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All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Modeling the Formation of Hydrate-Filled Veins in Fine-Grained Sediments from in Situ Microbial Methane

Continental margin sediments are dominantly fine-grained silt and clay, and methane hydrates in these sediments are often found in semi-vertical veins and fractures. In several instances, these hydrate veins occupy discrete depth intervals that are a few tens of meters thick and are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the gas hydrate stability zone (GHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. To investigate the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, compaction, solute diffusion, and microbial methane generation. Microbial methane generation depends on the amount of metabolizable organic carbon deposited at the seafloor, whose progressive degradation produces methane beneath the sulfate reduction zone. If the amount of organic carbon entering the methanogenic zone is kept constant in time, we found that the computed amounts of hydrate formed in discrete intervals within the GHSZ are well below those estimated from observations. On the other hand, if the deposition of organic carbon is higher in a given time interval, methane generation during burial is more intense in the corresponding sediment interval, resulting in enhanced hydrate formation. With variations in organic carbon deposition comparable to those generally observed in continental margins, our model was able to reproduce the methane hydrate contents that were estimated from drilling. These results support the suggestion that in situ microbial generation associated with transient organic carbon deposition is the source of methane that forms isolated intervals of hydrate-filled veins in fine-grained sediments.

58 GEOSCIENCES↗
NASA NTRS1993

Using rapid infrared forming to control interfaces in titanium-matrix composites

Control of the fiber-matrix reaction during composite fabrication is commonly achieved by shortening the processing time, coating the reinforcement with relatively inert materials, or adding alloying elements to retard the reaction. To minimize the processing time, a rapid IR forming (RIF) technique for metal-matrix composite fabrication has been developed. Experiments have shown that the RIF technique is a quick, simple, and low-cost process to fabricate titanium-alloy matrix composites reinforced with either silicon carbide or carbon fibers. Due to short processing times (typically on the order of 1-2 minutes in an inert atmosphere for composites with up to eight-ply reinforcements), the interfacial reaction is limited and well controlled. Composites fabricated by this technique have mechanical properties that are comparable to (in several cases, superior to) those made with conventional diffusion-bonding techniques.

Warrier, Sunil G.↗
DOE OSTI2020

Dissolution of Fluoride Salts in Hanford Tank Waste

The Direct Feed High-Level Waste (DFHLW) strategy seeks to bypass the Hanford Waste Treatment and Immobilization Plant Pretreatment Facility while retaining some processing functions to maximize waste feed loading and minimize high-level waste (HLW) waste volume. The DFHLW flowsheet needs leaching, washing, and solids concentration operations either in new or existing tanks. The effectiveness and efficiency of sludge washing has a substantial impact on DST space, mission duration, and the evaporation and low-activity waste (LAW) treatment operations required by these large wash-water additions. One target species requiring washing is fluoride. The HLW glass composition limits for fluorine drive operations to dissolve fluoride-bearing salts into the LAW fraction and thereby maximize waste loading in HLW glass. The fluoride in many high-level wastes at Hanford is predominantly in the form of fluoride-salt precipitates: villiaumite (NaF), kogarkoite (Na 3 FSO 4 ), and natrophosphate (Na 7 F(PO 4 ) 2 ·19H 2 O). Fluoride produces melter off-gas that creates corrosion risk in the off-gas system piping, while the sulfate and phosphate in the fluoride double salts kogarkoite and natrophosphate can be detrimental to glass waste loading. Fluoride salts are sparingly soluble, with solubilities ranging from approximately 40 to 130 kg per kL of pure water, and the dissolution kinetics of the three fluoride salts are not well known. Unexpected delays in a tank dissolution process could be encountered as a result of the lack of information about dissolution rates. In addition, if the double salts show transient non-stoichiometric dissolution of fluoride versus phosphate or sulfate, unexpectedly high concentrations of one of these other constituents could be produced. Washington River Protection Solutions authorized Pacific Northwest National Laboratory to collect the available data for fluoride salt dissolution rate, provide a scoping estimate of dissolution time if possible, and identify gaps in the understanding and predictive capability for estimating dissolution time. Open literature and Hanford reports were reviewed to document, understand, and (where possible) evaluate limitations on fluoride salt equilibria and dissolution kinetics, including both mass transport and surface reaction rate. Scoping estimates of dissolution time were made for mass-transfer-controlled dissolution of spherical particles of fluoride salts suspended in liquid. This is not the only potential governing mechanism; dissolution could be substantially slower if the surface reaction rate (the rate of release of ions from the surface) is the controlling mechanism. When the minimum amount of water for complete dissolution is used and the slip velocity between the liquid and suspended particles is less than or equal to the terminal settling velocity, the estimated mass-transfer rates allow 0.1 mm particles of fluoride salt to dissolve in minutes at 25 °C in water containing no other dissolved salts. Much larger solids, such as the 6-mm chunks that have been seen in heels, could take a few hours to more than a week to dissolve. The actual dissolution times will depend strongly on the actual slip velocity, the extent of particle suspension, constraint by surface reaction rates, the ratio of solvent to solid, and the presence of common ions that shift the solubility equilibria to restrict dissolution of fluoride salts.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2015

D 5h [PhSiO 1.5 ] 10 synthesis via F – catalyzed rearrangement of [PhSiO 1.5 ] n . An experimental/computational analysis of likely reaction pathways

We describe here in this paper the synthesis and analysis of the reaction pathways leading to formation of the rare D 5h decaphenylsilsesquioxane (SQ) [PhSiO 1.5 ] 10 via F – catalyzed rearrangement of [PhSiO 1.5 ] n n = 8, 12, and oligomers initially synthesized from PhSi(OEt) 3 . Isolated yields of ~50% [PhSiO 1.5 ] 10 are obtained via rearrangement of all starting materials. The recovered starting materials can be re-equilibrated using catalytic F – to generate similar yields in second batches. These yields arise because [PhSiO 1.5 ] 10 exhibits higher solubility and better energy stabilization (10 kcal mol –1 theory) in CH 2 Cl 2 compared to [PhSiO 1.5 ] 8 or [PhSiO 1.5 ] 12 . Reaction intermediates were identified using time dependent 19 F NMR and MALDI-ToF mass spectrometry eventually equilibrating to form the 8: 10 : 12 cages in a 1 : 3 : 1.3 equilibrium in CH 2 Cl 2 . Experimental results coupled with modeling using the Gamess computational package provide multiple reasonable pathways for SQ rearrangements to [RSiO 1.5 ] 10 , starting from [RSiO 1.5 ] 8 . Heats of reaction for interconversion of the model intermediates [HSiO 1.5 ] x determined computationally, were used to select the most reasonable reaction pathways. The findings support a mechanism involving activation and cleavage of a T 8 cage corner by F – attachment, followed by the corners stepwise removal as [ i.e. RSi(OH) 3 ], followed thereafter by reinsertion forming [RSiO 1.5 ] 9 –OH followed by, insertion of another corner to form [RSiO 1.5 ] 10 –(OH) 2 and finally condensation to give [RSiO 1.5 ] 10 . The most enthalpically favorable path (–24 kcal mol –1 ) involves a hybrid mechanism.

36 MATERIALS SCIENCE↗
DOE OSTI2019

The kinetic study of excited singlet oxygen atom O( 1 D) reactions with acetylene

Understanding the multi-channel dynamics of O( 1 D) reactions with unsaturated hydrocarbon molecules in low temperature reaction kinetics is critically important in stratospheric chemistry, plasma chemistry, plasma assisted fuel reforming, materials synthesis, and plasma assisted combustion. A photolysis flow reactor coupled with highly selective mid-infrared Faraday Rotation Spectroscopy (FRS) and direct ultraviolet-infrared (UV-IR) absorption spectroscopy (DAS) techniques was developed for the first time to study the multi-channel dynamics of excited singlet oxygen atom O( 1 D) reactions with C 2 H 2 and the kinetics of subsequent reactions. Time-resolved species concentrations of OH, HO 2 and H 2 O were obtained and used to develop a validated kinetic model of O(1D) reactions with C 2 H 2 . The branching ratios of O( 1 D) reaction with C 2 H 2 and subsequent HO 2 kinetics were also quantified. It is found that, contrary to O( 1 D) reactions with saturated alkanes, OH formation via direct H abstraction by O( 1 D) is negligible. The results revealed that two chain-branching and propagation reactions via direct O( 1 D) insertion are the major pathways for radical production. The present study clearly demonstrated the advantage of radical detection and kinetic studies using FRS in the effective suppression of absorption interference from non-paramagnetic hydrocarbons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Organic anion transporter 1 (OAT1/SLC22A6) enhances bioluminescence based on d-luciferin–luciferase reaction in living cells by facilitating the intracellular accumulation of d-luciferin

Highlights: • OAT1 expression in luciferase-expressing cells enhanced bioluminescence via the d-luciferin–luciferase reaction. • OAT1 mediated the intracellular accumulation of d-luciferin. • OAT1 increased visualization sensitivity of the bioluminescence emitted by the luciferase-expressing cells. Bioluminescence (BL) imaging based on d-luciferin (d-luc)–luciferase reaction allows noninvasive and real-time monitoring of luciferase-expressing cells. Because BL intensity depends on photons generated through the d-luc–luciferase reaction, an approach to increase intracellular levels of d-luc could improve the detection sensitivity. In the present study, we showed that organic anion transporter 1 (OAT1) is useful, as a d-luc transporter, in boosting the BL intensity in luciferase-expressing cells. Functional screening of several transporters showed that the expression of OAT1 in HEK293 cells stably expressing Pyrearinus termitilluminans luciferase (HEK293/eLuc) markedly enhanced BL intensity in the presence of d-luc. When OAT1 was transiently expressed in HEK293 cells, intracellular accumulation of d-luc was higher than that in control cells, and the specific d-luc uptake mediated by OAT1 was saturable with a Michaelis constant (K{sub m}) of 0.23 μM. The interaction between OAT1 and d-luc was verified using 6-carboxyfluorescein, a typical substrate of OAT1, which showed that d-luc inhibited the uptake of 6-carboxyfluorescein mediated by OAT1. BL intensity was concentration-dependent at steady states in HEK293/eLuc cells stably expressing OAT1, and followed Michaelis–Menten kinetics with an apparent K{sub m} of 0.36 μM. In addition, the enhanced BL was significantly inhibited by OAT1-specific inhibitors. Thus, OAT1-mediated transport of d-luc could be a rate-limiting step in the d-luc–luciferase reaction. Furthermore, we found that expressing OAT1 in HEK293/eLuc cells implanted subcutaneously in mice also significantly increased the BL after intraperitoneal injection of d-luc. Our findings suggest that because OAT1 is capable of transporting d-luc, it can also be used to improve visualization and monitoring of luciferase-expressing cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Temporal responsiveness of adipose-derived stem/stromal cell immune plasticity

Highlights: • Adipose-derived stem cells modulate immune responses in a plastic manner. • The persistence of pro- and anti-inflammatory phenotypes was explored over time. • IL-6 was present at all time points; IDO1 was induced after cytokine stimulation. • Phenotypes persisted 96–168 h after returning to control conditions. • Macrophages showed reaction to ASC culture but without time effect. We determined the role of time in adipose-derived stem/stromal cell (ASC) response to a model inflammatory environment. ASCs and other mesenchymal stem/stromal cells exhibit immune plasticity. We evaluated the persistence of pro- and anti-inflammatory phenotypes for ASCs exposed to a sustained or pulse inflammatory stimulus. Using qPCR, flow cytometry, and immunocytochemistry, we monitored the temporal expression and up-regulation patterns of a pro-inflammatory gene (caspase 1), a pleiotropic gene/protein (interleukin 6, IL-6), and an anti-inflammatory gene/protein (indoleamine 2, 3-dioxygenase, IDO1) after exposing ASCs to the cytokines tumor necrosis factor-α and interferon-γ. In response to sustained cytokine stimulation, we discovered that time played a role in the balance of pro- and anti-inflammatory ASC phenotypes. IL-6 was present at all time points for both cytokine-stimulated and non-stimulated conditions, whereas IDO1 was heterogeneously up-regulated in stimulated conditions at later time points. After a pulse stimulus, ASC immunoresponse remained consistent for 96–168 h. As a final measure of immune plasticity, we cultured cytokine-stimulated ASCs with blood-derived macrophages to observe macrophage polarization. While the presence of ASCs altered macrophage phenotype, there was no dependency on the length of ASC cytokine exposure time.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2010

Lunar Reconnaissance Orbiter (LRO) Thruster Control Mode Design and Flight Experience

National Aeronautics and Space Administration s (NASA) Goddard Space Flight Center (GSFC) in Greenbelt, MD, designed, built, tested, and launched the Lunar Reconnaissance Orbiter (LRO) from Cape Canaveral Air Force Station on June 18, 2009. The LRO spacecraft is the first operational spacecraft designed to support NASA s return to the Moon, as part of the Vision for Space Exploration. LRO was launched aboard an Atlas V 401 launch vehicle into a direct insertion trajectory to the Moon. Twenty-four hours after separation the propulsion system was used to perform a mid-course correction maneuver. Four days after the mid-course correction a series of propulsion maneuvers were executed to insert LRO into its commissioning orbit. The commission period lasted eighty days and this followed by a second set of thruster maneuvers that inserted LRO into its mission orbit. To date, the spacecraft has been gathering invaluable data in support of human s future return to the moon. The LRO Attitude Control Systems (ACS) contains two thruster based control modes: Delta-H and Delta-V. The design of the two controllers are similar in that they are both used for 3-axis control of the spacecraft with the Delta-H controller used for momentum management and the Delta-V controller used for orbit adjust and maintenance maneuvers. In addition to the nominal purpose of the thruster modes, the Delta-H controller also has the added capability of performing a large angle slew maneuver. A suite of ACS components are used by the thruster based control modes, for both initialization and control. For initialization purposes, a star tracker or the Kalman Filter solution is used for providing attitude knowledge and upon entrance into the thruster based control modes attitude knowledge is provided via rate propagation using a inertial reference unit (IRU). Rate information for the controller is also supplied by the IRU. Three-axis control of the spacecraft in the thruster modes is provided by eight 5-lbf class attitude control thrusters configured in two sets of four thrusters for redundancy purposes. Four additional 20-lbf class thrusters configured in two sets of two thrusters are used for Lunar Orbit Insertion maneuvers. The propulsion system is one the few systems on-board the LRO spacecraft that has built in redundancy. The Delta-H controller consists of a Proportional-Derivative (PD) controller with a structural filter on the thrusters and a Proportional controller on the reaction wheels. The PD control that employs the thrusters is used for attitude and rate control. The Proportional controller on the reaction wheels is used for commanding the wheels to a new momentum state. The ground commands used for the Delta-H controller are the system momentum vector, reaction wheel momentum, maximum expected command time, and which set of attitude control thrusters to use. The ability to command both the system momentum vector and reaction wheel momentum in the Delta-H controller provides both a capability and an additional source of operator error. Large angle slews via the Delta-H controller is achievable via this commands because these commands are used for the exit mode criteria. Setting these commands to non-consistent values prevents the mode from exiting nominally.

Hsu, Oscar C.↗
DOE OSTI2025

Cosmological parameter estimation with a joint-likelihood analysis of the cosmic microwave background and big bang nucleosynthesis

Here, we present a joint-likelihood analysis of big bang nucleosynthesis (BBN) and cosmic microwave background (CMB) data, consistently combining likelihoods and taking into account uncertainties in nuclear reaction rates for the first time. Bayesian inference is performed on the baryon abundance and the effective number of neutrino species, 𝑁 eff , using a CMB Boltzmann solver in combination with LINX , a new flexible and efficient BBN code. We marginalize over Planck nuisance parameters and nuclear rates to find 𝑁 eff =3.0⁢8$^{+0.15}_{−0.14}$, 2.9⁢4$^{+0.16}_{−0.15}$, or 2.96$^{+0.13}_{−0.14}$, for three separate reaction networks. This framework enables robust testing of the lambda cold dark matter paradigm and its variants with CMB and BBN data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Probe the Localized Electrochemical Environment Effects and Electrode Reaction Dynamics for Metal Batteries using In Situ 3D Microscopy

Uncontrollable dendrite growth is closely related to non-uniform reaction environments. However, there is a lack of understanding and analysis methods to probe the localized electrochemical environment (LEE). Here the effects of the LEE are investigated, including localized ion concentrations, current density, and electric potential, on metal plating/stripping dynamics and dendrite minimization. A novel in situ 3D microscopy technique is developed to image the morphology dynamics and deposition rate of Zn plating/stripping processes on 3D Zn–Mn anodes. Using the in situ 3D microscope, the electrode morphology changes during the reactions are directly imaged and Zn deposition rate maps at different time points are obtained. It is found that reaction kinetics are highly correlated to LEE and electrode morphology. To further quantify the LEE effects, the digital twin technique is employed that allows the accurate calculation of the electrochemical environments, such as localized ion concentrations, current density, and electric potential, which cannot be directly measured from experiments. We found that the curvature of the 3D electrode surface determines the LEE and significantly influences reaction kinetics. This provides a new strategy to minimize the dendrite formation by designing and optimizing the 3D geometry of the electrode to control the LEE.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Porous platinum mesoflowers with enhanced activity for methanol oxidation reaction

Porous Pt and Pt-Ag alloy mesoflowers (MFs) with about 2 {mu}m in diameter and high porosity were synthesized using Ag mesoflowers as sacrificial template by galvanic reaction. The silver content in Pt-Ag alloys can be facilely controlled by nitric acid treatment. And the pure Pt MFs can be obtained by selective removal of silver element from Pt{sub 72}Ag{sub 28} MFs electrochemically. Both Pt{sub 45}Ag{sub 55}, Pt{sub 72}Ag{sub 28} and pure Pt show a high catalytic performance in methanol oxidation reaction (MOR). Especially, pure Pt MFs exhibited a 2 to 3 times current density enhancement in MOR compared with the commercial used Pt black, which can be attributed to their porous nanostructure with 3-dimentional nature and small crystal sizes. - Graphical Abstract: The CVs of MOR on Pt (red) and Pt black (green) catalysts in 0.1 M HClO{sub 4} and 0.5 M CH{sub 3}OH for specific mass current. The insert shows the SEM images of two porous Pt MFs. Platinum mesoflowers (MFs) with about 2 {mu}m in diameter and high porosity were synthesised with Ag mesoflowers as sacrificial template by galvanic replacement. The porous Pt MFs exhibited a more than 3 times enhancement in electrocatalytic performance for methanol oxidation reaction compared the commercial used Pt black. Highlights: Black-Right-Pointing-Pointer Porous Pt and Pt-Ag mesoflowers (MFs) were synthesized using Ag MFs sacrifical template. Black-Right-Pointing-Pointer Pt MFs presents an improved catalytic activity in MOR compared with Pt black. Black-Right-Pointing-Pointer We provided a facile approach for the development of high performance Pt electrocatalysts for fuel cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Quantifying uncertainties due to optical potentials in one-neutron knockout reactions

One-neutron knockout reactions have been widely used to extract information about the single-particle structure of nuclei from the valley of stability to the drip lines. The interpretation of knockout data relies on reaction models, where the uncertainties are typically not accounted for. In this work, we quantify uncertainties of optical potentials used in these reaction models and propagate them, for the first time, to knockout observables using a Bayesian analysis. We study two reactions in the present paper, the first of which involves a loosely bound halo projectile, 11 Be, and the second a tightly bound projectile, 12 C. We first quantify the parametric uncertainties associated with phenomenological optical potentials. Complementing this approach, we also quantify the model uncertainties associated with the chiral forces that can be used to construct microscopic optical potentials. For the phenomenological study, we investigate the impact of the imaginary terms of the optical potential on the breakup and stripping components of the knockout cross sections as well as the impact of the angular range. For the 11 Be case, the theoretical uncertainty from the phenomenological method is on the order of the experimental uncertainty of the knockout observables; however, for the 12 C case, the theoretical uncertainty is significantly larger. Additionally, the widths of the uncertainty bands for the knockout observables obtained for the microscopic study and the phenomenological approach are of similar orders of magnitude. Based on this work we conclude that structure information inferred from the ratio of the knockout cross sections will carry a theoretical uncertainty of at least 20% for halo nuclei and at least 40% for tightly bound nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS2004

New Reduced Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes that are being developed at Glenn. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates were then used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx were obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3). The temperature of the gas entering the turbine (T4) was also correlated as a function of the initial combustor temperature (T3), equivalence ratio, water to fuel mass ratio, and pressure.

Molnar, Melissa↗
DOE OSTI2018

Total yield of reactive species originating from an atmospheric pressure plasma jet in real time

Abstract It is now well established that plasma-induced reactive species are key agents involved in many biochemical reactions. This work reports on the formation of plasma reactive species in an acidified ferrous sulfate (Fricke) solution interacting with an atmospheric pressure plasma jet (APPJ). A yield of ferric (Fe 3+ ) ions measured using in situ absorption spectroscopy was attributed to the formation of plasma reactive species provided and/or originated in the solution. The results indicated that the number of reactive species formed was proportional to plasma frequency and voltage. However, the Fe 3+ yield per pulse decreased with increased frequency. To obtain a better understanding of the processes and species involved in the chemical reactions due to plasma exposure, Fe 3+ yields were calculated and compared to the experimental data. At higher frequencies, there was insufficient time to complete all the reactions before the next pulse reached the solution; at lower frequencies, the Fe 3+ yield was higher because of the relatively longer time available for reactions to occur. In addition, the comparison between DNA damage levels and Fe 3+ yields was investigated under different experimental conditions in order to verify the usefulness of both the Fricke solution and the DNA molecule as a probe to characterize APPJs.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Real-time Atomic-scale Visualization of Reversible Copper Surface Activation during the CO Oxidation Reaction

Dynamic structural and chemical information of catalyst surface during a catalytic reaction is critical for deciphering the mechanisms governing the properties of catalysts. Transition-metal based catalysts have emerged as an important alternative to noble metal catalysts, but their catalytic mechanism remains largely elusive, complicated by dynamic structure and valence evolution. Herein, by using in situ aberration-corrected environmental transmission electron microscopy, we capture, for the first time at atomic level, the dynamic evolution of Cu surface during CO oxidation reaction. We discovered that, under reaction condition, the Cu surface is activated, typically involving 2-3 atomic layers with the formation of a reversible meta-stable phase that only exists during catalytic reactions. Further, we reveal the distinctive role of CO and O2 in the surface activation, featuring CO exposure to lead to surface roughening and consequently formation of low-coordinated Cu atoms, while O2 exposure to induce quasi-crystalline CuOx phase. Corrugated by DFT calculations, we rationalize crystalline CuOx reversibly transforms into the amorphous phase, acting as an active species to facilitate the interaction of gas reactants and catalyzing CO oxidation.

Luo, Langli↗
DOE OSTI2014

Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion

The currently existing theory of fluorescence correlation spectroscopy (FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in bulk solutions. For mesoscopic reaction-diffusion systems with nonlinear chemical reactions among a small number of molecules, a situation often encountered in single-cell biochemistry, it is expected that FCS time correlation functions of a reaction-diffusion system can deviate from the classic results of Elson and Magde [Biopolymers (1974) 13:1-27]. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems there are no closed solutions; therefore, stochastic Monte-Carlo simulations are carried out. We show that the deviation is small for a simple bimolecular reaction; the most significant deviations occur when the number of molecules is small and of the same order. Extending Delbrück-Gillespie’s theory for stochastic nonlinear reactions with rapidly stirring to reaction-diffusion systems provides a mesoscopic model for chemical and biochemical reactions at nanometric and mesoscopic level such as a single biological cell.

Del Razo, Mauricio↗
DOE OSTI2014

Dynamics and control of DNA sequence amplification

DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗