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At least 1,135 records · Page 63

Data-driven integration of genome-scale regulatory and metabolic network models

Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. Lastly, in this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.

59 BASIC BIOLOGICAL SCIENCES↗

A global solution to the Schrödinger equation: From Henstock to Feynman

One of the key elements of Feynman’s formulation of non-relativistic quantum mechanics is a so-called Feynman path integral. It plays an important role in the theory, but it appears as a postulate based on intuition, rather than a well-defined object. All previous attempts to supply Feynman’s theory with rigorous mathematics underpinning, based on the physical requirements, have not been satisfactory. The difficulty comes from the need to define a measure on the infinite dimensional space of paths and to create an integral that would possess all of the properties requested by Feynman. In the present paper, we consider a new approach to defining the Feynman path integral, based on the theory developed by Muldowney [A Modern Theory of Random Variable: With Applications in Stochastic Calcolus, Financial Mathematics, and Feynman Integration (John Wiley & Sons, Inc., New Jersey, 2012)]. Muldowney uses the Henstock integration technique and deals with non-absolute integrability of the Fresnel integrals, in order to obtain a representation of the Feynman path integral as a functional. This approach offers a mathematically rigorous definition supporting Feynman’s intuitive derivations. But in his work, Muldowney gives only local in space-time solutions. A physical solution to the non-relativistic Schrödinger equation must be global, and it must be given in the form of a unitary one-parameter group in L{sup 2}(ℝ{sup n}). The purpose of this paper is to show that a system of one-dimensional local Muldowney’s solutions may be extended to yield a global solution. Moreover, the global extension can be represented by a unitary one-parameter group acting in L{sup 2}(ℝ{sup n})

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Advancements in Development and Testing of Thermal Power Dispatch Simulators

Flexible plant operations and generation (FPOG) offer nuclear power plants (NPPs) the chance to leverage alternative, non-electric revenue streams while ensuring their continued role as reliable, clean, and constant sources of baseload electrical power. The excess thermal energy generated from NPPs during periods of low electricity demand can be channeled as raw materials to numerous industrial processes via a thermal power dispatch (TPD) system. Hydrogen production via high-temperature steam electrolysis (HTSE) is an optimal use case based on technical and economic feasibility. Researchers at Idaho National Laboratory (INL) have conducted previous works that developed and implemented TPD system models within the GSE Solutions Generic Pressurized Water Reactor (GPWR) simulator to support human-in-the-loop (HITL) scenario-based evaluations. The first part of this report documents modifications made to the GPWR TPD model and HMI from the previous iteration in line with a new Sargent and Lundy (S&L) TPD design with an automatic control system. The was done in collaboration with Westinghouse using their three-loop pressurizer water reactor (W3LPWR) simulator which contains an industrial grade automatic control system for the TPD. This was installed in the Human Systems Simulation Laboratory (HSSL) at INL. The second part of the report documents findings from an all-hands-on-deck integration and verification workshop that was conducted in the HSSL over several days. The research team comprised INL human factors and TPD experts, a nuclear engineer from GSE Solutions who implemented the revised TPD model for GPWR, the human-machine interface (HMI) prototyping and human factors team from the University of Idaho, and personnel with operations experience with pressurized water reactors. The workshop provided time and expertise to conduct the final activities to bring the operations, HMI, and simulator into a functional state. The goals of the integration and verification workshop were: 1. to install the revised GPWR TPD model into the HSSL 2. verify the TPD HMI prototype was functional 3. integrate the HTSE Simulink model to GPWR. 3. Issues were identified for resolution, but overall the workshop accomplished its goal to integrated and verify the majority of the intended functional. Future work will resolve the identified issues and use the integrated simulation to support an evaluation and demonstration in the next fiscal year.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A study of electroactive polyvinyl chloride (PVC) gel actuators through the use of the electric modulus formalism and cyclic linear voltage sweeps

The conductivity and dielectric properties are integral to the function of polyvinyl chloride (PVC) gel actuators. The frequency-dependent properties of PVC gel actuators are investigated here in terms of their impedance, permittivity, and for the first time, electric modulus. The data shows that PVC gels’ conductive properties are just as, if not more, important as their dielectric properties in electromechanical transduction applications. The electrode polarization (EP) and its impact on the impedance and dielectric spectra of PVC gels, as well as the developed asymmetric space charge at the anode, are discussed. The electric modulus and tan δ spectra are used for the fitting of Cole-Cole (CC) and Debye relaxation models for gels of varying plasticizer content. The electrostatic adhesive force for PVC gels of varying plasticizer is also measured, indicating large electrostatic adhesion (>2 N cm -2 ). A cyclic linear voltage sweep is used to clarify the dynamics of space charge within the gels. The peak current (associated with space charge development) is seen to be concurrent with the onset of mechanical deformation, showing the asymmetric charge as the origin of electromechanical transduction. Additionally, the maximum charge transferred (as measured by the integration of current over time) before space charge development is found to correlate with the electrostatic adhesive force measured for the gels, pointing to a new method of characterizing PVC gels for actuation.

Instruments & Instrumentation↗

Ultra-low temperature (≤300 °C) growth of Ge-rich SiGe by solid-liquid-coexisting annealing of a-GeSn/c-Si structures

Ultra-low temperature (≤300 °C) growth of Ge-rich SiGe on Si substrates is strongly desired to realize advanced electronic and optical devices, which can be merged onto Si large-scale integrated circuits (LSI). To achieve this, annealing characteristics of a-GeSn/c-Si structures are investigated under wide ranges of the initial Sn concentrations (0%–26%) and annealing conditions (300–1000 °C, 1 s–48 h). Epitaxial growth triggered by SiGe mixing is observed after annealing, where the annealing temperatures necessary for epitaxial growth significantly decrease with increasing initial Sn concentration and/or annealing time. As a result, Ge-rich (∼80%) SiGe layers with Sn concentrations of ∼2% are realized by ultra-low temperature annealing (300 °C, 48 h) for a sample with the initial Sn concentration of 26%. The annealing temperature (300 °C) is in the solid-liquid coexisting temperature region of the phase diagram for Ge-Sn system. From detailed analysis of crystallization characteristics and composition profiles in grown layers, it is suggested that SiGe mixing is generated by a liquid-phase reaction even at ultra-low temperatures far below the melting temperature of a-GeSn. This ultra-low-temperature growth technique of Ge-rich SiGe on Si substrates is expected to be useful to realize next-generation LSI, where various multi-functional devices are integrated on Si substrates.

36 MATERIALS SCIENCE↗

Thin-plate spline quadrature of geodetic integrals

Thin-plate spline functions (known for their flexibility and fidelity in representing experimental data) are especially well-suited for the numerical integration of geodetic integrals in the area where the integration is most sensitive to the data, i.e., in the immediate vicinity of the evaluation point. Spline quadrature rules are derived for the contribution of a circular innermost zone to Stoke's formula, to the formulae of Vening Meinesz, and to the recursively evaluated operator L(n) in the analytical continuation solution of Molodensky's problem. These rules are exact for interpolating thin-plate splines. In cases where the integration data are distributed irregularly, a system of linear equations needs to be solved for the quadrature coefficients. Formulae are given for the terms appearing in these equations. In case the data are regularly distributed, the coefficients may be determined once-and-for-all. Examples are given of some fixed-point rules. With such rules successive evaluation, within a circular disk, of the terms in Molodensky's series becomes relatively easy. The spline quadrature technique presented complements other techniques such as ring integration for intermediate integration zones.

Vangysen, Herman↗

Global optimization algorithms to compute thermodynamic equilibria in large complex systems with performance considerations

Several global optimization methods are reviewed that attempt to ensure that the integral Gibbs energy of a closed isothermal isobaric system is a global minimum to satisfy the necessary and sufficient conditions for thermodynamic equilibrium. In particular, the integral Gibbs energy function of a multicomponent system containing non-ideal phases may be highly non-linear and non-convex, which makes finding a global minimum a challenge. Consequently, a poor numerical approach may lead one to the false belief of equilibrium. Furthermore, confirming that one reaches a global minimum and that this is achieved with satisfactory computational performance becomes increasingly more challenging in systems containing many chemical elements and a correspondingly large number of species and phases. Several numerical methods that have been used for this specific purpose are reviewed with a benchmark study of three of the more promising methods using five case studies of varying complexity. A modification of the conventional Branch and Bound method is presented that is well suited to a wide array of thermodynamic applications, including complex phases with many constituents and sublattices, and ionic phases that must adhere to charge neutrality constraints. Also, a novel method is presented that efficiently solves the system of linear equations that exploits the unique structure of the Hessian matrix, which reduces the calculation from a O(N 3 ) operation to a O(N) operation. As a result, this combined approach demonstrates efficiency, reliability and capabilities that are favorable for integration of thermodynamic computations into multi-physics codes with inherent performance considerations.

97 MATHEMATICS AND COMPUTING↗

Exploring the Connection Between Sampling Problems in Bayesian Inference and Statistical Mechanics

The Bayesian and statistical mechanical communities often share the same objective in their work - estimating and integrating probability distribution functions (pdfs) describing stochastic systems, models or processes. Frequently, these pdfs are complex functions of random variables exhibiting multiple, well separated local minima. Conventional strategies for sampling such pdfs are inefficient, sometimes leading to an apparent non-ergodic behavior. Several recently developed techniques for handling this problem have been successfully applied in statistical mechanics. In the multicanonical and Wang-Landau Monte Carlo (MC) methods, the correct pdfs are recovered from uniform sampling of the parameter space by iteratively establishing proper weighting factors connecting these distributions. Trivial generalizations allow for sampling from any chosen pdf. The closely related transition matrix method relies on estimating transition probabilities between different states. All these methods proved to generate estimates of pdfs with high statistical accuracy. In another MC technique, parallel tempering, several random walks, each corresponding to a different value of a parameter (e.g. "temperature"), are generated and occasionally exchanged using the Metropolis criterion. This method can be considered as a statistically correct version of simulated annealing. An alternative approach is to represent the set of independent variables as a Hamiltonian system. Considerab!e progress has been made in understanding how to ensure that the system obeys the equipartition theorem or, equivalently, that coupling between the variables is correctly described. Then a host of techniques developed for dynamical systems can be used. Among them, probably the most powerful is the Adaptive Biasing Force method, in which thermodynamic integration and biased sampling are combined to yield very efficient estimates of pdfs. The third class of methods deals with transitions between states described by rate constants. These problems are isomorphic with chemical kinetics problems. Recently, several efficient techniques for this purpose have been developed based on the approach originally proposed by Gillespie. Although the utility of the techniques mentioned above for Bayesian problems has not been determined, further research along these lines is warranted

Pohorille, Andrew↗

On exact-WKB analysis, resurgent structure, and quantization conditions

There are two well-known approaches to studying nonperturbative aspects of quantum mechanical systems: saddle point analysis of the partition functions in Euclidean path integral formulation and the exact-WKB analysis based on the wave functions in the Schrödinger equation. In this work, based on the quantization conditions obtained from the exact-WKB method, we determine the relations between the two formalism and in particular show how the two Stokes phenomena are connected to each other: the Stokes phenomenon leading to the ambiguous contribution of different sectors of the path integral formulation corresponds to the change of the “topology” of the Stoke curves in the exact-WKB analysis. We also clarify the equivalence of different quantization conditions including Bohr-Sommerfeld, path integral and Gutzwiller’s ones. In particular, by reorganizing the exact quantization condition, we improve Gutzwiller’s analysis in a crucial way by bion contributions (incorporating complex periodic paths) and turn it into an exact result. Furthermore, we argue the novel meaning of quasi-moduli integral and provide a relation between the Maslov index and the intersection number of Lefschetz thimbles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Calculation of the Full Scattering Amplitude without Partial Wave Decomposition II: Inclusion of Exchange

As is well known, the full scattering amplitude can be expressed as an integral involving the complete scattering wave function. We have shown that the integral can be simplified and used in a practical way. Initial application to electron-hydrogen scattering without exchange was highly successful. The Schrodinger equation (SE), which can be reduced to a 2d partial differential equation (pde), was solved using the finite element method. We have now included exchange by solving the resultant SE, in the static exchange approximation, which is reducible to a pair of coupled pde's. The resultant scattering amplitudes, both singlet and triplet, calculated as a function of energy are in excellent agreement with converged partial wave results.

Shertzer, Janine↗

Calculation of the Full Scattering Amplitude without Partial Wave Decomposition II

As is well known, the full scattering amplitude can be expressed as an integral involving the complete scattering wave function. We have shown that the integral can be simplified and used in a practical way. Initial application to electron-hydrogen scattering without exchange was highly successful. The Schrodinger equation (SE) can be reduced to a 2d partial differential equation (pde), and was solved using the finite element method. We have now included exchange by solving the resultant SE, in the static exchange approximation. The resultant equation can be reduced to a pair of coupled pde's, to which the finite element method can still be applied. The resultant scattering amplitudes, both singlet and triplet, as a function of angle can be calculated for various energies. The results are in excellent agreement with converged partial wave results.

Shertzer, J.↗

Two-photon excitation cross-section in light and intermediate atoms

The method of explicit summation over the intermediate states is used along with LS coupling to derive an expression for two-photon absorption cross section in light and intermediate atoms in terms of integrals over radial wave functions. Two selection rules, one exact and one approximate, are also derived. In evaluating the radial integrals, for low-lying levels, the Hartree-Fock wave functions, and for high-lying levels, hydrogenic wave functions obtained by the quantum defect method are used. A relationship between the cross section and the oscillator strengths is derived. Cross sections due to selected transitions in nitrogen, oxygen, and chlorine are given. The expression for the cross section is useful in calculating the two-photon absorption in light and intermediate atoms.

Omidvar, K.↗

Integrated Hourly Meteorological Database of 20 Meteorological Stations (1981-2022) for Watershed Function SFA Hydrological Modeling

This dataset contains (a) a script “R_met_integrated_for_modeling.R”, and (b) associated input CSV files: 3 CSV files per location to create a 5-variable integrated meteorological dataset file (air temperature, precipitation, wind speed, relative humidity, and solar radiation) for 19 meteorological stations and 1 location within Trail Creek from the modeling team within the East River Community Observatory as part of the Watershed Function Scientific Focus Area (SFA). As meteorological forcings varied across the watershed, a high-frequency database is needed to ensure consistency in the data analysis and modeling. We evaluated several data sources, including gridded meteorological products and field data from meteorological stations. We determined that our modeling efforts required multiple data sources to meet all their needs. As output, this dataset contains (c) a single CSV data file (*_1981-2022.csv) for each location (20 CSV output files total) containing hourly time series data for 1981 to 2022 and (d) five PNG files of time series and density plots for each variable per location (100 PNG files). Detailed location metadata is contained within the Integrated_Met_Database_Locations.csv file for each point location included within this dataset, obtained from Varadharajan et al., 2023 doi:10.15485/1660962. This dataset also includes (e) a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and (f) a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type. Review the (g) ReadMe_Integrated_Met_Database.pdf file for additional details on the script, methods, and structure of the dataset.The script integrates Northwest Alliance for Computational Science and Engineering’s PRISM gridded data product, National Oceanic and Atmospheric Administration’s NCEP-NCAR Reanalysis 1 gridded data product (through the `RCNEP` R package, Kemp et al., doi:10.32614/CRAN.package.RNCEP), and analytical-based calculations. Further, this script downscales the input data into hourly frequency, which is necessary for the modeling efforts.

54 ENVIRONMENTAL SCIENCES↗

A comparative study of stability methods for flexible satellites.

This paper compares three approaches to the stability of hybrid dynamical systems, all three methods being based on the Liapunov direct method. The first method uses testing density functions, whereas the second involves defining certain integral coordinates. Both the method using testing density functions and the method of integral coordinates lead to closed-form stability criteria in terms of the system parameters. Criteria obtained using the method of integral coordinates are in general less restrictive than those derived by the method using testing density functions. On the other hand, the latter method is easier to apply and requires less work than the former. The third method is the standard modal analysis. The modal analysis generally yields more involved criteria, depending on the number of modes used to represent the elastic displacements. As an application, the attitude stability of an earth-pointing satellite with multi-elastic domains is investigated.

Meirovitch, L.↗

Identifying Dense NiSe 2 /CoSe 2 Heterointerfaces Coupled with Surface High-Valence Bimetallic Sites for Synergistically Enhanced Oxygen Electrocatalysis

Constructing heterostructures with abundant interfaces is essential for integrating the multiple functionalities in single entities. Herein, the synthesis of NiSe 2 /CoSe 2 heterostructures with different interfacial densities via an innovative strategy of successive ion injection is reported. The resulting hybrid electrocatalyst with dense heterointerfaces exhibits superior electrocatalytic properties in an alkaline electrolyte, superior to other benchmarks and precious metal catalysts. Advanced synchrotron techniques, post structural characterizations, and density functional theory (DFT) simulations reveal that the introduction of atomic-level interfaces can lower the oxidation overpotential of bimetallic Ni and Co active sites (whereas Ni$^{2+}$ can be more easily activated than Co$^{2+}$) and induce the electronic interaction between the core selenides and surface in situ generated oxides/hydroxides, which play a critical role in synergistically reducing energetic barriers and accelerating reaction kinetics for catalyzing the oxygen evolution. Hence, the heterointerface structure facilitates the catalytic performance enhancement via increasing the intrinsic reactivity of metallic atoms and enhancing the synergistic effect between the inner selenides and surface oxidation species. This work not only complements the understanding on the origins of the activity of electrocatalysts based on metal selenides, but also sheds light on further surface and interfacial engineering of advanced hybrid materials.

36 MATERIALS SCIENCE↗

Biocatalytic Yarn for Peroxide Decomposition with Controlled Liquid Transport

In this study, a robust biocatalytic yarn with controllable liquid transport properties is created by coating thin layers of chitosan containing catalase onto a cellulosic yarn. The resulting material integrates enzyme catalytic functionality with protective coating properties of chitosan and structural functionality of the textile. Mild immobilization conditions and good affinity between the two polysaccharides minimize enzyme inactivation during the preparation steps and prevent enzyme from leaching during peroxide decomposition testing and washing, providing a novel and versatile enzyme immobilization strategy. The catalytic efficiency of enzymes in a reaction containing solid, liquid, and gas phases is facilitated when dissolved enzyme substrate is transported by liquid flowing through the coated textile structure. The flow-through configuration decomposes at least two times more peroxide in a twenty-times smaller reaction zone volume compared to a stirred tank configuration. Liquid transport through the yarn and liquid spatial distribution within the yarn are investigated by in situ neutron radiography and neutron computed tomography, revealing a constrained wicking mechanism that benefits biocatalytic yarn performance. This new class of sustainable and flexible biocatalytic textile matrices has beneficial multifunctional properties, not previously described, that are applicable for numerous small- and large-scale applications including controlled flow reactors and reactive filtration.

36 MATERIALS SCIENCE↗

Selective Synthesis of a Series of Isostructural M II Cu I Heterobimetallic Complexes Spontaneously Assembled by an Unsymmetrical Naphthyridine‐Based Ligand

Abstract Metal–metal cooperation is integral to the function of many enzymes and materials, and model complexes hold enormous potential for providing insights into the capabilities of analogous multimetallic cores. However, the selective synthesis of heterobimetallic complexes still presents a significant challenge, especially for systems that hold the metals in close proximity and feature open or reactive coordination sites for both metals. To address this issue, a rigid, naphthyridine‐based dinucleating ligand featuring distinct binding environments was synthesized. This ligand enables the selective synthesis of a series of M II Cu I bimetallic complexes (M=Mn, Fe, Co, Ni, Cu, Zn), in which each metal center exclusively occupies its preferred binding pocket, from simple chloride salts. The precision of this selectivity is evident from cyclic voltammetry, ESI‐MS and anomalous X‐ray diffraction measurements.

Nicolay, Amélie↗

Natural and anthropogenic controls on lake water‐level decline and evaporation‐to‐inflow ratio in the conterminous United States

Abstract Lake water levels are integral to lake function, but hydrologic changes from land and water management may alter lake fluctuations beyond natural ranges. We constructed a conceptual model of multifaceted drivers of lake water levels and evaporation‐to‐inflow ratio (Evap : Inflow). Using a structural equation modeling framework, we tested our model on (1) a national subset of lakes in the conterminous United States with minimal water management to describe natural drivers of lake hydrology and (2) five ecoregional subsets of lakes to explore regional variation in water management effects. Our model fits the national and ecoregional datasets and explained up to 47% of variation in Evap : Inflow, 38% of vertical water level decline, and 79% of horizontal water level decline (littoral exposure). For lakes with minimal water management, Evap : Inflow was related to lake depth ( β = −0.31) and surface inflow ( β = −0.44); vertical decline was related to annual climate (e.g., precipitation β = −0.18) and water management ( β = −0.21); and horizontal decline was largely related to vertical decline ( β = 0.73) and lake morphometry (e.g., depth β = −0.18). Anthropogenic effects varied by ecoregion and likely reflect differences in regional water management and climate. In the West, water management indicators were related to greater vertical decline ( β = 0.38), whereas in the Midwest, these indicators were related to more stable and full lake levels ( β = −0.22) even during drought conditions. National analyses show how human water use interacts with regional climate resulting in contrasting impacts to lake hydrologic variation in the United States.

Fergus, C. Emi↗