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At least 1,585 records · Page 88

nn-PINNs: Non-Newtonian physics-informed neural networks for complex fluid modeling

Time- and rate-dependent material functions in non-Newtonian fluids in response to different deformation fields pose a challenge in integrating different constitutive models into conventional computational fluid dynamic platforms. Considering their relevance in many industrial and natural settings alike, robust data-driven frameworks that enable accurate modeling of these complex fluids are of great interest. The main goal is to solve the coupled Partial Differential Equations (PDEs) consisting of the constitutive equations that relate the shear stress to the deformation and fully capture the behavior of the fluid under various flow protocols with different boundary conditions. Here, in this work, we present non-Newtonian physics-informed neural networks (nn-PINNs) for solving systems of coupled PDEs adopted for complex fluid flow modeling. The proposed nn-PINN method is employed to solve the constitutive models in conjunction with conservation of mass and momentum by benefiting from Automatic Differentiation (AD) in neural networks, hence avoiding the mesh generation step. nn-PINNs are tested for a number of different complex fluids with different constitutive models and for several flow protocols. These include a range of Generalized Newtonian Fluid (GNF) empirical constitutive models, as well as some phenomenological models with memory effects and thixotropic timescales. nn-PINNs are found to obtain the correct solution of complex fluids in spatiotemporal domains with good accuracy compared to the ground truth solution. We also present applications of nn-PINNs for complex fluid modeling problems with unknown boundary conditions on the surface, and show that our approach can successfully recover the velocity and stress fields across the domain, including the boundaries, given some sparse velocity measurements.

42 ENGINEERING↗

Visible-light H 2 evolution using dye-sensitized TiO 2 : effects of physicochemical properties of TiO 2 on excited carrier dynamics and activity

Dye-sensitized photocatalysts have emerged as promising materials for solar-driven water splitting due to their ability to utilize visible light, in contrast to conventional wide-band-gap semiconductors. However, the relationship between semiconductor properties and charge carrier dynamics remains insufficiently understood. In this study, we investigated Pt/TiO 2 systems sensitized with a visible-light-absorbing Ru(II) polypyridyl complex (RuP), focusing on how the crystal phase and specific surface area of TiO 2 influence excited carrier dynamics and H 2 evolution activity. To isolate the effects of TiO 2 properties, Pt and RuP loadings were standardized across samples. Emission lifetime analysis showed similarly efficient electron injection from RuP to TiO 2 in all cases, suggesting that injection efficiency does not account for observed differences in activity. Transient absorption measurements revealed that back electron transfer (BET) rates depended strongly on the TiO 2 phase, with anatase and P25 exhibiting slower BET and higher activity for H 2 evolution than rutile. The highest apparent quantum yield for H 2 evolution was 12.0% at 450 nm. Among anatase samples, larger surface areas correlated with higher activity, while smaller-area samples exhibited slower BET rates but still low H 2 evolution activity, implying a role for RuP dye–dye interactions in performance loss. This was further supported by improvements in H 2 evolution activity by lowering RuP loading or adding co-adsorbents. Overall, these results demonstrate that both BET suppression and control over RuP dye aggregation are essential for designing efficient dye-sensitized photocatalytic systems.

Harada, Kakeru [Institute of Science Tokyo (Japan)↗

Efficient approach to obtain free energy gradient using QM/MM MD simulation

The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means of FEG and the nudged elastic band (NEB) method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Mechanism of RanGTP priming H2A-H2B release from Kap114 in an atypical RanGTP•Kap114•H2A-H2B complex

Previously, we showed that the nuclear import receptor Importin-9 wraps around the H2A-H2B core to chaperone and transport it from the cytoplasm to the nucleus. However, unlike most nuclear import systems where RanGTP dissociates cargoes from their importins, RanGTP binds stably to the Importin-9•H2A-H2B complex, and formation of the ternary RanGTP•Importin-9•H2A-H2B complex facilitates H2A-H2B release to the assembling nucleosome. It was unclear how RanGTP and the cargo H2A-H2B can bind simultaneously to an importin, and how interactions of the three components position H2A-H2B for release. Here, we show cryo-EM structures of Importin-9•RanGTP and of its yeast homolog Kap114, including Kap114•RanGTP, Kap114•H2A-H2B, and RanGTP•Kap114•H2A-H2B, to explain how the conserved Kap114 binds H2A-H2B and RanGTP simultaneously and how the GTPase primes histone transfer to the nucleosome. In the ternary complex, RanGTP binds to the N-terminal repeats of Kap114 in the same manner as in the Kap114/Importin-9•RanGTP complex, and H2A-H2B binds via its acidic patch to the Kap114 C-terminal repeats much like in the Kap114/Importin-9•H2A-H2B complex. Ran binds to a different conformation of Kap114 in the ternary RanGTP•Kap114•H2A-H2B complex. Here, Kap114 no longer contacts the H2A-H2B surface proximal to the H2A docking domain that drives nucleosome assembly, positioning it for transfer to the assembling nucleosome or to dedicated H2A-H2B chaperones in the nucleus.

59 BASIC BIOLOGICAL SCIENCES↗

Validation of a mixture-averaged thermal diffusion model for premixed lean hydrogen flames

The mixture-averaged thermal diffusion model originally proposed by Chapman and Cowling is validated using multiple flame configurations. Simulations using detailed hydrogen chemistry are done on one-, two-, and three-dimensional flames. The analysis spans flat and stretched, steady and unsteady, and laminar and turbulent flames. Quantitative and qualitative results using the thermal diffusion model compare very well with the more complex multicomponent diffusion model. Comparisons are made using flame speeds, surface areas, species profiles, and chemical source terms. Once validated, this model is applied to three-dimensional laminar and turbulent flames. For these cases, thermal diffusion causes an increase in the propagation speed of the flames as well as increased product chemical source terms in regions of high positive curvature. The results illustrate the necessity for including thermal diffusion, and the accuracy and computational efficiency of the mixture-averaged thermal diffusion model.

Schlup, Jason↗

ESTIMATING THE HEIGHT OF CMEs ASSOCIATED WITH A MAJOR SEP EVENT AT THE ONSET OF THE METRIC TYPE II RADIO BURST DURING SOLAR CYCLES 23 AND 24

We studied the coronal mass ejection (CME) height at the onset of 59 metric type II radio bursts associated with major solar energetic particle (SEP) events, excluding ground level enhancements (GLEs), during solar cycles 23 and 24. We calculated CME heights using a simple flare-onset method used by Gopalswamy et al. to estimate CME heights at the metric type II onset for cycle 23 GLEs. We found the mean CME height for non-GLE events (1.72 R{sub ☉}) to be ∼12% greater than that (1.53 R{sub ☉}) for cycle 23 GLEs. The difference could be caused by more impulsive acceleration of the GLE-associated CMEs. For cycle 24 non-GLE events, we compared the CME heights obtained using the flare-onset method and the three-dimensional spherical-shock fitting method and found the correlation to be good (CC = 0.68). We found the mean CME height for cycle 23 non-GLE events (1.79 R{sub ☉}) to be greater than that for cycle 24 non-GLE events (1.58 R{sub ☉}), but statistical tests do not definitely reject the possibility of coincidence. We suggest that the lower formation height of the shocks during cycle 24 indicates a change in the Alfvén speed profile because solar magnetic fields are weaker and plasma density levels are closer to the surface than usual during cycle 24. We also found that complex type III bursts showing diminution of type III emission in the 7–14 MHz frequency range are more likely associated with events with a CME height at the type II onset above 2 R{sub ☉}, supporting suggestions that the CME/shock structure causes the feature.

79 ASTRONOMY AND ASTROPHYSICS↗

Nonevaporable getter coating chambers for extreme high vacuum

Techniques for NEG coating a large diameter chamber are presented along with vacuum measurements in the chamber using several pumping configurations, with base pressure as low as 1.56x10^-12 Torr (N2 equivalent) with only a NEG coating and small ion pump. We then describe modifications to the NEG coating process to coat complex geometry chambers for ultra-cold atom trap experiments. Surface analysis of NEG coated samples are used to measure composition and morphology of the thin films. Finally, pressure measurements are compared for two NEG coated polarized electron source chambers: the 130 kV polarized electron source at Jefferson Lab and the upgraded 350 kV polarized 2 electron source, both of which are approaching or within the extreme high vacuum (XHV) range, defined as P<7.5x10^-13 Torr.

47 OTHER INSTRUMENTATION↗

Subsurface catalysis-mediated selectivity of dehydrogenation reaction

Progress in heterogeneous catalysis is often hampered by the difficulties of constructing active architectures and understanding reaction mechanisms at the molecular level due to the structural complexity of practical catalysts, in particular for multicomponent catalysts. Although surface science experiments and theoretical simulations help understand the detailed reaction mechanisms over model systems, the direct study of the nature of nanoparticle catalysts remains a grand challenge. This paper describes a facile construction of well-defined Pt-skin catalysts modified by different 3d transition metal (3dTM) atoms in subsurface regions. However, on the catalyst containing both surface and subsurface 3dTMs, the selectivity of propane dehydrogenation decreases in the sequences of Pt ~ PtFe > PtCo > PtNi due to the easier C–C cracking on exposed Co and Ni sites. After the exposed 3dTMs were removed completely, the C 3 H 6 selectivity was found to increase markedly in the row Pt < PtNi@Pt < PtCo@Pt < PtFe@Pt, which is in line with the calculated trend of d-band center shifting. The established relationship between reactivity and d-band center shifting illustrates the role of subsurface catalysis in dehydrogenation reaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Glucan Binding Protein C of Streptococcus mutans Mediates both Sucrose-Independent and Sucrose-Dependent Adherence

The high-resolution structure of glucan binding protein C (GbpC) at 1.14 Å, a sucrose-dependent virulence factor of the dental caries pathogen Streptococcus mutans , has been determined. GbpC shares not only structural similarities with the V regions of AgI/II and SspB but also functional adherence to salivary agglutinin (SAG) and its scavenger receptor cysteine-rich domains (SRCRs). This is not only a newly identified function for GbpC but also an additional fail-safe binding mechanism for S. mutans . Despite the structural similarities with S. mutans antigen I/II (AgI/II) and SspB of Streptococcus gordonii , GbpC remains unique among these surface proteins in its propensity to adhere to dextran/glucans. The complex crystal structure of GbpC with dextrose (β- d -glucose; Protein Data Bank ligand BGC) highlights exclusive structural features that facilitate this interaction with dextran. Targeted deletion mutant studies on GbpC's divergent loop region in the vicinity of a highly conserved calcium binding site confirm its role in biofilm formation. Finally, we present a model for adherence to dextran. The structure of GbpC highlights how artfully microbes have engineered the lectin-like folds to broaden their functional adherence repertoire.

Mieher, Joshua L.↗

A Novel Method for Diagnosing Land–Atmosphere Coupling Sensitivity in a Single-Column Model

The response of boundary layer properties and cloudiness to changes in surface evaporative fraction (EF) is investigated in a single-column model to quantify the locally coupled impact of subgrid surface variations on the atmosphere during summer. Sensitive coupling days are defined when the model atmosphere exhibits large variations across a range of EFs centered on the analyzed value. Coupling sensitivity exists as both positive feedback (cloudiness increases with EF) and negative feedback (clouds increase with decreasing EF) regimes. The positive regime manifests in shallow convection situations, which are capped by a strengthened inversion and subsidence, restricting the vertical extent of convection to just above the boundary layer. Surfaces with larger EF (greater surface latent heat flux) can inject more moisture into the vertically confined system, lowering the cloud base and an increasing cloud liquid water path (LWP). Negative feedback regimes tend to manifest when large-scale deep convection, such as from mesoscale convective systems and fronts, is advected through the domain, where convection strengthens over surfaces with a lower EF (greater surface sensible heat flux). The invigoration of these systems by the land surface leads to an increase in LWP through strengthened updrafts and stronger coupling between the boundary layer and the free atmosphere. These results apply in the absence of heterogeneity-induced mesoscale circulations, providing a one-dimensional dynamical perspective on the effect of surface heterogeneity. Finally, this study provides a framework of intermediate complexity, lying between parcel theory and high-resolution coupled land–atmosphere modeling, and therefore isolates the relevant first-order processes in land–atmosphere interactions.

54 ENVIRONMENTAL SCIENCES↗

ReACT Methodology Proof of Concept Final Report

The Department of Energy’s Office of Electricity Delivery and Energy Reliability (DOE-OE) funded INL Researchers to evaluate a novel process for assessing and mitigating cyber security risks. The proof of concept level of the method was tested in an industry environment. This case study, plus additional case studies will support the further development of the method into a tool to assist industry in securing their critical networks. This report provides an understanding of the process developed in the Response Analysis and Characterization Tool (ReACT) project. This report concludes with lessons learned and a roadmap for final development of these tools for use by industry.

99 GENERAL AND MISCELLANEOUS↗

Identifying the Critical Links in Road Transportation Networks: Centrality-based approach utilizing structural properties

Surface transportation road networks share structural properties similar to other complex networks (e.g., social networks, information networks, biological networks, and so on). This research investigates the structural properties of road networks for any possible correlation with the traffic characteristics such as link flows those determined independently. Additionally, we define a criticality index for the links of the road network that identifies the relative importance in the network. We tested our hypotheses with two sample road networks. Results show that, correlation exists between the link flows and centrality measures of a link of the road (dual graph approach is followed) and the criticality index is found to be effective for one test network to identify the vulnerable nodes.

99 GENERAL AND MISCELLANEOUS↗

Progression to Compatibility Evaluations in Flowing Molten Salts

Molten salt compatibility with structural alloys has been identified as a key issue for the development of Generation 3 concentrating solar power (CSP) systems with thermal storage. To accelerate this evaluation to pumped systems, the goal of this project was to conduct thermal convection loop (TCL) experiments with a peak temperature of ≥700°C and a typical temperature gradient of ~100°C. The experiments indicated that conventional ~16wt.%Cr Ni-based alloys are compatible up to 700°C with purified (i.e. low O) or dried (low H₂O) industrial-sourced Mg-K-Na chloride salt with <10 μm/yr loss. This two-year project was conducted based on the experimental and mechanistic understanding developed more than 60 years ago at Oak Ridge National Laboratory (ORNL). The first TCL experiment met the <15 μm/yr corrosion metric for this project with specimens of Ni-based alloy 600 exposed at 580°-700°C for 1000 h and post-exposure room temperature tensile tests showed minimal degradation. The second TCL experiment successfully deployed an electrochemical sensor from Argonne National Laboratory and had a peak temperature of 750°C but only ran for ~110 h due to a furnace failure. Both experiments used highly purified industrial-sourced salt with an O content of ~3 μg O/g salt and a Mg addition of 0.04 wt.%. In the second year, the Chloride Collective developed a more economical drying procedure such that the O content was much higher (>20,000 μg O/g salt). A third TCL experiment was conducted with a sensor and a peak temperature of 700°C using dried salt from the same industrial source and increased NaCl content (~20 wt.%). In addition to a 0.05% Mg addition to the salt, a Mg coupon was added in the coldest part of the loop which dissolved during the experiment. Again, small mass changes were noted for specimens of alloys 600 and C276 but the values were slightly higher than those measured in purified salt with Mg. A thin non-continuous and non-adherent oxide layer was deposited on most specimens containing Mg, Si and Al but Cr depletion also was observed. Both years included facilities qualification crucible experiments and then capsule experiments to confirm a baseline isothermal reaction rate. The first year capsule experiment led to the conclusion that the two-stage ORNL purification process using NH₄Cl and CCl₄ left the salt with a high Cl potential and a Mg addition (~0.05wt.%) was needed to lower the potential. The second year capsule experiments at 600° and 700°C found little difference in depth of attack for 0-0.25%Mg additions. In general, the complex reactions where salt can be trapped in the porous surface layer of metal indicated that mass change is an unreliable metric and average depth of Cr depletion is a better metric for assessing the extent of attack. These results have created a new baseline that is contrary to the recent published literature for chloride salts where mass losses have been reported that can be extrapolated to very significant annual metal loss rates. Chloride salt corrosion can be controlled and the results also indicate that salt purification to low O levels may not be necessary. However, additional TCL experiments are needed at different times and temperatures to generate important engineering information such as temperature dependent corrosion rates and reaction rate laws for extrapolation to long-term behavior and isolate the effect of salt additives and impurities.

36 MATERIALS SCIENCE↗

Characterization of MtoD from Sideroxydans lithotrophicus : a cytochrome c electron shuttle used in lithoautotrophic growth

The autotrophic Sideroxydans lithotrophicus ES-1 can grow by coupling the oxidation of ferrous iron to the reduction of oxygen. Soluble ferrous iron is oxidized at the surface of the cell by an MtoAB porin-cytochrome complex that functions as an electron conduit through the outer membrane. Electrons are then transported to the cytoplasmic membrane where they are used to generate proton motive force (PMF) (for ATP synthesis) and NADH for autotrophic processes such as carbon fixation. As part of the mtoAB gene cluster, S. lithotrophicus also contains the gene mtoD that is proposed to encode a cytochrome c protein. We isolated mtoD from a Shewanella oneidensis expression system where the mtoD gene was expressed on a pBAD plasmid vector. Biochemical, biophysical, and crystallographic characterization of the purified MtoD revealed it as an 11 kDa monomeric protein containing a single heme. Sequence and structural alignment indicated that MtoD belonged to the class-1 cytochrome c family and had a similar fold to ferricytochrome c552 family, however the MtoD heme is bis-histidine coordinated and is substantially more exposed than the hemes of other family members. The reduction potential of the MtoD heme at pH 7 was +155 mV vs. Standard Hydrogen Electrode, which is approximately 100 mV lower than that of mitochondrial cytochrome c. Consideration of the properties of MtoD in the context of the potential respiratory partners identified from the genome suggests that MtoD could associate to multiple electron transfer partners as the primary periplasmic electron shuttle.

59 BASIC BIOLOGICAL SCIENCES↗

Binding of Campylobacter jejuni FliW Adjacent to the CsrA RNA-Binding Pockets Modulates CsrA Regulatory Activity

Campylobacter jejuni CsrA is an mRNA-binding, post-transcriptional regulator that controls many metabolic- and virulence-related characteristics of this important pathogen. In contrast to E. coli CsrA, whose activity is modulated by binding to small non-coding RNAs (sRNAs), C. jejuni CsrA activity is controlled by binding to the CsrA antagonist FliW. In this study, we identified the FliW binding site on CsrA. Deletion of the C-terminus of C. jejuni CsrA, which is extended relative to sRNA-binding CsrA proteins, abrogated FliW binding. Bacterial two-hybrid experiments were used to assess the interaction of FliW with wild-type CsrA and mutants thereof, in which every amino acid was individually mutated. Two CsrA mutations (V51A and N55A) resulted in a significant decrease in FliW binding. The V51A and N55A mutants also showed a decrease in CsrA-FliW complex formation, as assessed by size-exclusion chromatography and surface plasmon resonance. These residues were highly conserved in bacterial species containing CsrA orthologs whose activities are predicted to be regulated by FliW. The location of FliW binding was immediately adjacent to the two RNA-binding sites of the CsrA homodimer, suggesting the model that FliW binding to CsrA modulates its ability to bind to its mRNA targets either by steric hindrance, electrostatic repulsion, or by altering the overall structure of the RNA-binding sites.

59 BASIC BIOLOGICAL SCIENCES↗

MULTI-WAVELENGTH POLARIMETRY AND SPECTRAL STUDY OF THE M87 JET DURING 2002–2008

We present a multi-wavelength polarimetric and spectral study of the M87 jet obtained at sub-arcsecond resolution between 2002 and 2008. The observations include multi-band archival VLA polarimetry data sets along with Hubble Space Telescope ( HST ) imaging polarimetry. These observations have better angular resolution than previous work by factors of 2–3 and in addition, allow us to explore the time domain. These observations envelop the huge flare in HST-1 located 0.″86 from the nucleus. The increased resolution enables us to view more structure in each knot, showing several resolved sub-components. We also see apparent helical structure in the polarization vectors in several knots, with polarization vectors turning either clockwise or counterclockwise near the flux maxima in various places as well as showing filamentary undulations. Some of these characteristics are correlated with flux and polarization maxima while others are not. We also examine the total flux and fractional polarization and look for changes in both radio and optical since the observations of Perlman et al. (1999) and test them against various models based on shocks and instabilities in the jet. Our results are broadly consistent with previous spine-sheath models and recollimation shock models; however, they require additional combinations of features to explain the observed complexity, e.g., shearing of magnetic field lines near the jet surface and compression of the toroidal component near shocks. In particular, in many regions we find apparently helical features both in total flux and polarization. We discuss the physical interpretation of these features.

79 ASTRONOMY AND ASTROPHYSICS↗

How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4

The Nef protein of HIV-1 downregulates the cell surface co-receptor CD4 by hijacking the clathrin adaptor complex AP-2. The structural basis for the hijacking of AP-2 by Nef is revealed by a 2.9 Å crystal structure of Nef bound to the α and σ2 subunits of AP-2. Nef binds to AP-2 via its central loop (residues 149-179) and its core. The determinants for Nef binding include residues that directly contact AP-2 and others that stabilize the binding-competent conformation of the central loop. Residues involved in both direct and indirect interactions are required for the binding of Nef to AP-2 and for downregulation of CD4. These results lead to a model for the docking of the full AP-2 tetramer to membranes as bound to Nef, such that the cytosolic tail of CD4 is situated to interact with its binding site on Nef.

60 APPLIED LIFE SCIENCES↗

Additive Manufacturing Case Study

Geothermal technologies include an extremely wide range of products required for well construction, completion, production, intervention and surface energy conversion activities. Many of these products are geometrically complex, require multi-step and highly specialized fabrication processes, and are expensive due to the low production numbers typically associated with the geothermal market. These challenges along with the high temperature demands of the geothermal environment have also hindered the adoption of many tools routinely used in the oil & gas industry.Recent advancements in Additive Manufacturing (AM) materials of construction, build volumes and part quality have transitioned the technology from primarily cosmetic prototyping applications to the point where AM can be used to make production parts, even for the most demanding applications. These improved AM capabilities along with the inherent ability of AM to produce complex parts and, in some cases, geometries that cannot be manufactured using conventional casting, machining and joining fabrication approaches motivate an exploration of its potential to positively impact geothermal well construction and operations technologies.Sandia National Labs collaborated with Oak Ridge National Laboratory on a case study examining additive manufacturing opportunities for Geothermal applications. The study focused on designing components with improved performance characteristics that cannot be fabricated conventionally. A rotor for a downhole motor was chosen based on the potential for improving its rotational dynamics. Topology optimization was used as a design method to reduce the rotational inertia of the part while preserving sufficient rotational stiffness to transmit the torque required for the drilling application. The optimization resulted in a nearly 50% reduction in polar moment of inertia while maintaining other desired performance characteristics. The design developed using the topology optimization approach was fabricated using additive manufacturing and cannot be fabricated conventionally. This paper will discuss the design approach, performance improvements and manufacturing methods used to produce the part.

Polsky, Yarom↗