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At least 667 records · Page 37

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

We report the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

59 BASIC BIOLOGICAL SCIENCES↗

In situ liquid SIMS analysis of uranium oxide

Trace analysis of nuclear materials in solid particles collected in the environment or particles in liquid slurry generated in nuclear material manufacturing processes can pinpoint elemental, organic, and isotopic signatures of nuclear fuel cycle activities and processes. Such information can support nuclear safeguards programs by increasing our ability to detect undeclared nuclear materials, routine activities for safeguarding at declared facilities, and illicit activities. However, trace radioactive material analysis in liquids and slurries is challenging using bulk approaches. For example, one drawback of sensitive analysis such as inductively coupled plasma mass spectrometry (ICP-MS) is that sample is consumed or destroyed as a result of the technical approach. We developed a vacuum compatible microfluidic interface to enable surface analysis of liquids and liquid-solid interactions using time-of-flight secondary ion mass spectrometry (ToF-SIMS). In this work, we illustrate initial results of liquid standards containing uranium using in situ liquid SIMS. Specifically a series of diluted uranium standards used for ICPMS analysis were studied and the limit of detection was estimated. Since the liquid SIMS analysis is almost nondestructive, the same sample can be analyzed by other more destructive approaches afterwards or saved for future references. Consequently, multimodal analysis is possible. Our results demonstrate that in situ liquid SIMS can be used as a new approach to analyze radioactive materials in liquid and slurry forms of relevance to the IAEA safeguards missions.

In situ liquid ToF-SIMS, uranium, limit of detecti↗

Staying cool: The development of India's pioneering energy efficiency policy for chillers

Abstract Chillers are the key energy‐consuming piece of equipment in most large space cooling systems. They can account for more than 40% of total energy consumption in any typical commercial building and in specific industrial building installations depending on the product and process. With climate change driving rapidly rising demand for commercial and industrial cooling, especially in emerging economies, energy efficiency policies for chillers are crucial to moderate future electricity demand and thereby minimize greenhouse gas emissions. However, most developing and emerging economies lack energy efficiency policies for this significant and growing cooling equipment sector. India recently announced new energy efficiency policies for chillers, projected to avoid 28 TWh of electricity consumption and 23 million tons of CO 2 emissions cumulatively through 2030. This article presents a case study of the unique challenges and solutions required to design a new energy efficiency policy for chillers in India. First, the energy consumed in chiller systems is sensitive to building occupancy, load changes, seasonal variations, operation and maintenance, and climatic conditions. In order to address these sensitivities, the chiller testing standard in India factors local weather and temperature conditions into energy performance ratings to account for these sensitivities. Further, every large chiller is a customized product, therefore developing a viable policy and implementation process required collaboration with international and national experts in standardization, manufacturers, building consultants, and testing laboratories. This article is categorized under: Energy Efficiency > Economics and Policy Solar Energy: Thermal ‐‐> Climate and Environment

Mukherjee, P. K.↗

Using Low-Cost “Garage Band” Recording Technology for Acquiring High Resolution High-Speed Data

The Oak Ridge National Laboratory (ORNL) has developed and tested a novel system architecture for acquiring high fidelity high-speed data. The approach uses a consumer grade audio recording device that is normally associated with “garage band” recording of music. ORNL has coupled this low-cost data acquisition hardware with computing technology running open-source software. The main advantage of this approach is per-channel cost; an instrument grade data acquisition system typically costs between $800 to $2000 per channel compared to less than $50 per channel for these consumer grade components. Three systems, each featuring four channels, have been deployed for acquiring data from geophones and the electrical supply system that supports the High Flux Isotope Reactor (HFIR) and the Radiochemical Engineering Development Center (REDC) at ORNL. Each channel samples at 96 kHz at 24-bit resolution. The deployed systems operate continuously 24/7 and produce about 4 terabytes of data per month per system. This paper provides a technical overview of this approach, its implementation, and some preliminary results from qualification testing. This work was conducted in support of the Multi-Informatics for Nuclear Operations Scenarios (MINOS).Keywords: Data acquisition Measurement Informatics

Wetherington Jr, G↗

Analyzing the Energy and Power Consumption of Remote Memory Accesses in the OpenSHMEM Model

PGAS models like OpenSHMEM provide interfaces to explicitly initiate one-sided remote memory accesses among processes. In addition, the model also provides synchronizing barriers to ensure a consistent view of the distributed memory at different phases of an application. The incorrect use of such interfaces affects the scalability achievable while using a parallel programming model. This study aims at understanding the effects of these constructs on the energy and power consumption behavior of OpenSHMEM applications. Our experiments show that cost incurred in terms of the total energy and power consumed depends on multiple factors across the software and hardware stack. We conclude that there is a significant impact on the power consumed by the CPU and DRAM due to multiple factors including the design of the data transfer patterns within an application, the design of the communication protocols within a middleware, the architectural constraints laid by the interconnect solutions, and also the levels of memory hierarchy within a compute node. This work motivates treating energy and power consumption as important factors while designing compute solutions for current and future distributed systems.

Jana, Siddhartha↗

Ecosystem-Level Biomimicry for the Built Environment: Adopting Systems Ecology Principles for the Control of Heterogeneous Energy Systems

This paper presents, to our knowledge, the first system-level engineering study to bio-mimic the cybernetics and flow dynamics of energy resources in natural ecosystems for the control of heterogeneous energy infrastructures in the built environment. To this end, we introduce a novel Biomimetic Pulsing State (BPS) control that functionally mimics mature ecosystems. A preliminary Modelica-based case study features a single-family residential building with electrical and HVAC subsystems. The BPS control objective is to minimize the energy exchange between the building and the grid for the purposes of future self-supporting buildings and grid stability. The building contains PV, a wind turbine, a battery storage system, and a fan coil/heat pump HVAC system served by an ambient district energy network. Evaluating the control performance (BPS vs. constant setpoint) over several renewable energy scenarios (net importer, net zero, net exporter), simulation results show how the building's HVAC system can dynamically adjust its electrical load and temperatures to the electrical system's net energy status in real-time with BPS control. As a net importer, the heat pump consumed 29% less energy and its peak power reduced by 15% with BPS control compared to the constant setpoint case, with the zone air temperature 1 degree C lower on average. As a net exporter, the heat pump effectively consumed the same energy, but the peak power increased by 34% with BPS control, while the zone air temperature was 1 degree C higher when renewable energy was abundant, preheating the home. BPS and constant setpoint control produced comparable results under a net zero scenario. While further evaluation is essential, BPS control may help communities meet their sustainability and resiliency targets as they transition towards fully distributed and renewable energy grids.

biomimicry↗

Bioaccumulation of Cr, Ni, Cd and Pb in the Economically Important Freshwater Fish Schizothorax plagiostomus from Three Rivers of Malakand Division, Pakistan: Risk Assessment for Human Health

Contamination of freshwater ecosystems such as rivers with hazardous heavy metals is an environmental problem of public health concern. Accumulation of potentially toxic heavy metals in freshwater fish causes a potential health threat to their consumers including humans. The present research aimed to (1) investigate the accumulation of four potentially toxic heavy metals viz. Cr, Ni, Cd and Pb in muscle tissue of the commercially important freshwater fish Schizothorax plagiostomus at different sites of River Swat, River Panjkora and River Barandu in northern Pakistan (2) to compare gross metal accumulation in the fish samples by calculating metal pollution index (MPI) and (3) to assess potential risk to the health of the fish consumers. Samples were analyzed for the heavy metals by flame atomic absorption spectrophotometry (FAAS). Risk analysis showed that Ni risk was higher at River Panjkora and River Barandu, Pb risk was higher at River Swat and River Panjkora while Cd risk was quite low at all the three rivers.

54 ENVIRONMENTAL SCIENCES↗

Exposure assessment of process-related contaminants in food by biomarker monitoring

Exposure assessment is a fundamental part of the risk assessment paradigm, but can often present a number of challenges and uncertainties. This is especially the case for process contaminants formed during the processing, e.g. heating of food, since they are in part highly reactive and/or volatile, thus making exposure assessment by analysing contents in food unreliable. New approaches are therefore required to accurately assess consumer exposure and thus better inform the risk assessment. Such novel approaches may include the use of biomarkers, physiologically based kinetic (PBK) modelling-facilitated reverse dosimetry, and/or duplicate diet studies. This review focuses on the state of the art with respect to the use of biomarkers of exposure for the process contaminants acrylamide, 3-MCPD esters, glycidyl esters, furan and acrolein. From the overview presented, it becomes clear that the field of assessing human exposure to process-related contaminants in food by biomarker monitoring is promising and strongly developing. The current state of the art as well as the existing data gaps and challenges for the future were defined. They include (1) using PBK modelling and duplicate diet studies to establish, preferably in humans, correlations between external exposure and biomarkers; (2) elucidation of the possible endogenous formation of the process-related contaminants and the resulting biomarker levels; (3) the influence of inter-individual variations and how to include that in the biomarker-based exposure predictions; (4) the correction for confounding factors; (5) the value of the different biomarkers in relation to exposure scenario’s and risk assessment, and (6) the possibilities of novel methodologies. Here, in spite of these challenges it can be concluded that biomarker-based exposure assessment provides a unique opportunity to more accurately assess consumer exposure to process-related contaminants in food and thus to better inform risk assessment.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Automatic Organ Segmentation for CT Scans Based on Super-Pixel and Convolutional Neural Networks

Accurate segmentation of specific organ from computed tomography (CT) scans is a basic and crucial task for accurate diagnosis and treatment. To avoid time-consuming manual optimization and to help physicians distinguish diseases, an automatic organ segmentation framework is presented. The framework utilized convolution neural networks (CNN) to classify pixels. To reduce the redundant inputs, the simple linear iterative clustering (SLIC) of super-pixels and the support vector machine (SVM) classifier are introduced. To establish the perfect boundary of organs in one-pixel-level, the pixels need to be classified step-by-step. First, the SLIC is used to cut an image into grids and extract respective digital signatures. Next, the signature is classified by the SVM, and the rough edges are acquired. Finally, a precise boundary is obtained by the CNN, which is based on patches around each pixel-point. The framework is applied to abdominal CT scans of livers and high-resolution computed tomography (HRCT) scans of lungs. The experimental CT scans are derived from two public datasets (Sliver 07 and a Chinese local dataset). Experimental results show that the proposed method can precisely and efficiently detect the organs. This method consumes 38 s/slice for liver segmentation. The Dice coefficient of the liver segmentation results reaches to 97.43%. For lung segmentation, the Dice coefficient is 97.93%. This finding demonstrates that the proposed framework is a favorable method for lung segmentation of HRCT scans.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

RBMK Uranium-Erbium Fuel

The history of the development and adoption of erbium fuel in RBMK is described. Research performed at the end of the 1980s – beginning of 1990s led to the conclusion that the optimal method of decreasing the steam coefficient of reactivity in RBMK is to add a consumable absorber – erbium. Computational and experimental work on the safety validation of the new fuel made it possible to adopt this fuel first in RBMK-1500 and then in RBMK-1000. The use of uranium-erbium fuel in RBMK made it possible to increase reactor safety, provide the requisite conditions for modernizing control rods, reduce the acuteness of the problem of storing spent fuel, and improve the economic indices of the fuel cycle. Considering the heightened interest in the use of erbium as a consumable absorber in VVER and some other reactors, the experience gained in developing and operating uranium-erbium fuel for RBMK could be helpful.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Challenges in simulating economic effects of climate change on global agricultural markets

Abstract Many approaches have been used to investigate climate change impacts on agriculture. However, several caveats remain in this field: (i) analyses focus only on a few major crops, (ii) large differences in yield impacts are observed between projections from site-based crops models and Global Gridded Crop Models (GGCMs), (iii) climate change impacts on livestock are rarely quantified, and (iv) several causal relations among biophysical, environmental, and socioeconomic aspects are usually not taken into account. We investigate how assumptions about these four aspects affect agricultural markets, food supply, consumer well-being, and land use at global level by deploying a large-scale socioeconomic model of the global economy with detailed representation of the agricultural sector. We find global welfare impacts several times larger when climate impacts all crops and all livestock compared to a scenario with impacts limited to major crops. At the regional level, food budget can decrease by 10 to 25% in developing countries, challenging food security. The role of land area expansion as a major source of adaptation is highlighted. Climate impacts on crop yields from site-based process crop models generate more challenging socioeconomic outcomes than those from GGCMs. We conclude that the agricultural research community should expand efforts to estimate climate impacts on many more crops and livestock. Also, careful comparison of the GGCMs and traditional site-based process crop models is needed to understand their major implications for agricultural and food markets.

Gurgel, Angelo C. (ORCID:0000000183319508)↗

Comparison of microprecipitation methods for polonium source preparation for alpha spectrometry

Detection of radioactive isotopes of polonium is important for understanding natural processes, management and assessment of radioactive waste, and nuclear forensics applications. Further, the most common methods for preparation of polonium samples for alpha spectrometry are electrodeposition and spontaneous deposition which are time consuming. Here, we compare three approaches utilizing rapid microprecipitation from bismuth phosphate, copper sulfide, or tellurium alongside traditional spontaneous deposition methods. From these experiments, results show that copper sulfide microprecipitation recoveries are similar to spontaneous deposition on silver and less time consuming with an approximate five-fold decrease in preparation time, including in the presence of complex matrices like seawater.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Plug-in electric vehicle market penetration and incentives: a global review

Plug-in electric vehicles (PEVs) have been commercially available in the global market for about 3 years. Many countries have policies designed to stimulate consumer acceptance and accelerate market adoption. In the United States (U.S.), the biggest PEV market, sales have more than tripled since 2011. During the same period, PEV sales have increased, albeit slowly, in most western European countries. Notably, some European countries, such as Norway, showed strong increases mainly owing to generous incentives to PEV consumers. Japan is the second-largest PEV market in terms of number of vehicles sold. The Nissan battery electric vehicle (BEV) Leaf is the top-selling PEV model, with more than 100,000 units sold globally since its launch in 2010. In contrast, after 3 years of policy stimulation, PEV market share in China is still lower than 0.1 % of total car sales, and most of these vehicles were purchased by either central or local governments. However, PEV bus production in China has increased dramatically over last 3 years. These market trends, together with strong government policies, show that national and regional PEV-related incentives in selected countries can play an important role in jump-starting the PEV market.

Global vehicle sales↗

Power System Transient Stability Analysis through a Homotopy Analysis Method

As an important function of energy management systems (EMSs), online contingency analysis plays an important role in providing power system security warnings of instability. At present, N-1 contingency analysis still relies on time-consuming numerical integration. To save computational cost, the paper proposes a quasi-analytical method to evaluate transient stability through time domain periodic solutions’ frequency sensitivities against initial values. First, dynamic systems described in classical models are modified into damping free systems whose solutions are either periodic or expanded (non-convergent). Second, because the sensitivities experience sharp changes when periodic solutions vanish and turn into expanded solutions, transient stability is assessed using the sensitivity. Third, homotopy analysis is introduced to extract frequency information and evaluate the sensitivities only from initial values so that time consuming numerical integration is avoided. Finally, a simple case is presented to demonstrate application of the proposed method, and simulation results show that the proposed method is promising.

Wang, Shaobu↗

Behavioral modeling of on-demand mobility services: general framework and application to sustainable travel incentives

This paper presents a systematic way of understanding and modeling traveler behavior in response to on-demand mobility services. We explicitly consider the sequential and yet inter-connected decision-making stages specific to on-demand service usage. The framework includes a hybrid choice model for service subscription, and three logit mixture models with inter-consumer heterogeneity for the service access, menu product choice and opt-out choice. Different models are connected by feeding logsums. The proposed modeling framework is essential for accounting the impacts of real-time on-demand system's dynamics on traveler behaviors and capturing consumer heterogeneity, thus being greatly relevant for integrations in multi-modal dynamic simulators. The methodology is applied to a case study of an innovative personalized on-demand real-time system which incentivizes travelers to select more sustainable travel options. The data for model estimation is collected through a smartphone-based context-aware stated preference survey. Through model estimation, lower values of time are observed when the respondents opt to use the reward system. The perception of incentives and schedule delay by different population segments are quantified. These results are fundamental in setting the ground for different behavioral scenarios of such a new on-demand system. Here, the proposed methodology is flexible to be applied to model other on-demand mobility services such as ride-hailing services and the emerging mobility as a service.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Evaluating the contribution of plant metabolic pathways in the light to the ATP:NADPH demand using a meta-analysis of isotopically non-stationary metabolic flux analyses

Abstract Balancing the ATP: NADPH demand from plant metabolism with supply from photosynthesis is essential for preventing photodamage and operating efficiently, so understanding its drivers is important for integrating metabolism with the light reactions of photosynthesis and for bioengineering efforts that may radically change this demand. It is often assumed that the C3 cycle and photorespiration consume the largest amount of ATP and reductant in illuminated leaves and as a result mostly determine the ATP: NADPH demand. However, the quantitative extent to which other energy consuming metabolic processes contribute in large ways to overall ATP: NADPH demand remains unknown. Here, we used the metabolic flux networks of numerous recently published isotopically non-stationary metabolic flux analyses (INST-MFA) to evaluate flux through the C3 cycle, photorespiration, the oxidative pentose phosphate pathway, the tricarboxylic acid cycle, and starch/sucrose synthesis and characterize broad trends in the demand of energy across different pathways and compartments as well as in the overall ATP:NADPH demand. These data sets include a variety of species including Arabidopsis thaliana , Nicotiana tabacum , and Camelina sativa as well as varying environmental factors including high/low light, day length, and photorespiratory levels. Examining these datasets in aggregate reveals that ultimately the bulk of the energy flux occurred in the C3 cycle and photorespiration, however, the energy demand from these pathways did not determine the ATP: NADPH demand alone. Instead, a notable contribution was revealed from starch and sucrose synthesis which might counterbalance photorespiratory demand and result in fewer adjustments in mechanisms which balance the ATP deficit.

59 BASIC BIOLOGICAL SCIENCES↗

A Multilayer Model for Alumina Inclusion Transformation by Calcium in the Ladle Furnace

Calcium wire injection is widely used for modification of solid alumina inclusions to liquid or partially liquid calcium aluminate. In the present work, a multilayer growth model is proposed for modification of alumina inclusions. Diffusion through a multiphase product layer and mass transfer of solute through the boundary layer to the inclusion are taken into account in this model. It is assumed that the outer surface of the inclusion is thermodynamically in equilibrium with the local steel composition. The results show that the mass transfer of calcium through the boundary layer and within the inclusion is complete in a matter of seconds; furthermore, once the liquid calcium aluminate forms, it quickly consumes the other solid calcium aluminate phases. Because the calcium is so rapidly consumed by the inclusions, the rate of transformation in a calcium treatment process is controlled by the rate that calcium is supplied to the steel by the calcium bubbles.

36 MATERIALS SCIENCE↗

Detoxification and Fermentation of Pyrolytic Sugar for Ethanol Production

The sugars present in bio-oil produced by fast pyrolysis can potentially be fermented by microbial organisms to produce cellulosic ethanol. This study shows the potential for microbial digestion of the aqueous fraction of bio-oil in an enrichment medium to consume glucose and produce ethanol. In addition to glucose, inhibitors such as furans and phenols are present in the bio-oil. A pure glucose enrichment medium of 20 g/l was used as a standard to compare with glucose and aqueous fraction mixtures for digestion. Thirty percent by volume of aqueous fraction in media was the maximum additive amount that could be consumed and converted to ethanol. Inhibitors were removed by extraction, activated carbon, air stripping, and microbial methods. After economic analysis, the cost of ethanol using an inexpensive fermentation medium in a large scale plant is approximately $14 per gallon.

09 BIOMASS FUELS↗