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At least 505 records · Page 28

Integrative mapping reveals molecular features underlying the mechanism of nucleocytoplasmic transport

Nuclear pore complexes (NPCs) enable rapid, selective, and robust nucleocytoplasmic transport. To explain how transport emerges from the system components and their interactions, we used experimental data and theoretical information to construct an integrative Brownian dynamics model of transport through an NPC, coupled to a kinetic model of transport in the cell. The model recapitulates key aspects of transport for a wide range of molecular cargoes, including preribosomes and viral capsids. Our model quantifies how flexible phenylalanine-glycine (FG) repeat proteins create an entropic barrier to passive diffusion and how this barrier is selectively lowered in facilitated diffusion by the many transient interactions of nuclear transport receptors with the FG repeats. Selective transport is enhanced by “fuzzy” multivalent interactions, redundant FG repeat mass, coupling to the energy-dependent RanGTP concentration gradient, and exponential dependence of transport kinetics on the transport barrier. Our model will facilitate rational modulation of the NPC and its artificial mimics.

Raveh, Barak [School of Computer Science and Engin↗

Direct implicit and explicit energy-conserving particle-in-cell methods for modeling of capacitively coupled plasma devices

Achieving large-scale kinetic modeling is a crucial task for the development and optimization of modern plasma devices. With the trend of decreasing pressure in applications, such as plasma etching, kinetic simulations are necessary to self-consistently capture the particle dynamics. The standard, explicit, electrostatic, momentum-conserving particle-in-cell method suffers from restrictive stability constraints on spatial cell size and temporal time step, requiring resolution of the electron Debye length and electron plasma period, respectively. This results in a very high computational cost, making the technique prohibitive for large volume device modeling. We investigate the direct implicit algorithm and the explicit energy conserving algorithm as alternatives to the standard approach, both of which can reduce computational cost with a minimal (or controllable) impact on results. These algorithms are implemented into the well-tested EDIPIC-2D and LTP-PIC codes, and their performance is evaluated via 2D capacitively coupled plasma discharge simulations. The investigation reveals that both approaches enable the utilization of cell sizes larger than the Debye length, resulting in a reduced runtime, while incurring only minor inaccuracies in plasma parameters. The direct implicit method also allows for time steps larger than the electron plasma period; however, care must be taken to avoid numerical heating or cooling. It is demonstrated that by appropriately adjusting the ratio of cell size to time step, it is possible to mitigate this effect to an acceptable level.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

X-ray heating and electron temperature of laboratory photoionized plasmas

We discuss experimental and modeling results for the x-ray heating and temperature of laboratory photoionized plasmas. A method is used to extract electron temperature based on the analysis of transmission spectroscopy data that is independent of atomic kinetics modeling. Boltzmann kinetic and radiation-hydrodynamics simulations emphasized the critical interplay between atomic physics and heating in photoionized plasmas. They also demonstrated the dramatic impact of photoexcitation on excited state populations, line emissivity, and radiation cooling. Temperature calculations performed with astrophysical codes significantly overestimated the measurement.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

First steps toward predicting corrosion behavior of structural materials in molten salts

To address the need for physics-based models to predict corrosion behavior of materials in molten salts, here we propose potential methods to aid in selection of optimum materials for structural components in molten salt powered technologies. In the present work, the role of alloy thermodynamics and kinetics on governing corrosion rates of Ni-based alloys will be discussed combining experimental and computational methods. A few strategies are presented to quantify corrosion rates of Ni-based materials isothermally exposed in purified KCl-MgCl 2 salts at 600° C-800° C. The influence of capsule material, potential corrosion products and role of alloy composition on the observed corrosion rates was discussed with coupled thermodynamic-kinetic models. Larger depths of corrosion attack were observed in alloy 230 specimens compared to other alloys under similar conditions was attributed to the much higher chemical activity of Cr in the alloy that results in a larger Cr chemical potential gradient.

36 MATERIALS SCIENCE↗

Fast microflow kinetics and acid catalyst deactivation in glucose conversion to 5-hydroxymethylfurfural

5-Hydroxymethyl furfural (HMF) is an important platform chemical because it can be upgraded to various drop-in and performance-advantaged products. The cascade reaction of HMF production from glucose over a Lewis acid (CrCl 3 ) and a Brønsted acid (HCl) catalyst in aqueous media is investigated in a microreactor at short residence times and high temperatures. We study the formation of various chromium species using UV-visible spectrophotometry and elucidate the Cr(III) speciation. The catalyst reactivity increases sharply at short residence times, and then drops at long times. This indicates that the catalyst treatment plays a vital role in getting optimal reactivity, and recording the catalyst history is necessary. We develop a kinetic model to describe the catalyst speciation as well as the Lewis and Brønsted acid-catalyzed reaction kinetics using a hierarchical approach. Here, the model is in good agreement with experiments. We demonstrate the benefits of tandem Lewis-external added Brønsted acid catalysis in processing time, productivity, and catalyst stability. We apply this model to optimize the HMF yield and obtain ~36% yield at 200 °C in 7 min and report the highest productivity of ~15% yield per min, demonstrating the opportunity of reaching high productivity at short residence times.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Chemical models for simulating single-walled nanotube production in arc vaporization and laser ablation processes

Chemical kinetic models for the nucleation and growth of clusters and single-walled carbon nanotube (SWNT) growth are developed for numerical simulations of the production of SWNTs. Two models that involve evaporation and condensation of carbon and metal catalysts, a full model involving all carbon clusters up to C80, and a reduced model are discussed. The full model is based on a fullerene model, but nickel and carbon/nickel cluster reactions are added to form SWNTs from soot and fullerenes. The full model has a large number of species--so large that to incorporate them into a flow field computation for simulating laser ablation and arc processes requires that they be simplified. The model is reduced by defining large clusters that represent many various sized clusters. Comparisons are given between these models for cases that may be applicable to arc and laser ablation production. Solutions to the system of chemical rate equations of these models for a ramped temperature profile show that production of various species, including SWNTs, agree to within about 50% for a fast ramp, and within 10% for a slower temperature decay time.

Nanotubes, Carbon/chemistry↗

The Importance of Decarbonylation Mechanisms in the Atomic Layer Deposition of High-Quality Ru Films by Zero-Oxidation State Ru(DMBD)(CO) 3

Achieving facile nucleation of noble metal films through atomic layer deposition (ALD) is extremely challenging. To this end, η 4 -2,3-dimethylbutadiene ruthenium tricarbonyl (Ru(DMBD)(CO) 3 ), a zero-valent complex, has recently been reported to achieve good nucleation by ALD at relatively low temperatures and mild reaction conditions. Here, we study the growth mechanism of this precursor by in situ quartz-crystal microbalance and quadrupole mass spectrometry during Ru ALD, complemented by ex situ film characterization and kinetic modeling. These studies reveal that Ru(DMBD)(CO) 3 produces high-quality Ru films with excellent nucleation properties. This results in smooth, coalesced films even at low film thicknesses, all important traits for device applications. However, Ru deposition follows a kinetically limited decarbonylation reaction scheme, akin to typical CVD processes, with a strong dependence on both temperature and reaction timescale. The non-self-limiting nature of the kinetically driven mechanism presents both challenges for ALD implementation and opportunities for process tuning. By surveying reports of similar precursors, we suggest that the findings can be generalized to the broader class of zero-oxidation state carbonyl-based precursors used in thermal ALD, with insight into the design of effective saturation studies.

chemical vapor deposition↗

Shock Tube and Flame Speed Measurements of 2,4,4-Trimethyl-1-Pentene: A Co-Optima Biofuel

Abstract The combustion of 2,4,4-trimethyl-1-pentene (diisobutylene, C8H16), which is a biofuel and a component of surrogate fuels, is examined in this work. Carbon monoxide time–histories and ignition delay times are collected behind reflected shock waves utilizing a shock tube and mid-infrared laser absorption spectroscopy. Measurements were obtained near 10 atm pressure during stoichiometric oxidation of 0.15%C8H16/O2/Ar. Simulated results from chemical kinetic models are provided, and sensitivity analyses are used to discuss differences between models for both ignition delay times and carbon monoxide formation. In addition, laminar burning speeds are obtained at 1 atm, 428 K, and equivalence ratios, phi, between 0.91 and 1.52 inside a spherical chamber facility. Measured burning speeds are found to be less than that of ethanol over the equivalence ratio span. Burning speed measurements are compared to predictions of chemical kinetic mechanisms and are in agreement for the richest conditions; however, at lean conditions, the model predicts a far slower-burning speed. The maximum burning speed occurs at an equivalence ratio of 1.08 with a magnitude of 0.70 m/s. The current work provides the crucial experimental data needed for assessing the feasibility of this biofuel and for the development of future combustion chemical kinetics models.

Energy & Fuels↗

Development Of Thermodynamic and Kinetic Simulation Tools and Testing Procedures for Enhanced Durability of Concrete Containing Industrial By-Products

This project developed screening tools that enable evaluation of alternative cementitious binders that create concretes to significantly reduce energy and emissions while remaining cost competitive on both initial and long-term costs. The team began with the viewpoint that acceptance of new cementitious binder products has a substantially greater chance of successful implementation when capital investment is not excessive and the end product has customers that have experience and resources to use this. As such, a binder system that is based on portland cement with blended using industrial by-products (alternative cementitious materials) has the potential for dramatic and meaningful impact. The team has focused on developing implementable solutions in specifications and current practice. This however requires three main factors: 1) ability to screen byproducts and alternative materials for success, 2) ability to ‘treat’ materials chemically to enhance kinetics, and 3) ability to provide predictions of performance of both binders and concrete from first principles. The project developed/refined a state of the art and scientifically based screening test for SCM called the pozzolanic reactivity test. The team developed kinetic models to simulate these materials as well as experimental approaches to alter selected reactions. Simulation tools were developed that enable the performance of concrete to be predicted based on the chemistry and reactivity of the cement and alternative SCM. Specifically, this project: • enhanced the kinetic reactivity models for use in multi-scale computational programs that use thermodynamics to predict reaction products. 2 • developed scaling models to extend thermodynamic modeling to link these models with pore structure. This enables strength, transport property, and coupled transport prediction. • developed tools to predict performance of cementitious materials using the pozzolanic reactivity test and chemical composition. The predicted properties are consistent with AASHTO R101 and the CEB-FIP model code and can be measured using associated test procedures. • demonstrated mechanical and fracture based modeling tools that thermodynamic predictions and inputs to predict concrete service life. These results have been used to demonstrate the value of enabling specifications to include ASTM C 595 cement as well ASTM C150 cement. In addition, these products are being used to expedite the evaluation of alternative SCM to aide in determining which materials have potential value and what ‘compositions’ of blended cements merit further investment.

42 ENGINEERING↗

Pre-steady-state kinetics of nanocrystal:molybdenum nitrogenase biohybrids reveals hole-scavenging efficiency is critical to N 2 reduction

Molybdenum (Mo) nitrogenase is a two-component enzyme complex that catalyzes the reduction of dinitrogen to ammonia and protons to hydrogen gas. We have shown that electrons for dinitrogen reduction can be delivered photochemically to the catalytic MoFe protein component by cadmium sulfide (CdS) nanocrystals. In this study, we used electron paramagnetic resonance spectroscopy to measure the transient populations of catalytic intermediates. We fit the populations with a pre-steady-state kinetic model, which allowed us to distinguish between productive and non-productive reaction pathways and extract the rate constants for the reaction. Our results demonstrated that the rate of catalytic electron delivery into MoFe protein increased with the concentration of the sacrificial electron donor. This enabled electron delivery to exceed the rate of hydride protonation, a relaxation pathway that competes with N 2 binding. Thus, managing the balance between electron transfer and hole transfer reactions is required to achieve a kinetic regime that favors N 2 reduction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Experimental and computational study of phase space dynamics in strongly coupled plasmas with steep density gradients

Understanding how plasmas thermalize when density gradients are steep remains a fundamental challenge in plasma physics, with direct implications for fusion experiments and astrophysical phenomena. Standard hydrodynamic models break down in these regimes, and kinetic theories make predictions that have never been directly tested. Here, we present the first detailed phase-space measurements of a strongly coupled plasma as it evolves from sharp density gradients to thermal equilibrium. Using laser-induced fluorescence imaging of an ultracold calcium plasma, we track the complete ion distribution function f(x,v,t). We discover that commonly used kinetic models (Bhatnagar–Gross–Krook and Lenard–Bernstein) overpredict thermalization rates, even while correctly capturing the initial counterstreaming plasma formation. Our measurements reveal that the initial ion acceleration response scales linearly with electron temperature, and that the simulations underpredict the initial ion response. In our geometry we demonstrate the formation of well-controlled counterpropagating plasma beams. This experimental platform enables precision tests of kinetic theories and opens new possibilities for studying plasma stopping power and flow-induced instabilities in strongly coupled systems.

Bergeson, Scott (ORCID:0000000231249226)↗

Dynamic Interconversion of Metal Active Site Ensembles in Zeolite Catalysis

Catalysis science is founded on understanding the structure, number, and reactivity of active sites. Kinetic models that consider active sites to be static and noninteracting entities are routinely successful in describing the behavior of heterogeneous catalysts. Yet, active site ensembles often restructure in response to their external environment and even during steady-state catalytic turnover, sometimes requiring non-mean-field kinetic treatments to describe distance-dependent interactions among sites. Such behavior is being recognized more frequently in modern catalysis research, with the advent of experimental methods to quantify turnover rates with increasing precision, an expanding arsenal of operando characterization tools, and computational descriptions of atomic structure and motion at chemical potentials and timescales increasingly relevant to reaction conditions. This review focuses on dynamic changes to metal active site ensembles on zeolite supports, which are silica-based crystalline materials substituted with Al that generate binding sites for isolated and low-nuclearity metal site ensembles. Metal sites can become solvated and mobilized during reaction, facilitating interactions among sites that change their nuclearity and function. Such intersite communication can be regulated by the zeolite support, resulting in non-single-site and potentially non-mean-field kinetic behavior arising from mechanisms of catalytic action that combine elements of those canonically associated with homogeneous and heterogeneous catalysis. Here, we discuss recent literature examples that document dynamic active site behavior in metal-zeolites and outline methodologies to identify and interpret such behavior. We conclude with our outlook on future research directions to develop this evolving branch of catalysis science and harness it for practical applications.

operando characterization↗

DME-Propane Ignition Delay Time Measurements at Mixing Controlled Compression Ignition Engine-Relevant Conditions

The blend of dimethyl ether (DME, CH 3 OCH 3 ) and propane (C 3 H 8 ) is a potentially renewable fuel mixture that has the potential to replace diesel in compression ignition engines. The combination can potentially reduce particulate and greenhouse gas emissions compared to a conventional diesel engine operating under similar conditions. However, detailed conceptual and simulation studies must be conducted before adopting a new fuel on a compression ignition engine. For these simulations, accurate chemical kinetic models are necessary. However, the validity of chemical kinetic mechanisms in the literature is unknown for mixing controlled compression ignition (MCCI) engine operating conditions. Hence, in this work, we studied the ignition of dimethyl ether (DME) and propane blends in a shock tube at MCCI engine conditions. Ignition delay time (IDT) data was collected behind the reflected shock for DME-propane mixtures for heavy-duty compression ignition (CI) engine parameters. Undiluted experiments spanning temperatures of 700 to 1100 K and pressures of 55 to 84 bar for various blends (100% CH 3 OCH 3 / 0% C 3 H 8, 100% C 3 H 8 / 0% CH 3 OCH 3 , 60% CH 3 OCH 3 / 40% C 3 H 8 ) of DME and propane were combusted in synthetic air (21% O 2 / 79% N 2 ). Some experiments were conducted at higher pressures (90-120 bar) to understand model performance at these conditions. Comparisons of IDT were made with the predictions of recent chemical kinetic mechanisms for DME-propane mixture, including the Aramco3.0, NUIG, and Dames et al. mechanisms. All mechanisms overpredicted IDT compared to experimental values. Sensitivity analysis was conducted with Dames et al. model, and critical reactions sensitive to IDT of DME-propane mixture near 100 bar are outlined.

Mohammed, Zuhayr Pasha↗

Grain dynamics in zero gravity

The dynamics of granular materials has proved difficult to model, primarily because of the complications arising from inelastic losses, friction, packing, and the effect of many grains being in contact simultaneously. The kinetic model of granular systems is similar to the kinetic theory of gases, except that collisional energy losses are always present in the former and must be treated explicity. Few granular materials on Earth are describable by this limiting model, since gravity tends to collapse the grains into a high density state where Coulombic friction effects are dominant. The planned Space Station offers an unusual opportunity to test the kinetic grain model and to explore its predictions. Without gravity, the regime of low interparticle velocities (where an elastic description of the collision is still valid) can be investigated. This will allow for direct interpretation by dynamical computer simulations as well as by the kinetic theory. The dynamics of spherical grains inside a clear box would be examined. Results would be compared with the predictions of the kinetic theory and computer simulations.

Werner, B. T.↗

Rapid Construction of Validated Chemistry Models for Advanced Biofuels (Co-Optima Final Report)

Computer methods were developed and demonstrated that make it possible to predict the combustion and pyrolysis chemistry of proposed biofuels, even before the biofuels are ever manufactured or experimentally tested. The methods are based on first-principles calculations of reaction rates and equilibria. A large number of complicated calculations are required, so we developed a computer workflow that automates many of the steps. With the chemical structure of the biofuel and the system conditions (temperature, pressure, compositions, etc.) as the input, the computer methods can construct a detailed kinetic model with refined parameters without intense human intervention. The automation of model construction makes it practical for a single engineer to make the predictions in a reasonable time period. The accuracy of the computer predictions was tested by measuring the time-profiles of various reaction intermediates (carbon monoxide, carbon dioxide, water, formaldehyde, methane, and ethylene) formed as the biofuels pyrolyze or ignite using sophisticated laser shock tube methods. Several biofuels, including methyl propyl ether, cyclopentanone, butyl acetate isomers, etc., were carefully studied to demonstrate the validity of the proposed computational and experimental methodology. This research project opens up the possibility for assessing some proposed biofuels on the computer without expensive experimental campaigns. The new computer methods are open source and well-documented, allowing a knowledgeable modeler to easily access the developed methods and implement them in their work routine. Moreover, they are also convenient and powerful, promising for developing the fuel chemistry models needed for use in engine simulators, facilitating co-optimization of new engine designs with new fuels.

09 BIOMASS FUELS↗

The topside ionosphere - A region of dynamic transition

The review article concentrates on dynamic processes at work in the topside ionosphere (between the F2 peak and about 3000 km) where the H ion dominates and ionic reactions can be neglected. The history of ionosphere and plasmasphere research using radio waves is reviewed. Low-speed and high-speed multispecies plasma ion flow is studied with various models (13-moment approximation, 5-moment approximation, kinetic models of the polar wind). Experimental observations of the plasmapause, results of vertical soundings of the topside, and global pole-to-pole distributions of ion composition, plasma temperature, and electron density are reviewed.

Banks, P. M.↗

Analysis of He-N2-CO2-UF6 laser system

Direct nuclear pumping of a CO2 laser system by the U-235(n,ff)FF reaction is examined. Calculations based on a kinetic model which takes into consideration all relevant kinetic processes indicate that dissociation of CO2 prevents the efficient operation of a nuclear pumped CO2 laser system.

Hassan, H. A.↗