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Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through “wildcards” representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.

59 BASIC BIOLOGICAL SCIENCES↗

Reactive Transport Modeling of Mineral Precipitation and Carbon Trapping in Discrete Fracture Networks

In this study we use numerical experiments to analyze reactive flow and transport behavior in discrete intersecting fracture networks, focusing on (a) how reaction-induced changes in physical and chemical properties affect flow connectivity and (b) how fracture networks developed in the Earth's critical zone contribute to carbon sequestration via mineral weathering reactions. In the first part of the study, we used two-dimensional reactive flow and transport simulations to analyze the impacts of mixing in a natural discrete fracture network. We concluded that reaction-induced changes can substantially alter the flow connectivity, especially at fracture intersections. The second set of simulations considered the problem of natural weathering of fractured mafic and ultramafic rocks in the partially saturated Earth's critical zone as a function of infiltration rates, fracture permeability, and partially saturated flow parameters. As a model system, we considered an incongruent reaction network with dissolution of forsterite and precipitation of magnesite. The behavior is complex in terms of the rate-controlling processes because of the multicomponent nature of the system as shown by the grid Peclet number: the CO 2 behavior is gas diffusion-controlled in the partially saturated zone, while the rate of water flow via the Damkӧhler number controls Mg 2+ transport through the fracture network. The amounts of carbon that can be trapped are modest, but the naturally fractured domain considered here provides a useful “base case” against which various engineered solutions can be compared.

58 GEOSCIENCES↗

VRA Modeling, phase 1

The destruction of organic contaminants in waste water for closed systems, such as that of Space Station, is crucial due to the need for recycling the waste water. A co-current upflow bubble column using oxygen as the gas phase oxidant and packed with catalyst particles consisting of a noble metal on an alumina substrate is being developed for this process. The objective of this study is to develop a plug-flow model that will predict the performance of this three phase reactor system in destroying a multicomponent mixture of organic contaminants in water. Mass balances on a series of contaminants and oxygen in both the liquid and gas phases are used to develop this model. These mass balances incorporate the gas-to-liquid and liquid-to-particle mass transfer coefficients, the catalyst effectiveness factor, and intrinsic reaction rate. To validate this model, a bench scale reactor has been tested at Michigan Technological University at elevated pressures (50-83 psig,) and a temperature range of 200 to 290 F. Feeds consisting of five dilute solutions of ethanol (approx. 10 ppm), chlorobenzene (approx. 20 ppb), formaldehyde (approx. 100 ppb), dimethyl sulfoxide (DMSO approx. 300 ppb), and urea (approx. 20 ppm) in water were tested individually with an oxygen mass flow rate of 0.009 lb/h. The results from these individual tests were used to develop the kinetic parameter inputs necessary for the computer model. The computer simulated results are compared to the experimental data obtained for all 5 components run in a mixture on the differential test column for a range of reactor contact times.

Kindt, Louis M.↗

Thermodynamic Activity Measurements with Knudsen Cell Mass Spectrometry

Coupling the Knudsen effusion method with mass spectrometry has proven to be one of the most useful experimental techniques for studying the equilibrium between condensed phases and complex vapors. The Knudsen effusion method involves placing a condensed sample in a Knudsen cell, a small "enclosure", that is uniformly heated and held until equilibrium is attained between the condensed and vapor phases. The vapor is continuously sampled by effusion through a small orifice in the cell. A molecular beam is formed from the effusing vapor and directed into a mass spectrometer for identification and pressure measurement of the species in the vapor phase. Knudsen cell mass spectrometry (KCMS) has been used for nearly fifty years now and continues to be a leading technique for obtaining thermodynamic data. Indeed, much of the well-established vapor specie data in the JANAF tables has been obtained from this technique. This is due to the extreme versatility of the technique. All classes of materials can be studied and all constituents of the vapor phase can be measured over a wide range of pressures (approximately 10(exp -4) to 10(exp -11) bar) and temperatures (500-2800 K). The ability to selectively measure different vapor species makes KCMS a very powerful tool for the measurement of component activities in metallic and ceramic solutions. Today several groups are applying KCMS to measure thermodynamic functions in multicomponent metallic and ceramic systems. Thermodynamic functions, especially component activities, are extremely important in the development of CALPHAD (Calculation of Phase Diagrams) type thermodynamic descriptions. These descriptions, in turn, are useful for modeling materials processing and predicting reactions such as oxide formation and fiber/matrix interactions. The leading experimental methods for measuring activities are the Galvanic cell or electro-motive force (EMF) technique and the KCMS technique. Each has specific advantages, depending on material and conditions. The EMF technique is suitable for lower temperature measurements, provided a suitable cell can be constructed. KCMS is useful for higher temperature measurements in a system with volatile components. In this paper, we briefly review the KCMS technique and identify the major experimental issues that must be addressed for precise measurements. These issues include temperature measurements, cell material and cell design and absolute pressure calibration. The resolution of these issues are discussed together with some recent examples of measured thermodynamic data.

Copland, Evan H.↗

Kinetic Growth of Multicomponent Microcompartment Shells

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Altogether, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

defects↗

Ion Clusters in Multicomponent Solutions Determined from X-ray PDF and SAXS Analysis: The NaNO 2 –NaOH–H 2 O System

Here, this study explores ion cluster formation in the NaNO 2 –NaOH–H 2 O system to understand how ion cluster formation is influenced by the composition in multicomponent mixtures. X-ray pair distribution function (PDF) and small-angle X-ray scattering (SAXS) identified complex ion clusters in concentrated NaNO 2 and NaOH solutions as well as their mixtures. PDF analysis showed that the Na–O distance depended primarily on total Na + concentrations rather than anion composition, whereas the nitrite-water oxygen distance stayed the same regardless of concentration or composition. This result indicates that the nitrite ion hydration was relatively independent of composition. SAXS confirms local fluctuations and coherent clusters with notable size differences between NaOH and NaNO 2 solutions. SAXS analysis of mixed solutions shows that their clusters are an average of the individual solutions, indicating mixed clusters.

Reynolds, Jacob G. [Central Plateau Cleanup Compan↗

Gels and gel-derived glasses in the Na2O-B2O3-SiO2 system

The containerless melting of high-purity multicomponent homogeneous gels and gel-monoliths offers a unique approach to making ultrapure multicomponent optical glasses in the reduced gravity environment of space. Procedures for preparing and characterizing gels and gel-derived glasses in the Na2O-B2O3-SiO2 system are described. Preparation is based on the polymerization reactions of alkoxysilane with trimethyl borate or boric acid and a suitable sodium compound. The chemistry of the gelling process is discussed in terms of process parameters and the gel compositions. The physicochemical nature of gels prepared by three different procedures were found to be significantly different. IR absorption spectra indicate finite differences in the molecular structures of the different gels. The melting of the gel powders and the transformation of porous gel-monoliths to transparent 'glass' without melting are described.

Mukherjee, S. P.↗

Mapping Thermoelectric Transport in a Multicomponent Alloy Space

Abstract Interest in high entropy alloy thermoelectric materials is predicated on achieving ultralow lattice thermal conductivity κ L through large compositional disorder. However, here it is shown that for a given mechanism, such as mass contrast phonon scattering, κ L will be minimized along the binary alloy with highest mass contrast, such that adding an intermediate mass atom to increase atomic disorder can increase thermal conductivity. Only when each component adds an independent scattering mechanism (such as adding strain fluctuation to an existing mass fluctuation) is there a benefit. In addition, both charge carriers and heat‐carrying phonons are known to experience scattering due to alloying effects, leading to a trade‐off in thermoelectric performance. Analytic transport models are applied, based on perturbation and effective medium theories, to predict how alloy scattering will affect the thermal and electronic transport across the full compositional range of several pseudo‐ternary and pseudo‐quaternary alloy systems. To do so, a multicomponent extension is demonstrated to both thermal and electronic binary alloy scattering models based on the virtual crystal approximation. Finally, it is shown that common functional forms used in computational thermodynamics can be applied to this problem to further generalize the scattering behavior that is modeled.

36 MATERIALS SCIENCE↗

A Phase-Field Study on Internal to External Oxidation Transition in High-Temperature Structural Alloys

Structural alloys applied at high temperatures rely on an external dense layer of oxide scale for protection. As some reactive alloy components are selectively oxidized internally, understanding how these dispersed metal oxide particles reach the surface to form a protective scale—the so-called internal to external oxidation transition—is crucial for designing these alloys. While the literature is replete with experimental studies on oxidation of alloys, there is a lack of computational studies in this realm due to the complex nature of coupled reaction and diffusion processes in multicomponent multi-phase alloy systems. In this work, we apply a recently developed phase-field model to simulate the oxidation processes under different compositions and nucleation scenarios to gain insights into how a continuous oxide scale can be established. The results show that while alloy composition is critical for internal to external oxidation transition, the oxide nuclei size, shape and distribution also have significant impact on the transition kinetics.

36 MATERIALS SCIENCE↗

Separation of volatile organic contaminants from water using a direct-contact dehumidifier: An experimental study and modeling

A packed-bed, direct-contact dehumidifier (PB-DCD) has been developed to selectively condense water from a gaseous mixture of organic contaminants. In this process, hot air is humidified by mixing with wastewater vapor in a static mixer and is dehumidified by subcooled fresh water passing through the PB-DCD in a counter-current configuration. The goal of this study is to understand the relationship between various operating parameters and how they affect separation of isopropyl alcohol (IPA) from the gaseous mixture with the purpose of expanding the investigation to other contaminants in the future. The process has been successfully used to separate IPA from wastewater. Different parameters including the concentration of IPA in water, feed temperature, air-to-vapor ratio, and cooling-water-to-vapor mass ratio, as well as residence time were examined to determine their influence on contaminant separation and clean water recovery rate. The Buckingham Pi theorem was applied to reduce the number of studying variables by generating non-dimensional groups. Experiments were performed to determine the relationship between the non-dimensional parameters and model mass transfer in the system. Mass transfer coefficients for multicomponent gaseous mixture condensation in a packed-bed direct contact condenser column are calculated and a modified correlation of mass transfer is developed. The parameters of the mass transfer model are obtained from operating conditions of the PB-DCD, stream conditions and thermodynamic properties. A modified Sherwood correlation is developed to predict IPA separation from a gaseous mixture consisting of air, water, and IPA. The modified Sherwood correlation is applied to successfully predict the Sherwood number with a mean absolute error equal to 6.6 %. According to the experimental results, the maximum IPA separation achieved was 76.3 %, which corresponds to a water recovery rate of 58.7 %.

42 ENGINEERING↗

Multi-Scale Modeling Framework for Mercury Biogeochemistry

Multi-Scale modeling of mercury (Hg) geochemical speciation and reactions has been performed by integrating atomistic quantum chemical calculations with continuum scale speciation models. Major progress has been made in the improvement of quantum chemical models to calculate critical thermodynamic data for Hg complexes in aquatic environments. Rapid and reliable quantum chemical approaches have been developed for calculating acid dissociation constants (pK a ) and stability constants (log K), with calculated mean unsigned errors of 0.5 and 1.5 log units, respectively for ligand molecules and Hg complexes. At the continuum scale, systematic analysis of uncertainty propagation in mercury (Hg) speciation modeling has been conducted and was used to identify environmental conditions under which thermodynamic constant uncertainties are significant and recommended to be accounted for. The integrated framework for multi-scale modeling of mercury geochemistry is open to the research community through the web-based multiscale modeling aqueous speciation resource, AQUA-MER. The improved quantum chemical approaches for thermodynamic constant calculations are accessible through AQUA-MER and can be used to provide the missing constants in the continuum scale speciation calculations. In addition to low molecular mass Hg complex speciation, modeling natural aquatic environments also involve the transport of high molecular weight dissolved organic matter (DOM) in reactive flows simultaneously with equilibrium and kinetic reactions. To this end, atomistic MD simulations were performed to capture the details of aggregation, mechanisms and distribution of functional groups in DOM at the molecular level. The elemental composition and calculated bulk properties of the DOM models are in close agreement with experimental measurements. A travel-time based reactive transport model in the hyporheic zone of stream corridors was established for the multicomponent Hg-DOM-S system and implemented through PFLOTRAN.

54 ENVIRONMENTAL SCIENCES↗

Carbon dioxide capture system and spectroscopic evaluation thereof

A chemical processing system for removing carbon dioxide from a gas mixture using a multicomponent amine-based scrubbing solution includes a spectroscopic evaluation system with a liquid contact probe for spectroscopic investigation, an energy source connected with the liquid contact probe to provide the spectroscopic stimulation energy to the probe, a spectrometer connected with the liquid contact probe to detect the spectroscopic response energy to the probe and to output spectral data corresponding to the spectroscopic response energy, and a machine learning spectral data analyzer connected to the spectrometer for evaluation of the spectral data to determine a concentration value for each of water, amine component and captured carbon dioxide in the scrubbing solution, the machine learning spectral data analyzer being trained for each such component over a corresponding trained concentration range, and optionally over a trained temperature range to provide a temperature-compensated concentration value.

Panaccione, Charles↗

Multicomponent gas mixture parametric CFD study of condensation heat transfer in small modular reactor system safety

Safety is always the primary concern for designing and analyzing nuclear reactor systems. The requirements for the safety margin for advanced small modular reactor (SMR) systems are targeted even higher than the conventional commercial large-scale nuclear reactors incorporating the passive and inherent safety systems. The SMR systems are designed with the condensation passive containment cooling system (PCCS), which plays a critical role in removing reactor heat during a steam release accident case. However, the presence of non-condensable gas (NCG), like air, reduces the heat transfer performance. This physics phenomenon becomes multifactorial for nuclear reactor containment during a fuel failure accident case that releases hydrogen gas. Besides, the mixture component of steam-air-hydrogen varies in reactor accident cases, which need simulation and validation keeping parameters of importance. Reviews showed that previous studies for SMR’s PCCCS did not cover the condensation heat transfer (CHT) in the presence of multicomponent NCG mixture parametric computational fluid dynamics (CFD) simulation and validation, making a research gap in the SMR design safety. A comprehensive CHT parametric CFD study was performed for SMR PCCS to fill this research gap. This study used experimental data as simulation 3D physics domain inlet and outlet boundary conditions. However, the wall boundary conditions were constant temperature, curve-fit, and annular coolant for verifying the turbulence models. Parametric simulations were performed, verified, and optimized for steam-NCGs mixtures. The multicomponent gases, multiphase mixtures, and fluid film condensation models were applied with associated turbulence models. The results of the parametric study were evaluated for realistic reactor conditions. Results showed that parametric study provided critical insight about the dependency of multicomponent gas mixture parameters that supports reactor safety design, analysis, and licensing.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Doppler global velocimetry

A new program to develop a Doppler Global Velocimeter (DGV) for application in the High angle-of-Attack Technology Program is discussed. The Flight research instrument system will make non-intrusive multicomponent velocity measurements of the vortical flow field around an aircraft in flight. The DGV will provide a means to obtain airborne experimental data to evaluate and refine computational fluid dynamic models and to correlate with wind-tunnel data sets. The primary use of the instrument system will be to provide a flexible research tool to map the 3D velocity field at various locations around an aircraft during high angle-of-attack maneuvers at subsonic, transonic, and supersonic speeds. Other potential applications may include shock definition and interactions, external stores flow interactions, rotary flow field definition, non-steady flow field definition, measurement of inlet and duct flow field, and measurement of hypersonic flow field in flight.

Usry, Jim↗

Ablation, Thermal Response, and Chemistry Program for Analysis of Thermal Protection Systems

In previous work, the authors documented the Multicomponent Ablation Thermochemistry (MAT) and Fully Implicit Ablation and Thermal response (FIAT) programs. In this work, key features from MAT and FIAT were combined to create the new Fully Implicit Ablation, Thermal response, and Chemistry (FIATC) program. FIATC is fully compatible with FIAT (version 2.5) but has expanded capabilities to compute the multispecies surface chemistry and ablation rate as part of the surface energy balance. This new methodology eliminates B' tables, provides blown species fractions as a function of time, and enables calculations that would otherwise be impractical (e.g. 4+ dimensional tables) such as pyrolysis and ablation with kinetic rates or unequal diffusion coefficients. Equations and solution procedures are presented, then representative calculations of equilibrium and finite-rate ablation in flight and ground-test environments are discussed.

Milos, Frank S.↗

Transport equations for multicomponent anisotropic space plasmas - A review

An attempt is made to present a unified approach to the study of transport phenomena in multicomponent anisotropic space plasmas. In particular, a system of generalized transport equations is presented that can be applied to widely different plasma flow conditions. The generalized transport equations can describe subsonic and supersonic flows, collision-dominated and collisionless flows, plasma flows in rapidly changing magnetic field configurations, multicomponent plasma flows with large temperature differences between the interacting species, and plasma flows that contain anisotropic temperature distributions. In addition, if Maxwell's equations of electricity and magnetism are added to the system of transport equations, they can be used to model electrostatic shocks, double layers, and magnetic merging processes. These transport equations also contain terms which act to regulate both the heat flow and temperature anisotropy, processes which appear to be operating in the solar wind.

Barakat, A. R.↗