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At least 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Structure-Based Analysis of Boronic Acids as Inhibitors of Acinetobacter -Derived Cephalosporinase-7, a Unique Class C β-Lactamase

Acinetobacter baumannii is a multidrug resistant pathogen that infects more than 12 000 patients each year in the US. Much of the resistance to β-lactam antibiotics in Acinetobacter spp. is mediated by class C β-lactamases known as Acinetobacter-derived cephalosporinases (ADCs). ADCs are unaffected by clinically used β-lactam-based β-lactamase inhibitors. In this study, five boronic acid transition state analog inhibitors (BATSIs) were evaluated for inhibition of the class C cephalosporinase ADC-7. Our goal was to explore the properties of BATSIs designed to probe the R1 binding site. K i values ranged from low micromolar to subnanomolar, and circular dichroism (CD) demonstrated that each inhibitor stabilizes the β-lactamase–inhibitor complexes. Additionally, X-ray crystal structures of ADC-7 in complex with five inhibitors were determined (resolutions from 1.80 to 2.09 Å). In the ADC-7/CR192 complex, the BATSI with the lowest K i (0.45 nM) and greatest ΔT m (+9 °C), a trifluoromethyl substituent, interacts with Arg340. Arg340 is unique to ADCs and may play an important role in the inhibition of ADC-7. Here, the ADC-7/BATSI complexes determined in this study shed light into the unique recognition sites in ADC enzymes and also offer insight into further structure-based optimization of these inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

ABSTRACT Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ- d -Glu-A 2 pm (A 2 pm is diaminopimelic acid) cysteine amidase (or dl -endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l -Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. IMPORTANCE Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases.

Xu, Qingping↗
DOE OSTI2015

Origin of the spin reorientation transitions in (Fe 1–x Co x ) 2 B alloys

Low-temperature measurements of the magnetocrystalline anisotropy energy K in (Fe 1–x Co x ) 2 B alloys are reported, and the origin of this anisotropy is elucidated using a first-principles electronic structure analysis. The calculated concentration dependence K(x) with a maximum near x = 0.3 and a minimum near x = 0.8 is in excellent agreement with experiment. This dependence is traced down to spin-orbital selection rules and the filling of electronic bands with increasing electronic concentration. In conclusion, at the optimal Co concentration, K depends strongly on the tetragonality and doubles under a modest 3% increase of the c/a ratio, suggesting that the magnetocrystalline anisotropy can be further enhanced using epitaxial or chemical strain.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Computational screening of dopants for photocatalytic two-electron reduction of CO 2 on anatase (101) surfaces

We have carried out first-principles calculations to explore reaction mechanisms of the 2e reduction of CO 2 to HCOOH or CO in photochemical reactions catalyzed by anatase (101) surface. Two energetically competitive reaction pathways to HCOOH were identified, which involve initial 1e (via bidentate) and 2e (via monodentate) reduction steps, respectively. The pathways of producing CO were also explored. From the electronic structure analysis, we have shown the role of the anatase surface in facilitating electron and proton transfer in CO 2 reduction. Based on the determined rate-limiting step, we have carried out screening of substitutional surface cation doping and found metallic elements that could substantially lower the reaction barriers. Finally, a simple model describing the relationship between the activation barriers and the binding energies of CO 2 - to the dopant surface site is proposed.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Analysis of structure and deformation behavior of AISI 316L tensile specimens from the second operational target module at the Spallation Neutron Source

In an earlier publication, tensile testing was performed on specimens removed from the first two operational targets of the Spallation Neutron Source (SNS). There were several anomalous features in the results. First, some specimens had very large elongations (up to 57%) while others had significantly smaller values. Second, there was a larger than the usual amount of data scatter in the elongation results. Third, the stress-strain diagrams of nominally similar specimens spanned a wide range of behavior ranging from expected irradiation-induced hardening to varying levels of force drop after yield point and indirect signs of "traveling deformation wave" behavior associated with strain-induced martensite formation. To investigate the cause(s) of such variable tensile behavior, several specimens from Target 2, spanning the range of observed tensile behavior, were chosen for detailed microstructural examination using electron backscattering analysis (EBSD). It was also shown that the steel employed in the construction of the target contained an unexpected bimodal grain size distribution, containing very large out-of-specification grains surrounded by necklaces of grains of within-specification sizes. The large grains were frequently comparable to the width of the gauge section of the tensile specimen. Moreover, the propensity to form martensite during deformation was shown to be accelerated by radiation but also to be very sensitive to the relative orientation of the grains with respect to the tensile axis. Specimens having large grains in the gauge that were most favorably oriented for production of martensite strongly exhibited the traveling deformation wave phenomenon, while those specimens with less favorably oriented grains had lesser or no degree of the wave effect, thereby accounting for the larger than expected data scatter.

316L↗
DOE OSTI2021

MITR DDE End Fitting Structural Rigidity Analysis

As a part of the design of the MITR Design Demonstration Element (DDE), a new design for the end fittings must be considered to meet specific experiment needs, e.g., compatibility with the geometrical restrictions of the DDE testing location (BR2 test reactor located in Mol, Belgium), and to allow for proper inspection of these test elements during the experiments. The design of the MITR DDE end fittings is substantially different from the design of the end fittings of the MITR LEU fuel elements, with the DDE end fittings considerably smaller in overall size and weight. Consequently, the stiffness of the end fittings as well as of the entire fuel element is affected. The end fittings in the MITR LEU fuel element are designed primarily for proper handling and flow distribution. The stiffness of the end fittings also constitutes a fraction of the total stiffness of the entire fuel element. It is debatable to what extent the end fittings provide the structural rigidity necessary for the fuel element to properly respond to potential loadings. It is presumed that the bulk of the overall stiffness of the element is derived from swaging multiple fuel plates into the side plates. However, the contribution of stiffness from various components of the MITR LEU fuel element and MITR DDE has not been determined so far. The primary objective of the work presented in this report was to assess the extent to which the stiffness of the end fitting in the MITR DDE contributes to the stiffness of the entire fuel element, and how it compares to the equivalent stiffness of the end fitting in the MITR LEU fuel element. Several simplified load cases were analyzed for that purpose using the geometries of the MITR LEU fuel element, MITR DDE, as well as that of the MITR DDE without the top end fitting.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2015

Identification and Structure-Function Analysis of Subfamily Selective G Protein-Coupled Receptor Kinase Inhibitors

Selective inhibitors of individual subfamilies of G protein-coupled receptor kinases (GRKs) would serve as useful chemical probes as well as leads for therapeutic applications ranging from heart failure to Parkinson’s disease. To identify such inhibitors, differential scanning fluorimetry was used to screen a collection of known protein kinase inhibitors that could increase the melting points of the two most ubiquitously expressed GRKs: GRK2 and GRK5. Enzymatic assays on 14 of the most stabilizing hits revealed that three exhibit nanomolar potency of inhibition for individual GRKs, some of which exhibiting orders of magnitude selectivity. Most of the identified compounds can be clustered into two chemical classes: indazole/dihydropyrimidine-containing compounds that are selective for GRK2 and pyrrolopyrimidine-containing compounds that potently inhibit GRK1 and GRK5 but with more modest selectivity. The two most potent inhibitors representing each class, GSK180736A and GSK2163632A, were cocrystallized with GRK2 and GRK1, and their atomic structures were determined to 2.6 and 1.85 Å spacings, respectively. GSK180736A, developed as a Rho-associated, coiled-coil-containing protein kinase inhibitor, binds to GRK2 in a manner analogous to that of paroxetine, whereas GSK2163632A, developed as an insulin-like growth factor 1 receptor inhibitor, occupies a novel region of the GRK active site cleft that could likely be exploited to achieve more selectivity. However, neither compound inhibits GRKs more potently than their initial targets. This data provides the foundation for future efforts to rationally design even more potent and selective GRK inhibitors.

Homan, Kristoff T.↗
NASA NTRSDate not supplied

Multidisciplinary Design Optimization of a Transonic Truss-Braced Wing using Physics-Based Models

Economic and environmental forces have placed pressure on the aviation industry to produce future aircraft designs with substantial improvements over those flying today. In order to meet these ambitious goals, new concepts such as the Transonic Truss-Braced Wing (TTBW) are being considered which diverge from the traditional tube-and-wing design. While this concept offers potential performance benefits over its traditional counterpart, it also features more coupling between various physics disciplines that must be considered during the design of the concept. This unique challenge provides a ripe opportunity for the application of multidisciplinary design optimization tool sets. The final work will couple together the mission analysis capability of Aviary with OpenAeroStruct for aerodynamic analysis and TACS for structural analysis. Using these tools we will preform a design optimization on the TTBW concept minimizing design fuel burn. The optimization will include design variables for mission trajectory, wing geometry, and structural sizing variables.

mbsae↗
DOE OSTI2015

Preparation and characterization of polymer blend based on sulfonated poly (ether ether ketone) and polyetherimide (SPEEK/PEI) as proton exchange membranes for fuel cells

Blends of sulfonated poly (ether ether ketone) (SPEEK) and polyetherimide (PEI) were prepared in five different weight ratios using N-methyl-2-pyrrolidone (NMP) as solvent by the solution cast technique. The degree of sulfonation (DS) of the sulfonated PEEK was determined from deuterated dimethyl sulfoxide (DMSO-d{sub 6}) solution of the purified polymer using {sup 1}H NMR method. The properties studied in the present investigation includes conductivity, water uptake, thermal stability and structure analysis of pure SPEEK as well as SPEEK-PEI polymer blend membranes. The experimental results show that the conductivity of the membranes increased with increase in temperature from 30 to 80°C, except for that of pure SPEEK membrane which increased with temperature from 30 to 60°C while its conductivity decreased with increasing temperature from 60 to 80°C. The conductivity of 70wt.%SPEEK-30wt.%PEI blend membrane at 80% relative humidity (RH) is found to be 1.361 × 10{sup −3} Scm{sup −1} at 30°C and 3.383 × 10{sup −3} Scm{sup −1} at 80°C respectively. It was also found that water uptake and thermal stability of the membranes slightly improved upon blending with PEI. Structure analysis was carried out using Fourier Transform Infrared (FTIR) spectroscopy which revealed considerable interactions between sulfonic acid group of SPEEK and imide groups of PEI. Modification of SPEEK by blending with PEI shows good potential for improving the electrical and physical properties of proton exchange membranes.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Carbon diffusion in molten uranium: an ab initio molecular dynamics study

In this work we used ab initio molecular dynamics (AIMD) within the framework of density functional theory (DFT) and the projector-augmented wave (PAW) method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activation energy for carbon was nearly twice that of uranium: 0.55±0.03 eV for carbon compared to 0.32±0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.

Molecular dynamics computer simulation, Nuclear Pr↗
DOE OSTI2015

Synthesis, crystal structure, thermal analysis and dielectric properties of [(C{sub 4}H{sub 9}){sub 4}N]{sub 3}Bi{sub 2}Cl{sub 9} compound

A new organic–inorganic tri-tetrabutylammonium nonachlorobibismuthate(III) compound was prepared. It was found to crystallize in the monoclinic system (P2{sub 1}/n space group) with the following lattice parameters: a=11.32(2) Å, b=22.30(3) Å, c=28.53(2) Å and β=96.52(0)°. The [Bi{sub 2}Cl{sub 9}]{sup 3−} anions are surrounded by six [(C{sub 4}H{sub 9})N]{sup +} cations, forming an octahedral configuration. These octahedra are sharing corners in order to provide the tri-dimensional network cohesion. The differential scanning calorimetry reveals four order-disorder reversible phase transitions located at 214, 238, 434 and 477 K. The Raman and infrared spectra confirm the presence of both cationic [(C{sub 4}H{sub 9})N]{sup +} and anionic [Bi{sub 2}Cl{sub 9}]{sup 3−} parts. The dielectric parameters, real and imaginary dielectric permittivity (ε′ and ε″), and dielectric loss tangent (tg δ), were measured in the frequency range of 209 kHz–5 MHz at different temperatures. The variations of dielectric dispersion (ε') and dielectric absorption (ε″) with frequency show a distribution of relaxation times, which is probably related to the change in the dynamical state of the [(C{sub 4}H{sub 9}){sub 4}N]{sup +} cations and the [Bi{sub 2}Cl{sub 9}]{sup 3−} anions. - Graphical abstract: Projection of the atomic arrangement of the [(C{sub 4}H{sub 9}){sub 4}N]{sub 3}Bi{sub 2}Cl{sub 9} compound along the b axis. - Highlights: • The structure of the (TBA){sub 3}Bi{sub 2}Cl{sub 9} compound was solved and reported. • The cristal belongs to the monoclinic system with P2{sub 1}/n space group. • DSC discloses four order–disorder reversible phases transitions. • The temperature-dependent permittivity ε' and ε″ has been investigated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

A single mutation in Taiwanese H6N1 influenza hemagglutinin switches binding to human‐type receptors

Abstract In June 2013, the first case of human infection with an avian H6N1 virus was reported in a Taiwanese woman. Although this was a single non‐fatal case, the virus continues to circulate in Taiwanese poultry. As with any emerging avian virus that infects humans, there is concern that acquisition of human‐type receptor specificity could enable transmission in the human population. Despite mutations in the receptor‐binding pocket of the human H6N1 isolate, it has retained avian‐type (NeuAcα2‐3Gal) receptor specificity. However, we show here that a single nucleotide substitution, resulting in a change from Gly to Asp at position 225 (G225D), completely switches specificity to human‐type (NeuAcα2‐6Gal) receptors. Significantly, G225D H6 loses binding to chicken trachea epithelium and is now able to bind to human tracheal tissue. Structural analysis reveals that Asp225 directly interacts with the penultimate Gal of the human‐type receptor, stabilizing human receptor binding.

de Vries, Robert P.↗
DOE OSTI2022

Magnetic Gears: The Key to Robust, Cost-Effective Hydropower Drivetrains

Based on previous demonstrated success at fabricating 5 and 10 kW scale magnetic gearbox (MGB) prototypes, Emrgy and its partners (the project team) proposed to design and construct a 100 kW scale MGB with a 30:1 gear ratio for the low-head hydro applications. The Statement of Project Objectives included tasks covering: 1) Market Applicability; 2) Technical Metrics; 3) Design (initial); 4) Electromagnetic (EM) Load and Structural Analysis; 5) Modal Analysis; 6) Sealing Design and 7) Final Design during Budget Period 1. Budget Period 2 included tasks covering: 1) Materials Procurement and Test Plan Development; 2) Assembly; and 3) Testing. The Market Applicability study (Task 1) led to a clear conclusion and recommendation toward “Low Head” technologies for maximum market share of both New Stream Reach development as well as powering Non-Powered Dams. The findings of this study also identified the opportunity for a larger scale magnetic gearbox-based drive train as a function of increased torque, as opposed to increased speed. The Technical Metrics Study (Task 2) concluded a horizontal orientation was preferred, examined potential loss mechanisms, concluded that a Halbach Array magnetic design was preferred, established a 30:1 gear ratio as optimal, and established a power rating of 100 kW as optimal. The subsequent initial and final detailed design process included electro-magnetic (EM) load and structural analysis (Task 4), a Modal analysis (for vibration) (Task 5), and a sealing design (Task 6) to assure water impermeability. The final design package (Task 7) included 729 individual parts, 117 unique part numbers, and 15 assemblies. In order to facilitate procurement, the full bill of materials was broken down into several sub-components: 1) custom magnetic parts; 2) custom machined parts; 3) custom casted parts; and 4) commercial off the shelf (COTS) parts. The casted parts were fabricated by Oak Ridge National Laboratory (ORNL) via a Cooperative Research and Development Agreement (CRADA) with Emrgy and funded by the Advanced Manufacturing Office (AMO). The procurement effort (Task 8) ultimately covered three time periods based on challenges encountered in meeting the budgeted cost for the prototype. Following the first effort in the early stages of Budget Period 2 in 2017, a no-cost time extension was granted to seek alternative fabrication and procurement options. The project was re-booted in 2020 based on the new ORNL CRADA that would focus on five (5) of the more difficult and expensive parts using their advanced manufacturing expertise. Procurement efforts for the other custom machined parts resulted in quotations that still exceeded the budget by more than $\$$100k. This was, in part, also due to the concurrent COVID-19 pandemic that caused both supply chain disruptions and labor shortages. As the project continued, pricing and availability degraded further. In Q2 FY’22, it was decided to not proceed with the fabrication of the prototype (Task 9) based on budgetary limitations. Outcomes included a full and detailed design of a 100 kW magnetic gearbox and associated indented bill of materials (BOM) and CAD drawings, a full assembly instruction manual with an associated BOM for materials necessary to support assembly, the fabrication of the double Halbach magnetic array for the rotor/stator system, fabrication of five (5) sand-casted/machined parts (via CRADA with ORNL) and an initial draft of a comprehensive testing plan. The most significant non-outcome was the actual fabrication and testing of the prototype gearbox based on budget limitations. Lessons learned included the need for an Application / Design / Cost trade analysis to better elucidate the cost potential of the MGB in the projected volumes anticipated for future demand. This would better establish the efficacy of the original cost target ($\$$0.80/Watt) and/or the need for reconsideration of designs and applications. Likewise, additional consideration of the prototype nature of the gearbox – single use, short lifetime, etc. - either as a separate exercise or in place of the design process completed, to reduce the cost of the demonstration prototype device. Additionally, project continuity was cited as a significant risk based on the loss of the primary design engineering firm after Budget Period 1. A design analysis exercise was conducted at the conclusion of the project to identify potential areas for cost reduction. One concept considered was the removal of the inner ring of magnets (with associated changes in the outer ring magnets) to enable a horizontal collapse of the design. It was estimated this could reduce cost by 10-25% without impacting performance.

13 HYDRO ENERGY↗
DOE OSTI2023

Exploring the Performance Boundaries of a Small Reconfigurable Multi-Mission UAV through Multidisciplinary Analysis

The performance of a small reconfigurable unmanned aerial vehicle (UAV) is evaluated, combining a multidisciplinary approach in the computational analysis of additive manufactured structures, fluid dynamics, and experiments. Reconfigurable UAVs promise cost savings and efficiency, without sacrificing performance, while demonstrating versatility to fulfill different mission profiles. The use of computational fluid dynamics (CFD) in UAV design produces higher accuracy aerodynamic data, which is particularly important for complex aircraft concepts such as blended wing bodies. To address challenges relating to anisotropic materials, the Tsai–Wu failure criterion is applied to the structural analysis, using CFD solutions as load inputs. Aerodynamic performance results show the low-speed variant attains an endurance of 1 h, 48 min, whereas its high-speed counterpart is 29 min at a 66.7% higher cruise speed. Each variant serves different aspects of small UAS deployment, with low speed envisioned for high-endurance surveying, and high speed for long-range or time-critical missions such as delivery. The experimental and simulation results suggest room for design iteration, in wing area and geometry adjustments. Structural simulations demonstrated the need for airframe improvements to the low-speed configuration. This paper highlights the potential of reconfigurable UAVs to be useful across multiple industries, advocating for further research and design improvements.

42 ENGINEERING↗
DOE OSTI2025

Mapping the structural–mechanical landscape of amorphous carbon with ReaxFF molecular dynamics

We use ReaxFF molecular dynamics (MD) to investigate the relationship between structural and mechanical properties in bulk and nanostructured amorphous carbon (a-C). The liquid-quench MD method is used to generate isotropic bulk samples with mass densities ranging from 0.96 to 3.29 g/cm3. Structural analysis identifies two types of structures with distinct short- and medium-range order: lower-density sp2-dominated a-C, which is characterized by a bimodal ring-size distribution, and higher-density sp3-dominated tetrahedral amorphous carbon (ta-C), exhibiting a unimodal ring-size distribution. Stress–strain MD simulations and analysis reveal how an atomistic structure impacts elastic properties and post-yield atomic rearrangements. All stretched structures demonstrate elastic isotropy and plasticity driven by a ring-size expansion mechanism reflected in changes in ring statistics. The plastic region is substantially larger in ta-C than in a-C due to the post-yield shift from sp3 to sp2 C dominant bonding. In both a-C and ta-C, ultimate failure occurs when a reactive crack, traversed by long sp chains, forms and propagates predominantly perpendicular to the direction of the applied strain. Oxygen infiltration into the fractured region significantly reduces stress resistance, primarily through the early rupture of long sp chains. MD simulations and analysis are extended to a-C slabs, a-C nanotubes, and partially a-C nanotubes. The latter nanostructure highlights the differences between the elastically isotropic a-C walls, which develop circumferential cracking, and the crystalline walls, which tear along crystallographic directions. These results provide a strong foundation for further computational characterization of a-C materials.

Dernov, A. (ORCID:0009000004220973)↗
DOE OSTI2013

A (S)TEM Gas Cell Holder with Localized Laser Heating for In Situ Experiments

The advent of aberration correction for transmission electron microscopy has transformed atomic resolution imaging into a nearly routine technique for structural analysis. Now an emerging frontier in electron microscopy is the development of in situ capabilities to observe reactions at atomic resolution in real time and within realistic environments. Here we present a new in situ gas cell holder that is designed for compatibility with a wide variety of sample type (i.e., dimpled 3-mm discs, standard mesh grids, various types of focused ion beam lamellae attached to half grids). Its capabilities include localized heating and precise control of the gas pressure and composition while simultaneously allowing atomic resolution imaging at ambient pressure. The results show that 0.25-nm lattice fringes are directly visible for nanoparticles imaged at ambient pressure with gas path lengths up to 20 μm. Additionally, we quantitatively demonstrate that while the attainable contrast and resolution decrease with increasing pressure and gas path length, resolutions better than 0.2 nm should be accessible at ambient pressure with gas path lengths less than the 15 μm utilized for these experiments.

aberration correction↗
DOE OSTI2017

Kinetic characterization of Vibrio cholerae ApbE: Substrate specificity and regulatory mechanisms

ApbE is a member of a novel family of flavin transferases that incorporates flavin mononucleotide (FMN) to subunits of diverse respiratory complexes, which fulfill important homeostatic functions. In this work a detailed characterization of Vibrio cholerae ApbE physiologic activity, substrate specificity and pH dependency was carried out. The data obtained show novel characteristics of the regulation and function of this family. For instance, our experiments indicate that divalent cations are essential for ApbE function, and that the selectivity depends largely on size and the coordination sphere of the cation. Our data also show that ApbE regulation by pH, ADP and potassium is an important mechanism that enhances the adaptation, survival and colonization of V. cholerae in the small intestine. Moreover, studies of the pH-dependency of the activity show that the reaction is favored under alkaline conditions, with a pKa of 8.4. These studies, together with sequence and structure analysis allowed us to identify His257, which is absolutely conserved in the family, as a candidate for the residue whose deprotonation controls the activity. Remarkably, the mutant H257G abolished the flavin transfer activity, strongly indicating that this residue plays an important role in the catalytic mechanism of ApbE.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

An analysis of the structure of an n-dodecane spray flame using TPDF modelling

With a view to understanding ignition and combustion behaviours in diesel engines, this study investigates several aspects of ignition and combustion of an n-dodecane spray in a high pressure, high temperature chamber, known as Spray A, using data resulting from modelling using the transported probability density function (TPDF) method. The model has been validated comprehensively with good to excellent agreement in our previous work against all available experimental data including for mixture-fraction and velocity fields in non-reacting cases, and flame lift-off length and ignition delay in reacting cases. This good agreement encourages further investigation of the numerical model results to help understand the structure of this flame, which serves to complement the experimental information that is available, which is very limited due to the difficult experimental conditions in which this flame exists. For example, quantitative experimental measurements of local mixture-fraction, temperature, velocity gradients, etc. are not yet possible in reacting cases. Analysis of the model results shows that two-stage ignition is found to occur across the ambient temperature conditions considered: the first stage is rapidly initiated on the lean side where temperatures are high and sequentially moves to richer, cooler conditions. The first stage is extremely resilient to turbulence, occurring in a region of very low Damkohler number. The second stage of ignition occurs first in rich mixtures in a region behind the head of the fuel jet where mixture gradients are low, and appears to be influenced strongly by turbulence. Relative to a homogeneous reactor, it is delayed on the lean side but advanced on the rich side, suggesting entrainment and mixing from the early igniting lean regions into richer mixtures is an important moderator of the ignition process. The second-stage ignition front propagates at very high velocities initially, suggesting it is a sequential ignition moving according to gradients of ignition delay and/or residence time. The flame stabilises however on the lean side in a region of much lower velocity, where turbulent velocity fluctuations are sufficiently high such that turbulent transport influences the propagation. It stabilises in a region of low Damkohler number which implies that a competition of chemistry versus micro-mixing might also be involved in stabilisation. The stabilisation mechanism is investigated by an analysis of the transport budgets, showing the flame is stabilised by autoignition but moderated by turbulent diffusion. Further analysis of the flame index supports this stabilisation mechanism, and demonstrates the simultaneous existence of non-premixed and premixed combustion modes in the same flame. Analysis of the flow fields also reveals that local entrainment and dilatation are important flow features near the flame base. (C) 2015 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Diesel↗