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At least 253 records · Page 14

How we compute N matters to estimates of mixing in stratified flows

We know that most commonly used models for turbulent mixing in the ocean rely on a background stratification against which turbulence must work to stir the fluid. While this background stratification is typically well defined in idealized numerical models, it is more difficult to capture in observations. Here, a potential discrepancy in ocean mixing estimates due to the chosen calculation of the background stratification is explored using direct numerical simulation data of breaking internal waves on slopes. There are two different methods for computing the buoyancy frequency $N$ , one based on a three-dimensionally sorted density field (often used in numerical models) and the other based on locally sorted vertical density profiles (often used in the field), are used to quantify the effect of $N$ on turbulence quantities. It is shown that how $N$ is calculated changes not only the flux Richardson number $R_{f}$ , which is often used to parameterize turbulent mixing, but also the turbulence activity number or the Gibson number $Gi$ , leading to potential errors in estimates of the mixing efficiency using $Gi$ -based parameterizations.

42 ENGINEERING↗

Modern Approaches to Exact Diagonalization and Selected Configuration Interaction with the Adaptive Sampling CI Method

Recent advances in selected configuration interaction methods have made them competitive with the most accurate techniques available and, hence, creating an increasingly powerful tool for solving quantum Hamiltonians. In this work, we build on recent advances from the adaptive sampling configuration interaction (ASCI) algorithm. We show that a useful paradigm for generating efficient selected CI/exact diagonalization algorithms is driven by fast sorting algorithms, much in the same way iterative diagonalization is based on the paradigm of matrix vector multiplication. We present several new algorithms for all parts of performing a selected CI, which includes new ASCI search, dynamic bit masking, fast orbital rotations, fast diagonal matrix elements, and residue arrays. The ASCI search algorithm can be used in several different modes, which includes an integral driven search and a coefficient driven search. The algorithms presented here are fast and scalable, and we find that because they are built on fast sorting algorithms they are more efficient than all other approaches we considered. After introducing these techniques, we present ASCI results applied to a large range of systems and basis sets to demonstrate the types of simulations that can be practically treated at the full-CI level with modern methods and hardware, presenting double- and triple-ζ benchmark data for the G1 data set. The largest of these calculations is Si$_2$H$_6$ which is a simulation of 34 electrons in 152 orbitals. We also present some preliminary results for fast deterministic perturbation theory simulations that use hash functions to maintain high efficiency for treating large basis sets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Click-Chemistry-Based Free Azide versus Azido Sugar Detection Enables Rapid In Vivo Screening of Glycosynthase Activity

Engineering of carbohydrate-active enzymes such as glycosynthases to enable chemoenzymatic synthesis of bespoke oligosaccharides has been limited by the lack of suitable ultrahigh-throughput screening methods capable of robustly detecting either starting substrates or end-products of the glycosidic bond formation reaction. Currently, there are limited screening methods available for rapid and highly sensitive single-cell-based screening of glycosynthase enzymes employing azido sugars as activated donor glycosyl substrates. Here, we report a fluorescence-based approach employing click-chemistry for the selective detection of glycosyl azides as substrates versus free inorganic azides as reaction products that facilitated an ultrahigh-throughput in vivo single-cell-based assay of glycosynthase activity. This assay was developed based on the distinct differences observed in relative fluorescence intensity of the triazole-containing fluorophore product formed during the click-chemistry reaction of organic glycosyl azides versus inorganic azides. This discovery formed the basis for proof of concept validation of a directed evolution methodology for screening and sorting glycosynthase mutants capable of synthesis of targeted fucosylated oligosaccharides. Our screening approach facilitated fluorescence-activated cell sorting of an error-prone polymerase chain reaction-based mutant library of fucosynthases expressed in Escherichia coli to identify several novel mutants that showed increased activity for ß-fucosyl azide-activated donor sugars toward desired acceptor sugars (e.g., pNP-xylose and lactose). Finally, we discuss avenues for improving this proof of concept in vivo assay method to identify better glycosynthase mutants and further demonstrate the broader applicability of this screening methodology for synthesis of bespoke glycans.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

L -Value and Energy Dependence of 0.1–50 keV O + , He + , and H + Ions for CME and CIR Storms Over the Entire Van Allen Probes Era

Our studies report the first observation of L -value and energy sorted correlation of differential fluxes of 0.1–50 keV O + , He + , and H + ions with different geophysical parameters for 29 Coronal Mass Ejected (CME) and 40 Corotating Interaction Region (CIR)-driven geomagnetic storms during the entire Van Allen Probes era. For both solar wind drivers, ions with ≥1 keV energies show more variability in response to the solar wind changes, while the lower energy (<1 keV) ions are relatively stable. During the in-storm interval, O + ions show maximum flux enhancement and become further prominent during CME storms. O + ion (≥10 keV) fluxes show good correlation with – $V_{sw}B_z$, and Sym-H index during CME-driven storms in the L ~2.5–5.5. Apart from this, the average duration of persistence ($\langleΔt\rangle$) for enhanced fluxes is higher for CIR-driven storms with $\langleΔt\rangle_{O^+}>\langleΔt\rangle_{He^+}>\langleΔt\rangle_{H^+}$ at E ≤ 50 keV in the L ~2.5–5.5. Moreover, the observed value of $\langleΔt\rangle_i$ (where $\textit{i}$ is O + , H + or He + ) increases with the increasing L . Further, we discuss the plausible mechanisms to provide a comprehensive overview of L -values and energy sorted O + , He + and H + ion dynamics for two different categories of solar wind drivers.

79 ASTRONOMY AND ASTROPHYSICS↗

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt

The intestinal epithelium is replaced weekly by non-quiescent stem cells with kinetics that rely on a rapid loss of stemness and choice for secretory or absorptive lineage differentiation. To determine how the cellular transcriptome and proteome changes during these transitions, we developed a new cell sorting method to purify stem cells, secretory and absorptive progenitor cells, and mature, differentiated cells. Transcriptome analyses revealed that as stem cells transition to the progenitor stage, alternative mRNA splicing and polyadenylation dominate changes in the transcriptome. In contrast, as progenitors differentiate into mature cell types, alterations in gene expression and mRNA levels drive the changes. RNA processing targets mRNAs encoding regulators of cell cycle, RNA regulators, cell adhesion, SUMOylation, and Wnt and Notch signaling. Additionally, global proteome profiling of sorted cell populations detected >2,800 proteins and revealed RNA:protein patterns of abundance and correlation. Paired together, these data highlight new potentials for autocrine and feedback regulation and provide new insights into cell state transitions in the crypt.

59 BASIC BIOLOGICAL SCIENCES↗

The influence of curvature on domain distribution in binary mixture membranes

Curvature-induced domain sorting, a strategy exploited by cells to organize membrane components, is a promising mechanism to control self-assembly of materials. To comprehend this phenomenon, we explore the effects of curvature on component rearrangement in thin polymer films and lipid bilayers supported on sinusoidal substrates. Self-consistent field theory (SCFT), specifically, was used to study the spatial distribution of polymers in blends containing conformationally asymmetric chains. In addition, coarse-grained molecular dynamics (MD) simulations were used to probe the arrangement of rigid lipid domains in a relatively soft lipid matrix. Besides the expected preference of rigid species localizing in regions with low mean curvature, both systems exhibit unexpected localization of rigid components in comparatively high curvature regions. The origins of this unexpected sorting are discussed in terms of entropic and enthalpic contributions. In summary, this study demonstrates that domain distribution strongly depends on local topography and further highlights the collective effects that thermodynamic forces have on the morphological behavior of membranes.

36 MATERIALS SCIENCE↗

Economic evaluation of infrastructures for thermochemical upcycling of post-consumer plastic waste

Thermochemical technologies, such as pyrolysis, offer a potentially scalable pathway for upcycling diverse types of plastic waste (PW) into value-added chemicals. However, deploying these technologies in waste management infrastructures is not straightforward because such systems involve a wide range of interdependent stakeholders, processing facilities, and products. In this work, we present a holistic optimization framework that integrates value-chain analysis, techno-economic analysis, and life-cycle analysis for investigating the economic viability and environmental benefits of upcycling infrastructures that collect, sort, clean, and process post-consumer PW for producing virgin polymer resins. The framework is applied to a case study in the upper Midwest region of the US. Our analysis reveals that the infrastructures are economically viable and could activate a regional circular economy that generates over 1 billion USD in annual profit. Moreover, our analysis reveals that this economy can reduce the carbon footprint of PW incineration by half. Our framework also determines the inherent values of post-consumer PW and of derived products such as plastic bales and pyrolysis oil; we find that, in these infrastructures, PW becomes a highly valuable feedstock with a market value of 500 USD per tonne. Here, we discuss how this market value can generate incentives that foster more effective waste pre-sorting practices by consumers that can help bypass material recycling facilities and increase total system profit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatial proteomics reveals signal sequence characteristics correlated with localization in cyanobacteria

Abstract Cyanobacteria have an inner and outer cell membrane enclosing the periplasm and cell wall and an additional set of internal membranes (called the thylakoid membranes) enclosing the thylakoid lumen. The periplasm and thylakoid lumen have unique proteomes, but the mechanisms regulating protein sorting to these locations have remained elusive. Here, proximity-based proteomics using the engineered peroxidase APEX2 was performed in the cyanobacteria Synechococcus sp. PCC 7002 to profile the proteomes of the cytoplasm, thylakoid lumen, and the periplasm and outer membrane (P-OM). Our analyses revealed specific roles for the thylakoid lumen in photosynthesis and energy generation, as well as roles for the periplasm in metabolite transport and binding, cell motility, and cell wall maintenance. Forty proteins localized to both the thylakoid lumen and the P-OM; however, their biological functions remain unclear. We also analyzed the correlation between signal sequence characteristics and differential protein localization to either the thylakoid lumen or the P-OM. In PCC 7002, as well as Synechocystis sp. PCC 6803 and Nostoc sp. PCC 7120, thylakoid lumen proteins translocated across membranes via the Secretory (Sec) system possessed more hydrophobic and alpha-helical signal sequence H-regions than P-OM proteins. The signal sequences of homologous proteins in Gloeobacter violaceus PCC 7421, a cyanobacterial species with a combined thylakoid lumen and periplasmic space, did not exhibit such differences. Therefore, the pattern of increased H-region hydrophobicity and alpha helix content is specific to cyanobacteria with a separate thylakoid lumen space and likely contributes to proper protein sorting between the thylakoid lumen and periplasm.

Plant Sciences↗

Large inflationary logarithms in a nontrivial nonlinear sigma model

Loops of inflationary gravitons are known to induce large temporal and spatial logarithms that can cause perturbation theory to break down. Nonlinear sigma models possess the same kind of derivative interactions and induce the same sorts of large logarithms, without the complicated index structure and potential gauge problem. Previous studies have examined models with zero field space curvature that can be reduced to free field theories by local, invertible field redefinitions. Here we study a model that cannot be so reduced and still shows the same sorts of large logarithms. Additionally, we compute the evolution of the background at 1-loop and 2-loop orders, and we find the 1-loop β and γ functions.

79 ASTRONOMY AND ASTROPHYSICS↗

DC Link Voltage Balancing of the Active Front-End for the Extreme Fast Charging Stations

One of the most important challenges of the extreme fast charging (XFC) stations is to balance the DC link voltages of the active front-end (AFE). The multilevel cascaded H-bridge (CHB) converter is a great topology for the AFE applications due to the high power density, low total harmonic distortion (THD), and a low number of active and passive components. In this paper, a technique is proposed for balancing DC-link capacitor voltages of a three-phase CHB converter, when a phase shiftPWM modulation technique is used on all cells of the converter. To reach this goal, the redundant states of the CHB converters are used for generating different AC voltage levels by sorting the voltages of the converters. The proposed voltage balancing technique uses the principles that are employed for the DC link voltage balancing of the low-frequency modulation techniques to balance the DC link voltages of the CHB converter. As shown in this paper, the DC link voltages of the CHB converter can accurately be balanced very fast without using PI controllers, which are used in the conventional DC link voltage balancing techniques. A controller also is proposed which will be used to control the dq currents of the CHB converter. To verify the advantages of the proposed technique, the simulation results of the proposed technique will be carried out in a three-phase 7-cell CHB AFE.

Grid-tied converters, cascaded H-bridge, DC link v↗

A Novel Resilience-Oriented Cellular Grid Formation Approach for Distribution Systems with Behind-the-Meter Distributed Energy Resources

This paper presents a resilience-oriented cellular grid formation approach to achieve scalable and reconfigurable community microgrid operations for distribution systems with behind-the-meter distributed energy resources. A set of interconnected solar photovoltaics, energy storage systems, and load is termed as a cell, implying a subset of the grid that can operate independently using its own resources. Cells are identified such that each cell inherently has sufficient energy resources to black start and can provide a certain level of backup power for its load under the loss of utility power supply. The proposed cell formation approach builds on a unique self-organizing map-based method (SomRes) to quantify a system's resilience. Using SomRes and a non-dominated sorting-based genetic algorithm (NSGA-II), a fast and efficient cell formation algorithm is developed to identify cells in a distribution system that are resilient against extreme events. The efficacy of the proposed approach is demonstrated on a numerical model of a real distribution feeder in Colorado, United States.

distributed energy resource↗

Power System Event Identification Based on Deep Neural Network With Information Loading

Online power system event identification and classification are crucial to enhancing the reliability of transmission systems. In this study, we develop a deep neural network (DNN) based approach to identify and classify power system events by leveraging real-world measurements from hundreds of phasor measurement units (PMUs) and labels from thousands of events. Two innovative designs are embedded into the baseline model built on convolutional neural networks (CNNs) to improve the event classification accuracy. First, we propose a graph signal processing based PMU sorting algorithm to improve the learning efficiency of CNNs. Second, we deploy information loading based regularization to strike the right balance between memorization and generalization for the DNN. Numerical results based on real-world dataset from the Eastern Interconnection of the U.S power transmission grid show that the combination of PMU based sorting and the information loading based regularization techniques help the proposed DNN approach achieve highly accurate event identification and classification results.

24 POWER TRANSMISSION AND DISTRIBUTION↗

The intrinsically disordered nature of the peroxisomal protein translocation machinery

Despite having a membrane that is impermeable to all but the smallest of metabolites, peroxisomes acquire their newly synthesized (cytosolic) matrix proteins in an already folded conformation. In some cases, even oligomeric proteins have been reported to translocate the organelle membrane. The protein sorting machinery that accomplishes this feat must be rather flexible and, unsurprisingly, several of its key components have large intrinsically disordered domains. Here, we provide an overview on these domains and their interactions trying to infer their functional roles in this protein sorting pathway.

Barros‐Barbosa, Aurora↗

Peptidoglycan Contribution to the B Cell Superantigen Activity of Staphylococcal Protein A

Staphylococcus aureus causes reiterative and chronic persistent infections. This can be explained by the formidable ability of this pathogen to escape immune surveillance mechanisms. Cells of S. aureus display the abundant staphylococcal protein A (SpA). SpA binds to immunoglobulin (Ig) molecules and coats the bacterial surface to prevent phagocytic uptake. SpA also binds and cross-links variable heavy 3 (V H 3) idiotype (IgM) B cell receptors, promoting B cell expansion and the secretion of nonspecific V H 3-IgM via a mechanism requiring CD4 + T cell help. SpA binding to antibodies is mediated by the N-terminal Ig-binding domains (IgBDs). The so-called region X, uncharacterized LysM domain, and C-terminal LPXTG sorting signal for peptidoglycan attachment complete the linear structure of the protein. Here, we report that both the LysM domain and the LPXTG motif sorting signal are required for the B cell superantigen activity of SpA in a mouse model of infection. SpA molecules purified from staphylococcal cultures are sufficient to exert B cell superantigen activity and promote immunoglobulin secretion as long as they carry intact LysM and LPXTG motif domains with bound peptidoglycan fragments. The LysM domain binds the glycan chains of peptidoglycan fragments, whereas the LPXTG motif is covalently linked to wall peptides lacking glycan. These findings emphasize the complexity of SpA interactions with B cell receptors.

59 BASIC BIOLOGICAL SCIENCES↗

Modern status of photonuclear data

The reliability of experimental cross sections obtained for (γ, 1n), (γ, 2n), and (γ, 3n) partial photoneutron reactions using beams of quasimonoenergetic annihilation photons and bremsstrahlung is analyzed by employing data for a large number of medium-heavy and heavy nuclei, including those of {sup 63,65}Cu, {sup 80}Se, {sup 90,91,94}Zr, {sup 115}In, {sup 112−124}Sn, {sup 133}Cs, {sup 138}Ba, {sup 159}Tb, {sup 181}Ta, {sup 186−192}Os, {sup 197}Au, {sup 208}Pb, and {sup 209}Bi. The ratios of the cross sections of definite partial reactions to the cross section of the neutron-yield reaction, F{sub i} = σ(γ, in)/σ(γ, xn), are used as criteria of experimental-data reliability. By definition, positive values of these ratios should not exceed the upper limits of 1.00, 0.50, 0.33,... for i = 1, 2, 3,..., respectively. For many nuclei, unreliable values of the above ratios were found to correlate clearly in various photon-energy regions F{sub i} with physically forbidden negative values of cross sections of partial reactions. On this basis, one can conclude that correspondent experimental data are unreliable. Significant systematic uncertainties of the methods used to determine photoneutron multiplicity are shown to be the main reason for this. New partial-reaction cross sections that satisfy the above data-reliability criteria were evaluated within an experimental–theoretical method [σ{sup eval}(γ, in) = F{sub i}{sup theor} (γ, in) × σ{sup expt}(γ, xn)] by employing the ratios F{sub i}{sup theor} (γ, in) calculated on the basis of a combined photonuclear-reaction model. It was obtained that cross sections evaluated in this way deviate substantially from the results of many experiments performed via neutron-multiplicity sorting, but, at the same time, agree with the results of alternative activation experiments. Prospects of employing methods that would provide, without recourse to photoneutron-multiplicity sorting, reliable data on cross sections of partial photoneutron reactions are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Detection of UV Radiation from Extensive Air Showers: Prospects for Cherenkov Gamma-Ray Astronomy

Cherenkov emission of extensive air showers (EAS) from cosmic gamma rays and cosmic-ray protons has been modelled. Spectral density of such emission in the 240–700 nm band has been determined for 3 GeV–10 TeV primaries of both sorts. It has been shown that the ratio of EAS Cherenkov emission fluxes in the optical and ultraviolet (UV) bands substantially depends on the sort of the primary, so the ratio can be employed to select gamma-ray events from the background produced by cosmic rays. Detection of EAS Cherenkov emission with specialized silicon photomultipliers sensitive in the UV band would allow one to substantially extend the duty cycle of a Cherenkov gamma-ray telescope, as it would be possible to observe the showers during moonlit nights. The UV-sensitive silicon photomultipliers developed at the Ioffe Institute would allow to detect gamma-ray-induced EAS at the Cherenkov gamma-ray observatory ALEGRO over a threshold of about 40 GeV at 5 km above sea level and about 80 GeV at 2 km above sea level.

79 ASTRONOMY AND ASTROPHYSICS↗

Computational Complexity of Neuromorphic Algorithms

Neuromorphic computing has several characteristics that make it an extremely compelling computing paradigm for post Moore computation. Some of these characteristics include intrinsic parallelism, inherent scalability, collocated processing and memory, and event-driven computation. While these characteristics impart energy efficiency to neuromorphic systems, they do come with their own set of challenges. One of the biggest challenges in neuromorphic computing is to establish the theoretical underpinnings of the computational complexity of neuromorphic algorithms. In this paper, we take the first steps towards defining the space and time complexity of neuromorphic algorithms. Specifically, we describe a model of neuromorphic computation and state the assumptions that govern the computational complexity of neuromorphic algorithms. Next, we present a theoretical framework to define the computational complexity of a neuromorphic algorithm. We explicitly define what space and time complexities mean in the context of neuromorphic algorithms based on our model of neuromorphic computation. Finally, we leverage our approach and define the computational complexities of six neuromorphic algorithms: constant function, successor function, predecessor function, projection function, neuromorphic sorting algorithm and neighborhood subgraph extraction algorithm.

Date, Prasanna↗

Divergence Reduction in Monte Carlo Neutron Transport with On-GPU Asynchronous Scheduling

While Monte Carlo Neutron Transport (MCNT) is near-embarrasingly parallel, the effectively unpredictable lifetime of neutrons can lead to divergence when MCNT is evaluated on GPUs. Divergence is the phenomenon of adjacent threads in a warp executing different control flow paths; on GPUS, it reduces performance because each work group may only execute one path at a time. The process of Thread Data Remapping (TDR) resolves these discrepancies by moving data across hardware such that data in the same warp will be processed through similar paths. A common issue among prior implementations of TDR is the synchronous nature of its remapping and processing cycles, which exhaustively sort data produced by prior processing passes and exhaustively evaluate the sorted data. In another work, we defined a method of remapping data through an asynchronous scheduler which allows for work to be stored in shared memory and deferred arbitrarily until that work is a viable option for low-divergence evaluation. This article surveys a wider set of cases, with the goal of characterizing performance trends across a more comprehensive set of parameters. These parameters include cross sections of scattering/capturing/fission, use of implicit capture, source neutron counts, simulation time spans, and tuned memory allocations. Across these cases, we have recorded minimum and average execution times, as well as a heuristically tuned near-optimal memory allocation size for both synchronous and asynchronous scheduling. Across the collected data, it is shown that the asynchronous method is faster and more memory efficient in the majority of cases, and that it requires less tuning to achieve competitive performance.

Computer Science↗