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At least 91 records · Page 5

Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria

ABSTRACT Brucella abortus σ E1 is an EcfG family sigma factor that regulates the transcription of dozens of genes in response to diverse stress conditions and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon, bab1_0223-bab1_0226 , is among the most highly activated gene sets in the σ E1 regulon. The proteins encoded by the operon resemble quaternary ammonium-compatible solute importers but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized. Transcription of yehZYXW is activated by the general stress sigma factor σ S in Enterobacteriaceae , which suggests a functional role for this transport system in bacterial stress response across the classes Alphaproteobacteria and Gammaproteobacteria . We present evidence that B. abortus YehZYXW does not function as an importer of known compatible solutes under physiological conditions and does not contribute to the virulence defect of a σ E1 -null strain. The sole in vitro phenotype associated with genetic disruption of this putative transport system is reduced growth in the presence of high Li + ion concentrations. A crystal structure of B. abortus YehZ revealed a class II periplasmic binding protein fold with significant structural homology to Archaeoglobus fulgidus ProX, which binds glycine betaine. However, the structure of the YehZ ligand-binding pocket is incompatible with high-affinity binding to glycine betaine. This is consistent with weak measured binding of YehZ to glycine betaine and related compatible solutes. We conclude that YehZYXW is a conserved, stress-regulated transport system that is phylogenetically and functionally distinct from quaternary ammonium-compatible solute importers. IMPORTANCE Brucella abortus σ E1 regulates transcription in response to stressors encountered in its mammalian host and is necessary for maintenance of chronic infection in a mouse model. The functions of the majority of genes regulated by σ E1 remain undefined. We present a functional/structural analysis of a conserved putative membrane transport system (YehZYXW) whose expression is strongly activated by σ E1 . Though annotated as a quaternary ammonium osmolyte uptake system, experimental physiological studies and measured ligand-binding properties of the periplasmic binding protein (PBP), YehZ, are inconsistent with this function. A crystal structure of B. abortus YehZ provides molecular insight into differences between bona fide quaternary ammonium osmolyte importers and YehZ-related proteins, which form a distinct phylogenetic and functional group of PBPs.

ABC transporter↗

History-dependent ion transport through conical nanopipettes and the implications in energy conversion dynamics at nanoscale interfaces

The dynamics of ion transport at nanostructured substrate–solution interfaces play vital roles in high-density energy conversion, stochastic chemical sensing and biosensing, membrane separation, nanofluidics and fundamental nanoelectrochemistry. Advancements in these applications require a fundamental understanding of ion transport at nanoscale interfaces. The understanding of the dynamic or transient transport, and the key physical process involved, is limited, which contrasts sharply with widely studied steady-state ion transport features at atomic and nanometer scale interfaces. Here we report striking time-dependent ion transport characteristics at nanoscale interfaces in current–potential (I–V) measurements and theoretical analyses. First, a unique non-zero I–V cross-point and pinched I–V curves are established as signatures to characterize the dynamics of ion transport through individual conical nanopipettes. Moreoever, ion transport against a concentration gradient is regulated by applied and surface electrical fields. The concept of ion pumping or separation is demonstrated via the selective ion transport against concentration gradients through individual nanopipettes. Third, this dynamic ion transport process under a predefined salinity gradient is discussed in the context of nanoscale energy conversion in supercapacitor type charging–discharging, as well as chemical and electrical energy conversion. Our analysis of the emerging current–potential features establishes the urgently needed physical foundation for energy conversion employing ordered nanostructures. The elucidated mechanism and established methodology can be generalized into broadly-defined nanoporous materials and devices for improved energy, separation and sensing applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modulated heat pulse propagation and partial transport barriers in chaotic magnetic fields

Direct numerical simulations of the time dependent parallel heat transport equation modeling heat pulses driven by power modulation in three-dimensional chaotic magnetic fields are presented. The numerical method is based on the Fourier formulation of a Lagrangian-Green's function method that provides an accurate and efficient technique for the solution of the parallel heat transport equation in the presence of harmonic power modulation. The numerical results presented provide conclusive evidence that even in the absence of magnetic flux surfaces, chaotic magnetic field configurations with intermediate levels of stochasticity exhibit transport barriers to modulated heat pulse propagation. In particular, high-order islands and remnants of destroyed flux surfaces (Cantori) act as partial barriers that slow down or even stop the propagation of heat waves at places where the magnetic field connection length exhibits a strong gradient. Results on modulated heat pulse propagation in fully stochastic fields and across magnetic islands are also presented. In qualitative agreement with recent experiments in large helical device and DIII-D, it is shown that the elliptic (O) and hyperbolic (X) points of magnetic islands have a direct impact on the spatio-temporal dependence of the amplitude of modulated heat pulses.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Steady-State Gyrokinetics Transport Code (SSGKT), A Scientific Application Partnership with the Framework Application for Core-Edge Transport Simulations, Final Report

This project initiated the development of TGYRO - a steady-state Gyrokinetic transport code (SSGKT) that integrates micro-scale GYRO turbulence simulations into a framework for practical multi-scale simulation of conventional tokamaks as well as future reactors. Using a lightweight master transport code, multiple independent (each massively parallel) gyrokinetic simulations are coordinated. The capability to evolve profiles using the TGLF model was also added to TGYRO and represents a more typical use-case for TGYRO. The goal of the project was to develop a steady-state Gyrokinetic transport code (SSGKT) that integrates micro-scale gyrokinetic turbulence simulations into a framework for practical multi-scale simulation of a burning plasma core ? the International Thermonuclear Experimental Reactor (ITER) in particular. This multi-scale simulation capability will be used to predict the performance (the fusion energy gain, Q) given the H-mode pedestal temperature and density. At present, projections of this type rely on transport models like GLF23, which are based on rather approximate fits to the results of linear and nonlinear simulations. Our goal is to make these performance projections with precise nonlinear gyrokinetic simulations. The method of approach is to use a lightweight master transport code to coordinate multiple independent (each massively parallel) gyrokinetic simulations using the GYRO code. This project targets the practical multi-scale simulation of a reactor core plasma in order to predict the core temperature and density profiles given the H-mode pedestal temperature and density. A master transport code will provide feedback to O(16) independent gyrokinetic simulations (each massively parallel). A successful feedback scheme offers a novel approach to predictive modeling of an important national and international problem. Success in this area of fusion simulations will allow US scientists to direct the research path of ITER over the next two decades. The design of an efficient feedback algorithm is a serious numerical challenge. Although the power source and transport balance coding in the master are standard, it is nontrivial to design a feedback loop that can cope with outputs that are both intermittent and extremely expensive. A prototypical feedback scheme has already been successfully demonstrated for a single global GYRO simulation, although the robustness and efficiency are likely far from optimal. Once the transport feedback scheme is perfected, it could, in principle, be embedded into any of the more elaborate transport codes (ONETWO, TRANSP, and CORSICA), or adopted by other FSP-related multi-scale projects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Transport dynamics of self-consistent, near-marginal drift-wave turbulence. II. Characterization of transport by means of passive scalars

From theoretical and modeling points of view, following Lagrangian trajectories is the most straightforward way to characterize the transport dynamics. In real plasmas, following Lagrangian trajectories is difficult or impossible. Using a blob of passive scalar (a tracer blob) allows a quasi-Lagrangian view of the dynamics. Using a simple two-dimensional electrostatic plasma turbulence model, this work demonstrates that the evolution of the tracers and the passive scalar field is equivalent between these two fluid transport viewpoints. When both the tracers and the passive scalar evolve in tandem and closely resemble stable distributions, namely, Gaussian distributions, the underlying turbulent transport character can be recovered from the temporal scaling of the second moments of both. This local transport approach corroborates the use of passive scalar as a turbulent transport measurement. The correspondence between the local transport character and the underlying transport is quantified for different transport regimes ranging from subdiffusive to superdiffusive. In conclusion, this correspondence is limited to the initial time periods of the spread of both the tracers and the passive scalar in the given transport regimes

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Theory of transport in high bootstrap fraction H-modes with internal transport barriers

A review of the recent progress in understanding the transport in fully non-inductive, high bootstrap fraction H-mode discharges, developed on the DIII-D tokamak, is given in this paper. Experiments have demonstrated improved energy confinement due to the formation of an internal transport barrier in high bootstrap fraction H-mode discharges. Gyrokinetic analysis, and quasi-linear predictive modeling, demonstrates that the observed transport barrier is due to the suppression of turbulence, primarily due to the large Shafranov shift. E×B velocity shear does not play a significant role in the transport barrier due to the high safety factor. The ion energy transport is reduced to neoclassical for DIII-D discharges and electron energy and particle transport is reduced, but still turbulent, within the barrier. Deeper into the plasma, high levels of electron transport are observed. The electron energy transport in DIII-D is found to be due to electromagnetically enhanced electron scale modes. A contribution from fast ion driven instabilities is also possible. The kinetic ballooning mode plays a strong role in the region between the internal and H-mode edge transport barriers with two types of self-organized pedestal states observed.

Physics↗

Utilizing ink composition to tune bulk-electrode gas transport, performance, and operational robustness for a Fe-N-C catalyst in polymer electrolyte fuel cell

With lower site density and turnover frequency, platinum group metal (PGM)-free catalysts based electrodes are often greater than 50 mu m thick in order to increase performance across the fuel cell operating range. Consequently, PGM-free electrodes have an additional bulk electrode transport resistance beyond the local or aggregate level transport in thin platinum-based electrodes. In parallel to the development of more active and durable PGM-free catalysts, advancements in understanding the interplay between PGM-free electrode fabrication, bulk-electrode transport, proton conductivity and performance are needed. Here, the relationship between ionic and gas phase transport through the electrode thickness is modified by adjusting electrocatalyst and ionomer flocculation/interaction at the ink level. The influence of the ink composition (water/n-propanol content) is examined via various in-situ electrochemical and ex-situ characterization techniques and the resulting electrode structure/performance relationship contrasted with electrode performance robustness across a range of relative humidity (RH). For the electrocatalyst examined here, a water-rich (82 wt% H2O) ink formulation was favorable for operation at high RH due to improved molecular diffusion through larger electrode pores. In contrast, the improved interactions between ionomer and electrocatalyst enabled a more robust electrode and higher performance during low RH operation for the 50 wt% H2O content ink.

08 HYDROGEN↗

Stochastic modeling of phosphorus transport in the Three Gorges Reservoir by incorporating variability associated with the phosphorus partition coefficient

Phosphorus (P) fate and transport plays a crucial role in the ecology of rivers and reservoirs in which eutrophication is limited by P. A key uncertainty in models used to help manage P in such systems is the partitioning of P to suspended and bed sediments. By analyzing data from field and laboratory experiments, we stochastically characterize the variability of the partition coefficient (Kd) and derive spatio-temporal solutions for P transport in the Three Gorges Reservoir (TGR). We formulate a set of stochastic partial different equations (SPDEs) to simulate P transport by randomly sampling Kd from the measured distributions, to obtain statistical descriptions of the P concentration and retention in the TGR. The correspondence between predicted and observed P concentrations and P retention in the TGR combined with the ability to effectively characterize uncertainty suggests that a model that incorporates the observed variability can better describe P dynamics and more effectively serve as a tool for P management in the system. This study highlights the importance of considering parametric uncertainty in estimating uncertainty/variability associated with simulated P transport.

Partition coefficient↗

Validation metrics for turbulent plasma transport

Developing accurate models of plasma dynamics is essential for confident predictive modeling of current and future fusion devices. In modern computer science and engineering, formal verification and validation processes are used to assess model accuracy and establish confidence in the predictive capabilities of a given model. This paper provides an overview of the key guiding principles and best practices for the development of validation metrics, illustrated using examples from investigations of turbulent transport in magnetically confined plasmas. Particular emphasis is given to the importance of uncertainty quantification and its inclusion within the metrics, and the need for utilizing synthetic diagnostics to enable quantitatively meaningful comparisons between simulation and experiment. As a starting point, the structure of commonly used global transport model metrics and their limitations is reviewed. An alternate approach is then presented, which focuses upon comparisons of predicted local fluxes, fluctuations, and equilibrium gradients against observation. The utility of metrics based upon these comparisons is demonstrated by applying them to gyrokinetic predictions of turbulent transport in a variety of discharges performed on the DIII-D tokamak [J. L. Luxon, Nucl. Fusion 42, 614 (2002)], as part of a multi-year transport model validation activity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

What Matters for the Charge Transport of 2D Perovskites?

Abstract Compared to 3D perovskites, 2D perovskites exhibit excellent stability, structural diversity, and tunable bandgaps, making them highly promising for applications in solar cells, light‐emitting diodes, and photodetectors. However, the trade‐off for worse charge transport is a critical issue that needs to be addressed. This comprehensive review first discusses the structure of 3D and 2D metal halide perovskites, then summarizes the significant factors influencing charge transport in detail and provides a brief overview of the testing methods. Subsequently, various strategies to improve the charge transport are presented, including tuning A′‐site organic spacer cations, A‐site cations, B‐site metal cations, and X‐site halide ions. Finally, an outlook on the future development of improving the 2D perovskites’ charge transport is discussed.

Zhang, Yixin↗

Investigation of the Selectivity of Carrier Transport Layers in Wide-Bandgap Perovskite Solar Cells

Excellent contact passivation and selectivity are prerequisites to realize the full potential of high-material-quality perovskite solar cells, first to maximize the internal voltage (or quasi-Fermi-level separation) iV within the absorber, then to translate this high internal voltage into a high external voltage V. Experimental quantification of contact passivation and selectivity is, thus, key to improving device performance. Here, open-circuit measurements of iV oc and V oc , combined with surface photovoltage measurements, are used to systematically quantify the passivation—using iVoc as a metric—and the selectivity—defined as Soc=V oc /iV oc —of a range of common carrier transport layers to wide-bandgap (1.67 eV) perovskite absorbers. The resulting solar cells suffer from large voltage deficits, particularly when NiO x is used as the hole transport layer, even though it provides better passivation than its polymer-based counterparts (PTAA and PTAA/PFN). This indicates a poor selectivity of NiO x (Soc<0.81 for NiO x -based devices), whereas devices using polymer-based hole transport layers exhibit high selectivity (S oc =0.94–0.95). In agreement with recent reports, this low selectivity is attributed to the formation of an interlayer of non-perovskite material with high resistance to holes at the perovskite/NiO x interface. These measurements also imply that the selectivity of the C60-based electron transport layers is relatively good.

carrier transport layers↗

Stability and accuracy of 3D neutron transport simulations using the 2D/1D method in MPACT

A consistent “2D/1D” neutron transport method is derived from the 3D Boltzmann transport equation, to calculate fuel-pin-resolved neutron fluxes for realistic full-core Pressurized Water Reactor (PWR) problems. The 2D/1D method employs the Method of Characteristics to discretize the radial variables and a lower order transport solution to discretize the axial variable. This paper describes the theory of the 2D/1D method and its implementation in the MPACT code, which has become the whole-core deterministic neutron transport solver for the Consortium for Advanced Simulations of Light Water Reactors (CASL) core simulator VERA-CS. Several applications have been performed on both leadership-class and industry-class computing clusters. Results are presented for whole-core solutions of the Watts Bar Nuclear Power Station Unit 1 and compared to both continuous-energy Monte Carlo results and plant data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites

Human FABP5 and FABP7 are intracellular endocannabinoid transporters. SBFI-26 is an $α$-truxillic acid 1-naphthyl monoester that competitively inhibits the activities of FABP5 and FABP7 and produces antinociceptive and anti-inflammatory effects in mice. The synthesis of SBFI-26 yields several stereoisomers, and it is not known how the inhibitor binds the transporters. Here we report co-crystal structures of SBFI-26 in complex with human FABP5 and FABP7 at 2.2 and 1.9 Å resolution, respectively. We found that only $(S)$-SBFI-26 was present in the crystal structures. The inhibitor largely mimics the fatty acid binding pattern, but it also has several unique interactions. Notably, the FABP7 complex corroborates key aspects of the ligand binding pose at the canonical site previously predicted by virtual screening. In FABP5, SBFI-26 was unexpectedly found to bind at the substrate entry portal region in addition to binding at the canonical ligand-binding pocket. Our structural and binding energy analyses indicate that both $R$ and $S$ forms appear to bind the transporter equally well. We suggest that the $S$ enantiomer observed in the crystal structures may be a result of the crystallization process selectively incorporating the $(S)$-SBFI-26–FABP complexes into the growing lattice, or that the $S$ enantiomer may bind to the portal site more rapidly than to the canonical site, leading to an increased local concentration of the $S$ enantiomer for binding to the canonical site. Our work reveals two binding poses of SBFI-26 in its target transporters. We surmise this knowledge will guide the development of more potent FABP inhibitors based upon the SBFI-26 scaffold.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-fluid transport code modeling of time-dependent recycling in ELMy H-mode

Simulations of a high-confinement-mode (H-mode) tokamak discharge with infrequent giant type-I ELMs are performed by the multi-fluid, multi-species, two-dimensional transport code UEDGE-MB, which incorporates the Macro-Blob approach for intermittent non-diffusive transport due to filamentary coherent structures observed during the Edge Localized Modes (ELMs) and simple time-dependent multi-parametric models for cross-field plasma transport coefficients and working gas inventory in material surfaces. Temporal evolutions of pedestal plasma profiles, divertor recycling, and wall inventory in a sequence of ELMs are studied and compared to the experimental time-dependent data. Short- and long-time-scale variations of the pedestal and divertor plasmas where the ELM is described as a sequence of macro-blobs are discussed. It is shown that the ELM recovery includes the phase of relatively dense and cold post-ELM divertor plasma evolving on a several ms scale, which is set by the transport properties of H-mode barrier. The global gas balance in the discharge is also analyzed. The calculated rates of working gas deposition during each ELM and wall outgassing between ELMs are compared to the ELM particle losses from the pedestal and neutral-beam-injection fueling rate, correspondingly. A sensitivity study of the pedestal and divertor plasmas to model assumptions for gas deposition and release on material surfaces is presented. The performed simulations show that the dynamics of pedestal particle inventory is dominated by the transient intense gas deposition into the wall during each ELM followed by continuous gas release between ELMs at roughly a constant rate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Quasiparticle band structures and thermoelectric transport properties of p-type SnSe

We used density functional and many-body perturbation theory to calculate the quasiparticle band structures and electronic transport parameters of p-type SnSe both for the low-temperature Pnma and high-temperature Cmcm phases. The Pnma phase has an indirect band gap of 0.829 eV, while the Cmcm has a direct band gap of 0.464 eV. Both phases exhibit multiple local band extrema within an energy range comparable to the thermal energy of carriers from the global extrema. We calculated the electronic transport coefficients as a function of doping concentration and temperature for single-crystal and polycrystalline materials to understand the previous experimental measurements. The electronic transport coefficients are highly anisotropic and are strongly affected by bipolar transport effects at high temperature. Our results indicate that SnSe exhibits optimal thermoelectric performance at high temperature when doped in the 10{sup 19}–10{sup 20 }cm{sup −3} range.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗