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At least 343 records · Page 19

Development of a kinetic model to describe six types of symbiotic interactions in a formate utilizing microalgae-bacteria cultivation system

This study investigated an algae/formate-utilizing-bacteria system that has been developed for carbon capture. This photomixotrophic consortium consumed formate to support bacterial growth so that the resulting respiration CO 2 could be simultaneously used by algae to avoid CO 2 gas-lipid mass transfer limitation. To understand biomass growth and population interactions in this unique system, a kinetic model has been developed to describe algae and bacteria multiplication, formate and nitrogen utilizations, CO 2 mass transfer, O 2 generation and consumption, lighting condition and shading effect. The simulation indicated that this ecosystem could form six types of interactions (mutualism, commensalism, parasitism, neutralism, amensalism, and competition) depending on the light intensity and nutrient availability. Furthermore, the simulation of both batch culture and chemostat, along with parameter sensitivity tests and experimental observations, offered insights into optimal applications of algae-bacteria consortium based photobiorefinery.

59 BASIC BIOLOGICAL SCIENCES↗

Re-evaluating cloud chamber constraints on depositional ice growth in cirrus clouds – Part 1: Model description and sensitivity tests

Abstract. Ice growth from vapor deposition is an important process for the evolution of cirrus clouds, but the physics of depositional ice growth at the low temperatures (<235 K) characteristic of the upper troposphere and lower stratosphere is not well understood. Surface attachment kinetics, generally parameterized as a deposition coefficient αD, control ice crystal habit and also may limit growth rates in certain cases, but significant discrepancies between experimental measurements have not been satisfactorily explained. Experiments on single ice crystals have previously indicated the deposition coefficient is a function of temperature and supersaturation, consistent with growth mechanisms controlled by the crystal's surface characteristics. Here we use observations from cloud chamber experiments in the Aerosol Interactions and Dynamics in the Atmosphere (AIDA) aerosol and cloud chamber to evaluate surface kinetic models in realistic cirrus conditions. These experiments have rapidly changing temperature, pressure, and ice supersaturation such that depositional ice growth may evolve from diffusion limited to surface kinetics limited over the course of a single experiment. In Part 1, we describe the adaptation of a Lagrangian parcel model with the Diffusion Surface Kinetics Ice Crystal Evolution (DiSKICE) model (Zhang and Harrington, 2014) to the AIDA chamber experiments. We compare the observed ice water content and saturation ratios to that derived under varying assumptions for ice surface growth mechanisms for experiments simulating ice clouds between 180 and 235 K and pressures between 150 and 300 hPa. We found that both heterogeneous and homogeneous nucleation experiments at higher temperatures (>205 K) could generally be modeled consistently with either a constant deposition coefficient or the DiSKICE model assuming growth on isometric crystals via abundant surface dislocations. Lower-temperature experiments showed more significant deviations from any depositional growth model, with different ice growth rates for heterogeneous and homogeneous nucleation experiments.

54 ENVIRONMENTAL SCIENCES↗

Non-compact oxide-island growth induced by surface phase transition of the intermetallic NiAl during vacuum annealing

Crystal structure and composition are inter-dependent and decoupling their effects on surface reactivity is challenging. Using low-energy electron microscopy to spatially and temporally resolve the oxide film growth during the oxidation of NiAl(100), we differentiate such coupled effects by monitoring oxide growth while simultaneously fine-tuning the surface structure and composition during oxidation. We demonstrate that the oxidation of chemically ordered surfaces results in compact oxide island growth whereas non-compact oxide growth during the surface phase transition. By incorporating the surface phase transition induced chemical disordering into kinetic Monte Carlo simulations, we illustrate that the non-compact oxide growth is induced by the composition effect on the surface diffusion of oxygen, which can be described by the concept of “ant in the labyrinth”.

36 MATERIALS SCIENCE↗

Modeling of Lithium Nucleation and Plating Kinetics Under Fast Charge Conditions

The onset of lithium nucleation and subsequent plating on the graphite particles is a challenging problem in the design of fast charging batteries. Here, a variational phase field formulation has been developed to initiate the nucleation of lithium particles based on the local plating overpotential conditions and allowing to predict the lithium plating under fast charge conditions. The model demonstrates that (1) at small charging current density, there is no nucleation and plating of metallic lithium, and no effect on the intercalation kinetics; (2) at intermediate charging current densities, initially a stagnated growth from isolated lithium nuclei is observed followed by a continuous growth of metallic lithium; (3) at large charging current densities, a continuous growth of metallic lithium resulting from coalescence of small nuclei into large nuclei decreases the excess interfacial energy, which in turn slows down the intercalation kinetics. The formulation sets the stage for predicting and evaluating the influence of various electrolyte compositions, graphite particle morphologies and electrode loadings on the nucleation and plating dynamics under fast charge conditions.

25 ENERGY STORAGE↗

Numerical Mixing Suppresses Submesoscale Baroclinic Instabilities Over Sloping Bathymetry

Abstract The impacts of spurious numerical salinity mixing on the larger‐scale flow and tracer fields are characterized using idealized simulations. The idealized model is motivated by realistic simulations of the Texas‐Louisiana shelf and features oscillatory near‐inertial wind forcing. can exceed the physical mixing from the turbulence closure in frontal zones and within the mixed layer. This suggests that simulated mixing processes in frontal zones are driven largely by . Near‐inertial alongshore wind stress amplitude is varied to identify a base case that maximizes the ratio of to in simulations with no prescribed horizontal mixing. We then test the sensitivity of the base case with three tracer advection schemes (MPDATA, U3HC4, and HSIMT) and conduct ensemble runs with perturbed bathymetry. Instability growth is evaluated using the volume‐integrated eddy kinetic energy and available potential energy . While all schemes have similar total mixing, the HSIMT simulations have over double the volume‐integrated and 20% less relative to other schemes, which suppresses the release of and reduces the by roughly 25%. This results in reduced isohaline variability and steeper isopycnals, evidence that enhanced suppresses instability growth. Differences in and between the MPDATA and U3HC4 simulations are marginal. However, the U3HC4 simulations have 25% more . Experiments with variable horizontal viscosity and diffusivity coefficients show that small amounts of prescribed horizontal mixing improve the representation of the ocean state for all advection schemes by reducing the and increasing the .

54 ENVIRONMENTAL SCIENCES↗

Simultaneous imaging and diffraction in the dynamic diamond anvil cell

The ability to visualize a sample undergoing a pressure-induced phase transition allows for the determination of kinetic parameters, such as the nucleation and growth rates of the high-pressure phase. For samples that are opaque to visible light (such as metallic systems), it is necessary to rely on x-ray imaging methods for sample visualization. Here, we present an experimental platform developed at beamline P02.2 at the PETRA III synchrotron radiation source, which is capable of performing simultaneous x-ray imaging and diffraction of samples that are dynamically compressed in piezo-driven diamond anvil cells. This setup utilizes a partially coherent monochromatic x-ray beam to perform lensless phase contrast imaging, which can be carried out using either a parallel- or focused-beam configuration. The capabilities of this platform are illustrated by experiments on dynamically compressed Ga and Ar. Melting and solidification were identified based on the observation of solid/liquid phase boundaries in the x-ray images and corresponding changes in the x-ray diffraction patterns collected during the transition, with significant edge enhancement observed in the x-ray images collected using the focused-beam. These results highlight the suitability of this technique for a variety of purposes, including melt curve determination.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Turbulence in Core-collapse Supernovae

It is understood in a general sense that turbulent fluid motion below the shock front in a core-collapse supernova stiffens the effective equation of state of the fluid and aids in the revival of the explosion. However, when one wishes to be precise and quantify the amount of turbulence in a supernova simulation, one immediately encounters the problem that turbulence is difficult to define and measure. Using the 3D magnetohydrodynamic code ELEPHANT, we study how different definitions of turbulence change one’s conclusions about the amount of turbulence in a supernova and the extent to which it helps the explosion. We find that, while all the definitions of turbulence we use lead to a qualitatively similar growth pattern over time of the turbulent kinetic energy in the gain region, the total amount of turbulent kinetic energy, and especially the ratios of turbulent to total kinetic energy, distinguish them. Some of the definitions appear to indicate turbulence is a necessary contributor to the explosion, and others indicate it is not. The different definitions also produce turbulence maps with different correlations with maps of the enstrophy, a quantity widely regarded as also indicating the presence of turbulence. We also compute the turbulent adiabatic index and observe that, in regions of low enstrophy, this quantity is sensitive to the definition used. As a consequence, the effective adiabatic index depends upon the method used to measure the turbulence, and thus it alters one’s conclusions regarding the impact of turbulence within the supernova.

computational astronomy↗

Elucidating the formation mechanisms of zeolites using data-driven modelling and in-situ characterization

Zeolites are the main solid catalysts used by the chemical industry. The use of zeolites in separations and as shape selective catalysts requires control of the width and connectivity of their pores. 235 distinct zeolite frameworks have been synthesized to date, of over 2 million that have been proposed. Recent work indicates that the limitation is in large part kinetic: new synthetic pathways are required to access new zeolites. Organic cations are used to direct the synthesis towards specific zeolites. However, the molecular mechanisms by which cations direct the nucleation towards specific zeolites is not known. Elucidating these mechanisms is key to realize new zeolites for catalysis and separations, and is the focus of this project. This project developed and implemented a synergistic, data-driven computational and experimental approach to resolve the molecular pathways of nucleation, growth, and polymorph selection of zeolites and the role of organic cations in directing their formation. The project developed computationally efficient and accurate models for the study of the nucleation and growth of pure silica zeolites in molecular simulations, using machine learning with data from experiments. Simulations with these models were integrated with scanning tunneling electron microscopy, computer vision, and deep learning to unveil the molecular pathways of formation of a zeolite. Of particular interest in this project was to elucidate the role of amorphous precursors in the nucleation of the zeolite. Previous experiments indicate that zeolites are born within non-crystalline aggregates in which the silicates and organic cations have local and medium range order similar to that of the zeolite. The organic cations that direct the formation of zeolites and those that direct the formation of ordered mesoporous silicas are similar. We hypothesized that the frustrated attraction that for large organic cations leads to the formation of stable mesophases that direct the synthesis of mesoporous silicas, could promote the formation of metastable mesophases that can assist in the nucleation and polymorph selection of zeolites. The simulations resolved how structure directing agents build crystalline order and showed that mesoscopic pre-ordering occurs is not required to facilitate the nucleation of zeolites, because the synthesis occurs at high driving forces, where the barriers for nucleation are negligible. This project unveiled that polymorph selection in zeolite synthesis occurs after nucleation, opening a distinct area of control through the kinetics of growth and not through nucleation barriers.

36 MATERIALS SCIENCE↗

Wire directed energy deposition of steel-aluminum structures using cold metal transfer process

In this study, a sharp transition from 316L stainless steel to 4043 aluminum alloy was fabricated using wire directed energy deposition (DED) via the cold metal transfer (CMT) process. The CMT process with its inherently low heat input, led to a significant reduction in intermetallic thickness at the bi-metallic interface compared to blown powder DED technique reported in the literature resulting in superior properties when compared to those of dissimilar steel-aluminum welds. Thermo-kinetic modeling confirmed that the intermetallic formation is through a classical nucleation and growth mechanism, and the fraction and thickness can be controlled by adjusting CMT process parameters to kinetically arrest or minimize the intermetallic formation. These findings underscore the efficacy of CMT-based wire DED for fabrication of steel-aluminum bi-metallic structures.

36 MATERIALS SCIENCE↗

Reduction kinetics of hercynite redox materials for solar thermochemical water splitting

Solar thermochemical water splitting (STWS) using a hercynite redox cycle is a promising technology for producing renewable H 2 . Here, the reduction kinetics of hercynite (FeAl 2 O 4 ) is evaluated using thermogravimetric and XRD analyses. The results indicate that as-prepared hercynite materials undergo reduction via two different reaction mechanisms. The reaction first proceeds by a nucleation and growth mechanism (AE1), followed by a third-order kinetic model (F3). XRD analyses show the occurrence of superstoichiometric oxygen in the spinel structure of FeAl 2 O 4+δ in the second reaction mechanism, which indicates the formation of cationic vacancies. TGA and XRD analyses confirm that hercynite maintains its spinel structure when the materials are thermally reduced and oxidized with steam. Differential scanning calorimetry (DSC) performed on FeAl 2 O 4 particles shows two heats of reaction in agreement with the two observed mechanisms. This is the first kinetics study to report on the thermal reduction of hercynite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Epitaxial 2D Magnet and Topological Insulator Heterostructures

I will discuss our latest advances on the epitaxial growth of 2D van der Waals (vdW) magnets and their integration with topological insulators (TI). This work is motivated by the realization of topological phases such as the quantum anomalous Hall effect and highly efficient spin-orbit torque produced by TIs. Our initial studies of MnSe2 growth on Bi2Se3 showed a tendency for the interdiffusion of Mn into the Bi2Se3. This ultimately led to the synthesis of MnBi2Se4 (MBS), a new magnetic TI. Interestingly, the vdW phase is not the thermodynamically stable phase and bulk crystals do not exist, so the epitaxial stabilization of MBS creates the opportunity to explore the magnetic and topological properties of this material. We find that MBS is a layered antiferromagnet, similar to MnBi2Te4, but a difference is that the magnetic moments lie in the plane of the film. Angle resolved photoemission experiments show the presence of a topological surface state with Dirac dispersion. For bilayers of 2D magnets and TIs, we have developed FGT films on Bi2Te3. We first optimized FGT by studying its growth on Ge(111) substrates, where we find that kinetic considerations play a major role. Using cross-sectional scanning transmission electron microscopy and scanning tunneling microscopy, we optimize the FGT films to have atomically smooth surfaces and abrupt interfaces with the Ge(111). Subsequently, we have developed the growth of FGT on Bi2Te3 for the integration of 2D magnets with Tis. Interestingly, we observe room temperature ferromagnetism in FGT/Bi2Te3 heterostructures by varying the growth conditions.

Kawakami, Roland↗

The effects of calcium hydroxide and activator chemistry on alkali-activated metakaolin pastes

The impact of calcium hydroxide as an additive in sodium hydroxide- and silicate-activated metakaolin pastes is presented with a primary aim to ascertain the specific effects of calcium on the reaction kinetics and phase formation. FTIR and XRD are employed to understand the interaction of calcium hydroxide (10 wt% replacement of metakaolin) in 1, 5 and 10 M NaOH-activated pastes (and equivalent molarity Na{sub 2}SiO{sub 3}-activated pastes), with a focus on its impact on the nanoscale properties of the sodium-alumino-silicate-hydrate (N-A-S-(H)) gel. In situ FTIR and ICC are used to assess the impact of calcium hydroxide on the reaction kinetics, including the rate of metakaolin dissolution and associated rate of N-A-S-(H) gel growth. It is found that calcium hydroxide is effective at accelerating the reaction kinetics of 5 M Na{sub 2}SiO{sub 3}-activated metakaolin due to the formation of an initial calcium-rich gel that promotes additional metakaolin dissolution and enhances N-A-S-(H) gel formation.

36 MATERIALS SCIENCE↗

In-situ re-crystallization of heavily-irradiated Gd 2 Ti 2 O 7

Gadolinium titanate (Gd 2 Ti 2 O 7 , or GTO) and other lanthanide pyrochlores are interesting candidates for actinide waste disposal and fast ion conduction because the relevant material properties are intimately dependent on local cation structure. Therefore, a deep understanding of the kinetics associated with cation ordering and disordering is required if such material properties are to be tuned for specific device designs. To this end, single crystals of GTO were irradiated with 190 keV helium ions to a total fluence of 1 × 10 17 ions/cm 2 , amorphizing the sample surface to a depth of ~1 μm and resulting in significant He bubble accumulation. FIB lamellae lifted out from the irradiated sections were examined during heat treatment in the (scanning) transmission electron microscope. Two distinct stages of the re-crystallization of the amorphized material were observed. The material near the end of the ions’ range transformed first and with the same orientation as the pristine material. This was due to the close proximity of the pristine material and the presence of small defect fluorite seeds, but the propagation of this growth front was frustrated by the large pores (formerly bubbles) in the He accumulation layer. This was followed by heterogeneous nucleation of new crystallites at random orientations at the top of the He accumulation layer, which is attributed to the high surface area associated with the many small He bubbles in that region. Finally, it is inferred that the kinetics of grain growth in this material are significantly faster than the kinetics of grain nucleation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sulfate adenylyl transferase kinetics and mechanisms of metabolic inhibitors of microbial sulfate respiration

Abstract Sulfate analog oxyanions that function as selective metabolic inhibitors of dissimilatory sulfate reducing microorganisms (SRM) are widely used in ecological studies and industrial applications. As such, it is important to understand the mode of action and mechanisms of tolerance or adaptation to these compounds. Different oxyanions vary widely in their inhibitory potency and mechanism of inhibition, but current evidence suggests that the sulfate adenylyl transferase/ATP sulfurylase (Sat) enzyme is an important target. We heterologously expressed and purified the Sat from the model SRM, Desulfovibrio alaskensis G20. With this enzyme we determined the turnover kinetics (kcat, KM) for alternative substrates (molybdate, selenate, arsenate, monofluorophosphate, and chromate) and inhibition constants (KI) for competitive inhibitors (perchlorate, chlorate, and nitrate). These measurements enable the first quantitative comparisons of these compounds as substrates or inhibitors of a purified Sat from a respiratory sulfate reducer. We compare predicted half-maximal inhibitory concentrations (IC50) based on Sat kinetics with measured IC50 values against D. alaskensis G20 growth and discuss our results in light of known mechanisms of sensitivity or resistance to oxyanions. This analysis helps with the interpretation of recent adaptive laboratory evolution studies and illustrates the value of interpreting gene–microbe–environment interactions through the lens of enzyme kinetics.

Carlson, Hans K. (ORCID:0000000215835313)↗

Repulsive expansion dynamics in colony growth and gene expression

Spatial expansion of a population of cells can arise from growth of microorganisms, plant cells, and mammalian cells. It underlies normal or dysfunctional tissue development, and it can be exploited as the foundation for programming spatial patterns. This expansion is often driven by continuous growth and division of cells within a colony, which in turn pushes the peripheral cells outward. This process generates a repulsion velocity field at each location within the colony. Here we show that this process can be approximated as coarse-grained repulsive-expansion kinetics. This framework enables accurate and efficient simulation of growth and gene expression dynamics in radially symmetric colonies with homogenous z-directional distribution. It is robust even if cells are not spherical and vary in size. The simplicity of the resulting mathematical framework also greatly facilitates generation of mechanistic insights.

59 BASIC BIOLOGICAL SCIENCES↗

Probing the Mechanism of Cadmium Sulfide Cluster Nucleation and Growth via Sequential Infiltration Synthesis

Few-atom metal chalcogenide clusters may be realized through the sequential infiltration of metal–organic precursors in polymer films. However, the underlying nucleation and growth mechanisms that allow for cluster synthesis with near atomic-scale precision are not fully resolved. The kinetics of the sequential infiltration synthesis (SIS) method that control the nucleation and growth mechanisms of primarily Cd 4 S 4 -core clusters within a poly­(4-vinylpyridine) (P4VP) matrix are probed with in situ UV–visible absorbance spectroscopy. Density functional theory (DFT) calculations that allow simulation of the optical properties of cluster fragments further reveal the thermodynamics that guide cluster growth within the P4VP matrix. Here, we conclude that a reactive capture mechanism for cluster nucleation and growth is dominant, although transient dimethyl cadmium adduction to the polymer backbone may contribute to cluster nucleation under shorter metal–organic purge process conditions. Grazing incidence X-ray diffraction (GI-XRD) and X-ray absorption spectroscopy (XAS) analyses further corroborate the cluster size and atom connectivity throughout the stepwise synthesis.

Jayaweera, Nuwanthaka P. [Argonne National Laborat↗

Transformation of an Embedded Five-Membered Ring in Polycyclic Aromatic Hydrocarbons via the Hydrogen-Abstraction–Acetylene-Addition Mechanism: A Theoretical Study

Five-membered rings are constituents of many polycyclic aromatic hydrocarbons (PAHs) and their presence on the edges of large PAHs has been repeatedly observed experimentally. However, modern kinetic combustion models often do not consider the growth of PAHs through the transformation of the five-membered rings. Here, in connection with the above, we carried out a theoretical study of the mechanism of Hydrogen-Abstraction-aCetylene-Addition (HACA) transformation of an embedded five-membered ring on the armchair PAH edge to a six-membered ring, considering cyclopenta[d,e,f]phenanthrene (4,5-methylenephenanthrene) as a prototype system for this process. The potential energy surface for the reactions of cyclopenta[d,e,f]phenanthrenyl radicals produced by direct H abstractions from cyclopenta[d,e,f]phenanthrene with acetylene has been compiled at the G3(MP2,CC)//B3LYP/6-311G(d,p) level of theory including zero-point vibrational energy corrections. The computed energies and molecular parameters were then used to solve the Rice-Ramsperger-Kassel-Marcus Master Equation (RRKM-ME) in order to calculate reaction rate at various pressures and temperatures, which were fitted to modified Arrhenius equation for further kinetic modeling. The results show that the HACA transformation of the embedded five-membered ring to a six-membered ring is possible, albeit slow. The most viable reaction mechanism involves the R2 + C 2 H 2 reaction, where the acetylene molecules adds to a σ-radical in the six-membered ring adjacent to the five-membered ring via a low entrance barrier. The predominant product of R2 + C 2 H 2 is predicted to be 3 ethynyl 4H cyclopenta[def]phenanthrene Pr5 via immediate H elimination from the initial addition complex. Next, Pr5 undergoes H-assisted isomerization to 4aH-pentaleno[4,3,2,1-cdef]phenanthrene Pr4, and the latter adds an H atom eventually forming the 1-pyrenylmethyl radical Pr3: R2 + C 2 H 2 ⇌ 3 ethynyl 4H cyclopenta[def]phenanthrene (Pr5) + H ⇌ 4aH-pentaleno[4,3,2,1-cdef]phenanthrene (Pr4) + H Pr5 + H ⇌ Pr4 + H Pr4 + H → 1-pyrenylmethyl (Pr3) This HACA sequence may be competitive with the methyl radical addition to the R1 radical formed by H abstraction from the CH 2 group in the five-membered ring of cyclopenta[d,e,f]phenanthrene, which provides a pathway to pyrene following two H atom losses. Relative contributions of the two mechanisms of the five- to six-membered ring transformation would strongly depend on the branching ratios of the R1 and R2 radicals produced by the H abstractions and the available concentration of C 2 H 2 vs. CH 3 and hence differ in different flames.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling soot growth in Comp-B using a detonation history

A chemical kinetics procedure for soot formation calculation is summarized. By importing Lagrangian hydrodynamic calculations, species history is consistently accounted for. Detonation product composition is assumed in region with the burnt high explosive (HE). Soot formation is calculated using the density and energy obtained in the hydrodynamics calculation of HE detonation. Ideal gas equation-of-state (EOS) with temperature-dependent specific heat is used in the HE product region. Sample calculations show reasonably-expected temperature and soot formation.

42 ENGINEERING↗