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At least 649 records · Page 36

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Efficient Thermal Processes Using Alternating Electromagnetic Field for Methodical and Selective Release of Hydrogen Isotopes

The controlled and selective release of hydrogen isotopes from Lanthanum-Nickel-Aluminum (LANA) materials was achieved using an alternating electromagnetic field (AEMF). Here, in the presence of the AEMF, the rate of desorption for D 2 was faster than for H 2 . In a closed system, compared to control experiments with helium, hydrogen-loaded LANA samples showed a significant increase in pressure which illustrates the desorption of hydrogen from the applied AEMF. An exponential increase in the hydrogen release rate was observed with increased AEMF strength. Additionally, hydrogen release from LANA confined in a subzero environment (-78°C) using an AEMF was demonstrated. These results demonstrate that the LANA material can be heated directly using alternating electromagnetic fields rather than indirectly to rapidly and selectively desorb hydrogen isotopes. The rapid response and difference in desorption kinetics for different hydrogen isotopes in the presence of the alternating electromagnetic fields provide a promising pathway for applications requiring controlled release of hydrogen and separation of its isotopes.

07 ISOTOPE AND RADIATION SOURCES↗

Advected carbon younger than the sediment fuels microbial metabolism in a pumped deep aquifer

Ever deeper wells are drilled worldwide to pump potable groundwater. Recent studies argue that overpumping compresses clays and releases reactive dissolved organic carbon (DOC), which in turn drives a series of microbial reactions that affect groundwater potability including arsenic concentrations. Here, we use a novel method to measure the radiocarbon ages of microbial RNA to determine the source of reactive or metabolizable DOC and argue against the compression of clays as the sole source of carbon. We show that microbial RNA (5,230; 5,550; 6,250 yr; n = 3 wells), DOC (280-10,800 yr; n = 13), and methane (modern to 6,240 yr; n = 3), from an overpumped deep aquifer in Bangladesh are much younger than the overlying clay layers deposited during the Pleistocene over 12,000 years ago. Mass-balance indicates that at least half of the carbon incorporated into RNA has to come from reactive DOC or methane that is advected downward via vertical recharge. This metabolism of advected organic carbon could have implications for the quality of water pumped from deep aquifers.

Biological and medical sciences↗

Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome

In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.

60 APPLIED LIFE SCIENCES↗

ADETS User Manual

ADETS (Automated DEpletion Transport System) calculates coupled neutronic/isotopic results for nuclear systems and produces a large number of criticality and burnup results based on various material feed/removal specifications, power(s), and time intervals. ADETS is a fully automated tool that links the LANL MCNP Monte Carlo transport code with the SCALE system, specifically ORIGEN-ARP (radioactive decay and burnup code). Additionally, ADETS can compute the dose at various distances of the reactor using a point gamma source, whose characteristics are computed by ORIGEN-ARP. In addition, ADETS is fully coupled with the Uncertanty Quantification, Probabilistic Risk Assessment, Parameter Optimization and Data Analysis code RAVEN (developed at the Idaho National Laboratory as well). RAVEN is released with ADETS but MCNP and SCALE (ORIGEN-ARP) are not included.

42 ENGINEERING↗

Second Target Station Project: STS Cross-Directorate Workshop on Hydrogen Fuel

Hydrogen, particularly green hydrogen produced through electrolysis using renewable energy, is poised to play a critical role in decarbonizing the global economy. Its ability to address the intermittency of renewable energy sources and decarbonize hard-to-electrify sectors positions it as a vital component of a sustainable energy future. Interest in hydrogen as a clean energy carrier is in a decade of unprecedented growth, with dozens of countries having released national hydrogen strategies contributing to a global hydrogen economy. In 2021, the Department of Energy (DOE) announced the Hydrogen Shot, the first of the Energy Earthshot Initiatives, which aims to lower the cost of clean hydrogen to $\$$1/kg by 2031. This initiative was followed by a considerable increase in funding for hydrogen technologies through the Bipartisan Infrastructure Law (BIL), with $\$$18 billion recently announced for regional demonstration projects (Hydrogen Hubs) and another $\$$11.5 billion aimed at research and development of electrolyzers, fuel cells, manufacturing, and recycling. The 2023 U.S. National Clean Hydrogen Strategy and Roadmap identifies the cost of clean hydrogen as a critical challenge for achieving economic scale. This includes the cost of hydrogen production by electrolysis, delivery and dispensing, onboard storage, and end-use technologies like fuel cells. Fundamental research and development into catalysts, component architectures, and material durability are critical to lower the costs of these vital technologies aimed at achieving a net-zero carbon emission economy by 2050.

08 HYDROGEN↗

End-Use Savings Shapes Measure Documentation: Heat Pump Rooftop Units with Original Fuel Backup

This documentation focuses on a single end-use savings shape measure—heat pump rooftop units with supplemental heat that matches the original fuel type of the replaced system; if the existing system used electric resistance heating, the supplemental heating source is electric resistance. If it was a natural gas furnace, the supplemental system is modeled as natural gas. This is a modification to the heat pump rooftop unit with electric supplemental heat measure from the Commercial EUSS 2023 Release 1 dataset. This document will primarily discuss the supplemental heating change for the heat pump RTU measure. For a comprehensive overview of the fundamental modeling methodology and background of the heat pump RTU measure, including performance curves and other key assumptions, please review the documentation for the original heat pump rooftop unit with electric supplemental heat.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

TRUST-EABM End-of-Year Report: Release FY20

The Delivery Environments (DE) program work package Testbeds to Reduce Uncertainties in Simulations and Tests (TRUST) is designed to quantify and reduce the uncertainty associated with experimental testing and numerical simulation of large engineering assemblies to support the efficient and responsive development of future systems. Because engineering assemblies contain a large number of uncertainty sources, well-characterized testbeds must be designed to isolate individual uncertainty sources. Once quantified, uncertainty sources can be compared to direct research and development funding towards the largest sources driving behavior of interest. Quantified uncertainty may also be propagated through engineering simulations to determine quantitative confidence in simulation predictions and for comparison against uncertainty in the experimental measurements.

97 MATHEMATICS AND COMPUTING↗

Fuel Injection Dynamics and Composition Effects on RDE Performance

Rotating detonation engines (RDEs) provide a promising route to substantially increasing cycle efficiency in stationary gas turbines. Much of this increase relies on the ability to achieve consistent pressure gain within the combustor. In particular, the design of injectors that feed fuel and air into the detonation channel plays a crucial role. Such injectors have to ensure proper mixing of fuel and oxidizer, while minimizing backflow of detonation products into the feed plenums, and reduce susceptibility to the complex wave structures that exist within the combustor. From a practical perspective, such RDEs also need to operate with variable fuel composition. When fuel mixtures with components that possess vastly different oxidation pathways and time-scales are used, there could be additional losses through deflagrative burning instead of detonation-driven heat release. Such sensitivity to the complete flow path is akin to the physics of thermoacoustic instabilities in conventional gas turbines. In this sense, RDEs pose a unique research challenge: the performance of the device relies on the small-scale heat release process, which is highly dependent on the flow interactions within the full-scale system. As a result, canonical flow configurations, instrumented with detailed diagnostics or modeled using high-fidelity tools, but only focus on the small-scale processes will not contain the key system-level interactions. At the same time, macroscopic measurements and models that only capture system-level performance will not provide insight into the key sources of pressure losses. These couplings and sensitivities provide a formidable challenge to both experimental and simulation studies of the effects Thus, a joint experimental/computational program designed specifically to address these challenges was undertaken in this program. The focus of this program was on two key topics: a) the interaction between injector flow and the overall wave dynamics within the combustor, and b) the deflagration/detonation structure in multi-component fuels that are of practical interest. Both topics involve interaction of small-scale heat release processes with the geometry-dependent wave structure. Studies focused on the study of full-scale RDE systems, based on a 6-inch conventional annular geometry. Experimentally RDEs were studied using a combination of diagnostics. A combination of optical diagnostics and aero-thermo-acoustic analysis based on a combination of spectral and mode decomposition analysis was used to identify the dynamics of the detonation wave and other secondary waves that exist in the system. These studies have helped the identification and investigation of injector and detonation dynamics arising from coupling, and how they affect RDE mixing, detonation structure, operability and performance. Performance of RDEs was investigated through thrust stand measurements, which was used to evaluate the effective pressure gain generated by the system through the concept of equivalent available pressure. Optical diagnostics were developed and implemented to investigate the distribution of heat release, across the detonation wave. Novel optical diagnostics of NIR imaging was also developed and applied to investigate the high temperature / high pressure distribution across the detonation wave. In order to complement the experiments, the computational tools were geared to simulate the full experimental setup. GPU-based acceleration of the models and computations were developed to enable rapid simulation of the full system. In addition, the use of adaptive mesh refinement, and unstructured grid formulation, enabled the investigation of realistic geometries studied in the laboratory. The simulations produced a wealth of detail on the structure of the detonation wave under different operating conditions. Emphasis was placed on quantifying mixture pre-burning and the impact on wave propagation and structure.

03 NATURAL GAS↗

Assessing the Impact of Renewable Energy Sources to Achieve Net Zero Emissions

The mass generation of green energy through the pathway of Renewable Energy Sources (RES), is one of the major decisive components contributing to the concept of decarbonization. The energy sector assessment reveals that out of per kWh energy produced, renewable energy emits between 9 and 1000 gCO2 equivalent on a life-cycle basis. Contemplating the literature and the latest reports released by world-wide energy department(s), this study presents a comprehensive concept of carbon footprint, its causes and effects including major impact on biodiversity and human life. The study discusses the substantial steps taken by developing countries like India in leveraging RES for the production of energy and its progressive impact on ecology. The discussion would be inclusive of major change and transformation which has brought significant drop of 16% in the greenhouse gas (GHG) emissions by installation of 104.9 GW of RES excluding Hydro. The appropriate steps taken forward therefore align with the Sustainable Development Goals (SDGs) of the United Nation (UN) in achieving net zero emission (NZE).

decarbonization↗

Preface: special issues on photosystem II

Here, the appearance of oxygenic photosynthesis 3–4 billion years ago is arguably one of the most important evolutionary developments which radically transformed both the biotic and abiotic landscapes of Earth. The presence of molecular oxygen enabled the evolution of complex lifeforms requiring large amounts of chemical energy which could only be produced by aerobic respiration. Additionally, molecular oxygen remodeled the geochemistry of the planet during its transition from a reducing to an oxidizing atmosphere during the Great Oxidation Event. Central to these processes is Photosystem II (PS II), the light energy-driven, water-plastoquinone oxidoreductase which initially evolved in cyanobacteria and subsequently was incorporated, along with Photosystem I (PS I), the cytochrome b 6 f complex and the Ndh complex, into all algae and higher plants by the process of endosymbiosis. This membrane protein complex releases molecular oxygen and protons as the byproducts of water splitting and produces plastoquinol, which provides reducing equivalents that are used sequentially by the cytochrome b 6 /f complex, PS I, and ultimately, as NADPH + H + , by the Calvin–Benson–Bassham cycle. Additionally, the protons released by PS II (and those pumped by the cytochrome b 6 /f complex and the NDH complex (during cyclic electron transfer)) form the proton motive force that drives ATP synthesis via the ATP Synthase, thus providing the chemical energy source for carbon fixation.

59 BASIC BIOLOGICAL SCIENCES↗

Reduction of CO to Methanol with Recyclable Organic Hydrides

We report the reaction steps for the selective conversion of a transition metal carbonyl complex to a hydroxymethyl complex that releases methanol upon irradiation with visible light have been successfully quantified in acetonitrile solution with dihydrobenzimidazole organic hydride reductants. Dihydrobenzimidazole reductants have been shown to be inactive toward H 2 generation in the presence of a wide range of proton sources and have been regenerated electrochemically or photochemically. Specifically, the reaction of cis-[Ru(bpy) 2 (CO) 2 ] 2+ (bpy = 2,2'-bipyridine) with one equivalent of a dihydrobenzimidazole quantitatively yields a formyl complex, cis-[Ru(bpy) 2 (CO)(CHO)] + , and the corresponding benzimidazolium on a seconds time scale. Kinetic experiments revealed a first-order dependence on the benzimidazole hydride concentration and an unusually large kinetic isotope effect, inconsistent with direct hydride transfer and more likely to occur by an electron transfer-proton-coupled electron transfer (EΤ-PCET) or related mechanism. Further reduction/protonation of cis-[Ru(bpy) 2 (CO)(CHO)] + with two equivalents of the organic hydride yields the hydroxymethyl complex cis-[Ru(bpy) 2 (CO)(CH 2 OH)] + . Visible light excitation of cis-[Ru(bpy) 2 (CO)(CH 2 OH)] + in the presence of excess organic hydride was shown to yield free methanol. Identification and quantification of methanol as the sole CO reduction product was confirmed by 1 H NMR spectroscopy and gas chromatography. The high selectivity and mild reaction conditions suggest a viable approach for methanol production from CO, and from CO 2 through cascade catalysis, with renewable organic hydrides that bear similarities to Nature's NADPH/NADP + .

14 SOLAR ENERGY↗

Analysis of near-field and far-field aerosol dispersion for microreactors

The current paper presents a simulation-based analysis of aerosol dispersion in the near-field and far-field of a generic, conceptual microreactor operating at pressures close to the ambient pressure; therefore, in the event of an accident that causes radionuclide leakage from the microreactor containment, the radionuclide particles are less likely to travel too far from the reactor, as opposed to conventional reactors. Accordingly, the presented work provides estimates of average and 95-percentile values of the relative effluent concentration. A parametric study is then performed to narrow down the parameters which affect the aerosol dispersion characteristics most significantly. Simulations were performed in the computer code ARCON96, and the parameters found to affect aerosol dispersion characteristics are the atmospheric stability class, and the distance between the release point and the receptor. It is recommended that the computer code RADTRAD be used to calculate actual dosage over distance, using the outputs from ARCON96 as inputs, along with reactor-specific core term inventories. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Round 3 Update of Stress Testing Results for Organic Light-Emitting Diode Panels and Luminaires

Organic light-emitting diode (OLED) sources are a potential solid-state lighting technology for use in indoor lighting applications. Some of the advantages offered by OLEDs include thin profiles, low glare, diffuse lighting, and unique form factors. The U.S. Department of Energy (DOE) has released six technical reports focused on OLED technologies to provide information and analysis to the lighting industry. These reports include the evaluation of two different field deployment sites, a market analysis, a tear-down analysis, and two independent assessments of the performance of select commercially available OLED products. This report builds on earlier DOE efforts with OLED technology by updating information about previously benchmarked commercial OLED products. Specifically, this report provides updated findings about the robustness and reliability of commercial OLED products.

42 ENGINEERING↗

Computational Fluid Dynamics Modeling to Simulate a Combined Reforming Process for Syngas and Hydrogen Production

An Oxygen Transport Membrane (OTM) combined reforming technology for producing syngas and hydrogen integrates the advantages of multiple processes—steam methane reforming (SMR), autothermal reforming (ATR), an air separation unit (ASU)—into a single integrated technology. The OTM consists of a primary reforming tube, in which desulfurized natural gas is partially reformed by steam at high pressure in the presence of a metal catalyst. This process is followed in series by a ceramic OTM with a secondary reformer, in which residual methane reforms and O 2 - ions react with a portion of the CO and H 2 fuel to provide the heat to support both primary and secondary reforming. Although the OTM combined reformer technology for syngas and H 2 production has been substantially developed in the last decade, several challenges that affect the overall production efficiency and reliability are yet to be fully understood, addressed, and resolved. Therefore, developing Computational Fluid Dynamics (CFD) models that incorporate fluid dynamics, mass transport, kinetics, heat transport, and structural mechanics is critical to understanding and minimizing the probability of tube failures during the startup and operation. In this report, an exhaustive literature review was performed to survey the current state of technology for producing syngas and H 2 using either conventional or renewable energy sources. The feedstocks reviewed include natural gas and coal for the conventional technologies, whereas biomass, solar, wind, and nuclear energy for the renewable technologies. The existing industry-grade COMSOL multiphysics models of OTM were upgraded for the latest software release. In addition, they were improved to help achieve grid and solver independence and were successfully ported on the ORNL high-performance computing clusters to speed up their run times. A 42% reduction in the simulation run time was achieved. A new higher-fidelity CFD model of an OTM tube was developed in the StarCCM+ simulation platform. This new model was designed to simulate various physics using first principles, e.g., turbulent flow, heat transfer, and chemical reactions while avoiding unnecessary simplifications. The resulting predictions were qualitatively assessed and provided useful insights into the multiphysics complexity of an OTM tube.

08 HYDROGEN↗

Fission Matrix Processing Using the MCNP6.3 HDF5 Restart File

This paper describes an approach to interrogating the fission matrix available in the HDF5-formatted restart file (also known as the “runtape” file), which is produced by the upcoming public release of the MCNP R code, version 6.3. The fission matrix, its eigenvalues, and its eigenvectors, are important tools for characterizing fissile systems such as research and power reactors and for accelerating the convergence of the Monte Carlo fission-source site distribution.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Precursor Analysis Report: Cyber Attack on Thyssenkrupp Blast Furnace 2014

The Cyber Attack on Thyssenkrupp Blast Furnace 2014 Precursor Analysis Report leverages publicly available information about the Thyssenkrupp Steel Mill cyber attack and catalogs anomalous observables for each technique employed in the attack. This analysis is based upon the methodology of the Cybersecurity for the Operational Technology Environment (CyOTE) program. In December 2014, the German Government’s Federal Office for Information Security (BSI) released a report detailing a cyber attack on a German steel mill that occurred earlier that year, though exact dates and details of the attack were not revealed. While the report did not specify the name of the company, multiple sources identified the victim as one of Europe’s largest steel manufacturers, Thyssenkrupp AG. Further, Thyssenkrupp announced on 16 May of that year that Europe’s largest blast furnace, “Schwelgern 2,” located at its facility in Duisburg, Germany, would be offline for several weeks for repairs and upgrades, suggesting Schwelgern 2 was likely the target of the attack. The attack began in early 2014, when adversaries infiltrated the victim steel mill’s Information Technology (IT) network via a spearphishing campaign, then worked their way into the Operational Technology (OT) environment, where they executed software that caused denial of service, denial of control, and eventually a loss of control. This led to the blast furnace shutting down without proper safety procedures, resulting in catastrophic physical damage. No lives were lost in the incident, but ThyssenKrupp suffered $4 million in damage to the blast furnace and an additional $6 million in lost revenue. The adversaries required specialized knowledge and expertise in steel production, which enabled them to compromise a variety of internal systems and components across both IT and OT networks. The attack also demonstrated detailed knowledge of the industrial control systems (ICS) and production processes being used. This combination resulted in one of the earliest known publicly reported cybersecurity incidents resulting in physical damage to ICS equipment. Researchers and analysts identified 19 unique techniques (used in a sequence of 20 steps) utilized during the attack with a total of 454 observables using MITRE ATT&CK® for Industrial Control Systems. The CyOTE program assesses observables accompanying techniques used prior to the triggering event to identify opportunities to detect malicious activity. If observables accompanying the attack techniques are perceived and investigated prior to the triggering event, earlier comprehension of malicious activity can take place. Fifteen of the identified techniques used during the Thyssenkrupp cyber attack were precursors to the triggering event. Analysis identified 369 observables associated with these precursor techniques, 316 of which were assessed to have an increased likelihood of being perceived in the 120 days preceding the triggering event. The response and comprehension time could have been reduced if the observables had been identified earlier. The information gathered in this report contributes to a library of observables tied to a repository of artifacts, data sources, and technique detection references for practitioners and developers to support the comprehension of indicators of attack. Asset owners and operators can use these products if they experience similar observables or to prepare for comparable scenarios.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Unveiling Hidden Lyman Alpha Emitters in the DESI DR1 Data

We present an automatic method based on machine-learning convolutional neural network (CNN) architecture to detect Lyman alpha emitters (LAE) hidden in the Data Release 1 spectroscopic dataset of the Dark Energy Spectroscopic Instrument (DESI). Those LAEs mostly have incorrect redshift estimations because the current DESI pipeline is not designed to detect and measure the redshifts of galaxies at $z>2$. To uncover those sources, we first visually inspect thousands of DESI spectra and construct a sample, consisting of both LAEs and non-LAEs, for training and testing the CNN-based model to (1) detect LAEs in DESI spectra and (2) determine their Ly$α$ redshifts. The final model yields $95.2\%$ purity and $95.9\%$ completeness for detecting LAEs. We apply this model to approximately $2\times10^{6}$ spectra of sources targeted as emission-line galaxies and detect 19,685 LAEs from $z\sim2$ to $3.5$ within 12 minutes with a single GPU, illustrating the high efficiency of this model for identifying LAEs. The detected LAEs are mostly at the bright end of the luminosity function with Ly$α$ luminosity $L_{\rm Lyα} \gtrsim 10^{43}$ erg/s. The high signal-to-noise composite spectrum of the detected LAEs further shows various spectral features, including P-Cygni profiles of metal lines and MgII emission lines, possible indicators of Lyman continuum escape fraction, revealing the rich astrophysical information in this LAE sample. Finally, this sample can be used to train and validate the pipelines for redshift determination of LAEs for the preparation of the DESI-II survey.

Chan, Jui-Kuan [Taiwan, Natl. Taiwan U.] (ORCID:00↗