functions during pathogenesis in both iron acquisition from lactoferrin (Lf), and in providing protection against the cationic antimicrobial peptide lactoferricin (Lfcn). While previous studies support a dual role for LbpB, exactly how these ligands interact with LbpB has remained unknown. Here, we present the structures of LbpB from N. meningitidis and N. gonorrhoeae in complex with human holo-Lf, forming a 1:1 complex and confirmed by size-exclusion chromatography small-angle X-ray scattering. LbpB consists of N- and C-lobes with the N-lobe interacting extensively with the C-lobe of Lf. Our structures provide insight into LbpB’s preference towards holo-Lf, and our mutagenesis and binding studies show that Lf and Lfcn bind independently. Our studies provide the molecular details for how LbpB serves to capture and preserve Lf in an iron-bound state for delivery to the membrane transporter LbpA for iron piracy, and as an antimicrobial peptide sink to evade host immune defenses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Deep-Learning-Enabled Crack Detection and Analysis in Commercial Lithium-Ion Battery Cathodes

We report in Li-ion batteries, the mechanical degradation initiated by micro cracks is one of the bottlenecks for enhancing the performance. Quantifying the crack formation and evolution in complex composite electrodes can provide important insights into electrochemical behaviors under prolonged and/or aggressive cycling. However, observation and interpretation of the complicated crack patterns in battery electrodes through imaging experiments are often time-consuming, labor intensive, and subjective. Herein, a deep learning-based approach is developed to extract the crack patterns from nanoscale hard X-ray holo-tomography data of a commercial 18650-type battery cathode. Efficient and effective quantification of the damage heterogeneity with automation and statistical significance is demonstrated. The crack characteristics are further associated with the active particles’ packing densities and a potentially viable architectural design is discussed for suppressing the structural degradation in an industry-relevant battery configuration.

25 ENERGY STORAGE↗
DOE OSTI2020

An efficient, conservative, time-implicit solver for the fully kinetic arbitrary-species 1D-2V Vlasov-Ampère system

In this paper, we consider the solution of the fully kinetic (including electrons) Vlasov-Ampère system in a one-dimensional physical space and two-dimensional velocity space (1D-2V) for an arbitrary number of species with a time-implicit Eulerian algorithm. The problem of velocity-space meshing for disparate thermal and bulk velocities is dealt with by an adaptive coordinate transformation of the Vlasov equation for each species, which is then discretized, including the resulting inertial terms. Mass, momentum, and energy are conserved, and Gauss's law is enforced to within the nonlinear convergence tolerance of the iterative solver through a set of nonlinear constraint functions while permitting significant flexibility in choosing discretizations in time, configuration, and velocity space. We mitigate the temporal stiffness introduced by, e.g., the plasma frequency through the use of high-order/low-order (HOLO) acceleration of the iterative implicit solver. We present several numerical results for canonical problems of varying degrees of complexity, including the multiscale ion-acoustic shock wave problem, which demonstrate the efficacy, accuracy, and efficiency of the scheme.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Structure and specificity of several triclocarban-binding single domain camelid antibody fragments

The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. Their interactions with proteins have been well-studied, but considerably less work has been done to characterize their ability to bind haptens. Here, a high-resolution structural study of three nanobodies (T4, T9, and T10) which have been shown to bind triclocarban (TCC, 3-(4-chlorophenyl)-1-(3,4-dichlorophenyl)urea) with near-nanomolar affinity shows that binding occurs in a tunnel largely formed by CDR1 rather than a surface or lateral binding mode seen in other nanobody-hapten interactions. Additional significant interactions are formed with a non-hypervariable loop, sometimes dubbed “CDR4”. A comparison of apo and holo forms of T9 and T10 shows that the binding site undergoes little conformational change upon binding of TCC. Structures of three nanobody-TCC complexes demonstrated there was not a standard binding mode. T4 and T9 have a high degree of sequence identity and bind the hapten in a nearly identical manner, while the more divergent T10 binds TCC in a slightly displaced orientation with the urea moiety rotated approximately 180° along the long axis of the molecule. In addition to methotrexate, this is the second report of haptens binding in a tunnel formed by CDR1, suggesting that compounds with similar hydrophobicity and shape could be recognized by nanobodies in analogous fashion. Structure-guided mutations failed to improve binding affinity for T4 and T9 underscoring the high degree of natural optimization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Holographic entropy inequalities and gapped phases of matter

Here, we extend our studies of holographic entropy inequalities to gapped phases of matter. For any number of regions, we determine the linear entropy inequalities satisfied by systems in which the entanglement entropy satisfies an exact area law. In particular, we find that all holographic entropy inequalities are valid in such systems. In gapped systems with topological order, the “cyclic inequalities” derived recently for the holo-graphic entanglement entropy generalize the Kitaev-Preskill formula for the topological entanglement entropy. Finally, we propose a candidate linear inequality for general 4-party quantum states.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

A holographic model for black hole complementarity

Here, we explore a version of black hole complementarity, where an approximate semiclassical effective field theory for interior infalling degrees of freedom emerges holo-graphically from an exact evolution of exterior degrees of freedom. The infalling degrees of freedom have a complementary description in terms of outgoing Hawking radiation and must eventually decohere with respect to the exterior Hamiltonian, leading to a breakdown of the semiclassical description for an infaller. Trace distance is used to quantify the difference between the complementary time evolutions, and to define a decoherence time. We propose a dictionary where the evolution with respect to the bulk effective Hamiltonian corresponds to mean field evolution in the holographic theory. In a particular model for the holographic theory, which exhibits fast scrambling, the decoherence time coincides with the scrambling time. The results support the hypothesis that decoherence of the infalling holographic state and disruptive bulk effects near the curvature singularity are comple-mentary descriptions of the same physics, which is an important step toward resolving the black hole information paradox.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

The Effect of Salts in Promoting Specific and Competitive Interactions between Zinc Finger Proteins and Metals

Specific protein–metal interactions (PMIs) fulfill essential functions in cells and organic bodies, and activation of these functions in vivo are mostly modulated by the complex environmental factors, including pH value, small biomolecules, and salts. Specifically, the role of salts in promoting specific PMIs and their competition among various metals has remained untapped mainly due to the difficulty to distinguish nonspecific PMIs from specific PMIs by classic spectroscopic techniques. Herein, we report Hofmeister salts differentially promote the specific PMIs by combining nanoelectrospray ionization mass spectrometry and spectroscopic techniques (fluorescence measurement and circular dichroism). Furthermore, to explore the influence of salts in competitive binding between metalloproteins and various metals, we designed a series of competitive experiments and applied to a well-defined model system, the competitive binding of zinc (II) and arsenic (III) to holo-promyelocytic leukemia protein (PML). These experiments not only provided new insights at the molecular scale as complementary to previous NMR and spectroscopic results, but also deduced the relative binding ability between zinc finger proteins and metals at the molecular scale, which avoids the mass spectrometric titration-based determination of binding constants that is frequently affected and often degraded by variable solution conditions including salt contents. .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗