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At least 487 records · Page 27

A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions

Abstract Metabolism has been a major field of study in the last years, mainly due to its importance in understanding cell physiology and certain disease phenotypes due to its deregulation. Genome-scale metabolic models (GSMMs) have been established as important tools to help achieve a better understanding of human metabolism. Towards this aim, advances in systems biology and bioinformatics have allowed the reconstruction of several human GSMMs, although some limitations and challenges remain, such as the lack of external identifiers for both metabolites and reactions. A pipeline was developed to integrate multiple GSMMs, starting by retrieving information from the main human GSMMs and evaluating the presence of external database identifiers and annotations for both metabolites and reactions. Information from metabolites was included into a graph database with omics data repositories, allowing clustering of metabolites through their similarity regarding database cross-referencing. Metabolite annotation of several older GSMMs was enriched, allowing the identification and integration of common entities. Using this information, as well as other metrics, we successfully integrated reactions from these models. These methods can be leveraged towards the creation of a unified consensus model of human metabolism.

Vieira, Vítor↗

Distributed Queries of Large Numerical Data Sets

We have extended a previously developed high-level data model, which combines numerical quantities and meta-data into a unified hybrid model, to distributed data. An elegant query language based on SQL is extended further to allow queries against such a distributed hybrid data base. The extension is realized by allowing statements in a non-SQL programming language to be embedded in SQL view definitions.

Nemes, Richard M.↗

Improving a Multilevel Turbulence Closure Model for a Shallow Lake in Comparison With Other 1-D Models

Lakes differ from lands in water availability, heat capacity, albedo, and roughness, which affect local surface-atmospheric interactions. This study modified a multilevel upper ocean model (UOM) for lake applications and evaluated its performance in Lake Taihu (China) with comprehensive measurements against three popular one-dimensional (1-D) lake models. These models were based on different concepts, including the self-similarity (FLake), the wind-driven eddy diffusion (LISSS), the k-ε turbulence closure (SIMSTRAT), and a simplified turbulence closure (UOM). The surface flux scheme in these models was unified to exclude the discrepancies in representing air-lake exchanges. All models in their default formulations presented obvious cold water temperature biases and largely underestimated the lake surface temperature (LST) diurnal range. For each model, these deficiencies were significantly reduced by incorporating new physics schemes or calibrated tunable parameters based on systematic sensitivity tests. The primary modifications for UOM included (1) a new scheme of decreased surface roughness lengths to better characterize the shallow lake, (2) a solar radiation penetration scheme with increased light extinction coefficient and surface absorption fraction to account for the high water turbidity, and (3) turbulent Prandtl number increased by a factor of 20 to reduce the turbulent vertical mixing. All other models were improved in these three aspects (roughness, extinction, and mixing) within their original formulations. Given these improvements, UOM showed superior performance to other models in capturing LST diurnal cycle and daily to seasonal variations, as well as summer-autumn vertical stratification changes. The new UOM is well suited for application in shallow lakes.

54 ENVIRONMENTAL SCIENCES↗

Ion Dynamics Model for Collisionless Radio Frequency Sheaths

Full scale reactor model based on fluid equations is widely used to analyze high density plasma reactors. It is well known that the submillimeter scale sheath in front of a biased electrode supporting the wafer is difficult to resolve in numerical simulations, and the common practice is to use results for electric field from some form of analytical sheath model as boundary conditions for full scale reactor simulation. There are several sheath models in the literature ranging from Child's law to a recent unified sheath model [P. A. Miller and M. E. Riley, J. Appl. Phys. 82, 3689 (1997)l. In the present work, the cold ion fluid equations in the radio frequency sheath are solved numerically to show that the spatiotemporal variation of ion flux inside the sheath, commonly ignored in analytical models, is important in determining the electric field and ion energy at the electrode. Consequently, a semianalytical model that includes the spatiotemporal variation of ion flux is developed for use as boundary condition in reactor simulations. This semianalytical model is shown to yield results for sheath properties in close agreement with numerical solutions.

Bose, Deepak↗

TPSAS-NF1676L-11382-DND

Long-range transport of ozone precursor species and carbonaceous aerosols emitted by wildfires may affect the atmospheric composition and regional climate far away from the location of the fires. Major outbreaks of fires occurred in 3 areas of Asia, Kazakhstan, Siberia, and Thailand, during the spring of 2008. Satellite and aircraft-based observations and trajectory studies have identified the transit of the plumes from these fires across the Pacific. We have conducted simulations of the effects of these fires on the atmospheric composition using the Real-time Air Quality Modeling System (RAQMS). RAQMS is a global scale meteorological and chemical modeling system with unified (stratosphere/troposphere) chemistry module. Model results, for example, indicate that increases of 10 ppbv in upper tropospheric ozone at 180W longitude and northern mid-latitudes in April, 2008 could be attributed to these fires. Large increases in aerosol optical depth due to carbonaceous aerosols are also seen nearer the fire location. Both tropospheric ozone and carbonaceous aerosols influence the atmospheric energy balance and climate. We use an off-line radiative transfer model along with the RAQMS chemical and aerosol analyses to calculate the direct radiative forcing during April, 2008, due to Asian wildfire emissions. Arctic indirect radiative forcing due to these emissions are evaluated using RAQMS aerosol extinction analyses in conjunction with MODIS retrievals of cloud liquid water and effective radius. We will discuss the radiative forcing results and the relative influences of the different fire events.

Murali Natarajan↗

Precision Higgs Boson Physics and Implications for Beyond the Standard Model Physics Theories

The discovery of the Higgs boson is one of science's most impressive recent achievements. We have taken a leap forward in understanding what is at the heart of elementary particle mass generation. We now have a significant opportunity to develop even deeper understanding of how the fundamental laws of nature are constructed. As such, we need intense focus from the scientific community to put this discovery in its proper context, to realign and narrow our understanding of viable theory based on this positive discovery, and to detail the implications the discovery has for theories that attempt to answer questions beyond what the Standard Model can explain. This project's first main object is to develop a state-of-the-art analysis of precision Higgs boson physics. This is to be done in the tradition of the electroweak precision measurements of the LEP/SLC era. Indeed, the electroweak precision studies of the past are necessary inputs to the full precision Higgs program. Calculations will be presented to the community of Higgs boson observables that detail just how well various couplings of the Higgs boson can be measured, and more. These will be carried out using state-of-the-art theory computations coupled with the new experimental results coming in from the LHC. The project's second main objective is to utilize the results obtained from LHC Higgs boson experiments and the precision analysis, along with the direct search studies at LHC, and discern viable theories of physics beyond the Standard Model that unify physics to a deeper level. Studies will be performed on supersymmetric theories, theories of extra spatial dimensions (and related theories, such as compositeness), and theories that contain hidden sector states uniquely accessible to the Higgs boson. In addition, if data becomes incompatible with the Standard Model's low-energy effective lagrangian, new physics theories will be developed that explain the anomaly and put it into a more unified framework beyond the Standard Model.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Higgs quadruplet for the type III seesaw model and implications for {mu}{yields}e{gamma} and {mu}-e conversion

In the type III seesaw model, the heavy neutrinos are contained in leptonic triplet representations. The Yukawa couplings of the triplet fermion and the left-handed neutrinos with the doublet Higgs field produce the Dirac mass terms. Together with the Majorana masses for the leptonic triplets, the light neutrinos obtain nonzero seesaw masses. We point out that it is also possible to have a quadruplet Higgs field to produce the Dirac mass terms to facilitate the seesaw mechanism. The vacuum expectation value of the quadruplet Higgs is constrained to be small by electroweak precision data. Therefore, the Yukawa couplings of a quadruplet can be much larger than those for a doublet. We also find that unlike the usual type III seesaw model where at least two copies of leptonic triplets are needed, with both doublet and quadruplet Higgs representations, just one leptonic triplet is possible to have a phenomenologically acceptable model because light neutrino masses can receive sizable contributions at both tree and one-loop levels. Large Yukawa couplings of the quadruplet can induce observable effects for lepton flavor violating processes {mu}{yields}e{gamma} and {mu}-e conversion. Implications of the recent {mu}{yields}e{gamma} limit from MEG and the limit on {mu}-e conversion on Au are also given. Some interesting collider signatures for the doubly charged Higgs boson in the quadruplet are discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Simulation of Flow in Multi-Scale Porous Media Using the Lattice Boltzmann Method on Quadtree Grids

Abstract The unified lattice Boltzmann model is extended to the quadtree grids for simulation of fluid flow through porous media. The unified lattice Boltzmann model is capable of simulating flow in porous media at various scales or in systems where multiple length scales coexist. The quadtree grid is able to provide a high-resolution approximation to complex geometries, with great flexibility to control local grid density. The combination of the unified lattice Boltzmann model and the quadtree grids results in an efficient numerical model for calculating permeability of multi-scale porous media. The model is used for permeability calculation for three systems, including a fractured system used in a previous study, a Voronoi tessellation system, and a computationally-generated pore structure of fractured shale. The results are compared with those obtained using the conventional lattice Boltzmann model or the unified lattice Boltzmann model on rectangular or uniform square grid. It is shown that the proposed model is an accurate and efficient tool for flow simulation in multi-scale porous media. In addition, for the fractured shale, the contribution of flow in matrix and fractures to the overall permeability of the fractured shale is studied systematically.

Earth Sciences↗

A perspective on coherent structures and conceptual models for turbulent boundary layer physics

Direct numerical simulations of turbulent boundary layers have been analyzed to develop a unified conceptual model for the kinematics of coherent motions in low Reynolds number canonical turbulent boundary layers. All classes of coherent motions are considered in the model, including low-speed streaks, ejections and sweeps, vortical structures, near-wall and outer-region shear layers, sublayer pockets, and large-scale outer-region eddies. The model reflects the conclusions from the study of the simulated boundary layer that vortical structures are directly associated with the production of turbulent shear stresses, entrainment, dissipation of turbulence kinetic energy, and the fluctuating pressure field. These results, when viewed from the perspective of the large body of published work on the subject of coherent motions, confirm that vortical structures may be considered the central dynamic element in the maintenance of turbulence in the canonical boundary layer. Vortical structures serve as a framework on which to construct a unified picture of boundary layer structure, providing a means to relate the many known structural elements in a consistent way.

Robinson, Stephen K.↗

Unified Viscoplastic Behavior of Metal Matrix Composites

The need for unified constitutive models was recognized more than a decade ago in the results of phenomenological tests on monolithic metals that exhibited strong creep-plasticity interaction. Recently, metallic alloys have been combined to form high-temperature ductile/ductile composite materials, raising the natural question of whether these metallic composites exhibit the same phenomenological features as their monolithic constituents. This question is addressed in the context of a limited, yet definite (to illustrate creep/plasticity interaction) set of experimental data on the model metal matrix composite (MMC) system W/Kanthal. Furthermore, it is demonstrated that a unified viscoplastic representation, extended for unidirectional composites and correlated to W/Kanthal, can accurately predict the observed longitudinal composite creep/plasticity interaction response and strain rate dependency. Finally, the predicted influence of fiber orientation on the creep response of W/Kanthal is illustrated.

Arnold, S. M.↗

Enhanced simulation software for rocket turbopump, turbulent, annular liquid seals

One of the main objectives of this work is to develop a new dynamic analysis for liquid annular seals with arbitrary profile and to analyze a general distorted interstage seal of the space shuttle main engine high pressure oxygen turbopump (SSME-ATD-HPOTP). The dynamic analysis developed is based on a method originally proposed by Nelson and Nguyen. A simpler scheme based on cubic splines is found to be computationally more efficient and has better convergence properties at higher eccentricities. The first order solution of the original analysis is modified by including a more exact solution that takes into account the variation of perturbed variables along the circumference. A new set of equations for dynamic analysis are derived based on this more general model. A unified solution procedure that is valid for both Moody's and Hirs' friction models is presented. Dynamic analysis is developed for three different models: constant properties, variable properties, and thermal effects with variable properties. Arbitrarily varying seal profiles in both axial and circumferential directions are considered. An example case of an elliptical seal with varying degrees of axial curvature is analyzed in detail. A case study based on predicted clearances of an interstage seal of the SSME-ATD-HPOTP is presented. Dynamic coefficients based on external specified load are introduced to analyze seals that support a preload. The other objective of this work is to study the effect of large rotor displacements of SSME-ATD-HPOTP on the dynamics of the annular seal and the resulting transient motion. One task is to identify the magnitude of motion of the rotor about the centered position and establish limits of effectiveness of using current linear models. This task is accomplished by solving the bulk flow model seal governing equations directly for transient seal forces for any given type of motion, including motion with large eccentricities. Based on the above study, an equivalence is established between linearized coefficients based transient motion and the same motion as predicted by the original governing equations. An innovative method is developed to model nonlinearities in an annular seal based on dynamic coefficients computed at various static eccentricities. This method is thoroughly tested for various types of transient motion using bulk flow model results as a benchmark.

Padavala, Satya↗

Multiscale equatorial electrojet turbulence: Energy conservation, coupling, and cascades in a baseline 2-D fluid model

In this paper, progress in understanding the coupling between plasma instabilities in the equatorial electrojet based on a unified fluid model is reported. Simulations with parameters set to various ionospheric background conditions revealed properties of the gradient-drift and Farley-Buneman instabilities. Notably, sharper density gradients increase linear growth rates at all scales, whereas variations in cross-field E × B drift velocity only affect small-scale instabilities. A formalism defining turbulent fluctuation energy for the system is introduced, and the turbulence is analyzed within this framework. This exercise serves as a useful verification test of the numerical simulations and also elucidates the physics underlying the ionospheric turbulence. Various physical mechanisms involved in the energetics are categorized as sources, sinks, nonlinear transfer, and cross-field coupling. The physics of the nonlinear transfer terms is studied to identify their roles in producing energy cascades, which explain the generation of small-scale structures that are stable in the linear regime. The theory of two-step energy cascading to generate the 3 m plasma irregularities in the equatorial electrojet is verified for the first time in the fluid regime. Finally, in addition, the nonlinearity of the system allows the possibility of an inverse energy cascade, potentially responsible for generating large-scale plasma structures at the top of the electrojet as found in different rocket and radar observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Unified concept of effective one component plasma for hot dense plasmas

Orbital-free molecular dynamics simulations are used to benchmark two popular models for hot dense plasmas: the one component plasma (OCP) and the Yukawa model. A unified concept emerges where an effective OCP (EOCP) is constructed from the short-range structure of the plasma. An unambiguous ionization and the screening length can be defined and used for a Yukawa system, which reproduces the long-range structure with finite compressibility. Similarly, the dispersion relation of longitudinal waves is consistent with the screened model at vanishing wave number but merges with the OCP at high wave number. Additionally, the EOCP reproduces the overall relaxation time scales of the correlation functions associated with ionic motion. Lastly, in the hot dense regime, this unified concept of EOCP can be fruitfully applied to deduce properties such as the equation of state, ionic transport coefficients, and the ion feature in x-ray Thomson scattering experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A unified thermionic and thermionic-field emission (TE–TFE) model for ideal Schottky reverse-bias leakage current

We present a unified thermionic emission (TE) and thermionic-field emission (TFE) model for the ideal reverse-bias leakage current in Schottky junctions. The unified TE–TFE analytical model advances upon previous analytical TFE models by Murphy–Good and Padovani–Stratton, which are the two most widely adopted models by the community, in two major aspects: (i) the applicability of the TFE expression therein is extended to near-zero surface electric fields by an error-function correction, allowing for the calculation of the total current by a nontrivial sum of TE (over-the-barrier current) and TFE (below-the-barrier current) contributions; therefore, an accurate description of the TE-to-TFE transition region is captured analytically for the first time; (ii) image-force lowering is considered with much-simpler correction terms. Comparisons with the reference numerical model show that the unified TE–TFE model has excellent accuracy, as well as a 10 000× reduction in computation time. The unified model is further tested against experimental data from Schottky barrier diodes based on Si, 4H-SiC, GaN, and β-Ga 2 O 3 , revealing accurate extractions of barrier heights and correct descriptions of the ideal reverse leakage characteristics. With the extended applicable range, improved accuracy, and computational efficiency, the unified TE–TFE model is highly valuable for the design and analysis of devices based on Schottky junctions, as well as for potential integration in technology computer-aided design (TCAD) tools.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

National Energy Water Treatment & Speciation (NEWTS): A Water & Critical Mineral Database and Dashboard

The scarcity of water resources, the need for beneficial water reuse, and the challenges of wastewater treatment are becoming increasingly pressing in economic, social, and environmental domains. Addressing these concerns requires effective treatment strategies to manage wastewater streams and tackle environmental and economic issues. Furthermore, the recovery of critical minerals from the waste streams associated with energy production holds the promise of offsetting treatment costs and securing local sources of valuable minerals. However, relevant data on these waste streams are dispersed and challenging to locate. The process of ingesting such data into modeling software often involves multiple steps, requiring data restructuring to meet software-input requirements. The non-standardized reporting of water data makes data aggregation and reformatting a time-consuming process. Additionally, essential attributes necessary for modeling water treatment and mineral scale formation are frequently missing. Moreover, data gaps vary depending on the region of interest. Consequently, there is a pressing need for high-quality energy-water composition data that can be easily imported into water chemistry modeling software. To address this need, the National Energy Technology Laboratory has created the National Energy Water Treatment and Speciation (NEWTS) Database and Dashboard—a free online tool catering to community leaders and water researchers. NEWTS facilitates a comprehensive understanding of the composition of energy-related wastewater streams in the United States. The datasets provide detailed concentrations and speciation of major and minor aqueous compounds in energy-related wastewater streams, including power plant leachate, acid mine drainage, brackish water, and oil and gas produced water across the United States. Many of the aqueous species are critical minerals (Li, REEs) in high demand to modernize the world’s energy infrastructure. Many of the datasets also contain volumetric flow-rates needed to model the treatment and reuse scenarios in advanced aqueous chemistry software programs. The NEWTS Database and Dashboard offer public access to hitherto challenging-to-access datasets, presented in a standardized format that is tailored for easy input into aqueous chemistry modeling software. By performing the work needed to transform dispersed, disparate data sources into unified, model-ready datasets, NEWTS serves as an essential resource in advancing water treatment research and sustainable water resource management.

produced water management↗

Constitutive modeling for isotropic materials

The fourth and final year of the HOST project with the initial objective of developing a unified constitutive model for finite element structural analysis of turbine engine hot section components is discussed. The final year's work was primarily concerned with the study of nonisothermal problems and the potential for thermal history effects to occur explicitly in the constitutive equations.

Lindholm, Ulric S.↗