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At least 325 records · Page 18

Structural basis for the subtype-selectivity of K Ca 2.2 channel activators

Small-conductance (K Ca 2.2) and intermediate-conductance (K Ca 3.1) Ca 2+ -activated K + channels are gated by a Ca 2+ -calmodulin dependent mechanism. NS309 potentiates the activity of both K Ca 2.2 and K Ca 3.1, while rimtuzalcap selectively activates K Ca 2.2. Rimtuzalcap has been used in clinical trials for the treatment of spinocerebellar ataxia and essential tremor. We report cryo-electron microscopy structures of NS309-bound K Ca 2.2 and K Ca 3.1, in addition to structures of rimtuzalcap-bound K Ca 2.2 and mutant K Ca 3.1_R355K. The different conformations of calmodulin and the cytoplasmic HC helices in the two channels underlie the subtype-selectivity of rimtuzalcap for K Ca 2.2. NS309 binds to pre-existing pockets in both channels, while the bulkier rimtuzalcap binds in an induced-fit pocket in K Ca 2.2 requiring conformational changes. In K Ca 2.2, calmodulin’s N-lobes are sufficiently far apart to enable conformational changes to accommodate either NS309 or rimtuzalcap. In K Ca 3.1, calmodulin’s N-lobes are closer to each other and constrained by K Ca 3.1’s HC helices, which allows binding of NS309 but not rimtuzalcap. Replacement of arginine-355 in K Ca 3.1’s HB helix with lysine (K Ca 3.1_R355K) allows the binding of rimtuzalcap and renders the mutant channel sensitive to rimtuzalcap. These structures provide a framework for structure-based drug design targeting K Ca 2.2 channels.

Nam, Young-Woo [Chapman Univ., Irvine, CA (United ↗

Global terrestrial nitrogen fixation and its modification by agriculture

Biological nitrogen fixation (BNF) is the largest natural source of new nitrogen (N) that supports terrestrial productivity, yet estimates of global terrestrial BNF remain highly uncertain. Here, in this study, we show that this uncertainty is partly because of sampling bias, as field BNF measurements in natural terrestrial ecosystems occur where N fixers are 17 times more prevalent than their mean abundances worldwide. To correct this bias, we develop new estimates of global terrestrial BNF by upscaling field BNF measurements using spatially explicit abundances of all major biogeochemical N-fixing niches. We find that natural biomes sustain lower BNF, 65 (52–77) Tg N yr −1 , than previous empirical bottom-up estimates, with most BNF occurring in tropical forests and drylands. We also find high agricultural BNF in croplands and cultivated pastures, 56 (54–58) Tg N yr −1 . Agricultural BNF has increased terrestrial BNF by 64% and total terrestrial N inputs from all sources by 60% over pre-industrial levels. Our results indicate that BNF may impose stronger constraints on the carbon sink in natural terrestrial biomes and represent a larger source of agricultural N than is generally considered in analyses of the global N cycle, with implications for proposed safe operating limits for N use.

Reis Ely, Carla R. [Oregon State Univ., Corvallis,↗

A global dataset of terrestrial biological nitrogen fixation

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha −1 y −1 ), the percentage of nitrogen derived from the atmosphere (%N dfa ), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

Reis Ely, Carla R. [Oregon State Univ., Corvallis,↗

Bayesian optimization of laser wakefield acceleration via spectral pulse shaping

In this paper, we investigate the effect of spectral pulse shaping of the laser driver on the performance of channel-guided, laser–plasma accelerators. The study was carried out with the assistance of Bayesian optimization using particle-in-cell simulations. We used a realistic plasma profile based on a novel optical-field-ionized channel technique with ionization injection and low, on-axis plasma densities to maximize the energy gain of the electron bunch trailing the laser. Spectral shaping allows us to modify the temporal profile of the laser driver while keeping the laser energy constant, affecting the acceleration and injection processes. In addition, we consider how modifying the plasma channel parameters may affect the target outputs. Given the complexity and breadth of the parameter space in question, we used numerical optimization to identify high-performing configurations. In particular, we found laser profiles with additional spectral content that, when used with optimal plasma channel parameters, result in charge content an order of magnitude higher than the baseline Gaussian case while also increasing the mean energy of the electron bunch.

Physics - Plasma physics↗

Overestimated natural biological nitrogen fixation translates to an exaggerated CO 2 fertilization effect in Earth system models

CO 2 fertilization of the terrestrial biosphere is limited by nitrogen. Biological nitrogen fixation (BNF) is the dominant natural nitrogen source to the terrestrial biosphere and can alleviate nitrogen limitation but is poorly constrained in Earth system models (ESMs). Here, in this study, we compare terrestrial BNF from an ensemble of ESMs of the 6th Coupled Model Intercomparison Project to a new global synthesis of observations across natural and agricultural biomes. We find that compared to observations, ESMs underestimate agricultural BNF but overestimate natural BNF in the present day by over 50%. Natural BNF is overestimated in the most productive ecosystems that contribute most to the terrestrial carbon sink (forests and grasslands). ESMs with different BNF representations yield a range of BNF responses to CO 2 enrichment. Some ESMs with phenomenological representations of BNF predict a natural BNF increase in response to a doubling of CO 2 that aligns with a meta-analysis of CO 2 enrichment experiments (31% increase) but fail to account for the substantial carbon cost of BNF. In contrast, ESMs with mechanistic representations of BNF account for its carbon cost as well as its regulation by nitrogen limitation but overestimate the BNF response to a doubling of CO 2 (135% increase). Overall, all current BNF representations in ESMs fall short of fully capturing its response to rising atmospheric CO 2 . Finally, we find a positive correlation between modeled present-day natural BNF and the CO 2 fertilization effect across ESMs, suggesting that overestimated natural BNF translates to an exaggerated CO 2 fertilization effect of approximately 11% in ESMs.

Biological nitrogen fixation↗

Anisotropic Thermal Transport in Quasi-2D Ruddlesden-Popper Hybrid Perovskite Superlattices

Two-dimensional hybrid metal-halide perovskites (2D-MHPs) have emerged as important solution-processed semiconductors with favorable optical and electronic properties for diverse applications in photovoltaics, optoelectronics, and spintronics. The quasi-2D layered structures, featuring large acoustic impedance mismatches between the organic and inorganic sublattices, are expected to result in distinct and anisotropic thermal transport properties along the cross-plane and in-plane directions. Here, we introduce transducer-free vibrational-pump-visible-probe (VPVP) approaches that enable accurate quantification of anisotropic thermal transport properties in various archetypical single-crystalline 2D-MHPs. Specifically, using VPVP spectroscopy and VPVP microscopy, we measure the anisotropic thermal diffusivities of 2D-MHPs with systematically varied Pb-I octahedral layer thicknesses, as well as organic spacer types and lengths, revealing how these structural parameters alter the cross-plane and in-plane thermal transport properties in distinct ways. While diffuse interface scattering plays an important role in dictating cross-plane thermal transport, in-plane thermal transport is primarily determined by phonon transport within interconnected inorganic layers. Density functional theory incorporating four-phonon scatterings provides further insight into the low thermal conductivity and modest thermal conduction anisotropy in 2D-MHPs. Our work demonstrates a new all-optical and noncontact method, which requires minimal sample preparation and allows direct visualization of cross-plane and in-plane thermal transport, potentially compatible with sample environments. The demonstrated VPVP approaches can advance understanding of thermal transport in 2D-MHPs as well as wide-ranging hybrid and polymeric semiconductors beyond 2D-MHPs.

36 MATERIALS SCIENCE↗

Occupant-Centric Demand Response for Thermostatically-Controlled Home Loads

Efficiently managing energy usage to balance supply and demand on the electric grid is crucial, especially with the widespread deployment of distributed variable renewable electricity generation. This paper introduces two duty-cycle control methods for heating systems, adjusting thermostat setpoints to limit and shift electricity demand. The control approaches employ innovative techniques, such as adaptive duty cycling, to prioritize household thermal comfort while reducing peak demand. These control methods can respond to signals from the electric grid, including demand targets and time-of-use tariffs, and were tested physically on an electric furnace and heat pump in a test home during winter conditions in 2021 and 2022. The results are given as average demand reductions and energy use impacts with respect to the average indoor-outdoor temperature difference during the control period. For heat pumps, demand limiting control reduced power by 18.5% and 23.3% for indoor-outdoor temperature differences of 30°F and 40°F. Preheating-based demand shifting achieved reductions of 34.8% and 33.2% for the same temperature differences. Electric furnace tests showed demand reductions of 33.8% and 25.3% for demand limiting, and 56.1% and 45.7% for preheating-based demand shifting. These findings highlight the potential for innovative control methods to enhance grid efficiency and reduce energy consumption.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

G-Mapper: Learning a Cover in the Mapper Construction

The Mapper algorithm is a visualization technique in topological data analysis (TDA) that outputs a graph reflecting the structure of a given dataset. However, the Mapper algorithm requires tuning several parameters in order to generate a “nice” Mapper graph. This paper focuses on selecting the cover parameter. We present an algorithm that optimizes the cover of a Mapper graph by splitting a cover repeatedly according to a statistical test for normality. Our algorithm is based on G-means clustering, which searches for the optimal number of clusters in 𝑘-means by iteratively applying the Anderson–Darling test. Our splitting procedure employs a Gaussian mixture model to carefully choose the cover according to the distribution of the given data. In conclusion, experiments for synthetic and real-world datasets demonstrate that our algorithm generates covers so that the Mapper graphs retain the essence of the datasets, while also running significantly faster than a previous iterative method.

G-means clustering↗

Exercise alters molecular profiles of inflammation and substrate metabolism in human white adipose tissue

White adipose tissue (WAT) plays a significant role in whole body energy homeostasis, and its excess typifies obesity. In addition to WAT quantity, perturbations in the basic cellular processes of WAT (i.e., quality) are also associated with obesity and metabolic disease. Exercise training alleviates metabolic perturbations associated with obesity; however, the underlying molecular mechanisms that drive these metabolic adaptations in WAT are not well described. For this work, abdominal subcutaneous WAT biopsies were collected after an acute bout of exercise (1 day after) at baseline and following 3 wk of supervised aerobic training in sedentary overweight women (n = 6) without alterations in body weight and fat mass. RNA-seq, global proteomics, and phosphoproteomics in WAT revealed training-induced changes in 1,527 transcripts, 154 proteins, and 144 phosphosites, respectively. Training decreased abundance of transcripts and proteins involved in inflammation and components of the extracellular matrix and increased abundance of transcripts and proteins related to fatty acid esterification and lipolysis. In summary, short-term aerobic training significantly reduces local inflammation and increases lipid metabolism in WAT of sedentary overweight women—independent of alterations in body and fat mass. As such, some of the health benefits of aerobic training may occur through molecular alterations in WAT (i.e., enhanced quality) rather than a sheer reduction in WAT quantity.

60 APPLIED LIFE SCIENCES↗

R-Stream

R-Stream version 3.21.3, including its TensorFlow front-end (TFRCC) and LLVM 9 front-end. This version includes the features developed in the Portacy Phase II contract. R-Stream is a source-to-source automatic parallelization engine. For usage, please refer to the manuals (In particular, user guide and release notes) available in the package.

Meister, Benoit [Reservoir Labs, Inc., Portland, O↗

A Roadmap for the Future of Systems Biology in Cancer Research

Cancer systems biology seeks to understand how cancer arises as a system of interconnected molecules, cells, and tissues, with the goal of understanding, predicting, and controlling the disease. In the last decade, the field has rapidly grown as advances in experimental, computational, and analytic technologies have improved our ability to capture and recapitulate the complexities of cancer at multiple scales. However, the field’s promise to understand how specific molecular changes give rise to altered cancer outcomes remains incompletely fulfilled. Fortunately, an opportunity exists to accelerate progress by better coordinating modeling and data-gathering efforts across the cancer systems biology community. This will create the foundation for building accurate, multiscale cancer models that can better predict and identify improved therapeutic interventions. Here, in this study, we outline some of the current challenges in cancer systems biology research, how they can be addressed, and actions that the community can take to accelerate progress in the field.

Modeling & Simulation↗

Turbulence and Cloudiness in Cumulus-Topped Marine Boundary Layers

Turbulence and cloudiness in cumulus-topped marine boundary layers are studied using data from the Atmospheric Radiation Measurement (ARM) Eastern North Atlantic (ENA) site. The analysis includes eight periods of nonprecipitating shallow cumulus clouds, spanning 141 h and encompassing 603 individual clouds. On average, the cumulus had bases at 558 m, were 99 m thick, had a chord length of 500 m, and exhibited an hourly base-layer cloudiness of 12%. Changes in cloud fraction were primarily driven by variations in cloud number not chord length. High-resolution Doppler lidar and cloud radar observations were used to estimate updraft and downdraft mass fluxes in the cumulus base layer under both clear and cloudy regions. Cloudy updrafts contributed only ∼23% of the total updraft mass flux at cloud base, indicating that most upward mass flux originated from clear-air eddies. Updraft strength, rather than updraft fraction, was found to predominantly control both clear and cloudy updraft mass fluxes. Cloud-base cloudiness strongly correlated with cloudy updraft mass flux but showed negligible correlation with clear-air updraft mass flux. Clear-air downdraft mass flux exhibited a strong relationship with the ratio of surface buoyancy to inversion strength. Mesoscale analysis revealed that moist patches had greater cloudiness, updraft mass flux, and vertical velocity variance compared to dry patches. Additionally, mesoscale base-layer cloud fraction was highly and significantly correlated with cloudy updraft mass flux in both dry and moist environments. Results presented herein have implications for cumulus parameterization development along with climatological and model evaluation studies conducted at the ENA site.

cumulus clouds↗

Scalable multilevel Monte Carlo methods exploiting parallel redistribution on coarse levels

Here, we study an element agglomeration coarsening strategy that requires data redistribution at coarse levels when the number of coarse elements becomes smaller than the number of MPI processes used on the finest level. The overall procedure generates coarse elements (general unstructured unions of fine grid elements) within the framework of element-based algebraic multigrid methods (or AMGe) studied previously. The AMGe-generated coarse spaces have the ability to exhibit approximation properties of the same order as the fine-level spaces since by construction they contain the piecewise polynomials of the same order as on the fine level. These approximation properties are key for the successful use of AMGe in multilevel solvers for nonlinear partial differential equations as well as for multilevel Monte Carlo (MLMC) simulations. The ability to coarsen without being constrained by the number of MPI processes, as described in the present paper, allows to improve the scalability of these solvers as well as the overall MLMC method. The paper illustrates this latter fact with detailed scalability study of MLMC simulations applied to model Darcy equations with a stochastic log-normal permeability field.

AMGe↗

Improved Calculation of the Young’s Modulus of Rectangular Prisms from Their Resonant Frequency Overtones by Identifying Appropriate Shear Constants

Young’s modulus is an important parameter for characterizing the strength of, and wave propagation through, a given material. This study improves the estimation of Young’s modulus using the impulse excitation technique based on an experimental analysis of 19 borosilicate glass bars. Analysis of the frequency equations relating Young’s modulus to the out-of-plane and in-plane flexural resonant frequencies of rectangular prisms has been conducted for both the fundamental frequency and its overtones at higher orders of vibration. Furthermore, the Young’s moduli of three novaculite rocks with various porosities were then measured up to the seventh order of vibration to validate the optimum shear constant equation for estimating Young’s modulus. Young’s modulus was found to be nearly frequency independent for these rock samples.

Impulse excitation↗

The Implications of Advanced Manufacturing in a Connected Economy Moving Towards a Smart, Sustainable, and Productive Economy

This report intends to provide a comprehensive overview of information and communications technologies (ICT), which play increasingly vital roles in the United States (U.S.) and global economies and continue to evolve rapidly as both technological capabilities and needs grow in tandem. To underscore the importance of the sector, the U.S. Congress recently passed a $\$$20–$\$$50 billion federal program Creating Helpful Incentives to Produce Semiconductors Act (CHIPS Act) to spur the competitiveness of the U.S. semiconductor industry and encourage U.S. investment, often complemented by state-level incentives (Kessler 2022).

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Electrical Validation Testing for ORPC MHK Generator, Modification 6: ORPC SBV for MHK Generator System (CRADA Final Report)

For the U.S. Department of Energy’s (DOE) 2016 Small Business Voucher for Marine and Hydrokinetic (MHK) System, Second Round 2016, ORPC intends to work with the National Renewable Energy Laboratory (NREL) to perform dynamometer testing of the MHK generator systems and its associated controls and inverters. ORPC will provide the generator, variable frequency drives (VFD), controls, and inverter for this testing. NREL will utilize the NREL Energy Systems Integration Facility (ESIF) and dynamometer facilities at the National Wind Technology Center (NWTC) for this work. Modification 6: Additionally, NREL will conduct a feasibility study for implementing passive DC rectification at the turbine.

17 WIND ENERGY↗

Standard Library Plant Controller Model Specification for a Grid-Forming Hybrid Control Inverter-Based Resource (REPCGFM_C1)

This document describes a standard library plant controller model to interface with the grid-forming hybrid control inverter-based resource (IBR) model. The initial version of model specification was jointly developed by Pacific Northwest National Laboratory (PNNL), Tesla Energy, and EPRI, and it was revised multiple times later to incorporate suggestions from WECC MVS members. Tesla Energy provided main control algorithms to support the development of this model specification. This standard library model is developed to help the utility industry better understand the GFM technology. The model could be used to represent equipment for long-term planning studies where vendor-specific models are not available. As equipment matures and improves, standard library models will be updated to capture the new functionalities of GFMs. It is not intended that these models will always remain representative of all future GFM technologies.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Standard Library Grid-Forming Hybrid Control Inverter-Based Resource Model Specification (REGFM_C1)

This document describes a standard library grid-forming (GFM) hybrid control inverter-based resource (IBR) model. The GFM hybrid control approach implements both a typical GFM control and a typical grid-following (GFL) control inside one single inverter simultaneously, so that it can take advantage of both methods without comprising the benefits of a typical GFM. The initial version of model specification was jointly developed by Pacific Northwest National Laboratory (PNNL), Tesla Energy, and EPRI, and it was revised multiple times later to incorporate suggestions from WECC MVS members. Tesla Energy provided main control blocks to support the development of this model specification. This standard library model is developed to help the utility industry better understand the GFM technology. The model could be used to represent equipment for long-term planning studies where vendor-specific models are not available. As equipment matures and improves, standard library models will be updated to capture the new functionalities of GFMs. It is not intended that these models will always remain representative of all future GFM technologies.

24 POWER TRANSMISSION AND DISTRIBUTION↗