A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions.

PubMed

Chang, Ivan; Baldi, Pierre

2013-05-15

Oxidoreductases are a fundamental class of enzymes responsible for the catalysis of oxidation-reduction reactions, crucial in most bioenergetic metabolic pathways. From their common root in the ancient prebiotic environment, oxidoreductases have evolved into diverse and elaborate protein structures with specific kinetic properties and mechanisms adapted to their individual functional roles and environmental conditions. While accurate kinetic modeling of oxidoreductases is thus important, current models suffer from limitations to the steady-state domain, lack empirical validation or are too specialized to a single system or set of conditions. To address these limitations, we introduce a novel unifying modeling framework for kinetic descriptions of oxidoreductases. The framework is based on a set of seven elementary reactions that (i) form the basis for 69 pairs of enzyme state transitions for encoding various specific microscopic intra-enzyme reaction networks (micro-models), and (ii) lead to various specific macroscopic steady-state kinetic equations (macro-models) via thermodynamic assumptions. Thus, a synergistic bridge between the micro and macro kinetics can be achieved, enabling us to extract unitary rate constants, simulate reaction variance and validate the micro-models using steady-state empirical data. To help facilitate the application of this framework, we make available RedoxMech: a Mathematica™ software package that automates the generation and customization of micro-models. The Mathematica™ source code for RedoxMech, the documentation and the experimental datasets are all available from: http://www.igb.uci.edu/tools/sb/metabolic-modeling. pfbaldi@ics.uci.edu Supplementary data are available at Bioinformatics online.

The Validity of Quasi-Steady-State Approximations in Discrete Stochastic Simulations

PubMed Central

Kim, Jae Kyoung; Josić, Krešimir; Bennett, Matthew R.

2014-01-01

In biochemical networks, reactions often occur on disparate timescales and can be characterized as either fast or slow. The quasi-steady-state approximation (QSSA) utilizes timescale separation to project models of biochemical networks onto lower-dimensional slow manifolds. As a result, fast elementary reactions are not modeled explicitly, and their effect is captured by nonelementary reaction-rate functions (e.g., Hill functions). The accuracy of the QSSA applied to deterministic systems depends on how well timescales are separated. Recently, it has been proposed to use the nonelementary rate functions obtained via the deterministic QSSA to define propensity functions in stochastic simulations of biochemical networks. In this approach, termed the stochastic QSSA, fast reactions that are part of nonelementary reactions are not simulated, greatly reducing computation time. However, it is unclear when the stochastic QSSA provides an accurate approximation of the original stochastic simulation. We show that, unlike the deterministic QSSA, the validity of the stochastic QSSA does not follow from timescale separation alone, but also depends on the sensitivity of the nonelementary reaction rate functions to changes in the slow species. The stochastic QSSA becomes more accurate when this sensitivity is small. Different types of QSSAs result in nonelementary functions with different sensitivities, and the total QSSA results in less sensitive functions than the standard or the prefactor QSSA. We prove that, as a result, the stochastic QSSA becomes more accurate when nonelementary reaction functions are obtained using the total QSSA. Our work provides an apparently novel condition for the validity of the QSSA in stochastic simulations of biochemical reaction networks with disparate timescales. PMID:25099817

Hierarchical calibration and validation for modeling bench-scale solvent-based carbon capture. Part 1: Non-reactive physical mass transfer across the wetted wall column: Original Research Article: Hierarchical calibration and validation for modeling bench-scale solvent-based carbon capture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Chao; Xu, Zhijie; Lai, Canhai

A hierarchical model calibration and validation is proposed for quantifying the confidence level of mass transfer prediction using a computational fluid dynamics (CFD) model, where the solvent-based carbon dioxide (CO2) capture is simulated and simulation results are compared to the parallel bench-scale experimental data. Two unit problems with increasing level of complexity are proposed to breakdown the complex physical/chemical processes of solvent-based CO2 capture into relatively simpler problems to separate the effects of physical transport and chemical reaction. This paper focuses on the calibration and validation of the first unit problem, i.e. the CO2 mass transfer across a falling ethanolaminemore » (MEA) film in absence of chemical reaction. This problem is investigated both experimentally and numerically using nitrous oxide (N2O) as a surrogate for CO2. To capture the motion of gas-liquid interface, a volume of fluid method is employed together with a one-fluid formulation to compute the mass transfer between the two phases. Bench-scale parallel experiments are designed and conducted to validate and calibrate the CFD models using a general Bayesian calibration. Two important transport parameters, e.g. Henry’s constant and gas diffusivity, are calibrated to produce the posterior distributions, which will be used as the input for the second unit problem to address the chemical adsorption of CO2 across the MEA falling film, where both mass transfer and chemical reaction are involved.« less

Comparison of DSMC Reaction Models with QCT Reaction Rates for Nitrogen

DTIC Science & Technology

2016-07-17

The U.S. Government is joint author of the work and has the right to use, modify, reproduce, release, perform, display, or disclose the work. 13...Distribution A: Approved for Public Release, Distribution Unlimited PA #16299 Introduction • Comparison with measurements is final goal • Validation...model verification and parameter adjustment • Four chemistry models: total collision energy (TCE), quantum kinetic (QK), vibration-dissociation favoring

Modeling a Packed Bed Reactor Utilizing the Sabatier Process

NASA Technical Reports Server (NTRS)

Shah, Malay G.; Meier, Anne J.; Hintze, Paul E.

2017-01-01

A numerical model is being developed using Python which characterizes the conversion and temperature profiles of a packed bed reactor (PBR) that utilizes the Sabatier process; the reaction produces methane and water from carbon dioxide and hydrogen. While the specific kinetics of the Sabatier reaction on the RuAl2O3 catalyst pellets are unknown, an empirical reaction rate equation1 is used for the overall reaction. As this reaction is highly exothermic, proper thermal control is of the utmost importance to ensure maximum conversion and to avoid reactor runaway. It is therefore necessary to determine what wall temperature profile will ensure safe and efficient operation of the reactor. This wall temperature will be maintained by active thermal controls on the outer surface of the reactor. Two cylindrical PBRs are currently being tested experimentally and will be used for validation of the Python model. They are similar in design except one of them is larger and incorporates a preheat loop by feeding the reactant gas through a pipe along the center of the catalyst bed. The further complexity of adding a preheat pipe to the model to mimic the larger reactor is yet to be implemented and validated; preliminary validation is done using the smaller PBR with no reactant preheating. When mapping experimental values of the wall temperature from the smaller PBR into the Python model, a good approximation of the total conversion and temperature profile has been achieved. A separate CFD model incorporates more complex three-dimensional effects by including the solid catalyst pellets within the domain. The goal is to improve the Python model to the point where the results of other reactor geometry can be reasonably predicted relatively quickly when compared to the much more computationally expensive CFD approach. Once a reactor size is narrowed down using the Python approach, CFD will be used to generate a more thorough prediction of the reactors performance.

SurfKin: an ab initio kinetic code for modeling surface reactions.

PubMed

Le, Thong Nguyen-Minh; Liu, Bin; Huynh, Lam K

2014-10-05

In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas-surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water-gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts. Copyright © 2014 Wiley Periodicals, Inc.

Finding Furfural Hydrogenation Catalysts via Predictive Modelling

PubMed Central

Strassberger, Zea; Mooijman, Maurice; Ruijter, Eelco; Alberts, Albert H; Maldonado, Ana G; Orru, Romano V A; Rothenberg, Gadi

2010-01-01

Abstract We combine multicomponent reactions, catalytic performance studies and predictive modelling to find transfer hydrogenation catalysts. An initial set of 18 ruthenium-carbene complexes were synthesized and screened in the transfer hydrogenation of furfural to furfurol with isopropyl alcohol complexes gave varied yields, from 62% up to >99.9%, with no obvious structure/activity correlations. Control experiments proved that the carbene ligand remains coordinated to the ruthenium centre throughout the reaction. Deuterium-labelling studies showed a secondary isotope effect (kH:kD=1.5). Further mechanistic studies showed that this transfer hydrogenation follows the so-called monohydride pathway. Using these data, we built a predictive model for 13 of the catalysts, based on 2D and 3D molecular descriptors. We tested and validated the model using the remaining five catalysts (cross-validation, R2=0.913). Then, with this model, the conversion and selectivity were predicted for four completely new ruthenium-carbene complexes. These four catalysts were then synthesized and tested. The results were within 3% of the model’s predictions, demonstrating the validity and value of predictive modelling in catalyst optimization. PMID:23193388

A more robust model of the biodiesel reaction, allowing identification of process conditions for significantly enhanced rate and water tolerance.

PubMed

Eze, Valentine C; Phan, Anh N; Harvey, Adam P

2014-03-01

A more robust kinetic model of base-catalysed transesterification than the conventional reaction scheme has been developed. All the relevant reactions in the base-catalysed transesterification of rapeseed oil (RSO) to fatty acid methyl ester (FAME) were investigated experimentally, and validated numerically in a model implemented using MATLAB. It was found that including the saponification of RSO and FAME side reactions and hydroxide-methoxide equilibrium data explained various effects that are not captured by simpler conventional models. Both the experiment and modelling showed that the "biodiesel reaction" can reach the desired level of conversion (>95%) in less than 2min. Given the right set of conditions, the transesterification can reach over 95% conversion, before the saponification losses become significant. This means that the reaction must be performed in a reactor exhibiting good mixing and good control of residence time, and the reaction mixture must be quenched rapidly as it leaves the reactor. Copyright © 2014 Elsevier Ltd. All rights reserved.

Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds

PubMed Central

Alves, Vinicius M.; Muratov, Eugene; Fourches, Denis; Strickland, Judy; Kleinstreuer, Nicole; Andrade, Carolina H.; Tropsha, Alexander

2015-01-01

Repetitive exposure to a chemical agent can induce an immune reaction in inherently susceptible individuals that leads to skin sensitization. Although many chemicals have been reported as skin sensitizers, there have been very few rigorously validated QSAR models with defined applicability domains (AD) that were developed using a large group of chemically diverse compounds. In this study, we have aimed to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitization, and employ these models as a virtual screening tool for identifying putative sensitizers among environmental chemicals. We followed best practices for model building and validation implemented with our predictive QSAR workflow using random forest modeling technique in combination with SiRMS and Dragon descriptors. The Correct Classification Rate (CCR) for QSAR models discriminating sensitizers from non-sensitizers were 71–88% when evaluated on several external validation sets, within a broad AD, with positive (for sensitizers) and negative (for non-sensitizers) predicted rates of 85% and 79% respectively. When compared to the skin sensitization module included in the OECD QSAR toolbox as well as to the skin sensitization model in publicly available VEGA software, our models showed a significantly higher prediction accuracy for the same sets of external compounds as evaluated by Positive Predicted Rate, Negative Predicted Rate, and CCR. These models were applied to identify putative chemical hazards in the ScoreCard database of possible skin or sense organ toxicants as primary candidates for experimental validation. PMID:25560674

Structure-reactivity modeling using mixture-based representation of chemical reactions.

PubMed

Polishchuk, Pavel; Madzhidov, Timur; Gimadiev, Timur; Bodrov, Andrey; Nugmanov, Ramil; Varnek, Alexandre

2017-09-01

We describe a novel approach of reaction representation as a combination of two mixtures: a mixture of reactants and a mixture of products. In turn, each mixture can be encoded using an earlier reported approach involving simplex descriptors (SiRMS). The feature vector representing these two mixtures results from either concatenated product and reactant descriptors or the difference between descriptors of products and reactants. This reaction representation doesn't need an explicit labeling of a reaction center. The rigorous "product-out" cross-validation (CV) strategy has been suggested. Unlike the naïve "reaction-out" CV approach based on a random selection of items, the proposed one provides with more realistic estimation of prediction accuracy for reactions resulting in novel products. The new methodology has been applied to model rate constants of E2 reactions. It has been demonstrated that the use of the fragment control domain applicability approach significantly increases prediction accuracy of the models. The models obtained with new "mixture" approach performed better than those required either explicit (Condensed Graph of Reaction) or implicit (reaction fingerprints) reaction center labeling.

Validation of chemistry models employed in a particle simulation method

NASA Technical Reports Server (NTRS)

Haas, Brian L.; Mcdonald, Jeffrey D.

1991-01-01

The chemistry models employed in a statistical particle simulation method, as implemented in the Intel iPSC/860 multiprocessor computer, are validated and applied. Chemical relaxation of five-species air in these reservoirs involves 34 simultaneous dissociation, recombination, and atomic-exchange reactions. The reaction rates employed in the analytic solutions are obtained from Arrhenius experimental correlations as functions of temperature for adiabatic gas reservoirs in thermal equilibrium. Favorable agreement with the analytic solutions validates the simulation when applied to relaxation of O2 toward equilibrium in reservoirs dominated by dissociation and recombination, respectively, and when applied to relaxation of air in the temperature range 5000 to 30,000 K. A flow of O2 over a circular cylinder at high Mach number is simulated to demonstrate application of the method to multidimensional reactive flows.

Resolution of Forces and Strain Measurements from an Acoustic Ground Test

NASA Technical Reports Server (NTRS)

Smith, Andrew M.; LaVerde, Bruce T.; Hunt, Ronald; Waldon, James M.

2013-01-01

The Conservatism in Typical Vibration Tests was Demonstrated: Vibration test at component level produced conservative force reactions by approximately a factor of 4 (approx.12 dB) as compared to the integrated acoustic test in 2 out of 3 axes. Reaction Forces Estimated at the Base of Equipment Using a Finite Element Based Method were Validated: FEM based estimate of interface forces may be adequate to guide development of vibration test criteria with less conservatism. Element Forces Estimated in Secondary Structure Struts were Validated: Finite element approach provided best estimate of axial strut forces in frequency range below 200 Hz where a rigid lumped mass assumption for the entire electronics box was valid. Models with enough fidelity to represent diminishing apparent mass of equipment are better suited for estimating force reactions across the frequency range. Forward Work: Demonstrate the reduction in conservatism provided by; Current force limited approach and an FEM guided approach. Validate proposed CMS approach to estimate coupled response from uncoupled system characteristics for vibroacoustics.

Validation of the MCNP computational model for neutron flux distribution with the neutron activation analysis measurement

NASA Astrophysics Data System (ADS)

Tiyapun, K.; Chimtin, M.; Munsorn, S.; Somchit, S.

2015-05-01

The objective of this work is to demonstrate the method for validating the predication of the calculation methods for neutron flux distribution in the irradiation tubes of TRIGA research reactor (TRR-1/M1) using the MCNP computer code model. The reaction rate using in the experiment includes 27Al(n, α)24Na and 197Au(n, γ)198Au reactions. Aluminium (99.9 wt%) and gold (0.1 wt%) foils and the gold foils covered with cadmium were irradiated in 9 locations in the core referred to as CT, C8, C12, F3, F12, F22, F29, G5, and G33. The experimental results were compared to the calculations performed using MCNP which consisted of the detailed geometrical model of the reactor core. The results from the experimental and calculated normalized reaction rates in the reactor core are in good agreement for both reactions showing that the material and geometrical properties of the reactor core are modelled very well. The results indicated that the difference between the experimental measurements and the calculation of the reactor core using the MCNP geometrical model was below 10%. In conclusion the MCNP computational model which was used to calculate the neutron flux and reaction rate distribution in the reactor core can be used for others reactor core parameters including neutron spectra calculation, dose rate calculation, power peaking factors calculation and optimization of research reactor utilization in the future with the confidence in the accuracy and reliability of the calculation.

Semisupervised Gaussian Process for Automated Enzyme Search.

PubMed

Mellor, Joseph; Grigoras, Ioana; Carbonell, Pablo; Faulon, Jean-Loup

2016-06-17

Synthetic biology is today harnessing the design of novel and greener biosynthesis routes for the production of added-value chemicals and natural products. The design of novel pathways often requires a detailed selection of enzyme sequences to import into the chassis at each of the reaction steps. To address such design requirements in an automated way, we present here a tool for exploring the space of enzymatic reactions. Given a reaction and an enzyme the tool provides a probability estimate that the enzyme catalyzes the reaction. Our tool first considers the similarity of a reaction to known biochemical reactions with respect to signatures around their reaction centers. Signatures are defined based on chemical transformation rules by using extended connectivity fingerprint descriptors. A semisupervised Gaussian process model associated with the similar known reactions then provides the probability estimate. The Gaussian process model uses information about both the reaction and the enzyme in providing the estimate. These estimates were validated experimentally by the application of the Gaussian process model to a newly identified metabolite in Escherichia coli in order to search for the enzymes catalyzing its associated reactions. Furthermore, we show with several pathway design examples how such ability to assign probability estimates to enzymatic reactions provides the potential to assist in bioengineering applications, providing experimental validation to our proposed approach. To the best of our knowledge, the proposed approach is the first application of Gaussian processes dealing with biological sequences and chemicals, the use of a semisupervised Gaussian process framework is also novel in the context of machine learning applied to bioinformatics. However, the ability of an enzyme to catalyze a reaction depends on the affinity between the substrates of the reaction and the enzyme. This affinity is generally quantified by the Michaelis constant KM. Therefore, we also demonstrate using Gaussian process regression to predict KM given a substrate-enzyme pair.

Modelling of polymer photodegradation for solar cell modules

NASA Technical Reports Server (NTRS)

Somersall, A. C.; Guillet, J. E.

1981-01-01

A computer program developed to model and calculate by numerical integration the varying concentrations of chemical species formed during photooxidation of a polymeric material over time, using as input data a choice set of elementary reactions, corresponding rate constants and a convenient set of starting conditions is evaluated. Attempts were made to validate the proposed mechanism by experimentally monitoring the photooxidation products of small liquid alkane which are useful starting models for ethylene segments of polymers like EVA. The model system proved in appropriate for the intended purposes. Another validation model is recommended.

Gas-phase reactions of uranate ions, UO(2)(-), UO(3)(-), UO(4)(-), and UO(4)H(-), with methanol: a convergence of experiment and theory.

PubMed

Michelini, Maria Del Carmen; Marçalo, Joaquim; Russo, Nino; Gibson, John K

2010-04-19

Bimolecular reactions of uranium oxide molecular anions with methanol have been studied experimentally, by Fourier transform ion cyclotron resonance mass spectrometry, and computationally, by density functional theory (DFT). The primary goals were to provide fundamental insights into mechanistic and structural details of model reactions of uranium oxides with organics, and to examine the validity of theoretical modeling of these types of reactions. The ions UO(3)(-), UO(4)(-), and UO(4)H(-) each reacted with methanol to give a singular product; the primary products each exhibited sequential reactions with two additional methanol molecules to again give singular products. The observed reactions were elimination of water, formaldehyde, or hydrogen, and in one case addition of a methanol molecule. The potential energy profiles were computed for each reaction, and isotopic labeling experiments were performed to probe the validity of the computed mechanisms and structures-in each case where the experiments could be compared with the theory there was concurrence, clearly establishing the efficacy of the employed DFT methodologies for these and related reaction systems. The DFT results were furthermore in accord with the surprisingly inert nature of UO(2)(-). The results provide a basis to understand mechanisms of key reactions of uranium oxides with organics, and a foundation to extend DFT methodologies to more complex actinide systems which are not amenable to such direct experimental studies.

Assisted Sonication vs Conventional Transesterification Numerical Simulation and Sensitivity Study

NASA Astrophysics Data System (ADS)

Janajreh, Isam; Noorul Hussain, Mohammed; El Samad, Tala

2015-10-01

Transeterification is known as slow reaction that can take over several hours to complete as the two immiscible liquid reactants combine to form biodiesel and the less favorable glycerol. The quest of finding the perfect catalyst, optimal operational conditions, and reactor configuration to accelerate the reaction in mere few minutes that ensures high quality biodiesel, in economically viable way is coming along with sonication. This drastic reduction is a key enabler for the development of a continuous processing that otherwise is fairly costly and low throughput using conventional method. The reaction kinetics of sonication assisted as inferred by several authors is several time faster and this work implements these rates in a high fidelity numerical simulation model. This flow model is based on Navier-Stokes equations coupled with energy equation for non-isothermal flow and the transport equations of the multiple reactive species. The model is initially validated against experimental data from previous work of the authors using an annular reactor configuration. Following the validation, comparison of the reaction rate is shown to gain more insight to the distribution of the reaction and its attained rates. The two models (conventional and sonication) then compared on the basis of their sensitivity to the methane to oil molar ratio as the most pronounced process parameter. Both the exit reactor yield and the distribution of the species are evaluated with favorable yield under sonication process. These results pave the way to build a more robust process intensified reactor having an integrated selective heterogeneous catalyst to steer the reaction. This can avoid the downstream cleaning processes, cutting reaction time, and render economic benefit to the process.

Kinetic modeling of electro-Fenton reaction in aqueous solution.

PubMed

Liu, H; Li, X Z; Leng, Y J; Wang, C

2007-03-01

To well describe the electro-Fenton (E-Fenton) reaction in aqueous solution, a new kinetic model was established according to the generally accepted mechanism of E-Fenton reaction. The model has special consideration on the rates of hydrogen peroxide (H(2)O(2)) generation and consumption in the reaction solution. The model also embraces three key operating factors affecting the organic degradation in the E-Fenton reaction, including current density, dissolved oxygen concentration and initial ferrous ion concentration. This analytical model was then validated by the experiments of phenol degradation in aqueous solution. The experiments demonstrated that the H(2)O(2) gradually built up with time and eventually approached its maximum value in the reaction solution. The experiments also showed that phenol was degraded at a slow rate at the early stage of the reaction, a faster rate during the middle stage, and a slow rate again at the final stage. It was confirmed in all experiments that the curves of phenol degradation (concentration vs. time) appeared to be an inverted "S" shape. The experimental data were fitted using both the normal first-order model and our new model, respectively. The goodness of fittings demonstrated that the new model could better fit the experimental data than the first-order model appreciably, which indicates that this analytical model can better describe the kinetics of the E-Fenton reaction mathematically and also chemically.

Heating-Rate-Coupled Model for Hydrogen Reduction of JSC-1A

NASA Technical Reports Server (NTRS)

Hegde, U.; Balasubramaniam, R.; Gokoglu, S. A.

2010-01-01

A previously developed and validated model for hydrogen reduction of JSC-1A for a constant reaction-bed temperature is extended to account for reaction during the bed heat-up period. A quasisteady approximation is used wherein an expression is derived for a single average temperature of reaction during the heat-up process by employing an Arrhenius expression for regolith conversion. Subsequently, the regolith conversion during the heat-up period is obtained by using this representative temperature. Accounting for the reaction during heat-up provides a better estimate of the reaction time needed at the desired regolith-bed operating temperature. Implications for the efficiency of the process, as measured by the energy required per unit mass of oxygen produced, are also indicated.

Modelling of spatial contaminant probabilities of occurrence of chlorinated hydrocarbons in an urban aquifer.

PubMed

Greis, Tillman; Helmholz, Kathrin; Schöniger, Hans Matthias; Haarstrick, Andreas

2012-06-01

In this study, a 3D urban groundwater model is presented which serves for calculation of multispecies contaminant transport in the subsurface on the regional scale. The total model consists of two submodels, the groundwater flow and reactive transport model, and is validated against field data. The model equations are solved applying finite element method. A sensitivity analysis is carried out to perform parameter identification of flow, transport and reaction processes. Coming from the latter, stochastic variation of flow, transport, and reaction input parameters and Monte Carlo simulation are used in calculating probabilities of pollutant occurrence in the domain. These probabilities could be part of determining future spots of contamination and their measure of damages. Application and validation is exemplarily shown for a contaminated site in Braunschweig (Germany), where a vast plume of chlorinated ethenes pollutes the groundwater. With respect to field application, the methods used for modelling reveal feasible and helpful tools to assess natural attenuation (MNA) and the risk that might be reduced by remediation actions.

Topological characterization versus synchronization for assessing (or not) dynamical equivalence

NASA Astrophysics Data System (ADS)

Letellier, Christophe; Mangiarotti, Sylvain; Sendiña-Nadal, Irene; Rössler, Otto E.

2018-04-01

Model validation from experimental data is an important and not trivial topic which is too often reduced to a simple visual inspection of the state portrait spanned by the variables of the system. Synchronization was suggested as a possible technique for model validation. By means of a topological analysis, we revisited this concept with the help of an abstract chemical reaction system and data from two electrodissolution experiments conducted by Jack Hudson's group. The fact that it was possible to synchronize topologically different global models led us to conclude that synchronization is not a recommendable technique for model validation. A short historical preamble evokes Jack Hudson's early career in interaction with Otto E. Rössler.

Unimolecular diffusion-mediated reactions with a nonrandom time-modulated absorbing barrier

NASA Technical Reports Server (NTRS)

Bashford, D.; Weaver, D. L.

1986-01-01

A diffusion-reaction model with time-dependent reactivity is formulated and applied to unimolecular reactions. The model is solved exactly numerically and approximately analytically for the unreacted fraction as a function of time. It is shown that the approximate analytical solution is valid even when the system is far from equilibrium, and when the reactivity probability is more complicated than a square-wave function of time. A discussion is also given of an approach to problems of this type using a stochastically fluctuating reactivity, and the first-passage time for a particular example is derived.

Modeling and simulation of pressure waves generated by nano-thermite reactions

NASA Astrophysics Data System (ADS)

Martirosyan, Karen S.; Zyskin, Maxim; Jenkins, Charles M.; (Yuki) Horie, Yasuyuki

2012-11-01

This paper reports the modeling of pressure waves from the explosive reaction of nano-thermites consisting of mixtures of nanosized aluminum and oxidizer granules. Such nanostructured thermites have higher energy density (up to 26 kJ/cm3) and can generate a transient pressure pulse four times larger than that from trinitrotoluene (TNT) based on volume equivalence. A plausible explanation for the high pressure generation is that the reaction times are much shorter than the time for a shock wave to propagate away from the reagents region so that all the reaction energy is dumped into the gaseous products almost instantaneously and thereby a strong shock wave is generated. The goal of the modeling is to characterize the gas dynamic behavior for thermite reactions in a cylindrical reaction chamber and to model the experimentally measured pressure histories. To simplify the details of the initial stage of the explosive reaction, it is assumed that the reaction generates a one dimensional shock wave into an air-filled cylinder and propagates down the tube in a self-similar mode. Experimental data for Al/Bi2O3 mixtures were used to validate the model with attention focused on the ratio of specific heats and the drag coefficient. Model predictions are in good agreement with the measured pressure histories.

A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions.

PubMed

Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C; Brooks, Scott C; Pace, Molly N; Kim, Young-Jin; Jardine, Philip M; Watson, David B

2007-06-16

This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.

Modeling of the oxidation of methyl esters—Validation for methyl hexanoate, methyl heptanoate, and methyl decanoate in a jet-stirred reactor

PubMed Central

Glaude, Pierre Alexandre; Herbinet, Olivier; Bax, Sarah; Biet, Joffrey; Warth, Valérie; Battin-Leclerc, Frédérique

2013-01-01

The modeling of the oxidation of methyl esters was investigated and the specific chemistry, which is due to the presence of the ester group in this class of molecules, is described. New reactions and rate parameters were defined and included in the software EXGAS for the automatic generation of kinetic mechanisms. Models generated with EXGAS were successfully validated against data from the literature (oxidation of methyl hexanoate and methyl heptanoate in a jet-stirred reactor) and a new set of experimental results for methyl decanoate. The oxidation of this last species was investigated in a jet-stirred reactor at temperatures from 500 to 1100 K, including the negative temperature coefficient region, under stoichiometric conditions, at a pressure of 1.06 bar and for a residence time of 1.5 s: more than 30 reaction products, including olefins, unsaturated esters, and cyclic ethers, were quantified and successfully simulated. Flow rate analysis showed that reactions pathways for the oxidation of methyl esters in the low-temperature range are similar to that of alkanes. PMID:23710076

Model validation of simple-graph representations of metabolism

PubMed Central

Holme, Petter

2009-01-01

The large-scale properties of chemical reaction systems, such as metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information, lists of chemical reactions, available in databases. Even for the simplest type of graph representation, this reduction can be done in several ways. We investigate different simple network representations by testing how well they encode information about one biologically important network structure—network modularity (the propensity for edges to be clustered into dense groups that are sparsely connected between each other). To achieve this goal, we design a model of reaction systems where network modularity can be controlled and measure how well the reduction to simple graphs captures the modular structure of the model reaction system. We find that the network types that best capture the modular structure of the reaction system are substrate–product networks (where substrates are linked to products of a reaction) and substance networks (with edges between all substances participating in a reaction). Furthermore, we argue that the proposed model for reaction systems with tunable clustering is a general framework for studies of how reaction systems are affected by modularity. To this end, we investigate statistical properties of the model and find, among other things, that it recreates correlations between degree and mass of the molecules. PMID:19158012

A measurement model for general noise reaction in response to aircraft noise.

PubMed

Kroesen, Maarten; Schreckenberg, Dirk

2011-01-01

In this paper a measurement model for general noise reaction (GNR) in response to aircraft noise is developed to assess the performance of aircraft noise annoyance and a direct measure of general reaction as indicators of this concept. For this purpose GNR is conceptualized as a superordinate latent construct underlying particular manifestations. This conceptualization is empirically tested through estimation of a second-order factor model. Data from a community survey at Frankfurt Airport are used for this purpose (N=2206). The data fit the hypothesized factor structure well and support the conceptualization of GNR as a superordinate construct. It is concluded that noise annoyance and a direct measure of general reaction to noise capture a large part of the negative feelings and emotions in response to aircraft noise but are unable to capture all relevant variance. The paper concludes with recommendations for the valid measurement of community reaction and several directions for further research.

Noble metal catalyzed aqueous phase hydrogenation and hydrodeoxygenation of lignin-derived pyrolysis oil and related model compounds.

PubMed

Mu, Wei; Ben, Haoxi; Du, Xiaotang; Zhang, Xiaodan; Hu, Fan; Liu, Wei; Ragauskas, Arthur J; Deng, Yulin

2014-12-01

Aqueous phase hydrodeoxygenation of lignin pyrolysis oil and related model compounds were investigated using four noble metals supported on activated carbon. The hydrodeoxygenation of guaiacol has three major reaction pathways and the demethylation reaction, mainly catalyzed by Pd, Pt and Rh, produces catechol as the products. The presence of catechol and guaiacol in the reaction is responsible for the coke formation and the catalysts deactivation. As expected, there was a significant decrease in the specific surface area of Pd, Pt and Rh catalysts during the catalytic reaction because of the coke deposition. In contrast, no catechol was produced from guaiacol when Ru was used so a completely hydrogenation was accomplished. The lignin pyrolysis oil upgrading with Pt and Ru catalysts further validated the reaction mechanism deduced from model compounds. Fully hydrogenated bio-oil was produced with Ru catalyst. Copyright © 2014 Elsevier Ltd. All rights reserved.

Iterated reaction graphs: simulating complex Maillard reaction pathways.

PubMed

Patel, S; Rabone, J; Russell, S; Tissen, J; Klaffke, W

2001-01-01

This study investigates a new method of simulating a complex chemical system including feedback loops and parallel reactions. The practical purpose of this approach is to model the actual reactions that take place in the Maillard process, a set of food browning reactions, in sufficient detail to be able to predict the volatile composition of the Maillard products. The developed framework, called iterated reaction graphs, consists of two main elements: a soup of molecules and a reaction base of Maillard reactions. An iterative process loops through the reaction base, taking reactants from and feeding products back to the soup. This produces a reaction graph, with molecules as nodes and reactions as arcs. The iterated reaction graph is updated and validated by comparing output with the main products found by classical gas-chromatographic/mass spectrometric analysis. To ensure a realistic output and convergence to desired volatiles only, the approach contains a number of novel elements: rate kinetics are treated as reaction probabilities; only a subset of the true chemistry is modeled; and the reactions are blocked into groups.

Modeling marine oily wastewater treatment by a probabilistic agent-based approach.

PubMed

Jing, Liang; Chen, Bing; Zhang, Baiyu; Ye, Xudong

2018-02-01

This study developed a novel probabilistic agent-based approach for modeling of marine oily wastewater treatment processes. It begins first by constructing a probability-based agent simulation model, followed by a global sensitivity analysis and a genetic algorithm-based calibration. The proposed modeling approach was tested through a case study of the removal of naphthalene from marine oily wastewater using UV irradiation. The removal of naphthalene was described by an agent-based simulation model using 8 types of agents and 11 reactions. Each reaction was governed by a probability parameter to determine its occurrence. The modeling results showed that the root mean square errors between modeled and observed removal rates were 8.73 and 11.03% for calibration and validation runs, respectively. Reaction competition was analyzed by comparing agent-based reaction probabilities, while agents' heterogeneity was visualized by plotting their real-time spatial distribution, showing a strong potential for reactor design and process optimization. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of a Detailed Volumetric Finite Element Model of the Spine to Simulate Surgical Correction of Spinal Deformities

PubMed Central

Driscoll, Mark; Mac-Thiong, Jean-Marc; Labelle, Hubert; Parent, Stefan

2013-01-01

A large spectrum of medical devices exists; it aims to correct deformities associated with spinal disorders. The development of a detailed volumetric finite element model of the osteoligamentous spine would serve as a valuable tool to assess, compare, and optimize spinal devices. Thus the purpose of the study was to develop and initiate validation of a detailed osteoligamentous finite element model of the spine with simulated correction from spinal instrumentation. A finite element of the spine from T1 to L5 was developed using properties and geometry from the published literature and patient data. Spinal instrumentation, consisting of segmental translation of a scoliotic spine, was emulated. Postoperative patient and relevant published data of intervertebral disc stress, screw/vertebra pullout forces, and spinal profiles was used to evaluate the models validity. Intervertebral disc and vertebral reaction stresses respected published in vivo, ex vivo, and in silico values. Screw/vertebra reaction forces agreed with accepted pullout threshold values. Cobb angle measurements of spinal deformity following simulated surgical instrumentation corroborated with patient data. This computational biomechanical analysis validated a detailed volumetric spine model. Future studies seek to exploit the model to explore the performance of corrective spinal devices. PMID:23991426

Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alves, Vinicius M.; Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599; Muratov, Eugene

Repetitive exposure to a chemical agent can induce an immune reaction in inherently susceptible individuals that leads to skin sensitization. Although many chemicals have been reported as skin sensitizers, there have been very few rigorously validated QSAR models with defined applicability domains (AD) that were developed using a large group of chemically diverse compounds. In this study, we have aimed to compile, curate, and integrate the largest publicly available dataset related to chemically-induced skin sensitization, use this data to generate rigorously validated and QSAR models for skin sensitization, and employ these models as a virtual screening tool for identifying putativemore » sensitizers among environmental chemicals. We followed best practices for model building and validation implemented with our predictive QSAR workflow using Random Forest modeling technique in combination with SiRMS and Dragon descriptors. The Correct Classification Rate (CCR) for QSAR models discriminating sensitizers from non-sensitizers was 71–88% when evaluated on several external validation sets, within a broad AD, with positive (for sensitizers) and negative (for non-sensitizers) predicted rates of 85% and 79% respectively. When compared to the skin sensitization module included in the OECD QSAR Toolbox as well as to the skin sensitization model in publicly available VEGA software, our models showed a significantly higher prediction accuracy for the same sets of external compounds as evaluated by Positive Predicted Rate, Negative Predicted Rate, and CCR. These models were applied to identify putative chemical hazards in the Scorecard database of possible skin or sense organ toxicants as primary candidates for experimental validation. - Highlights: • It was compiled the largest publicly-available skin sensitization dataset. • Predictive QSAR models were developed for skin sensitization. • Developed models have higher prediction accuracy than OECD QSAR Toolbox. • Putative chemical hazards in the Scorecard database were found using our models.« less

A stochastic modeling of isotope exchange reactions in glutamine synthetase

NASA Astrophysics Data System (ADS)

Kazmiruk, N. V.; Boronovskiy, S. E.; Nartsissov, Ya R.

2017-11-01

The model presented in this work allows simulation of isotopic exchange reactions at chemical equilibrium catalyzed by a glutamine synthetase. To simulate the functioning of the enzyme the algorithm based on the stochastic approach was applied. The dependence of exchange rates for 14C and 32P on metabolite concentration was estimated. The simulation results confirmed the hypothesis of the ascertained validity for preferred order random binding mechanism. Corresponding values of K0.5 were also obtained.

Laminar flamelet modeling of turbulent diffusion flames

NASA Technical Reports Server (NTRS)

Mell, W. E.; Kosaly, G.; Planche, O.; Poinsot, T.; Ferziger, J. H.

1990-01-01

In modeling turbulent combustion, decoupling the chemistry from the turbulence is of great practical significance. In cases in which the equilibrium chemistry model breaks down, laminar flamelet modeling (LFM) is a promising approach to decoupling. Here, the validity of this approach is investigated using direct numerical simulation of a simple chemical reaction in two-dimensional turbulence.

Localization of (photo)respiration and CO2 re-assimilation in tomato leaves investigated with a reaction-diffusion model

PubMed Central

Berghuijs, Herman N. C.; Yin, Xinyou; Ho, Q. Tri; Verboven, Pieter; Nicolaï, Bart M.

2017-01-01

The rate of photosynthesis depends on the CO2 partial pressure near Rubisco, Cc, which is commonly calculated by models using the overall mesophyll resistance. Such models do not explain the difference between the CO2 level in the intercellular air space and Cc mechanistically. This problem can be overcome by reaction-diffusion models for CO2 transport, production and fixation in leaves. However, most reaction-diffusion models are complex and unattractive for procedures that require a large number of runs, like parameter optimisation. This study provides a simpler reaction-diffusion model. It is parameterized by both leaf physiological and leaf anatomical data. The anatomical data consisted of the thickness of the cell wall, cytosol and stroma, and the area ratios of mesophyll exposed to the intercellular air space to leaf surfaces and exposed chloroplast to exposed mesophyll surfaces. The model was used directly to estimate photosynthetic parameters from a subset of the measured light and CO2 response curves; the remaining data were used for validation. The model predicted light and CO2 response curves reasonably well for 15 days old tomato (cv. Admiro) leaves, if (photo)respiratory CO2 release was assumed to take place in the inner cytosol or in the gaps between the chloroplasts. The model was also used to calculate the fraction of CO2 produced by (photo)respiration that is re-assimilated in the stroma, and this fraction ranged from 56 to 76%. In future research, the model should be further validated to better understand how the re-assimilation of (photo)respired CO2 is affected by environmental conditions and physiological parameters. PMID:28880924

Localization of (photo)respiration and CO2 re-assimilation in tomato leaves investigated with a reaction-diffusion model.

PubMed

Berghuijs, Herman N C; Yin, Xinyou; Ho, Q Tri; Retta, Moges A; Verboven, Pieter; Nicolaï, Bart M; Struik, Paul C

2017-01-01

The rate of photosynthesis depends on the CO2 partial pressure near Rubisco, Cc, which is commonly calculated by models using the overall mesophyll resistance. Such models do not explain the difference between the CO2 level in the intercellular air space and Cc mechanistically. This problem can be overcome by reaction-diffusion models for CO2 transport, production and fixation in leaves. However, most reaction-diffusion models are complex and unattractive for procedures that require a large number of runs, like parameter optimisation. This study provides a simpler reaction-diffusion model. It is parameterized by both leaf physiological and leaf anatomical data. The anatomical data consisted of the thickness of the cell wall, cytosol and stroma, and the area ratios of mesophyll exposed to the intercellular air space to leaf surfaces and exposed chloroplast to exposed mesophyll surfaces. The model was used directly to estimate photosynthetic parameters from a subset of the measured light and CO2 response curves; the remaining data were used for validation. The model predicted light and CO2 response curves reasonably well for 15 days old tomato (cv. Admiro) leaves, if (photo)respiratory CO2 release was assumed to take place in the inner cytosol or in the gaps between the chloroplasts. The model was also used to calculate the fraction of CO2 produced by (photo)respiration that is re-assimilated in the stroma, and this fraction ranged from 56 to 76%. In future research, the model should be further validated to better understand how the re-assimilation of (photo)respired CO2 is affected by environmental conditions and physiological parameters.

Numerical simulation of two-dimensional flow over a heated carbon surface with coupled heterogeneous and homogeneous reactions

NASA Astrophysics Data System (ADS)

Johnson, Ryan Federick; Chelliah, Harsha Kumar

2017-01-01

For a range of flow and chemical timescales, numerical simulations of two-dimensional laminar flow over a reacting carbon surface were performed to understand further the complex coupling between heterogeneous and homogeneous reactions. An open-source computational package (OpenFOAM®) was used with previously developed lumped heterogeneous reaction models for carbon surfaces and a detailed homogeneous reaction model for CO oxidation. The influence of finite-rate chemical kinetics was explored by varying the surface temperatures from 1800 to 2600 K, while flow residence time effects were explored by varying the free-stream velocity up to 50 m/s. The reacting boundary layer structure dependence on the residence time was analysed by extracting the ratio of chemical source and species diffusion terms. The important contributions of radical species reactions on overall carbon removal rate, which is often neglected in multi-dimensional simulations, are highlighted. The results provide a framework for future development and validation of lumped heterogeneous reaction models based on multi-dimensional reacting flow configurations.

Application of the DART Code for the Assessment of Advanced Fuel Behavior

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rest, J.; Totev, T.

2007-07-01

The Dispersion Analysis Research Tool (DART) code is a dispersion fuel analysis code that contains mechanistically-based fuel and reaction-product swelling models, a one dimensional heat transfer analysis, and mechanical deformation models. DART has been used to simulate the irradiation behavior of uranium oxide, uranium silicide, and uranium molybdenum aluminum dispersion fuels, as well as their monolithic counterparts. The thermal-mechanical DART code has been validated against RERTR tests performed in the ATR for irradiation data on interaction thickness, fuel, matrix, and reaction product volume fractions, and plate thickness changes. The DART fission gas behavior model has been validated against UO{sub 2}more » fission gas release data as well as measured fission gas-bubble size distributions. Here DART is utilized to analyze various aspects of the observed bubble growth in U-Mo/Al interaction product. (authors)« less

Supercritical water oxidation of quinazoline: Reaction kinetics and modeling.

PubMed

Gong, Yanmeng; Guo, Yang; Wang, Shuzhong; Song, Wenhan; Xu, Donghai

2017-03-01

This paper presents a first quantitative kinetic model for supercritical water oxidation (SCWO) of quinazoline that describes the formation and interconversion of intermediates and final products at 673-873 K. The set of 11 reaction pathways for phenol, pyrimidine, naphthalene, NH 3 , etc, involved in the simplified reaction network proved sufficient for fitting the experimental results satisfactorily. We validated the model prediction ability on CO 2 yields at initial quinazoline loading not used in the parameter estimation. Reaction rate analysis and sensitivity analysis indicate that nearly all reactions reach their thermodynamic equilibrium within 300 s. The pyrimidine yielding from quinazoline is the dominant ring-opening pathway and provides a significant contribution to CO 2 formation. Low sensitivity of NH 3 decomposition rate to concentration confirms its refractory nature in SCWO. Nitrogen content in liquid products decreases whereas that in gaseous phase increases as reaction time prolonged. The nitrogen predicted by the model in gaseous phase combined with the experimental nitrogen in liquid products gives an accurate nitrogen balance of conversion process. Copyright © 2016 Elsevier Ltd. All rights reserved.

STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies.

PubMed

Hepburn, Iain; Chen, Weiliang; Wils, Stefan; De Schutter, Erik

2012-05-10

Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. We describe STEPS, a stochastic reaction-diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction-diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. STEPS simulates models of cellular reaction-diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/

Validation of a dynamic linked segment model to calculate joint moments in lifting.

PubMed

de Looze, M P; Kingma, I; Bussmann, J B; Toussaint, H M

1992-08-01

A two-dimensional dynamic linked segment model was constructed and applied to a lifting activity. Reactive forces and moments were calculated by an instantaneous approach involving the application of Newtonian mechanics to individual adjacent rigid segments in succession. The analysis started once at the feet and once at a hands/load segment. The model was validated by comparing predicted external forces and moments at the feet or at a hands/load segment to actual values, which were simultaneously measured (ground reaction force at the feet) or assumed to be zero (external moments at feet and hands/load and external forces, beside gravitation, at hands/load). In addition, results of both procedures, in terms of joint moments, including the moment at the intervertebral disc between the fifth lumbar and first sacral vertebra (L5-S1), were compared. A correlation of r = 0.88 between calculated and measured vertical ground reaction forces was found. The calculated external forces and moments at the hands showed only minor deviations from the expected zero level. The moments at L5-S1, calculated starting from feet compared to starting from hands/load, yielded a coefficient of correlation of r = 0.99. However, moments calculated from hands/load were 3.6% (averaged values) and 10.9% (peak values) higher. This difference is assumed to be due mainly to erroneous estimations of the positions of centres of gravity and joint rotation centres. The estimation of the location of L5-S1 rotation axis can affect the results significantly. Despite the numerous studies estimating the load on the low back during lifting on the basis of linked segment models, only a few attempts to validate these models have been made. This study is concerned with the validity of the presented linked segment model. The results support the model's validity. Effects of several sources of error threatening the validity are discussed. Copyright © 1992. Published by Elsevier Ltd.

Determination of kinetic data for soot oxidation: Modeling of competition between oxygen diffusion and reaction during thermogravimetric analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilot, P.; Bonnefoy, F.; Marcuccilli, F.

1993-10-01

Kinetic data concerning carbon black oxidation in the temperature range between 600 and 900 C have been obtained using thermogravimetric analysis. Modeling of diffusion in a boundary layer above the pan and inside the porous medium coupled to oxygen reaction with carbon black is necessary to obtain kinetic constants as a function of temperature. These calculations require the knowledge of the oxidation rate at a given constant temperature as a function of the initial mass loading m[sub o]. This oxidation rate, expressed in milligrams of soot consumed per second and per milligram of initial soot loading, decreases when m[sub o]more » increases, in agreement with a reaction in an intermediary regime where the kinetics and the oxygen diffusion operate. The equivalent diffusivity of oxygen inside the porous medium is evaluated assuming two degrees of porosity: between soot aggregates and inside each aggregate. Below 700 C an activation energy of about 103 kJ/mol can be related to a combustion reaction probably kinetically controlled. Beyond 700 C the activation energy of about 20 kJ/ mol corresponds to a reaction essentially controlled by oxygen diffusion leading to a constant density oxidation with oxygen consumption at or near the particle surface. To validate these data, they are used in the modeling of a Diesel particulate trap regeneration. In this particular case, the oxidizing flux is forced across the carbon black deposit, oxygen diffusion being insignificant. A good agreement between experimental results and model predictions is obtained, proving the rate constants validity.« less

[Preliminary study on evaluation system of mental workers strain based on primary and middle school teachers].

PubMed

Lian, Yulong; Liu, Jiwen; Zhang, Chen; Yuan, Fang

2010-09-01

To use primary and middle schools teacher as samples to preliminarily build the mental work stress effect evaluation system, providing the methological platform for the research on the stress effect mechanism and mental workers interference measures. 851 teachers in primary and middle schools were selected with randomly stratified cluster methods. Use ISTA 6.0 and Life Events Evaluation Table to measure the stress factors, and use Work Tension Reaction Questionnaire, Symptom Self-Evaluation Table Questionnaire, and General Happiness Sensing Table to measure psychological stress reaction, blood sugar and blood fat, blood cortical, ACTH, nerve behavior function, for measuring physiological stress reaction. The Comprehensive Working Ability Index Table to measure working ability. And then use the mathematical model to build the mental workers stress effect evaluation system. And apply the simple random sampling method to select 400 environmental protection workers to perform cross effect validation. The model fits relatively well (RMSEA = 0.100, GFI = 0.93, NNFI = 1.00, CFI = 1.00) and conforms with the theory, reflecting the loads of the indice, such as, working stress reaction, psychological stress reaction, physiological stress reaction and working ability, are relatively high. At the same time, the stress reaction of those 4 dimensions can fit the 2-grade factor (stress effect) very well. The physiological stress reaction is negatively correlated (P < 0.05) with the working stress reaction, psychological stress reaction, working ability decrease, while is positively correlated (P < 0.05) with the working stress, psychological stress reaction, physiological stress reaction and working ability decrease. The social support is the protection factor for working stress, psychological stress reaction, physiological stress reaction and working ability decrease (gamma(s) are -0.55, -0.77, 0.73, -0.79, respectively, P < 0.05). While working stress factors, social life stress factors and dangerous individual characters are the risk factors (P < 0.05) for working stress, psychological stress reaction, physiological stress reaction increase and the working ability decrease. The utilization of the environment protection workers further validates this model. It conforms with the theory to evaluate the mental workers stress effects from the 4 dimensions, working stress, psychological stress reaction, physiological stress reaction, and working ability. And these 4 dimensions influence each other, and also are mutually different. The working and social life stress factors influence the stress effects with certain degrees. This evaluation model can tentatively be the methodological basis for the mental workers occupational stress evaluation.

Chemical structure-based predictive model for the oxidation of trace organic contaminants by sulfate radical.

PubMed

Ye, Tiantian; Wei, Zongsu; Spinney, Richard; Tang, Chong-Jian; Luo, Shuang; Xiao, Ruiyang; Dionysiou, Dionysios D

2017-06-01

Second-order rate constants [Formula: see text] for the reaction of sulfate radical anion (SO 4 •- ) with trace organic contaminants (TrOCs) are of scientific and practical importance for assessing their environmental fate and removal efficiency in water treatment systems. Here, we developed a chemical structure-based model for predicting [Formula: see text] using 32 molecular fragment descriptors, as this type of model provides a quick estimate at low computational cost. The model was constructed using the multiple linear regression (MLR) and artificial neural network (ANN) methods. The MLR method yielded adequate fit for the training set (R training 2 =0.88,n=75) and reasonable predictability for the validation set (R validation 2 =0.62,n=38). In contrast, the ANN method produced a more statistical robustness but rather poor predictability (R training 2 =0.99andR validation 2 =0.42). The reaction mechanisms of SO 4 •- reactivity with TrOCs were elucidated. Our result shows that the coefficients of functional groups reflect their electron donating/withdrawing characters. For example, electron donating groups typically exhibit positive coefficients, indicating enhanced SO 4 •- reactivity. Electron withdrawing groups exhibit negative values, indicating reduced reactivity. With its quick and accurate features, we applied this structure-based model to 55 discrete TrOCs culled from the Contaminant Candidate List 4, and quantitatively compared their removal efficiency with SO 4 •- and OH in the presence of environmental matrices. This high-throughput model helps prioritize TrOCs that are persistent to SO 4 •- based oxidation technologies at the screening level, and provide diagnostics of SO 4 •- reaction mechanisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

A novel approach of modeling continuous dark hydrogen fermentation.

PubMed

Alexandropoulou, Maria; Antonopoulou, Georgia; Lyberatos, Gerasimos

2018-02-01

In this study a novel modeling approach for describing fermentative hydrogen production in a continuous stirred tank reactor (CSTR) was developed, using the Aquasim modeling platform. This model accounts for the key metabolic reactions taking place in a fermentative hydrogen producing reactor, using fixed stoichiometry but different reaction rates. Biomass yields are determined based on bioenergetics. The model is capable of describing very well the variation in the distribution of metabolic products for a wide range of hydraulic retention times (HRT). The modeling approach is demonstrated using the experimental data obtained from a CSTR, fed with food industry waste (FIW), operating at different HRTs. The kinetic parameters were estimated through fitting to the experimental results. Hydrogen and total biogas production rates were predicted very well by the model, validating the basic assumptions regarding the implicated stoichiometric biochemical reactions and their kinetic rates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Shear-induced reaction-limited aggregation kinetics of Brownian particles at arbitrary concentrations

NASA Astrophysics Data System (ADS)

Zaccone, Alessio; Gentili, Daniele; Wu, Hua; Morbidelli, Massimo

2010-04-01

The aggregation of interacting Brownian particles in sheared concentrated suspensions is an important issue in colloid and soft matter science per se. Also, it serves as a model to understand biochemical reactions occurring in vivo where both crowding and shear play an important role. We present an effective medium approach within the Smoluchowski equation with shear which allows one to calculate the encounter kinetics through a potential barrier under shear at arbitrary colloid concentrations. Experiments on a model colloidal system in simple shear flow support the validity of the model in the concentration range considered. By generalizing Kramers' rate theory to the presence of shear and collective hydrodynamics, our model explains the significant increase in the shear-induced reaction-limited aggregation kinetics upon increasing the colloid concentration.

Global reaction mechanism for the auto-ignition of full boiling range gasoline and kerosene fuels

NASA Astrophysics Data System (ADS)

Vandersickel, A.; Wright, Y. M.; Boulouchos, K.

2013-12-01

Compact reaction schemes capable of predicting auto-ignition are a prerequisite for the development of strategies to control and optimise homogeneous charge compression ignition (HCCI) engines. In particular for full boiling range fuels exhibiting two stage ignition a tremendous demand exists in the engine development community. The present paper therefore meticulously assesses a previous 7-step reaction scheme developed to predict auto-ignition for four hydrocarbon blends and proposes an important extension of the model constant optimisation procedure, allowing for the model to capture not only ignition delays, but also the evolutions of representative intermediates and heat release rates for a variety of full boiling range fuels. Additionally, an extensive validation of the later evolutions by means of various detailed n-heptane reaction mechanisms from literature has been presented; both for perfectly homogeneous, as well as non-premixed/stratified HCCI conditions. Finally, the models potential to simulate the auto-ignition of various full boiling range fuels is demonstrated by means of experimental shock tube data for six strongly differing fuels, containing e.g. up to 46.7% cyclo-alkanes, 20% napthalenes or complex branched aromatics such as methyl- or ethyl-napthalene. The good predictive capability observed for each of the validation cases as well as the successful parameterisation for each of the six fuels, indicate that the model could, in principle, be applied to any hydrocarbon fuel, providing suitable adjustments to the model parameters are carried out. Combined with the optimisation strategy presented, the model therefore constitutes a major step towards the inclusion of real fuel kinetics into full scale HCCI engine simulations.

Numerical Investigation of Desulfurization Kinetics in Gas-Stirred Ladles by a Quick Modeling Analysis Approach

NASA Astrophysics Data System (ADS)

Cao, Qing; Nastac, Laurentiu; Pitts-Baggett, April; Yu, Qiulin

2018-03-01

A quick modeling analysis approach for predicting the slag-steel reaction and desulfurization kinetics in argon gas-stirred ladles has been developed in this study. The model consists of two uncoupled components: (i) a computational fluid dynamics (CFD) model for predicting the fluid flow and the characteristics of slag-steel interface, and (ii) a multicomponent reaction kinetics model for calculating the desulfurization evolution. The steel-slag interfacial area and mass transfer coefficients predicted by the CFD simulation are used as the processing data for the reaction model. Since the desulfurization predictions are uncoupled from the CFD simulation, the computational time of this uncoupled predictive approach is decreased by at least 100 times for each case study when compared with the CFD-reaction kinetics fully coupled model. The uncoupled modeling approach was validated by comparing the evolution of steel and slag compositions with the experimentally measured data during ladle metallurgical furnace (LMF) processing at Nucor Steel Tuscaloosa, Inc. Then, the validated approach was applied to investigate the effects of the initial steel and slag compositions, as well as different types of additions during the refining process on the desulfurization efficiency. The results revealed that the sulfur distribution ratio and the desulfurization reaction can be promoted by making Al and CaO additions during the refining process. It was also shown that by increasing the initial Al content in liquid steel, both Al oxidation and desulfurization rates rapidly increase. In addition, it was found that the variation of the initial Si content in steel has no significant influence on the desulfurization rate. Lastly, if the initial CaO content in slag is increased or the initial Al2O3 content is decreased in the fluid-slag compositional range, the desulfurization rate can be improved significantly during the LMF process.

Numerical Investigation of Desulfurization Kinetics in Gas-Stirred Ladles by a Quick Modeling Analysis Approach

NASA Astrophysics Data System (ADS)

Cao, Qing; Nastac, Laurentiu; Pitts-Baggett, April; Yu, Qiulin

2018-06-01

A quick modeling analysis approach for predicting the slag-steel reaction and desulfurization kinetics in argon gas-stirred ladles has been developed in this study. The model consists of two uncoupled components: (i) a computational fluid dynamics (CFD) model for predicting the fluid flow and the characteristics of slag-steel interface, and (ii) a multicomponent reaction kinetics model for calculating the desulfurization evolution. The steel-slag interfacial area and mass transfer coefficients predicted by the CFD simulation are used as the processing data for the reaction model. Since the desulfurization predictions are uncoupled from the CFD simulation, the computational time of this uncoupled predictive approach is decreased by at least 100 times for each case study when compared with the CFD-reaction kinetics fully coupled model. The uncoupled modeling approach was validated by comparing the evolution of steel and slag compositions with the experimentally measured data during ladle metallurgical furnace (LMF) processing at Nucor Steel Tuscaloosa, Inc. Then, the validated approach was applied to investigate the effects of the initial steel and slag compositions, as well as different types of additions during the refining process on the desulfurization efficiency. The results revealed that the sulfur distribution ratio and the desulfurization reaction can be promoted by making Al and CaO additions during the refining process. It was also shown that by increasing the initial Al content in liquid steel, both Al oxidation and desulfurization rates rapidly increase. In addition, it was found that the variation of the initial Si content in steel has no significant influence on the desulfurization rate. Lastly, if the initial CaO content in slag is increased or the initial Al2O3 content is decreased in the fluid-slag compositional range, the desulfurization rate can be improved significantly during the LMF process.

Chemical Memory Reactions Induced Bursting Dynamics in Gene Expression

PubMed Central

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems. PMID:23349679

Chemical memory reactions induced bursting dynamics in gene expression.

PubMed

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.

Non-equilibrium effects in high temperature chemical reactions

NASA Technical Reports Server (NTRS)

Johnson, Richard E.

1987-01-01

Reaction rate data were collected for chemical reactions occurring at high temperatures during reentry of space vehicles. The principle of detailed balancing is used in modeling kinetics of chemical reactions at high temperatures. Although this principle does not hold for certain transient or incubation times in the initial phase of the reaction, it does seem to be valid for the rates of internal energy transitions that occur within molecules and atoms. That is, for every rate of transition within the internal energy states of atoms or molecules, there is an inverse rate that is related through an equilibrium expression involving the energy difference of the transition.

Informing neutron capture nucleosynthesis on short-lived nuclei with (d,p) reactions

NASA Astrophysics Data System (ADS)

Cizewski, Jolie A.; Ratkiewicz, Andrew; Escher, Jutta E.; Lepailleur, Alexandre; Pain, Steven D.; Potel, Gregory

2018-01-01

Neutron capture on unstable nuclei is important in understanding abundances in r-process nucleosynthesis. Previously, the non-elastic breakup of the deuteron in the (d,p) reaction has been shown to provide a neutron that can be captured by the nucleus and the gamma-ray decay of the subsequent compound nucleus can be modelled to predict the gamma-ray decay of the compound nucleus in the (n,γ) reaction. Preliminary results from the 95Mo(d,pγ) reaction in normal kinematics support the (d,pγ) reaction as a valid surrogate for neutron capture. The techniques to measure the (d,pγ) reaction in inverse kinematics have been developed.

SSER: Species specific essential reactions database.

PubMed

Labena, Abraham A; Ye, Yuan-Nong; Dong, Chuan; Zhang, Fa-Z; Guo, Feng-Biao

2017-04-19

Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction is catalyzed by multiple enzymes, then inhibiting the reaction would be a better option than targeting the enzymes or the corresponding enzyme-encoding gene. The existing databases such as BRENDA, BiGG, KEGG, Bio-models, Biosilico, and many others offer useful and comprehensive information on biochemical reactions. But none of these databases especially focus on essential reactions. Therefore, building a centralized repository for this class of reactions would be of great value. Here, we present a species-specific essential reactions database (SSER). The current version comprises essential biochemical and transport reactions of twenty-six organisms which are identified via flux balance analysis (FBA) combined with manual curation on experimentally validated metabolic network models. Quantitative data on the number of essential reactions, number of the essential reactions associated with their respective enzyme-encoding genes and shared essential reactions across organisms are the main contents of the database. SSER would be a prime source to obtain essential reactions data and related gene and metabolite information and it can significantly facilitate the metabolic network models reconstruction and analysis, and drug target discovery studies. Users can browse, search, compare and download the essential reactions of organisms of their interest through the website http://cefg.uestc.edu.cn/sser .

Numerical modeling study on the epitaxial growth of silicon from dichlorosilane

NASA Astrophysics Data System (ADS)

Zaidi, Imama; Jang, Yeon-Ho; Ko, Dong Guk; Im, Ik-Tae

2018-02-01

Computer simulations play an important role in determining the optimal design parameters for chemical vapor deposition (CVD) reactors, such as flow rates, positions of the inlet and outlet orifices, and rotational rates, etc. Reliability of the results of these simulations depends on the set of chemical reaction used to represent the process of deposition in the reactor. Aim of the present work is to validate the simple empirical reaction to model the epitaxial growth of silicon for a Dichlorosilane-H2 (DCS)-H2 system. Governing equations for continuity, momentum, energy, and reacting species are solved numerically using the finite volume method. The agreement between experimental and predicted growth rates for various DCS flow rates is shown to be satisfactory. The increase in growth rate with the increase in pressure is in accordance with the available data. Based on the validated chemical reaction model, a study was carried out to analyze the uniformity of the silicon layer thickness for two different flow rates in a planetary reactor. It was concluded that, based on the operating conditions, the uniformity of the silicon layer over the wafer is independent of the satellite rotational rate in the reactor.

Finite Element Study of a Lumbar Intervertebral Disc Nucleus Replacement Device.

PubMed

Coogan, Jessica S; Francis, W Loren; Eliason, Travis D; Bredbenner, Todd L; Stemper, Brian D; Yoganandan, Narayan; Pintar, Frank A; Nicolella, Daniel P

2016-01-01

Nucleus replacement technologies are a minimally invasive alternative to spinal fusion and total disc replacement that have the potential to reduce pain and restore motion for patients with degenerative disc disease. Finite element modeling can be used to determine the biomechanics associated with nucleus replacement technologies. The current study focuses on a new nucleus replacement device designed as a conforming silicone implant with an internal void. A validated finite element model of the human lumbar L3-L4 motion segment was developed and used to investigate the influence of the nucleus replacement device on spine biomechanics. In addition, the effect of device design changes on biomechanics was determined. A 3D, L3-L4 finite element model was constructed from medical imaging data. Models were created with the normal intact nucleus, the nucleus replacement device, and a solid silicone implant. Probabilistic analysis was performed on the normal model to provide quantitative validation metrics. Sensitivity analysis was performed on the silicone Shore A durometer of the device. Models were loaded under axial compression followed by flexion/extension, lateral bending, or axial rotation. Compressive displacement, endplate stresses, reaction moment, and annulus stresses were determined and compared between the different models. The novel nucleus replacement device resulted in similar compressive displacement, endplate stress, and annulus stress and slightly higher reaction moment compared with the normal nucleus. The solid implant resulted in decreased displacement, increased endplate stress, decreased annulus stress, and decreased reaction moment compared with the novel device. With increasing silicone durometer, compressive displacement decreased, endplate stress increased, reaction moment increased, and annulus stress decreased. Finite element analysis was used to show that the novel nucleus replacement device results in similar biomechanics compared with the normal intact nucleus.

Finite Element Study of a Lumbar Intervertebral Disc Nucleus Replacement Device

PubMed Central

Coogan, Jessica S.; Francis, W. Loren; Eliason, Travis D.; Bredbenner, Todd L.; Stemper, Brian D.; Yoganandan, Narayan; Pintar, Frank A.; Nicolella, Daniel P.

2016-01-01

Nucleus replacement technologies are a minimally invasive alternative to spinal fusion and total disc replacement that have the potential to reduce pain and restore motion for patients with degenerative disc disease. Finite element modeling can be used to determine the biomechanics associated with nucleus replacement technologies. The current study focuses on a new nucleus replacement device designed as a conforming silicone implant with an internal void. A validated finite element model of the human lumbar L3–L4 motion segment was developed and used to investigate the influence of the nucleus replacement device on spine biomechanics. In addition, the effect of device design changes on biomechanics was determined. A 3D, L3–L4 finite element model was constructed from medical imaging data. Models were created with the normal intact nucleus, the nucleus replacement device, and a solid silicone implant. Probabilistic analysis was performed on the normal model to provide quantitative validation metrics. Sensitivity analysis was performed on the silicone Shore A durometer of the device. Models were loaded under axial compression followed by flexion/extension, lateral bending, or axial rotation. Compressive displacement, endplate stresses, reaction moment, and annulus stresses were determined and compared between the different models. The novel nucleus replacement device resulted in similar compressive displacement, endplate stress, and annulus stress and slightly higher reaction moment compared with the normal nucleus. The solid implant resulted in decreased displacement, increased endplate stress, decreased annulus stress, and decreased reaction moment compared with the novel device. With increasing silicone durometer, compressive displacement decreased, endplate stress increased, reaction moment increased, and annulus stress decreased. Finite element analysis was used to show that the novel nucleus replacement device results in similar biomechanics compared with the normal intact nucleus. PMID:27990418

Modeling the formation of N-nitrosodimethylamine (NDMA) from the reaction of natural organic matter (NOM) with monochloramine.

PubMed

Chen, Zhuo; Valentine, Richard L

2006-12-01

This paper presents mechanistic studies on the formation of NDMA, a newly identified chloramination disinfection byproduct, from reactions of monochloramine with natural organic matter. A kinetic model was developed to validate proposed reactions and to predict NDMA formation in chloraminated water during the time frame of 1-5 days. This involved incorporating NDMA formation reactions into an established comprehensive model describing the oxidation of humic-type natural organic matter by monochloramine. A rate-limiting step involving the oxidation of NOM is theorized to control the rate of NDMA formation which is assumed to be proportional to the rate of NOM oxidized by monochloramine. The applicability of the model to describe NDMA formation in the presence of three NOM sources over a wide range in water quality (i.e., pH, DOC, and ammonia concentrations) was evaluated. Results show that with accurate measurement of monochloramine demand for a specific supply, NDMA formation could be modeled over an extended range of experimental conditions by considering a single NOM source-specific value of thetaNDMA, a stoichiometric coefficient relating the amount of NDMA produced to the amount of NOM oxidized, and several kinetic parameters describing NOM oxidation. Furthermore, the oxidation of NOM is the rate-limiting step governing NDMA formation. This suggests that NDMA formation over a 1-5 day time frame may be estimated from information on the chloramine or free chlorine demand of the NOM and the source-specific linear relationship between this demand and NDMA formation. Although the proposed model has not yet been validated for shorter time periods that may better characterize the residence time in some distribution systems, the improved understanding of the important reactions governing NDMA formation and the resulting model should benefit the water treatment industry as a tool in developing strategies that minimize NDMA formation.

Assessing PTSD in the military: Validation of a scale distributed to Danish soldiers after deployment since 1998.

PubMed

Karstoft, Karen-Inge; Andersen, Søren B; Nielsen, Anni B S

2017-06-01

Since 1998, soldiers deployed to war zones with the Danish Defense (≈31,000) have been invited to fill out a questionnaire on post-mission reactions. This provides a unique data source for studying the psychological toll of war. Here, we validate a measure of PTSD-symptoms from the questionnaire. Soldiers from two cohorts deployed to Afghanistan with the International Security Assistance Force (ISAF) in 2009 (ISAF7, N = 334) and 2013 (ISAF15, N = 278) filled out a standard questionnaire (Psychological Reactions following International Missions, PRIM) concerning a range of post-deployment reactions including symptoms of PTSD (PRIM-PTSD). They also filled out a validated measure of PTSD-symptoms in DSM-IV, the PTSD-checklist (PCL). We tested reliability of PRIM-PTSD by estimating Cronbach's alpha, and tested validity by correlating items, clusters, and overall scale with corresponding items in the PCL. Furthermore, we conducted two confirmatory factor analytic models to test the factor structure of PRIM-PTSD, and tested measurement invariance of the selected model. Finally, we established a screening and a clinical cutoff score by application of ROC analysis. We found high internal consistency of the PRIM-PTSD (Cronbach's alpha = 0.88; both cohorts), strong item-item (0.48-0.83), item-cluster (0.43-0.72), cluster-cluster (0.71-0.82) and full-scale (0.86-0.88) correlations between PRIM-PTSD and PCL. The factor analyses showed adequate fit of a one-factor model, which was also found to display strong measurement invariance across cohorts. ROC curve analysis established cutoff scores for screening (sensitivity = 1, specificity = 0.93) and clinical use (sensitivity = 0.71, specificity = 0.98). In conclusion, we find that PRIM-PTSD is a valid measure for assessing PTSD-symptoms in Danish soldiers following deployment. © 2017 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

Finite element code development for modeling detonation of HMX composites

NASA Astrophysics Data System (ADS)

Duran, Adam V.; Sundararaghavan, Veera

2017-01-01

In this work, we present a hydrodynamics code for modeling shock and detonation waves in HMX. A stable efficient solution strategy based on a Taylor-Galerkin finite element (FE) discretization was developed to solve the reactive Euler equations. In our code, well calibrated equations of state for the solid unreacted material and gaseous reaction products have been implemented, along with a chemical reaction scheme and a mixing rule to define the properties of partially reacted states. A linear Gruneisen equation of state was employed for the unreacted HMX calibrated from experiments. The JWL form was used to model the EOS of gaseous reaction products. It is assumed that the unreacted explosive and reaction products are in both pressure and temperature equilibrium. The overall specific volume and internal energy was computed using the rule of mixtures. Arrhenius kinetics scheme was integrated to model the chemical reactions. A locally controlled dissipation was introduced that induces a non-oscillatory stabilized scheme for the shock front. The FE model was validated using analytical solutions for SOD shock and ZND strong detonation models. Benchmark problems are presented for geometries in which a single HMX crystal is subjected to a shock condition.

On The Validity of the Assumed PDF Method for Modeling Binary Mixing/Reaction of Evaporated Vapor in GAS/Liquid-Droplet Turbulent Shear Flow

NASA Technical Reports Server (NTRS)

Miller, R. S.; Bellan, J.

1997-01-01

An Investigation of the statistical description of binary mixing and/or reaction between a carrier gas and an evaporated vapor species in two-phase gas-liquid turbulent flows is perfomed through both theroetical analysis and comparisons with results from direct numerical simulations (DNS) of a two-phase mixing layer.

Development of a model for predicting reaction rate constants of organic chemicals with ozone at different temperatures.

PubMed

Li, Xuehua; Zhao, Wenxing; Li, Jing; Jiang, Jingqiu; Chen, Jianji; Chen, Jingwen

2013-08-01

To assess the persistence and fate of volatile organic compounds in the troposphere, the rate constants for the reaction with ozone (kO3) are needed. As kO3 values are only available for hundreds of compounds, and experimental determination of kO3 is costly and time-consuming, it is of importance to develop predictive models on kO3. In this study, a total of 379 logkO3 values at different temperatures were used to develop and validate a model for the prediction of kO3, based on quantum chemical descriptors, Dragon descriptors and structural fragments. Molecular descriptors were screened by stepwise multiple linear regression, and the model was constructed by partial least-squares regression. The cross validation coefficient QCUM(2) of the model is 0.836, and the external validation coefficient Qext(2) is 0.811, indicating that the model has high robustness and good predictive performance. The most significant descriptor explaining logkO3 is the BELm2 descriptor with connectivity information weighted atomic masses. kO3 increases with increasing BELm2, and decreases with increasing ionization potential. The applicability domain of the proposed model was visualized by the Williams plot. The developed model can be used to predict kO3 at different temperatures for a wide range of organic chemicals, including alkenes, cycloalkenes, haloalkenes, alkynes, oxygen-containing compounds, nitrogen-containing compounds (except primary amines) and aromatic compounds. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modeling biomass gasification in circulating fluidized beds

NASA Astrophysics Data System (ADS)

Miao, Qi

In this thesis, the modeling of biomass gasification in circulating fluidized beds was studied. The hydrodynamics of a circulating fluidized bed operating on biomass particles were first investigated, both experimentally and numerically. Then a comprehensive mathematical model was presented to predict the overall performance of a 1.2 MWe biomass gasification and power generation plant. A sensitivity analysis was conducted to test its response to several gasifier operating conditions. The model was validated using the experimental results obtained from the plant and two other circulating fluidized bed biomass gasifiers (CFBBGs). Finally, an ASPEN PLUS simulation model of biomass gasification was presented based on minimization of the Gibbs free energy of the reaction system at chemical equilibrium. Hydrodynamics plays a crucial role in defining the performance of gas-solid circulating fluidized beds (CFBs). A 2-dimensional mathematical model was developed considering the hydrodynamic behavior of CFB gasifiers. In the modeling, the CFB riser was divided into two regions: a dense region at the bottom and a dilute region at the top of the riser. Kunii and Levenspiel (1991)'s model was adopted to express the vertical solids distribution with some other assumptions. Radial distributions of bed voidage were taken into account in the upper zone by using Zhang et al. (1991)'s correlation. For model validation purposes, a cold model CFB was employed, in which sawdust was transported with air as the fluidizing agent. A comprehensive mathematical model was developed to predict the overall performance of a 1.2 MWe biomass gasification and power generation demonstration plant in China. Hydrodynamics as well as chemical reaction kinetics were considered. The fluidized bed riser was divided into two distinct sections: (a) a dense region at the bottom of the bed where biomass undergoes mainly heterogeneous reactions and (b) a dilute region at the top where most of homogeneous reactions occur in gas phase. Each section was divided into a number of small cells, over which mass and energy balances were applied. Due to the high heating rate in circulating fluidized bed, the pyrolysis was considered instantaneous. A number of homogeneous and heterogeneous reactions were considered in the model. Mass transfer resistance was considered negligible since the reactions were under kinetic control due to good gas-solid mixing. The model is capable of predicting the bed temperature distribution along the gasifier, the concentration and distribution of each species in the vertical direction of the bed, the composition and lower heating value (LHV) of produced gas, the gasification efficiency, the overall carbon conversion and the produced gas production rate. A sensitivity analysis was performed to test its response to several gasifier operating conditions. The model sensitivity analysis showed that equivalence ratio (ER), bed temperature, fluidization velocity, biomass feed rate and moisture content had various effects on the gasifier performance. However, the model was more sensitive to variations in ER and bed temperature. The model was validated using the experimental results obtained from the demonstration plant. The reactor was operated on rice husk at various ERs, fluidization velocities and biomass feed rates. The model gave reasonable predictions. The model was also validated by comparing the simulation results with two other different size CFBBGs using different biomass feedstock, and it was concluded that the developed model can be applied to other CFBBGs using various biomass fuels and having comparable reactor geometries. A thermodynamic model was developed under ASPEN PLUS environment. Using the approach of Gibbs free energy minimization, the model was essentially independent of kinetic parameters. A sensitivity analysis was performed on the model to test its response to operating variables, including ER and biomass moisture content. The results showed that the ER has the most effect on the product gas composition and LHV. The simulation results were compared with the experimental data obtained from the demonstration plant. Keywords: Biomass gasification; Mathematical model; Circulating fluidized bed; Hydrodynamics; Kinetics; Sensitivity analysis; Validation; Equivalence ratio; Temperature; Feed rate; Moisture; Syngas composition; Lower heating value; Gasification efficiency; Carbon conversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mondy, Lisa Ann; Rao, Rekha Ranjana; Shelden, Bion

We are developing computational models to elucidate the expansion and dynamic filling process of a polyurethane foam, PMDI. The polyurethane of interest is chemically blown, where carbon dioxide is produced via the reaction of water, the blowing agent, and isocyanate. The isocyanate also reacts with polyol in a competing reaction, which produces the polymer. Here we detail the experiments needed to populate a processing model and provide parameters for the model based on these experiments. The model entails solving the conservation equations, including the equations of motion, an energy balance, and two rate equations for the polymerization and foaming reactions,more » following a simplified mathematical formalism that decouples these two reactions. Parameters for the polymerization kinetics model are reported based on infrared spectrophotometry. Parameters describing the gas generating reaction are reported based on measurements of volume, temperature and pressure evolution with time. A foam rheology model is proposed and parameters determined through steady-shear and oscillatory tests. Heat of reaction and heat capacity are determined through differential scanning calorimetry. Thermal conductivity of the foam as a function of density is measured using a transient method based on the theory of the transient plane source technique. Finally, density variations of the resulting solid foam in several simple geometries are directly measured by sectioning and sampling mass, as well as through x-ray computed tomography. These density measurements will be useful for model validation once the complete model is implemented in an engineering code.« less

ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

PubMed

Kayala, Matthew A; Baldi, Pierre

2012-10-22

Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of ReactionPredictor are available via the chemoinformatics portal http://cdb.ics.uci.edu/.

Three-dimensional computational fluid dynamics modelling and experimental validation of the Jülich Mark-F solid oxide fuel cell stack

NASA Astrophysics Data System (ADS)

Nishida, R. T.; Beale, S. B.; Pharoah, J. G.; de Haart, L. G. J.; Blum, L.

2018-01-01

This work is among the first where the results of an extensive experimental research programme are compared to performance calculations of a comprehensive computational fluid dynamics model for a solid oxide fuel cell stack. The model, which combines electrochemical reactions with momentum, heat, and mass transport, is used to obtain results for an established industrial-scale fuel cell stack design with complex manifolds. To validate the model, comparisons with experimentally gathered voltage and temperature data are made for the Jülich Mark-F, 18-cell stack operating in a test furnace. Good agreement is obtained between the model and experiment results for cell voltages and temperature distributions, confirming the validity of the computational methodology for stack design. The transient effects during ramp up of current in the experiment may explain a lower average voltage than model predictions for the power curve.

Animal models of 'anxiety': where next?

PubMed

Rodgers, R J

1997-11-01

Numerous procedures have been developed to facilitate preclinical research on the behavioural pharmacology of anxiety and, as a result of this application, are often referred to as animal models of 'anxiety'. This is an unfortunate misnomer, not only because of the apparent inability of many tests to detect novel anxiolytics consistently, but also because the term implies that anxiety is a unitary emotion. Such difficulties have arisen largely as a consequence of test development strategies which, by emphasizing pharmacological (i.e. benzodiazepine) validation, have yielded models predictive of a specific type of anxiolytic activity. The present review argues that the refinement of existing tests as well as the development of new procedures requires urgent attention to the much neglected issue of behavioural validation. From an evolutionary perspective, normal human anxiety may be conceptualized as a repertoire of defence reactions tailored to meet different forms of threats, and disorders of anxiety as the inappropriate activation or exaggeration of these usually adaptive response patterns. In this context, consideration of the defensive reactions typically observed in our animal models reveals substantially greater commonality in the behavioural effects of benzodiazepine and 5-HT1A anxiolytics than would otherwise be apparent. Therefore, with the exception of the conventional plus-maze paradigm (discussed at some length), better correspondence is seen in tests involving unconditioned response to potential threat (e.g. social interaction, distress vocalizations and light/dark exploration) than in tests of conditioned fear reactions. Even within the latter grouping, however, greater commonality is seen in procedures based on reactions to proximal threat (e.g. freezing, startle, ultrasonic vocalizations, burying) than those involving reactions to distal threat (e.g. avoidance/flight). Significantly, very similar findings have been reported in tests specifically designed to study defensive reactions (e.g. rat and mouse defence test batteries) or which incorporate a more detailed knowledge of defence into established procedures (e.g. ethological plus-maze and defensive burying paradigms). Furthermore, recent evidence also suggests that drugs with proved clinical efficacy in panic attacks/panic disorder have reliably stronger effects on flight responses than other components of the defensive repertoire. It is concluded that a focus on defensive behaviour patterns improves test validity (predictive/face/construct), offers a more rational basis for test selection in drug development programmes, and provides a firmer theoretical framework for future methodological and therapeutic advance.

Versatile fusion source integrator AFSI for fast ion and neutron studies in fusion devices

NASA Astrophysics Data System (ADS)

Sirén, Paula; Varje, Jari; Äkäslompolo, Simppa; Asunta, Otto; Giroud, Carine; Kurki-Suonio, Taina; Weisen, Henri; JET Contributors, The

2018-01-01

ASCOT Fusion Source Integrator AFSI, an efficient tool for calculating fusion reaction rates and characterizing the fusion products, based on arbitrary reactant distributions, has been developed and is reported in this paper. Calculation of reactor-relevant D-D, D-T and D-3He fusion reactions has been implemented based on the Bosch-Hale fusion cross sections. The reactions can be calculated between arbitrary particle populations, including Maxwellian thermal particles and minority energetic particles. Reaction rate profiles, energy spectra and full 4D phase space distributions can be calculated for the non-isotropic reaction products. The code is especially suitable for integrated modelling in self-consistent plasma physics simulations as well as in the Serpent neutronics calculation chain. Validation of the model has been performed for neutron measurements at the JET tokamak and the code has been applied to predictive simulations in ITER.

Models in the Design and Validation of Eddy Current Inspection for Cracking in the Shuttle Reaction Control System Thruster

NASA Technical Reports Server (NTRS)

Aldrin, John C.; Williams, Phillip A.; Wincheski, Russell (Buzz) A.

2008-01-01

A case study is presented for using models in eddy current NDE design for crack detection in Shuttle Reaction Control System thruster components. Numerical methods were used to address the complex geometry of the part and perform parametric studies of potential transducer designs. Simulations were found to show agreement with experimental results. Accurate representation of the coherent noise associated with the measurement and part geometry was found to be critical to properly evaluate the best probe designs.

Spallation reactions: A successful interplay between modeling and applications

NASA Astrophysics Data System (ADS)

David, J.-C.

2015-06-01

The spallation reactions are a type of nuclear reaction which occur in space by interaction of the cosmic rays with interstellar bodies. The first spallation reactions induced with an accelerator took place in 1947 at the Berkeley cyclotron (University of California) with 200MeV deuterons and 400MeV alpha beams. They highlighted the multiple emission of neutrons and charged particles and the production of a large number of residual nuclei far different from the target nuclei. In the same year, R. Serber described the reaction in two steps: a first and fast one with high-energy particle emission leading to an excited remnant nucleus, and a second one, much slower, the de-excitation of the remnant. In 2010 IAEA organized a workshop to present the results of the most widely used spallation codes within a benchmark of spallation models. If one of the goals was to understand the deficiencies, if any, in each code, one remarkable outcome points out the overall high-quality level of some models and so the great improvements achieved since Serber. Particle transport codes can then rely on such spallation models to treat the reactions between a light particle and an atomic nucleus with energies spanning from few tens of MeV up to some GeV. An overview of the spallation reactions modeling is presented in order to point out the incomparable contribution of models based on basic physics to numerous applications where such reactions occur. Validations or benchmarks, which are necessary steps in the improvement process, are also addressed, as well as the potential future domains of development. Spallation reactions modeling is a representative case of continuous studies aiming at understanding a reaction mechanism and which end up in a powerful tool.

Integrated computational model of the bioenergetics of isolated lung mitochondria

PubMed Central

Zhang, Xiao; Jacobs, Elizabeth R.; Camara, Amadou K. S.; Clough, Anne V.

2018-01-01

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria. PMID:29889855

Integrated computational model of the bioenergetics of isolated lung mitochondria.

PubMed

Zhang, Xiao; Dash, Ranjan K; Jacobs, Elizabeth R; Camara, Amadou K S; Clough, Anne V; Audi, Said H

2018-01-01

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria.

Accurate atom-mapping computation for biochemical reactions.

PubMed

Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

2012-11-26

The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

Development of Chemistry Triangle Oriented Module on Topic of Reaction Rate for Senior High School Level Grade XI Chemistry Learning.

NASA Astrophysics Data System (ADS)

Sari, D. R.; Hardeli; Bayharti

2018-04-01

This study aims to produce chemistry triangle oriented module on topic of reaction rate, and to reveal the validity and practicality level of the generated module. The type of research used is EducationalDesign Research (EDR) with development model is Plompmodel. This model consists of three phases, which are preliminary research, prototyping phase, and assessment phase. The instrument used in this research is questionnaire validity and practicality. The data of the research were analyzed by using Kappa Cohen formula. The chemistry triangle oriented module validation sheet was given to 5 validators consisting of 3 chemistry lecturers and 2 high school chemistry teachers, while the practicality sheet was given to 2 chemistry teachers, 6 students of SMAN 10 Padang grade XII MIA 5 on the small groupevaluation and 25 students of SMAN 10 Padang grade XII MIA 6 on the field test. Based on the questionnaire validity analysis, the validity level of the module is very high with the value of kappa moment 0.87. The level of practicality based on teacher questionnaire response is very high category with a kappa moment value 0.96. Based on the questionnaire of student responses on small group evaluation, the level of practicality is very high category with a kappa moment 0.81, and the practicality is very high category with kappa moment value 0.83 based on questionnaire of student response on field test.

Geochemical Reaction Mechanism Discovery from Molecular Simulation

DOE PAGES

Stack, Andrew G.; Kent, Paul R. C.

2014-11-10

Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineralmore » surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.« less

Finite element modeling of contaminant transport in soils including the effect of chemical reactions.

PubMed

Javadi, A A; Al-Najjar, M M

2007-05-17

The movement of chemicals through soils to the groundwater is a major cause of degradation of water resources. In many cases, serious human and stock health implications are associated with this form of pollution. Recent studies have shown that the current models and methods are not able to adequately describe the leaching of nutrients through soils, often underestimating the risk of groundwater contamination by surface-applied chemicals, and overestimating the concentration of resident solutes. Furthermore, the effect of chemical reactions on the fate and transport of contaminants is not included in many of the existing numerical models for contaminant transport. In this paper a numerical model is presented for simulation of the flow of water and air and contaminant transport through unsaturated soils with the main focus being on the effects of chemical reactions. The governing equations of miscible contaminant transport including advection, dispersion-diffusion and adsorption effects together with the effect of chemical reactions are presented. The mathematical framework and the numerical implementation of the model are described in detail. The model is validated by application to a number of test cases from the literature and is then applied to the simulation of a physical model test involving transport of contaminants in a block of soil with particular reference to the effects of chemical reactions. Comparison of the results of the numerical model with the experimental results shows that the model is capable of predicting the effects of chemical reactions with very high accuracy. The importance of consideration of the effects of chemical reactions is highlighted.

Assessing Cognitive Performance in Badminton Players: A Reproducibility and Validity Study

PubMed Central

van de Water, Tanja; Faber, Irene; Elferink-Gemser, Marije

2017-01-01

Abstract Fast reaction and good inhibitory control are associated with elite sports performance. To evaluate the reproducibility and validity of a newly developed Badminton Reaction Inhibition Test (BRIT), fifteen elite (25 ± 4 years) and nine non-elite (24 ± 4 years) Dutch male badminton players participated in the study. The BRIT measured four components: domain-general reaction time, badminton-specific reaction time, domain-general inhibitory control and badminton-specific inhibitory control. Five participants were retested within three weeks on the badminton-specific components. Reproducibility was acceptable for badminton-specific reaction time (ICC = 0.626, CV = 6%) and for badminton-specific inhibitory control (ICC = 0.317, CV = 13%). Good construct validity was shown for badminton-specific reaction time discriminating between elite and non-elite players (F = 6.650, p < 0.05). Elite players did not outscore non-elite players on domain-general reaction time nor on both components of inhibitory control (p > 0.05). Concurrent validity for domain-general reaction time was good, as it was associated with a national ranking for elite (p = 0.70, p < 0.01) and non-elite (p = 0.70, p < 0.05) players. No relationship was found between the national ranking and badminton-specific reaction time, nor both components of inhibitory control (p > 0.05). In conclusion, reproducibility and validity of inhibitory control assessment was not confirmed, however, the BRIT appears a reproducible and valid measure of reaction time in badminton players. Reaction time measured with the BRIT may provide input for training programs aiming to improve badminton players’ performance. PMID:28210347

Assessing Cognitive Performance in Badminton Players: A Reproducibility and Validity Study.

PubMed

van de Water, Tanja; Huijgen, Barbara; Faber, Irene; Elferink-Gemser, Marije

2017-01-01

Fast reaction and good inhibitory control are associated with elite sports performance. To evaluate the reproducibility and validity of a newly developed Badminton Reaction Inhibition Test (BRIT), fifteen elite (25 ± 4 years) and nine non-elite (24 ± 4 years) Dutch male badminton players participated in the study. The BRIT measured four components: domain-general reaction time, badminton-specific reaction time, domain-general inhibitory control and badminton-specific inhibitory control. Five participants were retested within three weeks on the badminton-specific components. Reproducibility was acceptable for badminton-specific reaction time (ICC = 0.626, CV = 6%) and for badminton-specific inhibitory control (ICC = 0.317, CV = 13%). Good construct validity was shown for badminton-specific reaction time discriminating between elite and non-elite players (F = 6.650, p < 0.05). Elite players did not outscore non-elite players on domain-general reaction time nor on both components of inhibitory control (p > 0.05). Concurrent validity for domain-general reaction time was good, as it was associated with a national ranking for elite (p = 0.70, p < 0.01) and non-elite (p = 0.70, p < 0.05) players. No relationship was found between the national ranking and badminton-specific reaction time, nor both components of inhibitory control (p > 0.05). In conclusion, reproducibility and validity of inhibitory control assessment was not confirmed, however, the BRIT appears a reproducible and valid measure of reaction time in badminton players. Reaction time measured with the BRIT may provide input for training programs aiming to improve badminton players' performance.

Computational Steroidogenesis Model To Predict Biochemical Responses to Endocrine Active Chemicals: Model Development and Cross Validation

EPA Science Inventory

Steroids, which have an important role in a wide range of physiological processes, are synthesized primarily in the gonads and adrenal glands through a series of enzyme-mediated reactions. The activity of steroidogenic enzymes can be altered by a variety of endocrine active chem...

Mathematical model of the direct reduction of dust composite pellets containing zinc and iron

NASA Astrophysics Data System (ADS)

An, Xiu-wei; Wang, Jing-song; She, Xue-feng; Xue, Qing-guo

2013-07-01

Direct reduction of dust composite pellets containing zinc and iron was examined by simulating the conditions of actual production process of a rotary hearth furnace (RHF) in laboratory. A mathematical model was constructed to study the reduction kinetics of iron oxides and ZnO in the dust composite pellets. It was validated by comparing the calculated values with experimental results. The effects of furnace temperature, pellet radius, and pellet porosity on the reduction were investigated by the model. It is shown that furnace temperature has obvious influence on both of the reduction of iron oxides and ZnO, but the influence of pellet radius and porosity is much smaller. Model calculations suggest that both of the reduction of iron oxides and ZnO are under mixed control with interface reactions and Boudouard reaction in the early stage, but only with interface reactions in the later stage.

An improved swarm optimization for parameter estimation and biological model selection.

PubMed

Abdullah, Afnizanfaizal; Deris, Safaai; Mohamad, Mohd Saberi; Anwar, Sohail

2013-01-01

One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data.

Ranking and validation of the spallation models for description of intermediate mass fragment emission from p + Ag collisions at 480 MeV incident proton beam energy

NASA Astrophysics Data System (ADS)

Sharma, Sushil K.; Kamys, Bogusław; Goldenbaum, Frank; Filges, Detlef

2016-06-01

Double-differential cross-sections d2σ/dΩ dE for isotopically identified intermediate mass fragments ( 6Li up to 27Mg from nuclear reactions induced by 480 MeV protons impinging on a silver target were analyzed in the frame of a two-step model. The first step of the reaction was described by the intranuclear cascade model INCL4.6 and the second one by four different models (ABLA07,GEM2, GEMINI++, and SMM). The experimental spectra reveal the presence of low-energy, isotropic as well as high-energy, forward-peaked contributions. The INCL4.6 model offers a possibility to describe the latter contribution for light intermediate mass fragments by coalescence of the emitted nucleons. The qualitative agreement of the model predictions with the data was observed but the high-energy tails of the spectra were significantly overestimated. The shape of the isotropic part of the spectra was reproduced by all four models. The GEM2 model strongly underestimated the value of the cross-sections for heavier IMF whereas the SMM and ABLA07 models generally overestimated the data. The best quantitative description of the data was offered by GEMINI++, however, a discrepancy between the data and the model cross-sections still remained for almost all reaction products, especially at forward angles. It indicates that non-equilibrium processes are present which cannot be reproduced by the applied models. The goodness of the data description was judged quantitatively using two statistical deviation factors, the H-factor and the M-factor, as a tool for ranking and validation of the theoretical models.

Accurate prediction of severe allergic reactions by a small set of environmental parameters (NDVI, temperature).

PubMed

Notas, George; Bariotakis, Michail; Kalogrias, Vaios; Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

2015-01-01

Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions.

Accurate Prediction of Severe Allergic Reactions by a Small Set of Environmental Parameters (NDVI, Temperature)

PubMed Central

Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

2015-01-01

Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions. PMID:25794106

Determination of osthol and its metabolites in a phase I reaction system and the Caco-2 cell model by HPLC-UV and LC-MS/MS

PubMed Central

Yuan, Zhenting; Xu, Haiyan; Wang, Ke; Zhao, Zhonghua; Hu, Ming

2012-01-01

A straightforward and sensitive reversed-phase high-performance liquid chromatography (HPLC) assay was developed and validated for the analysis of osthol and its phase I metabolites (internal standard: umbelliferone). The method was validated for the determination of osthol with respect to selectivity, precision, linearity, limit of detection, recovery, and stability. The linear response range was 0.47 ~ 60 μM, and the average recoveries ranged from 98 to 101%. The inter-day and intra-day relative standard deviations were both less than 5%. Using this method, we showed that more than 80% of osthol was metabolized in 20 min in a phase I metabolic reaction system. Transport experiments in the Caco-2 cell culture model indicated that osthol was easily absorbed with high absorptive permeability (>10×10-6 cm/sec). The permeability did not display concentration-dependence or vectorial-dependence and is mildly temperature sensitive (activation energy less than 10 Kcal/mole), indicating passive mechanism of transport. When analyzed by LC-MS/MS, five metabolites were detected in a phase I reaction system and in the receiver side of a modified Caco-2 cell model, which was supplemented with the phase I reaction system. The major metabolites appeared to be desmethyl-osthol and multiple isomers of dehydro-osthol. In conclusion, a likely cause of poor osthol bioavailability is rapid phase I metabolism via the cytochrome P-450 pathways. PMID:19304430

Kinetic mechanism of molecular energy transfer and chemical reactions in low-temperature air-fuel plasmas.

PubMed

Adamovich, Igor V; Li, Ting; Lempert, Walter R

2015-08-13

This work describes the kinetic mechanism of coupled molecular energy transfer and chemical reactions in low-temperature air, H2-air and hydrocarbon-air plasmas sustained by nanosecond pulse discharges (single-pulse or repetitive pulse burst). The model incorporates electron impact processes, state-specific N(2) vibrational energy transfer, reactions of excited electronic species of N(2), O(2), N and O, and 'conventional' chemical reactions (Konnov mechanism). Effects of diffusion and conduction heat transfer, energy coupled to the cathode layer and gasdynamic compression/expansion are incorporated as quasi-zero-dimensional corrections. The model is exercised using a combination of freeware (Bolsig+) and commercial software (ChemKin-Pro). The model predictions are validated using time-resolved measurements of temperature and N(2) vibrational level populations in nanosecond pulse discharges in air in plane-to-plane and sphere-to-sphere geometry; temperature and OH number density after nanosecond pulse burst discharges in lean H(2)-air, CH(4)-air and C(2)H(4)-air mixtures; and temperature after the nanosecond pulse discharge burst during plasma-assisted ignition of lean H2-mixtures, showing good agreement with the data. The model predictions for OH number density in lean C(3)H(8)-air mixtures differ from the experimental results, over-predicting its absolute value and failing to predict transient OH rise and decay after the discharge burst. The agreement with the data for C(3)H(8)-air is improved considerably if a different conventional hydrocarbon chemistry reaction set (LLNL methane-n-butane flame mechanism) is used. The results of mechanism validation demonstrate its applicability for analysis of plasma chemical oxidation and ignition of low-temperature H(2)-air, CH(4)-air and C(2)H(4)-air mixtures using nanosecond pulse discharges. Kinetic modelling of low-temperature plasma excited propane-air mixtures demonstrates the need for development of a more accurate 'conventional' chemistry mechanism. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Kinetics of enzymatic trans-esterification of glycerides for biodiesel production.

PubMed

Calabrò, Vincenza; Ricca, Emanuele; De Paola, Maria Gabriela; Curcio, Stefano; Iorio, Gabriele

2010-08-01

In this paper, the reaction of enzymatic trans-esterification of glycerides with ethanol in a reaction medium containing hexane at a temperature of 37 degrees C has been studied. The enzyme was Lipase from Mucor miehei, immobilized on ionic exchange resin, aimed at achieving high catalytic specific surface and recovering, regenerating and reusing the biocatalyst. A kinetic analysis has been carried out to identify the reaction path; the rate equation and kinetic parameters have been also calculated. The kinetic model has been validated by comparison between predicted and experimental results. Mass transport resistances estimation was undertaken in order to verify that the kinetics found was intrinsic. Model potentialities in terms of reactors design and optimization are also shown.

On the validity of specific rate constants (kSA) in Fe0/H2O systems.

PubMed

Noubactep, C

2009-05-30

The validity of the specific reaction rate constants (k(SA)) in modelling contaminant removal in Fe(0)/H(2)O systems is questioned. It is shown that the current k(SA)-model does not consider the large reactive surface area provided by the in-situ formed oxide film, and thus the adsorptive interactions between contaminants and film materials. Furthermore, neither the dynamic nature of film formation nor the fact that the Fe(0) surface is shielded by the film is considered. Suggestions are made how the k(SA)-model could be further developed to meet its original goal.

Reaction Force of Micro-scale Liquid Droplets Constrained Between Parallel Plates through CFD

NASA Astrophysics Data System (ADS)

Free, Robert; Hekiri, Haider; Hawa, Takumi

2012-02-01

Micro-scale liquid droplets responding to depression between parallel plates are investigated analytically and numerically. The functional dependence of the reaction force accrued in such droplets on droplet size, surface tension, depression amount, and contact angle is explored. For both the 2D and 3D case, an analytical model is developed based on first principles. Computational fluid dynamics is then utilized to evaluate the validity of these models. The reaction force is highly nonlinear, initially increasing very slowly with increasing depression of the droplet, but eventually moving asymptotically to infinity. The force scales linearly with both the droplet free radius and surface tension of the liquid, but has a much more complicated dependence on the contact angle and depression. Explicit expressions for the reaction force have been determined, showing these dependencies. The 3D model has been largely supported by the CFD results. It very accurately predicts the reaction force on the upper plate as the droplet is crushed, accounting for the effect of contact angle, surface tension, and droplet size.

Simulation of unsteady flows by the DSMC macroscopic chemistry method

NASA Astrophysics Data System (ADS)

Goldsworthy, Mark; Macrossan, Michael; Abdel-jawad, Madhat

2009-03-01

In the Direct Simulation Monte-Carlo (DSMC) method, a combination of statistical and deterministic procedures applied to a finite number of 'simulator' particles are used to model rarefied gas-kinetic processes. In the macroscopic chemistry method (MCM) for DSMC, chemical reactions are decoupled from the specific particle pairs selected for collisions. Information from all of the particles within a cell, not just those selected for collisions, is used to determine a reaction rate coefficient for that cell. Unlike collision-based methods, MCM can be used with any viscosity or non-reacting collision models and any non-reacting energy exchange models. It can be used to implement any reaction rate formulations, whether these be from experimental or theoretical studies. MCM has been previously validated for steady flow DSMC simulations. Here we show how MCM can be used to model chemical kinetics in DSMC simulations of unsteady flow. Results are compared with a collision-based chemistry procedure for two binary reactions in a 1-D unsteady shock-expansion tube simulation. Close agreement is demonstrated between the two methods for instantaneous, ensemble-averaged profiles of temperature, density and species mole fractions, as well as for the accumulated number of net reactions per cell.

On the Green's function of the partially diffusion-controlled reversible ABCD reaction for radiation chemistry codes

NASA Astrophysics Data System (ADS)

Plante, Ianik; Devroye, Luc

2015-09-01

Several computer codes simulating chemical reactions in particles systems are based on the Green's functions of the diffusion equation (GFDE). Indeed, many types of chemical systems have been simulated using the exact GFDE, which has also become the gold standard for validating other theoretical models. In this work, a simulation algorithm is presented to sample the interparticle distance for partially diffusion-controlled reversible ABCD reaction. This algorithm is considered exact for 2-particles systems, is faster than conventional look-up tables and uses only a few kilobytes of memory. The simulation results obtained with this method are compared with those obtained with the independent reaction times (IRT) method. This work is part of our effort in developing models to understand the role of chemical reactions in the radiation effects on cells and tissues and may eventually be included in event-based models of space radiation risks. However, as many reactions are of this type in biological systems, this algorithm might play a pivotal role in future simulation programs not only in radiation chemistry, but also in the simulation of biochemical networks in time and space as well.

DFT-based prediction of reactivity of short-chain alcohol dehydrogenase

NASA Astrophysics Data System (ADS)

Stawoska, I.; Dudzik, A.; Wasylewski, M.; Jemioła-Rzemińska, M.; Skoczowski, A.; Strzałka, K.; Szaleniec, M.

2017-06-01

The reaction mechanism of ketone reduction by short chain dehydrogenase/reductase, ( S)-1-phenylethanol dehydrogenase from Aromatoleum aromaticum, was studied with DFT methods using cluster model approach. The characteristics of the hydride transfer process were investigated based on reaction of acetophenone and its eight structural analogues. The results confirmed previously suggested concomitant transfer of hydride from NADH to carbonyl C atom of the substrate with proton transfer from Tyr to carbonyl O atom. However, additional coupled motion of the next proton in the proton-relay system, between O2' ribose hydroxyl and Tyr154 was observed. The protonation of Lys158 seems not to affect the pKa of Tyr154, as the stable tyrosyl anion was observed only for a neutral Lys158 in the high pH model. The calculated reaction energies and reaction barriers were calibrated by calorimetric and kinetic methods. This allowed an excellent prediction of the reaction enthalpies (R2 = 0.93) and a good prediction of the reaction kinetics (R2 = 0.89). The observed relations were validated in prediction of log K eq obtained for real whole-cell reactor systems that modelled industrial synthesis of S-alcohols.

Multi-dimensional modelling of gas turbine combustion using a flame sheet model in KIVA II

NASA Technical Reports Server (NTRS)

Cheng, W. K.; Lai, M.-C.; Chue, T.-H.

1991-01-01

A flame sheet model for heat release is incorporated into a multi-dimensional fluid mechanical simulation for gas turbine application. The model assumes that the chemical reaction takes place in thin sheets compared to the length scale of mixing, which is valid for the primary combustion zone in a gas turbine combustor. In this paper, the details of the model are described and computational results are discussed.

Optimization strategies for radiation induced grafting of 4-vinylpyridine onto poly(ethylene-co-tetraflouroethene) film using Box-Behnken design

NASA Astrophysics Data System (ADS)

Mahmoud Nasef, Mohamed; Shamsaei, Ezzatollah; Ghassemi, Payman; Ahmed Aly, Amgad; Hamid Yahaya, Abdul

2012-04-01

The radiation induced grafting of 4-vinylpyridine (4-VP) onto poly(ethylene-co-tetrafluoroethene) (ETFE) was optimized using the Box-Behnken factorial design available in the response surface method (RSM). The optimized grafting parameters; absorbed dose, monomer concentration, grafting time and reaction temperature were varied in four levels to quantify their effect on the grafting yield (GY). The validity of the statistical model was supported by the small deviation between the predicted (GY=61%) and experimental (GY=57%) values. The optimum conditions for enhancing GY were determined at the following values: monomer concentration of 48 vol%, absorbed dose of 64 kGy, reaction time of 4 h and temperature of 68 °C. A comparison was made between the optimization model developed for the present grafting system and that for grafting of 1-vinylimidazole (1-VIm) onto ETFE to confirm the validly and reliability of the Box-Behnken for the optimization of various radiation induced grafting reactions. Fourier transform infrared (FTIR), thermogravimetric analysis (TGA) and X-ray diffraction (XRD) were used to investigate the properties of the obtained films and provide evidence for grafting.

Combustion chamber analysis code

NASA Technical Reports Server (NTRS)

Przekwas, A. J.; Lai, Y. G.; Krishnan, A.; Avva, R. K.; Giridharan, M. G.

1993-01-01

A three-dimensional, time dependent, Favre averaged, finite volume Navier-Stokes code has been developed to model compressible and incompressible flows (with and without chemical reactions) in liquid rocket engines. The code has a non-staggered formulation with generalized body-fitted-coordinates (BFC) capability. Higher order differencing methodologies such as MUSCL and Osher-Chakravarthy schemes are available. Turbulent flows can be modeled using any of the five turbulent models present in the code. A two-phase, two-liquid, Lagrangian spray model has been incorporated into the code. Chemical equilibrium and finite rate reaction models are available to model chemically reacting flows. The discrete ordinate method is used to model effects of thermal radiation. The code has been validated extensively against benchmark experimental data and has been applied to model flows in several propulsion system components of the SSME and the STME.

Assessment of tautomer distribution using the condensed reaction graph approach

NASA Astrophysics Data System (ADS)

Gimadiev, T. R.; Madzhidov, T. I.; Nugmanov, R. I.; Baskin, I. I.; Antipin, I. S.; Varnek, A.

2018-03-01

We report the first direct QSPR modeling of equilibrium constants of tautomeric transformations (logK T ) in different solvents and at different temperatures, which do not require intermediate assessment of acidity (basicity) constants for all tautomeric forms. The key step of the modeling consisted in the merging of two tautomers in one sole molecular graph ("condensed reaction graph") which enables to compute molecular descriptors characterizing entire equilibrium. The support vector regression method was used to build the models. The training set consisted of 785 transformations belonging to 11 types of tautomeric reactions with equilibrium constants measured in different solvents and at different temperatures. The models obtained perform well both in cross-validation (Q2 = 0.81 RMSE = 0.7 logK T units) and on two external test sets. Benchmarking studies demonstrate that our models outperform results obtained with DFT B3LYP/6-311 ++ G(d,p) and ChemAxon Tautomerizer applicable only in water at room temperature.

Semiclassical Calculation of Reaction Rate Constants for Homolytical Dissociations

NASA Technical Reports Server (NTRS)

Cardelino, Beatriz H.

2002-01-01

There is growing interest in extending organometallic chemical vapor deposition (OMCVD) to III-V materials that exhibit large thermal decomposition at their optimum growth temperature, such as indium nitride. The group III nitrides are candidate materials for light-emitting diodes and semiconductor lasers operating into the blue and ultraviolet regions. To overcome decomposition of the deposited compound, the reaction must be conducted at high pressures, which causes problems of uniformity. Microgravity may provide the venue for maintaining conditions of laminar flow under high pressure. Since the selection of optimized parameters becomes crucial when performing experiments in microgravity, efforts are presently geared to the development of computational OMCVD models that will couple the reactor fluid dynamics with its chemical kinetics. In the present study, we developed a method to calculate reaction rate constants for the homolytic dissociation of III-V compounds for modeling OMCVD. The method is validated by comparing calculations with experimental reaction rate constants.

Finite element code development for modeling detonation of HMX composites

NASA Astrophysics Data System (ADS)

Duran, Adam; Sundararaghavan, Veera

2015-06-01

In this talk, we present a hydrodynamics code for modeling shock and detonation waves in HMX. A stable efficient solution strategy based on a Taylor-Galerkin finite element (FE) discretization was developed to solve the reactive Euler equations. In our code, well calibrated equations of state for the solid unreacted material and gaseous reaction products have been implemented, along with a chemical reaction scheme and a mixing rule to define the properties of partially reacted states. A linear Gruneisen equation of state was employed for the unreacted HMX calibrated from experiments. The JWL form was used to model the EOS of gaseous reaction products. It is assumed that the unreacted explosive and reaction products are in both pressure and temperature equilibrium. The overall specific volume and internal energy was computed using the rule of mixtures. Arrhenius kinetics scheme was integrated to model the chemical reactions. A locally controlled dissipation was introduced that induces a non-oscillatory stabilized scheme for the shock front. The FE model was validated using analytical solutions for sod shock and ZND strong detonation models and then used to perform 2D and 3D shock simulations. We will present benchmark problems for geometries in which a single HMX crystal is subjected to a shock condition. Our current progress towards developing microstructural models of HMX/binder composite will also be discussed.

Heterogenous Combustion of Porous Graphite Particles in Normal and Microgravity

NASA Technical Reports Server (NTRS)

Chelliah, Harsha K.; Miller, Fletcher J.; Delisle, Andrew J.

2001-01-01

Combustion of solid fuel particles has many important applications, including power generation and space propulsion systems. The current models available for describing the combustion process of these particles, especially porous solid particles, include various simplifying approximations. One of the most limiting approximations is the lumping of the physical properties of the porous fuel with the heterogeneous chemical reaction rate constants. The primary objective of the present work is to develop a rigorous model that could decouple such physical and chemical effects from the global heterogeneous reaction rates. For the purpose of validating this model, experiments with porous graphite particles of varying sizes and porosity are being performed. The details of this experimental and theoretical model development effort are described.

Assessing Environmental Consequences of Ticcing in Youth with Chronic Tic Disorders: The Tic Accommodation and Reactions Scale

PubMed Central

Capriotti, Matthew R.; Piacentini, John C.; Himle, Michael B.; Ricketts, Emily J.; Espil, Flint M.; Lee, Han Joo; Turkel, Jennifer E.; Woods, Douglas W.

2015-01-01

Tics associated with Tourette syndrome and other chronic tic disorders (CTDs) often draw social reactions and disrupt ongoing behavior. In some cases, such tic-related consequences may function to alter moment-to-moment and future tic severity. These observations have been incorporated into contemporary biopsychosocial models of CTD phenomenology, but systematic research detailing the nature of the relationship between environmental consequences and ticcing remains scarce. This study describes the development of the Tic Accommodation and Reactions Scale (TARS), a measure of the number and frequency of immediate consequences for ticcing experienced by youth with CTDs. Thirty eight youth with CTDs and their parents completed the TARS as part of a broader assessment of CTD symptoms and psychosocial functioning. The TARS demonstrated good psychometric properties (i.e., internal consistency, parent-child agreement, convergent validity, discriminant validity). Differences between parent-reported and child-reported data indicated that children may provide more valid reports of tic-contingent consequences than parents. Although preliminary, results of this study suggest that the TARS is a psychometrically sound measure of tic-related consequences suited for future research in youth with CTDs. PMID:27076696

UTCI-Fiala multi-node model of human heat transfer and temperature regulation

NASA Astrophysics Data System (ADS)

Fiala, Dusan; Havenith, George; Bröde, Peter; Kampmann, Bernhard; Jendritzky, Gerd

2012-05-01

The UTCI-Fiala mathematical model of human temperature regulation forms the basis of the new Universal Thermal Climate Index (UTC). Following extensive validation tests, adaptations and extensions, such as the inclusion of an adaptive clothing model, the model was used to predict human temperature and regulatory responses for combinations of the prevailing outdoor climate conditions. This paper provides an overview of the underlying algorithms and methods that constitute the multi-node dynamic UTCI-Fiala model of human thermal physiology and comfort. Treated topics include modelling heat and mass transfer within the body, numerical techniques, modelling environmental heat exchanges, thermoregulatory reactions of the central nervous system, and perceptual responses. Other contributions of this special issue describe the validation of the UTCI-Fiala model against measured data and the development of the adaptive clothing model for outdoor climates.

Combustion Of Porous Graphite Particles In Oxygen Enriched Air

NASA Technical Reports Server (NTRS)

Delisle, Andrew J.; Miller, Fletcher J.; Chelliah, Harsha K.

2003-01-01

Combustion of solid fuel particles has many important applications, including power generation and space propulsion systems. The current models available for describing the combustion process of these particles, especially porous solid particles, include various simplifying approximations. One of the most limiting approximations is the lumping of the physical properties of the porous fuel with the heterogeneous chemical reaction rate constants [1]. The primary objective of the present work is to develop a rigorous modeling approach that could decouple such physical and chemical effects from the global heterogeneous reaction rates. For the purpose of validating this model, experiments with porous graphite particles of varying sizes and porosity are being performed under normal and micro gravity.

Quasiclassical trajectory calculations to evaluate a kinematic constraint on internal energy in suprathreshold collision energy abstraction reactions

NASA Astrophysics Data System (ADS)

Shuman, Nicholas S.; Mihok, Morgan; Fistik, Margaret; Valentini, James J.

2005-08-01

Experimentally observed product quantum state distributions across a wide range of abstraction reactions at suprathreshold collision energies have shown a strong bias against product internal energy. Only a fraction, sometimes quite a small fraction, of the energetically accessible product quantum states are populated. Picconatto et al. [J. Chem. Phys. 114, 1663 (2001)] noted a simple mathematical relationship between the highest-energy rovibrational states observed and the kinematics of the reaction system. They proposed a reaction model based on reaction kinematics that quantitatively explains this behavior. The model is in excellent agreement with measured quantum state distributions. The assumptions of the model invoke detailed characteristics of reactive trajectories at suprathreshold collision energies. Here we test those assumptions using quasiclassical trajectory calculations for the abstraction reactions H +HCl→H2+Cl, D +HCl→HD+Cl, and H +DCl→HD+Cl. Trajectories were run on a potential-energy surface calculated with a London-Eyring-Polyani-Sato function with a localized 3-center term (LEPS-3C) previously shown to accurately reproduce experimentally observed product state distributions for the H +HCl abstraction reaction. The trajectories sample collision energies near threshold and also substantially above it. Although the trajectories demonstrate some aspects of the model, they show that it is not valid. However, the inadequacy of the proposed model does not invalidate the apparent kinematic basis of the observed energy constraint. The present results show that there must be some other molecular behavior rooted in the reaction kinematics that is the explanation and the source of the constraint.

Cross section of α-induced reactions on iridium isotopes obtained from thick target yield measurement for the astrophysical γ process

NASA Astrophysics Data System (ADS)

Szücs, T.; Kiss, G. G.; Gyürky, Gy.; Halász, Z.; Fülöp, Zs.; Rauscher, T.

2018-01-01

The stellar reaction rates of radiative α-capture reactions on heavy isotopes are of crucial importance for the γ process network calculations. These rates are usually derived from statistical model calculations, which need to be validated, but the experimental database is very scarce. This paper presents the results of α-induced reaction cross section measurements on iridium isotopes carried out at first close to the astrophysically relevant energy region. Thick target yields of 191Ir(α,γ)195Au, 191Ir(α,n)194Au, 193Ir(α,n)196mAu, 193Ir(α,n)196Au reactions have been measured with the activation technique between Eα = 13.4 MeV and 17 MeV. For the first time the thick target yield was determined with X-ray counting. This led to a previously unprecedented sensitivity. From the measured thick target yields, reaction cross sections are derived and compared with statistical model calculations. The recently suggested energy-dependent modification of the α + nucleus optical potential gives a good description of the experimental data.

Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems.

PubMed

Camunas-Soler, Joan; Alemany, Anna; Ritort, Felix

2017-01-27

Thermodynamic bulk measurements of binding reactions rely on the validity of the law of mass action and the assumption of a dilute solution. Yet, important biological systems such as allosteric ligand-receptor binding, macromolecular crowding, or misfolded molecules may not follow these assumptions and may require a particular reaction model. Here we introduce a fluctuation theorem for ligand binding and an experimental approach using single-molecule force spectroscopy to determine binding energies, selectivity, and allostery of nucleic acids and peptides in a model-independent fashion. A similar approach could be used for proteins. This work extends the use of fluctuation theorems beyond unimolecular folding reactions, bridging the thermodynamics of small systems and the basic laws of chemical equilibrium. Copyright © 2017, American Association for the Advancement of Science.

A Pre-Steady State Kinetic Analysis of the αY60W mutant of trans-3-Chloroacrylic Acid Dehalogenase: Implications for the Mechanism of the Wild-type Enzyme†

PubMed Central

Huddleston, Jamison P.; Schroeder, Gottfried K.; Johnson, Kenneth A.; Whitman, Christian P.

2012-01-01

The bacterial degradation of the nematicide 1,3-dichloropropene, an isomeric mixture, requires the action of trans- and cis-3-chloracrylic acid dehalogenase (CaaD and cis-CaaD, respectively). Both enzymes are tautomerase superfamily members and share a core catalytic mechanism for the hydrolytic dehalogenation of the respective isomer of 3-haloacrylate. The observation that cis-CaaD requires two additional residues raises the question of how CaaD carries out a comparable reaction with fewer catalytic residues. As part of an effort to determine the basis for the apparently simpler CaaD-catalyzed reaction, the kinetic mechanism was determined by stopped-flow and chemical quench techniques using a fluorescent mutant form of the enzyme, αY60W-CaaD, and trans-3-bromoacrylate as the substrate. The data from these experiments as well as bromide inhibition studies are best accommodated by a six-step model that provides individual rate constants for substrate binding, chemistry, and a proposed conformational change occurring after chemistry followed by release of malonate semialdehyde and bromide. The conformational change and product release rates are comparable and together they limit the rate of turnover. The kinetic analysis and modeling studies validate the αY60W-CaaD mutant as an accurate reporter of active site events during the course of the enzyme-catalyzed reaction. The kinetic mechanism for the αY60W-CaaD-catalyzed reaction is comparable to that obtained for the cis-CaaD-catalyzed reaction. The kinetic model and the validated αY60W-CaaD mutant set the stage for an analysis of active site mutants to explore the contributions of individual catalytic residues and the basis for the simplicity of the reaction. PMID:23110338

Fate of sessile droplet chemical agents in environmental substrates in the presence of physiochemical processes

NASA Astrophysics Data System (ADS)

Navaz, H. K.; Dang, A. L.; Atkinson, T.; Zand, A.; Nowakowski, A.; Kamensky, K.

2014-05-01

A general-purpose multi-phase and multi-component computer model capable of solving the complex problems encountered in the agent substrate interaction is developed. The model solves the transient and time-accurate mass and momentum governing equations in a three dimensional space. The provisions for considering all the inter-phase activities (solidification, evaporation, condensation, etc.) are included in the model. The chemical reactions among all phases are allowed and the products of the existing chemical reactions in all three phases are possible. The impact of chemical reaction products on the transport properties in porous media such as porosity, capillary pressure, and permeability is considered. Numerous validations for simulants, agents, and pesticides with laboratory and open air data are presented. Results for chemical reactions in the presence of pre-existing water in porous materials such as moisture, or separated agent and water droplets on porous substrates are presented. The model will greatly enhance the capabilities in predicting the level of threat after any chemical such as Toxic Industrial Chemicals (TICs) and Toxic Industrial Materials (TIMs) release on environmental substrates. The model's generality makes it suitable for both defense and pharmaceutical applications.

Modeling the oxidation kinetics of sono-activated persulfate's process on the degradation of humic acid.

PubMed

Songlin, Wang; Ning, Zhou; Si, Wu; Qi, Zhang; Zhi, Yang

2015-03-01

Ultrasound degradation of humic acid has been investigated in the presence of persulfate anions at ultrasonic frequency of 40 kHz. The effects of persulfate anion concentration, ultrasonic power input, humic acid concentration, reaction time, solution pH and temperature on humic acid removal efficiency were studied. It is found that up to 90% humic acid removal efficiency was achieved after 2 h reaction. In this system, sulfate radicals (SO₄⁻·) were considered to be the mainly oxidant to mineralize humic acid while persulfate anion can hardly react with humic acid directly. A novel kinetic model based on sulfate radicals (SO₄⁻·) oxidation was established to describe the humic acid mineralization process mathematically and chemically in sono-activated persulfate system. According to the new model, ultrasound power, persulfate dosage, solution pH and reaction temperature have great influence on humic acid degradation. Different initial concentration of persulfate anions and humic acid, ultrasonic power, initial pH and reaction temperature have been discussed to valid the effectiveness of the model, and the simulated data showed new model had good agreement with the experiments data.

Electrodisintegration of Li 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bishop, G. R.; Bernheim, M.

1963-06-01

For the ( γ,n) reaction in Li 6 a model in which Li 6 splits into a deuteron and an alpha particle that separately absorb the photon energy was recently proposed. The model was tested by studying the inelastic scattering of 101.4-Mev electrons from Li 6. Expressions for the cross sections were obtained, and values calculated for a form factor in the cross sections confirm the validity of the model.

A Mathematical Model for the Multiphase Transport and Reaction Kinetics in a Ladle with Bottom Powder Injection

NASA Astrophysics Data System (ADS)

Lou, Wentao; Zhu, Miaoyong

2017-12-01

A computation fluid dynamics-population balance model-simultaneous reaction model (CFD-PBM-SRM) coupled model has been proposed to study the multiphase flow behavior and refining reaction kinetics in a ladle with bottom powder injection, and some new and important phenomena and mechanisms are presented. For the multiphase flow behavior, the effects of bubbly plume flow, powder particle motion, particle-particle collision and growth, particle-bubble collision and adhesion, and powder particle removal into top slag are considered. For the reaction kinetics, the mechanisms of multicomponent simultaneous reactions, including Al, S, Si, Mn, Fe, and O, at the multi-interface, including top slag-liquid steel interface, air-liquid steel interface, powder droplet-liquid steel interface, and bubble-liquid steel interface, are presented, and the effect of sulfur solubility in the powder droplet on the desulfurization is also taken into account. Model validation is carried out using hot tests in a 2-t induction furnace with bottom powder injection. The result shows that the powder particles gradually disperse in the entire furnace; in the vicinity of the bottom slot plugs, the desulfurization product CaS is liquid phase, while in the upper region of the furnace, the desulfurization product CaS is solid phase. The predicted sulfur contents by the present model agree well with the measured data in the 2-t furnace with bottom powder injection.

Modeling non-equilibrium mass transport in biologically reactive porous media

NASA Astrophysics Data System (ADS)

Davit, Yohan; Debenest, Gérald; Wood, Brian D.; Quintard, Michel

2010-09-01

We develop a one-equation non-equilibrium model to describe the Darcy-scale transport of a solute undergoing biodegradation in porous media. Most of the mathematical models that describe the macroscale transport in such systems have been developed intuitively on the basis of simple conceptual schemes. There are two problems with such a heuristic analysis. First, it is unclear how much information these models are able to capture; that is, it is not clear what the model's domain of validity is. Second, there is no obvious connection between the macroscale effective parameters and the microscopic processes and parameters. As an alternative, a number of upscaling techniques have been developed to derive the appropriate macroscale equations that are used to describe mass transport and reactions in multiphase media. These approaches have been adapted to the problem of biodegradation in porous media with biofilms, but most of the work has focused on systems that are restricted to small concentration gradients at the microscale. This assumption, referred to as the local mass equilibrium approximation, generally has constraints that are overly restrictive. In this article, we devise a model that does not require the assumption of local mass equilibrium to be valid. In this approach, one instead requires only that, at sufficiently long times, anomalous behaviors of the third and higher spatial moments can be neglected; this, in turn, implies that the macroscopic model is well represented by a convection-dispersion-reaction type equation. This strategy is very much in the spirit of the developments for Taylor dispersion presented by Aris (1956). On the basis of our numerical results, we carefully describe the domain of validity of the model and show that the time-asymptotic constraint may be adhered to even for systems that are not at local mass equilibrium.

Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

NASA Astrophysics Data System (ADS)

Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; Regan, John M.; Mench, Matthew M.

2016-10-01

This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions in a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.

Modeling and validation of single-chamber microbial fuel cell cathode biofilm growth and response to oxidant gas composition

DOE PAGES

Ou, Shiqi; Zhao, Yi; Aaron, Douglas S.; ...

2016-08-15

This work describes experiments and computational simulations to analyze single-chamber, air-cathode microbial fuel cell (MFC) performance and cathodic limitations in terms of current generation, power output, mass transport, biomass competition, and biofilm growth. Steady-state and transient cathode models were developed and experimentally validated. Two cathode gas mixtures were used to explore oxygen transport in the cathode: the MFCs exposed to a helium-oxygen mixture (heliox) produced higher current and power output than the group of MFCs exposed to air or a nitrogen-oxygen mixture (nitrox), indicating a dependence on gas-phase transport in the cathode. Multi-substance transport, biological reactions, and electrochemical reactions inmore » a multi-layer and multi-biomass cathode biofilm were also simulated in a transient model. The transient model described biofilm growth over 15 days while providing insight into mass transport and cathodic dissolved species concentration profiles during biofilm growth. Lastly, simulation results predict that the dissolved oxygen content and diffusion in the cathode are key parameters affecting the power output of the air-cathode MFC system, with greater oxygen content in the cathode resulting in increased power output and fully-matured biomass.« less

Nuclear reaction measurements on tissue-equivalent materials and GEANT4 Monte Carlo simulations for hadrontherapy

NASA Astrophysics Data System (ADS)

De Napoli, M.; Romano, F.; D'Urso, D.; Licciardello, T.; Agodi, C.; Candiano, G.; Cappuzzello, F.; Cirrone, G. A. P.; Cuttone, G.; Musumarra, A.; Pandola, L.; Scuderi, V.

2014-12-01

When a carbon beam interacts with human tissues, many secondary fragments are produced into the tumor region and the surrounding healthy tissues. Therefore, in hadrontherapy precise dose calculations require Monte Carlo tools equipped with complex nuclear reaction models. To get realistic predictions, however, simulation codes must be validated against experimental results; the wider the dataset is, the more the models are finely tuned. Since no fragmentation data for tissue-equivalent materials at Fermi energies are available in literature, we measured secondary fragments produced by the interaction of a 55.6 MeV u-1 12C beam with thick muscle and cortical bone targets. Three reaction models used by the Geant4 Monte Carlo code, the Binary Light Ions Cascade, the Quantum Molecular Dynamic and the Liege Intranuclear Cascade, have been benchmarked against the collected data. In this work we present the experimental results and we discuss the predictive power of the above mentioned models.

Quantum Yield of Cyclobutane Pyrimidine Dimer Formation Via the Triplet Channel Determined by Photosensitization.

PubMed

Liu, Lizhe; Pilles, Bert M; Gontcharov, Julia; Bucher, Dominik B; Zinth, Wolfgang

2016-01-21

UV-induced formation of the cyclobutane pyrimidine dimer (CPD) lesion is investigated by stationary and time-resolved photosensitization experiments. The photosensitizer 2'-methoxyacetophenone with high intersystem crossing efficiency and large absorption cross-section in the UV-A range was used. A diffusion controlled reaction model is presented. Time-resolved experiments confirmed the validity of the reaction model and provided information on the dynamics of the triplet sensitization process. With a series of concentration dependent stationary illumination experiments, we determined the quantum efficiency for CPD formation from the triplet state of the thymine dinucleotide TpT to be 4 ± 0.2%.

The efficiency of driving chemical reactions by a physical non-equilibrium is kinetically controlled.

PubMed

Göppel, Tobias; Palyulin, Vladimir V; Gerland, Ulrich

2016-07-27

An out-of-equilibrium physical environment can drive chemical reactions into thermodynamically unfavorable regimes. Under prebiotic conditions such a coupling between physical and chemical non-equilibria may have enabled the spontaneous emergence of primitive evolutionary processes. Here, we study the coupling efficiency within a theoretical model that is inspired by recent laboratory experiments, but focuses on generic effects arising whenever reactant and product molecules have different transport coefficients in a flow-through system. In our model, the physical non-equilibrium is represented by a drift-diffusion process, which is a valid coarse-grained description for the interplay between thermophoresis and convection, as well as for many other molecular transport processes. As a simple chemical reaction, we consider a reversible dimerization process, which is coupled to the transport process by different drift velocities for monomers and dimers. Within this minimal model, the coupling efficiency between the non-equilibrium transport process and the chemical reaction can be analyzed in all parameter regimes. The analysis shows that the efficiency depends strongly on the Damköhler number, a parameter that measures the relative timescales associated with the transport and reaction kinetics. Our model and results will be useful for a better understanding of the conditions for which non-equilibrium environments can provide a significant driving force for chemical reactions in a prebiotic setting.

Chemical reaction networks as a model to describe UVC- and radiolytically-induced reactions of simple compounds.

PubMed

Dondi, Daniele; Merli, Daniele; Albini, Angelo; Zeffiro, Alberto; Serpone, Nick

2012-05-01

When a chemical system is submitted to high energy sources (UV, ionizing radiation, plasma sparks, etc.), as is expected to be the case of prebiotic chemistry studies, a plethora of reactive intermediates could form. If oxygen is present in excess, carbon dioxide and water are the major products. More interesting is the case of reducing conditions where synthetic pathways are also possible. This article examines the theoretical modeling of such systems with random-generated chemical networks. Four types of random-generated chemical networks were considered that originated from a combination of two connection topologies (viz., Poisson and scale-free) with reversible and irreversible chemical reactions. The results were analyzed taking into account the number of the most abundant products required for reaching 50% of the total number of moles of compounds at equilibrium, as this may be related to an actual problem of complex mixture analysis. The model accounts for multi-component reaction systems with no a priori knowledge of reacting species and the intermediates involved if system components are sufficiently interconnected. The approach taken is relevant to an earlier study on reactions that may have occurred in prebiotic systems where only a few compounds were detected. A validation of the model was attained on the basis of results of UVC and radiolytic reactions of prebiotic mixtures of low molecular weight compounds likely present on the primeval Earth.

Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling.

PubMed

Schaefer, C; Jansen, A P J

2013-02-07

We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature.

Kinetic analysis of overlapping multistep thermal decomposition comprising exothermic and endothermic processes: thermolysis of ammonium dinitramide.

PubMed

Muravyev, Nikita V; Koga, Nobuyoshi; Meerov, Dmitry B; Pivkina, Alla N

2017-01-25

This study focused on kinetic modeling of a specific type of multistep heterogeneous reaction comprising exothermic and endothermic reaction steps, as exemplified by the practical kinetic analysis of the experimental kinetic curves for the thermal decomposition of molten ammonium dinitramide (ADN). It is known that the thermal decomposition of ADN occurs as a consecutive two step mass-loss process comprising the decomposition of ADN and subsequent evaporation/decomposition of in situ generated ammonium nitrate. These reaction steps provide exothermic and endothermic contributions, respectively, to the overall thermal effect. The overall reaction process was deconvoluted into two reaction steps using simultaneously recorded thermogravimetry and differential scanning calorimetry (TG-DSC) curves by considering the different physical meanings of the kinetic data derived from TG and DSC by P value analysis. The kinetic data thus separated into exothermic and endothermic reaction steps were kinetically characterized using kinetic computation methods including isoconversional method, combined kinetic analysis, and master plot method. The overall kinetic behavior was reproduced as the sum of the kinetic equations for each reaction step considering the contributions to the rate data derived from TG and DSC. During reproduction of the kinetic behavior, the kinetic parameters and contributions of each reaction step were optimized using kinetic deconvolution analysis. As a result, the thermal decomposition of ADN was successfully modeled as partially overlapping exothermic and endothermic reaction steps. The logic of the kinetic modeling was critically examined, and the practical usefulness of phenomenological modeling for the thermal decomposition of ADN was illustrated to demonstrate the validity of the methodology and its applicability to similar complex reaction processes.

Evaluation of a Genome-Scale In Silico Metabolic Model for Geobacter metallireducens Using Proteomic Data from a Field Biostimulation Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fang, Yilin; Wilkins, Michael J.; Yabusaki, Steven B.

2012-12-12

Biomass and shotgun global proteomics data that reflected relative protein abundances from samples collected during the 2008 experiment at the U.S. Department of Energy Integrated Field-Scale Subsurface Research Challenge site in Rifle, Colorado, provided an unprecedented opportunity to validate a genome-scale metabolic model of Geobacter metallireducens and assess its performance with respect to prediction of metal reduction, biomass yield, and growth rate under dynamic field conditions. Reconstructed from annotated genomic sequence, biochemical, and physiological data, the constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes.more » Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low fluxes through amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.« less

Reaction time as an indicator of insufficient effort: Development and validation of an embedded performance validity parameter.

PubMed

Stevens, Andreas; Bahlo, Simone; Licha, Christina; Liske, Benjamin; Vossler-Thies, Elisabeth

2016-11-30

Subnormal performance in attention tasks may result from various sources including lack of effort. In this report, the derivation and validation of a performance validity parameter for reaction time is described, using a set of malingering-indices ("Slick-criteria"), and 3 independent samples of participants (total n =893). The Slick-criteria yield an estimate of the probability of malingering based on the presence of an external incentive, evidence from neuropsychological testing, from self-report and clinical data. In study (1) a validity parameter is derived using reaction time data of a sample, composed of inpatients with recent severe brain lesions not involved in litigation and of litigants with and without brain lesion. In study (2) the validity parameter is tested in an independent sample of litigants. In study (3) the parameter is applied to an independent sample comprising cooperative and non-cooperative testees. Logistic regression analysis led to a derived validity parameter based on median reaction time and standard deviation. It performed satisfactorily in studies (2) and (3) (study 2 sensitivity=0.94, specificity=1.00; study 3 sensitivity=0.79, specificity=0.87). The findings suggest that median reaction time and standard deviation may be used as indicators of negative response bias. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The single-zone numerical model of homogeneous charge compression ignition engine performance

NASA Astrophysics Data System (ADS)

Fedyanov, E. A.; Itkis, E. M.; Kuzmin, V. N.; Shumskiy, S. N.

2017-02-01

The single-zone model of methane-air mixture combustion in the Homogeneous Charge Compression Ignition engine was developed. First modeling efforts resulted in the selection of the detailed kinetic reaction mechanism, most appropriate for the conditions of the HCCI process. Then, the model was completed so as to simulate the performance of the four-stroke engine and was coupled by physically reasonable adjusting functions. Validation of calculations against experimental data showed acceptable agreement.

Computational Fluid Dynamics Modeling of Nickel Hydrogen Batteries

NASA Technical Reports Server (NTRS)

Cullion, R.; Gu, W. B.; Wang, C. Y.; Timmerman, P.

2000-01-01

An electrochemical Ni-H2 battery model has been expanded to include thermal effects. A thermal energy conservation equation was derived from first principles. An electrochemical and thermal coupled model was created by the addition of this equation to an existing multiphase, electrochemical model. Charging at various rates was investigated and the results validated against experimental data. Reaction currents, pressure changes, temperature profiles, and concentration variations within the cell are predicted numerically and compared with available data and theory.

Generating functionals and Gaussian approximations for interruptible delay reactions

NASA Astrophysics Data System (ADS)

Brett, Tobias; Galla, Tobias

2015-10-01

We develop a generating functional description of the dynamics of non-Markovian individual-based systems in which delay reactions can be terminated before completion. This generalizes previous work in which a path-integral approach was applied to dynamics in which delay reactions complete with certainty. We construct a more widely applicable theory, and from it we derive Gaussian approximations of the dynamics, valid in the limit of large, but finite, population sizes. As an application of our theory we study predator-prey models with delay dynamics due to gestation or lag periods to reach the reproductive age. In particular, we focus on the effects of delay on noise-induced cycles.

Segmental Dynamics of Forward Fall Arrests: System Identification Approach

PubMed Central

Kim, Kyu-Jung; Ashton-Miller, James A.

2009-01-01

Background Fall-related injuries are multifaceted problems, necessitating thorough biodynamic simulation to identify critical biomechanical factors. Methods A 2-degree-of-freedom discrete impact model was constructed through system identification and validation processes using the experimental data to understand dynamic interactions of various biomechanical parameters in bimanual forward fall arrests. Findings The bimodal reaction force response from the identified models had small identification errors for the first and second force peaks less than 3.5% and high coherence between the measured and identified model responses (R2=0.95). Model validation with separate experimental data also demonstrated excellent validation accuracy and coherence, less than 7% errors and R2=0.87, respectively. The first force peak was usually greater than the second force peak and strongly correlated with the impact velocity of the upper extremity, while the second force peak was associated with the impact velocity of the body. The impact velocity of the upper extremity relative to the body could be a major risk factor to fall-related injuries as observed from model simulations that a 75% faster arm movement relative to the falling speed of the body alone could double the first force peak from soft landing, thereby readily exceeding the fracture strength of the distal radius. Interpretation Considering that the time-critical nature of falling often calls for a fast arm movement, the use of the upper extremity in forward fall arrests is not biomechanically justified unless sufficient reaction time and coordinated protective motion of the upper extremity are available. PMID:19250726

Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations for solvent-based carbon capture. Part 2: Chemical absorption across a wetted wall column: Original Research Article: Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Chao; Xu, Zhijie; Lai, Kevin

Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO2) capture. To generate data for WWC model validation, CO2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO2 in MEA. In addition, the overall mass transfer coefficient predictedmore » using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO2 reaction rate constants after using the N2O/CO2 analogy method. The calibrated model can be used to predict the CO2 mass transfer in a WWC for a wider range of operating conditions.« less

Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations for solvent-based carbon capture. Part 2: Chemical absorption across a wetted wall column: Original Research Article: Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations

DOE PAGES

Wang, Chao; Xu, Zhijie; Lai, Kevin; ...

2017-10-24

Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO2) capture. To generate data for WWC model validation, CO2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO2 in MEA. In addition, the overall mass transfer coefficient predictedmore » using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO2 reaction rate constants after using the N2O/CO2 analogy method. The calibrated model can be used to predict the CO2 mass transfer in a WWC for a wider range of operating conditions.« less

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Minjing; Qian, Wei-jun; Gao, Yuqian

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes asmore » time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates« less

Effect of friction on electron transfer: The two reaction coordinate case

NASA Astrophysics Data System (ADS)

Onuchic, José Nelson

1987-04-01

Electron transfer is a very important reaction in many biological processes such as photosynthesis and oxidative phosphorylation. In many of these reactions, most of the interesting dynamics can be included by using two reaction coordinates: one fast (local high frequency vibration modes) and one slow (outersphere modes such as solvent polarization). We report a model to describe this problem, which uses path integral techniques to calculate electron transfer rates, and also to obtain the Fokker-Planck equations associated with this model. Different limiting cases lead to qualitatively different results such as exponential or nonexponential time decay for the donor survival probability. Conditions for the validity of the adiabatic or the nonadiabatic limits will be discussed. Application of this model to real systems is proposed, in particular for a porphyrin rigidly linked to a quinone, which is a very interesting model compound for primary events of photosynthesis. This model can also be used for other multicoordinate biological reactions such as ligand binding to heme proteins. Also, in the concluding part of Sec. III, we discuss the important limit where the fast vibronic mode is much faster than all the other nuclear modes coupled to the problem. In this limit the fast mode ``renormalizes'' the electronic matrix element, and this considerably simplifies the treatment of the problem, reducing it to coupling only to the slow modes.

An Improved Swarm Optimization for Parameter Estimation and Biological Model Selection

PubMed Central

Abdullah, Afnizanfaizal; Deris, Safaai; Mohamad, Mohd Saberi; Anwar, Sohail

2013-01-01

One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data. PMID:23593445

Termolecular ion-molecule reactions in Titan's atmosphere. IV. A search made at up to 1 micron in pure hydrocarbons

NASA Technical Reports Server (NTRS)

Anicich, Vincent G.; Wilson, Paul; McEwan, Murray J.

2003-01-01

The results of a study of ion-molecule reactions occurring in pure methane, acetylene, ethylene, ethane, propyne, propene, propane, and diacetylene at pressures up to 40 microns of pressure are reported. A variety of experimental methods are used: The standard double resonance in an ICR, for determination of the precursor ions and the modulated double resonance ejection in an ICR, for the determination of the daughter ions. The FA-SIFT technique was used for validation and examination of termolecular reactions with rate coefficients that are less than 10(-26) cm(6) s(-1). An extensive database of reaction kinetics already exists for many of these reactions. The main point of this study was the determination of the accuracy of this database and to search for any missing reactions and reaction channels that may have been omitted from earlier investigations. A specific objective of this work was to extend the study to the highest pressures possible to find out if there were any important termolecular reaction channels occurring. A new approach was used here. In the pure hydrocarbon gases the mass spectra were followed as a function of the pressure changes of the gas. An initial guess was first made using the current literature as a source of the reaction kinetics that were expected. A model of the ion abundances was produced from the solution of the partial differential equations in terms of reaction rate coefficients and initial abundances. The experimental data was fitted to the model for all of the pressures by a least squares minimization to the reaction rate coefficients and initial abundances. The reaction rate coefficients obtained from the model were then compared to the literature values. Several new channels and reactions were discovered when the modeled fits were compared to the actual data. This is all explained in the text and the implications of these results are discussed for the Titan atmosphere.

Intervertebral reaction force prediction using an enhanced assembly of OpenSim models.

PubMed

Senteler, Marco; Weisse, Bernhard; Rothenfluh, Dominique A; Snedeker, Jess G

2016-01-01

OpenSim offers a valuable approach to investigating otherwise difficult to assess yet important biomechanical parameters such as joint reaction forces. Although the range of available models in the public repository is continually increasing, there currently exists no OpenSim model for the computation of intervertebral joint reactions during flexion and lifting tasks. The current work combines and improves elements of existing models to develop an enhanced model of the upper body and lumbar spine. Models of the upper body with extremities, neck and head were combined with an improved version of a lumbar spine from the model repository. Translational motion was enabled for each lumbar vertebrae with six controllable degrees of freedom. Motion segment stiffness was implemented at lumbar levels and mass properties were assigned throughout the model. Moreover, body coordinate frames of the spine were modified to allow straightforward variation of sagittal alignment and to simplify interpretation of results. Evaluation of model predictions for level L1-L2, L3-L4 and L4-L5 in various postures of forward flexion and moderate lifting (8 kg) revealed an agreement within 10% to experimental studies and model-based computational analyses. However, in an extended posture or during lifting of heavier loads (20 kg), computed joint reactions differed substantially from reported in vivo measures using instrumented implants. We conclude that agreement between the model and available experimental data was good in view of limitations of both the model and the validation datasets. The presented model is useful in that it permits computation of realistic lumbar spine joint reaction forces during flexion and moderate lifting tasks. The model and corresponding documentation are now available in the online OpenSim repository.

A Mathematical Model for Reactions During Top-Blowing in the AOD Process: Validation and Results

NASA Astrophysics Data System (ADS)

Visuri, Ville-Valtteri; Järvinen, Mika; Kärnä, Aki; Sulasalmi, Petri; Heikkinen, Eetu-Pekka; Kupari, Pentti; Fabritius, Timo

2017-06-01

In earlier work, a fundamental mathematical model was proposed for side-blowing operation in the argon oxygen decarburization (AOD) process. In the preceding part "Derivation of the Model," a new mathematical model was proposed for reactions during top-blowing in the AOD process. In this model it was assumed that reactions occur simultaneously at the surface of the cavity caused by the gas jet and at the surface of the metal droplets ejected from the metal bath. This paper presents validation and preliminary results with twelve industrial heats. In the studied heats, the last combined-blowing stage was altered so that oxygen was introduced from the top lance only. Four heats were conducted using an oxygen-nitrogen mixture (1:1), while eight heats were conducted with pure oxygen. Simultaneously, nitrogen or argon gas was blown via tuyères in order to provide mixing that is comparable to regular practice. The measured carbon content varied from 0.4 to 0.5 wt pct before the studied stage to 0.1 to 0.2 wt pct after the studied stage. The results suggest that the model is capable of predicting changes in metal bath composition and temperature with a reasonably high degree of accuracy. The calculations indicate that the top slag may supply oxygen for decarburization during top-blowing. Furthermore, it is postulated that the metal droplets generated by the shear stress of top-blowing create a large mass exchange area, which plays an important role in enabling the high decarburization rates observed during top-blowing in the AOD process. The overall rate of decarburization attributable to top-blowing in the last combined-blowing stage was found to be limited by the mass transfer of dissolved carbon.

Classifying vulnerability to sleep deprivation using baseline measures of psychomotor vigilance.

PubMed

Patanaik, Amiya; Kwoh, Chee Keong; Chua, Eric C P; Gooley, Joshua J; Chee, Michael W L

2015-05-01

To identify measures derived from baseline psychomotor vigilance task (PVT) performance that can reliably predict vulnerability to sleep deprivation. Subjects underwent total sleep deprivation and completed a 10-min PVT every 1-2 h in a controlled laboratory setting. Participants were categorized as vulnerable or resistant to sleep deprivation, based on a median split of lapses that occurred following sleep deprivation. Standard reaction time, drift diffusion model (DDM), and wavelet metrics were derived from PVT response times collected at baseline. A support vector machine model that incorporated maximum relevance and minimum redundancy feature selection and wrapper-based heuristics was used to classify subjects as vulnerable or resistant using rested data. Two academic sleep laboratories. Independent samples of 135 (69 women, age 18 to 25 y), and 45 (3 women, age 22 to 32 y) healthy adults. In both datasets, DDM measures, number of consecutive reaction times that differ by more than 250 ms, and two wavelet features were selected by the model as features predictive of vulnerability to sleep deprivation. Using the best set of features selected in each dataset, classification accuracy was 77% and 82% using fivefold stratified cross-validation, respectively. In both datasets, DDM measures, number of consecutive reaction times that differ by more than 250 ms, and two wavelet features were selected by the model as features predictive of vulnerability to sleep deprivation. Using the best set of features selected in each dataset, classification accuracy was 77% and 82% using fivefold stratified cross-validation, respectively. Despite differences in experimental conditions across studies, drift diffusion model parameters associated reliably with individual differences in performance during total sleep deprivation. These results demonstrate the utility of drift diffusion modeling of baseline performance in estimating vulnerability to psychomotor vigilance decline following sleep deprivation. © 2015 Associated Professional Sleep Societies, LLC.

Thermally multiplexed polymerase chain reaction.

PubMed

Phaneuf, Christopher R; Pak, Nikita; Saunders, D Curtis; Holst, Gregory L; Birjiniuk, Joav; Nagpal, Nikita; Culpepper, Stephen; Popler, Emily; Shane, Andi L; Jerris, Robert; Forest, Craig R

2015-07-01

Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously-each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.

Validation of the concentration profiles obtained from the near infrared/multivariate curve resolution monitoring of reactions of epoxy resins using high performance liquid chromatography as a reference method.

PubMed

Garrido, M; Larrechi, M S; Rius, F X

2007-03-07

This paper reports the validation of the results obtained by combining near infrared spectroscopy and multivariate curve resolution-alternating least squares (MCR-ALS) and using high performance liquid chromatography as a reference method, for the model reaction of phenylglycidylether (PGE) and aniline. The results are obtained as concentration profiles over the reaction time. The trueness of the proposed method has been evaluated in terms of lack of bias. The joint test for the intercept and the slope showed that there were no significant differences between the profiles calculated spectroscopically and the ones obtained experimentally by means of the chromatographic reference method at an overall level of confidence of 5%. The uncertainty of the results was estimated by using information derived from the process of assessment of trueness. Such operational aspects as the cost and availability of instrumentation and the length and cost of the analysis were evaluated. The method proposed is a good way of monitoring the reactions of epoxy resins, and it adequately shows how the species concentration varies over time.

Comparison of 3D dynamic virtual model to link segment model for estimation of net L4/L5 reaction moments during lifting.

PubMed

Abdoli-Eramaki, Mohammad; Stevenson, Joan M; Agnew, Michael J; Kamalzadeh, Amin

2009-04-01

The purpose of this study was to validate a 3D dynamic virtual model for lifting tasks against a validated link segment model (LSM). A face validation study was conducted by collecting x, y, z coordinate data and using them in both virtual and LSM models. An upper body virtual model was needed to calculate the 3D torques about human joints for use in simulated lifting styles and to estimate the effect of external mechanical devices on human body. Firstly, the model had to be validated to be sure it provided accurate estimates of 3D moments in comparison to a previously validated LSM. Three synchronised Fastrak units with nine sensors were used to record data from one male subject who completed dynamic box lifting under 27 different load conditions (box weights (3), lifting techniques (3) and rotations (3)). The external moments about three axes of L4/L5 were compared for both models. A pressure switch on the box was used to denote the start and end of the lift. An excellent agreement [image omitted] was found between the two models for dynamic lifting tasks, especially for larger moments in flexion and extension. This virtual model was considered valid for use in a complete simulation of the upper body skeletal system. This biomechanical virtual model of the musculoskeletal system can be used by researchers and practitioners to give a better tool to study the causes of LBP and the effect of intervention strategies, by permitting the researcher to see and control a virtual subject's motions.

Evaluation of a genome-scale in silico metabolic model for Geobacter metallireducens by using proteomic data from a field biostimulation experiment.

PubMed

Fang, Yilin; Wilkins, Michael J; Yabusaki, Steven B; Lipton, Mary S; Long, Philip E

2012-12-01

Accurately predicting the interactions between microbial metabolism and the physical subsurface environment is necessary to enhance subsurface energy development, soil and groundwater cleanup, and carbon management. This study was an initial attempt to confirm the metabolic functional roles within an in silico model using environmental proteomic data collected during field experiments. Shotgun global proteomics data collected during a subsurface biostimulation experiment were used to validate a genome-scale metabolic model of Geobacter metallireducens-specifically, the ability of the metabolic model to predict metal reduction, biomass yield, and growth rate under dynamic field conditions. The constraint-based in silico model of G. metallireducens relates an annotated genome sequence to the physiological functions with 697 reactions controlled by 747 enzyme-coding genes. Proteomic analysis showed that 180 of the 637 G. metallireducens proteins detected during the 2008 experiment were associated with specific metabolic reactions in the in silico model. When the field-calibrated Fe(III) terminal electron acceptor process reaction in a reactive transport model for the field experiments was replaced with the genome-scale model, the model predicted that the largest metabolic fluxes through the in silico model reactions generally correspond to the highest abundances of proteins that catalyze those reactions. Central metabolism predicted by the model agrees well with protein abundance profiles inferred from proteomic analysis. Model discrepancies with the proteomic data, such as the relatively low abundances of proteins associated with amino acid transport and metabolism, revealed pathways or flux constraints in the in silico model that could be updated to more accurately predict metabolic processes that occur in the subsurface environment.

Quantum chemical modeling of enzymatic reactions: the case of histone lysine methyltransferase.

PubMed

Georgieva, Polina; Himo, Fahmi

2010-06-01

Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods. Copyright 2010 Wiley Periodicals, Inc.

Verification Test of the SURF and SURFplus Models in xRage: Part II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Menikoff, Ralph

2016-06-20

The previous study used an underdriven detonation wave (steady ZND reaction zone profile followed by a scale invariant rarefaction wave) for PBX 9502 as a validation test of the implementation of the SURF and SURFplus models in the xRage code. Even with a fairly fine uniform mesh (12,800 cells for 100mm) the detonation wave profile had limited resolution due to the thin reaction zone width (0.18mm) for the fast SURF burn rate. Here we study the effect of finer resolution by comparing results of simulations with cell sizes of 8, 2 and 1 μm, which corresponds to 25, 100 andmore » 200 points within the reaction zone. With finer resolution the lead shock pressure is closer to the von Neumann spike pressure, and there is less noise in the rarefaction wave due to fluctuations within the reaction zone. As a result the average error decreases. The pointwise error is still dominated by the smearing the pressure kink in the vicinity of the sonic point which occurs at the end of the reaction zone.« less

Simulation of Fusion Plasmas

ScienceCinema

Holland, Chris [UC San Diego, San Diego, California, United States

2017-12-09

The upcoming ITER experiment (www.iter.org) represents the next major milestone in realizing the promise of using nuclear fusion as a commercial energy source, by moving into the “burning plasma” regime where the dominant heat source is the internal fusion reactions. As part of its support for the ITER mission, the US fusion community is actively developing validated predictive models of the behavior of magnetically confined plasmas. In this talk, I will describe how the plasma community is using the latest high performance computing facilities to develop and refine our models of the nonlinear, multiscale plasma dynamics, and how recent advances in experimental diagnostics are allowing us to directly test and validate these models at an unprecedented level.

Development of esMOCA Biomechanic, Motion Capture Instrumentation for Biomechanics Analysis

NASA Astrophysics Data System (ADS)

Arendra, A.; Akhmad, S.

2018-01-01

This study aims to build motion capture instruments using inertial measurement unit sensors to assist in the analysis of biomechanics. Sensors used are accelerometer and gyroscope. Estimation of orientation sensors is done by digital motion processing in each sensor nodes. There are nine sensor nodes attached to the upper limbs. This sensor is connected to the pc via a wireless sensor network. The development of kinematics and inverse dynamamic models of the upper limb is done in simulink simmechanic. The kinematic model receives streaming data of sensor nodes mounted on the limbs. The output of the kinematic model is the pose of each limbs and visualized on display. The dynamic inverse model outputs the reaction force and reaction moment of each joint based on the limb motion input. Model validation in simulink with mathematical model of mechanical analysis showed results that did not differ significantly

MT3DMS: Model use, calibration, and validation

USGS Publications Warehouse

Zheng, C.; Hill, Mary C.; Cao, G.; Ma, R.

2012-01-01

MT3DMS is a three-dimensional multi-species solute transport model for solving advection, dispersion, and chemical reactions of contaminants in saturated groundwater flow systems. MT3DMS interfaces directly with the U.S. Geological Survey finite-difference groundwater flow model MODFLOW for the flow solution and supports the hydrologic and discretization features of MODFLOW. MT3DMS contains multiple transport solution techniques in one code, which can often be important, including in model calibration. Since its first release in 1990 as MT3D for single-species mass transport modeling, MT3DMS has been widely used in research projects and practical field applications. This article provides a brief introduction to MT3DMS and presents recommendations about calibration and validation procedures for field applications of MT3DMS. The examples presented suggest the need to consider alternative processes as models are calibrated and suggest opportunities and difficulties associated with using groundwater age in transport model calibration.

Machine Learning in Computer-Aided Synthesis Planning.

PubMed

Coley, Connor W; Green, William H; Jensen, Klavs F

2018-05-15

Computer-aided synthesis planning (CASP) is focused on the goal of accelerating the process by which chemists decide how to synthesize small molecule compounds. The ideal CASP program would take a molecular structure as input and output a sorted list of detailed reaction schemes that each connect that target to purchasable starting materials via a series of chemically feasible reaction steps. Early work in this field relied on expert-crafted reaction rules and heuristics to describe possible retrosynthetic disconnections and selectivity rules but suffered from incompleteness, infeasible suggestions, and human bias. With the relatively recent availability of large reaction corpora (such as the United States Patent and Trademark Office (USPTO), Reaxys, and SciFinder databases), consisting of millions of tabulated reaction examples, it is now possible to construct and validate purely data-driven approaches to synthesis planning. As a result, synthesis planning has been opened to machine learning techniques, and the field is advancing rapidly. In this Account, we focus on two critical aspects of CASP and recent machine learning approaches to both challenges. First, we discuss the problem of retrosynthetic planning, which requires a recommender system to propose synthetic disconnections starting from a target molecule. We describe how the search strategy, necessary to overcome the exponential growth of the search space with increasing number of reaction steps, can be assisted through a learned synthetic complexity metric. We also describe how the recursive expansion can be performed by a straightforward nearest neighbor model that makes clever use of reaction data to generate high quality retrosynthetic disconnections. Second, we discuss the problem of anticipating the products of chemical reactions, which can be used to validate proposed reactions in a computer-generated synthesis plan (i.e., reduce false positives) to increase the likelihood of experimental success. While we introduce this task in the context of reaction validation, its utility extends to the prediction of side products and impurities, among other applications. We describe neural network-based approaches that we and others have developed for this forward prediction task that can be trained on previously published experimental data. Machine learning and artificial intelligence have revolutionized a number of disciplines, not limited to image recognition, dictation, translation, content recommendation, advertising, and autonomous driving. While there is a rich history of using machine learning for structure-activity models in chemistry, it is only now that it is being successfully applied more broadly to organic synthesis and synthesis design. As reported in this Account, machine learning is rapidly transforming CASP, but there are several remaining challenges and opportunities, many pertaining to the availability and standardization of both data and evaluation metrics, which must be addressed by the community at large.

Development of an Advanced Computational Model for OMCVD of Indium Nitride

NASA Technical Reports Server (NTRS)

Cardelino, Carlos A.; Moore, Craig E.; Cardelino, Beatriz H.; Zhou, Ning; Lowry, Sam; Krishnan, Anantha; Frazier, Donald O.; Bachmann, Klaus J.

1999-01-01

An advanced computational model is being developed to predict the formation of indium nitride (InN) film from the reaction of trimethylindium (In(CH3)3) with ammonia (NH3). The components are introduced into the reactor in the gas phase within a background of molecular nitrogen (N2). Organometallic chemical vapor deposition occurs on a heated sapphire surface. The model simulates heat and mass transport with gas and surface chemistry under steady state and pulsed conditions. The development and validation of an accurate model for the interactions between the diffusion of gas phase species and surface kinetics is essential to enable the regulation of the process in order to produce a low defect material. The validation of the model will be performed in concert with a NASA-North Carolina State University project.

Computational Fluid Dynamic Modeling of Zinc Slag Fuming Process in Top-Submerged Lance Smelting Furnace

NASA Astrophysics Data System (ADS)

Huda, Nazmul; Naser, Jamal; Brooks, Geoffrey; Reuter, Markus A.; Matusewicz, Robert W.

2012-02-01

Slag fuming is a reductive treatment process for molten zinciferous slags for extracting zinc in the form of metal vapor by injecting or adding a reductant source such as pulverized coal or lump coal and natural gas. A computational fluid dynamic (CFD) model was developed to study the zinc slag fuming process from imperial smelting furnace (ISF) slag in a top-submerged lance furnace and to investigate the details of fluid flow, reaction kinetics, and heat transfer in the furnace. The model integrates combustion phenomena and chemical reactions with the heat, mass, and momentum interfacial interaction between the phases present in the system. A commercial CFD package AVL Fire 2009.2 (AVL, Graz, Austria) coupled with a number of user-defined subroutines in FORTRAN programming language were used to develop the model. The model is based on three-dimensional (3-D) Eulerian multiphase flow approach, and it predicts the velocity and temperature field of the molten slag bath, generated turbulence, and vortex and plume shape at the lance tip. The model also predicts the mass fractions of slag and gaseous components inside the furnace. The model predicted that the percent of ZnO in the slag bath decreases linearly with time and is consistent broadly with the experimental data. The zinc fuming rate from the slag bath predicted by the model was validated through macrostep validation process against the experimental study of Waladan et al. The model results predicted that the rate of ZnO reduction is controlled by the mass transfer of ZnO from the bulk slag to slag-gas interface and rate of gas-carbon reaction for the specified simulation time studied. Although the model is based on zinc slag fuming, the basic approach could be expanded or applied for the CFD analysis of analogous systems.

Center for Modeling of Turbulence and Transition (CMOTT): Research Briefs, 1992

NASA Technical Reports Server (NTRS)

Liou, William W. (Editor)

1992-01-01

The progress is reported of the Center for Modeling of Turbulence and Transition (CMOTT). The main objective of the CMOTT is to develop, validate and implement the turbulence and transition models for practical engineering flows. The flows of interest are three-dimensional, incompressible and compressible flows with chemical reaction. The research covers two-equation (e.g., k-e) and algebraic Reynolds-stress models, second moment closure models, probability density function (pdf) models, Renormalization Group Theory (RNG), Large Eddy Simulation (LES) and Direct Numerical Simulation (DNS).

Liquid chromatography coupled to quadrupole-time of flight tandem mass spectrometry based quantitative structure-retention relationships of amino acid analogues derivatized via n-propyl chloroformate mediated reaction.

PubMed

Kritikos, Nikolaos; Tsantili-Kakoulidou, Anna; Loukas, Yannis L; Dotsikas, Yannis

2015-07-17

In the current study, quantitative structure-retention relationships (QSRR) were constructed based on data obtained by a LC-(ESI)-QTOF-MS/MS method for the determination of amino acid analogues, following their derivatization via chloroformate esters. Molecules were derivatized via n-propyl chloroformate/n-propanol mediated reaction. Derivatives were acquired through a liquid-liquid extraction procedure. Chromatographic separation is based on gradient elution using methanol/water mixtures from a 70/30% composition to an 85/15% final one, maintaining a constant rate of change. The group of examined molecules was diverse, including mainly α-amino acids, yet also β- and γ-amino acids, γ-amino acid analogues, decarboxylated and phosphorylated analogues and dipeptides. Projection to latent structures (PLS) method was selected for the formation of QSRRs, resulting in a total of three PLS models with high cross-validated coefficients of determination Q(2)Y. For this reason, molecular structures were previously described through the use of descriptors. Through stratified random sampling procedures, 57 compounds were split to a training set and a test set. Model creation was based on multiple criteria including principal component significance and eigenvalue, variable importance, form of residuals, etc. Validation was based on statistical metrics Rpred(2),QextF2(2),QextF3(2) for the test set and Roy's metrics rm(Av)(2) and rm(δ)(2), assessing both predictive stability and internal validity. Based on aforementioned models, simplified equivalent were then created using a multi-linear regression (MLR) method. MLR models were also validated with the same metrics. The suggested models are considered useful for the estimation of retention times of amino acid analogues for a series of applications. Copyright © 2015 Elsevier B.V. All rights reserved.

Reaction Wheel Disturbance Model Extraction Software - RWDMES

NASA Technical Reports Server (NTRS)

Blaurock, Carl

2009-01-01

The RWDMES is a tool for modeling the disturbances imparted on spacecraft by spinning reaction wheels. Reaction wheels are usually the largest disturbance source on a precision pointing spacecraft, and can be the dominating source of pointing error. Accurate knowledge of the disturbance environment is critical to accurate prediction of the pointing performance. In the past, it has been difficult to extract an accurate wheel disturbance model since the forcing mechanisms are difficult to model physically, and the forcing amplitudes are filtered by the dynamics of the reaction wheel. RWDMES captures the wheel-induced disturbances using a hybrid physical/empirical model that is extracted directly from measured forcing data. The empirical models capture the tonal forces that occur at harmonics of the spin rate, and the broadband forces that arise from random effects. The empirical forcing functions are filtered by a physical model of the wheel structure that includes spin-rate-dependent moments (gyroscopic terms). The resulting hybrid model creates a highly accurate prediction of wheel-induced forces. It accounts for variation in disturbance frequency, as well as the shifts in structural amplification by the whirl modes, as the spin rate changes. This software provides a point-and-click environment for producing accurate models with minimal user effort. Where conventional approaches may take weeks to produce a model of variable quality, RWDMES can create a demonstrably high accuracy model in two hours. The software consists of a graphical user interface (GUI) that enables the user to specify all analysis parameters, to evaluate analysis results and to iteratively refine the model. Underlying algorithms automatically extract disturbance harmonics, initialize and tune harmonic models, and initialize and tune broadband noise models. The component steps are described in the RWDMES user s guide and include: converting time domain data to waterfall PSDs (power spectral densities); converting PSDs to order analysis data; extracting harmonics; initializing and simultaneously tuning a harmonic model and a wheel structural model; initializing and tuning a broadband model; and verifying the harmonic/broadband/structural model against the measurement data. Functional operation is through a MATLAB GUI that loads test data, performs the various analyses, plots evaluation data for assessment and refinement of analysis parameters, and exports the data to documentation or downstream analysis code. The harmonic models are defined as specified functions of frequency, typically speed-squared. The reaction wheel structural model is realized as mass, damping, and stiffness matrices (typically from a finite element analysis package) with the addition of a gyroscopic forcing matrix. The broadband noise model is realized as a set of speed-dependent filters. The tuning of the combined model is performed using nonlinear least squares techniques. RWDMES is implemented as a MATLAB toolbox comprising the Fit Manager for performing the model extraction, Data Manager for managing input data and output models, the Gyro Manager for modifying wheel structural models, and the Harmonic Editor for evaluating and tuning harmonic models. This software was validated using data from Goodrich E wheels, and from GSFC Lunar Reconnaissance Orbiter (LRO) wheels. The validation testing proved that RWDMES has the capability to extract accurate disturbance models from flight reaction wheels with minimal user effort.

Kinetic approach for the enzymatic determination of levodopa and carbidopa assisted by multivariate curve resolution-alternating least squares.

PubMed

Grünhut, Marcos; Garrido, Mariano; Centurión, Maria E; Fernández Band, Beatriz S

2010-07-12

A combination of kinetic spectroscopic monitoring and multivariate curve resolution-alternating least squares (MCR-ALS) was proposed for the enzymatic determination of levodopa (LVD) and carbidopa (CBD) in pharmaceuticals. The enzymatic reaction process was carried out in a reverse stopped-flow injection system and monitored by UV-vis spectroscopy. The spectra (292-600 nm) were recorded throughout the reaction and were analyzed by multivariate curve resolution-alternating least squares. A small calibration matrix containing nine mixtures was used in the model construction. Additionally, to evaluate the prediction ability of the model, a set with six validation mixtures was used. The lack of fit obtained was 4.3%, the explained variance 99.8% and the overall prediction error 5.5%. Tablets of commercial samples were analyzed and the results were validated by pharmacopeia method (high performance liquid chromatography). No significant differences were found (alpha=0.05) between the reference values and the ones obtained with the proposed method. It is important to note that a unique chemometric model made it possible to determine both analytes simultaneously. Copyright 2010 Elsevier B.V. All rights reserved.

Nuclear Reaction Models Responsible for Simulation of Neutron-induced Soft Errors in Microelectronics

NASA Astrophysics Data System (ADS)

Watanabe, Y.; Abe, S.

2014-06-01

Terrestrial neutron-induced soft errors in MOSFETs from a 65 nm down to a 25 nm design rule are analyzed by means of multi-scale Monte Carlo simulation using the PHITS-HyENEXSS code system. Nuclear reaction models implemented in PHITS code are validated by comparisons with experimental data. From the analysis of calculated soft error rates, it is clarified that secondary He and H ions provide a major impact on soft errors with decreasing critical charge. It is also found that the high energy component from 10 MeV up to several hundreds of MeV in secondary cosmic-ray neutrons has the most significant source of soft errors regardless of design rule.

Novel particle tracking algorithm based on the Random Sample Consensus Model for the Active Target Time Projection Chamber (AT-TPC)

NASA Astrophysics Data System (ADS)

Ayyad, Yassid; Mittig, Wolfgang; Bazin, Daniel; Beceiro-Novo, Saul; Cortesi, Marco

2018-02-01

The three-dimensional reconstruction of particle tracks in a time projection chamber is a challenging task that requires advanced classification and fitting algorithms. In this work, we have developed and implemented a novel algorithm based on the Random Sample Consensus Model (RANSAC). The RANSAC is used to classify tracks including pile-up, to remove uncorrelated noise hits, as well as to reconstruct the vertex of the reaction. The algorithm, developed within the Active Target Time Projection Chamber (AT-TPC) framework, was tested and validated by analyzing the 4He+4He reaction. Results, performance and quality of the proposed algorithm are presented and discussed in detail.

Combined expectancies: electrophysiological evidence for the adjustment of expectancy effects

PubMed Central

Mattler, Uwe; van der Lugt, Arie; Münte, Thomas F

2006-01-01

Background When subjects use cues to prepare for a likely stimulus or a likely response, reaction times are facilitated by valid cues but prolonged by invalid cues. In studies on combined expectancy effects, two cues can independently give information regarding two dimensions of the forthcoming task. In certain situations, cueing effects on one dimension are reduced when the cue on the other dimension is invalid. According to the Adjusted Expectancy Model, cues affect different processing levels and a mechanism is presumed which is sensitive to the validity of early level cues and leads to online adjustment of expectancy effects at later levels. To examine the predictions of this model cueing of stimulus modality was combined with response cueing. Results Behavioral measures showed the interaction of cueing effects. Electrophysiological measures of the lateralized readiness potential (LRP) and the N200 amplitude confirmed the predictions of the model. The LRP showed larger effects of response cues on response activation when modality cues were valid rather than invalid. N200 amplitude was largest with valid modality cues and invalid response cues, medium with invalid modality cues, and smallest with two valid cues. Conclusion Findings support the view that the validity of early level expectancies modulates the effects of late level expectancies, which included response activation and response conflict in the present study. PMID:16674805

Elementary reaction modeling of reversible CO/CO2 electrochemical conversion on patterned nickel electrodes

NASA Astrophysics Data System (ADS)

Luo, Yu; Shi, Yixiang; Li, Wenying; Cai, Ningsheng

2018-03-01

CO/CO2 are the major gas reactant/product in the fuel electrode of reversible solid oxide cells (RSOC). This study proposes a two-charge-transfer-step mechanism to describe the reaction and transfer processes of CO-CO2 electrochemical conversion on a patterned Ni electrode of RSOC. An elementary reaction model is developed to couple two charge transfer reactions, C(Ni)+O2-(YSZ) ↔ CO(Ni)+(YSZ) +2e- and CO(Ni)+O2-(YSZ) ↔ CO2(Ni)+(YSZ)+2e-, with adsorption/desorption, surface chemical reactions and surface diffusion. This model well validates in both solid oxide electrolysis cell (SOEC) and solid oxide fuel cell (SOFC) modes by the experimental data from a patterned Ni electrode with 10 μm stripe width at different pCO (0-0.25 atm), pCO2 (0-0.35 atm) and operating temperature (600-700 °C). This model indicates SOEC mode is dominated by charge transfer step C(Ni)+O2-(YSZ)↔CO(Ni)+(YSZ) +2e-, while SOFC mode by CO(Ni)+ O2-(YSZ)↔CO2(Ni)+(YSZ)+2e- on the patterned Ni electrode. The sensitivity analysis shows charge transfer step is the major rate-determining step for RSOC, besides, surface diffusion of CO and CO2 as well as CO2 adsorption also plays a significant role in the electrochemical reaction of SOEC while surface diffusion of CO and CO2 desorption could be co-limiting in SOFC.

A systematic review of validated methods for identifying hypersensitivity reactions other than anaphylaxis (fever, rash, and lymphadenopathy), using administrative and claims data.

PubMed

Schneider, Gary; Kachroo, Sumesh; Jones, Natalie; Crean, Sheila; Rotella, Philip; Avetisyan, Ruzan; Reynolds, Matthew W

2012-01-01

The Food and Drug Administration's Mini-Sentinel pilot program aims to conduct active surveillance to refine safety signals that emerge for marketed medical products. A key facet of this surveillance is to develop and understand the validity of algorithms for identifying health outcomes of interest from administrative and claims data. This article summarizes the process and findings of the algorithm review of hypersensitivity reactions. PubMed and Iowa Drug Information Service searches were conducted to identify citations applicable to the hypersensitivity reactions of health outcomes of interest. Level 1 abstract reviews and Level 2 full-text reviews were conducted to find articles using administrative and claims data to identify hypersensitivity reactions and including validation estimates of the coding algorithms. We identified five studies that provided validated hypersensitivity-reaction algorithms. Algorithm positive predictive values (PPVs) for various definitions of hypersensitivity reactions ranged from 3% to 95%. PPVs were high (i.e. 90%-95%) when both exposures and diagnoses were very specific. PPV generally decreased when the definition of hypersensitivity was expanded, except in one study that used data mining methodology for algorithm development. The ability of coding algorithms to identify hypersensitivity reactions varied, with decreasing performance occurring with expanded outcome definitions. This examination of hypersensitivity-reaction coding algorithms provides an example of surveillance bias resulting from outcome definitions that include mild cases. Data mining may provide tools for algorithm development for hypersensitivity and other health outcomes. Research needs to be conducted on designing validation studies to test hypersensitivity-reaction algorithms and estimating their predictive power, sensitivity, and specificity. Copyright © 2012 John Wiley & Sons, Ltd.

A systematic review of validated methods for identifying transfusion-related ABO incompatibility reactions using administrative and claims data.

PubMed

Carnahan, Ryan M; Kee, Vicki R

2012-01-01

This paper aimed to systematically review algorithms to identify transfusion-related ABO incompatibility reactions in administrative data, with a focus on studies that have examined the validity of the algorithms. A literature search was conducted using PubMed, Iowa Drug Information Service database, and Embase. A Google Scholar search was also conducted because of the difficulty identifying relevant studies. Reviews were conducted by two investigators to identify studies using data sources from the USA or Canada because these data sources were most likely to reflect the coding practices of Mini-Sentinel data sources. One study was found that validated International Classification of Diseases (ICD-9-CM) codes representing transfusion reactions. None of these cases were ABO incompatibility reactions. Several studies consistently used ICD-9-CM code 999.6, which represents ABO incompatibility reactions, and a technical report identified the ICD-10 code for these reactions. One study included the E-code E8760 for mismatched blood in transfusion in the algorithm. Another study reported finding no ABO incompatibility reaction codes in the Healthcare Cost and Utilization Project Nationwide Inpatient Sample database, which contains data of 2.23 million patients who received transfusions, raising questions about the sensitivity of administrative data for identifying such reactions. Two studies reported perfect specificity, with sensitivity ranging from 21% to 83%, for the code identifying allogeneic red blood cell transfusions in hospitalized patients. There is no information to assess the validity of algorithms to identify transfusion-related ABO incompatibility reactions. Further information on the validity of algorithms to identify transfusions would also be useful. Copyright © 2012 John Wiley & Sons, Ltd.

Sample distribution in peak mode isotachophoresis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubin, Shimon; Schwartz, Ortal; Bercovici, Moran, E-mail: mberco@technion.ac.il

We present an analytical study of peak mode isotachophoresis (ITP), and provide closed form solutions for sample distribution and electric field, as well as for leading-, trailing-, and counter-ion concentration profiles. Importantly, the solution we present is valid not only for the case of fully ionized species, but also for systems of weak electrolytes which better represent real buffer systems and for multivalent analytes such as proteins and DNA. The model reveals two major scales which govern the electric field and buffer distributions, and an additional length scale governing analyte distribution. Using well-controlled experiments, and numerical simulations, we verify andmore » validate the model and highlight its key merits as well as its limitations. We demonstrate the use of the model for determining the peak concentration of focused sample based on known buffer and analyte properties, and show it differs significantly from commonly used approximations based on the interface width alone. We further apply our model for studying reactions between multiple species having different effective mobilities yet co-focused at a single ITP interface. We find a closed form expression for an effective-on rate which depends on reactants distributions, and derive the conditions for optimizing such reactions. Interestingly, the model reveals that maximum reaction rate is not necessarily obtained when the concentration profiles of the reacting species perfectly overlap. In addition to the exact solutions, we derive throughout several closed form engineering approximations which are based on elementary functions and are simple to implement, yet maintain the interplay between the important scales. Both the exact and approximate solutions provide insight into sample focusing and can be used to design and optimize ITP-based assays.« less

Irreversible thermodynamics of Poisson processes with reaction.

PubMed

Méndez, V; Fort, J

1999-11-01

A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics.

Validation of predicted patellofemoral mechanics in a finite element model of the healthy and cruciate-deficient knee.

PubMed

Ali, Azhar A; Shalhoub, Sami S; Cyr, Adam J; Fitzpatrick, Clare K; Maletsky, Lorin P; Rullkoetter, Paul J; Shelburne, Kevin B

2016-01-25

Healthy patellofemoral (PF) joint mechanics are critical to optimal function of the knee joint. Patellar maltracking may lead to large joint reaction loads and high stresses on the articular cartilage, increasing the risk of cartilage wear and the onset of osteoarthritis. While the mechanical sources of PF joint dysfunction are not well understood, links have been established between PF tracking and abnormal kinematics of the tibiofemoral (TF) joint, specifically following cruciate ligament injury and repair. The objective of this study was to create a validated finite element (FE) representation of the PF joint in order to predict PF kinematics and quadriceps force across healthy and pathological specimens. Measurements from a series of dynamic in-vitro cadaveric experiments were used to develop finite element models of the knee for three specimens. Specimens were loaded under intact, ACL-resected and both ACL and PCL-resected conditions. Finite element models of each specimen were constructed and calibrated to the outputs of the intact knee condition, and subsequently used to predict PF kinematics, contact mechanics, quadriceps force, patellar tendon moment arm and patellar tendon angle of the cruciate resected conditions. Model results for the intact and cruciate resected trials successfully matched experimental kinematics (avg. RMSE 4.0°, 3.1mm) and peak quadriceps forces (avg. difference 5.6%). Cruciate resections demonstrated either increased patellar tendon loads or increased joint reaction forces. The current study advances the standard for evaluation of PF mechanics through direct validation of cruciate-resected conditions including specimen-specific representations of PF anatomy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Surface-mediated nucleation in the solid-state polymorph transformation of terephthalic acid.

PubMed

Beckham, Gregg T; Peters, Baron; Starbuck, Cindy; Variankaval, Narayan; Trout, Bernhardt L

2007-04-18

A molecular mechanism for nucleation for the solid-state polymorph transformation of terephthalic acid is presented. New methods recently developed in our group, aimless shooting and likelihood maximization, are employed to construct a model for the reaction coordinate for the two system sizes studied. The reaction coordinate approximation is validated using the committor probability analysis. The transformation proceeds via a localized, elongated nucleus along the crystal edge formed by fluctuations in the supramolecular synthons, suggesting a nucleation and growth mechanism in the macroscopic system.

An Investigation of a Hybrid Mixing Model for PDF Simulations of Turbulent Premixed Flames

NASA Astrophysics Data System (ADS)

Zhou, Hua; Li, Shan; Wang, Hu; Ren, Zhuyin

2015-11-01

Predictive simulations of turbulent premixed flames over a wide range of Damköhler numbers in the framework of Probability Density Function (PDF) method still remain challenging due to the deficiency in current micro-mixing models. In this work, a hybrid micro-mixing model, valid in both the flamelet regime and broken reaction zone regime, is proposed. A priori testing of this model is first performed by examining the conditional scalar dissipation rate and conditional scalar diffusion in a 3-D direct numerical simulation dataset of a temporally evolving turbulent slot jet flame of lean premixed H2-air in the thin reaction zone regime. Then, this new model is applied to PDF simulations of the Piloted Premixed Jet Burner (PPJB) flames, which are a set of highly shear turbulent premixed flames and feature strong turbulence-chemistry interaction at high Reynolds and Karlovitz numbers. Supported by NSFC 51476087 and NSFC 91441202.

Investigation of Coal-biomass Catalytic Gasification using Experiments, Reaction Kinetics and Computational Fluid Dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Battaglia, Francine; Agblevor, Foster; Klein, Michael

A collaborative effort involving experiments, kinetic modeling, and computational fluid dynamics (CFD) was used to understand co-gasification of coal-biomass mixtures. The overall goal of the work was to determine the key reactive properties for coal-biomass mixed fuels. Sub-bituminous coal was mixed with biomass feedstocks to determine the fluidization and gasification characteristics of hybrid poplar wood, switchgrass and corn stover. It was found that corn stover and poplar wood were the best feedstocks to use with coal. The novel approach of this project was the use of a red mud catalyst to improve gasification and lower gasification temperatures. An important resultsmore » was the reduction of agglomeration of the biomass using the catalyst. An outcome of this work was the characterization of the chemical kinetics and reaction mechanisms of the co-gasification fuels, and the development of a set of models that can be integrated into other modeling environments. The multiphase flow code, MFIX, was used to simulate and predict the hydrodynamics and co-gasification, and results were validated with the experiments. The reaction kinetics modeling was used to develop a smaller set of reactions for tractable CFD calculations that represented the experiments. Finally, an efficient tool was developed, MCHARS, and coupled with MFIX to efficiently simulate the complex reaction kinetics.« less

Dual neutral particle induced transmutation in CINDER2008

NASA Astrophysics Data System (ADS)

Martin, W. J.; de Oliveira, C. R. E.; Hecht, A. A.

2014-12-01

Although nuclear transmutation methods for fission have existed for decades, the focus has been on neutron-induced reactions. Recent novel concepts have sought to use both neutrons and photons for purposes such as active interrogation of cargo to detect the smuggling of highly enriched uranium, a concept that would require modeling the transmutation caused by both incident particles. As photonuclear transmutation has yet to be modeled alongside neutron-induced transmutation in a production code, new methods need to be developed. The CINDER2008 nuclear transmutation code from Los Alamos National Laboratory is extended from neutron applications to dual neutral particle applications, allowing both neutron- and photon-induced reactions for this modeling with a focus on fission. Following standard reaction modeling, the induced fission reaction is understood as a two-part reaction, with an entrance channel to the excited compound nucleus, and an exit channel from the excited compound nucleus to the fission fragmentation. Because photofission yield data-the exit channel from the compound nucleus-are sparse, neutron fission yield data are used in this work. With a different compound nucleus and excitation, the translation to the excited compound state is modified, as appropriate. A verification and validation of these methods and data has been performed. This has shown that the translation of neutron-induced fission product yield sets, and their use in photonuclear applications, is appropriate, and that the code has been extended correctly.

Increased efficacy for in-house validation of real-time PCR GMO detection methods.

PubMed

Scholtens, I M J; Kok, E J; Hougs, L; Molenaar, B; Thissen, J T N M; van der Voet, H

2010-03-01

To improve the efficacy of the in-house validation of GMO detection methods (DNA isolation and real-time PCR, polymerase chain reaction), a study was performed to gain insight in the contribution of the different steps of the GMO detection method to the repeatability and in-house reproducibility. In the present study, 19 methods for (GM) soy, maize canola and potato were validated in-house of which 14 on the basis of an 8-day validation scheme using eight different samples and five on the basis of a more concise validation protocol. In this way, data was obtained with respect to the detection limit, accuracy and precision. Also, decision limits were calculated for declaring non-conformance (>0.9%) with 95% reliability. In order to estimate the contribution of the different steps in the GMO analysis to the total variation variance components were estimated using REML (residual maximum likelihood method). From these components, relative standard deviations for repeatability and reproducibility (RSD(r) and RSD(R)) were calculated. The results showed that not only the PCR reaction but also the factors 'DNA isolation' and 'PCR day' are important factors for the total variance and should therefore be included in the in-house validation. It is proposed to use a statistical model to estimate these factors from a large dataset of initial validations so that for similar GMO methods in the future, only the PCR step needs to be validated. The resulting data are discussed in the light of agreed European criteria for qualified GMO detection methods.

Impulsive synchronization of stochastic reaction-diffusion neural networks with mixed time delays.

PubMed

Sheng, Yin; Zeng, Zhigang

2018-07-01

This paper discusses impulsive synchronization of stochastic reaction-diffusion neural networks with Dirichlet boundary conditions and hybrid time delays. By virtue of inequality techniques, theories of stochastic analysis, linear matrix inequalities, and the contradiction method, sufficient criteria are proposed to ensure exponential synchronization of the addressed stochastic reaction-diffusion neural networks with mixed time delays via a designed impulsive controller. Compared with some recent studies, the neural network models herein are more general, some restrictions are relaxed, and the obtained conditions enhance and generalize some published ones. Finally, two numerical simulations are performed to substantiate the validity and merits of the developed theoretical analysis. Copyright © 2018 Elsevier Ltd. All rights reserved.

FTIR Study of Comustion Species in Several Regions of a Candle Flame

NASA Astrophysics Data System (ADS)

White, Allen R.

2013-06-01

The complex chemical structure of the fuel in a candle flame, parafin, is broken down into smaller hydrocarbons in the dark region just above the candle wick during combustion. This creates fuel-rich, fuel-lean, hydrocarbon reaction, and combustion product regions in the flame during combustion that are spectroscopically rich, particularly in the infrared. IR emissions were measured for each reaction region via collection optics focused into an FTIR and used to identify IR active species present in that region and, when possible, temperature of the sampling region. The results of the measurements are useful for combustion reaction modeling as well as for future validation of mass spectroscopy sampling systems.

Modeling shock-driven reaction in low density PMDI foam

NASA Astrophysics Data System (ADS)

Brundage, Aaron; Alexander, C. Scott; Reinhart, William; Peterson, David

Shock experiments on low density polyurethane foams reveal evidence of reaction at low impact pressures. However, these reaction thresholds are not evident over the low pressures reported for historical Hugoniot data of highly distended polyurethane at densities below 0.1 g/cc. To fill this gap, impact data given in a companion paper for polymethylene diisocyanate (PMDI) foam with a density of 0.087 g/cc were acquired for model validation. An equation of state (EOS) was developed to predict the shock response of these highly distended materials over the full range of impact conditions representing compaction of the inert material, low-pressure decomposition, and compression of the reaction products. A tabular SESAME EOS of the reaction products was generated using the JCZS database in the TIGER equilibrium code. In particular, the Arrhenius Burn EOS, a two-state model which transitions from an unreacted to a reacted state using single step Arrhenius kinetics, as implemented in the shock physics code CTH, was modified to include a statistical distribution of states. Hence, a single EOS is presented that predicts the onset to reaction due to shock loading in PMDI-based polyurethane foams. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's NNSA under Contract DE-AC04-94AL85000.

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

NASA Astrophysics Data System (ADS)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations for solvent-based carbon capture. Part 2: Chemical absorption across a wetted wall column: Original Research Article: Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Chao; Xu, Zhijie; Lai, Kevin

The first part of this paper (Part 1) presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO2) capture. To generate data for WWC model validation, CO2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work has the ability to account for both chemical absorption and desorption of CO2 in MEA. In addition,more » the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry’s constant and gas diffusivity in the non-reacting nitrous oxide (N2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO2 reaction rate constants after using the N2O/CO2 analogy method. The calibrated model can be used to predict the CO2 mass transfer in a WWC for a wider range of operating conditions.« less

Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations for solvent-based carbon capture. Part 2: Chemical absorption across a wetted wall column: Original Research Article: Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Chao; Xu, Zhijie; Lai, Kevin

Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO 2) capture. In this study, to generate data for WWC model validation, CO 2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO 2 in MEA. In addition,more » the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO 2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N 2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO 2 reaction rate constants after using the N 2O/CO 2 analogy method. Finally, the calibrated model can be used to predict the CO 2 mass transfer in a WWC for a wider range of operating conditions.« less

Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations for solvent-based carbon capture. Part 2: Chemical absorption across a wetted wall column: Original Research Article: Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations

DOE PAGES

Wang, Chao; Xu, Zhijie; Lai, Kevin; ...

2017-10-24

Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO 2) capture. In this study, to generate data for WWC model validation, CO 2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO 2 in MEA. In addition,more » the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO 2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N 2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO 2 reaction rate constants after using the N 2O/CO 2 analogy method. Finally, the calibrated model can be used to predict the CO 2 mass transfer in a WWC for a wider range of operating conditions.« less

Development and Validation of a 3-Dimensional CFB Furnace Model

NASA Astrophysics Data System (ADS)

Vepsäläinen, Arl; Myöhänen, Karl; Hyppäneni, Timo; Leino, Timo; Tourunen, Antti

At Foster Wheeler, a three-dimensional CFB furnace model is essential part of knowledge development of CFB furnace process regarding solid mixing, combustion, emission formation and heat transfer. Results of laboratory and pilot scale phenomenon research are utilized in development of sub-models. Analyses of field-test results in industrial-scale CFB boilers including furnace profile measurements are simultaneously carried out with development of 3-dimensional process modeling, which provides a chain of knowledge that is utilized as feedback for phenomenon research. Knowledge gathered by model validation studies and up-to-date parameter databases are utilized in performance prediction and design development of CFB boiler furnaces. This paper reports recent development steps related to modeling of combustion and formation of char and volatiles of various fuel types in CFB conditions. Also a new model for predicting the formation of nitrogen oxides is presented. Validation of mixing and combustion parameters for solids and gases are based on test balances at several large-scale CFB boilers combusting coal, peat and bio-fuels. Field-tests including lateral and vertical furnace profile measurements and characterization of solid materials provides a window for characterization of fuel specific mixing and combustion behavior in CFB furnace at different loads and operation conditions. Measured horizontal gas profiles are projection of balance between fuel mixing and reactions at lower part of furnace and are used together with both lateral temperature profiles at bed and upper parts of furnace for determination of solid mixing and combustion model parameters. Modeling of char and volatile based formation of NO profiles is followed by analysis of oxidizing and reducing regions formed due lower furnace design and mixing characteristics of fuel and combustion airs effecting to formation ofNO furnace profile by reduction and volatile-nitrogen reactions. This paper presents CFB process analysis focused on combustion and NO profiles in pilot and industrial scale bituminous coal combustion.

A parallel reaction-transport model applied to cement hydration and microstructure development

NASA Astrophysics Data System (ADS)

Bullard, Jeffrey W.; Enjolras, Edith; George, William L.; Satterfield, Steven G.; Terrill, Judith E.

2010-03-01

A recently described stochastic reaction-transport model on three-dimensional lattices is parallelized and is used to simulate the time-dependent structural and chemical evolution in multicomponent reactive systems. The model, called HydratiCA, uses probabilistic rules to simulate the kinetics of diffusion, homogeneous reactions and heterogeneous phenomena such as solid nucleation, growth and dissolution in complex three-dimensional systems. The algorithms require information only from each lattice site and its immediate neighbors, and this localization enables the parallelized model to exhibit near-linear scaling up to several hundred processors. Although applicable to a wide range of material systems, including sedimentary rock beds, reacting colloids and biochemical systems, validation is performed here on two minerals that are commonly found in Portland cement paste, calcium hydroxide and ettringite, by comparing their simulated dissolution or precipitation rates far from equilibrium to standard rate equations, and also by comparing simulated equilibrium states to thermodynamic calculations, as a function of temperature and pH. Finally, we demonstrate how HydratiCA can be used to investigate microstructure characteristics, such as spatial correlations between different condensed phases, in more complex microstructures.

Prediction of metabolites of epoxidation reaction in MetaTox.

PubMed

Rudik, A V; Dmitriev, A V; Bezhentsev, V M; Lagunin, A A; Filimonov, D A; Poroikov, V V

2017-10-01

Biotransformation is a process of the chemical modifications which may lead to the reactive metabolites, in particular the epoxides. Epoxide reactive metabolites may cause the toxic effects. The prediction of such metabolites is important for drug development and ecotoxicology studies. Epoxides are formed by some oxidation reactions, usually catalysed by cytochromes P450, and represent a large class of three-membered cyclic ethers. Identification of molecules, which may be epoxidized, and indication of the specific location of epoxide functional group (which is called SOE - site of epoxidation) are important for prediction of epoxide metabolites. Datasets from 355 molecules and 615 reactions were created for training and validation. The prediction of SOE is based on a combination of LMNA (Labelled Multilevel Neighbourhood of Atom) descriptors and Bayesian-like algorithm implemented in PASS software and MetaTox web-service. The average invariant accuracy of prediction (AUC) calculated in leave-one-out and 20-fold cross-validation procedures is 0.9. Prediction of epoxide formation based on the created SAR model is included as the component of MetaTox web-service ( http://www.way2drug.com/mg ).

Extended lattice Boltzmann scheme for droplet combustion.

PubMed

Ashna, Mostafa; Rahimian, Mohammad Hassan; Fakhari, Abbas

2017-05-01

The available lattice Boltzmann (LB) models for combustion or phase change are focused on either single-phase flow combustion or two-phase flow with evaporation assuming a constant density for both liquid and gas phases. To pave the way towards simulation of spray combustion, we propose a two-phase LB method for modeling combustion of liquid fuel droplets. We develop an LB scheme to model phase change and combustion by taking into account the density variation in the gas phase and accounting for the chemical reaction based on the Cahn-Hilliard free-energy approach. Evaporation of liquid fuel is modeled by adding a source term, which is due to the divergence of the velocity field being nontrivial, in the continuity equation. The low-Mach-number approximation in the governing Navier-Stokes and energy equations is used to incorporate source terms due to heat release from chemical reactions, density variation, and nonluminous radiative heat loss. Additionally, the conservation equation for chemical species is formulated by including a source term due to chemical reaction. To validate the model, we consider the combustion of n-heptane and n-butanol droplets in stagnant air using overall single-step reactions. The diameter history and flame standoff ratio obtained from the proposed LB method are found to be in good agreement with available numerical and experimental data. The present LB scheme is believed to be a promising approach for modeling spray combustion.

In-line monitoring of cocrystallization process and quantification of carbamazepine-nicotinamide cocrystal using Raman spectroscopy and chemometric tools.

PubMed

Soares, Frederico L F; Carneiro, Renato L

2017-06-05

A cocrystallization process may involve several molecular species, which are generally solid under ambient conditions. Thus, accurate monitoring of different components that might appear during the reaction is necessary, as well as quantification of the final product. This work reports for the first time the synthesis of carbamazepine-nicotinamide cocrystal in aqueous media with a full conversion. The reactions were monitored by Raman spectroscopy coupled with Multivariate Curve Resolution - Alternating Least Squares, and the quantification of the final product among its coformers was performed using Raman spectroscopy and Partial Least Squares regression. The slurry reaction was made in four different conditions: room temperature, 40°C, 60°C and 80°C. The slurry reaction at 80°C enabled a full conversion of initial substrates into the cocrystal form, using water as solvent for a greener method. The employment of MCR-ALS coupled with Raman spectroscopy enabled to observe the main steps of the reactions, such as drug dissolution, nucleation and crystallization of the cocrystal. The PLS models gave mean errors of cross validation around 2.0 (% wt/wt), and errors of validation between 2.5 and 8.2 (% wt/wt) for all components. These were good results since the spectra of cocrystals and the physical mixture of the coformers present some similar peaks. Copyright © 2017 Elsevier B.V. All rights reserved.

In-line monitoring of cocrystallization process and quantification of carbamazepine-nicotinamide cocrystal using Raman spectroscopy and chemometric tools

NASA Astrophysics Data System (ADS)

Soares, Frederico L. F.; Carneiro, Renato L.

2017-06-01

A cocrystallization process may involve several molecular species, which are generally solid under ambient conditions. Thus, accurate monitoring of different components that might appear during the reaction is necessary, as well as quantification of the final product. This work reports for the first time the synthesis of carbamazepine-nicotinamide cocrystal in aqueous media with a full conversion. The reactions were monitored by Raman spectroscopy coupled with Multivariate Curve Resolution - Alternating Least Squares, and the quantification of the final product among its coformers was performed using Raman spectroscopy and Partial Least Squares regression. The slurry reaction was made in four different conditions: room temperature, 40 °C, 60 °C and 80 °C. The slurry reaction at 80 °C enabled a full conversion of initial substrates into the cocrystal form, using water as solvent for a greener method. The employment of MCR-ALS coupled with Raman spectroscopy enabled to observe the main steps of the reactions, such as drug dissolution, nucleation and crystallization of the cocrystal. The PLS models gave mean errors of cross validation around 2.0 (% wt/wt), and errors of validation between 2.5 and 8.2 (% wt/wt) for all components. These were good results since the spectra of cocrystals and the physical mixture of the coformers present some similar peaks.

A diffusion-reaction scheme for modeling ignition and self-propagating reactions in Al/CuO multilayered thin films

NASA Astrophysics Data System (ADS)

Lahiner, Guillaume; Nicollet, Andrea; Zapata, James; Marín, Lorena; Richard, Nicolas; Rouhani, Mehdi Djafari; Rossi, Carole; Estève, Alain

2017-10-01

Thermite multilayered films have the potential to be used as local high intensity heat sources for a variety of applications. Improving the ability of researchers to more rapidly develop Micro Electro Mechanical Systems devices based on thermite multilayer films requires predictive modeling in which an understanding of the relationship between the properties (ignition and flame propagation), the multilayer structure and composition (bilayer thicknesses, ratio of reactants, and nature of interfaces), and aspects related to integration (substrate conductivity and ignition apparatus) is achieved. Assembling all these aspects, this work proposes an original 2D diffusion-reaction modeling framework to predict the ignition threshold and reaction dynamics of Al/CuO multilayered thin films. This model takes into consideration that CuO first decomposes into Cu2O, and then, released oxygen diffuses across the Cu2O and Al2O3 layers before reacting with pure Al to form Al2O3. This model is experimentally validated from ignition and flame velocity data acquired on Al/CuO multilayers deposited on a Kapton layer. This paper discusses, for the first time, the importance of determining the ceiling temperature above which the multilayers disintegrate, possibly before their complete combustion, thus severely impacting the reaction front velocity and energy release. This work provides a set of heating surface areas to obtain the best ignition conditions, i.e., with minimal ignition power, as a function of the substrate type.

Network Thermodynamic Curation of Human and Yeast Genome-Scale Metabolic Models

PubMed Central

Martínez, Verónica S.; Quek, Lake-Ee; Nielsen, Lars K.

2014-01-01

Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. PMID:25028891

Psychometrics in Psychological Research: Role Model or Partner in Science?

ERIC Educational Resources Information Center

Sijtsma, Klaas

2006-01-01

This is a reaction to Borsboom's (2006) discussion paper on the issue that psychology takes so little notice of the modern developments in psychometrics, in particular, latent variable methods. Contrary to Borsboom, it is argued that latent variables are summaries of interesting data properties, that construct validation should involve studying…

Chemical Kinetics, Heat Transfer, and Sensor Dynamics Revisited in a Simple Experiment

ERIC Educational Resources Information Center

Sad, Maria E.; Sad, Mario R.; Castro, Alberto A.; Garetto, Teresita F.

2008-01-01

A simple experiment about thermal effects in chemical reactors is described, which can be used to illustrate chemical reactor models, the determination and validation of their parameters, and some simple principles of heat transfer and sensor dynamics. It is based in the exothermic reaction between aqueous solutions of sodium thiosulfate and…

Nuclear Structure of 186Re

DTIC Science & Technology

2016-12-24

D population-depopulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 AME Atomic Mass Evaluation...this mass region are important for validating models of nuclear structure and reactions. The ENSDF feeds a specific data library relevant to nuclear...spherically asymmetric. Spherical asymmetry is common for nuclei between shell closures, such as those in the mid-shell 150  A  190 mass range of interest

Development and Validation of a Mathematical Model for Olive Oil Oxidation

NASA Astrophysics Data System (ADS)

Rahmouni, K.; Bouhafa, H.; Hamdi, S.

2009-03-01

A mathematical model describing the stability or the susceptibility to oxidation of extra virgin olive oil has been developed. The model has been resolved by an iterative method using differential finite method. It was validated by experimental data of extra virgin olive oil (EVOO) oxidation. EVOO stability was tested by using a Rancimat at four different temperatures 60, 70, 80 and 90° C until peroxide accumulation reached 20 [meq/kg]. Peroxide formation is speed relatively slow; fits zero order reaction with linear regression coefficients varying from 0, 98 to 0, 99. The mathematical model was used to predict the shelf life of bulk conditioned olive oil. This model described peroxide accumulation inside a container in excess of oxygen as a function of time at various positions from the interface air/oil. Good correlations were obtained between theoretical and experimental values.

Thermo-chemical Ice Penetrator for Icy Moons

NASA Astrophysics Data System (ADS)

Arenberg, J. W.; Lee, G.; Harpole, G.; Zamel, J.; Sen, B.; Ross, F.; Retherford, K. D.

2016-12-01

The ability to place sensors or to take samples below the ice surface enables a wide variety of potential scientific investigations. Penetrating an ice cap can be accomplished via a mechanical drill, laser drill, kinetic impactor, or heated penetrator. This poster reports on the development of technology for the latter most option, namely a self-heated probe driven by an exothermic chemical reaction: a Thermo-chemical ice penetrator (TChIP). Our penetrator design employs a eutectic mix of alkali metals that produce an exothermic reaction upon contact with an icy surface. This reaction increases once the ice starts melting, so no external power is required. This technology is inspired by a classified Cold-War era program developed at Northrop Grumman for the US Navy. Terrestrial demonstration of this technology took place in the Arctic; however, this device cannot be considered high TRL for application at the icy moons of the solar system due to the environmental differences between Earth's Arctic and the icy moons. These differences demand a TChIP design specific to these cold, low mass, airless worlds. It is expected that this model of TChIP performance will be complex, incorporating all of the forces on the penetrator, gravity, the thermo-chemistry at the interface between penetrator and ice, and multi-phase heat and mass transport, and hydrodynamics. Our initial efforts are aimed at the development of a validated set of tools and simulations to predict the performance of the penetrator for both the environment found on these icy moons and for a terrestrial environment. The purpose of the inclusion of the terrestrial environment is to aid in model validation. Once developed and validated, our models will allow us to design penetrators for a specific scientific application on a specific body. This poster discusses the range of scientific investigations that are enabled by TChIP. We also introduce the development plan to advance TChIP to the point where it can be considered for infusion into a program.

Technology for a Thermo-chemical Ice Penetrator for Icy Moons

NASA Astrophysics Data System (ADS)

Arenberg, Jonathan; Harpole, George; Zamel, James; Sen, Bashwar; Lee, Greg; Ross, Floyd; Retherford, Kurt D.

2016-10-01

The ability to place sensors or to take samples below the ice surface enables a wide variety of potential scientific investigations. Penetrating an ice cap can be accomplished via a mechanical drill, laser drill, kinetic impactor, or heated penetrator. This poster reports on the development of technology for the latter most option, namely a self-heated probe driven by an exothermic chemical reaction: a Thermo-chemical ice penetrator (TChIP). Our penetrator design employs a eutectic mix of alkali metals that produce an exothermic reaction upon contact with an icy surface. This reaction increases once the ice starts melting, so no external power is required. This technology is inspired by a classified Cold-War era program developed at Northrop Grumman for the US Navy. Terrestrial demonstration of this technology took place in the Arctic; however, this device cannot be considered high TRL for application at the icy moons of the solar system due to the environmental differences between Earth's Arctic and the icy moons. These differences demand a TChIP design specific to these cold, low mass, airless worlds. It is expected that this model of TChIP performance will be complex, incorporating all of the forces on the penetrator, gravity, the thermo-chemistry at the interface between penetrator and ice, and multi-phase heat and mass transport, and hydrodynamics. Our initial efforts are aimed at the development of a validated set of tools and simulations to predict the performance of the penetrator for both the environment found on these icy moons and for a terrestrial environment. The purpose of the inclusion of the terrestrial environment is to aid in model validation. Once developed and validated, our models will allow us to design penetrators for a specific scientific application on a specific body. This poster discusses the range of scientific investigations that are enabled by TChIP. We also introduce the development plan to advance TChIP to the point where it can be considered for infusion into a program.

Construction of reactive potential energy surfaces with Gaussian process regression: active data selection

NASA Astrophysics Data System (ADS)

Guan, Yafu; Yang, Shuo; Zhang, Dong H.

2018-04-01

Gaussian process regression (GPR) is an efficient non-parametric method for constructing multi-dimensional potential energy surfaces (PESs) for polyatomic molecules. Since not only the posterior mean but also the posterior variance can be easily calculated, GPR provides a well-established model for active learning, through which PESs can be constructed more efficiently and accurately. We propose a strategy of active data selection for the construction of PESs with emphasis on low energy regions. Through three-dimensional (3D) example of H3, the validity of this strategy is verified. The PESs for two prototypically reactive systems, namely, H + H2O ↔ H2 + OH reaction and H + CH4 ↔ H2 + CH3 reaction are reconstructed. Only 920 and 4000 points are assembled to reconstruct these two PESs respectively. The accuracy of the GP PESs is not only tested by energy errors but also validated by quantum scattering calculations.

Development of an Uncertainty Quantification Predictive Chemical Reaction Model for Syngas Combustion

DOE PAGES

Slavinskaya, N. A.; Abbasi, M.; Starcke, J. H.; ...

2017-01-24

An automated data-centric infrastructure, Process Informatics Model (PrIMe), was applied to validation and optimization of a syngas combustion model. The Bound-to-Bound Data Collaboration (B2BDC) module of PrIMe was employed to discover the limits of parameter modifications based on uncertainty quantification (UQ) and consistency analysis of the model–data system and experimental data, including shock-tube ignition delay times and laminar flame speeds. Existing syngas reaction models are reviewed, and the selected kinetic data are described in detail. Empirical rules were developed and applied to evaluate the uncertainty bounds of the literature experimental data. Here, the initial H 2/CO reaction model, assembled frommore » 73 reactions and 17 species, was subjected to a B2BDC analysis. For this purpose, a dataset was constructed that included a total of 167 experimental targets and 55 active model parameters. Consistency analysis of the composed dataset revealed disagreement between models and data. Further analysis suggested that removing 45 experimental targets, 8 of which were self-inconsistent, would lead to a consistent dataset. This dataset was subjected to a correlation analysis, which highlights possible directions for parameter modification and model improvement. Additionally, several methods of parameter optimization were applied, some of them unique to the B2BDC framework. The optimized models demonstrated improved agreement with experiments compared to the initially assembled model, and their predictions for experiments not included in the initial dataset (i.e., a blind prediction) were investigated. The results demonstrate benefits of applying the B2BDC methodology for developing predictive kinetic models.« less

Development of an Uncertainty Quantification Predictive Chemical Reaction Model for Syngas Combustion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slavinskaya, N. A.; Abbasi, M.; Starcke, J. H.

An automated data-centric infrastructure, Process Informatics Model (PrIMe), was applied to validation and optimization of a syngas combustion model. The Bound-to-Bound Data Collaboration (B2BDC) module of PrIMe was employed to discover the limits of parameter modifications based on uncertainty quantification (UQ) and consistency analysis of the model–data system and experimental data, including shock-tube ignition delay times and laminar flame speeds. Existing syngas reaction models are reviewed, and the selected kinetic data are described in detail. Empirical rules were developed and applied to evaluate the uncertainty bounds of the literature experimental data. Here, the initial H 2/CO reaction model, assembled frommore » 73 reactions and 17 species, was subjected to a B2BDC analysis. For this purpose, a dataset was constructed that included a total of 167 experimental targets and 55 active model parameters. Consistency analysis of the composed dataset revealed disagreement between models and data. Further analysis suggested that removing 45 experimental targets, 8 of which were self-inconsistent, would lead to a consistent dataset. This dataset was subjected to a correlation analysis, which highlights possible directions for parameter modification and model improvement. Additionally, several methods of parameter optimization were applied, some of them unique to the B2BDC framework. The optimized models demonstrated improved agreement with experiments compared to the initially assembled model, and their predictions for experiments not included in the initial dataset (i.e., a blind prediction) were investigated. The results demonstrate benefits of applying the B2BDC methodology for developing predictive kinetic models.« less

Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

PubMed Central

Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane; Zarecki, Raphy; Ruppin, Eytan; Hanson, Andrew D.; Henry, Christopher S.

2015-01-01

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes. PMID:25806041

Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

DOE PAGES

Seaver, Samuel M.D.; Bradbury, Louis M.T.; Frelin, Océane; ...

2015-03-10

There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions andmore » possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.« less

On-the-Fly Kinetic Monte Carlo Simulation of Aqueous Phase Advanced Oxidation Processes.

PubMed

Guo, Xin; Minakata, Daisuke; Crittenden, John

2015-08-04

We have developed an on-the-fly kinetic Monte Carlo (KMC) model to predict the degradation mechanisms and fates of intermediates and byproducts that are produced during aqueous-phase advanced oxidation processes (AOPs). The on-the-fly KMC model is composed of a reaction pathway generator, a reaction rate constant estimator, a mechanistic reduction module, and a KMC solver. The novelty of this work is that we develop the pathway as we march forward in time rather than developing the pathway before we use the KMC method to solve the equations. As a result, we have fewer reactions to consider, and we have greater computational efficiency. We have verified this on-the-fly KMC model for the degradation of polyacrylamide (PAM) using UV light and titanium dioxide (i.e., UV/TiO2). Using the on-the-fly KMC model, we were able to predict the time-dependent profiles of the average molecular weight for PAM. The model provided detailed and quantitative insights into the time evolution of the molecular weight distribution and reaction mechanism. We also verified our on-the-fly KMC model for the destruction of (1) acetone, (2) trichloroethylene (TCE), and (3) polyethylene glycol (PEG) for the ultraviolet light and hydrogen peroxide AOP. We demonstrated that the on-the-fly KMC model can achieve the same accuracy as the computer-based first-principles KMC (CF-KMC) model, which has already been validated in our earlier work. The on-the-fly KMC is particularly suitable for molecules with large molecular weights (e.g., polymers) because the degradation mechanisms for large molecules can result in hundreds of thousands to even millions of reactions. The ordinary differential equations (ODEs) that describe the degradation pathways cannot be solved using traditional numerical methods, but the KMC can solve these equations.

A novel phenomenological multi-physics model of Li-ion battery cells

NASA Astrophysics Data System (ADS)

Oh, Ki-Yong; Samad, Nassim A.; Kim, Youngki; Siegel, Jason B.; Stefanopoulou, Anna G.; Epureanu, Bogdan I.

2016-09-01

A novel phenomenological multi-physics model of Lithium-ion battery cells is developed for control and state estimation purposes. The model can capture electrical, thermal, and mechanical behaviors of battery cells under constrained conditions, e.g., battery pack conditions. Specifically, the proposed model predicts the core and surface temperatures and reaction force induced from the volume change of battery cells because of electrochemically- and thermally-induced swelling. Moreover, the model incorporates the influences of changes in preload and ambient temperature on the force considering severe environmental conditions electrified vehicles face. Intensive experimental validation demonstrates that the proposed multi-physics model accurately predicts the surface temperature and reaction force for a wide operational range of preload and ambient temperature. This high fidelity model can be useful for more accurate and robust state of charge estimation considering the complex dynamic behaviors of the battery cell. Furthermore, the inherent simplicity of the mechanical measurements offers distinct advantages to improve the existing power and thermal management strategies for battery management.

Theoretical and Numerical Investigation of the Cavity Evolution in Gypsum Rock

NASA Astrophysics Data System (ADS)

Li, Wei; Einstein, Herbert H.

2017-11-01

When water flows through a preexisting cylindrical tube in gypsum rock, the nonuniform dissolution alters the tube into an enlarged tapered tube. A 2-D analytical model is developed to study the transport-controlled dissolution in an enlarged tapered tube, with explicit consideration of the tapered geometry and induced radial flow. The analytical model shows that the Graetz solution can be extended to model dissolution in the tapered tube. An alternative form of the governing equations is proposed to take advantage of the invariant quantities in the Graetz solution to facilitate modeling cavity evolution in gypsum rock. A 2-D finite volume model was developed to validate the extended Graetz solution. The time evolution of the transport-controlled and the reaction-controlled dissolution models for a single tube with time-invariant flow rate are compared. This comparison shows that for time-invariant flow rate, the reaction-controlled dissolution model produces a positive feedback between the tube enlargement and dissolution, while the transport-controlled dissolution does not.

Applying the Rule Space Model to Develop a Learning Progression for Thermochemistry

NASA Astrophysics Data System (ADS)

Chen, Fu; Zhang, Shanshan; Guo, Yanfang; Xin, Tao

2017-12-01

We used the Rule Space Model, a cognitive diagnostic model, to measure the learning progression for thermochemistry for senior high school students. We extracted five attributes and proposed their hierarchical relationships to model the construct of thermochemistry at four levels using a hypothesized learning progression. For this study, we developed 24 test items addressing the attributes of exothermic and endothermic reactions, chemical bonds and heat quantity change, reaction heat and enthalpy, thermochemical equations, and Hess's law. The test was administered to a sample base of 694 senior high school students taught in 3 schools across 2 cities. Results based on the Rule Space Model analysis indicated that (1) the test items developed by the Rule Space Model were of high psychometric quality for good analysis of difficulties, discriminations, reliabilities, and validities; (2) the Rule Space Model analysis classified the students into seven different attribute mastery patterns; and (3) the initial hypothesized learning progression was modified by the attribute mastery patterns and the learning paths to be more precise and detailed.

Analysis of JSI TRIGA MARK II reactor physical parameters calculated with TRIPOLI and MCNP.

PubMed

Henry, R; Tiselj, I; Snoj, L

2015-03-01

New computational model of the JSI TRIGA Mark II research reactor was built for TRIPOLI computer code and compared with existing MCNP code model. The same modelling assumptions were used in order to check the differences of the mathematical models of both Monte Carlo codes. Differences between the TRIPOLI and MCNP predictions of keff were up to 100pcm. Further validation was performed with analyses of the normalized reaction rates and computations of kinetic parameters for various core configurations. Copyright © 2014 Elsevier Ltd. All rights reserved.

Computational and experimental analysis of DNA shuffling

PubMed Central

Maheshri, Narendra; Schaffer, David V.

2003-01-01

We describe a computational model of DNA shuffling based on the thermodynamics and kinetics of this process. The model independently tracks a representative ensemble of DNA molecules and records their states at every stage of a shuffling reaction. These data can subsequently be analyzed to yield information on any relevant metric, including reassembly efficiency, crossover number, type and distribution, and DNA sequence length distributions. The predictive ability of the model was validated by comparison to three independent sets of experimental data, and analysis of the simulation results led to several unique insights into the DNA shuffling process. We examine a tradeoff between crossover frequency and reassembly efficiency and illustrate the effects of experimental parameters on this relationship. Furthermore, we discuss conditions that promote the formation of useless “junk” DNA sequences or multimeric sequences containing multiple copies of the reassembled product. This model will therefore aid in the design of optimal shuffling reaction conditions. PMID:12626764

Kinetic Monte Carlo modeling of chemical reactions coupled with heat transfer.

PubMed

Castonguay, Thomas C; Wang, Feng

2008-03-28

In this paper, we describe two types of effective events for describing heat transfer in a kinetic Monte Carlo (KMC) simulation that may involve stochastic chemical reactions. Simulations employing these events are referred to as KMC-TBT and KMC-PHE. In KMC-TBT, heat transfer is modeled as the stochastic transfer of "thermal bits" between adjacent grid points. In KMC-PHE, heat transfer is modeled by integrating the Poisson heat equation for a short time. Either approach is capable of capturing the time dependent system behavior exactly. Both KMC-PHE and KMC-TBT are validated by simulating pure heat transfer in a rod and a square and modeling a heated desorption problem where exact numerical results are available. KMC-PHE is much faster than KMC-TBT and is used to study the endothermic desorption of a lattice gas. Interesting findings from this study are reported.

Kinetic Monte Carlo modeling of chemical reactions coupled with heat transfer

NASA Astrophysics Data System (ADS)

Castonguay, Thomas C.; Wang, Feng

2008-03-01

In this paper, we describe two types of effective events for describing heat transfer in a kinetic Monte Carlo (KMC) simulation that may involve stochastic chemical reactions. Simulations employing these events are referred to as KMC-TBT and KMC-PHE. In KMC-TBT, heat transfer is modeled as the stochastic transfer of "thermal bits" between adjacent grid points. In KMC-PHE, heat transfer is modeled by integrating the Poisson heat equation for a short time. Either approach is capable of capturing the time dependent system behavior exactly. Both KMC-PHE and KMC-TBT are validated by simulating pure heat transfer in a rod and a square and modeling a heated desorption problem where exact numerical results are available. KMC-PHE is much faster than KMC-TBT and is used to study the endothermic desorption of a lattice gas. Interesting findings from this study are reported.

A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

PubMed Central

2012-01-01

Background Yarrowia lipolytica is an oleaginous yeast which has emerged as an important microorganism for several biotechnological processes, such as the production of organic acids, lipases and proteases. It is also considered a good candidate for single-cell oil production. Although some of its metabolic pathways are well studied, its metabolic engineering is hindered by the lack of a genome-scale model that integrates the current knowledge about its metabolism. Results Combining in silico tools and expert manual curation, we have produced an accurate genome-scale metabolic model for Y. lipolytica. Using a scaffold derived from a functional metabolic model of the well-studied but phylogenetically distant yeast S. cerevisiae, we mapped conserved reactions, rewrote gene associations, added species-specific reactions and inserted specialized copies of scaffold reactions to account for species-specific expansion of protein families. We used physiological measures obtained under lab conditions to validate our predictions. Conclusions Y. lipolytica iNL895 represents the first well-annotated metabolic model of an oleaginous yeast, providing a base for future metabolic improvement, and a starting point for the metabolic reconstruction of other species in the Yarrowia clade and other oleaginous yeasts. PMID:22558935

A variable turbulent Prandtl and Schmidt number model study for scramjet applications

NASA Astrophysics Data System (ADS)

Keistler, Patrick

A turbulence model that allows for the calculation of the variable turbulent Prandtl (Prt) and Schmidt (Sct) numbers as part of the solution is presented. The model also accounts for the interactions between turbulence and chemistry by modeling the corresponding terms. Four equations are added to the baseline k-zeta turbulence model: two equations for enthalpy variance and its dissipation rate to calculate the turbulent diffusivity, and two equations for the concentrations variance and its dissipation rate to calculate the turbulent diffusion coefficient. The underlying turbulence model already accounts for compressibility effects. The variable Prt /Sct turbulence model is validated and tuned by simulating a wide variety of experiments. Included in the experiments are two-dimensional, axisymmetric, and three-dimensional mixing and combustion cases. The combustion cases involved either hydrogen and air, or hydrogen, ethylene, and air. Two chemical kinetic models are employed for each of these situations. For the hydrogen and air cases, a seven species/seven reaction model where the reaction rates are temperature dependent and a nine species/nineteen reaction model where the reaction rates are dependent on both pressure and temperature are used. For the cases involving ethylene, a 15 species/44 reaction reduced model that is both pressure and temperature dependent is used, along with a 22 species/18 global reaction reduced model that makes use of the quasi-steady-state approximation. In general, fair to good agreement is indicated for all simulated experiments. The turbulence/chemistry interaction terms are found to have a significant impact on flame location for the two-dimensional combustion case, with excellent experimental agreement when the terms are included. In most cases, the hydrogen chemical mechanisms behave nearly identically, but for one case, the pressure dependent model would not auto-ignite at the same conditions as the experiment and the other chemical model. The model was artificially ignited in that case. For the cases involving ethylene combustion, the chemical model has a profound impact on the flame size, shape, and ignition location. However, without quantitative experimental data, it is difficult to determine which one is more suitable for this particular application.

Virtual experiments, physical validation: dental morphology at the intersection of experiment and theory

PubMed Central

Anderson, P. S. L.; Rayfield, E. J.

2012-01-01

Computational models such as finite-element analysis offer biologists a means of exploring the structural mechanics of biological systems that cannot be directly observed. Validated against experimental data, a model can be manipulated to perform virtual experiments, testing variables that are hard to control in physical experiments. The relationship between tooth form and the ability to break down prey is key to understanding the evolution of dentition. Recent experimental work has quantified how tooth shape promotes fracture in biological materials. We present a validated finite-element model derived from physical compression experiments. The model shows close agreement with strain patterns observed in photoelastic test materials and reaction forces measured during these experiments. We use the model to measure strain energy within the test material when different tooth shapes are used. Results show that notched blades deform materials for less strain energy cost than straight blades, giving insights into the energetic relationship between tooth form and prey materials. We identify a hypothetical ‘optimal’ blade angle that minimizes strain energy costs and test alternative prey materials via virtual experiments. Using experimental data and computational models offers an integrative approach to understand the mechanics of tooth morphology. PMID:22399789

Nuclear Reaction Models Responsible for Simulation of Neutron-induced Soft Errors in Microelectronics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watanabe, Y., E-mail: watanabe@aees.kyushu-u.ac.jp; Abe, S.

Terrestrial neutron-induced soft errors in MOSFETs from a 65 nm down to a 25 nm design rule are analyzed by means of multi-scale Monte Carlo simulation using the PHITS-HyENEXSS code system. Nuclear reaction models implemented in PHITS code are validated by comparisons with experimental data. From the analysis of calculated soft error rates, it is clarified that secondary He and H ions provide a major impact on soft errors with decreasing critical charge. It is also found that the high energy component from 10 MeV up to several hundreds of MeV in secondary cosmic-ray neutrons has the most significant sourcemore » of soft errors regardless of design rule.« less

Three-Dimensional Simulation of Ultrasound-Induced Microalgal Cell Disruption.

PubMed

Wang, M; Yuan, W; Hale, Andy

2016-03-01

The three-dimensional distribution (x, y, and z) of ultrasound-induced microalgal cell disruption in a sonochemical reactor was predicted by solving the Helmholtz equation using a three-dimensional acoustic module in the COMSOL Multiphysics software. The simulated local ultrasound pressure at any given location (x, y, and z) was found to correlate with cell disruption of a freshwater alga, Scenedesmus dimorphus, represented by the change of algal cell particle/debris concentration, chlorophyll-a fluorescence density (CAFD), and Nile red stained lipid fluorescence density (LFD), which was also validated by the model reaction of potassium iodide oxidation (the Weissler reaction). Furthermore, the effect of ultrasound power intensity and processing duration on algal cell disruption was examined to address the limitation of the model.

Consistent Estimation of Gibbs Energy Using Component Contributions

PubMed Central

Milo, Ron; Fleming, Ronan M. T.

2013-01-01

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism. PMID:23874165

A chemical and fluid dynamic study of the chemical vapor deposition of aluminum nitride in a vertical reactor

NASA Astrophysics Data System (ADS)

Bather, Wayne Anthony

The metalorganic chemical vapor deposition (MOCVD) growth of compound semiconductors has become important in producing many high performance electronic and optoelectronic devices from the wide bandgaps III-V nitrides, for example, aluminum nitride (AlN). A systematic theoretical and experimental investigation of the chemistry and mass transport process in a MOCVD system can yield predictive models of the deposition process. The chemistries and fluid dynamics of the MOCVD growth of AlN in a vertical reactor is analyzed and characterized in order to parameterize and model the deposition process. A Fourier Transform Infrared (FTIR) spectroscopic study of the predeposition reactions between trimethylaluminum (TMAl) and ammonia (NHsb3) is carried out in a static gas cell to examine the primary homogeneous gas phase reactions, pyrolysis of the reactants, and adduct formation, possibly accompanied by elimination reactions. A series of reactions, based on laboratory studies and literature review, is then proposed to model the deposition process. All pertinent kinetic, thermochemical, and transport properties were obtained. Utilizing a mass transport model, we performed computational fluid dynamics calculations using the FLUENT software package. We determined temperature, velocity, and concentration profiles, along with deposition rates inside the experimental vertical CVD reactor in the Howard University Material Science Research Center of Excellence. Experimental deposition rate data were found to be in good agreement with those predicted from the simulations, thus validating the proposed model. The control of the homogeneous gas phase reaction leading to the formation and subsequent decomposition of the adduct is critical to the formation of device-grade AlN films. Many basic processes occurring during MOCVD of AlN are still not completely understood, and none of the detailed surface reaction mechanisms are known.

Waste tyre pyrolysis: modelling of a moving bed reactor.

PubMed

Aylón, E; Fernández-Colino, A; Murillo, R; Grasa, G; Navarro, M V; García, T; Mastral, A M

2010-12-01

This paper describes the development of a new model for waste tyre pyrolysis in a moving bed reactor. This model comprises three different sub-models: a kinetic sub-model that predicts solid conversion in terms of reaction time and temperature, a heat transfer sub-model that calculates the temperature profile inside the particle and the energy flux from the surroundings to the tyre particles and, finally, a hydrodynamic model that predicts the solid flow pattern inside the reactor. These three sub-models have been integrated in order to develop a comprehensive reactor model. Experimental results were obtained in a continuous moving bed reactor and used to validate model predictions, with good approximation achieved between the experimental and simulated results. In addition, a parametric study of the model was carried out, which showed that tyre particle heating is clearly faster than average particle residence time inside the reactor. Therefore, this fast particle heating together with fast reaction kinetics enables total solid conversion to be achieved in this system in accordance with the predictive model. Copyright © 2010 Elsevier Ltd. All rights reserved.

Complete integrability of information processing by biochemical reactions

PubMed Central

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-01-01

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling – based on spin systems – has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis–Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy – based on completely integrable hydrodynamic-type systems of PDEs – which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions. PMID:27812018

Complete integrability of information processing by biochemical reactions

NASA Astrophysics Data System (ADS)

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-11-01

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling - based on spin systems - has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis-Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy - based on completely integrable hydrodynamic-type systems of PDEs - which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions.

Complete integrability of information processing by biochemical reactions.

PubMed

Agliari, Elena; Barra, Adriano; Dello Schiavo, Lorenzo; Moro, Antonio

2016-11-04

Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical kinetics, (anti-)ferromagnetic spin models in statistical mechanics and operational amplifiers/flip-flops in cybernetics. The underlying modeling - based on spin systems - has been proved to be accurate for a wide class of systems matching classical (e.g. Michaelis-Menten, Hill, Adair) scenarios in the infinite-size approximation. However, the current research in biochemical information processing has been focusing on systems involving a relatively small number of units, where this approximation is no longer valid. Here we show that the whole statistical mechanical description of reaction kinetics can be re-formulated via a mechanical analogy - based on completely integrable hydrodynamic-type systems of PDEs - which provides explicit finite-size solutions, matching recently investigated phenomena (e.g. noise-induced cooperativity, stochastic bi-stability, quorum sensing). The resulting picture, successfully tested against a broad spectrum of data, constitutes a neat rationale for a numerically effective and theoretically consistent description of collective behaviors in biochemical reactions.

Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong

2014-12-10

Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverifiedmore » reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.« less

Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling

PubMed Central

Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R.; Jijakli, Kenan; Salehi-Ashtiani, Kourosh

2014-01-01

Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates. PMID:25540776

Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling.

PubMed

Chaiboonchoe, Amphun; Dohai, Bushra Saeed; Cai, Hong; Nelson, David R; Jijakli, Kenan; Salehi-Ashtiani, Kourosh

2014-01-01

Metabolic modeling provides the means to define metabolic processes at a systems level; however, genome-scale metabolic models often remain incomplete in their description of metabolic networks and may include reactions that are experimentally unverified. This shortcoming is exacerbated in reconstructed models of newly isolated algal species, as there may be little to no biochemical evidence available for the metabolism of such isolates. The phenotype microarray (PM) technology (Biolog, Hayward, CA, USA) provides an efficient, high-throughput method to functionally define cellular metabolic activities in response to a large array of entry metabolites. The platform can experimentally verify many of the unverified reactions in a network model as well as identify missing or new reactions in the reconstructed metabolic model. The PM technology has been used for metabolic phenotyping of non-photosynthetic bacteria and fungi, but it has not been reported for the phenotyping of microalgae. Here, we introduce the use of PM assays in a systematic way to the study of microalgae, applying it specifically to the green microalgal model species Chlamydomonas reinhardtii. The results obtained in this study validate a number of existing annotated metabolic reactions and identify a number of novel and unexpected metabolites. The obtained information was used to expand and refine the existing COBRA-based C. reinhardtii metabolic network model iRC1080. Over 254 reactions were added to the network, and the effects of these additions on flux distribution within the network are described. The novel reactions include the support of metabolism by a number of d-amino acids, l-dipeptides, and l-tripeptides as nitrogen sources, as well as support of cellular respiration by cysteamine-S-phosphate as a phosphorus source. The protocol developed here can be used as a foundation to functionally profile other microalgae such as known microalgae mutants and novel isolates.

Development of a modified independent parallel reactions kinetic model and comparison with the distributed activation energy model for the pyrolysis of a wide variety of biomass fuels.

PubMed

Sfakiotakis, Stelios; Vamvuka, Despina

2015-12-01

The pyrolysis of six waste biomass samples was studied and the fuels were kinetically evaluated. A modified independent parallel reactions scheme (IPR) and a distributed activation energy model (DAEM) were developed and their validity was assessed and compared by checking their accuracy of fitting the experimental results, as well as their prediction capability in different experimental conditions. The pyrolysis experiments were carried out in a thermogravimetric analyzer and a fitting procedure, based on least squares minimization, was performed simultaneously at different experimental conditions. A modification of the IPR model, considering dependence of the pre-exponential factor on heating rate, was proved to give better fit results for the same number of tuned kinetic parameters, comparing to the known IPR model and very good prediction results for stepwise experiments. Fit of calculated data to the experimental ones using the developed DAEM model was also proved to be very good. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dynamic modeling and validation of a lignocellulosic enzymatic hydrolysis process--a demonstration scale study.

PubMed

Prunescu, Remus Mihail; Sin, Gürkan

2013-12-01

The enzymatic hydrolysis process is one of the key steps in second generation biofuel production. After being thermally pretreated, the lignocellulosic material is liquefied by enzymes prior to fermentation. The scope of this paper is to evaluate a dynamic model of the hydrolysis process on a demonstration scale reactor. The following novel features are included: the application of the Convection-Diffusion-Reaction equation to a hydrolysis reactor to assess transport and mixing effects; the extension of a competitive kinetic model with enzymatic pH dependency and hemicellulose hydrolysis; a comprehensive pH model; and viscosity estimations during the course of reaction. The model is evaluated against real data extracted from a demonstration scale biorefinery throughout several days of operation. All measurements are within predictions uncertainty and, therefore, the model constitutes a valuable tool to support process optimization, performance monitoring, diagnosis and process control at full-scale studies. Copyright © 2013 Elsevier Ltd. All rights reserved.

Comparative simulation of a fluidised bed reformer using industrial process simulators

NASA Astrophysics Data System (ADS)

Bashiri, Hamed; Sotudeh-Gharebagh, Rahmat; Sarvar-Amini, Amin; Haghtalab, Ali; Mostoufi, Navid

2016-08-01

A simulation model is developed by commercial simulators in order to predict the performance of a fluidised bed reformer. As many physical and chemical phenomena take place in the reformer, two sub-models (hydrodynamic and reaction sub-models) are needed. The hydrodynamic sub-model is based on the dynamic two-phase model and the reaction sub-model is derived from the literature. In the overall model, the bed is divided into several sections. In each section, the flow of the gas is considered as plug flow through the bubble phase and perfectly mixed through the emulsion phase. Experimental data from the literature were used to validate the model. Close agreement was found between the model of both ASPEN Plus (ASPEN PLUS 2004 ©) and HYSYS (ASPEN HYSYS 2004 ©) and the experimental data using various sectioning of the reactor ranged from one to four. The experimental conversion lies between one and four sections as expected. The model proposed in this work can be used as a framework in developing the complicated models for non-ideal reactors inside of the process simulators.

Validation of DSMC results for chemically nonequilibrium air flows against measurements of the electron number density in RAM-C II flight experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shevyrin, Alexander A.; Vashchenkov, Pavel V.; Bondar, Yevgeniy A.

An ionized flow around the RAM C-II vehicle in the range of altitudes from 73 to 81 km is studied by the Direct Simulation Monte Carlo (DSMC) method with three models of chemical reactions. It is demonstrated that vibration favoring in reactions of dissociation of neutral molecules affects significantly the predicted values of plasma density in the shock layer, and good agreement between the results of experiments and DSMC computations can be achieved in terms of the plasma density as a function of the flight altitude.

Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data

PubMed Central

Bandaru, Pradeep; Bansal, Mukesh

2011-01-01

Abstract We present a step towards the metabolome-wide computational inference of cellular metabolic reaction networks from metabolic profiling data, such as mass spectrometry. The reconstruction is based on identification of irreducible statistical interactions among the metabolite activities using the ARACNE reverse-engineering algorithm and on constraining possible metabolic transformations to satisfy the conservation of mass. The resulting algorithms are validated on synthetic data from an abridged computational model of Escherichia coli metabolism. Precision rates upwards of 50% are routinely observed for identification of full metabolic reactions, and recalls upwards of 20% are also seen. PMID:21314454

Estimating reaction rate coefficients within a travel-time modeling framework.

PubMed

Gong, R; Lu, C; Wu, W-M; Cheng, H; Gu, B; Watson, D; Jardine, P M; Brooks, S C; Criddle, C S; Kitanidis, P K; Luo, J

2011-01-01

A generalized, efficient, and practical approach based on the travel-time modeling framework is developed to estimate in situ reaction rate coefficients for groundwater remediation in heterogeneous aquifers. The required information for this approach can be obtained by conducting tracer tests with injection of a mixture of conservative and reactive tracers and measurements of both breakthrough curves (BTCs). The conservative BTC is used to infer the travel-time distribution from the injection point to the observation point. For advection-dominant reactive transport with well-mixed reactive species and a constant travel-time distribution, the reactive BTC is obtained by integrating the solutions to advective-reactive transport over the entire travel-time distribution, and then is used in optimization to determine the in situ reaction rate coefficients. By directly working on the conservative and reactive BTCs, this approach avoids costly aquifer characterization and improves the estimation for transport in heterogeneous aquifers which may not be sufficiently described by traditional mechanistic transport models with constant transport parameters. Simplified schemes are proposed for reactive transport with zero-, first-, nth-order, and Michaelis-Menten reactions. The proposed approach is validated by a reactive transport case in a two-dimensional synthetic heterogeneous aquifer and a field-scale bioremediation experiment conducted at Oak Ridge, Tennessee. The field application indicates that ethanol degradation for U(VI)-bioremediation is better approximated by zero-order reaction kinetics than first-order reaction kinetics. Copyright © 2010 The Author(s). Journal compilation © 2010 National Ground Water Association.

Estimating Reaction Rate Coefficients Within a Travel-Time Modeling Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gong, R; Lu, C; Luo, Jian

A generalized, efficient, and practical approach based on the travel-time modeling framework is developed to estimate in situ reaction rate coefficients for groundwater remediation in heterogeneous aquifers. The required information for this approach can be obtained by conducting tracer tests with injection of a mixture of conservative and reactive tracers and measurements of both breakthrough curves (BTCs). The conservative BTC is used to infer the travel-time distribution from the injection point to the observation point. For advection-dominant reactive transport with well-mixed reactive species and a constant travel-time distribution, the reactive BTC is obtained by integrating the solutions to advective-reactive transportmore » over the entire travel-time distribution, and then is used in optimization to determine the in situ reaction rate coefficients. By directly working on the conservative and reactive BTCs, this approach avoids costly aquifer characterization and improves the estimation for transport in heterogeneous aquifers which may not be sufficiently described by traditional mechanistic transport models with constant transport parameters. Simplified schemes are proposed for reactive transport with zero-, first-, nth-order, and Michaelis-Menten reactions. The proposed approach is validated by a reactive transport case in a two-dimensional synthetic heterogeneous aquifer and a field-scale bioremediation experiment conducted at Oak Ridge, Tennessee. The field application indicates that ethanol degradation for U(VI)-bioremediation is better approximated by zero-order reaction kinetics than first-order reaction kinetics.« less

An energy-dependent numerical model for the condensation probability, γ j

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerby, Leslie Marie

The “condensation” probability, γ j, is an important variable in the preequilibrium stage of nuclear spallation reactions. It represents the probability that p j excited nucleons (excitons) will “condense” to form complex particle type j in the excited residual nucleus. In addition, it has a significant impact on the emission width, or probability of emitting fragment type j from the residual nucleus. Previous formulations for γ j were energy-independent and valid for fragments up to 4He only. This paper explores the formulation of a new model for γ j, one which is energy-dependent and valid for up to 28Mg, andmore » which provides improved fits compared to experimental fragment spectra.« less

An energy-dependent numerical model for the condensation probability, γ j

DOE PAGES

Kerby, Leslie Marie

2016-12-09

The “condensation” probability, γ j, is an important variable in the preequilibrium stage of nuclear spallation reactions. It represents the probability that p j excited nucleons (excitons) will “condense” to form complex particle type j in the excited residual nucleus. In addition, it has a significant impact on the emission width, or probability of emitting fragment type j from the residual nucleus. Previous formulations for γ j were energy-independent and valid for fragments up to 4He only. This paper explores the formulation of a new model for γ j, one which is energy-dependent and valid for up to 28Mg, andmore » which provides improved fits compared to experimental fragment spectra.« less

Correlating Reactivity and Selectivity to Cyclopentadienyl Ligand Properties in Rh(III)-Catalyzed C-H Activation Reactions: An Experimental and Computational Study.

PubMed

Piou, Tiffany; Romanov-Michailidis, Fedor; Romanova-Michaelides, Maria; Jackson, Kelvin E; Semakul, Natthawat; Taggart, Trevor D; Newell, Brian S; Rithner, Christopher D; Paton, Robert S; Rovis, Tomislav

2017-01-25

Cp X Rh(III)-catalyzed C-H functionalization reactions are a proven method for the efficient assembly of small molecules. However, rationalization of the effects of cyclopentadienyl (Cp X ) ligand structure on reaction rate and selectivity has been viewed as a black box, and a truly systematic study is lacking. Consequently, predicting the outcomes of these reactions is challenging because subtle variations in ligand structure can cause notable changes in reaction behavior. A predictive tool is, nonetheless, of considerable value to the community as it would greatly accelerate reaction development. Designing a data set in which the steric and electronic properties of the Cp X Rh(III) catalysts were systematically varied allowed us to apply multivariate linear regression algorithms to establish correlations between these catalyst-based descriptors and the regio-, diastereoselectivity, and rate of model reactions. This, in turn, led to the development of quantitative predictive models that describe catalyst performance. Our newly described cone angles and Sterimol parameters for Cp X ligands served as highly correlative steric descriptors in the regression models. Through rational design of training and validation sets, key diastereoselectivity outliers were identified. Computations reveal the origins of the outstanding stereoinduction displayed by these outliers. The results are consistent with partial η 5 -η 3 ligand slippage that occurs in the transition state of the selectivity-determining step. In addition to the instructive value of our study, we believe that the insights gained are transposable to other group 9 transition metals and pave the way toward rational design of C-H functionalization catalysts.

Determination of rate constants and branching ratios for TCE degradation by zero-valent iron using a chain decay multispecies model.

PubMed

Hwang, Hyoun-Tae; Jeen, Sung-Wook; Sudicky, Edward A; Illman, Walter A

2015-01-01

The applicability of a newly-developed chain-decay multispecies model (CMM) was validated by obtaining kinetic rate constants and branching ratios along the reaction pathways of trichloroethene (TCE) reduction by zero-valent iron (ZVI) from column experiments. Changes in rate constants and branching ratios for individual reactions for degradation products over time for two columns under different geochemical conditions were examined to provide ranges of those parameters expected over the long-term. As compared to the column receiving deionized water, the column receiving dissolved CaCO3 showed higher mean degradation rates for TCE and all of its degradation products. However, the column experienced faster reactivity loss toward TCE degradation due to precipitation of secondary carbonate minerals, as indicated by a higher value for the ratio of maximum to minimum TCE degradation rate observed over time. From the calculated branching ratios, it was found that TCE and cis-dichloroethene (cis-DCE) were dominantly dechlorinated to chloroacetylene and acetylene, respectively, through reductive elimination for both columns. The CMM model, validated by the column test data in this study, provides a convenient tool to determine simultaneously the critical design parameters for permeable reactive barriers and natural attenuation such as rate constants and branching ratios. Copyright © 2015 Elsevier B.V. All rights reserved.

Network thermodynamic curation of human and yeast genome-scale metabolic models.

PubMed

Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K

2014-07-15

Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The Ca(2+)-EDTA chelation as standard reaction to validate Isothermal Titration Calorimeter measurements (ITC).

PubMed

Ràfols, Clara; Bosch, Elisabeth; Barbas, Rafael; Prohens, Rafel

2016-07-01

A study about the suitability of the chelation reaction of Ca(2+)with ethylenediaminetetraacetic acid (EDTA) as a validation standard for Isothermal Titration Calorimeter measurements has been performed exploring the common experimental variables (buffer, pH, ionic strength and temperature). Results obtained in a variety of experimental conditions have been amended according to the side reactions involved in the main process and to the experimental ionic strength and, finally, validated by contrast with the potentiometric reference values. It is demonstrated that the chelation reaction performed in acetate buffer 0.1M and 25°C shows accurate and precise results and it is robust enough to be adopted as a standard calibration process. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of Two Predictive Models for Short-Term Mortality in Patients after Severe Traumatic Brain Injury.

PubMed

Kesmarky, Klara; Delhumeau, Cecile; Zenobi, Marie; Walder, Bernhard

2017-07-15

The Glasgow Coma Scale (GCS) and the Abbreviated Injury Score of the head region (HAIS) are validated prognostic factors in traumatic brain injury (TBI). The aim of this study was to compare the prognostic performance of an alternative predictive model including motor GCS, pupillary reactivity, age, HAIS, and presence of multi-trauma for short-term mortality with a reference predictive model including motor GCS, pupil reaction, and age (IMPACT core model). A secondary analysis of a prospective epidemiological cohort study in Switzerland including patients after severe TBI (HAIS >3) with the outcome death at 14 days was performed. Performance of prediction, accuracy of discrimination (area under the receiver operating characteristic curve [AUROC]), calibration, and validity of the two predictive models were investigated. The cohort included 808 patients (median age, 56; interquartile range, 33-71), median GCS at hospital admission 3 (3-14), abnormal pupil reaction 29%, with a death rate of 29.7% at 14 days. The alternative predictive model had a higher accuracy of discrimination to predict death at 14 days than the reference predictive model (AUROC 0.852, 95% confidence interval [CI] 0.824-0.880 vs. AUROC 0.826, 95% CI 0.795-0.857; p < 0.0001). The alternative predictive model had an equivalent calibration, compared with the reference predictive model Hosmer-Lemeshow p values (Chi2 8.52, Hosmer-Lemeshow p = 0.345 vs. Chi2 8.66, Hosmer-Lemeshow p = 0.372). The optimism-corrected value of AUROC for the alternative predictive model was 0.845. After severe TBI, a higher performance of prediction for short-term mortality was observed with the alternative predictive model, compared with the reference predictive model.

Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

PubMed

Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

2013-01-01

The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more detailed mathematical models.

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

PubMed Central

Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

2013-01-01

The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more detailed mathematical models. PMID:24244124

DEVELOPMENT OF A VALIDATED MODEL FOR USE IN MINIMIZING NOx EMISSIONS AND MAXIMIZING CARBON UTILIZATION WHEN CO-FIRING BIOMASS WITH COAL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larry G. Felix; P. Vann Bush

2002-10-26

This is the eighth Quarterly Technical Report for DOE Cooperative Agreement No. DE-FC26-00NT40895. A statement of the project objectives is included in the Introduction of this report. The final biomass co-firing test burn was conducted during this quarter. In this test (Test 14), up to 20% by weight dry switchgrass was comilled with Jim Walters No.7 mine coal and injected through the single-register burner. Jim Walters No.7 coal is a low-volatility, low-sulfur ({approx}0.7% S) Eastern bituminous coal. The results of this test are presented in this quarterly report. Progress has continued to be made in implementing a modeling approach tomore » combine reaction times and temperature distributions from computational fluid dynamic models of the pilot-scale combustion furnace with char burnout and chemical reaction kinetics to predict NO{sub x} emissions and unburned carbon levels in the furnace exhaust. The REI Configurable Fireside Simulator (CFS) is now in regular use. Presently, the CFS is being used to generate CFD calculations for completed tests with Powder River Basin coal and low-volatility (Jim Walters No.7 Mine) coal. Niksa Energy Associates will use the results of these CFD simulations to complete their validation of the NOx/LOI predictive model. Work has started on the project final report.« less

A systems biology approach to investigate the antimicrobial activity of oleuropein.

PubMed

Li, Xianhua; Liu, Yanhong; Jia, Qian; LaMacchia, Virginia; O'Donoghue, Kathryn; Huang, Zuyi

2016-12-01

Oleuropein and its hydrolysis products are olive phenolic compounds that have antimicrobial effects on a variety of pathogens, with the potential to be utilized in food and pharmaceutical products. While the existing research is mainly focused on individual genes or enzymes that are regulated by oleuropein for antimicrobial activities, little work has been done to integrate intracellular genes, enzymes and metabolic reactions for a systematic investigation of antimicrobial mechanism of oleuropein. In this study, the first genome-scale modeling method was developed to predict the system-level changes of intracellular metabolism triggered by oleuropein in Staphylococcus aureus, a common food-borne pathogen. To simulate the antimicrobial effect, an existing S. aureus genome-scale metabolic model was extended by adding the missing nitric oxide reactions, and exchange rates of potassium, phosphate and glutamate were adjusted in the model as suggested by previous research to mimic the stress imposed by oleuropein on S. aureus. The developed modeling approach was able to match S. aureus growth rates with experimental data for five oleuropein concentrations. The reactions with large flux change were identified and the enzymes of fifteen of these reactions were validated by existing research for their important roles in oleuropein metabolism. When compared with experimental data, the up/down gene regulations of 80% of these enzymes were correctly predicted by our modeling approach. This study indicates that the genome-scale modeling approach provides a promising avenue for revealing the intracellular metabolism of oleuropein antimicrobial properties.

DSMC simulations of shock tube experiments for the dissociation rate of nitrogen

NASA Astrophysics Data System (ADS)

Bird, G. A.

2012-11-01

The DSMC method has been used to simulate the flow associated with several experiments that led to predictions of the dissociation rate in nitrogen. One involved optical interferometry to determine the density behind strong shock wave and the other involved the measurement of the shock tube end-wall pressure after the reflection of a similar shock wave. DSMC calculations for the un-reflected shock wave were made with the older TCE model that converts rate coefficients to reaction cross-sections, with the newer Q-K model that predicts the rates and with a set of reaction cross-sections for nitrogen dissociation from QCT calculations. A comparison of the resulting density profiles with the measured profile provides a test of the validity of the DSMC chemistry models. The DSMC reaction rates were sampled directly in the DSMC calculation, both far downstream where the flow is in equilibrium and in the non-equilibrium region immediately behind the shock. This permits a critical evaluation of data reduction procedures that were employed to deduce the dissociation rate from the measured quantities.

Estimated congener specific gas-phase atmospheric behavior and fractionation of perfluoroalkyl compounds: rates of reaction with atmospheric oxidants, air-water partitioning, and wet/dry deposition lifetimes.

PubMed

Rayne, Sierra; Forest, Kaya; Friesen, Ken J

2009-08-01

A quantitative structure-activity model has been validated for estimating congener specific gas-phase hydroxyl radical reaction rates for perfluoroalkyl sulfonic acids (PFSAs), carboxylic acids (PFCAs), aldehydes (PFAls) and dihydrates, fluorotelomer olefins (FTOls), alcohols (FTOHs), aldehydes (FTAls), and acids (FTAcs), and sulfonamides (SAs), sulfonamidoethanols (SEs), and sulfonamido carboxylic acids (SAAs), and their alkylated derivatives based on calculated semi-empirical PM6 method ionization potentials. Corresponding gas-phase reaction rates with nitrate radicals and ozone have also been estimated using the computationally derived ionization potentials. Henry's law constants for these classes of perfluorinated compounds also appear to be reasonably approximated by the SPARC software program, thereby allowing estimation of wet and dry atmospheric deposition rates. Both congener specific gas-phase atmospheric and air-water interface fractionation of these compounds is expected, complicating current source apportionment perspectives and necessitating integration of such differential partitioning influences into future multimedia models. The findings will allow development and refinement of more accurate and detailed local through global scale atmospheric models for the atmospheric fate of perfluoroalkyl compounds.

Application of CFD modelling at a full-scale ozonation plant for the removal of micropollutants from secondary effluent.

PubMed

Launer, M; Lyko, S; Fahlenkamp, H; Jagemann, P; Ehrhard, P

2013-01-01

Since November 2009, Germany's first full-scale ozonation plant for tertiary treatment of secondary effluent is in continuous operation. A kinetic model was developed and combined with the commercial computational fluid dynamics (CFD) software ANSYS(®) CFX(®) to simulate the removal of micropollutants from secondary effluents. Input data like reaction rate constants and initial concentrations of bulk components of the effluent organic matter (EfOM) were derived from experimental batch tests. Additionally, well-known correlations for the mass transfer were implemented into the simulation model. The CFD model was calibrated and validated by full-scale process data and by analytical measurements for micropollutants. The results show a good consistency of simulated values and measured data. Therewith, the validated CFD model described in this study proved to be suited for the application of secondary effluent ozonation. By implementing site-specific ozone exposition and the given reactor geometry the described CFD model can be easily adopted for similar applications.

Experimental evidence of quantum radiation reaction in aligned crystals.

PubMed

Wistisen, Tobias N; Di Piazza, Antonino; Knudsen, Helge V; Uggerhøj, Ulrik I

2018-02-23

Quantum radiation reaction is the influence of multiple photon emissions from a charged particle on the particle's dynamics, characterized by a significant energy-momentum loss per emission. Here we report experimental radiation emission spectra from ultrarelativistic positrons in silicon in a regime where quantum radiation reaction effects dominate the positron's dynamics. Our analysis shows that while the widely used quantum approach is overall the best model, it does not completely describe all the data in this regime. Thus, these experimental findings may prompt seeking more generally valid methods to describe quantum radiation reaction. This experiment is a fundamental test of quantum electrodynamics in a regime where the dynamics of charged particles is strongly influenced not only by the external electromagnetic fields but also by the radiation field generated by the charges themselves and where each photon emission may significantly reduce the energy of the charge.

The equilibrium assumption is valid for the kinetic treatment of most time-dependent protein-modification reactions.

PubMed Central

Brocklehurst, K

1979-01-01

To facilitate mechanistic interpretation of the kinetics of time-dependent inhibition of enzymes and of similar protein modification reactions, it is important to know when the equilibrium assumption may be applied to the model: formula: (see text). The conventional criterion of quasi-equilibrium, k + 2 less than k-1, is not always easy to assess, particularly when k + 2 cannot be separately determined. It is demonstrated that the condition k + 2 less than k-1 is necessarily true, however, when the value of the apparent second-order rate constant for the modification reaction is much smaller than the value of k + 1. Since k + 1 is commonly at least 10(7)M-1.S-1 for substrates, it is probable that the equilibrium assumption may be properly applied to most irreversible inhibitions and modification reactions. PMID:518556

QSAR models for degradation of organic pollutants in ozonation process under acidic condition.

PubMed

Zhu, Huicen; Guo, Weimin; Shen, Zhemin; Tang, Qingli; Ji, Wenchao; Jia, Lijuan

2015-01-01

Although some researches about the degradation of organic pollutants have been carried out during recent years, reaction rate constants are available only for homologue compounds with similar structures or components. Therefore, it is of great significance to find a universal relationship between reaction rate and certain parameters of several diverse organic pollutants. In this study, removal ratio and kinetics of 33 kinds of organic substances were investigated by ozonation process, including azo dyes, heterocyclic compounds, ionic compounds and so on. Most quantum chemical parameters were conducted by using Gaussian 09 at the DFT B3LYP/6-311G level, including μ, q H(+), q(C)minq(C)max, ELUMO and EHOMO. Other descriptors, bond order (BO) as well as Fukui indices (f(+), f(-) and f(0)), were calculated by Material Studio 6.1 at Dmol(3)/GGA-BLYP/DNP(3.5) basis for each organic compound. The recommended model for predicting rate constants was lnk'=1.978-95.484f(0)x-3.350q(C)min+38.221f(+)x, which had the squared regression coefficient R(2)=0.763 and standard deviation SD=0.716. The results of t test and the Fisher test suggested that the model exhibited optimum stability. Also, the model was validated by internal and external validations. Recommended QSAR model showed that the highest f(0) value of main-chain carbons (f(0)x) is more closely related to lnk' than other quantum descriptors. Copyright © 2014 Elsevier Ltd. All rights reserved.

Nickel sensitisation in mice: a critical appraisal.

PubMed

Johansen, Pål; Wäckerle-Men, Ying; Senti, Gabriela; Kündig, Thomas M

2010-06-01

The market release of new domestic and industrial chemical and metal products requires certain safety certification, including testing for skin sensitisation. Although various official guidelines have described how such testing is to be done, the validity of the available test models are in part dubious, for which reason regulatory agencies and research aim to further improve and generalise the models for testing of skin sensitisation. We applied a recently published murine model of nickel allergy as to test its applicability in a regulatory setting and to study and better understand the events leading to type-IV hypersensitivity. Nickel was chosen as model hapten since it induces allergic contact dermatitis with high incidence in the general population. Typically, C57BL/6 mice were sensitised and challenged by intradermal applications of nickel, and cutaneous inflammation was analysed by the mouse ear-swelling test, by histology, and by lymphocyte reactivity in vitro. Surprisingly, the study suggested that the skin reactions observed were results of irritant reactions rather than of adaptive immune responses. Non-sensitised mice responded with cutaneous inflammation and in vitro lymphocyte reactivity which were comparable with nickel-sensitised mice. Furthermore, histological examinations as well as experiments in T-cell deficient mice demonstrated that lymphocytes were not involved and that nickel caused an irritant contact dermatitis rather a true allergic type-IV contact dermatitis. The authors question the validity of the described murine model of nickel allergy. Copyright 2010 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.

Genome-wide association analysis to identify genotype × environment interaction for milk protein yield and level of somatic cell score as environmental descriptors in German Holsteins.

PubMed

Streit, M; Reinhardt, F; Thaller, G; Bennewitz, J

2013-01-01

Genotype by environment interaction (G × E) has been widely reported in dairy cattle. If the environment can be measured on a continuous scale, reaction norms can be applied to study G × E. The average herd milk production level has frequently been used as an environmental descriptor because it is influenced by the level of feeding or the feeding regimen. Another important environmental factor is the level of udder health and hygiene, for which the average herd somatic cell count might be a descriptor. In the present study, we conducted a genome-wide association analysis to identify single nucleotide polymorphisms (SNP) that affect intercept and slope of milk protein yield reaction norms when using the average herd test-day solution for somatic cell score as an environmental descriptor. Sire estimates for intercept and slope of the reaction norms were calculated from around 12 million daughter records, using linear reaction norm models. Sires were genotyped for ~54,000 SNP. The sire estimates were used as observations in the association analysis, using 1,797 sires. Significant SNP were confirmed in an independent validation set consisting of 500 sires. A known major gene affecting protein yield was included as a covariable in the statistical model. Sixty (21) SNP were confirmed for intercept with P ≤ 0.01 (P ≤ 0.001) in the validation set, and 28 and 11 SNP, respectively, were confirmed for slope. Most but not all SNP affecting slope also affected intercept. Comparison with an earlier study revealed that SNP affecting slope were, in general, also significant for slope when the environment was modeled by the average herd milk production level, although the two environmental descriptors were poorly correlated. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A Mechanism-Based Model for the Prediction of the Metabolic Sites of Steroids Mediated by Cytochrome P450 3A4.

PubMed

Dai, Zi-Ru; Ai, Chun-Zhi; Ge, Guang-Bo; He, Yu-Qi; Wu, Jing-Jing; Wang, Jia-Yue; Man, Hui-Zi; Jia, Yan; Yang, Ling

2015-06-30

Early prediction of xenobiotic metabolism is essential for drug discovery and development. As the most important human drug-metabolizing enzyme, cytochrome P450 3A4 has a large active cavity and metabolizes a broad spectrum of substrates. The poor substrate specificity of CYP3A4 makes it a huge challenge to predict the metabolic site(s) on its substrates. This study aimed to develop a mechanism-based prediction model based on two key parameters, including the binding conformation and the reaction activity of ligands, which could reveal the process of real metabolic reaction(s) and the site(s) of modification. The newly established model was applied to predict the metabolic site(s) of steroids; a class of CYP3A4-preferred substrates. 38 steroids and 12 non-steroids were randomly divided into training and test sets. Two major metabolic reactions, including aliphatic hydroxylation and N-dealkylation, were involved in this study. At least one of the top three predicted metabolic sites was validated by the experimental data. The overall accuracy for the training and test were 82.14% and 86.36%, respectively. In summary, a mechanism-based prediction model was established for the first time, which could be used to predict the metabolic site(s) of CYP3A4 on steroids with high predictive accuracy.

Oxidation of Carbon Fibers in a Cracked Ceramic Matrix Composite Modeled as a Function of Temperature

NASA Technical Reports Server (NTRS)

Halbig, Michael C.; Cawley, James D.; Eckel, Andrew J.

2003-01-01

The oxidation model simulates the oxidation of the reinforcing carbon fibers within a ceramic matrix composite material containing as-fabricated microcracks. The physics-based oxidation model uses theoretically and experimentally determined variables as input for the model. The model simulates the ingress of oxygen through microcracks into a two-dimensional plane within the composite material. Model input includes temperature, oxygen concentration, the reaction rate constant, the diffusion coefficient, and the crack opening width as a function of the mechanical and thermal loads. The model is run in an iterative process for a two-dimensional grid system in which oxygen diffuses through the porous and cracked regions of the material and reacts with carbon in short time steps. The model allows the local oxygen concentrations and carbon volumes from the edge to the interior of the composite to be determined over time. Oxidation damage predicted by the model was compared with that observed from microstructural analysis of experimentally tested composite material to validate the model for two temperatures of interest. When the model is run for low-temperature conditions, the kinetics are reaction controlled. Carbon and oxygen reactions occur relatively slowly. Therefore, oxygen can bypass the carbon near the outer edge and diffuse into the interior so that it saturates the entire composite at relatively high concentrations. The kinetics are limited by the reaction rate between carbon and oxygen. This results in an interior that has high local concentrations of oxygen and a similar amount of consumed carbon throughout the cross section. When the model is run for high-temperature conditions, the kinetics are diffusion controlled. Carbon and oxygen reactions occur very quickly. The carbon consumes oxygen as soon as it is supplied. The kinetics are limited by the relatively slow rate at which oxygen is supplied in comparison to the relatively fast rate at which carbon and oxygen reactions occur. This results in a sharp gradient in oxygen concentration from the edge where it is supplied to the nearest source of carbon, which is where the oxygen is quickly consumed. A moving reaction front is seen in which the outlaying carbon is consumed before the next inner layer of carbon begins to react.

A coupled CFD and two-phase substrate kinetic model for enzymatic hydrolysis of lignocellulose

NASA Astrophysics Data System (ADS)

Danes, Nicholas; Sitaraman, Hariswaran; Stickel, Jonathan; Sprague, Michael

2017-11-01

Cost-effective production of fuels from lignocellulosic biomass is an important subject of research in order to meet the world's current and future energy demands. Enzymatic hydrolysis is one of the several steps in the biochemical conversion of biomass into fuels. This process involves the interplay of non-Newtonian fluid dynamics that happen over tens of seconds coupled with chemical reactions that happen over several hours. In this work, we present a coupled CFD-reaction model for conversion of cellulose to sugars in a benchtop mixer reactor. A subcycling approach is used to circumvent the large time scale disparity between fluid dynamics and reactions. We will present a validation study of our simulations with experiments for well-mixed and stratified reactor scenarios along with predictions for conversion rates and product concentrations at varying impeller speeds and in scaled-up reactors. This work is funded by the Bioenergy Technology Office of DOE and the NSF's Enriched Doctoral Training program (DMS-1551229).

Biomass-derived oxygenate reforming on Pt(111): A demonstration of surface science using D-glucose and its model surrogate glycolaldehyde

NASA Astrophysics Data System (ADS)

McManus, Jesse R.; Yu, Weiting; Salciccioli, Michael; Vlachos, Dionisios G.; Chen, Jingguang G.; Vohs, John M.

2012-12-01

Molecules derived from cellulosic biomass, such as glucose, represent an important renewable feedstock for the production of hydrogen and hydrocarbon-based fuels and chemicals. Development of efficient catalysts for their reformation into useful products is needed; however, this requires a detailed understanding of their adsorption and reaction on catalytically active transition metal surfaces. In this paper we demonstrate that the standard surface science techniques routinely used to characterize the reaction of small molecules on metals are also amenable for use in studying the adsorption and reaction of complex biomass-derivatives on single crystal metal surfaces. In particular, Temperature Programmed Desorption (TPD) and High Resolution Electron Energy Loss Spectroscopy (HREELS) combined with Density Functional Theory (DFT) calculations were used to elucidate the adsorption configuration of D-glucose and glycolaldehye on Pt(111). Both molecules were found to adsorb in an η1 aldehyde configuration partially validating the use of simple, functionally-equivalent model compounds for surface studies of cellulosic oxygenates.

A new approach to synthesis of benzyl cinnamate: Optimization by response surface methodology.

PubMed

Zhang, Dong-Hao; Zhang, Jiang-Yan; Che, Wen-Cai; Wang, Yun

2016-09-01

In this work, the new approach to synthesis of benzyl cinnamate by enzymatic esterification of cinnamic acid with benzyl alcohol is optimized by response surface methodology. The effects of various reaction conditions, including temperature, enzyme loading, substrate molar ratio of benzyl alcohol to cinnamic acid, and reaction time, are investigated. A 5-level-4-factor central composite design is employed to search for the optimal yield of benzyl cinnamate. A quadratic polynomial regression model is used to analyze the experimental data at a 95% confidence level (P<0.05). The coefficient of determination of this model is found to be 0.9851. Three sets of optimum reaction conditions are established, and the verified experimental trials are performed for validating the optimum points. Under the optimum conditions (40°C, 31mg/mL enzyme loading, 2.6:1 molar ratio, 27h), the yield reaches 97.7%, which provides an efficient processes for industrial production of benzyl cinnamate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Kinetics of (reversible) internal reforming of methane in solid oxide fuel cells under stationary and APU conditions

NASA Astrophysics Data System (ADS)

Timmermann, H.; Sawady, W.; Reimert, R.; Ivers-Tiffée, E.

The internal reforming of methane in a solid oxide fuel cell (SOFC) is investigated and modeled for flow conditions relevant to operation. To this end, measurements are performed on anode-supported cells (ASC), thereby varying gas composition (y CO = 4-15%, yH2 = 5 - 17 % , yCO2 = 6 - 18 % , yH2O = 2 - 30 % , yCH4 = 0.1 - 20 %) and temperature (600-850 °C). In this way, operating conditions for both stationary applications (methane-rich pre-reformate) as well as for auxiliary power unit (APU) applications (diesel-POX reformate) are represented. The reforming reaction is monitored in five different positions alongside the anodic gas channel by means of gas chromatography. It is shown that methane is converted in the flow field for methane-rich gas compositions, whereas under operation with diesel reformate the direction of the reaction is reversed for temperatures below 675 °C, i.e. (exothermic) methanation occurs along the anode. Using a reaction model, a rate equation for reforming could be derived which is also valid in the case of methanation. By introducing this equation into the reaction model the methane conversion along a catalytically active Ni-YSZ cermet SOFC anode can be simulated for the operating conditions specified above.

Validation of the Instructional Materials Motivation Survey (IMMS) in a Self-Directed Instructional Setting Aimed at Working with Technology

ERIC Educational Resources Information Center

Loorbach, Nicole; Peters, Oscar; Karreman, Joyce; Steehouder, Michaël

2015-01-01

The ARCS Model of Motivational Design has been used myriad times to design motivational instructions that focus on attention, relevance, confidence and satisfaction in order to motivate students. The Instructional Materials Motivation Survey (IMMS) is a 36-item situational measure of people's reactions to instructional materials in the light…

VALIDATION TESTING OF NEW MECHANISMS WITH OUTDOOR CHAMBER DATA, VOLUME 3: CALCULATION OF PHOTOCHEMICAL REACTION PHOTOLYSIS RATES IN THE UNC OUTDOOR CHAMBER

EPA Science Inventory

A new model is described for computing in-chamber actinic flux using site specific conditions that include time of day, air pressure, total column ozone, total column water vapor, relative humidity, aerosol type, aerosol optical density at 500 nm, and the spectral albedo of the g...

Unsupported or Turned Against: Understanding How Two Types of Negative Social Reactions to Sexual Assault Relate to Post-Assault Outcomes.

PubMed

Relyea, Mark; Ullman, Sarah

2015-03-01

Social reactions to disclosures of sexual assault have significant effects on women's post-assault outcomes (see Ullman, 2010, for a review). The Social Reactions Questionnaire (SRQ; Ullman, 2000) measures these reactions (as reported by survivors) and aggregates them into positive and negative scales. However, studies indicate that only some "negative" reactions have a negative valence for survivors whereas others produce a mixed (positive and negative) valence. The current study compares a one-primary-factor model of "negative reactions" to a model with two primary factors that we have labeled "turning against" and "unsupportive acknowledgement." Results showed that although one primary factor was plausible, two primary factors provided a better fit to the data. To assess the discriminant validity of the two factors, we performed regressions predicting social support, psychological adjustment, and coping behaviors. Analyses supported the hypotheses that reactions of being turned against were related to social withdrawal, increased self-blame, and decreased sexual assertiveness whereas reactions of unsupportive acknowledgment were related to both adaptive and maladaptive coping. Against predictions, depression and PTSD were more related to receiving unsupportive acknowledgment than to receiving turning against reactions. Implications for interventions and research are discussed. Importantly, almost all women (94%) in our sample received reactions that acknowledged that an assault occurred but failed to provide support, and this lack of support was associated with worse coping than even more hostile reactions such as being blamed or stigmatized. Therefore, there seems a great need for effective programs to train community members to respond to survivors with the kind of emotional and tangible support that promotes better outcomes.

DART model for irradiation-induced swelling of uranium silicide dispersion fuel elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rest, J.; Hofman, G.L.

1999-04-01

Models for the interaction of uranium silicide dispersion fuels with an aluminum matrix, for the resultant reaction product swelling, and for the calculation of the stress gradient within the fuel particles are described within the context of DART fission-gas-induced swelling models. The effects of an aluminide shell on fuel particle swelling are evaluated. Validation of the model is demonstrated by comparing DART calculations with irradiation data for the swelling of U{sub 3}SiAl-Al and U{sub 3}Si{sub 2}-Al in variously designed dispersion fuel elements.

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.; Giese, Timothy J.; York, Darrin M.

2015-12-01

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom's local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion and dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the SN2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.

Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology

PubMed Central

Amemiya, Takahiro; Honma, Masashi; Kariya, Yoshiaki; Ghosh, Samik; Kitano, Hiroaki; Kurachi, Yoshihisa; Fujita, Ken-ichi; Sasaki, Yasutsuna; Homma, Yukio; Abernethy, Darrel R; Kume, Haruki; Suzuki, Hiroshi

2015-01-01

Background/Objectives: Targeted kinase inhibitors are an important class of agents in anticancer therapeutics, but their limited tolerability hampers their clinical performance. Identification of the molecular mechanisms underlying the development of adverse reactions will be helpful in establishing a rational method for the management of clinically adverse reactions. Here, we selected sunitinib as a model and demonstrated that the molecular mechanisms underlying the adverse reactions associated with kinase inhibitors can efficiently be identified using a systems toxicological approach. Methods: First, toxicological target candidates were short-listed by comparing the human kinase occupancy profiles of sunitinib and sorafenib, and the molecular mechanisms underlying adverse reactions were predicted by sequential simulations using publicly available mathematical models. Next, to evaluate the probability of these predictions, a clinical observation study was conducted in six patients treated with sunitinib. Finally, mouse experiments were performed for detailed confirmation of the hypothesized molecular mechanisms and to evaluate the efficacy of a proposed countermeasure against adverse reactions to sunitinib. Results: In silico simulations indicated the possibility that sunitinib-mediated off-target inhibition of phosphorylase kinase leads to the generation of oxidative stress in various tissues. Clinical observations of patients and mouse experiments confirmed the validity of this prediction. The simulation further suggested that concomitant use of an antioxidant may prevent sunitinib-mediated adverse reactions, which was confirmed in mouse experiments. Conclusions: A systems toxicological approach successfully predicted the molecular mechanisms underlying clinically adverse reactions associated with sunitinib and was used to plan a rational method for the management of these adverse reactions. PMID:28725458

Particle-scale CO2 adsorption kinetics modeling considering three reaction mechanisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suh, Dong-Myung; Sun, Xin

2013-09-01

In the presence of water (H2O), dry and wet adsorptions of carbon dioxide (CO2) and physical adsorption of H2O happen concurrently in a sorbent particle. The three reactions depend on each other and have a complicated, but important, effect on CO2 capturing via a solid sorbent. In this study, transport phenomena in the sorbent were modeled, including the tree reactions, and a numerical solving procedure for the model also was explained. The reaction variable distribution in the sorbent and their average values were calculated, and simulation results were compared with experimental data to validate the proposed model. Some differences, causedmore » by thermodynamic parameters, were observed between them. However, the developed model reasonably simulated the adsorption behaviors of a sorbent. The weight gained by each adsorbed species, CO2 and H2O, is difficult to determine experimentally. It is known that more CO2 can be captured in the presence of water. Still, it is not yet known quantitatively how much more CO2 the sorbent can capture, nor is it known how much dry and wet adsorptions separately account for CO2 capture. This study addresses those questions by modeling CO2 adsorption in a particle and simulating the adsorption process using the model. As adsorption temperature changed into several values, the adsorbed amount of each species was calculated. The captured CO2 in the sorbent particle was compared quantitatively between dry and wet conditions. As the adsorption temperature decreased, wet adsorption increased. However, dry adsorption was reduced.« less

Development of Diagnostic Biomarkers for Detecting Diabetic Retinopathy at Early Stages Using Quantitative Proteomics

PubMed Central

Min, Hophil; Kim, Sang Jin; Oh, Sohee; Kim, Kyunggon; Yu, Hyeong Gon; Park, Taesung; Kim, Youngsoo

2016-01-01

Diabetic retinopathy (DR) is a common microvascular complication caused by diabetes mellitus (DM) and is a leading cause of vision impairment and loss among adults. Here, we performed a comprehensive proteomic analysis to discover biomarkers for DR. First, to identify biomarker candidates that are specifically expressed in human vitreous, we performed data-mining on both previously published DR-related studies and our experimental data; 96 proteins were then selected. To confirm and validate the selected biomarker candidates, candidates were selected, confirmed, and validated using plasma from diabetic patients without DR (No DR) and diabetics with mild or moderate nonproliferative diabetic retinopathy (Mi or Mo NPDR) using semiquantitative multiple reaction monitoring (SQ-MRM) and stable-isotope dilution multiple reaction monitoring (SID-MRM). Additionally, we performed a multiplex assay using 15 biomarker candidates identified in the SID-MRM analysis, which resulted in merged AUC values of 0.99 (No DR versus Mo NPDR) and 0.93 (No DR versus Mi and Mo NPDR). Although further validation with a larger sample size is needed, the 4-protein marker panel (APO4, C7, CLU, and ITIH2) could represent a useful multibiomarker model for detecting the early stages of DR. PMID:26665153

Effect of nonlinearity in hybrid kinetic Monte Carlo-continuum models.

PubMed

Balter, Ariel; Lin, Guang; Tartakovsky, Alexandre M

2012-01-01

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a kinetic Monte Carlo (KMC) model for a surface to a finite-difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition-dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition-dissolution model including competitive adsorption, which leads to a nonlinear rate, and show that in this case the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.

Effect of Nonlinearity in Hybrid Kinetic Monte Carlo-Continuum Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balter, Ariel I.; Lin, Guang; Tartakovsky, Alexandre M.

2012-04-23

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a KMC model for a surface to a finite difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and also show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition/dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition/dissolution model including competitive adsorption, which leadsmore » to a nonlinear rate, and show that, in this case, the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.« less

Reactant conversion in homogeneous turbulence - Mathematical modeling, computational validations, and practical applications

NASA Technical Reports Server (NTRS)

Madnia, C. K.; Frankel, S. H.; Givi, P.

1992-01-01

The presently obtained closed-form analytical expressions, which predict the limiting rate of mean reactant conversion in homogeneous turbulent flows under the influence of a binary reaction, are derived via the single-point pdf method based on amplitude mapping closure. With this model, the maximum rate of the mean reactant's decay can be conveniently expressed in terms of definite integrals of the parabolic cylinder functions. The results obtained are shown to be in good agreement with data generated by direct numerical simulations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Shang-Min; Grosheintz, Luc; Kitzmann, Daniel

We present an open-source and validated chemical kinetics code for studying hot exoplanetary atmospheres, which we name VULCAN. It is constructed for gaseous chemistry from 500 to 2500 K, using a reduced C–H–O chemical network with about 300 reactions. It uses eddy diffusion to mimic atmospheric dynamics and excludes photochemistry. We have provided a full description of the rate coefficients and thermodynamic data used. We validate VULCAN by reproducing chemical equilibrium and by comparing its output versus the disequilibrium-chemistry calculations of Moses et al. and Rimmer and Helling. It reproduces the models of HD 189733b and HD 209458b by Mosesmore » et al., which employ a network with nearly 1600 reactions. We also use VULCAN to examine the theoretical trends produced when the temperature–pressure profile and carbon-to-oxygen ratio are varied. Assisted by a sensitivity test designed to identify the key reactions responsible for producing a specific molecule, we revisit the quenching approximation and find that it is accurate for methane but breaks down for acetylene, because the disequilibrium abundance of acetylene is not directly determined by transport-induced quenching, but is rather indirectly controlled by the disequilibrium abundance of methane. Therefore we suggest that the quenching approximation should be used with caution and must always be checked against a chemical kinetics calculation. A one-dimensional model atmosphere with 100 layers, computed using VULCAN, typically takes several minutes to complete. VULCAN is part of the Exoclimes Simulation Platform (ESP; exoclime.net) and publicly available at https://github.com/exoclime/VULCAN.« less

Titration Calorimetry Standards and the Precision of Isothermal Titration Calorimetry Data

PubMed Central

Baranauskienė, Lina; Petrikaitė, Vilma; Matulienė, Jurgita; Matulis, Daumantas

2009-01-01

Current Isothermal Titration Calorimetry (ITC) data in the literature have relatively high errors in the measured enthalpies of protein-ligand binding reactions. There is a need for universal validation standards for titration calorimeters. Several inorganic salt co-precipitation and buffer protonation reactions have been suggested as possible enthalpy standards. The performances of several commercial calorimeters, including the VP-ITC, ITC200, and Nano ITC-III, were validated using these suggested standard reactions. PMID:19582227

The Development of Valid Subtypes for Depression in Primary Care Settings

PubMed Central

Karasz, Alison

2009-01-01

A persistent theme in the debate on the classification of depressive disorders is the distinction between biological and environmental depressions. Despite decades of research, there remains little consensus on how to distinguish between depressive subtypes. This preliminary study describes a method that could be useful, if implemented on a larger scale, in the development of valid subtypes of depression in primary care settings, using explanatory models of depressive illness. Seventeen depressed Hispanic patients at an inner city general practice participated in explanatory model interviews. Participants generated illness narratives, which included details about symptoms, cause, course, impact, health seeking, and anticipated outcome. Two distinct subtypes emerged from the analysis. The internal model subtype was characterized by internal attributions, specifically the notion of an “injured self.” The external model subtype conceptualized depression as a reaction to life situations. Each subtype was associated with a distinct constellation of clinical features and health seeking experiences. Future directions for research using explanatory models to establish depressive subtypes are explored. PMID:18414123

A two-stage predictive model to simultaneous control of trihalomethanes in water treatment plants and distribution systems: adaptability to treatment processes.

PubMed

Domínguez-Tello, Antonio; Arias-Borrego, Ana; García-Barrera, Tamara; Gómez-Ariza, José Luis

2017-10-01

The trihalomethanes (TTHMs) and others disinfection by-products (DBPs) are formed in drinking water by the reaction of chlorine with organic precursors contained in the source water, in two consecutive and linked stages, that starts at the treatment plant and continues in second stage along the distribution system (DS) by reaction of residual chlorine with organic precursors not removed. Following this approach, this study aimed at developing a two-stage empirical model for predicting the formation of TTHMs in the water treatment plant and subsequently their evolution along the water distribution system (WDS). The aim of the two-stage model was to improve the predictive capability for a wide range of scenarios of water treatments and distribution systems. The two-stage model was developed using multiple regression analysis from a database (January 2007 to July 2012) using three different treatment processes (conventional and advanced) in the water supply system of Aljaraque area (southwest of Spain). Then, the new model was validated using a recent database from the same water supply system (January 2011 to May 2015). The validation results indicated no significant difference in the predictive and observed values of TTHM (R 2 0.874, analytical variance <17%). The new model was applied to three different supply systems with different treatment processes and different characteristics. Acceptable predictions were obtained in the three distribution systems studied, proving the adaptability of the new model to the boundary conditions. Finally the predictive capability of the new model was compared with 17 other models selected from the literature, showing satisfactory results prediction and excellent adaptability to treatment processes.

Combined Experimental and Computational Approach to Predict the Glass-Water Reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pierce, Eric M.; Bacon, Diana H.

2011-10-01

The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic timescales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models be validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test B, and pressurized unsaturated flow (PUF)], thereby reducingmore » the duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year-long PUF experiment was conducted with the Subsurface Transport Over Reactive Multiphases (STORM) code. Results show that parameterization of the computer model by combining direct bench scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year-long test duration, the rate decreased from 0.2 to 0.01 g/(m2 day) based on B release for low-activity waste glass LAWA44. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by four orders of magnitude) and suggests that the gel-layer properties are less protective under these dynamic conditions.« less

Combined Experimental and Computational Approach to Predict the Glass-Water Reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pierce, Eric M; Bacon, Diana

2011-01-01

The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic time-scales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models are validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test-B, and pressurized unsaturated flow (PUF)], thereby reducing themore » duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year long PUF experiment was conducted with the subsurface transport over reactive multi-phases code. Results show that parameterization of the computer model by combining direct bench-scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year long test duration, the rate decreased from 0.2 to 0.01 g/(m2 d) base on B release. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by 4 orders of magnitude) and suggest the gel-layer properties are less protective under these dynamic conditions.« less

Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective

PubMed Central

Subramanian, Abhishek; Jhawar, Jitesh; Sarkar, Ram Rup

2015-01-01

Leishmania infantum, causative agent of visceral leishmaniasis in humans, illustrates a complex lifecycle pertaining to two extreme environments, namely, the gut of the sandfly vector and human macrophages. Leishmania is capable of dynamically adapting and tactically switching between these critically hostile situations. The possible metabolic routes ventured by the parasite to achieve this exceptional adaptation to its varying environments are still poorly understood. In this study, we present an extensively reconstructed energy metabolism network of Leishmania infantum as an attempt to identify certain strategic metabolic routes preferred by the parasite to optimize its survival in such dynamic environments. The reconstructed network consists of 142 genes encoding for enzymes performing 237 reactions distributed across five distinct model compartments. We annotated the subcellular locations of different enzymes and their reactions on the basis of strong literature evidence and sequence-based detection of cellular localization signal within a protein sequence. To explore the diverse features of parasite metabolism the metabolic network was implemented and analyzed as a constraint-based model. Using a systems-based approach, we also put forth an extensive set of lethal reaction knockouts; some of which were validated using published data on Leishmania species. Performing a robustness analysis, the model was rigorously validated and tested for the secretion of overflow metabolites specific to Leishmania under varying extracellular oxygen uptake rate. Further, the fate of important non-essential amino acids in L. infantum metabolism was investigated. Stage-specific scenarios of L. infantum energy metabolism were incorporated in the model and key metabolic differences were outlined. Analysis of the model revealed the essentiality of glucose uptake, succinate fermentation, glutamate biosynthesis and an active TCA cycle as driving forces for parasite energy metabolism and its optimal growth. Finally, through our in silico knockout analysis, we could identify possible therapeutic targets that provide experimentally testable hypotheses. PMID:26367006

Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

PubMed Central

Nag, Ambarish; St. John, Peter C.; Crowley, Michael F.

2018-01-01

Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes the biosynthetic pathways for the main components of biomass—namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-α-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK and ACK enzymes are the most effective in increasing succinate production. PMID:29381705

Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes.

PubMed

Nag, Ambarish; St John, Peter C; Crowley, Michael F; Bomble, Yannick J

2018-01-01

Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes the biosynthetic pathways for the main components of biomass-namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-α-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK and ACK enzymes are the most effective in increasing succinate production.

Highly efficient enzymatic acetylation of flavonoids: Development of solvent-free process and kinetic evaluation

DOE PAGES

Milivojevic, Ana; Corovic, Marija; Carevic, Milica; ...

2017-09-23

Solubility and stability of flavonoid glycosides, valuable natural constituents of cosmetics and pharmaceuticals, could be improved by lipase-catalyzed acylation. Focus of this study was on development of eco-friendly process for the production of flavonoid acetates. By using phloridzin as model compound and triacetin as acetyl donor and solvent, 100% conversion and high productivity (23.32 g l –1 day –1) were accomplished. Complete conversions of two other glycosylated flavonoids, naringin and esculin, in solvent-free system were achieved, as well. Comprehensive kinetic mechanism based on two consecutive mono-substrate reactions was established where first one represents formation of flavonoid monoacetate and within secondmore » reaction diacetate is being produced from monoacetate. Both steps were regarded as reversible Michaelis-Menten reactions without inhibition. Apparent kinetic parameters for two consecutive reactions (V m constants for substrates and products and K m constants for forward and reverse reactions) were estimated for three examined acetyl acceptors and excellent fitting of experimental data (R 2 > 0.97) was achieved. Obtained results showed that derived kinetic model could be applicable for solvent-free esterifications of different flavonoid glycosides. As a result, it was valid for entire transesterification course (72 h of reaction) which, combined with complete conversions and green character of synthesis, represents firm basis for further process development.« less

Highly efficient enzymatic acetylation of flavonoids: Development of solvent-free process and kinetic evaluation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milivojevic, Ana; Corovic, Marija; Carevic, Milica

Solubility and stability of flavonoid glycosides, valuable natural constituents of cosmetics and pharmaceuticals, could be improved by lipase-catalyzed acylation. Focus of this study was on development of eco-friendly process for the production of flavonoid acetates. By using phloridzin as model compound and triacetin as acetyl donor and solvent, 100% conversion and high productivity (23.32 g l –1 day –1) were accomplished. Complete conversions of two other glycosylated flavonoids, naringin and esculin, in solvent-free system were achieved, as well. Comprehensive kinetic mechanism based on two consecutive mono-substrate reactions was established where first one represents formation of flavonoid monoacetate and within secondmore » reaction diacetate is being produced from monoacetate. Both steps were regarded as reversible Michaelis-Menten reactions without inhibition. Apparent kinetic parameters for two consecutive reactions (V m constants for substrates and products and K m constants for forward and reverse reactions) were estimated for three examined acetyl acceptors and excellent fitting of experimental data (R 2 > 0.97) was achieved. Obtained results showed that derived kinetic model could be applicable for solvent-free esterifications of different flavonoid glycosides. As a result, it was valid for entire transesterification course (72 h of reaction) which, combined with complete conversions and green character of synthesis, represents firm basis for further process development.« less

Mathematical model to analyze the dissolution behavior of metastable crystals or amorphous drug accompanied with a solid-liquid interface reaction.

PubMed

Hirai, Daiki; Iwao, Yasunori; Kimura, Shin-Ichiro; Noguchi, Shuji; Itai, Shigeru

2017-04-30

Metastable crystals and the amorphous state of poorly water-soluble drugs in solid dispersions (SDs), are subject to a solid-liquid interface reaction upon exposure to a solvent. The dissolution behavior during the solid-liquid interface reaction often shows that the concentration of drugs is supersaturated, with a high initial drug concentration compared with the solubility of stable crystals but finally approaching the latter solubility with time. However, a method for measuring the precipitation rate of stable crystals and/or the potential solubility of metastable crystals or amorphous drugs has not been established. In this study, a novel mathematical model that can represent the dissolution behavior of the solid-liquid interface reaction for metastable crystals or amorphous drug was developed and its validity was evaluated. The theory for this model was based on the Noyes-Whitney equation and assumes that the precipitation of stable crystals at the solid-liquid interface occurs through a first-order reaction. Moreover, two models were developed, one assuming that the surface area of the drug remains constant because of the presence of excess drug in the bulk and the other that the surface area changes in time-dependency because of agglomeration of the drug. SDs of Ibuprofen (IB)/polyvinylpyrrolidone (PVP) were prepared and their dissolution behaviors under non-sink conditions were fitted by the models to evaluate improvements in solubility. The model assuming time-dependent surface area showed good agreement with experimental values. Furthermore, by applying the model to the dissolution profile, parameters such as the precipitation rate and the potential solubility of the amorphous drug were successfully calculated. In addition, it was shown that the improvement in solubility with supersaturation was able to be evaluated quantitatively using this model. Therefore, this mathematical model would be a useful tool to quantitatively determine the supersaturation concentration of a metastable drug from solid dispersions. Copyright © 2017 Elsevier B.V. All rights reserved.

Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

PubMed

Faheem, Muhammad; Heyden, Andreas

2014-08-12

We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

Probabilistic models and uncertainty quantification for the ionization reaction rate of atomic Nitrogen

NASA Astrophysics Data System (ADS)

Miki, K.; Panesi, M.; Prudencio, E. E.; Prudhomme, S.

2012-05-01

The objective in this paper is to analyze some stochastic models for estimating the ionization reaction rate constant of atomic Nitrogen (N + e- → N+ + 2e-). Parameters of the models are identified by means of Bayesian inference using spatially resolved absolute radiance data obtained from the Electric Arc Shock Tube (EAST) wind-tunnel. The proposed methodology accounts for uncertainties in the model parameters as well as physical model inadequacies, providing estimates of the rate constant that reflect both types of uncertainties. We present four different probabilistic models by varying the error structure (either additive or multiplicative) and by choosing different descriptions of the statistical correlation among data points. In order to assess the validity of our methodology, we first present some calibration results obtained with manufactured data and then proceed by using experimental data collected at EAST experimental facility. In order to simulate the radiative signature emitted in the shock-heated air plasma, we use a one-dimensional flow solver with Park's two-temperature model that simulates non-equilibrium effects. We also discuss the implications of the choice of the stochastic model on the estimation of the reaction rate and its uncertainties. Our analysis shows that the stochastic models based on correlated multiplicative errors are the most plausible models among the four models proposed in this study. The rate of the atomic Nitrogen ionization is found to be (6.2 ± 3.3) × 1011 cm3 mol-1 s-1 at 10,000 K.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiegel, Aaron A.; Liu, Matthew J.; Hinsberg, William D.

Multiphase chemical reactions (gas + solid/liquid) involve a complex interplay between bulk and interface chemistry, diffusion, evaporation, and condensation. Reactions of atmospheric aerosols are an important example of this type of chemistry: the rich array of particle phase states and multiphase transformation pathways produce diverse but poorly understood interactions between chemistry and transport. Their chemistry is of intrinsic interest because of their role in controlling climate. Their characteristics also make them useful models for the study of principles of reactivity of condensed materials under confined conditions. Previously, we have reported a computational study of the oxidation chemistry of a liquidmore » aliphatic aerosol. In this study, we extend the calculations to investigate nearly the same reactions at a semisolid gas-aerosol interface. A reaction-diffusion model for heterogeneous oxidation of triacontane by hydroxyl radicals (OH) is described, and its predictions are compared to measurements of aerosol size and composition, which evolve continuously during oxidation. Our results are also explicitly compared to those obtained for the corresponding liquid system, squalane, to pinpoint salient elements controlling reactivity. The diffusive confinement of the free radical intermediates at the interface results in enhanced importance of a few specific chemical processes such as the involvement of aldehydes in fragmentation and evaporation, and a significant role of radical-radical reactions in product formation. The simulations show that under typical laboratory conditions semisolid aerosols have highly oxidized nanometer-scale interfaces that encapsulate an unreacted core and may confer distinct optical properties and enhanced hygroscopicity. This highly oxidized layer dynamically evolves with reaction, which we propose to result in plasticization. The validated model is used to predict chemistry under atmospheric conditions, where the OH radical concentration is much lower. The oxidation reactions are more strongly influenced by diffusion in the particle, resulting in a more liquid-like character.« less

A Bayesian network approach to knowledge integration and representation of farm irrigation: 1. Model development

NASA Astrophysics Data System (ADS)

Wang, Q. J.; Robertson, D. E.; Haines, C. L.

2009-02-01

Irrigation is important to many agricultural businesses but also has implications for catchment health. A considerable body of knowledge exists on how irrigation management affects farm business and catchment health. However, this knowledge is fragmentary; is available in many forms such as qualitative and quantitative; is dispersed in scientific literature, technical reports, and the minds of individuals; and is of varying degrees of certainty. Bayesian networks allow the integration of dispersed knowledge into quantitative systems models. This study describes the development, validation, and application of a Bayesian network model of farm irrigation in the Shepparton Irrigation Region of northern Victoria, Australia. In this first paper we describe the process used to integrate a range of sources of knowledge to develop a model of farm irrigation. We describe the principal model components and summarize the reaction to the model and its development process by local stakeholders. Subsequent papers in this series describe model validation and the application of the model to assess the regional impact of historical and future management intervention.

Detailed Modeling and Analysis of the CPFM Dataset

NASA Technical Reports Server (NTRS)

Swartz, William H.; Lloyd, Steven A.; DeMajistre, Robert

2004-01-01

A quantitative understanding of photolysis rate coefficients (or "j-values") is essential to determining the photochemical reaction rates that define ozone loss and other crucial processes in the atmosphere. j-Values can be calculated with radiative transfer models, derived from actinic flux observations, or inferred from trace gas measurements. The principal objective of this study is to cross-validate j-values from the Composition and Photodissociative Flux Measurement (CPFM) instrument during the Photochemistry of Ozone Loss in the Arctic Region In Summer (POLARIS) and SAGE I11 Ozone Loss and Validation Experiment (SOLVE) field campaigns with model calculations and other measurements and to use this detailed analysis to improve our ability to determine j-values. Another objective is to analyze the spectral flux from the CPFM (not just the j-values) and, using a multi-wavelength/multi-species spectral fitting technique, determine atmospheric composition.

Statistical Simulation of the Performance and Degradation of a PEMFC Membrane Electrode Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, David; Bellemare-Davis, Alexander; Karan, Kunal

2012-07-01

A 1-D MEA Performance model was developed that considered transport of liquid water, agglomerate catalyst structure, and the statistical variation of the MEA characteristic parameters. The model was validated against a low surface area carbon supported catalyst across various platinum loadings and operational conditions. The statistical variation was found to play a significant role in creating noise in the validation data and that there was a coupling effect between movement in material properties with liquid water transport. Further, in studying the low platinum loaded catalyst layers it was found that liquid water played a significant role in the increasing themore » overall transport losses. The model was then further applied to study platinum dissolution via potential cycling accelerated stress tests, in which the platinum was found to dissolve nearest the membrane effectively resulting in reaction distribution shifts within the layer.« less

Unsupported or Turned Against: Understanding How Two Types of Negative Social Reactions to Sexual Assault Relate to Post-Assault Outcomes

PubMed Central

Relyea, Mark; Ullman, Sarah

2013-01-01

Social reactions to disclosures of sexual assault have significant effects on women’s post-assault outcomes (see Ullman, 2010, for a review). The Social Reactions Questionnaire (SRQ; Ullman, 2000) measures these reactions (as reported by survivors) and aggregates them into positive and negative scales. However, studies indicate that only some “negative” reactions have a negative valence for survivors whereas others produce a mixed (positive and negative) valence. The current study compares a one-primary-factor model of “negative reactions” to a model with two primary factors that we have labeled “turning against” and “unsupportive acknowledgement.” Results showed that although one primary factor was plausible, two primary factors provided a better fit to the data. To assess the discriminant validity of the two factors, we performed regressions predicting social support, psychological adjustment, and coping behaviors. Analyses supported the hypotheses that reactions of being turned against were related to social withdrawal, increased self-blame, and decreased sexual assertiveness whereas reactions of unsupportive acknowledgment were related to both adaptive and maladaptive coping. Against predictions, depression and PTSD were more related to receiving unsupportive acknowledgment than to receiving turning against reactions. Implications for interventions and research are discussed. Importantly, almost all women (94%) in our sample received reactions that acknowledged that an assault occurred but failed to provide support, and this lack of support was associated with worse coping than even more hostile reactions such as being blamed or stigmatized. Therefore, there seems a great need for effective programs to train community members to respond to survivors with the kind of emotional and tangible support that promotes better outcomes. PMID:25750475

Validation in the clinical process: four settings for objectification of the subjectivity of understanding.

PubMed

Beland, H

1994-12-01

Clinical material is presented for discussion with the aim of exemplifying the author's conceptions of validation in a number of sessions and in psychoanalytic research and of making them verifiable, susceptible to consensus and/or falsifiable. Since Freud's postscript to the Dora case, the first clinical validation in the history of psychoanalysis, validation has been group-related and society-related, that is to say, it combines the evidence of subjectivity with the consensus of the research community (the scientific community). Validation verifies the conformity of the unconscious transference meaning with the analyst's understanding. The deciding criterion is the patient's reaction to the interpretation. In terms of the theory of science, validation in the clinical process corresponds to experimental testing of truth in the sphere of inanimate nature. Four settings of validation can be distinguished: the analyst's self-supervision during the process of understanding, which goes from incomprehension to comprehension (container-contained, PS-->D, selected fact); the patient's reaction to the interpretation (insight) and the analyst's assessment of the reaction; supervision and second thoughts; and discussion in groups and publications leading to consensus. It is a peculiarity of psychoanalytic research that in the event of positive validation the three criteria of truth (evidence, consensus and utility) coincide.

Diffuse charge and Faradaic reactions in porous electrodes

NASA Astrophysics Data System (ADS)

Biesheuvel, P. M.; Fu, Yeqing; Bazant, Martin Z.

2011-06-01

Porous electrodes instead of flat electrodes are widely used in electrochemical systems to boost storage capacities for ions and electrons, to improve the transport of mass and charge, and to enhance reaction rates. Existing porous electrode theories make a number of simplifying assumptions: (i) The charge-transfer rate is assumed to depend only on the local electrostatic potential difference between the electrode matrix and the pore solution, without considering the structure of the double layer (DL) formed in between; (ii) the charge-transfer rate is generally equated with the salt-transfer rate not only at the nanoscale of the matrix-pore interface, but also at the macroscopic scale of transport through the electrode pores. In this paper, we extend porous electrode theory by including the generalized Frumkin-Butler-Volmer model of Faradaic reaction kinetics, which postulates charge transfer across the molecular Stern layer located in between the electron-conducting matrix phase and the plane of closest approach for the ions in the diffuse part of the DL. This is an elegant and purely local description of the charge-transfer rate, which self-consistently determines the surface charge and does not require consideration of reference electrodes or comparison with a global equilibrium. For the description of the DLs, we consider the two natural limits: (i) the classical Gouy-Chapman-Stern model for thin DLs compared to the macroscopic pore dimensions, e.g., for high-porosity metallic foams (macropores >50 nm) and (ii) a modified Donnan model for strongly overlapping DLs, e.g., for porous activated carbon particles (micropores <2 nm). Our theory is valid for electrolytes where both ions are mobile, and it accounts for voltage and concentration differences not only on the macroscopic scale of the full electrode, but also on the local scale of the DL. The model is simple enough to allow us to derive analytical approximations for the steady-state and early transients. We also present numerical solutions to validate the analysis and to illustrate the evolution of ion densities, pore potential, surface charge, and reaction rates in response to an applied voltage.

Toward Construct Validation of a Transfer Climate Instrument. [and] Improving Positive Transfer: A Test of Relapse Prevention Training on Transfer Outcomes.

ERIC Educational Resources Information Center

Holton, Elwood F., III; And Others

1997-01-01

Includes "Toward Construct Validation of a Transfer Climate Instrument" (Holton et al.); "Improving Positive Transfer: A Test of Relapse Prevention Training on Transfer Outcomes" (Burke); "Invited Reaction: Progress or Relapse?" (Newstrom); "Invited Reaction: Theory, Research, and Practice" (Tang);…

Extension of the ratio method to low energy

DOE PAGES

Colomer, Frederic; Capel, Pierre; Nunes, F. M.; ...

2016-05-25

The ratio method has been proposed as a means to remove the reaction model dependence in the study of halo nuclei. Originally, it was developed for higher energies but given the potential interest in applying the method at lower energy, in this work we explore its validity at 20 MeV/nucleon. The ratio method takes the ratio of the breakup angular distribution and the summed angular distribution (which includes elastic, inelastic and breakup) and uses this observable to constrain the features of the original halo wave function. In this work we use the Continuum Discretized Coupled Channel method and the Coulomb-correctedmore » Dynamical Eikonal Approximation for the study. We study the reactions of 11Be on 12C, 40Ca and 208Pb at 20 MeV/nucleon. We compare the various theoretical descriptions and explore the dependence of our result on the core-target interaction. Lastly, our study demonstrates that the ratio method is valid at these lower beam energies.« less

A prediction model-based algorithm for computer-assisted database screening of adverse drug reactions in the Netherlands.

PubMed

Scholl, Joep H G; van Hunsel, Florence P A M; Hak, Eelko; van Puijenbroek, Eugène P

2018-02-01

The statistical screening of pharmacovigilance databases containing spontaneously reported adverse drug reactions (ADRs) is mainly based on disproportionality analysis. The aim of this study was to improve the efficiency of full database screening using a prediction model-based approach. A logistic regression-based prediction model containing 5 candidate predictors was developed and internally validated using the Summary of Product Characteristics as the gold standard for the outcome. All drug-ADR associations, with the exception of those related to vaccines, with a minimum of 3 reports formed the training data for the model. Performance was based on the area under the receiver operating characteristic curve (AUC). Results were compared with the current method of database screening based on the number of previously analyzed associations. A total of 25 026 unique drug-ADR associations formed the training data for the model. The final model contained all 5 candidate predictors (number of reports, disproportionality, reports from healthcare professionals, reports from marketing authorization holders, Naranjo score). The AUC for the full model was 0.740 (95% CI; 0.734-0.747). The internal validity was good based on the calibration curve and bootstrapping analysis (AUC after bootstrapping = 0.739). Compared with the old method, the AUC increased from 0.649 to 0.740, and the proportion of potential signals increased by approximately 50% (from 12.3% to 19.4%). A prediction model-based approach can be a useful tool to create priority-based listings for signal detection in databases consisting of spontaneous ADRs. © 2017 The Authors. Pharmacoepidemiology & Drug Safety Published by John Wiley & Sons Ltd.

On-lattice agent-based simulation of populations of cells within the open-source Chaste framework.

PubMed

Figueredo, Grazziela P; Joshi, Tanvi V; Osborne, James M; Byrne, Helen M; Owen, Markus R

2013-04-06

Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors; and ordinary differential equations for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here, we report on the creation of an agent-based multi-scale environment amalgamating the characteristics of these models within a Virtual Physiological Human (VPH) Exemplar Project. This project enables reuse, integration, expansion and sharing of the model and relevant data. The agent-based and reaction-diffusion parts of the multi-scale model have been implemented and are available for download as part of the latest public release of Chaste (Cancer, Heart and Soft Tissue Environment; http://www.cs.ox.ac.uk/chaste/), part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the 'what if' scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia (low oxygen levels). We conclude our work by summarizing the future steps for the expansion of the current system.

Developing a musculoskeletal model of the primate skull: predicting muscle activations, bite force, and joint reaction forces using multibody dynamics analysis and advanced optimisation methods.

PubMed

Shi, Junfen; Curtis, Neil; Fitton, Laura C; O'Higgins, Paul; Fagan, Michael J

2012-10-07

An accurate, dynamic, functional model of the skull that can be used to predict muscle forces, bite forces, and joint reaction forces would have many uses across a broad range of disciplines. One major issue however with musculoskeletal analyses is that of muscle activation pattern indeterminacy. A very large number of possible muscle force combinations will satisfy a particular functional task. This makes predicting physiological muscle recruitment patterns difficult. Here we describe in detail the process of development of a complex multibody computer model of a primate skull (Macaca fascicularis), that aims to predict muscle recruitment patterns during biting. Using optimisation criteria based on minimisation of muscle stress we predict working to balancing side muscle force ratios, peak bite forces, and joint reaction forces during unilateral biting. Validation of such models is problematic; however we have shown comparable working to balancing muscle activity and TMJ reaction ratios during biting to those observed in vivo and that peak predicted bite forces compare well to published experimental data. To our knowledge the complexity of the musculoskeletal model is greater than any previously reported for a primate. This complexity, when compared to more simple representations provides more nuanced insights into the functioning of masticatory muscles. Thus, we have shown muscle activity to vary throughout individual muscle groups, which enables them to function optimally during specific masticatory tasks. This model will be utilised in future studies into the functioning of the masticatory apparatus. Copyright © 2012 Elsevier Ltd. All rights reserved.

Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors.

PubMed

Nandi, Sisir; Monesi, Alessandro; Drgan, Viktor; Merzel, Franci; Novič, Marjana

2013-10-30

In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.

Correcting ligands, metabolites, and pathways

PubMed Central

Ott, Martin A; Vriend, Gert

2006-01-01

Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry) and that a considerable number (about one third) had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect) reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and visualization. It is freely available at provided that the copyright notice of all original data is cited. The database will be useful for querying and browsing biochemical pathways, and to obtain reference information for identifying compounds. However, these applications require that the underlying data be correct, and that is the focus of BioMeta. PMID:17132165

Microfluidic Injector Models Based on Artificial Neural Networks

DTIC Science & Technology

2005-06-15

medicine, and chemistry [1], [2]. They generally perform chemical analysis involving sample preparation, mixing , reaction, injection, separation analysis...algorithms have been validated against many ex- periments found in the literature demonstrating microfluidic mixing , joule heating, injection, and...385 [7] K. Seiler, Z. H. Fan, K. Fluri, and D. J. Harrison, “ Electroosmotic pump- ing and valveless control of fluid flow within a manifold of

Conflict: Operational Realism versus Analytical Rigor in Defense Modeling and Simulation

DTIC Science & Technology

2012-06-14

Campbell, Experimental and Quasi- Eperimental Designs for Generalized Causal Inference, Boston: Houghton Mifflin Company, 2002. [7] R. T. Johnson, G...experimentation? In order for an experiment to be considered rigorous, and the results valid, the experiment should be designed using established...addition to the interview, the pilots were administered a written survey, designed to capture their reactions regarding the level of realism present

The Cool Flames Experiment

NASA Technical Reports Server (NTRS)

Pearlman, Howard; Chapek, Richard; Neville, Donna; Sheredy, William; Wu, Ming-Shin; Tornabene, Robert

2001-01-01

A space-based experiment is currently under development to study diffusion-controlled, gas-phase, low temperature oxidation reactions, cool flames and auto-ignition in an unstirred, static reactor. At Earth's gravity (1g), natural convection due to self-heating during the course of slow reaction dominates diffusive transport and produces spatio-temporal variations in the thermal and thus species concentration profiles via the Arrhenius temperature dependence of the reaction rates. Natural convection is important in all terrestrial cool flame and auto-ignition studies, except for select low pressure, highly dilute (small temperature excess) studies in small vessels (i.e., small Rayleigh number). On Earth, natural convection occurs when the Rayleigh number (Ra) exceeds a critical value of approximately 600. Typical values of the Ra, associated with cool flames and auto-ignitions, range from 104-105 (or larger), a regime where both natural convection and conduction heat transport are important. When natural convection occurs, it alters the temperature, hydrodynamic, and species concentration fields, thus generating a multi-dimensional field that is extremely difficult, if not impossible, to be modeled analytically. This point has been emphasized recently by Kagan and co-workers who have shown that explosion limits can shift depending on the characteristic length scale associated with the natural convection. Moreover, natural convection in unstirred reactors is never "sufficiently strong to generate a spatially uniform temperature distribution throughout the reacting gas." Thus, an unstirred, nonisothermal reaction on Earth does not reduce to that generated in a mechanically, well-stirred system. Interestingly, however, thermal ignition theories and thermokinetic models neglect natural convection and assume a heat transfer correlation of the form: q=h(S/V)(T(bar) - Tw) where q is the heat loss per unit volume, h is the heat transfer coefficient, S/V is the surface to volume ratio, and (T(bar) - Tw ) is the spatially averaged temperature excess. This Newtonian form has been validated in spatially-uniform, well-stirred reactors, provided the effective heat transfer coefficient associated with the unsteady process is properly evaluated. Unfortunately, it is not a valid assumption for spatially-nonuniform temperature distributions induced by natural convection in unstirred reactors. "This is why the analysis of such a system is so difficult." Historically, the complexities associated with natural convection were perhaps recognized as early as 1938 when thermal ignition theory was first developed. In the 1955 text "Diffusion and Heat Exchange in Chemical Kinetics", Frank-Kamenetskii recognized that "the purely conductive theory can be applied at sufficiently low pressure and small dimensions of the vessel when the influence of natural convection can be disregarded." This was reiterated by Tyler in 1966 and further emphasized by Barnard and Harwood in 1974. Specifically, they state: "It is generally assumed that heat losses are purely conductive. While this may be valid for certain low pressure slow combustion regimes, it is unlikely to be true for the cool flame and ignition regimes." While this statement is true for terrestrial experiments, the purely conductive heat transport assumption is valid at microgravity (mu-g). Specifically, buoyant complexities are suppressed at mu-g and the reaction-diffusion structure associated with low temperature oxidation reactions, cool flames and auto-ignitions can be studied. Without natural convection, the system is simpler, does not require determination of the effective heat transfer coefficient, and is a testbed for analytic and numerical models that assume pure diffusive transport. In addition, mu-g experiments will provide baseline data that will improve our understanding of the effects of natural convection on Earth.

Using a bayesian latent class model to evaluate the utility of investigating persons with negative polymerase chain reaction results for pertussis.

PubMed

Tarr, Gillian A M; Eickhoff, Jens C; Koepke, Ruth; Hopfensperger, Daniel J; Davis, Jeffrey P; Conway, James H

2013-07-15

Pertussis remains difficult to control. Imperfect sensitivity of diagnostic tests and lack of specific guidance regarding interpretation of negative test results among patients with compatible symptoms may contribute to its spread. In this study, we examined whether additional pertussis cases could be identified if persons with negative pertussis test results were routinely investigated. We conducted interviews among 250 subjects aged ≤18 years with pertussis polymerase chain reaction (PCR) results reported from 2 reference laboratories in Wisconsin during July-September 2010 to determine whether their illnesses met the Centers for Disease Control and Prevention's clinical case definition (CCD) for pertussis. PCR validity measures were calculated using the CCD as the standard for pertussis disease. Two Bayesian latent class models were used to adjust the validity measures for pertussis detectable by 1) culture alone and 2) culture and/or more sensitive measures such as serology. Among 190 PCR-negative subjects, 54 (28%) had illnesses meeting the CCD. In adjusted analyses, PCR sensitivity and the negative predictive value were 1) 94% and 99% and 2) 43% and 87% in the 2 types of models, respectively. The models suggested that public health follow-up of reported pertussis patients with PCR-negative results leads to the detection of more true pertussis cases than follow-up of PCR-positive persons alone. The results also suggest a need for a more specific pertussis CCD.

Validation of a metabolic network for Saccharomyces cerevisiae using mixed substrate studies.

PubMed

Vanrolleghem, P A; de Jong-Gubbels, P; van Gulik, W M; Pronk, J T; van Dijken, J P; Heijnen, S

1996-01-01

Setting up a metabolic network model for respiratory growth of Saccharomyces cerevisiae requires the estimation of only two (energetic) stoichiometric parameters: (1) the operational PO ratio and (2) a growth-related maintenance factor k. It is shown, both theoretically and practically, how chemostat cultivations with different mixtures of two substrates allow unique values to be given to these unknowns of the proposed metabolic model. For the yeast and model considered, an effective PO ratio of 1.09 mol of ATP/mol of O (95% confidence interval 1.07-1.11) and a k factor of 0.415 mol of ATP/C-mol of biomass (0.385-0.445) were obtained from biomass substrate yield data on glucose/ethanol mixtures. Symbolic manipulation software proved very valuable in this study as it supported the proof of theoretical identifiability and significantly reduced the necessary computations for parameter estimation. In the transition from 100% glucose to 100% ethanol in the feed, four metabolic regimes occur. Switching between these regimes is determined by cessation of an irreversible reaction and initiation of an alternative reaction. Metabolic network predictions of these metabolic switches compared well with activity measurements of key enzymes. As a second validation of the network, the biomass yield of S. cerevisiae on acetate was also compared to the network prediction. An excellent agreement was found for a network in which acetate transport was modeled with a proton symport, while passive diffusion of acetate gave significantly higher yield predictions.

Review and analysis of high temperature chemical reactions and the effect of non-equilibrium conditions

NASA Technical Reports Server (NTRS)

Johnson, R. E.

1986-01-01

Chemical reactions at high temperatures have been considered extensively because of their importance to the heating effects on re-entry of space vehicles. Data on these reactions however, are not abundant and even when found there are discrepancies in data collected by various investigators. In particular, data for recombination reactions are calculated from the dissociation reactions or vice versa through the equilibrium constant. This involves the use of the principle of detailed balancing. This principle is discussed in reference to conditions where it is valid as well as to those where it is not valid. Related topics that merit further study or for which applicable information was available are briefly mentioned in an appendix to this report.

A statistical approach to develop a detailed soot growth model using PAH characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raj, Abhijeet; Celnik, Matthew; Shirley, Raphael

A detailed PAH growth model is developed, which is solved using a kinetic Monte Carlo algorithm. The model describes the structure and growth of planar PAH molecules, and is referred to as the kinetic Monte Carlo-aromatic site (KMC-ARS) model. A detailed PAH growth mechanism based on reactions at radical sites available in the literature, and additional reactions obtained from quantum chemistry calculations are used to model the PAH growth processes. New rates for the reactions involved in the cyclodehydrogenation process for the formation of 6-member rings on PAHs are calculated in this work based on density functional theory simulations. Themore » KMC-ARS model is validated by comparing experimentally observed ensembles on PAHs with the computed ensembles for a C{sub 2}H{sub 2} and a C{sub 6}H{sub 6} flame at different heights above the burner. The motivation for this model is the development of a detailed soot particle population balance model which describes the evolution of an ensemble of soot particles based on their PAH structure. However, at present incorporating such a detailed model into a population balance is computationally unfeasible. Therefore, a simpler model referred to as the site-counting model has been developed, which replaces the structural information of the PAH molecules by their functional groups augmented with statistical closure expressions. This closure is obtained from the KMC-ARS model, which is used to develop correlations and statistics in different flame environments which describe such PAH structural information. These correlations and statistics are implemented in the site-counting model, and results from the site-counting model and the KMC-ARS model are in good agreement. Additionally the effect of steric hindrance in large PAH structures is investigated and correlations for sites unavailable for reaction are presented. (author)« less

A framework for discrete stochastic simulation on 3D moving boundary domains

DOE PAGES

Drawert, Brian; Hellander, Stefan; Trogdon, Michael; ...

2016-11-14

We have developed a method for modeling spatial stochastic biochemical reactions in complex, three-dimensional, and time-dependent domains using the reaction-diffusion master equation formalism. In particular, we look to address the fully coupled problems that arise in systems biology where the shape and mechanical properties of a cell are determined by the state of the biochemistry and vice versa. To validate our method and characterize the error involved, we compare our results for a carefully constructed test problem to those of a microscale implementation. Finally, we demonstrate the effectiveness of our method by simulating a model of polarization and shmoo formationmore » during the mating of yeast. The method is generally applicable to problems in systems biology where biochemistry and mechanics are coupled, and spatial stochastic effects are critical.« less

Prediction and characterization of heat-affected zone formation due to neighboring nickel-aluminum multilayer foil reaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, David P.; Hirschfeld, Deidre A.; Hooper, Ryan J.

2015-09-01

Reactive multilayer foils have the potential to be used as local high intensity heat sources for a variety of applications. Much of the past research effort concerning these materials have focused on understanding the structure-property relationships of the foils that govern the energy released during a reaction. To enhance the ability of researchers to more rapidly develop technologies based on reactive multilayer foils, a deeper and more predictive understanding of the relationship between the heat released from the foil and microstructural evolution in the neighboring materials is needed. This work describes the development of a numerical model for the purposemore » of evaluating new foil-substrate combinations for screening and optimization. The model is experimentally validated using a commercially available Ni-Al multilayer foils and different alloys.« less

High-throughput amplification of mature microRNAs in uncharacterized animal models using polyadenylated RNA and stem-loop reverse transcription polymerase chain reaction.

PubMed

Biggar, Kyle K; Wu, Cheng-Wei; Storey, Kenneth B

2014-10-01

This study makes a significant advancement on a microRNA amplification technique previously used for expression analysis and sequencing in animal models without annotated mature microRNA sequences. As research progresses into the post-genomic era of microRNA prediction and analysis, the need for a rapid and cost-effective method for microRNA amplification is critical to facilitate wide-scale analysis of microRNA expression. To facilitate this requirement, we have reoptimized the design of amplification primers and introduced a polyadenylation step to allow amplification of all mature microRNAs from a single RNA sample. Importantly, this method retains the ability to sequence reverse transcription polymerase chain reaction (RT-PCR) products, validating microRNA-specific amplification. Copyright © 2014 Elsevier Inc. All rights reserved.

Tractable Chemical Models for CVD of Silicon and Carbon

NASA Technical Reports Server (NTRS)

Blanquet, E.; Gokoglu, S. A.

1993-01-01

Tractable chemical models are validated for the CVD of silicon and carbon. Dilute silane (SiH4) and methane (CH4) in hydrogen are chosen as gaseous precursors. The chemical mechanism for each systems Si and C is deliberately reduced to three reactions in the models: one in the gas phase and two at the surface. The axial-flow CVD reactor utilized in this study has well-characterized flow and thermal fields and provides variable deposition rates in the axial direction. Comparisons between the experimental and calculated deposition rates are made at different pressures and temperatures.

Fire Suppression M and S Validation (Status and Challenges), Systems Fire Protection Information Exchange

DTIC Science & Technology

2015-10-14

rate Kinetics •14 Species & 12 reactionsCombustion Model •Participating Media Discrete Ordinate Method •WSG model for CO2, H2O and SootRadiation Model...Inhibition of JP-8 Combustion Physical Acting Agents • Dilute heat • Dilute reactants Ex: water, nitrogen Chemical Acting Agents • Reduce flame...Release; distribution is unlimited 5 Overview of Reduced Kinetics Scheme for FM200 • R1: JP-8 + O2 => CO + CO2 + H2O • R2: CO + O2 <=> CO2 • R3: HFP + JP-8

DART model for irradiation-induced swelling of dispersion fuel elements including aluminum-fuel interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rest, J.; Hofman, G.L.

1997-12-01

The Dispersion Analysis Research Tool (DART) contains models for fission-gas-induced fuel swelling, interaction of fuel with the matrix aluminum, for the resultant reaction-product swelling, and for the calculation of the stress gradient within the fuel particle. The effects of an aluminide shell on fuel particle swelling are evaluated. Validation of the model is demonstrated by a comparison of DART calculations of fuel swelling of U{sub 3}SiAl-Al and U{sub 3}Si{sub 2}-Al for various dispersion fuel element designs with the data.

Grain shape influence on semiconducting metal oxide based gas sensor performance: modeling versus experiment.

PubMed

Rebholz, Julia; Bonanati, Peter; Weimar, Udo; Barsan, Nicolae

2014-06-01

A model for sensing with semiconducting metal oxide (SMOX)-based gas sensors was developed which takes the effect of the shape of the grains in the sensing layers into account. Its validity is limited to materials in which the grains of the SMOX sensing layer are large enough to have an undepleted bulk region (large grains). This means that in all experimental conditions, the SMOX properties ensure that the influence of surface phenomena is not extended to the whole grain. The model takes the surface chemistry and its impact on the electrical properties of the sensing material into consideration. In this way, it relates the sensor signal--defined as the relative change of the sensor's conductance--directly to the concentration of the target gas and also exhibits meaningful chemical parameters, such as the type of reactive oxygen species, the reaction constants, and the concentration of adsorption sites. The validity of the model is confirmed experimentally by applying it to data gathered by measuring homemade sensors in relevant conditions.

Modelling and validation of Proton exchange membrane fuel cell (PEMFC)

NASA Astrophysics Data System (ADS)

Mohiuddin, A. K. M.; Basran, N.; Khan, A. A.

2018-01-01

This paper is the outcome of a small scale fuel cell project. Fuel cell is an electrochemical device that converts energy from chemical reaction to electrical work. Proton Exchange Membrane Fuel Cell (PEMFC) is one of the different types of fuel cell, which is more efficient, having low operational temperature and fast start up capability results in high energy density. In this study, a mathematical model of 1.2 W PEMFC is developed and simulated using MATLAB software. This model describes the PEMFC behaviour under steady-state condition. This mathematical modeling of PEMFC determines the polarization curve, power generated, and the efficiency of the fuel cell. Simulation results were validated by comparing with experimental results obtained from the test of a single PEMFC with a 3 V motor. The performance of experimental PEMFC is little lower compared to simulated PEMFC, however both results were found in good agreement. Experiments on hydrogen flow rate also been conducted to obtain the amount of hydrogen consumed to produce electrical work on PEMFC.

Simplified Thermo-Chemical Modelling For Hypersonic Flow

NASA Astrophysics Data System (ADS)

Sancho, Jorge; Alvarez, Paula; Gonzalez, Ezequiel; Rodriguez, Manuel

2011-05-01

Hypersonic flows are connected with high temperatures, generally associated with strong shock waves that appear in such flows. At high temperatures vibrational degrees of freedom of the molecules may become excited, the molecules may dissociate into atoms, the molecules or free atoms may ionize, and molecular or ionic species, unimportant at lower temperatures, may be formed. In order to take into account these effects, a chemical model is needed, but this model should be simplified in order to be handled by a CFD code, but with a sufficient precision to take into account the physics more important. This work is related to a chemical non-equilibrium model validation, implemented into a commercial CFD code, in order to obtain the flow field around bodies in hypersonic flow. The selected non-equilibrium model is composed of seven species and six direct reactions together with their inverse. The commercial CFD code where the non- equilibrium model has been implemented is FLUENT. For the validation, the X38/Sphynx Mach 20 case is rebuilt on a reduced geometry, including the 1/3 Lref forebody. This case has been run in laminar regime, non catalytic wall and with radiative equilibrium wall temperature. The validated non-equilibrium model is applied to the EXPERT (European Experimental Re-entry Test-bed) vehicle at a specified trajectory point (Mach number 14). This case has been run also in laminar regime, non catalytic wall and with radiative equilibrium wall temperature.

Beam-tracing model for predicting sound fields in rooms with multilayer bounding surfaces

NASA Astrophysics Data System (ADS)

Wareing, Andrew; Hodgson, Murray

2005-10-01

This paper presents the development of a wave-based room-prediction model for predicting steady-state sound fields in empty rooms with specularly reflecting, multilayer surfaces. A triangular beam-tracing model with phase, and a transfer-matrix approach to model the surfaces, were involved. Room surfaces were modeled as multilayers of fluid, solid, or porous materials. Biot theory was used in the transfer-matrix formulation of the porous layer. The new model consisted of the transfer-matrix model integrated into the beam-tracing algorithm. The transfer-matrix model was validated by comparing predictions with those by theory, and with experiment. The test surfaces were a glass plate, double drywall panels, double steel panels, a carpeted floor, and a suspended-acoustical ceiling. The beam-tracing model was validated in the cases of three idealized room configurations-a small office, a corridor, and a small industrial workroom-with simple boundary conditions. The number of beams, the reflection order, and the frequency resolution required to obtain accurate results were investigated. Beam-tracing predictions were compared with those by a method-of-images model with phase. The model will be used to study sound fields in rooms with local- or extended-reaction multilayer surfaces.

Qualitative dynamics semantics for SBGN process description.

PubMed

Rougny, Adrien; Froidevaux, Christine; Calzone, Laurence; Paulevé, Loïc

2016-06-16

Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters. They allow to capture general features of systems dynamics, such as attractors or reachability properties, for which scalable analyses exist. The Systems Biology Graphical Notation Process Description language (SBGN-PD) has become a standard to represent reaction networks. However, no qualitative dynamics semantics taking into account all the main features available in SBGN-PD had been proposed so far. We propose two qualitative dynamics semantics for SBGN-PD reaction networks, namely the general semantics and the stories semantics, that we formalize using asynchronous automata networks. While the general semantics extends standard Boolean semantics of reaction networks by taking into account all the main features of SBGN-PD, the stories semantics allows to model several molecules of a network by a unique variable. The obtained qualitative models can be checked against dynamical properties and therefore validated with respect to biological knowledge. We apply our framework to reason on the qualitative dynamics of a large network (more than 200 nodes) modeling the regulation of the cell cycle by RB/E2F. The proposed semantics provide a direct formalization of SBGN-PD networks in dynamical qualitative models that can be further analyzed using standard tools for discrete models. The dynamics in stories semantics have a lower dimension than the general one and prune multiple behaviors (which can be considered as spurious) by enforcing the mutual exclusiveness between the activity of different nodes of a same story. Overall, the qualitative semantics for SBGN-PD allow to capture efficiently important dynamical features of reaction network models and can be exploited to further refine them.

Catalytic oxidation of toluene: comparative study over powder and monolithic manganese-nickel mixed oxide catalysts.

PubMed

Duplančić, Marina; Tomašić, Vesna; Gomzi, Zoran

2017-07-05

This paper is focused on development of the metal monolithic structure for total oxidation of toluene at low temperature. The well-adhered catalyst, based on the mixed oxides of manganese and nickel, is washcoated on the Al/Al 2 O 3 plates as metallic support. For the comparison purposes, results observed for the manganese-nickel mixed oxide supported on the metallic monolith are compared with those obtained using powder type of the same catalyst. Prepared manganese-nickel mixed oxides in both configurations show remarkable low-temperature activity for the toluene oxidation. The reaction temperature T 50 corresponding to 50% of the toluene conversion is observed at temperatures of ca. 400-430 K for the powder catalyst and at ca. 450-490 K for the monolith configuration. The appropriate mathematical models, such as one-dimensional (1D) pseudo-homogeneous model of the fixed bed reactor and the 1D heterogeneous model of the metal monolith reactor, are applied to describe and compare catalytic performances of both reactors. Validation of the applied models is performed by comparing experimental data with theoretical predictions. The obtained results confirmed that the reaction over the monolithic structure is kinetically controlled, while in the case of the powder catalyst the reaction rate is influenced by the intraphase diffusion.

Modelling and analysis of a direct ascorbic acid fuel cell

NASA Astrophysics Data System (ADS)

Zeng, Yingzhi; Fujiwara, Naoko; Yamazaki, Shin-ichi; Tanimoto, Kazumi; Wu, Ping

L-Ascorbic acid (AA), also known as vitamin C, is an environmentally-benign and biologically-friendly compound that can be used as an alternative fuel for direct oxidation fuel cells. While direct ascorbic acid fuel cells (DAAFCs) have been studied experimentally, modelling and simulation of these devices have been overlooked. In this work, we develop a mathematical model to describe a DAAFC and validate it with experimental data. The model is formulated by integrating the mass and charge balances, and model parameters are estimated by best-fitting to experimental data of current-voltage curves. By comparing the transient voltage curves predicted by dynamic simulation and experiments, the model is further validated. Various parameters that affect the power generation are studied by simulation. The cathodic reaction is found to be the most significant determinant of power generation, followed by fuel feed concentration and the mass-transfer coefficient of ascorbic acid. These studies also reveal that the power density steadily increases with respect to the fuel feed concentration. The results may guide future development and operation of a more efficient DAAFC.

Associations between beliefs about and reactions toward people who stutter.

PubMed

Arnold, Hayley S; Li, Jian

2016-03-01

This study sought to assess whether beliefs about people who stutter (PWS) predict intended behavioral and affective reactions toward them in a large and varied sample of respondents while taking into account familiarity with PWS and the demographic variables of age, education, and gender. Analyses were based on 2206 residents of the United States of America. The seemingly unrelated regression (SUR) technique was used to test the relationship between beliefs about PWS and behavioral and affective reactions toward PWS. Variables such as familiarity with PWS and demographic data were also controlled in the statistical model. Findings indicated that, when demographic variables and familiarity were taken into account, the accuracy of participants' beliefs about PWS significantly predicted their intended behavioral and affective reactions toward PWS. The participants' gender and familiarity with PWS were also associated with these reactions toward PWS. The finding of an association between beliefs and intended reactions validates attempts to improve public treatment of PWS through improving the accuracy of beliefs about PWS. Additionally, because familiarity with PWS is a significant predictor of helpful and positive reactions toward PWS, interventions involving PWS educating others through direct interpersonal interactions may be one effective way to improve public reactions toward individuals who stutter. Copyright © 2016 Elsevier Inc. All rights reserved.

A minimally-resolved immersed boundary model for reaction-diffusion problems

NASA Astrophysics Data System (ADS)

Pal Singh Bhalla, Amneet; Griffith, Boyce E.; Patankar, Neelesh A.; Donev, Aleksandar

2013-12-01

We develop an immersed boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a minimally-resolved "blob" using many fewer degrees of freedom per particle than standard discretization approaches. More complicated or more highly resolved particle shapes can be built out of a collection of reactive blobs. We demonstrate numerically that the blob model can provide an accurate representation at low to moderate packing densities of the reactive particles, at a cost not much larger than solving a Poisson equation in the same domain. Unlike multipole expansion methods, our method does not require analytically computed Green's functions, but rather, computes regularized discrete Green's functions on the fly by using a standard grid-based discretization of the Poisson equation. This allows for great flexibility in implementing different boundary conditions, coupling to fluid flow or thermal transport, and the inclusion of other effects such as temporal evolution and even nonlinearities. We develop multigrid-based preconditioners for solving the linear systems that arise when using implicit temporal discretizations or studying steady states. In the diffusion-limited case the resulting linear system is a saddle-point problem, the efficient solution of which remains a challenge for suspensions of many particles. We validate our method by comparing to published results on reaction-diffusion in ordered and disordered suspensions of reactive spheres.

Application of chemical reaction mechanistic domains to an ecotoxicity QSAR model, the KAshinhou Tool for Ecotoxicity (KATE).

PubMed

Furuhama, A; Hasunuma, K; Aoki, Y; Yoshioka, Y; Shiraishi, H

2011-01-01

The validity of chemical reaction mechanistic domains defined by skin sensitisation in the Quantitative Structure-Activity Relationship (QSAR) ecotoxicity system, KAshinhou Tools for Ecotoxicity (KATE), March 2009 version, has been assessed and an external validation of the current KATE system carried out. In the case of the fish end-point, the group of chemicals with substructures reactive to skin sensitisation always exhibited higher root mean square errors (RMSEs) than chemicals without reactive substructures under identical C- or log P-judgements in KATE. However, in the case of the Daphnia end-point this was not so, and the group of chemicals with reactive substructures did not always have higher RMSEs: the Schiff base mechanism did not function as a high error detector. In addition to the RMSE findings, the presence of outliers suggested that the KATE classification rules needs to be reconsidered, particularly for the amine group. Examination of the dependency of the organism on the toxic action of chemicals in fish and Daphnia revealed that some of the reactive substructures could be applied to the improvement of the KATE system. It was concluded that the reaction mechanistic domains of toxic action for skin sensitisation could provide useful complementary information in predicting acute aquatic ecotoxicity, especially at the fish end-point.

Development of a Stochastically-driven, Forward Predictive Performance Model for PEMFCs

NASA Astrophysics Data System (ADS)

Harvey, David Benjamin Paul

A one-dimensional multi-scale coupled, transient, and mechanistic performance model for a PEMFC membrane electrode assembly has been developed. The model explicitly includes each of the 5 layers within a membrane electrode assembly and solves for the transport of charge, heat, mass, species, dissolved water, and liquid water. Key features of the model include the use of a multi-step implementation of the HOR reaction on the anode, agglomerate catalyst sub-models for both the anode and cathode catalyst layers, a unique approach that links the composition of the catalyst layer to key properties within the agglomerate model and the implementation of a stochastic input-based approach for component material properties. The model employs a new methodology for validation using statistically varying input parameters and statistically-based experimental performance data; this model represents the first stochastic input driven unit cell performance model. The stochastic input driven performance model was used to identify optimal ionomer content within the cathode catalyst layer, demonstrate the role of material variation in potential low performing MEA materials, provide explanation for the performance of low-Pt loaded MEAs, and investigate the validity of transient-sweep experimental diagnostic methods.

Construction of combustion models for rapeseed methyl ester bio-diesel fuel for internal combustion engine applications.

PubMed

Golovitchev, Valeri I; Yang, Junfeng

2009-01-01

Bio-diesel fuels are non-petroleum-based diesel fuels consisting of long chain alkyl esters produced by the transesterification of vegetable oils, that are intended for use (neat or blended with conventional fuels) in unmodified diesel engines. There have been few reports of studies proposing theoretical models for bio-diesel combustion simulations. In this study, we developed combustion models based on ones developed previously. We compiled the liquid fuel properties, and the existing detailed mechanism of methyl butanoate ester (MB, C(5)H(10)O(2)) oxidation was supplemented by sub-mechanisms for two proposed fuel constituent components, C(7)H(16) and C(7)H(8)O (and then, by mp2d, C(4)H(6)O(2) and propyne, C(3)H(4)) to represent the combustion model for rapeseed methyl ester described by the chemical formula, C(19)H(34)O(2) (or C(19)H(36)O(2)). The main fuel vapor thermal properties were taken as those of methyl palmitate C(19)H(36)O(2) in the NASA polynomial form of the Burcat database. The special global reaction was introduced to "crack" the main fuel into its constituent components. This general reaction included 309 species and 1472 reactions, including soot and NO(x) formation processes. The detailed combustion mechanism was validated using shock-tube ignition-delay data under diesel engine conditions. For constant volume and diesel engine (Volvo D12C) combustion modeling, this mechanism could be reduced to 88 species participating in 363 reactions.

A comparative study on dynamic stiffness in typical finite element model and multi-body model of C6-C7 cervical spine segment.

PubMed

Wang, Yawei; Wang, Lizhen; Du, Chengfei; Mo, Zhongjun; Fan, Yubo

2016-06-01

In contrast to numerous researches on static or quasi-static stiffness of cervical spine segments, very few investigations on their dynamic stiffness were published. Currently, scale factors and estimated coefficients were usually used in multi-body models for including viscoelastic properties and damping effects, meanwhile viscoelastic properties of some tissues were unavailable for establishing finite element models. Because dynamic stiffness of cervical spine segments in these models were difficult to validate because of lacking in experimental data, we tried to gain some insights on current modeling methods through studying dynamic stiffness differences between these models. A finite element model and a multi-body model of C6-C7 segment were developed through using available material data and typical modeling technologies. These two models were validated with quasi-static response data of the C6-C7 cervical spine segment. Dynamic stiffness differences were investigated through controlling motions of C6 vertebrae at different rates and then comparing their reaction forces or moments. Validation results showed that both the finite element model and the multi-body model could generate reasonable responses under quasi-static loads, but the finite element segment model exhibited more nonlinear characters. Dynamic response investigations indicated that dynamic stiffness of this finite element model might be underestimated because of the absence of dynamic stiffen effect and damping effects of annulus fibrous, while representation of these effects also need to be improved in current multi-body model. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Application of Reactive Transport Modeling to Heap Bioleaching of Copper

NASA Astrophysics Data System (ADS)

Liu, W.

2017-12-01

Copper heap bioleaching is a complex industrial process that utilizes oxidative chemical leaching and microbial activities to extract copper from packed ore beds. Mathematical modelling is an effective tool for identifying key factors that determine the leaching performance. HeapSim is a modelling tool that incorporates all fundamental processes that occur in a heap under leach, such as the movement of leaching solution, chemical reaction kinetics, heat transfer, and microbial activities, to predict the leaching behavior of a heap. In this study, the HeapSim model was applied to simulate chalcocite heap bioleaching at Quebrada Blanca mine located in the Northern Chile. The main findings were that the model could be satisfactorily calibrated and validated to simulate chalcocite leaching. Heap temperature was sensitive to the changes in the raffinate temperature, raffinate flow rate, and the extent of pyrite oxidation. At high flow rates, heap temperature was controlled by the raffinate temperature. In contrast, heat removal by the raffinate solution flow was insignificant at low flow rates, leading to the accumulation of heat generated by pyrite reaction and therefore an increase in heap temperature.

A lumped model of venting during thermal runaway in a cylindrical Lithium Cobalt Oxide lithium-ion cell

NASA Astrophysics Data System (ADS)

Coman, Paul T.; Rayman, Sean; White, Ralph E.

2016-03-01

This paper presents a mathematical model built for analyzing the intricate thermal behavior of a 18650 LCO (Lithium Cobalt Oxide) battery cell during thermal runaway when venting of the electrolyte and contents of the jelly roll (ejecta) is considered. The model consists of different ODEs (Ordinary Differential Equations) describing reaction rates and electrochemical reactions, as well as the isentropic flow equations for describing electrolyte venting. The results are validated against experimental findings from Golubkov et al. [1] [Andrey W. Golubkov, David Fuchs, Julian Wagner, Helmar Wiltsche, Christoph Stangl, Gisela Fauler, Gernot Voitice Alexander Thaler and Viktor Hacker, RSC Advances, 4:3633-3642, 2014] for two cases - with flow and without flow. The results show that if the isentropic flow equations are not included in the model, the thermal runaway is triggered prematurely at the point where venting should occur. This shows that the heat dissipation due to ejection of electrolyte and jelly roll contents has a significant contribution. When the flow equations are included, the model shows good agreement with the experiment and therefore proving the importance of including venting.

Lagrangian simulation of mixing and reactions in complex geochemical systems

NASA Astrophysics Data System (ADS)

Engdahl, Nicholas B.; Benson, David A.; Bolster, Diogo

2017-04-01

Simulations of detailed geochemical systems have traditionally been restricted to Eulerian reactive transport algorithms. This note introduces a Lagrangian method for modeling multicomponent reaction systems. The approach uses standard random walk-based methods for the particle motion steps but allows the particles to interact with each other by exchanging mass of their various chemical species. The colocation density of each particle pair is used to calculate the mass transfer rate, which creates a local disequilibrium that is then relaxed back toward equilibrium using the reaction engine PhreeqcRM. The mass exchange is the only step where the particles interact and the remaining transport and reaction steps are entirely independent for each particle. Several validation examples are presented, which reproduce well-known analytical solutions. These are followed by two demonstration examples of a competitive decay chain and an acid-mine drainage system. The source code, entitled Complex Reaction on Particles (CRP), and files needed to run these examples are hosted openly on GitHub (https://github.com/nbengdahl/CRP), so as to enable interested readers to readily apply this approach with minimal modifications.

Recent advances in hypersonic technology

NASA Technical Reports Server (NTRS)

Dwoyer, Douglas L.

1990-01-01

This paper will focus on recent advances in hypersonic aerodynamic prediction techniques. Current capabilities of existing numerical methods for predicting high Mach number flows will be discussed and shortcomings will be identified. Physical models available for inclusion into modern codes for predicting the effects of transition and turbulence will also be outlined and their limitations identified. Chemical reaction models appropriate to high-speed flows will be addressed, and the impact of their inclusion in computational fluid dynamics codes will be discussed. Finally, the problem of validating predictive techniques for high Mach number flows will be addressed.

Numerical investigation of combustion field of hypervelocity scramjet engine

NASA Astrophysics Data System (ADS)

Zhang, Shikong; Li, Jiang; Qin, Fei; Huang, Zhiwei; Xue, Rui

2016-12-01

A numerical study of the ground testing of a hydrogen-fueled scramjet engine was undertaken using the commercial computational-fluid-dynamics code CFD++. The simulated Mach number was 12. A 7-species, 9-reaction-step hydrogen-air chemistry kinetics system was adopted for the Reynolds-averaged Navier-Stokes simulation. The two-equation SST turbulence model, which takes into account the wall functions, was used to handle the turbulence-chemistry interactions. The results were validated by experimentally measuring the wall pressure distribution, and the values obtained proved to be in good agreement. The flow pattern at non-reaction/reaction is presented, as are the results of analyzing the supersonic premix/non-premix flame structure, the reaction heat release distribution in different modes, and the change in the equivalence ratio. In this study, we realize the working mode of a hypervelocity engine and provide some suggestions for the combustion organization of the engine as well as offer insight into the potential for exploiting the processes of combustion and flow.

A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks

PubMed Central

Khammash, Mustafa

2014-01-01

Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology, epidemiology, immunology, systems biology and synthetic biology. It is now well-established that, for small population sizes, stochastic models for biochemical reaction networks are necessary to capture randomness in the interactions. The tools for analyzing such models, however, still lag far behind their deterministic counterparts. In this paper, we bridge this gap by developing a constructive framework for examining the long-term behavior and stability properties of the reaction dynamics in a stochastic setting. In particular, we address the problems of determining ergodicity of the reaction dynamics, which is analogous to having a globally attracting fixed point for deterministic dynamics. We also examine when the statistical moments of the underlying process remain bounded with time and when they converge to their steady state values. The framework we develop relies on a blend of ideas from probability theory, linear algebra and optimization theory. We demonstrate that the stability properties of a wide class of biological networks can be assessed from our sufficient theoretical conditions that can be recast as efficient and scalable linear programs, well-known for their tractability. It is notably shown that the computational complexity is often linear in the number of species. We illustrate the validity, the efficiency and the wide applicability of our results on several reaction networks arising in biochemistry, systems biology, epidemiology and ecology. The biological implications of the results as well as an example of a non-ergodic biological network are also discussed. PMID:24968191

Multiple model approach to evaluation of accelerated carbonation for steelmaking slag in a slurry reactor.

PubMed

Pan, Shu-Yuan; Liu, Hsing-Lu; Chang, E-E; Kim, Hyunook; Chen, Yi-Hung; Chiang, Pen-Chi

2016-07-01

Basic oxygen furnace slag (BOFS) exhibits highly alkaline properties due to its high calcium content, which is beneficial to carbonation reaction. In this study, accelerated carbonation of BOFS was evaluated under different reaction times, temperatures, and liquid-to-solid (L/S) ratios in a slurry reactor. CO2 mass balance within the slurry reactor was carried out to validate the technical feasibility of fixing gaseous CO2 into solid precipitates. After that, a multiple model approach, i.e., theoretical kinetics and empirical surface model, for carbonation reaction was presented to determine the maximal carbonation conversion of BOFS in a slurry reactor. On one hand, the reaction kinetics of BOFS carbonation was evaluated by the shrinking core model (SCM). Calcite (CaCO3) was identified as a reaction product through the scanning electronic microscopy and X-ray diffraction analyses, which provided the rationale of applying the SCM in this study. The rate-limiting step of carbonation was found to be ash-diffusion controlled, and the effective diffusivity for carbonation of BOFS in a slurry reactor were determined accordingly. On the other hand, the carbonation conversion of BOFS was predicted by the response surface methodology (RSM) via a nonlinear mathematical programming. According to the experimental data, the highest carbonation conversion of BOFS achieved was 57% under an L/S ratio of 20 mL g(-1), a CO2 flow rate of 0.1 L min(-1), and a pressure of 101.3 kPa at 50 °C for 120 min. Furthermore, the applications and limitations of SCM and RSM were examined and exemplified by the carbonation of steelmaking slags. Copyright © 2016 Elsevier Ltd. All rights reserved.

Produced water re-injection in a non-fresh water aquifer with geochemical reaction, hydrodynamic molecular dispersion and adsorption kinetics controlling: model development and numerical simulation

NASA Astrophysics Data System (ADS)

Obe, Ibidapo; Fashanu, T. A.; Idialu, Peter O.; Akintola, Tope O.; Abhulimen, Kingsley E.

2017-06-01

An improved produced water reinjection (PWRI) model that incorporates filtration, geochemical reaction, molecular transport, and mass adsorption kinetics was developed to predict cake deposition and injectivity performance in hydrocarbon aquifers in Nigeria oil fields. Thus, the improved PWRI model considered contributions of geochemical reaction, adsorption kinetics, and hydrodynamic molecular dispersion mechanism to alter the injectivity and deposition of suspended solids on aquifer wall resulting in cake formation in pores during PWRI and transport of active constituents in hydrocarbon reservoirs. The injectivity decline and cake deposition for specific case studies of hydrocarbon aquifers in Nigeria oil fields were characterized with respect to its well geometry, lithology, and calibrations data and simulated in COMSOL multiphysics software environment. The PWRI model was validated by comparisons to assessments of previous field studies based on data and results supplied by operator and regulator. The results of simulation showed that PWRI performance was altered because of temporal variations and declinations of permeability, injectivity, and cake precipitation, which were observed to be dependent on active adsorption and geochemical reaction kinetics coupled with filtration scheme and molecular dispersion. From the observed results and findings, transition time t r to cake nucleation and growth were dependent on aquifer constituents, well capacity, filtration coefficients, particle-to-grain size ratio, water quality, and more importantly, particle-to-grain adsorption kinetics. Thus, the results showed that injectivity decline and permeability damage were direct contributions of geochemical reaction, hydrodynamic molecular diffusion, and adsorption kinetics to the internal filtration mechanism, which are largely dependent on the initial conditions of concentration of active constituents of produced water and aquifer capacity.

Campaign 2 Level 2 Milestone Review 2009: Milestone # 3131 Grain Scale Simulation of Pore Collapse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwartz, A J

2009-09-28

The milestone reviewed on Sept. 16, 2009 was 'High-fidelity simulation of shock initiation of high explosives at the grain scale using coupled hydrodynamics, thermal transport and chemistry'. It is the opinion of the committee that the team has satisfied the milestone. A detailed description of how the goals were met is provided. The milestone leveraged capabilities from ASC Physics and Engineering Materials program combined with experimental input from Campaign 2. A combined experimental-multiscale simulation approach was used to create and validate the various TATB model components. At the lowest length scale, quantum chemical calculations were used to determine equations ofmore » state, thermal transport properties and reaction rates for TATB as it is decomposing. High-pressure experiments conducted in diamond anvil cells, gas guns and the Z machine were used to validate the EOS, thermal conductivity, specific heat and predictions of water formation. The predicted reaction networks and chemical kinetic equations were implemented in Cheetah and validated against the lower length scale data. Cheetah was then used within the ASC code ALE3D for high-resolution, thermo-mechanically coupled simulations of pore collapse at the micron size scale to predict conditions for detonation initiation.« less

Validating (d,p gamma) as a Surrogate for Neutron Capture

DOE PAGES

Ratkiewicz, A.; Cizewski, J.A.; Pain, S.D.; ...

2015-05-28

The r-process is responsible for creating roughly half of the elements heavier than iron. It has recently become understood that the rates at which neutron capture reactions proceed at late times in the r-process may dramatically affect the final abundance pattern. However, direct measurements of neutron capture reaction rates on exotic nuclei are exceptionally difficult, necessitating the development of indirect approaches such as the surrogate technique. The (d,pγ) reaction at low energies was identified as a promising surrogate for the (n,γ) reaction, as both reactions share many characteristics. We report on a program to validate (d,pγ) as a surrogate formore » (n,γ) using 95Mo as a target. The experimental campaign includes direct measurements of the γ-ray intensities from the decay of excited states populated in the 95Mo(n,γ) and 95Mo(d,pγ) reactions.« less

Study of 232Th(n, γ) and 232Th(n,f) reaction rates in a graphite moderated spallation neutron field produced by 1.6 GeV deuterons on lead target

NASA Astrophysics Data System (ADS)

Asquith, N. L.; Hashemi-Nezhad, S. R.; Westmeier, W.; Zhuk, I.; Tyutyunnikov, S.; Adam, J.

2015-02-01

The Gamma-3 assembly of the Joint Institute for Nuclear Research (JINR), Dubna, Russia is designed to emulate the neutron spectrum of a thermal Accelerator Driven System (ADS). It consists of a lead spallation target surrounded by reactor grade graphite. The target was irradiated with 1.6 GeV deuterons from the Nuclotron accelerator and the neutron capture and fission rate of 232Th in several locations within the assembly were experimentally measured. 232Th is a proposed fuel for envisaged Accelerator Driven Systems and these two reactions are fundamental to the performance and feasibility of 232Th in an ADS. The irradiation of the Gamma-3 assembly was also simulated using MCNPX 2.7 with the INCL4 intra-nuclear cascade and ABLA fission/evaporation models. Good agreement between the experimentally measured and calculated reaction rates was found. This serves as a good validation for the computational models and cross section data used to simulate neutron production and transport of spallation neutrons within a thermal ADS.

Linear scaling relationships and volcano plots in homogeneous catalysis - revisiting the Suzuki reaction.

PubMed

Busch, Michael; Wodrich, Matthew D; Corminboeuf, Clémence

2015-12-01

Linear free energy scaling relationships and volcano plots are common tools used to identify potential heterogeneous catalysts for myriad applications. Despite the striking simplicity and predictive power of volcano plots, they remain unknown in homogeneous catalysis. Here, we construct volcano plots to analyze a prototypical reaction from homogeneous catalysis, the Suzuki cross-coupling of olefins. Volcano plots succeed both in discriminating amongst different catalysts and reproducing experimentally known trends, which serves as validation of the model for this proof-of-principle example. These findings indicate that the combination of linear scaling relationships and volcano plots could serve as a valuable methodology for identifying homogeneous catalysts possessing a desired activity through a priori computational screening.

Symmetry Relations in Chemical Kinetics Arising from Microscopic Reversibility

NASA Astrophysics Data System (ADS)

Adib, Artur B.

2006-01-01

It is shown that the kinetics of time-reversible chemical reactions having the same equilibrium constant but different initial conditions are closely related to one another by a directly measurable symmetry relation analogous to chemical detailed balance. In contrast to detailed balance, however, this relation does not require knowledge of the elementary steps that underlie the reaction, and remains valid in regimes where the concept of rate constants is ill defined, such as at very short times and in the presence of low activation barriers. Numerical simulations of a model of isomerization in solution are provided to illustrate the symmetry under such conditions, and potential applications in protein folding or unfolding are pointed out.

Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nag, Ambarish; St. John, Peter C.; Crowley, Michael F.

Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes themore » biosynthetic pathways for the main components of biomass - namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-a-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK and ACK enzymes are the most effective in increasing succinate production.« less

Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

DOE PAGES

Nag, Ambarish; St. John, Peter C.; Crowley, Michael F.; ...

2018-01-30

Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes themore » biosynthetic pathways for the main components of biomass - namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-a-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK and ACK enzymes are the most effective in increasing succinate production.« less

Developing a 3-choice serial reaction time task for examining neural and cognitive function in an equine model.

PubMed

Roberts, Kirsty; Hemmings, Andrew J; McBride, Sebastian D; Parker, Matthew O

2017-12-01

Large animal models of human neurological disorders are advantageous compared to rodent models due to their neuroanatomical complexity, longevity and their ability to be maintained in naturalised environments. Some large animal models spontaneously develop behaviours that closely resemble the symptoms of neural and psychiatric disorders. The horse is an example of this; the domestic form of this species consistently develops spontaneous stereotypic behaviours akin to the compulsive and impulsive behaviours observed in human neurological disorders such as Tourette's syndrome. The ability to non-invasively probe normal and abnormal equine brain function through cognitive testing may provide an extremely useful methodological tool to assess brain changes associated with certain human neurological and psychiatric conditions. An automated operant system with the ability to present visual and auditory stimuli as well as dispense salient food reward was developed. To validate the system, ten horses were trained and tested using a standard cognitive task (three choice serial reaction time task (3-CSRTT)). All animals achieved total learning criterion and performed six probe sessions. Learning criterion was met within 16.30±0.79 sessions over a three day period. During six probe sessions, level of performance was maintained at 80.67±0.57% (mean±SEM) accuracy. This is the first mobile fully automated system developed to examine cognitive function in the horse. A fully-automated operant system for mobile cognitive function of a large animal model has been designed and validated. Horses pose an interesting complementary model to rodents for the examination of human neurological dysfunction. Copyright © 2017 Elsevier B.V. All rights reserved.

Innate defensive behaviour and panic-like reactions evoked by rodents during aggressive encounters with Brazilian constrictor snakes in a complex labyrinth: behavioural validation of a new model to study affective and agonistic reactions in a prey versus predator paradigm.

PubMed

Guimarães-Costa, Raquel; Guimarães-Costa, Maria Beatriz; Pippa-Gadioli, Leonardo; Weltson, Alfredo; Ubiali, Walter Adriano; Paschoalin-Maurin, Tatiana; Felippotti, Tatiana Tocchini; Elias-Filho, Daoud Hibrahim; Laure, Carlos Júlio; Coimbra, Norberto Cysne

2007-09-15

Defensive behaviour has been extensively studied, and non-invasive methodologies may be interesting approaches to analyzing the limbic system function as a whole. Using experimental models of animals in the state of anxiety has been fundamental in the search for new anxiolytic and antipanic compounds. The aim of this present work is to examine a new model for the study of affective behaviour, using a complex labyrinth consisting of an arena and galleries forming a maze. Furthermore, it aims to compare the defensive behaviour of Wistar rats, Mongolian gerbils and golden hamsters in a complex labyrinth, as well as the defensive behaviour of Meriones unguiculatus in aggressive encounters with either Epicrates cenchria assisi or Boa constrictor amarali in this same model. Among species presently studied, the Mongolian gerbils showed better performance in the exploration of both arena and galleries of the labyrinth, also demonstrating less latency in finding exits of the galleries. This increases the possibility of survival, as well as optimizes the events of encounter with the predator. The duration of alertness and freezing increased during confrontation with living Epicrates, as well as the duration of exploratory behaviour in the labyrinth. There was an increase in the number of freezing and alertness behaviours, as well as in duration of alertness during confrontations involving E.c. assisi, compared with behavioural reactions elicited by jirds in presence of B.c. amarali. Interestingly, the aggressive behaviour of Mongolian gerbils was more prominent against B.c. amarali compared with the other Boidae snake. E.c. assisi elicited more offensive attacks and exhibited a greater time period of body movement than B.c. amarali, which spent more time in the arena and in defensive immobility than the E.c. assisi. Considering that jirds evoked more fear-like reaction in contact with E.c. assisi, a fixed E.c. assisi kept in a hermetically closed acrylic box was used as control. In these prey/predator encounter-based experiments, there was an increase in the number of alertness and freezing behaviours exhibited by gerbils, and a decrease in the number of crossing elicited by them, when comparing confrontations between the living E.c. assisi and the control. The experiments were performed at 7.0 p.m. In the labyrinth, the snakes showed in confrontation similar performance to that observed in nature (organizing hunting behaviour, offensive/defensive attack, constriction, prey inspection and feeding behaviour), which were essential to the validity of the experiments and gave behavioural validation within the complex labyrinth.

Charge–transfer reaction of 2,3-dichloro-1,4-naphthoquinone with crizotinib: Spectrophotometric study, computational molecular modeling and use in development of microwell assay for crizotinib

PubMed Central

Alzoman, Nourah Z.; Alshehri, Jamilah M.; Darwish, Ibrahim A.; Khalil, Nasr Y.; Abdel-Rahman, Hamdy M.

2014-01-01

The reaction of 2,3-dichloro-1,4-naphthoquinone (DCNQ) with crizotinib (CZT; a novel drug used for treatment of non-small cell lung cancer) was investigated in different solvents of varying dielectric constants and polarity indexes. The reaction produced a red-colored product. Spectrophotometric investigations confirmed that the reaction proceeded through charge–transfer (CT) complex formation. The molar absorptivity of the complex was found to be linearly correlated with the dielectric constant and polarity index of the solvent; the correlation coefficients were 0.9567 and 0.9069, respectively. The stoichiometric ratio of DCNQ:CZT was found to be 2:1 and the association constant of the complex was found to be 1.07 × 102 l/mol. The kinetics of the reaction was studied; the order of the reaction, rate and rate constant were determined. Computational molecular modeling for the complex between DCNQ and CZT was conducted, the sites of interaction on CZT molecule were determined, and the mechanism of the reaction was postulated. The reaction was employed as a basis in the development of a novel 96-microwell assay for CZT in a linear range of 4–500 μg/ml. The assay limits of detection and quantitation were 2.06 and 6.23 μg/ml, respectively. The assay was validated as per the guidelines of the International Conference on Harmonization (ICH) and successfully applied to the analysis of CZT in its bulk and capsules with good accuracy and precision. The assay has high throughput and consumes a minimum volume of organic solvents thus it reduces the exposures of the analysts to the toxic effects of organic solvents, and significantly reduces the analysis cost. PMID:25685046

Optimizing LX-17 Thermal Decomposition Model Parameters with Evolutionary Algorithms

NASA Astrophysics Data System (ADS)

Moore, Jason; McClelland, Matthew; Tarver, Craig; Hsu, Peter; Springer, H. Keo

2017-06-01

We investigate and model the cook-off behavior of LX-17 because this knowledge is critical to understanding system response in abnormal thermal environments. Thermal decomposition of LX-17 has been explored in conventional ODTX (One-Dimensional Time-to-eXplosion), PODTX (ODTX with pressure-measurement), TGA (thermogravimetric analysis), and DSC (differential scanning calorimetry) experiments using varied temperature profiles. These experimental data are the basis for developing multiple reaction schemes with coupled mechanics in LLNL's multi-physics hydrocode, ALE3D (Arbitrary Lagrangian-Eulerian code in 2D and 3D). We employ evolutionary algorithms to optimize reaction rate parameters on high performance computing clusters. Once experimentally validated, this model will be scalable to a number of applications involving LX-17 and can be used to develop more sophisticated experimental methods. Furthermore, the optimization methodology developed herein should be applicable to other high explosive materials. This work was performed under the auspices of the U.S. DOE by LLNL under contract DE-AC52-07NA27344. LLNS, LLC.

Quantum and classical dynamics of water dissociation on Ni(111): A test of the site-averaging model in dissociative chemisorption of polyatomic molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Bin; Department of Chemical Physics, University of Science and Technology of China, Hefei 230026; Guo, Hua, E-mail: hguo@unm.edu

Recently, we reported the first highly accurate nine-dimensional global potential energy surface (PES) for water interacting with a rigid Ni(111) surface, built on a large number of density functional theory points [B. Jiang and H. Guo, Phys. Rev. Lett. 114, 166101 (2015)]. Here, we investigate site-specific reaction probabilities on this PES using a quasi-seven-dimensional quantum dynamical model. It is shown that the site-specific reactivity is largely controlled by the topography of the PES instead of the barrier height alone, underscoring the importance of multidimensional dynamics. In addition, the full-dimensional dissociation probability is estimated by averaging fixed-site reaction probabilities with appropriatemore » weights. To validate this model and gain insights into the dynamics, additional quasi-classical trajectory calculations in both full and reduced dimensions have also been performed and important dynamical factors such as the steering effect are discussed.« less

Influence of Wind Pressure on the Carbonation of Concrete

PubMed Central

Zou, Dujian; Liu, Tiejun; Du, Chengcheng; Teng, Jun

2015-01-01

Carbonation is one of the major deteriorations that accelerate steel corrosion in reinforced concrete structures. Many mathematical/numerical models of the carbonation process, primarily diffusion-reaction models, have been established to predict the carbonation depth. However, the mass transfer of carbon dioxide in porous concrete includes molecular diffusion and convection mass transfer. In particular, the convection mass transfer induced by pressure difference is called penetration mass transfer. This paper presents the influence of penetration mass transfer on the carbonation. A penetration-reaction carbonation model was constructed and validated by accelerated test results under high pressure. Then the characteristics of wind pressure on the carbonation were investigated through finite element analysis considering steady and fluctuating wind flows. The results indicate that the wind pressure on the surface of concrete buildings results in deeper carbonation depth than that just considering the diffusion of carbon dioxide. In addition, the influence of wind pressure on carbonation tends to increase significantly with carbonation depth. PMID:28793462

Influence of Wind Pressure on the Carbonation of Concrete.

PubMed

Zou, Dujian; Liu, Tiejun; Du, Chengcheng; Teng, Jun

2015-07-24

Carbonation is one of the major deteriorations that accelerate steel corrosion in reinforced concrete structures. Many mathematical/numerical models of the carbonation process, primarily diffusion-reaction models, have been established to predict the carbonation depth. However, the mass transfer of carbon dioxide in porous concrete includes molecular diffusion and convection mass transfer. In particular, the convection mass transfer induced by pressure difference is called penetration mass transfer. This paper presents the influence of penetration mass transfer on the carbonation. A penetration-reaction carbonation model was constructed and validated by accelerated test results under high pressure. Then the characteristics of wind pressure on the carbonation were investigated through finite element analysis considering steady and fluctuating wind flows. The results indicate that the wind pressure on the surface of concrete buildings results in deeper carbonation depth than that just considering the diffusion of carbon dioxide. In addition, the influence of wind pressure on carbonation tends to increase significantly with carbonation depth.

Methodology for modeling the mechanical interaction between a reaction wheel and a flexible structure

NASA Astrophysics Data System (ADS)

Elias, Laila M.; Dekens, Frank G.; Basdogan, Ipek; Sievers, Lisa A.; Neville, Timothy

2003-02-01

This paper presents a modeling methodology used to predict the performance of a flexible structure, such as a space telescope, in the presence of an on-board vibrational disturbance source, such as a reaction wheel assembly (RWA). Both decoupled and coupled analysis methods are presented. The decoupled method relies on blocked RWA disturbances, measured with the RWA hardmounted to a rigid surface. The coupled method corrects the blocked RWA disturbance boundary conditions using 'force filters' which depend on estimates of the interface accelerances of the RWA and spacecraft. Both methods were validated on the Micro-Precision Interferometer testbed at the Jet Propulsion Laboratory. Experimental results are encouraging, indicating that both methods provide sufficient accuracy compared to measured values; however, the coupled method provides the best results when the gyroscopic nature of the spinning RWA is captured in the RWA accelerance model. Additionally, the RWA disturbance cross spectral density terms are found to be influential.

New strategy to improve quality control of Montenegro skin test at the production level.

PubMed

Guedes, Deborah Carbonera; Minozzo, João Carlos; Pasquali, Aline Kuhn Sbruzzi; Faulds, Craig; Soccol, Carlos Ricardo; Thomaz-Soccol, Vanete

2017-01-01

The production of the Montenegro antigen for skin test poses difficulties regarding quality control. Here, we propose that certain animal models reproducing a similar immune response to humans may be used in the quality control of Montenegro antigen production. Fifteen Cavia porcellus (guinea pigs) were immunized with Leishmania amazonensis or Leishmania braziliensis , and, after 30 days, they were skin tested with standard Montenegro antigen. To validate C. porcellus as an animal model for skin tests, eighteen Mesocricetus auratus (hamsters) were infected with L. amazonensis or L. braziliensis , and, after 45 days, they were skin tested with standard Montenegro antigen. Cavia porcellus immunized with L. amazonensis or L. braziliensis , and hamsters infected with the same species presented induration reactions when skin tested with standard Montenegro antigen 48-72h after the test. The comparison between immunization methods and immune response from the two animal species validated C. porcellus as a good model for Montenegro skin test, and the model showed strong potential as an in vivo model in the quality control of the production of Montenegro antigen.

Chemical kinetic modeling of propene oxidation at low and intermediate temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilk, R.D.; Cernansky, N.P.; Pitz, W.J.

1986-01-13

A detailed chemical kinetic mechanism for propene oxidation is developed and used to model reactions in a static reactor at temperatures of 590 to 740/sup 0/K, equivalence ratios of 0.8 to 2.0, and a pressure of 600 torr. Modeling of hydrocarbon oxidation in this temperature range is important for the validation of detailed models to be used for performing calculations related to automotive engine knock. The model predicted induction periods and species concentrations for all the species measured experimentally in a static reactor by Wilk, Cernansky, and Cohen. The detailed model predicted a temperature region of approximately constant induction periodmore » which corresponded very closely to the region of negative temperature coefficient behavior found in the experiment. Overall, the calculated concentrations of acetaldehyde, ethene, and methane were somewhat low compared to the experimental measurements, and the calculated concentrations of formaldehyde and methanol were high. The characteristic s-shape of the fuel concentration history was well predicted. The importance of OH+C/sub 3/H/sub 6/ and related rections in determining product distributions and the importance of consumption reactions for allyl radicals was demonstrated by the modeling calculations. 18 refs., 4 figs., 1 tab.« less

Pyrolysis of reinforced polymer composites: Parameterizing a model for multiple compositions

NASA Astrophysics Data System (ADS)

Martin, Geraldine E.

A single set of material properties was developed to describe the pyrolysis of fiberglass reinforced polyester composites at multiple composition ratios. Milligram-scale testing was performed on the unsaturated polyester (UP) resin using thermogravimetric analysis (TGA) coupled with differential scanning calorimetry (DSC) to establish and characterize an effective semi-global reaction mechanism, of three consecutive first-order reactions. Radiation-driven gasification experiments were conducted on UP resin and the fiberglass composites at compositions ranging from 41 to 54 wt% resin at external heat fluxes from 30 to 70 kW m -2. The back surface temperature was recorded with an infrared camera and used as the target for inverse analysis to determine the thermal conductivity of the systematically isolated constituent species. Manual iterations were performed in a comprehensive pyrolysis model, ThermaKin. The complete set of properties was validated for the ability to reproduce the mass loss rate during gasification testing.

Maximization of fructose esters synthesis by response surface methodology.

PubMed

Neta, Nair Sampaio; Peres, António M; Teixeira, José A; Rodrigues, Ligia R

2011-07-01

Enzymatic synthesis of fructose fatty acid ester was performed in organic solvent media, using a purified lipase from Candida antartica B immobilized in acrylic resin. Response surface methodology with a central composite rotatable design based on five levels was implemented to optimize three experimental operating conditions (temperature, agitation and reaction time). A statistical significant cubic model was established. Temperature and reaction time were found to be the most significant parameters. The optimum operational conditions for maximizing the synthesis of fructose esters were 57.1°C, 100 rpm and 37.8 h. The model was validated in the identified optimal conditions to check its adequacy and accuracy, and an experimental esterification percentage of 88.4% (±0.3%) was obtained. These results showed that an improvement of the enzymatic synthesis of fructose esters was obtained under the optimized conditions. Copyright © 2011 Elsevier B.V. All rights reserved.

Thermo-Oxidative Induced Damage in Polymer Composites: Microstructure Image-Based Multi-Scale Modeling and Experimental Validation

NASA Astrophysics Data System (ADS)

Hussein, Rafid M.; Chandrashekhara, K.

2017-11-01

A multi-scale modeling approach is presented to simulate and validate thermo-oxidation shrinkage and cracking damage of a high temperature polymer composite. The multi-scale approach investigates coupled transient diffusion-reaction and static structural at macro- to micro-scale. The micro-scale shrinkage deformation and cracking damage are simulated and validated using 2D and 3D simulations. Localized shrinkage displacement boundary conditions for the micro-scale simulations are determined from the respective meso- and macro-scale simulations, conducted for a cross-ply laminate. The meso-scale geometrical domain and the micro-scale geometry and mesh are developed using the object oriented finite element (OOF). The macro-scale shrinkage and weight loss are measured using unidirectional coupons and used to build the macro-shrinkage model. The cross-ply coupons are used to validate the macro-shrinkage model by the shrinkage profiles acquired using scanning electron images at the cracked surface. The macro-shrinkage model deformation shows a discrepancy when the micro-scale image-based cracking is computed. The local maximum shrinkage strain is assumed to be 13 times the maximum macro-shrinkage strain of 2.5 × 10-5, upon which the discrepancy is minimized. The microcrack damage of the composite is modeled using a static elastic analysis with extended finite element and cohesive surfaces by considering the modulus spatial evolution. The 3D shrinkage displacements are fed to the model using node-wise boundary/domain conditions of the respective oxidized region. Microcrack simulation results: length, meander, and opening are closely matched to the crack in the area of interest for the scanning electron images.

Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; Giese, Timothy J.

2015-12-21

Accurate modeling of the molecular environment is critical in condensed phase simulations of chemical reactions. Conventional quantum mechanical/molecular mechanical (QM/MM) simulations traditionally model non-electrostatic non-bonded interactions through an empirical Lennard-Jones (LJ) potential which, in violation of intuitive chemical principles, is bereft of any explicit coupling to an atom’s local electronic structure. This oversight results in a model whereby short-ranged exchange-repulsion and long-ranged dispersion interactions are invariant to changes in the local atomic charge, leading to accuracy limitations for chemical reactions where significant atomic charge transfer can occur along the reaction coordinate. The present work presents a variational, charge-dependent exchange-repulsion andmore » dispersion model, referred to as the charge-dependent exchange and dispersion (QXD) model, for hybrid QM/MM simulations. Analytic expressions for the energy and gradients are provided, as well as a description of the integration of the model into existing QM/MM frameworks, allowing QXD to replace traditional LJ interactions in simulations of reactive condensed phase systems. After initial validation against QM data, the method is demonstrated by capturing the solvation free energies of a series of small, chlorine-containing compounds that have varying charge on the chlorine atom. The model is further tested on the S{sub N}2 attack of a chloride anion on methylchloride. Results suggest that the QXD model, unlike the traditional LJ model, is able to simultaneously obtain accurate solvation free energies for a range of compounds while at the same time closely reproducing the experimental reaction free energy barrier. The QXD interaction model allows explicit coupling of atomic charge with many-body exchange and dispersion interactions that are related to atomic size and provides a more accurate and robust representation of non-electrostatic non-bonded QM/MM interactions.« less

Mittag-Leffler synchronization of fractional neural networks with time-varying delays and reaction-diffusion terms using impulsive and linear controllers.

PubMed

Stamova, Ivanka; Stamov, Gani

2017-12-01

In this paper, we propose a fractional-order neural network system with time-varying delays and reaction-diffusion terms. We first develop a new Mittag-Leffler synchronization strategy for the controlled nodes via impulsive controllers. Using the fractional Lyapunov method sufficient conditions are given. We also study the global Mittag-Leffler synchronization of two identical fractional impulsive reaction-diffusion neural networks using linear controllers, which was an open problem even for integer-order models. Since the Mittag-Leffler stability notion is a generalization of the exponential stability concept for fractional-order systems, our results extend and improve the exponential impulsive control theory of neural network system with time-varying delays and reaction-diffusion terms to the fractional-order case. The fractional-order derivatives allow us to model the long-term memory in the neural networks, and thus the present research provides with a conceptually straightforward mathematical representation of rather complex processes. Illustrative examples are presented to show the validity of the obtained results. We show that by means of appropriate impulsive controllers we can realize the stability goal and to control the qualitative behavior of the states. An image encryption scheme is extended using fractional derivatives. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data

PubMed Central

2011-01-01

Background With the advent of high-throughput targeted metabolic profiling techniques, the question of how to interpret and analyze the resulting vast amount of data becomes more and more important. In this work we address the reconstruction of metabolic reactions from cross-sectional metabolomics data, that is without the requirement for time-resolved measurements or specific system perturbations. Previous studies in this area mainly focused on Pearson correlation coefficients, which however are generally incapable of distinguishing between direct and indirect metabolic interactions. Results In our new approach we propose the application of a Gaussian graphical model (GGM), an undirected probabilistic graphical model estimating the conditional dependence between variables. GGMs are based on partial correlation coefficients, that is pairwise Pearson correlation coefficients conditioned against the correlation with all other metabolites. We first demonstrate the general validity of the method and its advantages over regular correlation networks with computer-simulated reaction systems. Then we estimate a GGM on data from a large human population cohort, covering 1020 fasting blood serum samples with 151 quantified metabolites. The GGM is much sparser than the correlation network, shows a modular structure with respect to metabolite classes, and is stable to the choice of samples in the data set. On the example of human fatty acid metabolism, we demonstrate for the first time that high partial correlation coefficients generally correspond to known metabolic reactions. This feature is evaluated both manually by investigating specific pairs of high-scoring metabolites, and then systematically on a literature-curated model of fatty acid synthesis and degradation. Our method detects many known reactions along with possibly novel pathway interactions, representing candidates for further experimental examination. Conclusions In summary, we demonstrate strong signatures of intracellular pathways in blood serum data, and provide a valuable tool for the unbiased reconstruction of metabolic reactions from large-scale metabolomics data sets. PMID:21281499

Kinetic modeling of α-hydrogen abstractions from unsaturated and saturated oxygenate compounds by carbon-centered radicals.

PubMed

Paraskevas, Paschalis D; Sabbe, Maarten K; Reyniers, Marie-Françoise; Papayannakos, Nikos; Marin, Guy B

2014-06-23

Hydrogen abstractions are important elementary reactions in a variety of reacting media at high temperatures in which oxygenates and hydrocarbon radicals are present. Accurate kinetic data are obtained from CBS-QB3 ab initio (AI) calculations by using conventional transition-state theory within the high-pressure limit, including corrections for hindered rotation and tunneling. From the obtained results, a group-additive (GA) model is developed that allows the Arrhenius parameters and rate coefficients for abstraction of the α-hydrogen from a wide range of oxygenate compounds to be predicted at temperatures ranging from 300 to 1500 K. From a training set of 60 hydrogen abstractions from oxygenates by carbon-centered radicals, 15 GA values (ΔGAV°s) are obtained for both the forward and reverse reactions. Among them, four ΔGAV°s refer to primary contributions, and the remaining 11 ΔGAV°s refer to secondary ones. The accuracy of the model is further improved by introducing seven corrections for cross-resonance stabilization of the transition state from an additional set of 43 reactions. The determined ΔGAV°s are validated upon a test set of AI data for 17 reactions. The mean absolute deviation of the pre-exponential factors (log A) and activation energies (E(a)) for the forward reaction at 300 K are 0.238 log(m(3)  mol(-1)  s(-1)) and 1.5 kJ mol(-1), respectively, whereas the mean factor of deviation <ρ> between the GA-predicted and the AI-calculated rate coefficients is 1.6. In comparison with a compilation of 33 experimental rate coefficients, the <ρ> between the GA-predicted values and these experimental values is only 2.2. Hence, the constructed GA model can be reliably used in the prediction of the kinetics of α-hydrogen-abstraction reactions between a broad range of oxygenates and oxygenate radicals. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selection, calibration, and validation of models of tumor growth.

PubMed

Lima, E A B F; Oden, J T; Hormuth, D A; Yankeelov, T E; Almeida, R C

2016-11-01

This paper presents general approaches for addressing some of the most important issues in predictive computational oncology concerned with developing classes of predictive models of tumor growth. First, the process of developing mathematical models of vascular tumors evolving in the complex, heterogeneous, macroenvironment of living tissue; second, the selection of the most plausible models among these classes, given relevant observational data; third, the statistical calibration and validation of models in these classes, and finally, the prediction of key Quantities of Interest (QOIs) relevant to patient survival and the effect of various therapies. The most challenging aspects of this endeavor is that all of these issues often involve confounding uncertainties: in observational data, in model parameters, in model selection, and in the features targeted in the prediction. Our approach can be referred to as "model agnostic" in that no single model is advocated; rather, a general approach that explores powerful mixture-theory representations of tissue behavior while accounting for a range of relevant biological factors is presented, which leads to many potentially predictive models. Then representative classes are identified which provide a starting point for the implementation of OPAL, the Occam Plausibility Algorithm (OPAL) which enables the modeler to select the most plausible models (for given data) and to determine if the model is a valid tool for predicting tumor growth and morphology ( in vivo ). All of these approaches account for uncertainties in the model, the observational data, the model parameters, and the target QOI. We demonstrate these processes by comparing a list of models for tumor growth, including reaction-diffusion models, phase-fields models, and models with and without mechanical deformation effects, for glioma growth measured in murine experiments. Examples are provided that exhibit quite acceptable predictions of tumor growth in laboratory animals while demonstrating successful implementations of OPAL.

Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer.

PubMed

Köhler, Markus; Oßwald, Patrick; Krueger, Dominik; Whitside, Ryan

2018-02-19

This manuscript describes a high-temperature flow reactor experiment coupled to the powerful molecular beam mass spectrometry (MBMS) technique. This flexible tool offers a detailed observation of chemical gas-phase kinetics in reacting flows under well-controlled conditions. The vast range of operating conditions available in a laminar flow reactor enables access to extraordinary combustion applications that are typically not achievable by flame experiments. These include rich conditions at high temperatures relevant for gasification processes, the peroxy chemistry governing the low temperature oxidation regime or investigations of complex technical fuels. The presented setup allows measurements of quantitative speciation data for reaction model validation of combustion, gasification and pyrolysis processes, while enabling a systematic general understanding of the reaction chemistry. Validation of kinetic reaction models is generally performed by investigating combustion processes of pure compounds. The flow reactor has been enhanced to be suitable for technical fuels (e.g. multi-component mixtures like Jet A-1) to allow for phenomenological analysis of occurring combustion intermediates like soot precursors or pollutants. The controlled and comparable boundary conditions provided by the experimental design allow for predictions of pollutant formation tendencies. Cold reactants are fed premixed into the reactor that are highly diluted (in around 99 vol% in Ar) in order to suppress self-sustaining combustion reactions. The laminar flowing reactant mixture passes through a known temperature field, while the gas composition is determined at the reactors exhaust as a function of the oven temperature. The flow reactor is operated at atmospheric pressures with temperatures up to 1,800 K. The measurements themselves are performed by decreasing the temperature monotonically at a rate of -200 K/h. With the sensitive MBMS technique, detailed speciation data is acquired and quantified for almost all chemical species in the reactive process, including radical species.

Ductile mode grinding of reaction-bonded silicon carbide mirrors.

PubMed

Dong, Zhichao; Cheng, Haobo

2017-09-10

The demand for reaction-bonded silicon carbide (RB-SiC) mirrors has escalated recently with the rapid development of space optical remote sensors used in astronomy or Earth observation. However, RB-SiC is difficult to machine due to its high hardness. This study intends to perform ductile mode grinding to RB-SiC, which produces superior surface integrity and fewer subsurface damages, thus minimizing the workload of subsequent lapping and polishing. For this purpose, a modified theoretical model for grain depth of cut of grinding wheels is presented, which correlates various processing parameters and the material characteristics (i.e., elastic module) of a wheel's bonding matrix and workpiece. Ductile mode grinding can be achieved as the grain depth of cut of wheels decreases to be less than the critical cut depth of workpieces. The theoretical model gives a roadmap to optimize the grinding parameters for ductile mode grinding of RB-SiC and other ultra-hard brittle materials. Its feasibility was validated by experiments. With the optimized grinding parameters for RB-SiC, the ductile mode grinding produced highly specular surfaces (with roughness of ∼2.2-2.8  nm Ra), which means the material removal mechanism of RB-SiC is dominated by plastic deformation rather than brittle fracture. Contrast experiments were also conducted on fused silica, using the same grinding parameters; this produced only very rough surfaces, which further validated the feasibility of the proposed model.

Factor structure and validation of the Attentional Control Scale.

PubMed

Judah, Matt R; Grant, DeMond M; Mills, Adam C; Lechner, William V

2014-04-01

The Attentional Control Scale (ACS; Derryberry & Reed, 2002) has been used to assess executive control over attention in numerous studies, but no published data have examined the factor structure of the English version. The current studies addressed this need and tested the predictive and convergent validity of the ACS subscales. In Study 1, exploratory factor analysis yielded a two-factor model with Focusing and Shifting subscales. In Study 2, confirmatory factor analysis supported this model and suggested superior fit compared to the factor structure of the Icelandic version (Ólafsson et al., 2011). Study 3 examined correlations between the ACS subscales and measures of working memory, anxiety, and cognitive control. Study 4 examined correlations between the subscales and reaction times on a mixed-antisaccade task, revealing positive correlations for antisaccade performance and prosaccade latency with Focusing scores and between switch trial performance and Shifting scores. Additionally, the findings partially supported unique relationships between Focusing and trait anxiety and between Shifting and depression that have been noted in recent research. Although the results generally support the validity of the ACS, additional research using performance-based tasks is needed.

Strategies for carbohydrate model building, refinement and validation

PubMed Central

2017-01-01

Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein–sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade. PMID:28177313

Reexamining the nuclear structure of 154Gd in the dynamic pairing plus quadrupole model

NASA Astrophysics Data System (ADS)

Gupta, J. B.; Hamilton, J. H.

2017-05-01

In a previous study of the collective multiphonon bands in 154Gd, using the microscopic dynamic pairing plus quadrupole model, data for eight K bands were analyzed. In the last four decades, its decay scheme is significantly revised and the nuclear theory has undergone a significant change. Special focus is on new weak intensity transitions in several bands and on the reassigned levels in its decay scheme. The present study represents a detailed revised analysis of the collective even parity bands below 2.1 MeV. Also, a discussion is given on the nature of the Kπ=0+ excited bands, validity of band mixing approach, and of the assumption of shape coexistence of β band with ground band. Comparison is made with the X (5) analytical symmetry and the algebraic interacting boson model predictions. Discussion of the 2 n transfer reactions is given. The validity of the multiphonon view of the Kπ=4+ and 22+ bands is also studied.

Strategies for carbohydrate model building, refinement and validation.

PubMed

Agirre, Jon

2017-02-01

Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.

Neutron capture measurement on {sup 173}Lu at LANSCE with DANCE detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theroine, C.; Ebran, A.; Meot, V.

2013-06-10

The (n,{gamma}) cross section on the unstable {sup 173}Lu(t{sub 1/2} = 1.37y) has been measured from thermal energy up to 200 eV at Los Alamos Neutron Science Center (LANSCE) with The Detector for Advanced Neutron Capture Experiements (DANCE). The main aim of this study is to validate and optimize reaction models for unstable nucleus. A preliminary capture yield will be presented in this paper.

Thermal Modeling and Management of Solid Oxide Fuel Cells Operating with Internally Reformed Methane

NASA Astrophysics Data System (ADS)

Wu, Yiyang; Shi, Yixiang; Cai, Ningsheng; Ni, Meng

2018-06-01

A detailed three-dimensional mechanistic model of a large-scale solid oxide fuel cell (SOFC) unit running on partially pre-reformed methane is developed. The model considers the coupling effects of chemical and electrochemical reactions, mass transport, momentum and heat transfer in the SOFC unit. After model validation, parametric simulations are conducted to investigate how the methane pre-reforming ratio affects the transport and electrochemistry of the SOFC unit. It is found that the methane steam reforming reaction has a "smoothing effect", which can achieve more uniform distributions of gas compositions, current density and temperature among the cell plane. In the case of 1500 W/m2 power density output, adding 20% methane absorbs 50% of internal heat production inside the cell, reduces the maximum temperature difference inside the cell from 70 K to 22 K and reduces the cathode air supply by 75%, compared to the condition of completely pre-reforming of methane. Under specific operating conditions, the pre-reforming ratio of methane has an optimal range for obtaining a good temperature distribution and good cell performance.

Development and validation of chemistry agnostic flow battery cost performance model and application to nonaqueous electrolyte systems: Chemistry agnostic flow battery cost performance model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, Alasdair; Thomsen, Edwin; Reed, David

2016-04-20

A chemistry agnostic cost performance model is described for a nonaqueous flow battery. The model predicts flow battery performance by estimating the active reaction zone thickness at each electrode as a function of current density, state of charge, and flow rate using measured data for electrode kinetics, electrolyte conductivity, and electrode-specific surface area. Validation of the model is conducted using a 4kW stack data at various current densities and flow rates. This model is used to estimate the performance of a nonaqueous flow battery with electrode and electrolyte properties used from the literature. The optimized cost for this system ismore » estimated for various power and energy levels using component costs provided by vendors. The model allows optimization of design parameters such as electrode thickness, area, flow path design, and operating parameters such as power density, flow rate, and operating SOC range for various application duty cycles. A parametric analysis is done to identify components and electrode/electrolyte properties with the highest impact on system cost for various application durations. A pathway to 100$kWh -1 for the storage system is identified.« less

Organosolv delignification of Eucalyptus globulus: Kinetic study of autocatalyzed ethanol pulping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oliet, M.; Rodriguez, F.; Santos, A.

2000-01-01

The autocatalyzed delignification of Eucalyptus globulus in 50% ethanol (w/w) was modeled as the irreversible and consecutive dissolution of initial, bulk, and residual lignin. Their respective contributions to total lignin was estimated as 9, 75, and 16%. Isothermal pulping experiments were carried out to evaluate an empirical kinetic model among eight proposals corresponding to different reaction schemes. The calculated activation energy was found to be 96.5, 98.5, and 40.8 kJ/mol for initial, bulk, and residual delignification, respectively. The influence of hydrogen ion concentration was expressed by a power-law function model. The kinetic model developed here was validated using data frommore » nonisothermal pulping runs.« less

Quantitative structure-activity relationships for reactivities of sulfate and hydroxyl radicals with aromatic contaminants through single-electron transfer pathway.

PubMed

Luo, Shuang; Wei, Zongsu; Spinney, Richard; Villamena, Frederick A; Dionysiou, Dionysios D; Chen, Dong; Tang, Chong-Jian; Chai, Liyuan; Xiao, Ruiyang

2018-02-15

Sulfate radical anion (SO 4 •- ) and hydroxyl radical (OH) based advanced oxidation technologies has been extensively used for removal of aromatic contaminants (ACs) in waters. In this study, we investigated the Gibbs free energy (ΔG SET ∘ ) of the single electron transfer (SET) reactions for 76 ACs with SO 4 •- and OH, respectively. The result reveals that SO 4 •- possesses greater propensity to react with ACs through the SET channel than OH. We hypothesized that the electron distribution within the molecule plays an essential role in determining the ΔG SET ∘ and subsequent SET reactions. To test the hypothesis, a quantitative structure-activity relationship (QSAR) model was developed for predicting ΔG SET ∘ using the highest occupied molecular orbital energies (E HOMO ), a measure of electron distribution and donating ability. The standardized QSAR models are reported to be ΔG ° SET =-0.97×E HOMO - 181 and ΔG ° SET =-0.97×E HOMO - 164 for SO 4 •- and OH, respectively. The models were internally and externally validated to ensure robustness and predictability, and the application domain and limitations were discussed. The single-descriptor based models account for 95% of the variability for SO 4 •- and OH. These results provide the mechanistic insight into the SET reaction pathway of radical and non-radical bimolecular reactions, and have important applications for radical based oxidation technologies to remove target ACs in different waters. Copyright © 2017 Elsevier B.V. All rights reserved.

Implementation of a kappa-epsilon turbulence model to RPLUS3D code

NASA Technical Reports Server (NTRS)

Chitsomboon, Tawit

1992-01-01

The RPLUS3D code has been developed at the NASA Lewis Research Center to support the National Aerospace Plane (NASP) project. The code has the ability to solve three dimensional flowfields with finite rate combustion of hydrogen and air. The combustion process of the hydrogen-air system are simulated by an 18 reaction path, 8 species chemical kinetic mechanism. The code uses a Lower-Upper (LU) decomposition numerical algorithm as its basis, making it a very efficient and robust code. Except for the Jacobian matrix for the implicit chemistry source terms, there is no inversion of a matrix even though a fully implicit numerical algorithm is used. A k-epsilon turbulence model has recently been incorporated into the code. Initial validations have been conducted for a flow over a flat plate. Results of the validation studies are shown. Some difficulties in implementing the k-epsilon equations to the code are also discussed.

Implementation of a kappa-epsilon turbulence model to RPLUS3D code

NASA Astrophysics Data System (ADS)

Chitsomboon, Tawit

1992-02-01

The RPLUS3D code has been developed at the NASA Lewis Research Center to support the National Aerospace Plane (NASP) project. The code has the ability to solve three dimensional flowfields with finite rate combustion of hydrogen and air. The combustion process of the hydrogen-air system are simulated by an 18 reaction path, 8 species chemical kinetic mechanism. The code uses a Lower-Upper (LU) decomposition numerical algorithm as its basis, making it a very efficient and robust code. Except for the Jacobian matrix for the implicit chemistry source terms, there is no inversion of a matrix even though a fully implicit numerical algorithm is used. A k-epsilon turbulence model has recently been incorporated into the code. Initial validations have been conducted for a flow over a flat plate. Results of the validation studies are shown. Some difficulties in implementing the k-epsilon equations to the code are also discussed.

A fluorescence high throughput screening method for the detection of reactive electrophiles as potential skin sensitizers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Avonto, Cristina; Chittiboyina, Amar G.; Rua, Diego

2015-12-01

Skin sensitization is an important toxicological end-point in the risk assessment of chemical allergens. Because of the complexity of the biological mechanisms associated with skin sensitization, integrated approaches combining different chemical, biological and in silico methods are recommended to replace conventional animal tests. Chemical methods are intended to characterize the potential of a sensitizer to induce earlier molecular initiating events. The presence of an electrophilic mechanistic domain is considered one of the essential chemical features to covalently bind to the biological target and induce further haptenation processes. Current in chemico assays rely on the quantification of unreacted model nucleophiles aftermore » incubation with the candidate sensitizer. In the current study, a new fluorescence-based method, ‘HTS-DCYA assay’, is proposed. The assay aims at the identification of reactive electrophiles based on their chemical reactivity toward a model fluorescent thiol. The reaction workflow enabled the development of a High Throughput Screening (HTS) method to directly quantify the reaction adducts. The reaction conditions have been optimized to minimize solubility issues, oxidative side reactions and increase the throughput of the assay while minimizing the reaction time, which are common issues with existing methods. Thirty-six chemicals previously classified with LLNA, DPRA or KeratinoSens™ were tested as a proof of concept. Preliminary results gave an estimated 82% accuracy, 78% sensitivity, 90% specificity, comparable to other in chemico methods such as Cys-DPRA. In addition to validated chemicals, six natural products were analyzed and a prediction of their sensitization potential is presented for the first time. - Highlights: • A novel fluorescence-based method to detect electrophilic sensitizers is proposed. • A model fluorescent thiol was used to directly quantify the reaction products. • A discussion of the reaction workflow and critical parameters is presented. • The method could provide a useful tool to complement existing chemical assays.« less

Diffusive confinement of free radical intermediates in the OH radical oxidation of semisolid aerosols

DOE PAGES

Wiegel, Aaron A.; Liu, Matthew J.; Hinsberg, William D.; ...

2017-02-07

Multiphase chemical reactions (gas + solid/liquid) involve a complex interplay between bulk and interface chemistry, diffusion, evaporation, and condensation. Reactions of atmospheric aerosols are an important example of this type of chemistry: the rich array of particle phase states and multiphase transformation pathways produce diverse but poorly understood interactions between chemistry and transport. Their chemistry is of intrinsic interest because of their role in controlling climate. Their characteristics also make them useful models for the study of principles of reactivity of condensed materials under confined conditions. Previously, we have reported a computational study of the oxidation chemistry of a liquidmore » aliphatic aerosol. In this study, we extend the calculations to investigate nearly the same reactions at a semisolid gas-aerosol interface. A reaction-diffusion model for heterogeneous oxidation of triacontane by hydroxyl radicals (OH) is described, and its predictions are compared to measurements of aerosol size and composition, which evolve continuously during oxidation. Our results are also explicitly compared to those obtained for the corresponding liquid system, squalane, to pinpoint salient elements controlling reactivity. The diffusive confinement of the free radical intermediates at the interface results in enhanced importance of a few specific chemical processes such as the involvement of aldehydes in fragmentation and evaporation, and a significant role of radical-radical reactions in product formation. The simulations show that under typical laboratory conditions semisolid aerosols have highly oxidized nanometer-scale interfaces that encapsulate an unreacted core and may confer distinct optical properties and enhanced hygroscopicity. This highly oxidized layer dynamically evolves with reaction, which we propose to result in plasticization. The validated model is used to predict chemistry under atmospheric conditions, where the OH radical concentration is much lower. The oxidation reactions are more strongly influenced by diffusion in the particle, resulting in a more liquid-like character.« less

Cybernetic modeling based on pathway analysis for Penicillium chrysogenum fed-batch fermentation.

PubMed

Geng, Jun; Yuan, Jingqi

2010-08-01

A macrokinetic model employing cybernetic methodology is proposed to describe mycelium growth and penicillin production. Based on the primordial and complete metabolic network of Penicillium chrysogenum found in the literature, the modeling procedure is guided by metabolic flux analysis and cybernetic modeling framework. The abstracted cybernetic model describes the transients of the consumption rates of the substrates, the assimilation rates of intermediates, the biomass growth rate, as well as the penicillin formation rate. Combined with the bioreactor model, these reaction rates are linked with the most important state variables, i.e., mycelium, substrate and product concentrations. Simplex method is used to estimate the sensitive parameters of the model. Finally, validation of the model is carried out with 20 batches of industrial-scale penicillin cultivation.

Development and Implementation of Photonuclear Cross-Section Data for Mutually Coupled Neutron-Photon Transport Calculations in the Monte Carlo N-Particle (MCNP) Radiation Transport Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Morgan C.

2000-07-01

The fundamental motivation for the research presented in this dissertation was the need to development a more accurate prediction method for characterization of mixed radiation fields around medical electron accelerators (MEAs). Specifically, a model is developed for simulation of neutron and other particle production from photonuclear reactions and incorporated in the Monte Carlo N-Particle (MCNP) radiation transport code. This extension of the capability within the MCNP code provides for the more accurate assessment of the mixed radiation fields. The Nuclear Theory and Applications group of the Los Alamos National Laboratory has recently provided first-of-a-kind evaluated photonuclear data for a selectmore » group of isotopes. These data provide the reaction probabilities as functions of incident photon energy with angular and energy distribution information for all reaction products. The availability of these data is the cornerstone of the new methodology for state-of-the-art mutually coupled photon-neutron transport simulations. The dissertation includes details of the model development and implementation necessary to use the new photonuclear data within MCNP simulations. A new data format has been developed to include tabular photonuclear data. Data are processed from the Evaluated Nuclear Data Format (ENDF) to the new class ''u'' A Compact ENDF (ACE) format using a standalone processing code. MCNP modifications have been completed to enable Monte Carlo sampling of photonuclear reactions. Note that both neutron and gamma production are included in the present model. The new capability has been subjected to extensive verification and validation (V&V) testing. Verification testing has established the expected basic functionality. Two validation projects were undertaken. First, comparisons were made to benchmark data from literature. These calculations demonstrate the accuracy of the new data and transport routines to better than 25 percent. Second, the ability to calculate radiation dose due to the neutron environment around a MEA is shown. An uncertainty of a factor of three in the MEA calculations is shown to be due to uncertainties in the geometry modeling. It is believed that the methodology is sound and that good agreement between simulation and experiment has been demonstrated.« less

Evaluation of a simple test of reaction time for baseline concussion testing in a population of high school athletes.

PubMed

MacDonald, James; Wilson, Julie; Young, Julie; Duerson, Drew; Swisher, Gail; Collins, Christy L; Meehan, William P

2015-01-01

A common sequela of concussions is impaired reaction time. Computerized neurocognitive tests commonly measure reaction time. A simple clinical test for reaction time has been studied previously in college athletes; whether this test is valid and reliable when assessing younger athletes remains unknown. Our study examines the reliability and validity of this test in a population of high school athletes. Cross-sectional study. Two American High Schools. High school athletes (N = 448) participating in American football or soccer during the academic years 2011 to 2012 and 2012 to 2013. All study participants completed a computerized baseline neurocognitive assessment that included a measure of reaction time (RT comp), in addition to a clinical measure of reaction time that assessed how far a standard measuring device would fall prior to the athlete catching it (RT clin). Validity was assessed by determining the correlation between RT clin and RT comp. Reliability was assessed by measuring the intraclass correlation coefficients (ICCs) between the repeated measures of RT clin and RT comp taken 1 year apart. In the first year of study, RT clin and RT comp were positively but weakly correlated (rs = 0.229, P < 0.001). In the second year, there was no significant correlation between RT clin and RT comp (rs = 0.084, P = 0.084). Both RT clin [ICC = 0.608; 95% confidence interval (CI), 0.434-0.728] and RT comp (ICC = 0.691; 95% CI, 0.554-0.786) had marginal reliability. In a population of high school athletes, RT clin had poor validity when compared with RT comp as a standard. Both RT clin and RT comp had marginal test-retest reliability. Before considering the clinical use of RT clin in the assessment of sport-related concussions sustained by high school athletes, the factors affecting reliability and validity should be investigated further. Reaction time impairment commonly results from concussion and is among the most clinically important measures of the condition. The device evaluated in this study has previously been investigated as a reaction time measure in college athletes. This study investigates the clinical generalizability of the device in a younger population. A video abstract showing how the RT clin device is used in practice is available as Supplemental Digital Content 1, http://links.lww.com/JSM/A43.

Modelling nifedipine photodegradation, photostability and actinometric properties.

PubMed

Maafi, Wassila; Maafi, Mounir

2013-11-01

The photodegradation of drugs obeying unimolecular mechanisms such as that of nifedipine (NIF) were usually characterised in the literature by zero-, first- and second-order kinetics. This approach has been met with varying success. This paper addresses this issue and proposes a novel approach for unimolecular photodegradation kinetics. The photodegradation of the cardiovascular drug nifedipine is investigated within this framework. Experimental kinetic data of nifedipine photodegradation were obtained by continuous monochromatic irradiation and DAD analysis. Fourth-order Runge-Kutta calculated kinetic data served for the validation of the new semi-empirical integrated rate-law model proposed in this study. A new model equation has been developed and proposed which faithfully describes the kinetic behaviour of NIF in solution for non-isosbestic irradiations at wavelengths where both NIF and its photoproduct absorb. NIF absolute quantum yield values were determined and found to increase with irradiation wavelength according to a defined sigmoid relationship. The effects of increasing NIF or excipients' concentrations on NIF kinetics were successfully modelled and found to improve NIF photostability. The potential of NIF for actinometry has been explored and evaluated. A new reaction order (the so-called Φ-order) has been identified and specifically proposed for unimolecular photodegradation reactions. The semi-empirical and integrated rate-law models facilitated reliable kinetic studies of NIF photodegradation as an example of AB(1Φ) unimolecular reactions. It allowed filling a gap in kinetic studies of drugs since, thus far, thermal first-order or a combination of first- and zero- order kinetic equations were generally applied for drug photoreactions in the literature. Also, a new reaction order, the "Φ-order", has been evidenced and proposed as a specific alternative for photodegradation kinetics. Copyright © 2013 Elsevier B.V. All rights reserved.

Simulation studies in biochemical signaling and enzyme reactions

NASA Astrophysics Data System (ADS)

Nelatury, Sudarshan R.; Vagula, Mary C.

2014-06-01

Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

A 3D numerical study of LO2/GH2 supercritical combustion in the ONERA-Mascotte Test-rig configuration

NASA Astrophysics Data System (ADS)

Benmansour, Abdelkrim; Liazid, Abdelkrim; Logerais, Pierre-Olivier; Durastanti, Jean-Félix

2016-02-01

Cryogenic propellants LOx/H2 are used at very high pressure in rocket engine combustion. The description of the combustion process in such application is very complex due essentially to the supercritical regime. Ideal gas law becomes invalid. In order to try to capture the average characteristics of this combustion process, numerical computations are performed using a model based on a one-phase multi-component approach. Such work requires fluid properties and a correct definition of the mixture behavior generally described by cubic equations of state with appropriated thermodynamic relations validated against the NIST data. In this study we consider an alternative way to get the effect of real gas by testing the volume-weighted-mixing-law with association of the component transport properties using directly the NIST library data fitting including the supercritical regime range. The numerical simulations are carried out using 3D RANS approach associated with two tested turbulence models, the standard k-Epsilon model and the realizable k-Epsilon one. The combustion model is also associated with two chemical reaction mechanisms. The first one is a one-step generic chemical reaction and the second one is a two-step chemical reaction. The obtained results like temperature profiles, recirculation zones, visible flame lengths and distributions of OH species are discussed.

Numerical Modeling of Suspension HVOF Spray

NASA Astrophysics Data System (ADS)

Jadidi, M.; Moghtadernejad, S.; Dolatabadi, A.

2016-02-01

A three-dimensional two-way coupled Eulerian-Lagrangian scheme is used to simulate suspension high-velocity oxy-fuel spraying process. The mass, momentum, energy, and species equations are solved together with the realizable k-ɛ turbulence model to simulate the gas phase. Suspension is assumed to be a mixture of solid particles [mullite powder (3Al2O3·2SiO2)], ethanol, and ethylene glycol. The process involves premixed combustion of oxygen-propylene, and non-premixed combustion of oxygen-ethanol and oxygen-ethylene glycol. One-step global reaction is used for each mentioned reaction together with eddy dissipation model to compute the reaction rate. To simulate the droplet breakup, Taylor Analogy Breakup model is applied. After the completion of droplet breakup, and solvent evaporation/combustion, the solid suspended particles are tracked through the domain to determine the characteristics of the coating particles. Numerical simulations are validated against the experimental results in the literature for the same operating conditions. Seven or possibly eight shock diamonds are captured outside the nozzle. In addition, a good agreement between the predicted particle temperature, velocity, and diameter, and the experiment is obtained. It is shown that as the standoff distance increases, the particle temperature and velocity reduce. Furthermore, a correlation is proposed to determine the spray cross-sectional diameter and estimate the particle trajectories as a function of standoff distance.

Modeling Non-Steady Isotopologue and Isotopomer Speciation and Fractionation during Denitrification in Soils

NASA Astrophysics Data System (ADS)

Maggi, F.; Riley, W. J.

2009-12-01

The composition and location of 15N atoms on N2O isotopomers and isotopologues during isotope speciation has been used to characterize soil biological N cycling and N2O surface emissions. Although there exist few experimental observations, no attempt has been made to model N2O isotopomer speciation. The mathematical treatment of biological kinetic reactions in isotopic applications normally makes use of first-order and quasi steady-state complexation assumptions without taking into account changes in enzyme concentration, reaction stoichiometry, and isotopologue and isotopomer speciation. When multiatomic isotopically-labeled reactants are used in a multi-molecurar reaction, these assumptions may fail since they always lead to a constant fractionation factor and cannot describe speciation of isotopologues and isotopomers. We have developed a mathematical framework that is capable of describing isotopologue and isotopmer speciation and fractionation under the assumption of non-steady complexation during biological kinetic reactions that overcome the limitations mentioned above. This framework was applied to a case study of non-steady (variable and inverse) isotopic effects observed during N2O production and consumption in soils. Our mathematical treatment has led to generalized kinetic equations which replicate experimental observations with high accuracy and help interpret non-steady isotopic effects and isotopologue and isotopomer speciation. The kinetic equations introduced and applied here have general validity in describing isotopic effects in any biochemical reactions by considering: changing enzyme concentrations, mass and isotope conservation, and reaction stoichiometry. The equations also describe speciation of any isotopologue and isotopomer product from any isotopologue and isotopmer reactant.

Statistical Significance of the Maximum Hardness Principle Applied to Some Selected Chemical Reactions.

PubMed

Saha, Ranajit; Pan, Sudip; Chattaraj, Pratim K

2016-11-05

The validity of the maximum hardness principle (MHP) is tested in the cases of 50 chemical reactions, most of which are organic in nature and exhibit anomeric effect. To explore the effect of the level of theory on the validity of MHP in an exothermic reaction, B3LYP/6-311++G(2df,3pd) and LC-BLYP/6-311++G(2df,3pd) (def2-QZVP for iodine and mercury) levels are employed. Different approximations like the geometric mean of hardness and combined hardness are considered in case there are multiple reactants and/or products. It is observed that, based on the geometric mean of hardness, while 82% of the studied reactions obey the MHP at the B3LYP level, 84% of the reactions follow this rule at the LC-BLYP level. Most of the reactions possess the hardest species on the product side. A 50% null hypothesis is rejected at a 1% level of significance.

Analysis of dose rates received around the storage pool for irradiated control rods in a BWR nuclear power plant.

PubMed

Ródenas, J; Abarca, A; Gallardo, S

2011-08-01

BWR control rods are activated by neutron reactions in the reactor. The dose produced by this activity can affect workers in the area surrounding the storage pool, where activated rods are stored. Monte Carlo (MC) models for neutron activation and dose assessment around the storage pool have been developed and validated. In this work, the MC models are applied to verify the expected reduction of dose when the irradiated control rod is hanged in an inverted position into the pool. 2010 Elsevier Ltd. All rights reserved.

Visible-Light Actinometry and Intermittent Illumination as Convenient Tools to Study Ru(bpy)3Cl2 Mediated Photoredox Transformations

PubMed Central

Pitre, Spencer P.; McTiernan, Christopher D.; Vine, Wyatt; DiPucchio, Rebecca; Grenier, Michel; Scaiano, Juan C.

2015-01-01

Photoredox catalysis provides many green opportunities for radical-mediated synthetic transformations. However, the determination of the underlying mechanisms has been challenging due to lack of quantitative methods that can be easily implemented in synthetic labs, where this research tends to be centered. We report here on the development, characterization and calibration of a novel actinometer based on the photocatalyst tris(2,2′-bipyridyl)ruthenium(II) chloride (Ru(bpy)3Cl2). By using the same molecule as the photocatalyst and the actinometer, we eliminate problems associated with matching sample spectral distribution, lamp-sample spectral overlap and other problems intrinsic to doing quantitative photochemistry in a laboratory that has little expertise in this area. In order to validate our actinometer system in determining the quantum yield of a Ru(bpy)3Cl2 photosensitized reaction, we test the Ru(bpy)3Cl2 catalyzed oxidation of benzhydrol to benzophenone as a model chain reaction. We also revive the rotating sector method by updating the technique for modern LED technologies and demonstrate how intermittent illumination on the timescale of milliseconds to seconds can help probe a chain reaction, using the benzhydrol to benzophenone oxidation to validate the technique. We envision these methods to have great implications in the field of photoredox catalysis, providing researchers with valuable research tools. PMID:26578341

Mental State Assessment and Validation Using Personalized Physiological Biometrics

PubMed Central

Patel, Aashish N.; Howard, Michael D.; Roach, Shane M.; Jones, Aaron P.; Bryant, Natalie B.; Robinson, Charles S. H.; Clark, Vincent P.; Pilly, Praveen K.

2018-01-01

Mental state monitoring is a critical component of current and future human-machine interfaces, including semi-autonomous driving and flying, air traffic control, decision aids, training systems, and will soon be integrated into ubiquitous products like cell phones and laptops. Current mental state assessment approaches supply quantitative measures, but their only frame of reference is generic population-level ranges. What is needed are physiological biometrics that are validated in the context of task performance of individuals. Using curated intake experiments, we are able to generate personalized models of three key biometrics as useful indicators of mental state; namely, mental fatigue, stress, and attention. We demonstrate improvements to existing approaches through the introduction of new features. Furthermore, addressing the current limitations in assessing the efficacy of biometrics for individual subjects, we propose and employ a multi-level validation scheme for the biometric models by means of k-fold cross-validation for discrete classification and regression testing for continuous prediction. The paper not only provides a unified pipeline for extracting a comprehensive mental state evaluation from a parsimonious set of sensors (only EEG and ECG), but also demonstrates the use of validation techniques in the absence of empirical data. Furthermore, as an example of the application of these models to novel situations, we evaluate the significance of correlations of personalized biometrics to the dynamic fluctuations of accuracy and reaction time on an unrelated threat detection task using a permutation test. Our results provide a path toward integrating biometrics into augmented human-machine interfaces in a judicious way that can help to maximize task performance.

Mental State Assessment and Validation Using Personalized Physiological Biometrics.

PubMed

Patel, Aashish N; Howard, Michael D; Roach, Shane M; Jones, Aaron P; Bryant, Natalie B; Robinson, Charles S H; Clark, Vincent P; Pilly, Praveen K

2018-01-01

Mental state monitoring is a critical component of current and future human-machine interfaces, including semi-autonomous driving and flying, air traffic control, decision aids, training systems, and will soon be integrated into ubiquitous products like cell phones and laptops. Current mental state assessment approaches supply quantitative measures, but their only frame of reference is generic population-level ranges. What is needed are physiological biometrics that are validated in the context of task performance of individuals. Using curated intake experiments, we are able to generate personalized models of three key biometrics as useful indicators of mental state; namely, mental fatigue, stress, and attention. We demonstrate improvements to existing approaches through the introduction of new features. Furthermore, addressing the current limitations in assessing the efficacy of biometrics for individual subjects, we propose and employ a multi-level validation scheme for the biometric models by means of k -fold cross-validation for discrete classification and regression testing for continuous prediction. The paper not only provides a unified pipeline for extracting a comprehensive mental state evaluation from a parsimonious set of sensors (only EEG and ECG), but also demonstrates the use of validation techniques in the absence of empirical data. Furthermore, as an example of the application of these models to novel situations, we evaluate the significance of correlations of personalized biometrics to the dynamic fluctuations of accuracy and reaction time on an unrelated threat detection task using a permutation test. Our results provide a path toward integrating biometrics into augmented human-machine interfaces in a judicious way that can help to maximize task performance.

Validated spectrofluorimetric method for the determination of carbamazepine in pharmaceutical dosage forms after reaction with 4-chloro-7--nitrobenzo-2-oxa-1,3-diazole (NBD-Cl).

PubMed

Walash, Mohammed I; El-Enany, Nahed; Askar, Hanany

2015-11-01

A sensitive and simple spectrofluorimetric method has been developed and validated for the determination of the anti-epileptic drug carbamazepine (CBZ) in its dosage forms. The method was based on a nucleophilic substitution reaction of CBZ with 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) in borate buffer (pH 9) to form a highly fluorescent derivative that was measured at 530 nm after excitation at 460 nm. Factors affecting the formation of the reaction product were studied and optimized, and the reaction mechanism was postulated. The fluorescence-concentration plot is rectilinear over the range of 0.6-8 µg/mL with limit of detection of 0.06 µg/mL and limit of quantitation of 0.19 µg/mL. The method was applied to the analysis of commercial tablets and the results were in good agreement with those obtained using the reference method. Validation of the analytical procedures was evaluated according to ICH guidelines. Copyright © 2015 John Wiley & Sons, Ltd.

Thermal behavior in the cracking reaction zone of scramjet cooling channels at different channel aspect ratios

NASA Astrophysics Data System (ADS)

Zhang, Silong; Feng, Yu; Jiang, Yuguang; Qin, Jiang; Bao, Wen; Han, Jiecai; Haidn, Oskar J.

2016-10-01

To study the thermal behavior in the cracking reaction zone of regeneratively cooled scramjet cooling channels at different aspect ratios, 3-D model of fuel flow in terms of the fuel's real properties and cracking reaction is built and validated through experiments. The whole cooling channel is divided into non-cracking and cracking reaction zones. Only the cracking reaction zone is studied in this article. The simulation results indicate that the fuel conversion presents a similar distribution with temperature because the fuel conversion in scramjet cooling channels is co-decided by the temperature and velocity but the temperature plays the dominate role. For the cases given in this paper, increasing the channel aspect ratio will increase the pressure drop and it is not beneficial for reducing the wall temperature because of the much severer thermal stratification, larger conversion non-uniformity, the corresponding M-shape velocity profile which will cause local heat transfer deterioration and the decreased chemical heat absorption. And the decreased chemical heat absorption caused by stronger temperature and conversion non-uniformities is bad for the utilization of chemical heat sink, chemical recuperation process and the ignition performance.

In Silico Knockout Screening of Plasmodium falciparum Reactions and Prediction of Novel Essential Reactions by Analysing the Metabolic Network

PubMed Central

Isewon, Itunuoluwa; Aromolaran, Olufemi; Oladipupo, Olufunke

2018-01-01

Malaria is an infectious disease that affects close to half a million individuals every year and Plasmodium falciparum is a major cause of malaria. The treatment of this disease could be done effectively if the essential enzymes of this parasite are specifically targeted. Nevertheless, the development of the parasite in resisting existing drugs now makes discovering new drugs a core responsibility. In this study, a novel computational model that makes the prediction of new and validated antimalarial drug target cheaper, easier, and faster has been developed. We have identified new essential reactions as potential targets for drugs in the metabolic network of the parasite. Among the top seven (7) predicted essential reactions, four (4) have been previously identified in earlier studies with biological evidence and one (1) has been with computational evidence. The results from our study were compared with an extensive list of seventy-seven (77) essential reactions with biological evidence from a previous study. We present a list of thirty-one (31) potential candidates for drug targets in Plasmodium falciparum which includes twenty-four (24) new potential candidates for drug targets. PMID:29789805

Validation of absolute axial neutron flux distribution calculations with MCNP with 197Au(n,γ)198Au reaction rate distribution measurements at the JSI TRIGA Mark II reactor.

PubMed

Radulović, Vladimir; Štancar, Žiga; Snoj, Luka; Trkov, Andrej

2014-02-01

The calculation of axial neutron flux distributions with the MCNP code at the JSI TRIGA Mark II reactor has been validated with experimental measurements of the (197)Au(n,γ)(198)Au reaction rate. The calculated absolute reaction rate values, scaled according to the reactor power and corrected for the flux redistribution effect, are in good agreement with the experimental results. The effect of different cross-section libraries on the calculations has been investigated and shown to be minor. Copyright © 2013 Elsevier Ltd. All rights reserved.

Characterization of Aerodynamic Interactions with the Mars Science Laboratory Reaction Control System Using Computation and Experiment

NASA Technical Reports Server (NTRS)

Schoenenberger, Mark; VanNorman, John; Rhode, Matthew; Paulson, John

2013-01-01

On August 5 , 2012, the Mars Science Laboratory (MSL) entry capsule successfully entered Mars' atmosphere and landed the Curiosity rover in Gale Crater. The capsule used a reaction control system (RCS) consisting of four pairs of hydrazine thrusters to fly a guided entry. The RCS provided bank control to fly along a flight path commanded by an onboard computer and also damped unwanted rates due to atmospheric disturbances and any dynamic instabilities of the capsule. A preliminary assessment of the MSL's flight data from entry showed that the capsule flew much as predicted. This paper will describe how the MSL aerodynamics team used engineering analyses, computational codes and wind tunnel testing in concert to develop the RCS system and certify it for flight. Over the course of MSL's development, the RCS configuration underwent a number of design iterations to accommodate mechanical constraints, aeroheating concerns and excessive aero/RCS interactions. A brief overview of the MSL RCS configuration design evolution is provided. Then, a brief description is presented of how the computational predictions of RCS jet interactions were validated. The primary work to certify that the RCS interactions were acceptable for flight was centered on validating computational predictions at hypersonic speeds. A comparison of computational fluid dynamics (CFD) predictions to wind tunnel force and moment data gathered in the NASA Langley 31-Inch Mach 10 Tunnel was the lynch pin to validating the CFD codes used to predict aero/RCS interactions. Using the CFD predictions and experimental data, an interaction model was developed for Monte Carlo analyses using 6-degree-of-freedom trajectory simulation. The interaction model used in the flight simulation is presented.

Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations

PubMed Central

Baum, Katharina; Kofahl, Bente; Steuer, Ralf; Wolf, Jana

2016-01-01

Oscillations occur in a wide variety of cellular processes, for example in calcium and p53 signaling responses, in metabolic pathways or within gene-regulatory networks, e.g. the circadian system. Since it is of central importance to understand the influence of perturbations on the dynamics of these systems a number of experimental and theoretical studies have examined their robustness. The period of circadian oscillations has been found to be very robust and to provide reliable timing. For intracellular calcium oscillations the period has been shown to be very sensitive and to allow for frequency-encoded signaling. We here apply a comprehensive computational approach to study the robustness of period and amplitude of oscillatory systems. We employ different prototype oscillator models and a large number of parameter sets obtained by random sampling. This framework is used to examine the effect of three design principles on the sensitivities towards perturbations of the kinetic parameters. We find that a prototype oscillator with negative feedback has lower period sensitivities than a prototype oscillator relying on positive feedback, but on average higher amplitude sensitivities. For both oscillator types, the use of Michaelis-Menten instead of mass action kinetics in all degradation and conversion reactions leads to an increase in period as well as amplitude sensitivities. We observe moderate changes in sensitivities if replacing mass conversion reactions by purely regulatory reactions. These insights are validated for a set of established models of various cellular rhythms. Overall, our work highlights the importance of reaction kinetics and feedback type for the variability of period and amplitude and therefore for the establishment of predictive models. PMID:28027301

Quantitative DFT modeling of product concentration in organometallic reactions: Cu-mediated pentafluoroethylation of benzoic acid chlorides as a case study.

PubMed

Jover, Jesús

2017-11-08

DFT calculations are widely used for computing properties, reaction mechanisms and energy profiles in organometallic reactions. A qualitative agreement between the experimental and the calculated results seems to usually be enough to validate a computational methodology but recent advances in computation indicate that a nearly quantitative agreement should be possible if an appropriate DFT study is carried out. Final percent product concentrations, often reported as yields, are by far the most commonly reported properties in experimental metal-mediated synthesis studies but reported DFT studies have not focused on predicting absolute product amounts. The recently reported stoichiometric pentafluoroethylation of benzoic acid chlorides (R-C 6 H 4 COCl) with [(phen)Cu(PPh 3 )C 2 F 5 ] (phen = 1,10-phenanthroline, PPh 3 = triphenylphosphine) has been used as a case study to check whether the experimental product concentrations can be reproduced by any of the most popular DFT approaches with high enough accuracy. To this end, the Gibbs energy profile for the pentafluoroethylation of benzoic acid chloride has been computed using 14 different DFT methods. These computed Gibbs energy profiles have been employed to build kinetic models predicting the final product concentration in solution. The best results are obtained with the D3-dispersion corrected B3LYP functional, which has been successfully used afterwards to model the reaction outcomes of other simple (R = o-Me, p-Me, p-Cl, p-F, etc.) benzoic acid chlorides. The product concentrations of more complex reaction networks in which more than one position of the substrate may be activated by the copper catalyst (R = o-Br and p-I) are also predicted appropriately.

Comparison between PVI2D and Abreu–Johnson’s Model for Petroleum Vapor Intrusion Assessment

PubMed Central

Yao, Yijun; Wang, Yue; Verginelli, Iason; Suuberg, Eric M.; Ye, Jianfeng

2018-01-01

Recently, we have developed a two-dimensional analytical petroleum vapor intrusion model, PVI2D (petroleum vapor intrusion, two-dimensional), which can help users to easily visualize soil gas concentration profiles and indoor concentrations as a function of site-specific conditions such as source strength and depth, reaction rate constant, soil characteristics, and building features. In this study, we made a full comparison of the results returned by PVI2D and those obtained using Abreu and Johnson’s three-dimensional numerical model (AJM). These comparisons, examined as a function of the source strength, source depth, and reaction rate constant, show that PVI2D can provide similar soil gas concentration profiles and source-to-indoor air attenuation factors (within one order of magnitude difference) as those by the AJM. The differences between the two models can be ascribed to some simplifying assumptions used in PVI2D and to some numerical limitations of the AJM in simulating strictly piecewise aerobic biodegradation and no-flux boundary conditions. Overall, the obtained results show that for cases involving homogenous source and soil, PVI2D can represent a valid alternative to more rigorous three-dimensional numerical models. PMID:29398981

Information Foraging Theory in Software Maintenance

DTIC Science & Technology

2012-09-30

classified information, stamp classification level on the top and bottom of this page. 17. LIMITATION OF ABSTRACT. This block must be completed to assign a ...time: for example a time series plot of model reaction times to many (simulated) stimuli presented to it in a run • “ Statistical ” abstractions summed...shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number

Assessment of the 3He pressure inside the CABRI transient rods - Development of a surrogate model based on measurements and complementary CFD calculations

NASA Astrophysics Data System (ADS)

Clamens, Olivier; Lecerf, Johann; Hudelot, Jean-Pascal; Duc, Bertrand; Cadiou, Thierry; Blaise, Patrick; Biard, Bruno

2018-01-01

CABRI is an experimental pulse reactor, funded by the French Nuclear Safety and Radioprotection Institute (IRSN) and operated by CEA at the Cadarache research center. It is designed to study fuel behavior under RIA conditions. In order to produce the power transients, reactivity is injected by depressurization of a neutron absorber (3He) situated in transient rods inside the reactor core. The shapes of power transients depend on the total amount of reactivity injected and on the injection speed. The injected reactivity can be calculated by conversion of the 3He gas density into units of reactivity. So, it is of upmost importance to properly master gas density evolution in transient rods during a power transient. The 3He depressurization was studied by CFD calculations and completed with measurements using pressure transducers. The CFD calculations show that the density evolution is slower than the pressure drop. Surrogate models were built based on CFD calculations and validated against preliminary tests in the CABRI transient system. Studies also show that it is harder to predict the depressurization during the power transients because of neutron/3He capture reactions that induce a gas heating. This phenomenon can be studied by a multiphysics approach based on reaction rate calculation thanks to Monte Carlo code and study the resulting heating effect with the validated CFD simulation.

Extraterrestrial cold chemistry. A need for a specific database.

NASA Astrophysics Data System (ADS)

Pernot, P.; Carrasco, N.; Dobrijevic, M.; Hébrard, E.; Plessis, S.; Wakelam, V.

2008-09-01

The major resource databases for building chemical models for photochemistry in cold environments are mainly based on those designed for Earth atmospheric chemistry or combustion, in which reaction rates are reported for temperatures typically above 300 K [1,2]. Kinetic data measured at low temperatures are very sparse; for instance, in stateoftheart photochemical models of Titan atmosphere, less than 10% of the rates have been measured in the relevant temperature range (100200 K) [35]. In consequence, photochemical models rely mostly on lowT extrapolations by Arrheniustype laws. There is more and more evidence that this is often inappropriate [6], and low T extrapolations are hindered by very high uncertainty [3] (Fig.1). The predictions of models based on those extrapolations are expected to be very inaccurate [4,7]. We argue that there is not much sense in increasing the complexity of the present models as long as this predictivity issue has not been resolved. Fig. 1 Uncertainty of low temperature extrapolation for the N(2D) +C2H4 reaction rate, from measurements in the range 225 292 K [10], assuming an Arrhenius law (blue line). The sample of rate laws is generated by Monte Carlo uncertainty propagation after a Bayesian Data reAnalysis (BDA) of experimental data. A dialogue between modellers and experimentalists is necessary to improve this situation. Considering the heavy costs of low temperature reaction kinetics experiments, the identification of key reactions has to be based on an optimal strategy to improve the predictivity of photochemical models. This can be achieved by global sensitivity analysis, as illustrated on Titan atmospheric chemistry [8]. The main difficulty of this scheme is that it requires a lot of inputs, mainly the evaluation of uncertainty for extrapolated reaction rates. Although a large part has already been achieved by Hébrard et al. [3], extension and validation requires a group of experts. A new generation of collaborative kinetic database is needed to implement efficiently this scheme. The KIDA project [9], initiated by V. Wakelam for astrochemistry, has been joined by planetologists with similar prospects. EuroPlaNet will contribute to this effort through the organization of comities of experts on specific processes in atmospheric photochemistry.

Computer Aided Battery Engineering Consortium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pesaran, Ahmad

A multi-national lab collaborative team was assembled that includes experts from academia and industry to enhance recently developed Computer-Aided Battery Engineering for Electric Drive Vehicles (CAEBAT)-II battery crush modeling tools and to develop microstructure models for electrode design - both computationally efficient. Task 1. The new Multi-Scale Multi-Domain model framework (GH-MSMD) provides 100x to 1,000x computation speed-up in battery electrochemical/thermal simulation while retaining modularity of particles and electrode-, cell-, and pack-level domains. The increased speed enables direct use of the full model in parameter identification. Task 2. Mechanical-electrochemical-thermal (MECT) models for mechanical abuse simulation were simultaneously coupled, enabling simultaneous modelingmore » of electrochemical reactions during the short circuit, when necessary. The interactions between mechanical failure and battery cell performance were studied, and the flexibility of the model for various batteries structures and loading conditions was improved. Model validation is ongoing to compare with test data from Sandia National Laboratories. The ABDT tool was established in ANSYS. Task 3. Microstructural modeling was conducted to enhance next-generation electrode designs. This 3- year project will validate models for a variety of electrodes, complementing Advanced Battery Research programs. Prototype tools have been developed for electrochemical simulation and geometric reconstruction.« less

Probabilistic, sediment-geochemical parameterisation of the groundwater compartment of the Netherlands for spatially distributed, reactive transport modelling

NASA Astrophysics Data System (ADS)

Janssen, Gijs; Gunnink, Jan; van Vliet, Marielle; Goldberg, Tanya; Griffioen, Jasper

2017-04-01

Pollution of groundwater aquifers with contaminants as nitrate is a common problem. Reactive transport models are useful to predict the fate of such contaminants and to characterise the efficiency of mitigating or preventive measures. Parameterisation of a groundwater transport model on reaction capacity is a necessary step during building the model. Two Dutch, national programs are combined to establish a methodology for building a probabilistic model on reaction capacity of the groundwater compartment at the national scale: the Geological Survey program and the NHI Netherlands Hydrological Instrument program. Reaction capacity is considered as a series of geochemical characteristics that control acid/base condition, redox condition and sorption capacity. Five primary reaction capacity variables are characterised: 1. pyrite, 2. non-pyrite, reactive iron (oxides, siderite and glauconite), 3. clay fraction, 4. organic matter and 5. Ca-carbonate. Important reaction capacity variables that are determined by more than one solid compound are also deduced: 1. potential reduction capacity (PRC) by pyrite and organic matter, 2. cation-exchange capacity (CEC) by organic matter and clay content, 3. carbonate buffering upon pyrite oxidation (CPBO) by carbonate and pyrite. Statistical properties of these variables are established based on c. 16,000 sediment geochemical analyses. The first tens of meters are characterised based on 25 regions using combinations of lithological class and geological formation as strata. Because of both less data and more geochemical uniformity, the deeper subsurface is characterised in a similar way based on 3 regions. The statistical data is used as input in an algoritm that probabilistically calculates the reaction capacity per grid cell. First, the cumulative frequency distribution (cfd) functions are calculated from the statistical data for the geochemical strata. Second, all voxel cells are classified into the geochemical strata. Third, the cfd functions are used to put random reaction capacity variables into the hydrological voxel model. Here, the distribution can be conditioned on two variables. Two important variables are clay content and depth. The first is valid because more dense data is available for clay content than for geochemical variables as pyrite and probabilistic, lithological models are also built at TNO Geological Survey. The second is important to account for locally different depths at which the redox cline between NO3-rich and Fe(II)-rich groundwater occurs within the first tens of meters of the subsurface. An extensive data-set of groundwater quality analyses is used to derive criteria for depth variability of the redox cline. The result is a unique algoritm in order to obtain heterogeneous geochemical reaction capacity models of the entire groundwater compartment of the Netherlands.

Numerical model of spray combustion in a single cylinder diesel engine

NASA Astrophysics Data System (ADS)

Acampora, Luigi; Sequino, Luigi; Nigro, Giancarlo; Continillo, Gaetano; Vaglieco, Bianca Maria

2017-11-01

A numerical model is developed for predicting the pressure cycle from Intake Valve Closing (IVC) to the Exhaust Valve Opening (EVO) events. The model is based on a modified one-dimensional (1D) Musculus and Kattke spray model, coupled with a zero-dimensional (0D) non-adiabatic transient Fed-Batch reactor model. The 1D spray model provides an estimate of the fuel evaporation rate during the injection phenomenon, as a function of time. The 0D Fed-Batch reactor model describes combustion. The main goal of adopting a 0D (perfectly stirred) model is to use highly detailed reaction mechanisms for Diesel fuel combustion in air, while keeping the computational cost as low as possible. The proposed model is validated by comparing its predictions with experimental data of pressure obtained from an optical single cylinder Diesel engine.

Designing and encoding models for synthetic biology.

PubMed

Endler, Lukas; Rodriguez, Nicolas; Juty, Nick; Chelliah, Vijayalakshmi; Laibe, Camille; Li, Chen; Le Novère, Nicolas

2009-08-06

A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology 'loop'.

Numerical algebraic geometry for model selection and its application to the life sciences

PubMed Central

Gross, Elizabeth; Davis, Brent; Ho, Kenneth L.; Bates, Daniel J.

2016-01-01

Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation and model selection. These are all optimization problems, well known to be challenging due to nonlinearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data are available. Here, we consider polynomial models (e.g. mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry. Specifically, we use probability-one polynomial homotopy continuation methods to compute all critical points of the objective function, then filter to recover the global optima. Our approach exploits the geometrical structures relating models and data, and we demonstrate its utility on examples from cell signalling, synthetic biology and epidemiology. PMID:27733697

Validation of a multi-phase plant-wide model for the description of the aeration process in a WWTP.

PubMed

Lizarralde, I; Fernández-Arévalo, T; Beltrán, S; Ayesa, E; Grau, P

2018-02-01

This paper introduces a new mathematical model built under the PC-PWM methodology to describe the aeration process in a full-scale WWTP. This methodology enables a systematic and rigorous incorporation of chemical and physico-chemical transformations into biochemical process models, particularly for the description of liquid-gas transfer to describe the aeration process. The mathematical model constructed is able to reproduce biological COD and nitrogen removal, liquid-gas transfer and chemical reactions. The capability of the model to describe the liquid-gas mass transfer has been tested by comparing simulated and experimental results in a full-scale WWTP. Finally, an exploration by simulation has been undertaken to show the potential of the mathematical model. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamics of a Chlorophyll Dimer in Collective and Local Thermal Environments

DOE PAGES

Merkli, M.; Berman, Gennady Petrovich; Sayre, Richard Thomas; ...

2016-01-30

Here we present a theoretical analysis of exciton transfer and decoherence effects in a photosynthetic dimer interacting with collective (correlated) and local (uncorrelated) protein-solvent environments. Our approach is based on the framework of the spin-boson model. We derive explicitly the thermal relaxation and decoherence rates of the exciton transfer process, valid for arbitrary temperatures and for arbitrary (in particular, large) interaction constants between the dimer and the environments. We establish a generalization of the Marcus formula, giving reaction rates for dimer levels possibly individually and asymmetrically coupled to environments. We identify rigorously parameter regimes for the validity of the generalizedmore » Marcus formula. The existence of long living quantum coherences at ambient temperatures emerges naturally from our approach.« less

Liquid and Gas Phase Chemistry of Hypergolic Reactions between MMH and NTO or RFNA

NASA Astrophysics Data System (ADS)

Black, Ariel

Hypergolic systems rely on fuel and oxidizer propellant combinations that spontaneously ignite upon contact. Monomethylhydrazine (MMH) fuel and nitrogen tetroxide (NTO) - based oxidizers embody the state of the art for hypergolic propellants, although the health and safety hazards associated with these propellants demand investigation into less-toxic, high performance alternatives. In order to replicate the combustion characteristics of these highly reactive propellants, a detailed understanding of the full reaction process is necessary. Current reaction mechanisms and hypergolic ignition models generally assume that gas-phase chemistry dominates the interaction since the liquid-phase reactions occur on the order of microseconds. However, condensed-phase reactions produce intermediates integral to gas-phase initiation and development. Additional insight into the physical and chemical processes that dictate this liquid-phase chemistry is therefore essential. Concurrently, further examination of the gas-phase reactions leading to and immediately following ignition is also needed. A method devoted to the determination of the liquid phase hypergolic reaction mechanism and kinematic rate parameters for MMH-NTO and MMH-red fuming nitric acid (RFNA) is presented in this study. MMH-RFNA reaction chemistry is better understood and documented in literature than MMH-NTO and is examined for comparison and validation. Drop on pool experiments at a range of temperatures were initially undertaken using MMH and RFNA and then modified to accommodate the high vapor pressure of NTO. Using a temperature and atmosphere controlled droplet contact chamber, the liquid phases of MMH-RFNA and MMH-NTO were studied by capturing impacts at frame rates from 100,000 to 500,000 fps. This footage allowed for the identification of time delays between droplet contact and initial gas formation, enabling calibration of the Arrhenius pre-exponential factors and activation energies for a global, one-step liquid phase chemical reaction model. These defining constants have never before been experimentally determined for MMH-NTO and can be employed to improve the accuracy of CFD combustion simulations. Induction delay times for MMH-RFNA ranged from 30 to 100 microseconds, agreeing with previously reported data, while MMH-NTO delays varied from 10 to 100 microseconds. Advanced ultraviolet and visible (UV-Vis) spectroscopic techniques were applied to conventional drop test analysis in order to study the emitting species in MMH-NTO and MMH-RFNA combustion reactions. A streak camera coupled with a spectrometer provided temporally resolved spectra for species emitting wavelengths from 250 to 950 nm within a one millimeter diameter point of interest above the reaction. The spectra were compared to known MMH-RFNA gas-phase reaction mechanisms and spectroscopic data reported in literature in an attempt to partially validate the proposed full and reduced MMH-RFNA reaction mechanisms and derive a connection to elementary reactions of MMH-NTO. MMH-NTO consistently produced brighter flames than MMH-RFNA and as such generally generated higher intensity signals for a given spectrometer setting. Both propellant combinations revealed conclusive evidence of OH and NH radicals and probable evidence of CN and/or CH radicals. In most tests OH* yielded the highest intensity signals with both RFNA and NTO. MMH-NTO revealed greater NH* intensity than MMH-RFNA. Additionally, species appeared later but peaked sooner relative to ignition for MMH-RFNA than for MMH-NTO. Efforts to draw correlations between these experimental results and existing reaction mechanisms proved to be challenging and are ongoing. A dominant, high intensity signal characteristic of sodium was an unexpected, but apparently not uncommon, observation, with varying opinions as to its origin.

On the use temperature parameterized rate coefficients in the estimation of non-equilibrium reaction rates

NASA Astrophysics Data System (ADS)

Shizgal, Bernie D.; Chikhaoui, Aziz

2006-06-01

The present paper considers a detailed analysis of the nonequilibrium effects for a model reactive system with the Chapman-Eskog (CE) solution of the Boltzmann equation as well as an explicit time dependent solution. The elastic cross sections employed are a hard sphere cross section and the Maxwell molecule cross section. Reactive cross sections which model reactions with and without activation energy are used. A detailed comparison is carried out with these solutions of the Boltzmann equation and the approximation introduced by Cukrowski and coworkers [J. Chem. Phys. 97 (1992) 9086; Chem. Phys. 89 (1992) 159; Physica A 188 (1992) 344; Chem. Phys. Lett. A 297 (1998) 402; Physica A 275 (2000) 134; Chem. Phys. Lett. 341 (2001) 585; Acta Phys. Polonica B 334 (2003) 3607.] based on the temperature of the reactive particles. We show that the Cukrowski approximation has limited applicability for the large class of reactive systems studied in this paper. The explicit time dependent solutions of the Boltzmann equation demonstrate that the CE approach is valid only for very slow reactions for which the corrections to the equilibrium rate coefficient are very small.

Perspective: Size selected clusters for catalysis and electrochemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition,more » cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.« less

Perspective: Size selected clusters for catalysis and electrochemistry

DOE PAGES

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; ...

2018-03-15

We report that size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this Perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition,more » cluster-support interactions and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modelling based on density functional theory sampling of local minima and energy barriers or ab initio Molecular Dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Lastly, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.« less

Perspective: Size selected clusters for catalysis and electrochemistry

NASA Astrophysics Data System (ADS)

Halder, Avik; Curtiss, Larry A.; Fortunelli, Alessandro; Vajda, Stefan

2018-03-01

Size-selected clusters containing a handful of atoms may possess noble catalytic properties different from nano-sized or bulk catalysts. Size- and composition-selected clusters can also serve as models of the catalytic active site, where an addition or removal of a single atom can have a dramatic effect on their activity and selectivity. In this perspective, we provide an overview of studies performed under both ultra-high vacuum and realistic reaction conditions aimed at the interrogation, characterization, and understanding of the performance of supported size-selected clusters in heterogeneous and electrochemical reactions, which address the effects of cluster size, cluster composition, cluster-support interactions, and reaction conditions, the key parameters for the understanding and control of catalyst functionality. Computational modeling based on density functional theory sampling of local minima and energy barriers or ab initio molecular dynamics simulations is an integral part of this research by providing fundamental understanding of the catalytic processes at the atomic level, as well as by predicting new materials compositions which can be validated in experiments. Finally, we discuss approaches which aim at the scale up of the production of well-defined clusters for use in real world applications.

A toolbox model of evolution of metabolic pathways on networks of arbitrary topology.

PubMed

Pang, Tin Yau; Maslov, Sergei

2011-05-01

In prokaryotic genomes the number of transcriptional regulators is known to be proportional to the square of the total number of protein-coding genes. A toolbox model of evolution was recently proposed to explain this empirical scaling for metabolic enzymes and their regulators. According to its rules, the metabolic network of an organism evolves by horizontal transfer of pathways from other species. These pathways are part of a larger "universal" network formed by the union of all species-specific networks. It remained to be understood, however, how the topological properties of this universal network influence the scaling law of functional content of genomes in the toolbox model. Here we answer this question by first analyzing the scaling properties of the toolbox model on arbitrary tree-like universal networks. We prove that critical branching topology, in which the average number of upstream neighbors of a node is equal to one, is both necessary and sufficient for quadratic scaling. We further generalize the rules of the model to incorporate reactions with multiple substrates/products as well as branched and cyclic metabolic pathways. To achieve its metabolic tasks, the new model employs evolutionary optimized pathways with minimal number of reactions. Numerical simulations of this realistic model on the universal network of all reactions in the KEGG database produced approximately quadratic scaling between the number of regulated pathways and the size of the metabolic network. To quantify the geometrical structure of individual pathways, we investigated the relationship between their number of reactions, byproducts, intermediate, and feedback metabolites. Our results validate and explain the ubiquitous appearance of the quadratic scaling for a broad spectrum of topologies of underlying universal metabolic networks. They also demonstrate why, in spite of "small-world" topology, real-life metabolic networks are characterized by a broad distribution of pathway lengths and sizes of metabolic regulons in regulatory networks.

A multiphysics microstructure-resolved model for silicon anode lithium-ion batteries

NASA Astrophysics Data System (ADS)

Wang, Miao; Xiao, Xinran; Huang, Xiaosong

2017-04-01

Silicon (Si) is one of the most promising next generation anode materials for lithium-ion batteries (LIBs), but the use of Si in LIBs has been rather limited. The main challenge is its large volume change (up to 300%) during battery cycling. This can lead to the fracture of Si, failure at the interfaces between electrode components, and large dimensional change on the cell level. To optimize the Si electrode/battery design, a model that considers the interactions of different cell components is needed. This paper presents the development of a multiphysics microstructure-resolved model (MRM) for LIB cells with a-Si anode. The model considered the electrochemical reactions, Li transports in electrolyte and electrodes, dimensional changes and stresses, property evolution with the structure, and the coupling relationships. Important model parameters, such as the diffusivity, reaction rate constant, and apparent transfer coefficient, were determined by correlating the simulation results to experiments. The model was validated with experimental results in the literature. The use of this model was demonstrated in a parameter study of Si nanowall|Li cells. The specific and volumetric capacities of the cell as a function of the size, length/size ratio, spacing of the nanostructure, and Li+ concentration in electrolyte were investigated.

Reactant conversion in homogeneous turbulence: Mathematical modeling, computational validations and practical applications

NASA Technical Reports Server (NTRS)

Madnia, C. K.; Frankel, S. H.; Givi, P.

1992-01-01

Closed form analytical expressions are obtained for predicting the limited rate of reactant conversion in a binary reaction of the type F + rO yields (1 + r) Product in unpremixed homogeneous turbulence. These relations are obtained by means of a single point Probability Density Function (PDF) method based on the Amplitude Mapping Closure. It is demonstrated that with this model, the maximum rate of the reactants' decay can be conveniently expressed in terms of definite integrals of the Parabolic Cylinder Functions. For the cases with complete initial segregation, it is shown that the results agree very closely with those predicted by employing a Beta density of the first kind for an appropriately defined Shvab-Zeldovich scalar variable. With this assumption, the final results can also be expressed in terms of closed form analytical expressions which are based on the Incomplete Beta Functions. With both models, the dependence of the results on the stoichiometric coefficient and the equivalence ratio can be expressed in an explicit manner. For a stoichiometric mixture, the analytical results simplify significantly. In the mapping closure, these results are expressed in terms of simple trigonometric functions. For the Beta density model, they are in the form of Gamma Functions. In all the cases considered, the results are shown to agree well with data generated by Direct Numerical Simulations (DNS). Due to the simplicity of these expressions and because of nice mathematical features of the Parabolic Cylinder and the Incomplete Beta Functions, these models are recommended for estimating the limiting rate of reactant conversion in homogeneous reacting flows. These results also provide useful insights in assessing the extent of validity of turbulence closures in the modeling of unpremixed reacting flows. Some discussions are provided on the extension of the model for treating more complicated reacting systems including realistic kinetics schemes and multi-scalar mixing with finite rate chemical reactions in more complex configurations.

TH-C-BRD-04: Beam Modeling and Validation with Triple and Double Gaussian Dose Kernel for Spot Scanning Proton Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirayama, S; Takayanagi, T; Fujii, Y

2014-06-15

Purpose: To present the validity of our beam modeling with double and triple Gaussian dose kernels for spot scanning proton beams in Nagoya Proton Therapy Center. This study investigates the conformance between the measurements and calculation results in absolute dose with two types of beam kernel. Methods: A dose kernel is one of the important input data required for the treatment planning software. The dose kernel is the 3D dose distribution of an infinitesimal pencil beam of protons in water and consists of integral depth doses and lateral distributions. We have adopted double and triple Gaussian model as lateral distributionmore » in order to take account of the large angle scattering due to nuclear reaction by fitting simulated inwater lateral dose profile for needle proton beam at various depths. The fitted parameters were interpolated as a function of depth in water and were stored as a separate look-up table for the each beam energy. The process of beam modeling is based on the method of MDACC [X.R.Zhu 2013]. Results: From the comparison results between the absolute doses calculated by double Gaussian model and those measured at the center of SOBP, the difference is increased up to 3.5% in the high-energy region because the large angle scattering due to nuclear reaction is not sufficiently considered at intermediate depths in the double Gaussian model. In case of employing triple Gaussian dose kernels, the measured absolute dose at the center of SOBP agrees with calculation within ±1% regardless of the SOBP width and maximum range. Conclusion: We have demonstrated the beam modeling results of dose distribution employing double and triple Gaussian dose kernel. Treatment planning system with the triple Gaussian dose kernel has been successfully verified and applied to the patient treatment with a spot scanning technique in Nagoya Proton Therapy Center.« less

Supercomputer modeling of hydrogen combustion in rocket engines

NASA Astrophysics Data System (ADS)

Betelin, V. B.; Nikitin, V. F.; Altukhov, D. I.; Dushin, V. R.; Koo, Jaye

2013-08-01

Hydrogen being an ecological fuel is very attractive now for rocket engines designers. However, peculiarities of hydrogen combustion kinetics, the presence of zones of inverse dependence of reaction rate on pressure, etc. prevents from using hydrogen engines in all stages not being supported by other types of engines, which often brings the ecological gains back to zero from using hydrogen. Computer aided design of new effective and clean hydrogen engines needs mathematical tools for supercomputer modeling of hydrogen-oxygen components mixing and combustion in rocket engines. The paper presents the results of developing verification and validation of mathematical model making it possible to simulate unsteady processes of ignition and combustion in rocket engines.

Validation of MCNP NPP Activation Simulations for Decommissioning Studies by Analysis of NPP Neutron Activation Foil Measurement Campaigns

NASA Astrophysics Data System (ADS)

Volmert, Ben; Pantelias, Manuel; Mutnuru, R. K.; Neukaeter, Erwin; Bitterli, Beat

2016-02-01

In this paper, an overview of the Swiss Nuclear Power Plant (NPP) activation methodology is presented and the work towards its validation by in-situ NPP foil irradiation campaigns is outlined. Nuclear Research and consultancy Group (NRG) in The Netherlands has been given the task of performing the corresponding neutron metrology. For this purpose, small Aluminium boxes containing a set of circular-shaped neutron activation foils have been prepared. After being irradiated for one complete reactor cycle, the sets have been successfully retrieved, followed by gamma-spectrometric measurements of the individual foils at NRG. Along with the individual activities of the foils, the reaction rates and thermal, intermediate and fast neutron fluence rates at the foil locations have been determined. These determinations include appropriate corrections for gamma self-absorption and neutron self-shielding as well as corresponding measurement uncertainties. The comparison of the NPP Monte Carlo calculations with the results of the foil measurements is done by using an individual generic MCNP model functioning as an interface and allowing the simulation of individual foil activation by predetermined neutron spectra. To summarize, the comparison between calculation and measurement serve as a sound validation of the Swiss NPP activation methodology by demonstrating a satisfying agreement between measurement and calculation. Finally, the validation offers a chance for further improvements of the existing NPP models by ensuing calibration and/or modelling optimizations for key components and structures.

Computational models of the Posner simple and choice reaction time tasks

PubMed Central

Feher da Silva, Carolina; Baldo, Marcus V. C.

2015-01-01

The landmark experiments by Posner in the late 1970s have shown that reaction time (RT) is faster when the stimulus appears in an expected location, as indicated by a cue; since then, the so-called Posner task has been considered a “gold standard” test of spatial attention. It is thus fundamental to understand the neural mechanisms involved in performing it. To this end, we have developed a Bayesian detection system and small integrate-and-fire neural networks, which modeled sensory and motor circuits, respectively, and optimized them to perform the Posner task under different cue type proportions and noise levels. In doing so, main findings of experimental research on RT were replicated: the relative frequency effect, suboptimal RTs and significant error rates due to noise and invalid cues, slower RT for choice RT tasks than for simple RT tasks, fastest RTs for valid cues and slowest RTs for invalid cues. Analysis of the optimized systems revealed that the employed mechanisms were consistent with related findings in neurophysiology. Our models predict that (1) the results of a Posner task may be affected by the relative frequency of valid and neutral trials, (2) in simple RT tasks, input from multiple locations are added together to compose a stronger signal, and (3) the cue affects motor circuits more strongly in choice RT tasks than in simple RT tasks. In discussing the computational demands of the Posner task, attention has often been described as a filter that protects the nervous system, whose capacity is limited, from information overload. Our models, however, reveal that the main problems that must be overcome to perform the Posner task effectively are distinguishing signal from external noise and selecting the appropriate response in the presence of internal noise. PMID:26190997

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

PubMed Central

2011-01-01

Background Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications. Results We present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the hydrogenase reaction was found to have a strong effect on butanol formation--as experimentally observed. Conclusions Microbial production of butanol by C. beijerinckii offers a promising, sustainable, method for generation of this important chemical and potential biofuel. iCM925 is a predictive model that can accurately reproduce physiological behavior and provide insight into the underlying mechanisms of microbial butanol production. As such, the model will be instrumental in efforts to better understand, and metabolically engineer, this microorganism for improved butanol production. PMID:21846360

Development and evaluation of predictive model for bovine serum albumin-water partition coefficients of neutral organic chemicals.

PubMed

Ma, Guangcai; Yuan, Quan; Yu, Haiying; Lin, Hongjun; Chen, Jianrong; Hong, Huachang

2017-04-01

The binding of organic chemicals to serum albumin can significantly reduce their unbound concentration in blood and affect their biological reactions. In this study, we developed a new QSAR model for bovine serum albumin (BSA) - water partition coefficients (K BSA/W ) of neutral organic chemicals with large structural variance, logK BSA/W values covering 3.5 orders of magnitude (1.19-4.76). All chemical geometries were optimized by semi-empirical PM6 algorithm. Several quantum chemical parameters that reflect various intermolecular interactions as well as hydrophobicity were selected to develop QSAR model. The result indicates the regression model derived from logK ow , the most positive net atomic charges on an atom, Connolly solvent excluded volume, polarizability, and Abraham acidity could explain the partitioning mechanism of organic chemicals between BSA and water. The simulated external validation and cross validation verifies the developed model has good statistical robustness and predictive ability, thus can be used to estimate the logK BSA/W values for chemicals in application domain, accordingly to provide basic data for the toxicity assessment of the chemicals. Copyright © 2016 Elsevier Inc. All rights reserved.

Coupling crystal plasticity and phase-field damage to simulate β-HMX-based polymer-bonded explosive under shock load

NASA Astrophysics Data System (ADS)

Grilli, Nicolo; Dandekar, Akshay; Koslowski, Marisol

2017-06-01

The development of high explosive materials requires constitutive models that are able to predict the influence of microstructure and loading conditions on shock sensitivity. In this work a model at the continuum-scale for the polymer-bonded explosive constituted of β-HMX particles embedded in a Sylgard matrix is developed. It includes a Murnaghan equation of state, a crystal plasticity model, based on power-law slip rate and hardening, and a phase field damage model based on crack regularization. The temperature increase due to chemical reactions is introduced by a heat source term, which is validated using results from reactive molecular dynamics simulations. An initial damage field representing pre-existing voids and cracks is used in the simulations to understand the effect of these inhomogeneities on the damage propagation and shock sensitivity. We show the predictions of the crystal plasticity model and the effect of the HMX crystal orientation on the shock initiation and on the dissipated plastic work and damage propagation. The simulation results are validated with ultra-fast dynamic transmission electron microscopy experiments and x-ray experiments carried out at Purdue University. Membership Pending.

New insight into the ZnO sulfidation reaction: mechanism and kinetics modeling of the ZnS outward growth.

PubMed

Neveux, Laure; Chiche, David; Pérez-Pellitero, Javier; Favergeon, Loïc; Gay, Anne-Sophie; Pijolat, Michèle

2013-02-07

Zinc oxide based materials are commonly used for the final desulfurization of synthesis gas in Fischer-Tropsch based XTL processes. Although the ZnO sulfidation reaction has been widely studied, little is known about the transformation at the crystal scale, its detailed mechanism and kinetics. A model ZnO material with well-determined characteristics (particle size and shape) has been synthesized to perform this study. Characterizations of sulfided samples (using XRD, TEM and electron diffraction) have shown the formation of oriented polycrystalline ZnS nanoparticles with a predominant hexagonal form (wurtzite phase). TEM observations also have evidenced an outward development of the ZnS phase, showing zinc and oxygen diffusion from the ZnO-ZnS internal interface to the surface of the ZnS particle. The kinetics of ZnO sulfidation by H(2)S has been investigated using isothermal and isobaric thermogravimetry. Kinetic tests have been performed that show that nucleation of ZnS is instantaneous compared to the growth process. A reaction mechanism composed of eight elementary steps has been proposed to account for these results, and various possible rate laws have been determined upon approximation of the rate-determining step. Thermogravimetry experiments performed in a wide range of H(2)S and H(2)O partial pressures have shown that the ZnO sulfidation reaction rate has a nonlinear variation with H(2)S partial pressure at the same time no significant influence of water vapor on reaction kinetics has been observed. From these observations, a mixed kinetics of external interface reaction with water desorption and oxygen diffusion has been determined to control the reaction kinetics and the proposed mechanism has been validated. However, the formation of voids at the ZnO-ZnS internal interface, characterized by TEM and electron tomography, strongly slows down the reaction rate. Therefore, the impact of the decreasing ZnO-ZnS internal interface on reaction kinetics has been taken into account in the reaction rate expression. In this way the void formation at the interface has been modeled considering a random nucleation followed by an isotropic growth of cavities. Very good agreement has been observed between both experimental and calculated rates after taking into account the decrease in the ZnO-ZnS internal interface.

Indirect color prediction of amorphous carbohydrate melts as a function of thermal history.

PubMed

van Sleeuwen, Rutger M T; Gosse, Anaїck J; Normand, Valery

2013-07-01

Glassy carbohydrate microcapsules are widely used for the encapsulation of flavors in food applications, and are made using various thermal processes (for example, extrusion). During manufacturing, these carbohydrate melts are held at elevated temperatures and color can form due to nonenzymatic browning reactions. These reactions can negatively or positively affect the color and flavor of microcapsules. The rate of color formation of maltodextrin and maltodextrin/sucrose melts at elevated temperatures was determined spectrophotometrically and was found to follow pseudo zero-order kinetics. The effect of temperature was adequately modeled by an Arrhenius relationship. Reaction rate constants and Arrhenius parameters were determined for individual wavelengths in the visible range (360 to 700 nm at 1 nm intervals). Transient processes (temperature changes with time) were modeled as a sequence of small isothermal events, and the equivalent thermal history at a reference temperature calculated using the Arrhenius relationship. Therefore, spectral transmittance curves could be predicted with knowledge of the time/temperature relationship. Validation was conducted by subjecting both melts to a transient thermal history. Experimental transmittance spectrum compared favorably against predicted values. These spectra were optionally converted to any desirable color space (for example, CIELAB, XYZ, RGB) or derived parameter (for example, Browning Index). The tool could be used to better control nonenzymatic browning reactions in industrial food processes. © 2013 Institute of Food Technologists®

Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu

2014-01-21

The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents formore » a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible systems.« less

Validation of reference genes for quantitative gene expression analysis in experimental epilepsy.

PubMed

Sadangi, Chinmaya; Rosenow, Felix; Norwood, Braxton A

2017-12-01

To grasp the molecular mechanisms and pathophysiology underlying epilepsy development (epileptogenesis) and epilepsy itself, it is important to understand the gene expression changes that occur during these phases. Quantitative real-time polymerase chain reaction (qPCR) is a technique that rapidly and accurately determines gene expression changes. It is crucial, however, that stable reference genes are selected for each experimental condition to ensure that accurate values are obtained for genes of interest. If reference genes are unstably expressed, this can lead to inaccurate data and erroneous conclusions. To date, epilepsy studies have used mostly single, nonvalidated reference genes. This is the first study to systematically evaluate reference genes in male Sprague-Dawley rat models of epilepsy. We assessed 15 potential reference genes in hippocampal tissue obtained from 2 different models during epileptogenesis, 1 model during chronic epilepsy, and a model of noninjurious seizures. Reference gene ranking varied between models and also differed between epileptogenesis and chronic epilepsy time points. There was also some variance between the four mathematical models used to rank reference genes. Notably, we found novel reference genes to be more stably expressed than those most often used in experimental epilepsy studies. The consequence of these findings is that reference genes suitable for one epilepsy model may not be appropriate for others and that reference genes can change over time. It is, therefore, critically important to validate potential reference genes before using them as normalizing factors in expression analysis in order to ensure accurate, valid results. © 2017 Wiley Periodicals, Inc.

In Depth Analysis of AVCOAT TPS Response to a Reentry Flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Titov, E. V.; Kumar, Rakesh; Levin, D. A.

2011-05-20

Modeling of the high altitude portion of reentry vehicle trajectories with DSMC or statistical BGK solvers requires accurate evaluation of the boundary conditions at the ablating TPS surface. Presented in this article is a model which takes into account the complex ablation physics including the production of pyrolysis gases, and chemistry at the TPS surface. Since the ablation process is time dependent the modeling of the material response to the high energy reentry flow starts with the solution of the rarefied flow over the vehicle and then loosely couples with the material response. The objective of the present work ismore » to carry out conjugate thermal analysis by weakly coupling a flow solver to a material thermal response model. The latter model solves the one dimensional heat conduction equation accounting for the pyrolysis process that takes place in the reaction zone of an ablative thermal protection system (TPS) material. An estimate of the temperature range within which the pyrolysis reaction (decomposition and volatilization) takes place is obtained from Ref. [1]. The pyrolysis reaction results in the formation of char and the release of gases through the porous charred material. These gases remove additional amount of heat as they pass through the material, thus cooling the material (the process known as transpiration cooling). In the present work, we incorporate the transpiration cooling model in the material thermal response code in addition to the pyrolysis model. The flow in the boundary layer and in the vicinity of the TPS material is in the transitional flow regime. Therefore, we use a previously validated statistical BGK method to model the flow physics in the vicinity of the micro-cracks, since the BGK method allows simulations of flow at pressures higher than can be computed using DSMC.« less

Development of a QSAR model for predicting aqueous reaction rate constants of organic chemicals with hydroxyl radicals.

PubMed

Luo, Xiang; Yang, Xianhai; Qiao, Xianliang; Wang, Ya; Chen, Jingwen; Wei, Xiaoxuan; Peijnenburg, Willie J G M

2017-03-22

Reaction with hydroxyl radicals (˙OH) is an important removal pathway for organic pollutants in the aquatic environment. The aqueous reaction rate constant (k OH ) is therefore an important parameter for fate assessment of aquatic pollutants. Since experimental determination fails to meet the requirement of being able to efficiently handle numerous organic chemicals at limited cost and within a relatively short period of time, in silico methods such as quantitative structure-activity relationship (QSAR) models are needed to predict k OH . In this study, a QSAR model with a larger and wider applicability domain as compared with existing models was developed. Following the guidelines for the development and validation of QSAR models proposed by the Organization for Economic Co-operation and Development (OECD), the model shows satisfactory performance. The applicability domain of the model has been extended and contained chemicals that have rarely been covered in most previous studies. The chemicals covered in the current model contain functional groups including [double bond splayed left]C[double bond, length as m-dash]C[double bond splayed right], -C[triple bond, length as m-dash]C-, -C 6 H 5 , -OH, -CHO, -O-, [double bond splayed left]C[double bond, length as m-dash]O, -C[double bond, length as m-dash]O(O)-, -COOH, -C[triple bond, length as m-dash]N, [double bond splayed left]N-, -NH 2 , -NH-C(O)-, -NO 2 , -N[double bond, length as m-dash]C-N[double bond splayed right], [double bond splayed left]N-N[double bond splayed right], -N[double bond, length as m-dash]N-, -S-, -S-S-, -SH, -SO 3 , -SO 4 , -PO 4 , and -X (F, Cl, Br, and I).

Validation of lumbar spine loading from a musculoskeletal model including the lower limbs and lumbar spine.

PubMed

Actis, Jason A; Honegger, Jasmin D; Gates, Deanna H; Petrella, Anthony J; Nolasco, Luis A; Silverman, Anne K

2018-02-08

Low back mechanics are important to quantify to study injury, pain and disability. As in vivo forces are difficult to measure directly, modeling approaches are commonly used to estimate these forces. Validation of model estimates is critical to gain confidence in modeling results across populations of interest, such as people with lower-limb amputation. Motion capture, ground reaction force and electromyographic data were collected from ten participants without an amputation (five male/five female) and five participants with a unilateral transtibial amputation (four male/one female) during trunk-pelvis range of motion trials in flexion/extension, lateral bending and axial rotation. A musculoskeletal model with a detailed lumbar spine and the legs including 294 muscles was used to predict L4-L5 loading and muscle activations using static optimization. Model estimates of L4-L5 intervertebral joint loading were compared to measured intradiscal pressures from the literature and muscle activations were compared to electromyographic signals. Model loading estimates were only significantly different from experimental measurements during trunk extension for males without an amputation and for people with an amputation, which may suggest a greater portion of L4-L5 axial load transfer through the facet joints, as facet loads are not captured by intradiscal pressure transducers. Pressure estimates between the model and previous work were not significantly different for flexion, lateral bending or axial rotation. Timing of model-estimated muscle activations compared well with electromyographic activity of the lumbar paraspinals and upper erector spinae. Validated estimates of low back loading can increase the applicability of musculoskeletal models to clinical diagnosis and treatment. Copyright © 2017 Elsevier Ltd. All rights reserved.

Enzyme catalysis-electrophoresis titration for multiplex enzymatic assay via moving reaction boundary chip.

PubMed

Zhong, Ran; Xie, Haiyang; Kong, Fanzhi; Zhang, Qiang; Jahan, Sharmin; Xiao, Hua; Fan, Liuyin; Cao, Chengxi

2016-09-21

In this work, we developed the concept of enzyme catalysis-electrophoresis titration (EC-ET) under ideal conditions, the theory of EC-ET for multiplex enzymatic assay (MEA), and a related method based on a moving reaction boundary (MRB) chip with a collateral channel and cell phone imaging. As a proof of principle, the model enzymes horseradish peroxidase (HRP), laccase and myeloperoxidase (MPO) were chosen for the tests of the EC-ET model. The experiments revealed that the EC-ET model could be achieved via coupling EC with ET within a MRB chip; particularly the MEA analyses of catalysis rate, maximum rate, activity, Km and Kcat could be conducted via a single run of the EC-ET chip, systemically demonstrating the validity of the EC-ET theory. Moreover, the developed method had these merits: (i) two orders of magnitude higher sensitivity than a fluorescence microplate reader, (ii) simplicity and low cost, and (iii) fairly rapid (30 min incubation, 20 s imaging) analysis, fair stability (<5.0% RSD) and accuracy, thus validating the EC-ET method. Finally, the developed EC-ET method was used for the clinical assay of MPO activity in blood samples; the values of MPO activity detected via the EC-ET chip were in agreement with those obtained by a traditional fluorescence microplate reader, indicating the applicability of the EC-ET method. The work opens a window for the development of enzymatic research, enzyme assay, immunoassay, and point-of-care testing as well as titration, one of the oldest methods of analysis, based on a simple chip.

Reverse transcription quantitative real-time polymerase chain reaction reference genes in the spared nerve injury model of neuropathic pain: validation and literature search.

PubMed

Piller, Nicolas; Decosterd, Isabelle; Suter, Marc R

2013-07-10

The reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used, highly sensitive laboratory technique to rapidly and easily detect, identify and quantify gene expression. Reliable RT-qPCR data necessitates accurate normalization with validated control genes (reference genes) whose expression is constant in all studied conditions. This stability has to be demonstrated.We performed a literature search for studies using quantitative or semi-quantitative PCR in the rat spared nerve injury (SNI) model of neuropathic pain to verify whether any reference genes had previously been validated. We then analyzed the stability over time of 7 commonly used reference genes in the nervous system - specifically in the spinal cord dorsal horn and the dorsal root ganglion (DRG). These were: Actin beta (Actb), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal proteins 18S (18S), L13a (RPL13a) and L29 (RPL29), hypoxanthine phosphoribosyltransferase 1 (HPRT1) and hydroxymethylbilane synthase (HMBS). We compared the candidate genes and established a stability ranking using the geNorm algorithm. Finally, we assessed the number of reference genes necessary for accurate normalization in this neuropathic pain model. We found GAPDH, HMBS, Actb, HPRT1 and 18S cited as reference genes in literature on studies using the SNI model. Only HPRT1 and 18S had been once previously demonstrated as stable in RT-qPCR arrays. All the genes tested in this study, using the geNorm algorithm, presented gene stability values (M-value) acceptable enough for them to qualify as potential reference genes in both DRG and spinal cord. Using the coefficient of variation, 18S failed the 50% cut-off with a value of 61% in the DRG. The two most stable genes in the dorsal horn were RPL29 and RPL13a; in the DRG they were HPRT1 and Actb. Using a 0.15 cut-off for pairwise variations we found that any pair of stable reference gene was sufficient for the normalization process. In the rat SNI model, we validated and ranked Actb, RPL29, RPL13a, HMBS, GAPDH, HPRT1 and 18S as good reference genes in the spinal cord. In the DRG, 18S did not fulfill stability criteria. The combination of any two stable reference genes was sufficient to provide an accurate normalization.

Neutron capture on short-lived nuclei via the surrogate (d,pγ) reaction

NASA Astrophysics Data System (ADS)

Cizewski, Jolie A.; Ratkiewicz, Andrew

2018-05-01

Rapid r-process nucleosynthesis is responsible for the creation of about half of the elements heavier than iron. Neutron capture on shortlived nuclei in cold processes or during freeze out from hot processes can have a significant impact on the final observed r-process abundances. We are validating the (d,pγ) reaction as a surrogate for neutron capture with measurements on 95Mo targets and a focus on discrete transitions. The experimental results have been analyzed within the Hauser-Feshbach approach with non-elastic breakup of the deuteron providing a neutron to be captured. Preliminary results support the (d,pγ) reaction as a valid surrogate for neutron capture. We are poised to measure the (d,pγ) reaction in inverse kinematics with unstable beams following the development of the experimental techniques.

Diabatic models with transferrable parameters for generalized chemical reactions

NASA Astrophysics Data System (ADS)

Reimers, Jeffrey R.; McKemmish, Laura K.; McKenzie, Ross H.; Hush, Noel S.

2017-05-01

Diabatic models applied to adiabatic electron-transfer theory yield many equations involving just a few parameters that connect ground-state geometries and vibration frequencies to excited-state transition energies and vibration frequencies to the rate constants for electron-transfer reactions, utilizing properties of the conical-intersection seam linking the ground and excited states through the Pseudo Jahn-Teller effect. We review how such simplicity in basic understanding can also be obtained for general chemical reactions. The key feature that must be recognized is that electron-transfer (or hole transfer) processes typically involve one electron (hole) moving between two orbitals, whereas general reactions typically involve two electrons or even four electrons for processes in aromatic molecules. Each additional moving electron leads to new high-energy but interrelated conical-intersection seams that distort the shape of the critical lowest-energy seam. Recognizing this feature shows how conical-intersection descriptors can be transferred between systems, and how general chemical reactions can be compared using the same set of simple parameters. Mathematical relationships are presented depicting how different conical-intersection seams relate to each other, showing that complex problems can be reduced into an effective interaction between the ground-state and a critical excited state to provide the first semi-quantitative implementation of Shaik’s “twin state” concept. Applications are made (i) demonstrating why the chemistry of the first-row elements is qualitatively so different to that of the second and later rows, (ii) deducing the bond-length alternation in hypothetical cyclohexatriene from the observed UV spectroscopy of benzene, (iii) demonstrating that commonly used procedures for modelling surface hopping based on inclusion of only the first-derivative correction to the Born-Oppenheimer approximation are valid in no region of the chemical parameter space, and (iv), demonstrating the types of chemical reactions that may be suitable for exploitation as a chemical qubit in some quantum information processor.

[Animal models for assessment of GMO allergenicity: advantages and limitations].

PubMed

Adel-Patient, K; Wal, J M

2004-03-01

Incidence of IgE-mediated allergic reactions to foods is increasing as well as the severity of associated symptoms and numerous foods are now incriminated, probably in relation with modifications of dietary habits and increased exposure to new or modified food ingredients. Therefore, the introduction on the market of food composed of or derived from genetically modified organisms (GMOs) raised the question of their potential allergenicity. Particularly with regards to the allergenicity of a newly expressed protein, it is necessary to obtain, from several steps in the risk assessment process, a cumulative body of evidence which minimises any uncertainty. This may include the use of animal model despite no fully reliable validated model is available yet. Such animal models should allow to address 3 major issues: Is the novel protein a sensitizer, i.e. does it possess intrinsic properties that allow to sensitize a predisposed individual? Is the protein an elicitor i.e. is it able to elicit an allergic reaction in a sensitised individual? And is the protein an adjuvant, i.e. can it facilitate or enhance the sensitisation to an other protein? Animal models under investigation currently include mice, rats and guinea pigs but models such as dogs and swine also appeared a few years ago. The aim is to mimic the mechanism and characteristics of the sensitisation phase and/or the elicitation phase of the allergic reaction as it occurs in atopic humans. They are necessary because sensitisation studies can obviously not be done in human and because in vitro tests cannot reproduce the complexity of the immune system. We propose a mouse model which mimics both phases of the allergic reaction. It has permitted to evidence that biochemical and clinical manifestations occuring during the active phases of the allergic reaction differ according to the structure of the allergen used for the challenge. This may allow to compare the allergenic potential of a genetically modified protein with that of the conventional one and to identify possible unintended effects. However, pathogenesis of food allergy in human is very complex and multifactorial, including individual differences in susceptibility, environmental factors, conditions of exposure, ... No animal model can take into account all these factors and allow a reliable prediction of the prevalence and severity of allergic reactions which would result from the exposure to a (novel) protein. Nevertheless, point by point analysis using the different models available may provide useful informations on the potential allergenicity of a novel protein.

Preterm labor--modeling the uterine electrical activity from cellular level to surface recording.

PubMed

Rihana, S; Marque, C

2008-01-01

Uterine electrical activity is correlated to the appearance of uterine contractions. forceful contractions appear at the end of term. Therefore, understanding the genesis and the propagation of uterine electrical activity may provide an efficient tool to diagnose preterm labor. Moreover, the control of uterine excitability seems to have important consequences in the control of preterm labor. Modeling the electrical activity in uterine tissue is thus an important step in understanding physiological uterine contractile mechanisms and to permit uterine EMG simulation. Our model presented in this paper, incorporates ion channel models at the cell level, the reaction diffusion equations at the tissue level and the spatiotemporal integration at the uterine EMG reconstructed level. This model validates some key physiological observation hypotheses concerning uterine excitability and propagation.

Model of dissolution in the framework of tissue engineering and drug delivery.

PubMed

Sanz-Herrera, J A; Soria, L; Reina-Romo, E; Torres, Y; Boccaccini, A R

2018-05-22

Dissolution phenomena are ubiquitously present in biomaterials in many different fields. Despite the advantages of simulation-based design of biomaterials in medical applications, additional efforts are needed to derive reliable models which describe the process of dissolution. A phenomenologically based model, available for simulation of dissolution in biomaterials, is introduced in this paper. The model turns into a set of reaction-diffusion equations implemented in a finite element numerical framework. First, a parametric analysis is conducted in order to explore the role of model parameters on the overall dissolution process. Then, the model is calibrated and validated versus a straightforward but rigorous experimental setup. Results show that the mathematical model macroscopically reproduces the main physicochemical phenomena that take place in the tests, corroborating its usefulness for design of biomaterials in the tissue engineering and drug delivery research areas.

Recent Advances in Modeling Hugoniots with Cheetah

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glaesemann, K R; Fried, L E

2005-07-26

We describe improvements to the Cheetah thermochemical-kinetics code's equilibrium solver to enable it to find a wider range of thermodynamic states. Cheetah supports a wide range of elements, condensed detonation products, and gas phase reactions. Therefore, Cheetah can be applied to a wide range of shock problems involving both energetic and non-energetic materials. An improve equation of state is also introduced. New experimental validations of Cheetah's equation of state methodology have been performed, including both reacted and unreacted Hugoniots.

Recent Advances in Modeling Hugoniots with Cheetah

NASA Astrophysics Data System (ADS)

Glaesemann, K. R.; Fried, L. E.

2006-07-01

We describe improvements to the Cheetah thermochemical-kinetics code's equilibrium solver to enable it to find a wider range of thermodynamic states. Cheetah supports a wide range of elements, condensed detonation products, and gas phase reactions. Therefore, Cheetah can be applied to a wide range of shock problems involving both energetic and non-energetic materials. An improve equation of state is also introduced. New experimental validations of Cheetah's equation of state methodology have been performed, including both reacted and unreacted Hugoniots.

Lean Six Sigma Project - Defense Logistics Agency/Honeywell Long-Term Contract Model Using One-Pass Pricing for Sole-Source Spare Parts

DTIC Science & Technology

2011-02-18

Control Limit Lower Control Limit Reaction Plan 1 Complaints from other suppliers (synopsis, award) SCG During award process Identify Sole- Source...Parts 0.0 1.0 0.0 Evaluate complaint, if valid remove item from contract. 2 Tracking timeline for procurement/reviews SCG During pre- award process...Review Solicitation 100.0 Determine where the document stands in the approval process. Adjust milestones and followup . 3 FAR/DPAP guidance SCG

Underbody Blast Models of TBI Caused by Hyper-Acceleration and Secondary Head Impact

DTIC Science & Technology

2015-02-01

or behavioral indices of brain injury . 2.0 Technical Requirements: 2 Fig. 1. Diffusion tensor imaging of water diffusion in the internal capsule...demonstrates relative differences between blast (left) and sham (right) and also the similarities between the two animals in each group. vWF Bcl - 2 Fo ld...C ha ng e -8 -6 -4 - 2 0 2 4 6 8 10 12 ** ** Figure 6. Quantitative real-time polymerase chain reaction (qPCR) validation of vWF and Bcl - 2

Development and Validation of a Slurry Model for Chemical Hydrogen Storage in Fuel Cell Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brooks, Kriston P.; Pires, Richard P.; Simmons, Kevin L.

2014-07-25

The US Department of Energy's (DOE) Hydrogen Storage Engineering Center of Excellence (HSECoE) is developing models for hydrogen storage systems for fuel cell-based light duty vehicle applications for a variety of promising materials. These transient models simulate the performance of the storage system for comparison to the DOE’s Technical Targets and a set of four drive cycles. The purpose of this research is to describe the models developed for slurry-based chemical hydrogen storage materials. The storage systems of both a representative exothermic system based on ammonia borane and endothermic system based on alane were developed and modeled in Simulink®. Oncemore » complete the reactor and radiator components of the model were validated with experimental data. The model was then run using a highway cycle, an aggressive cycle, cold-start cycle and hot drive cycle. The system design was adjusted to meet these drive cycles. A sensitivity analysis was then performed to identify the range of material properties where these DOE targets and drive cycles could be met. Materials with a heat of reaction greater than 11 kJ/mol H2 generated and a slurry hydrogen capacity of greater than 11.4% will meet the on-board efficiency and gravimetric capacity targets, respectively.« less

The Arrhenius equation revisited.

PubMed

Peleg, Micha; Normand, Mark D; Corradini, Maria G

2012-01-01

The Arrhenius equation has been widely used as a model of the temperature effect on the rate of chemical reactions and biological processes in foods. Since the model requires that the rate increase monotonically with temperature, its applicability to enzymatic reactions and microbial growth, which have optimal temperature, is obviously limited. This is also true for microbial inactivation and chemical reactions that only start at an elevated temperature, and for complex processes and reactions that do not follow fixed order kinetics, that is, where the isothermal rate constant, however defined, is a function of both temperature and time. The linearity of the Arrhenius plot, that is, Ln[k(T)] vs. 1/T where T is in °K has been traditionally considered evidence of the model's validity. Consequently, the slope of the plot has been used to calculate the reaction or processes' "energy of activation," usually without independent verification. Many experimental and simulated rate constant vs. temperature relationships that yield linear Arrhenius plots can also be described by the simpler exponential model Ln[k(T)/k(T(reference))] = c(T-T(reference)). The use of the exponential model or similar empirical alternative would eliminate the confusing temperature axis inversion, the unnecessary compression of the temperature scale, and the need for kinetic assumptions that are hard to affirm in food systems. It would also eliminate the reference to the Universal gas constant in systems where a "mole" cannot be clearly identified. Unless proven otherwise by independent experiments, one cannot dismiss the notion that the apparent linearity of the Arrhenius plot in many food systems is due to a mathematical property of the model's equation rather than to the existence of a temperature independent "energy of activation." If T+273.16°C in the Arrhenius model's equation is replaced by T+b, where the numerical value of the arbitrary constant b is substantially larger than T and T(reference), the plot of Ln k(T) vs. 1/(T+b) will always appear almost perfectly linear. Both the modified Arrhenius model version having the arbitrary constant b, Ln[k(T)/k(T(reference)) = a[1/ (T(reference)+b)-1/ (T+b)], and the exponential model can faithfully describe temperature dependencies traditionally described by the Arrhenius equation without the assumption of a temperature independent "energy of activation." This is demonstrated mathematically and with computer simulations, and with reprocessed classical kinetic data and published food results.

Evaluation of Finite-Rate Gas/Surface Interaction Models for a Carbon Based Ablator

NASA Technical Reports Server (NTRS)

Chen, Yih-Kanq; Goekcen, Tahir

2015-01-01

Two sets of finite-rate gas-surface interaction model between air and the carbon surface are studied. The first set is an engineering model with one-way chemical reactions, and the second set is a more detailed model with two-way chemical reactions. These two proposed models intend to cover the carbon surface ablation conditions including the low temperature rate-controlled oxidation, the mid-temperature diffusion-controlled oxidation, and the high temperature sublimation. The prediction of carbon surface recession is achieved by coupling a material thermal response code and a Navier-Stokes flow code. The material thermal response code used in this study is the Two-dimensional Implicit Thermal-response and Ablation Program, which predicts charring material thermal response and shape change on hypersonic space vehicles. The flow code solves the reacting full Navier-Stokes equations using Data Parallel Line Relaxation method. Recession analyses of stagnation tests conducted in NASA Ames Research Center arc-jet facilities with heat fluxes ranging from 45 to 1100 wcm2 are performed and compared with data for model validation. The ablating material used in these arc-jet tests is Phenolic Impregnated Carbon Ablator. Additionally, computational predictions of surface recession and shape change are in good agreement with measurement for arc-jet conditions of Small Probe Reentry Investigation for Thermal Protection System Engineering.

An ab initio chemical reaction model for the direct simulation Monte Carlo study of non-equilibrium nitrogen flows.

PubMed

Mankodi, T K; Bhandarkar, U V; Puranik, B P

2017-08-28

A new ab initio based chemical model for a Direct Simulation Monte Carlo (DSMC) study suitable for simulating rarefied flows with a high degree of non-equilibrium is presented. To this end, Collision Induced Dissociation (CID) cross sections for N 2 +N 2 →N 2 +2N are calculated and published using a global complete active space self-consistent field-complete active space second order perturbation theory N 4 potential energy surface and quasi-classical trajectory algorithm for high energy collisions (up to 30 eV). CID cross sections are calculated for only a selected set of ro-vibrational combinations of the two nitrogen molecules, and a fitting scheme based on spectroscopic weights is presented to interpolate the CID cross section for all possible ro-vibrational combinations. The new chemical model is validated by calculating equilibrium reaction rate coefficients that can be compared well with existing shock tube and computational results. High-enthalpy hypersonic nitrogen flows around a cylinder in the transition flow regime are simulated using DSMC to compare the predictions of the current ab initio based chemical model with the prevailing phenomenological model (the total collision energy model). The differences in the predictions are discussed.

Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin in Populus trichocarpa[W

PubMed Central

Wang, Jack P.; Naik, Punith P.; Chen, Hsi-Chuan; Shi, Rui; Lin, Chien-Yuan; Liu, Jie; Shuford, Christopher M.; Li, Quanzi; Sun, Ying-Hsuan; Tunlaya-Anukit, Sermsawat; Williams, Cranos M.; Muddiman, David C.; Ducoste, Joel J.; Sederoff, Ronald R.; Chiang, Vincent L.

2014-01-01

We established a predictive kinetic metabolic-flux model for the 21 enzymes and 24 metabolites of the monolignol biosynthetic pathway using Populus trichocarpa secondary differentiating xylem. To establish this model, a comprehensive study was performed to obtain the reaction and inhibition kinetic parameters of all 21 enzymes based on functional recombinant proteins. A total of 104 Michaelis-Menten kinetic parameters and 85 inhibition kinetic parameters were derived from these enzymes. Through mass spectrometry, we obtained the absolute quantities of all 21 pathway enzymes in the secondary differentiating xylem. This extensive experimental data set, generated from a single tissue specialized in wood formation, was used to construct the predictive kinetic metabolic-flux model to provide a comprehensive mathematical description of the monolignol biosynthetic pathway. The model was validated using experimental data from transgenic P. trichocarpa plants. The model predicts how pathway enzymes affect lignin content and composition, explains a long-standing paradox regarding the regulation of monolignol subunit ratios in lignin, and reveals novel mechanisms involved in the regulation of lignin biosynthesis. This model provides an explanation of the effects of genetic and transgenic perturbations of the monolignol biosynthetic pathway in flowering plants. PMID:24619611

Low-energy (anti)neutrino physics with Borexino: Neutrinos from the primary proton-proton fusion process in the Sun

NASA Astrophysics Data System (ADS)

Mosteiro, P.; Bellini, G.; Benziger, J.; Bick, D.; Bonfini, G.; Bravo, D.; Caccianiga, B.; Cadonati, L.; Calaprice, F.; Caminata, A.; Cavalcante, P.; Chavarría, Á.; Chepurnov, A.; D'Angelo, D.; Davini, S.; Derbin, A.; Empl, A.; Etenko, A.; Fomenko, K.; Franco, D.; Gabriele, F.; Galbiati, C.; Gazzana, S.; Ghiano, C.; Giammarchi, M.; Göger-Neff, M.; Goretti, A.; Gromov, M.; Hagner, C.; Hungerford, E.; Ianni, Al.; Ianni, An.; Kobychev, V.; Korablëv, D.; Korga, G.; Kryn, D.; Laubenstein, M.; Lehnert, B.; Lewke, T.; Litvinovich, E.; Lombardi, F.; Lombardi, P.; Ludhova, L.; Lukyanchenko, G.; Machulin, I.; Manecki, S.; Maneschg, W.; Marcocci, S.; Meindl, Q.; Meroni, E.; Meyer, M.; Miramonti, L.; Misiaszek, M.; Montuschi, M.; Muratova, V.; Oberauer, L.; Obolensky, M.; Ortica, F.; Otis, K.; Pallavicini, M.; Papp, L.; Perasso, L.; Pocar, A.; Ranucci, G.; Razeto, A.; Re, A.; Romani, A.; Rossi, N.; Saldanha, R.; Salvo, C.; Schönert, S.; Simgen, H.; Skorokhvatov, M.; Smirnov, O.; Sotnikov, A.; Sukhotin, S.; Suvorov, Y.; Tartaglia, R.; Testera, G.; Vignaud, D.; Vogelaar, R. B.; von Feilitzsch, F.; Wang, H.; Winter, J.; Wojcik, M.; Wright, A.; Wurm, M.; Zaimidoroga, O.; Zavatarelli, S.; Zuber, K.; Zuzel, G.

2015-08-01

The Sun is fueled by a series of nuclear reactions that produce the energy that makes it shine. The primary reaction is the fusion of two protons into a deuteron, a positron and a neutrino. These neutrinos constitute the vast majority of neutrinos reaching Earth, providing us with key information about what goes on at the core of our star. Several experiments have now confirmed the observation of neutrino oscillations by detecting neutrinos from secondary nuclear processes in the Sun; this is the first direct spectral measurement of the neutrinos from the keystone proton-proton fusion. This observation is a crucial step towards the completion of the spectroscopy of pp-chain neutrinos, as well as further validation of the LMA-MSW model of neutrino oscillations.

Modeling the pH and temperature dependence of aqueousphase hydroxyl radical reaction rate constants of organic micropollutants using QSPR approach.

PubMed

Gupta, Shikha; Basant, Nikita

2017-11-01

Designing of advanced oxidation process (AOP) requires knowledge of the aqueous phase hydroxyl radical ( ● OH) reactions rate constants (k OH ), which are strictly dependent upon the pH and temperature of the medium. In this study, pH- and temperature-dependent quantitative structure-property relationship (QSPR) models based on the decision tree boost (DTB) approach were developed for the prediction of k OH of diverse organic contaminants following the OECD guidelines. Experimental datasets (n = 958) pertaining to the k OH values of aqueous phase reactions at different pH (n = 470; 1.4 × 10 6 to 3.8 × 10 10  M -1  s -1 ) and temperature (n = 171; 1.0 × 10 7 to 2.6 × 10 10  M -1  s -1 ) were considered and molecular descriptors of the compounds were derived. The Sanderson scale electronegativity, topological polar surface area, number of double bonds, and halogen atoms in the molecule, in addition to the pH and temperature, were found to be the relevant predictors. The models were validated and their external predictivity was evaluated in terms of most stringent criteria parameters derived on the test data. High values of the coefficient of determination (R 2 ) and small root mean squared error (RMSE) in respective training (> 0.972, ≤ 0.12) and test (≥ 0.936, ≤ 0.16) sets indicated high generalization and predictivity of the developed QSPR model. Other statistical parameters derived from the training and test data also supported the robustness of the models and their suitability for screening new chemicals within the defined chemical space. The developed QSPR models provide a valuable tool for predicting the ● OH reaction rate constants of emerging new water contaminants for their susceptibility to AOPs.

Modeling Low-temperature Geochemical Processes

NASA Astrophysics Data System (ADS)

Nordstrom, D. K.

2003-12-01

Geochemical modeling has become a popular and useful tool for a wide number of applications from research on the fundamental processes of water-rock interactions to regulatory requirements and decisions regarding permits for industrial and hazardous wastes. In low-temperature environments, generally thought of as those in the temperature range of 0-100 °C and close to atmospheric pressure (1 atm=1.01325 bar=101,325 Pa), complex hydrobiogeochemical reactions participate in an array of interconnected processes that affect us, and that, in turn, we affect. Understanding these complex processes often requires tools that are sufficiently sophisticated to portray multicomponent, multiphase chemical reactions yet transparent enough to reveal the main driving forces. Geochemical models are such tools. The major processes that they are required to model include mineral dissolution and precipitation; aqueous inorganic speciation and complexation; solute adsorption and desorption; ion exchange; oxidation-reduction; or redox; transformations; gas uptake or production; organic matter speciation and complexation; evaporation; dilution; water mixing; reaction during fluid flow; reaction involving biotic interactions; and photoreaction. These processes occur in rain, snow, fog, dry atmosphere, soils, bedrock weathering, streams, rivers, lakes, groundwaters, estuaries, brines, and diagenetic environments. Geochemical modeling attempts to understand the redistribution of elements and compounds, through anthropogenic and natural means, for a large range of scale from nanometer to global. "Aqueous geochemistry" and "environmental geochemistry" are often used interchangeably with "low-temperature geochemistry" to emphasize hydrologic or environmental objectives.Recognition of the strategy or philosophy behind the use of geochemical modeling is not often discussed or explicitly described. Plummer (1984, 1992) and Parkhurst and Plummer (1993) compare and contrast two approaches for modeling groundwater chemistry: (i) "forward modeling," which predicts water compositions from hypothesized reactions and user assumptions and (ii) "inverse modeling," which uses water, mineral, and isotopic compositions to constrain hypothesized reactions. These approaches simply reflect the amount of information one has to work with. With minimal information on a site, a modeler is forced to rely on forward modeling. Optimal information would include detailed mineralogy on drill cores or well cuttings combined with detailed water analyses at varying depths and sufficient spatial distribution to follow geochemical reactions and mixing of waters along defined flow paths. With optimal information, a modeler will depend on inverse modeling.This chapter outlines the main concepts and key developments in the field of geochemical modeling for low-temperature environments and illustrates their use with examples. It proceeds with a short discussion of what modeling is, continues with concepts and definitions commonly used, and follows with a short history of geochemical models, a discussion of databases, the codes that embody models, and recent examples of how these codes have been used in water-rock interactions. An important new stage of development seems to have been reached in this field with questions of reliability and validity of models. Future work will be obligated to document ranges of certainty and sources of uncertainty, sensitivity of models and codes to parameter errors and assumptions, propagation of errors, and delineation of the range of applicability.

From Power to Inaction.

PubMed

Durso, Geoffrey R O; Briñol, Pablo; Petty, Richard E

2016-12-01

Research has shown that people who feel powerful are more likely to act than those who feel powerless, whereas people who feel ambivalent are less likely to act than those whose reactions are univalent (entirely positive or entirely negative). But what happens when powerful people also are ambivalent? On the basis of the self-validation theory of judgment, we hypothesized that power and ambivalence would interact to predict individuals' action. Because power can validate individuals' reactions, we reasoned that feeling powerful strengthens whatever reactions people have during a decision. It can strengthen univalent reactions and increase action orientation, as shown in past research. Among people who hold an ambivalent judgment, however, those who feel powerful would be less action oriented than those who feel powerless. Two experiments provide evidence for this hypothesized interactive effect of power and ambivalence on individuals' action tendencies during both positive decisions (promoting an employee; Experiment 1) and negative decisions (firing an employee; Experiment 2). In summary, when individuals' reactions are ambivalent, power increases the likelihood of inaction.

ENDF/B-VIII.0: The 8th Major Release of the Nuclear Reaction Data Library with CIELO-project Cross Sections, New Standards and Thermal Scattering Data

NASA Astrophysics Data System (ADS)

Brown, D. A.; Chadwick, M. B.; Capote, R.; Kahler, A. C.; Trkov, A.; Herman, M. W.; Sonzogni, A. A.; Danon, Y.; Carlson, A. D.; Dunn, M.; Smith, D. L.; Hale, G. M.; Arbanas, G.; Arcilla, R.; Bates, C. R.; Beck, B.; Becker, B.; Brown, F.; Casperson, R. J.; Conlin, J.; Cullen, D. E.; Descalle, M.-A.; Firestone, R.; Gaines, T.; Guber, K. H.; Hawari, A. I.; Holmes, J.; Johnson, T. D.; Kawano, T.; Kiedrowski, B. C.; Koning, A. J.; Kopecky, S.; Leal, L.; Lestone, J. P.; Lubitz, C.; Márquez Damián, J. I.; Mattoon, C. M.; McCutchan, E. A.; Mughabghab, S.; Navratil, P.; Neudecker, D.; Nobre, G. P. A.; Noguere, G.; Paris, M.; Pigni, M. T.; Plompen, A. J.; Pritychenko, B.; Pronyaev, V. G.; Roubtsov, D.; Rochman, D.; Romano, P.; Schillebeeckx, P.; Simakov, S.; Sin, M.; Sirakov, I.; Sleaford, B.; Sobes, V.; Soukhovitskii, E. S.; Stetcu, I.; Talou, P.; Thompson, I.; van der Marck, S.; Welser-Sherrill, L.; Wiarda, D.; White, M.; Wormald, J. L.; Wright, R. Q.; Zerkle, M.; Žerovnik, G.; Zhu, Y.

2018-02-01

We describe the new ENDF/B-VIII.0 evaluated nuclear reaction data library. ENDF/B-VIII.0 fully incorporates the new IAEA standards, includes improved thermal neutron scattering data and uses new evaluated data from the CIELO project for neutron reactions on 1H, 16O, 56Fe, 235U, 238U and 239Pu described in companion papers in the present issue of Nuclear Data Sheets. The evaluations benefit from recent experimental data obtained in the U.S. and Europe, and improvements in theory and simulation. Notable advances include updated evaluated data for light nuclei, structural materials, actinides, fission energy release, prompt fission neutron and γ-ray spectra, thermal neutron scattering data, and charged-particle reactions. Integral validation testing is shown for a wide range of criticality, reaction rate, and neutron transmission benchmarks. In general, integral validation performance of the library is improved relative to the previous ENDF/B-VII.1 library.

Hydrolysis condensation reactions of titanium alkoxides in thin films: A study of the steric hindrance effect by X-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Barlier, Vincent; Bounor-Legaré, Véronique; Boiteux, Gisèle; Davenas, Joël; Léonard, Didier

2008-06-01

An original approach based on X-ray photoelectron spectroscopy (XPS) is proposed to study the influence of the surrounding humidity on the hydrolysis-condensation reactions of five titanium alkoxides in thin films. More precisely, the influence of the nature of the ligands (propoxide, butoxide, isopropoxide, phenoxide, and 9H-carbazole-9-yl-ethyl-oxy) on the reaction rate was evidenced. The reaction advancement was evaluated by comparing XPS chemical compositions to theoretical compositions calculated for all the possible rates. XPS chemical environment information allowed validating the reliability of this approach through the evaluation of the condensation state. In both approaches, the influence of the steric hindrance on the reactivity of titanium alkoxides was highlighted to be similar to what has been previously observed in solution. Theses results corroborate the validity of our XPS approach to determine titanium alkoxide hydrolysis-condensation reactions in the specific application of thin films.

Analysis of a water moderated critical assembly with anisn-Vitamin C

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, L.

1979-03-01

A tightly packed water moderated /sup 233/UO/sub 2/--ThO/sub 2/ critical assembly was analyzed with the Vitamin C library and the 1-D S/s n/ code, ANISN (S/sub 8/,P/sub 3/). The purpose of the study was to provide validation of this calculational model as applied to water-cooled hybrid fusion blankets. The quantities compared were the core eigenvalue and various activation shapes. The calculated eigenvalue was 1.02 +- 0.01. The /sup 233/U fission and /sup 232/Th capture shapes were found to be in good agreement (+-5%) with experiment, except near water--metal boundaries where differences up to 24% were observed. No such error peakingmore » was observed in the /sup 232/Th fast fission shape. We conclude that the model provides good volume averaged reaction rates in water-cooled systems. However, care must be exercised near water boundaries where thermally dependent reaction rates are significantly underestimated.« less

Simulation of Charge Collection in Diamond Detectors Irradiated with Deuteron-Triton Neutron Sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Milocco, Alberto; Trkov, Andrej; Pillon, Mario

2011-12-13

Diamond-based neutron spectrometers exhibit outstanding properties such as radiation hardness, low sensitivity to gamma rays, fast response and high-energy resolution. They represent a very promising application of diamonds for plasma diagnostics in fusion devices. The measured pulse height spectrum is obtained from the collection of helium and beryllium ions produced by the reactions on {sup 12}C. An original code is developed to simulate the production and the transport of charged particles inside the diamond detector. The ion transport methodology is based on the well-known TRIM code. The reactions of interest are triggered using the ENDF/B-VII.0 nuclear data for the neutronmore » interactions on carbon. The model is implemented in the TALLYX subroutine of the MCNP5 and MCNPX codes. Measurements with diamond detectors in a {approx}14 MeV neutron field have been performed at the FNG (Rome, Italy) and IRMM (Geel, Belgium) facilities. The comparison of the experimental data with the simulations validates the proposed model.« less

Gas-liquid countercurrent integration process for continuous biodiesel production using a microporous solid base KF/CaO as catalyst.

PubMed

Hu, Shengyang; Wen, Libai; Wang, Yun; Zheng, Xinsheng; Han, Heyou

2012-11-01

A continuous-flow integration process was developed for biodiesel production using rapeseed oil as feedstock, based on the countercurrent contact reaction between gas and liquid, separation of glycerol on-line and cyclic utilization of methanol. Orthogonal experimental design and response surface methodology were adopted to optimize technological parameters. A second-order polynomial model for the biodiesel yield was established and validated experimentally. The high determination coefficient (R(2)=98.98%) and the low probability value (Pr<0.0001) proved that the model matched the experimental data, and had a high predictive ability. The optimal technological parameters were: 81.5°C reaction temperature, 51.7cm fill height of catalyst KF/CaO and 105.98kPa system pressure. Under these conditions, the average yield of triplicate experiments was 93.7%, indicating the continuous-flow process has good potential in the manufacture of biodiesel. Copyright © 2012 Elsevier Ltd. All rights reserved.

Model-based complete enzymatic production of 3,6-anhydro-L-galactose from red algal biomass.

PubMed

Pathiraja, Duleepa; Lee, Saeyoung; Choi, In-Geol

2018-06-13

3,6-Anhydro-L-galactose (L-AHG) is a bioactive constituent of agar polysaccharides. To be used as a cosmetic or pharmaceutical ingredient, L-AHG is more favorably prepared by enzymatic saccharification of agar using a combination of agarolytic enzymes. Determining the optimum enzyme combination from natural repertoire is a bottleneck for designing an efficient enzymatic hydrolysis process. We consider all theoretical enzymatic saccharification routes in the natural agarolytic pathway of a marine bacterium, Saccharophagus degradans 2-40. Among these routes, three representative routes were determined by removing redundant enzymatic reactions. We simulated each L-AHG production route by simple kinetic models and validated the reaction feasibility by experimental procedure. The optimal enzyme mixture (with 67.3% maximum saccharification yield) was composed of endo-type β-agarase, exo-type β-agarase, agarooligosaccharolytic β-galactosidase and α-neoagarobiose hydrolase. This approach will reduce time and effort for developing a coherent enzymatic process to produce L-AHG on mass scale.

Time-Resolved Kinetic Chirped-Pulse Rotational Spectroscopy in a Room-Temperature Flow Reactor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zaleski, Daniel P.; Harding, Lawrence B.; Klippenstein, Stephen J.

Chirped-pulse Fourier transform millimeter-wave spectroscopy is a potentially powerful tool for studying chemical reaction dynamics and kinetics. Branching ratios of multiple reaction products and intermediates can be measured with unprecedented chemical specificity; molecular isomers, conformers, and vibrational states have distinct rotational spectra. Here we demonstrate chirped-pulse spectroscopy of vinyl cyanide photoproducts in a flow tube reactor at ambient temperature of 295 K and pressures of 1-10 mu bar. This in situ and time-resolved experiment illustrates the utility of this novel approach to investigating chemical reaction dynamics and kinetics. Following 193 nm photodissociation of CH2CHCN, we observe rotational relaxation of energizedmore » HCN, HNC, and HCCCN photoproducts with 10 mu s time resolution and sample the vibrational population distribution of HCCCN. The experimental branching ratio HCN/HCCCN is compared with a model based on RRKM theory using high-level ab initio calculations, which were in turn validated by comparisons to Active Thermochemical Tables enthalpies.« less

Time-Resolved Kinetic Chirped-Pulse Rotational Spectroscopy in a Room-Temperature Flow Reactor

DOE PAGES

Zaleski, Daniel P.; Harding, Lawrence B.; Klippenstein, Stephen J.; ...

2017-12-01

Chirped-pulse Fourier transform millimeter-wave spectroscopy is a potentially powerful tool for studying chemical reaction dynamics and kinetics. Branching ratios of multiple reaction products and intermediates can be measured with unprecedented chemical specificity; molecular isomers, conformers, and vibrational states have distinct rotational spectra. Here we demonstrate chirped-pulse spectroscopy of vinyl cyanide photoproducts in a flow tube reactor at ambient temperature of 295 K and pressures of 1-10 mu bar. This in situ and time-resolved experiment illustrates the utility of this novel approach to investigating chemical reaction dynamics and kinetics. Following 193 nm photodissociation of CH2CHCN, we observe rotational relaxation of energizedmore » HCN, HNC, and HCCCN photoproducts with 10 mu s time resolution and sample the vibrational population distribution of HCCCN. The experimental branching ratio HCN/HCCCN is compared with a model based on RRKM theory using high-level ab initio calculations, which were in turn validated by comparisons to Active Thermochemical Tables enthalpies.« less

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice–Ramsperger–Kassel theory

PubMed Central

Bao, Junwei Lucas; Zhang, Xin

2016-01-01

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C2F4), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice–Ramsperger–Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements. PMID:27834727

Barrierless association of CF2 and dissociation of C2F4 by variational transition-state theory and system-specific quantum Rice-Ramsperger-Kassel theory.

PubMed

Bao, Junwei Lucas; Zhang, Xin; Truhlar, Donald G

2016-11-29

Bond dissociation is a fundamental chemical reaction, and the first principles modeling of the kinetics of dissociation reactions with a monotonically increasing potential energy along the dissociation coordinate presents a challenge not only for modern electronic structure methods but also for kinetics theory. In this work, we use multifaceted variable-reaction-coordinate variational transition-state theory (VRC-VTST) to compute the high-pressure limit dissociation rate constant of tetrafluoroethylene (C 2 F 4 ), in which the potential energies are computed by direct dynamics with the M08-HX exchange correlation functional. To treat the pressure dependence of the unimolecular rate constants, we use the recently developed system-specific quantum Rice-Ramsperger-Kassel theory. The calculations are carried out by direct dynamics using an exchange correlation functional validated against calculations that go beyond coupled-cluster theory with single, double, and triple excitations. Our computed dissociation rate constants agree well with the recent experimental measurements.

Understanding Performance Limitations to Enable High Performance Magnesium-Ion Batteries

DOE PAGES

Kim, Sun Ung; Perdue, Brian; Apblett, Christopher A.; ...

2016-05-18

We developed a mathematical model in order to investigate the performance limiting factors of Mg-ion battery with a Chevrel phase (Mg xMo 6S 8) cathode and a Mg metal anode. Furthermore, the model was validated using experimental data from the literature [Cheng et al., Chem. Mater., 26, 4904 (2014)]. Two electrochemical reactions of the Chevrel phase with significantly different kinetics and solid diffusion were included in the porous electrode model, which captured the physics sufficiently well to generate charge curves of five rates (0.1C–2C) for two different particle sizes. Limitation analysis indicated that the solid diffusion and kinetics in themore » higher-voltage plateau limit the capacity and increase the overpotential in the Cheng et al.’s thin (20-μm) electrodes. The model reveals that the performance of the cells with reasonable thickness would also be subject to electrolyte-phase limitations. Finally, the simulation also suggested that the polarization losses on discharge will be lower than that on charge, because of the differences in the kinetics and solid diffusion between the two reactions of the Chevrel phase.« less

A theoretical model to determine the capacity performance of shape-specific electrodes

NASA Astrophysics Data System (ADS)

Yue, Yuan; Liang, Hong

2018-06-01

A theory is proposed to explain and predict the electrochemical process during reaction between lithium ions and electrode materials. In the model, the process of reaction is proceeded into two steps, surface adsorption and diffusion of lithium ions. The surface adsorption is an instantaneous process for lithium ions to adsorb onto the surface sites of active materials. The diffusion of lithium ions into particles is determined by the charge-discharge condition. A formula to determine the maximum specific capacity of active materials at different charging rates (C-rates) is derived. The maximum specific capacity is correlated to characteristic parameters of materials and cycling - such as size, aspect ratio, surface area, and C-rate. Analysis indicates that larger particle size or greater aspect ratio of active materials and faster C-rates can reduce maximum specific capacity. This suggests that reducing particle size of active materials and slowing the charge-discharge speed can provide enhanced electrochemical performance of a battery cell. Furthermore, the model is validated by published experimental results. This model brings new understanding in quantification of electrochemical kinetics and capacity performance. It enables development of design strategies for novel electrodes and future generation of energy storage devices.

Numerical simulations to model laser-driven coil-capacitor targets for generation of kilo-Tesla magnetic fields

NASA Astrophysics Data System (ADS)

Schillaci, F.; De Marco, M.; Giuffrida, L.; Fujioka, S.; Zhang, Z.; Korn, G.; Margarone, D.

2018-02-01

A coil-capacitor target is modeled using FEM simulations and analytical calculations, which allow to explain the time evolution of such complex target during magnetic field production driven by the flow of an extremely high current generated through the interaction with a high power laser. The numerical model includes a detailed study of the magnetic field produced by the coil-capacitor target, both in the static and transient cases, as well as magnetic force and Joule heating. The model is validated by experimental data reported in literature and can be of interest for several applications. As an example, the combination of two synchronized nanosecond lasers with the purpose of producing a plasma responsible of the proton-boron (p+ + 11B → 8.5 MeV + 3α) fusion reaction, and energizing two multi-turn coils with the main purpose of confining such a plasma could enhance the reaction rate. The preliminary conceptual design of a magnetic mirror configuration to be used for confining protons and boron ions up to a few MeV/u in a region of less than 1 mm2 is briefly reported.

Is there hope for multi-site complexation modeling?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bickmore, Barry R.; Rosso, Kevin M.; Mitchell, S. C.

2006-06-06

It has been shown here that the standard formulation of the MUSIC model does not deliver the molecular-scale insight into oxide surface reactions that it promises. The model does not properly divide long-range electrostatic and short-range contributions to acid-base reaction energies, and it does not treat solvation in a physically realistic manner. However, even if the current MUSIC model does not succeed in its ambitions, its ambitions are still reasonable. It was a pioneering attempt in that Hiemstra and coworkers recognized that intrinsic equilibrium constants, where the effects of long-range electrostatic effects have been removed, must be theoretically constrained priormore » to model fitting if there is to be any hope of obtaining molecular-scale insights from SCMs. We have also shown, on the other hand, that it may be premature to dismiss all valence-based models of acidity. Not only can some such models accurately predict intrinsic acidity constants, but they can also now be linked to the results of molecular dynamics simulations of solvated systems. Significant challenges remain for those interested in creating SCMs that are accurate at the molecular scale. It will only be after all model parameters can be predicted from theory, and the models validated against titration data that we will be able to begin to have some confidence that we really are adequately describing the chemical systems in question.« less

STEPS: efficient simulation of stochastic reaction–diffusion models in realistic morphologies

PubMed Central

2012-01-01

Background Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. Results We describe STEPS, a stochastic reaction–diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction–diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. Conclusion STEPS simulates models of cellular reaction–diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/ PMID:22574658

Idiosyncratic Adverse Drug Reactions: Current Concepts

PubMed Central

Naisbitt, Dean J.

2013-01-01

Idiosyncratic drug reactions are a significant cause of morbidity and mortality for patients; they also markedly increase the uncertainty of drug development. The major targets are skin, liver, and bone marrow. Clinical characteristics suggest that IDRs are immune mediated, and there is substantive evidence that most, but not all, IDRs are caused by chemically reactive species. However, rigorous mechanistic studies are very difficult to perform, especially in the absence of valid animal models. Models to explain how drugs or reactive metabolites interact with the MHC/T-cell receptor complex include the hapten and P-I models, and most recently it was found that abacavir can interact reversibly with MHC to alter the endogenous peptides that are presented to T cells. The discovery of HLA molecules as important risk factors for some IDRs has also significantly contributed to our understanding of these adverse reactions, but it is not yet clear what fraction of IDRs have a strong HLA dependence. In addition, with the exception of abacavir, most patients who have the HLA that confers a higher IDR risk with a specific drug will not have an IDR when treated with that drug. Interindividual differences in T-cell receptors and other factors also presumably play a role in determining which patients will have an IDR. The immune response represents a delicate balance, and immune tolerance may be the dominant response to a drug that can cause IDRs. PMID:23476052

Rate equation analysis of hydrogen uptake on Si (100) surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inanaga, S.; Rahman, F.; Khanom, F.

2005-09-15

We have studied the uptake process of H on Si (100) surfaces by means of rate equation analysis. Flowers' quasiequilibrium model for adsorption and desorption of H [M. C. Flowers, N. B. H. Jonathan, A. Morris, and S. Wright, Surf. Sci. 396, 227 (1998)] is extended so that in addition to the H abstraction (ABS) and {beta}{sub 2}-channel thermal desorption (TD) the proposed rate equation further includes the adsorption-induced desorption (AID) and {beta}{sub 1}-TD. The validity of the model is tested by the experiments of ABS and AID rates in the reaction system H+D/Si (100). Consequently, we find it canmore » well reproduce the experimental results, validating the proposed model. We find the AID rate curve as a function of surface temperature T{sub s} exhibits a clear anti-correlation with the bulk dangling bond density versus T{sub s} curve reported in the plasma-enhanced chemical vapor deposition (CVD) for amorphous Si films. The significance of the H chemistry in plasma-enhanced CVD is discussed.« less

Cycle life performance of rechargeable lithium ion batteries and mathematical modeling

NASA Astrophysics Data System (ADS)

Ning, Gang

Capacity fade of commercial Sony US 18650 Li-ion batteries cycled at high discharge rates was studied at ambient temperature. Battery cycled at the highest discharge rate (3 C) shows the largest internal resistance increase of 27.7% relative to the resistance of fresh battery. It's been observed anode carbon loses 10.6% of its capability to intercalate or deintercalate Li+ after it was subjected to 300 cycles at discharge rate of 3 C. This loss dominates capacity fade of full battery. A mechanism considering continuous parasitic reaction at anode/electrolyte interface and film thickening has been proposed. First principles based charge-discharge models to simulate cycle life behavior of rechargeable Li-ion batteries have been developed. In the generalized model, transport in both electrolyte phase and solid phase were simultaneously taken into account. Under mild charge-discharge condition, transport of lithium in the electrolyte phase has been neglected in the simplified model. Both models are based on loss of the active lithium ions due to the electrochemical parasitic reaction at anode/electrolyte interface and on rise of the anode film resistance. The effect of parameters such as depth of discharge (DOD), end of charge voltage (EOCV) and overvoltage of the parasitic reaction on the cycle life behavior of a battery has been analyzed. The experimental results obtained at a charge rate of 1 C, discharge rate of 0.5 C, EOCV of 4.0 V and DOD of 0.4 have been used to validate cycle life models. Good agreement between the simulations and the experiments has been achieved up to 1968 cycles with both models. Simulation of cycle life of battery under multiple cycling regimes has also been demonstrated.

Using the Training Reactions Questionnaire to Analyze the Reactions of University Students Undergoing Career-Related Training in Jordan: A Prospective Human Resource Development Approach

ERIC Educational Resources Information Center

Khasawneh, Samer; Al-Zawahreh, Abdelghafour

2015-01-01

The primary purpose of the present study was to validate Morgan and Casper's training reactions questionnaire (TRQ) for use in Jordan. The study also investigated the reactions of university students to career-related training programs. Another purpose of the study was to determine the impact of certain aspects of training programs on the overall…

Flame Chemiluminescence Rate Constants for Quantitative Microgravity Combustion Diagnostics

NASA Technical Reports Server (NTRS)

Luque, Jorge; Smith, Gregory P.; Jeffries, Jay B.; Crosley, David R.; Weiland, Karen (Technical Monitor)

2001-01-01

Absolute excited state concentrations of OH(A), CH(A), and C2(d) were determined in three low pressure premixed methane-air flames. Two dimensional images of chemiluminescence from these states were recorded by a filtered CCD camera, processed by Abel inversion, and calibrated against Rayleigh scattering, Using a previously validated 1-D flame model with known chemistry and excited state quenching rate constants, rate constants are extracted for the reactions CH + O2 (goes to) OH(A) + CO and C2H + O (goes to) CH(A) + CO at flame temperatures. Variations of flame emission intensities with stoichiometry agree well with model predictions.

XAFS of short-lived reduction products of structural and functional models of the [Fe Fe] hydrogenase H-cluster

NASA Astrophysics Data System (ADS)

Bondin, Mark I.; Borg, Stacey J.; Cheah, Mun-Hon; Best, Stephen P.

2006-11-01

Thiolate-bridged diiron compounds that are related to the active site of the [Fe-Fe] hydrogenase enzyme have been shown to act as electrocatalysts for reduction of protons. The use of XAFS for clarification of the structures of intermediates formed following reduction of related diiron carbonyl compounds is described. These measurements allow the determination of Fe-Fe and Fe-S bond lengths with good reliability and when used in conjunction with the standard bonding models this provides a means of validating the structures proposed for longer-lived ( t>20 s at -50 °C) reaction intermediates.

Automation on the generation of genome-scale metabolic models.

PubMed

Reyes, R; Gamermann, D; Montagud, A; Fuente, D; Triana, J; Urchueguía, J F; de Córdoba, P Fernández

2012-12-01

Nowadays, the reconstruction of genome-scale metabolic models is a nonautomatized and interactive process based on decision making. This lengthy process usually requires a full year of one person's work in order to satisfactory collect, analyze, and validate the list of all metabolic reactions present in a specific organism. In order to write this list, one manually has to go through a huge amount of genomic, metabolomic, and physiological information. Currently, there is no optimal algorithm that allows one to automatically go through all this information and generate the models taking into account probabilistic criteria of unicity and completeness that a biologist would consider. This work presents the automation of a methodology for the reconstruction of genome-scale metabolic models for any organism. The methodology that follows is the automatized version of the steps implemented manually for the reconstruction of the genome-scale metabolic model of a photosynthetic organism, Synechocystis sp. PCC6803. The steps for the reconstruction are implemented in a computational platform (COPABI) that generates the models from the probabilistic algorithms that have been developed. For validation of the developed algorithm robustness, the metabolic models of several organisms generated by the platform have been studied together with published models that have been manually curated. Network properties of the models, like connectivity and average shortest mean path of the different models, have been compared and analyzed.

Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

PubMed

Du, Bin; Zhang, Zhen; Grubner, Sharon; Yurkovich, James T; Palsson, Bernhard O; Zielinski, Daniel C

2018-06-05

Reaction-equilibrium constants determine the metabolite concentrations necessary to drive flux through metabolic pathways. Group-contribution methods offer a way to estimate reaction-equilibrium constants at wide coverage across the metabolic network. Here, we present an updated group-contribution method with 1) additional curated thermodynamic data used in fitting and 2) capabilities to calculate equilibrium constants as a function of temperature. We first collected and curated aqueous thermodynamic data, including reaction-equilibrium constants, enthalpies of reaction, Gibbs free energies of formation, enthalpies of formation, entropy changes of formation of compounds, and proton- and metal-ion-binding constants. Next, we formulated the calculation of equilibrium constants as a function of temperature and calculated the standard entropy change of formation (Δ f S ∘ ) using a model based on molecular properties. The median absolute error in estimating Δ f S ∘ was 0.013 kJ/K/mol. We also estimated magnesium binding constants for 618 compounds using a linear regression model validated against measured data. We demonstrate the improved performance of the current method (8.17 kJ/mol in median absolute residual) over the current state-of-the-art method (11.47 kJ/mol) in estimating the 185 new reactions added in this work. The efforts here fill in gaps for thermodynamic calculations under various conditions, specifically different temperatures and metal-ion concentrations. These, to our knowledge, new capabilities empower the study of thermodynamic driving forces underlying the metabolic function of organisms living under diverse conditions. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A fluorescence high throughput screening method for the detection of reactive electrophiles as potential skin sensitizers.

PubMed

Avonto, Cristina; Chittiboyina, Amar G; Rua, Diego; Khan, Ikhlas A

2015-12-01

Skin sensitization is an important toxicological end-point in the risk assessment of chemical allergens. Because of the complexity of the biological mechanisms associated with skin sensitization, integrated approaches combining different chemical, biological and in silico methods are recommended to replace conventional animal tests. Chemical methods are intended to characterize the potential of a sensitizer to induce earlier molecular initiating events. The presence of an electrophilic mechanistic domain is considered one of the essential chemical features to covalently bind to the biological target and induce further haptenation processes. Current in chemico assays rely on the quantification of unreacted model nucleophiles after incubation with the candidate sensitizer. In the current study, a new fluorescence-based method, 'HTS-DCYA assay', is proposed. The assay aims at the identification of reactive electrophiles based on their chemical reactivity toward a model fluorescent thiol. The reaction workflow enabled the development of a High Throughput Screening (HTS) method to directly quantify the reaction adducts. The reaction conditions have been optimized to minimize solubility issues, oxidative side reactions and increase the throughput of the assay while minimizing the reaction time, which are common issues with existing methods. Thirty-six chemicals previously classified with LLNA, DPRA or KeratinoSens™ were tested as a proof of concept. Preliminary results gave an estimated 82% accuracy, 78% sensitivity, 90% specificity, comparable to other in chemico methods such as Cys-DPRA. In addition to validated chemicals, six natural products were analyzed and a prediction of their sensitization potential is presented for the first time. Copyright © 2015 Elsevier Inc. All rights reserved.

Anticipatory Traumatic Reaction: Outcomes Arising From Secondary Exposure to Disasters and Large-Scale Threats.

PubMed

Hopwood, Tanya L; Schutte, Nicola S; Loi, Natasha M

2017-09-01

Two studies, with a total of 707 participants, developed and examined the reliability and validity of a measure for anticipatory traumatic reaction (ATR), a novel construct describing a form of distress that may occur in response to threat-related media reports and discussions. Exploratory and confirmatory factor analysis resulted in a scale comprising three subscales: feelings related to future threat; preparatory thoughts and actions; and disruption to daily activities. Internal consistency was .93 for the overall ATR scale. The ATR scale demonstrated convergent validity through associations with negative affect, depression, anxiety, stress, neuroticism, and repetitive negative thinking. The scale showed discriminant validity in relationships to Big Five characteristics. The ATR scale had some overlap with a measure of posttraumatic stress disorder, but also showed substantial separate variance. This research provides preliminary evidence for the novel construct of ATR as well as a measure of the construct. The ATR scale will allow researchers to further investigate anticipatory traumatic reaction in the fields of trauma, clinical practice, and social psychology.

A Dynamic/Anisotropic Low Earth Orbit (LEO) Ionizing Radiation Model

NASA Technical Reports Server (NTRS)

Badavi, Francis F.; West, Katie J.; Nealy, John E.; Wilson, John W.; Abrahms, Briana L.; Luetke, Nathan J.

2006-01-01

The International Space Station (ISS) provides the proving ground for future long duration human activities in space. Ionizing radiation measurements in ISS form the ideal tool for the experimental validation of ionizing radiation environmental models, nuclear transport code algorithms, and nuclear reaction cross sections. Indeed, prior measurements on the Space Transportation System (STS; Shuttle) have provided vital information impacting both the environmental models and the nuclear transport code development by requiring dynamic models of the Low Earth Orbit (LEO) environment. Previous studies using Computer Aided Design (CAD) models of the evolving ISS configurations with Thermo Luminescent Detector (TLD) area monitors, demonstrated that computational dosimetry requires environmental models with accurate non-isotropic as well as dynamic behavior, detailed information on rack loading, and an accurate 6 degree of freedom (DOF) description of ISS trajectory and orientation.

The effect of toxic carbon source on the reaction of activated sludge in the batch reactor.

PubMed

Wu, Changyong; Zhou, Yuexi; Zhang, Siyu; Xu, Min; Song, Jiamei

2018-03-01

The toxic carbon source can cause higher residual effluent dissolved organic carbon than easily biodegraded carbon source in activated sludge process. In this study, an integrated activated sludge model is developed as the tool to understand the mechanism of toxic carbon source (phenol) on the reaction, regarding the carbon flows during the aeration period in the batch reactor. To estimate the toxic function of phenol, the microbial cells death rate (k death ) is introduced into the model. The integrated model was calibrated and validated by the experimental data and it was found the model simulations matched the all experimental measurements. In the steady state, the toxicity of phenol can result in higher microbial cells death rate (0.1637 h -1 vs 0.0028 h -1 ) and decay rate coefficient of biomass (0.0115 h -1 vs 0.0107 h -1 ) than acetate. In addition, the utilization-associated products (UAP) and extracellular polymeric substances (EPS) formation coefficients of phenol are higher than that of acetate, indicating that more carbon flows into the extracellular components, such as soluble microbial products (SMP), when degrading toxic organics. In the non-steady state of feeding phenol, the yield coefficient for growth and maximum specific growth rate are very low in the first few days (1-10 d), while the decay rate coefficient of biomass and microbial cells death rate are relatively high. The model provides insights into the difference of the dynamic reaction with different carbon sources in the batch reactor. Copyright © 2017 Elsevier Ltd. All rights reserved.

A computational study of ultrafast acid dissociation and acid-base neutralization reactions. I. The model.

PubMed

Maurer, Patrick; Thomas, Vibin; Rivard, Ugo; Iftimie, Radu

2010-07-28

Ultrafast, time-resolved investigations of acid-base neutralization reactions have recently been performed using systems containing the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) and various Bronsted bases. Two conflicting neutralization mechanisms have been formulated by Mohammed et al. [Science 310, 83 (2005)] and Siwick et al. [J. Am. Chem. Soc. 129, 13412 (2007)] for the same acid-base system. Herein an ab initio molecular dynamics based computational model is formulated, which is able to investigate the validity of the proposed mechanisms in the general context of ground-state acid-base neutralization reactions. Our approach consists of using 2,4,6-tricyanophenol (exp. pKa congruent with 1) as a model for excited-state HPTS( *) (pKa congruent with 1.4) and carboxylate ions for the accepting base. We employ our recently proposed dipole-field/quantum mechanics (QM) treatment [P. Maurer and R. Iftimie, J. Chem. Phys. 132, 074112 (2010)] of the proton donor and acceptor molecules. This approach allows one to tune the free energy of neutralization to any desired value as well as model initial nonequilibrium hydration effects caused by a sudden increase in acidity, making it possible to achieve a more realistic comparison with experimental data than could be obtained via a full-QM treatment of the entire system. It is demonstrated that the dipole-field/QM model reproduces correctly key properties of the 2,4,6-tricyanophenol acid molecule including gas-phase proton dissociation energies and dipole moments, and condensed-phase hydration structure and pKa values.

Mining adverse drug reactions from online healthcare forums using hidden Markov model.

PubMed

Sampathkumar, Hariprasad; Chen, Xue-wen; Luo, Bo

2014-10-23

Adverse Drug Reactions are one of the leading causes of injury or death among patients undergoing medical treatments. Not all Adverse Drug Reactions are identified before a drug is made available in the market. Current post-marketing drug surveillance methods, which are based purely on voluntary spontaneous reports, are unable to provide the early indications necessary to prevent the occurrence of such injuries or fatalities. The objective of this research is to extract reports of adverse drug side-effects from messages in online healthcare forums and use them as early indicators to assist in post-marketing drug surveillance. We treat the task of extracting adverse side-effects of drugs from healthcare forum messages as a sequence labeling problem and present a Hidden Markov Model(HMM) based Text Mining system that can be used to classify a message as containing drug side-effect information and then extract the adverse side-effect mentions from it. A manually annotated dataset from http://www.medications.com is used in the training and validation of the HMM based Text Mining system. A 10-fold cross-validation on the manually annotated dataset yielded on average an F-Score of 0.76 from the HMM Classifier, in comparison to 0.575 from the Baseline classifier. Without the Plain Text Filter component as a part of the Text Processing module, the F-Score of the HMM Classifier was reduced to 0.378 on average, while absence of the HTML Filter component was found to have no impact. Reducing the Drug names dictionary size by half, on average reduced the F-Score of the HMM Classifier to 0.359, while a similar reduction to the side-effects dictionary yielded an F-Score of 0.651 on average. Adverse side-effects mined from http://www.medications.com and http://www.steadyhealth.com were found to match the Adverse Drug Reactions on the Drug Package Labels of several drugs. In addition, some novel adverse side-effects, which can be potential Adverse Drug Reactions, were also identified. The results from the HMM based Text Miner are encouraging to pursue further enhancements to this approach. The mined novel side-effects can act as early indicators for health authorities to help focus their efforts in post-marketing drug surveillance.

Perceived Parental Reactions to Adolescent Distress (PRAD): Development and Validation of a Brief Measure

PubMed Central

Barbot, Baptiste; Heinz, Sasha L.; Luthar, Suniya S.

2013-01-01

Although adolescence is a time of individuation with increased reliance on peers, research indicates that, despite a deliberate distancing from parents, adolescents continue to seek the support and console of parental attachment figures in times of distress. The Perceived Parental Reactions to Adolescent Distress (PRAD) is a brief self-report measure developed to examine adolescents’ perception of parental response under conditions of distress as measured by four conceptually and empirically distinct parental reactions to distress: Comfort, Self-focus, Avoidance and Harshness. Across two studies involving a total of 738 high school students, we developed the PRAD and substantiated its robust psychometric properties, including evidence for reliability as well as internal and criterion validity. Sources of individual differences in the test-scores were also explored. Empirical as well as practical importance of assessing parental reactions to adolescent distress is discussed with regard to both the attachment and adolescent development literature. PMID:23777451

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, D. A.; Chadwick, M. B.; Capote, R.

We describe the new ENDF/B-VIII.0 evaluated nuclear reaction data library. ENDF/B-VIII.0 fully incorporates the new IAEA standards, includes improved thermal neutron scattering data and uses new evaluated data from the CIELO project for neutron reactions on 1H, 16O, 56Fe, 235U, 238U and 239Pu described in companion papers in the present issue of Nuclear Data Sheets. The evaluations benefit from recent experimental data obtained in the U.S. and Europe, and improvements in theory and simulation. Notable advances include updated evaluated data for light nuclei, structural materials, actinides, fission energy release, prompt fission neutron and γ-ray spectra, thermal neutron scattering data, andmore » charged-particle reactions. Integral validation testing is shown for a wide range of criticality, reaction rate, and neutron transmission benchmarks. In general, integral validation performance of the library is improved relative to the previous ENDF/B-VII.1 library.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Rekha R.; Mondy, Lisa Ann; Noble, David R.

We are studying PMDI polyurethane with a fast catalyst, such that filling and polymerization occur simultaneously. The foam is over-packed to tw ice or more of its free rise density to reach the density of interest. Our approach is to co mbine model development closely with experiments to discover new physics, to parameterize models and to validate the models once they have been developed. The model must be able to repres ent the expansion, filling, curing, and final foam properties. PMDI is chemically blown foam, wh ere carbon dioxide is pr oduced via the reaction of water and isocyanate. Themore » isocyanate also re acts with polyol in a competing reaction, which produces the polymer. A new kinetic model is developed and implemented, which follows a simplified mathematical formalism that decouple s these two reactions. The model predicts the polymerization reaction via condensation chemis try, where vitrification and glass transition temperature evolution must be included to correctly predict this quantity. The foam gas generation kinetics are determined by tracking the molar concentration of both water and carbon dioxide. Understanding the therma l history and loads on the foam due to exothermicity and oven heating is very important to the results, since the kinetics and ma terial properties are all very sensitive to temperature. The conservation eq uations, including the e quations of motion, an energy balance, and thr ee rate equations are solved via a stabilized finite element method. We assume generalized-Newtonian rheology that is dependent on the cure, gas fraction, and temperature. The conservation equations are comb ined with a level set method to determine the location of the free surface over time. Results from the model are compared to experimental flow visualization data and post-te st CT data for the density. Seve ral geometries are investigated including a mock encapsulation part, two configur ations of a mock stru ctural part, and a bar geometry to specifically test the density model. We have found that the model predicts both average density and filling profiles well. However, it under predicts density gradients, especially in the gravity direction. Thoughts on m odel improvements are also discussed.« less

Flow optimization study of a batch microfluidics PET tracer synthesizing device

PubMed Central

Elizarov, Arkadij M.; Meinhart, Carl; van Dam, R. Michael; Huang, Jiang; Daridon, Antoine; Heath, James R.; Kolb, Hartmuth C.

2010-01-01

We present numerical modeling and experimental studies of flow optimization inside a batch microfluidic micro-reactor used for synthesis of human-scale doses of Positron Emission Tomography (PET) tracers. Novel techniques are used for mixing within, and eluting liquid out of, the coin-shaped reaction chamber. Numerical solutions of the general incompressible Navier Stokes equations along with time-dependent elution scalar field equation for the three dimensional coin-shaped geometry were obtained and validated using fluorescence imaging analysis techniques. Utilizing the approach presented in this work, we were able to identify optimized geometrical and operational conditions for the micro-reactor in the absence of radioactive material commonly used in PET related tracer production platforms as well as evaluate the designed and fabricated micro-reactor using numerical and experimental validations. PMID:21072595

Subject-specific finite element modelling of the human foot complex during walking: sensitivity analysis of material properties, boundary and loading conditions.

PubMed

Akrami, Mohammad; Qian, Zhihui; Zou, Zhemin; Howard, David; Nester, Chris J; Ren, Lei

2018-04-01

The objective of this study was to develop and validate a subject-specific framework for modelling the human foot. This was achieved by integrating medical image-based finite element modelling, individualised multi-body musculoskeletal modelling and 3D gait measurements. A 3D ankle-foot finite element model comprising all major foot structures was constructed based on MRI of one individual. A multi-body musculoskeletal model and 3D gait measurements for the same subject were used to define loading and boundary conditions. Sensitivity analyses were used to investigate the effects of key modelling parameters on model predictions. Prediction errors of average and peak plantar pressures were below 10% in all ten plantar regions at five key gait events with only one exception (lateral heel, in early stance, error of 14.44%). The sensitivity analyses results suggest that predictions of peak plantar pressures are moderately sensitive to material properties, ground reaction forces and muscle forces, and significantly sensitive to foot orientation. The maximum region-specific percentage change ratios (peak stress percentage change over parameter percentage change) were 1.935-2.258 for ground reaction forces, 1.528-2.727 for plantar flexor muscles and 4.84-11.37 for foot orientations. This strongly suggests that loading and boundary conditions need to be very carefully defined based on personalised measurement data.

Shielded Heavy-Ion Environment Linear Detector (SHIELD): an experiment for the Radiation and Technology Demonstration (RTD) Mission.

PubMed

Shavers, M R; Cucinotta, F A; Miller, J; Zeitlin, C; Heilbronn, L; Wilson, J W; Singleterry, R C

2001-01-01

Radiological assessment of the many cosmic ion species of widely distributed energies requires the use of theoretical transport models to accurately describe diverse physical processes related to nuclear reactions in spacecraft structures, planetary atmospheres and surfaces, and tissues. Heavy-ion transport models that were designed to characterize shielded radiation fields have been validated through comparison with data from thick-target irradiation experiments at particle accelerators. With the RTD Mission comes a unique opportunity to validate existing radiation transport models and guide the development of tools for shield design. For the first time, transport properties will be measured in free-space to characterize the shielding effectiveness of materials that are likely to be aboard interplanetary space missions. Target materials composed of aluminum, advanced composite spacecraft structure and other shielding materials, helium (a propellant) and tissue equivalent matrices will be evaluated. Large solid state detectors will provide kinetic energy and charge identification for incident heavy-ions and for secondary ions created in the target material. Transport calculations using the HZETRN model suggest that 8 g cm -2 thick targets would be adequate to evaluate the shielding effectiveness during solar minimum activity conditions for a period of 30 days or more.

Liquid Oxygen/Liquid Methane Integrated Propulsion System Test Bed

NASA Technical Reports Server (NTRS)

Flynn, Howard; Lusby, Brian; Villemarette, Mark

2011-01-01

In support of NASA?s Propulsion and Cryogenic Advanced Development (PCAD) project, a liquid oxygen (LO2)/liquid methane (LCH4) Integrated Propulsion System Test Bed (IPSTB) was designed and advanced to the Critical Design Review (CDR) stage at the Johnson Space Center. The IPSTB?s primary objectives are to study LO2/LCH4 propulsion system steady state and transient performance, operational characteristics and to validate fluid and thermal models of a LO2/LCH4 propulsion system for use in future flight design work. Two phase thermal and dynamic fluid flow models of the IPSTB were built to predict the system performance characteristics under a variety of operating modes and to aid in the overall system design work. While at ambient temperature and simulated altitude conditions at the White Sands Test Facility, the IPSTB and its approximately 600 channels of system instrumentation would be operated to perform a variety of integrated main engine and reaction control engine hot fire tests. The pressure, temperature, and flow rate data collected during this testing would then be used to validate the analytical models of the IPSTB?s thermal and dynamic fluid flow performance. An overview of the IPSTB design and analytical model development will be presented.

The origin of garnet in the anorthosite-charnockite suite of the Adirondacks

USGS Publications Warehouse

McLelland, J.M.; Whitney, P.R.

1977-01-01

Detailed analysis of textural and chemical criteria in rocks of the anorthosite-charnockite suite of the Adirondack Highlands suggests that development of garnet in silica-saturated rocks of the suite occurs according to the reaction: {Mathematical expression}, where ?? is a function of the distribution of Fe and Mg between the several coexisting ferromagnesian phases. Depending upon the relative amounts of Fe and Mg present, quartz may be either a reactant or a product. Using an aluminum-fixed reference frame, this reaction can be restated in terms of a set of balanced partial reactions describing the processes occurring in spatially separated domains within the rock. The fact that garnet invariably replaces plagioclase as opposed to the other reactant phases indicates that the aluminum-fixed model is valid as a first approximation. This reaction is univariant and produces unzoned garnet. It differs from a similar equation proposed by de Waard (1965) for the origin of garnet in Adirondack metabasic rocks, i.e. 6 Orthopyroxene+2 Anorthite = Clinopyroxene+Garnet+2 Quartz, the principle difference being that iron oxides (ilmenite and/or magnetite) are essential reactant phases in the present reactions. The product assemblage (garnet+clinopyroxene+plagioclase ?? orthopyroxene ?? quartz) is characteristic of the clinopyroxene-almandine subfacies of the granulite facies. ?? 1977 Springer-Verlag.

Catalytic conversion in nanoporous materials: Concentration oscillations and spatial correlations due to inhibited transport and intermolecular interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia, Andres; Evans, James W.

2016-11-03

We show that steady-state catalytic conversion in nanoporous materials can occur in a quasi-counter-diffusion mode with the reactant (product) concentration strongly decaying (growing) into the pore, but also with oscillations in the total concentration. These oscillations reflect the response of the fluid to the transition from an extended to a confined environment near the pore opening. We focus on the regime of strongly inhibited transport in narrow pores corresponding to single-file diffusion. Here, limited penetration of the reactant into the pores and the associated low reaction yield is impacted by strong spatial correlations induced by both reaction (non-equilibrium correlations) andmore » also by intermolecular interactions (thermodynamic correlations). We develop a generalized hydrodynamic formulation to effectively describe inhibited transport accounting for the effect of these correlations, and incorporate this description of transport into appropriate reaction-diffusion equations. These equations accurately describe both shorter-range concentration oscillations near the pore opening and the longer-range mesoscale variation of concentration profiles in the pore (and thus also describe reaction yield). Success of the analytic theory is validated by comparison with a precise kinetic Monte Carlo simulation of an appropriate molecular-level stochastic reaction-diffusion model. As a result, this work elucidates unconventional chemical kinetics in interacting confined systems.« less

Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zapol, Peter; Bourg, Ian; Criscenti, Louise Jacqueline

2011-10-01

This report summarizes research performed for the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Subcontinuum and Upscaling Task. The work conducted focused on developing a roadmap to include molecular scale, mechanistic information in continuum-scale models of nuclear waste glass dissolution. This information is derived from molecular-scale modeling efforts that are validated through comparison with experimental data. In addition to developing a master plan to incorporate a subcontinuum mechanistic understanding of glass dissolution into continuum models, methods were developed to generate constitutive dissolution rate expressions from quantum calculations, force field models were selected to generate multicomponent glass structures and gel layers,more » classical molecular modeling was used to study diffusion through nanopores analogous to those in the interfacial gel layer, and a micro-continuum model (K{mu}C) was developed to study coupled diffusion and reaction at the glass-gel-solution interface.« less

A Frequency-Domain Substructure System Identification Algorithm

NASA Technical Reports Server (NTRS)

Blades, Eric L.; Craig, Roy R., Jr.

1996-01-01

A new frequency-domain system identification algorithm is presented for system identification of substructures, such as payloads to be flown aboard the Space Shuttle. In the vibration test, all interface degrees of freedom where the substructure is connected to the carrier structure are either subjected to active excitation or are supported by a test stand with the reaction forces measured. The measured frequency-response data is used to obtain a linear, viscous-damped model with all interface-degree of freedom entries included. This model can then be used to validate analytical substructure models. This procedure makes it possible to obtain not only the fixed-interface modal data associated with a Craig-Bampton substructure model, but also the data associated with constraint modes. With this proposed algorithm, multiple-boundary-condition tests are not required, and test-stand dynamics is accounted for without requiring a separate modal test or finite element modeling of the test stand. Numerical simulations are used in examining the algorithm's ability to estimate valid reduced-order structural models. The algorithm's performance when frequency-response data covering narrow and broad frequency bandwidths is used as input is explored. Its performance when noise is added to the frequency-response data and the use of different least squares solution techniques are also examined. The identified reduced-order models are also compared for accuracy with other test-analysis models and a formulation for a Craig-Bampton test-analysis model is also presented.

Global Modelling of the total OH reactivity: validation against measurements and atmospheric implications of the 'missing' sink

NASA Astrophysics Data System (ADS)

Ferracci, Valerio; Archibald, Alexander T.; Pyle, John A.

2017-04-01

The removal of most trace gases emitted into the atmosphere is primarily initiated by reaction with the hydroxyl radical, OH. A number of field campaigns over the last two decades have observed the presence of a "missing" sink of the OH radical in a variety of regions across the planet, from urban areas to remote forests: comparison of the direct measurements of the OH loss rate, also known as total OH reactivity, with the sum of individual known OH sinks (obtained via the simultaneous detection of species such as volatile organic compounds and nitrogen oxides) indicated that, in some cases, up to 80% of the total OH loss rate was unaccounted for. The implications of this finding are significant, as a potentially major OH sink operating in the atmosphere is not currently accounted for in atmospheric models: the presence of an additional OH sink might, for instance, lead to an increase in the atmospheric lifetime of a number of trace species, including high-impact greenhouse gases such as methane. The only modelling of the total OH reactivity is currently performed on a regional scale; a thorough assessment of the impact of the missing sink on the chemistry and climate of the planet by global modelling is therefore highly desirable. In this work a chemistry-climate model (the Met Office's Unified Model with the United Kingdom Chemistry and Aerosols scheme, UM-UKCA) was used to calculate the total OH reactivity at the planetary boundary layer. The model output was validated against available field measurements to verify that the known OH sinks observed in the field were reproduced correctly by the model: a good agreement was found between the data from more than 30 field campaigns and the model output. Following this, the effects of introducing novel OH sinks in the chemistry scheme were investigated. The first step was the introduction in the model of the newly characterised reactions of peroxy radicals (RO2) with OH, the kinetics and products of which have only recently been studied in the laboratory. Results from the UM-UKCA model show that reaction with RO2 might represent a non-negligible OH sink in remote environments, but cannot reconcile field measurements of the total OH reactivity with the sum of the individual sinks. To address this, an unspecified additional sink was added to the model in a series of simulations reproducing different scenarios (e.g., different OH recycling probabilities through the oxidation of the additional sink) with a view to establishing the impact of the additional OH sink on the oxidative capacity of the lower atmosphere.

Real-time monitoring of disintegration activity of catalytic core domain of HIV-1 integrase using molecular beacon.

PubMed

Zhang, Da-wei; Zhao, Ming-ming; He, Hong-qiu; Guo, Shun-xing

2013-09-15

HIV-1 integrase, an essential enzyme for retroviral replication, is a validated target for anti-HIV therapy development. The catalytic core domain of integrase (IN-CCD) is capable of catalyzing disintegration reaction. In this work, a hairpin-shaped disintegration substrate was designed and validated by enzyme-linked immunosorbent assay; a molecular beacon-based assay was developed for disintegration reaction of IN-CCD. Results showed that the disintegration substrate could be recognized and catalyzed by IN-CCD, and the disintegration reaction can be monitored according to the increase of fluorescent signal. The assay can be applied to real-time detection of disintegration with advantages of simplicity, high sensitivity, and excellent specificity. Copyright © 2013 Elsevier Inc. All rights reserved.

Validated spectrophotometric methods for determination of sodium valproate based on charge transfer complexation reactions.

PubMed

Belal, Tarek S; El-Kafrawy, Dina S; Mahrous, Mohamed S; Abdel-Khalek, Magdi M; Abo-Gharam, Amira H

2016-02-15

This work presents the development, validation and application of four simple and direct spectrophotometric methods for determination of sodium valproate (VP) through charge transfer complexation reactions. The first method is based on the reaction of the drug with p-chloranilic acid (p-CA) in acetone to give a purple colored product with maximum absorbance at 524nm. The second method depends on the reaction of VP with dichlone (DC) in dimethylformamide forming a reddish orange product measured at 490nm. The third method is based upon the interaction of VP and picric acid (PA) in chloroform resulting in the formation of a yellow complex measured at 415nm. The fourth method involves the formation of a yellow complex peaking at 361nm upon the reaction of the drug with iodine in chloroform. Experimental conditions affecting the color development were studied and optimized. Stoichiometry of the reactions was determined. The proposed spectrophotometric procedures were effectively validated with respect to linearity, ranges, precision, accuracy, specificity, robustness, detection and quantification limits. Calibration curves of the formed color products with p-CA, DC, PA and iodine showed good linear relationships over the concentration ranges 24-144, 40-200, 2-20 and 1-8μg/mL respectively. The proposed methods were successfully applied to the assay of sodium valproate in tablets and oral solution dosage forms with good accuracy and precision. Assay results were statistically compared to a reference pharmacopoeial HPLC method where no significant differences were observed between the proposed methods and reference method. Copyright © 2015 Elsevier B.V. All rights reserved.

Validated spectrophotometric methods for determination of sodium valproate based on charge transfer complexation reactions

NASA Astrophysics Data System (ADS)

Belal, Tarek S.; El-Kafrawy, Dina S.; Mahrous, Mohamed S.; Abdel-Khalek, Magdi M.; Abo-Gharam, Amira H.

2016-02-01

This work presents the development, validation and application of four simple and direct spectrophotometric methods for determination of sodium valproate (VP) through charge transfer complexation reactions. The first method is based on the reaction of the drug with p-chloranilic acid (p-CA) in acetone to give a purple colored product with maximum absorbance at 524 nm. The second method depends on the reaction of VP with dichlone (DC) in dimethylformamide forming a reddish orange product measured at 490 nm. The third method is based upon the interaction of VP and picric acid (PA) in chloroform resulting in the formation of a yellow complex measured at 415 nm. The fourth method involves the formation of a yellow complex peaking at 361 nm upon the reaction of the drug with iodine in chloroform. Experimental conditions affecting the color development were studied and optimized. Stoichiometry of the reactions was determined. The proposed spectrophotometric procedures were effectively validated with respect to linearity, ranges, precision, accuracy, specificity, robustness, detection and quantification limits. Calibration curves of the formed color products with p-CA, DC, PA and iodine showed good linear relationships over the concentration ranges 24-144, 40-200, 2-20 and 1-8 μg/mL respectively. The proposed methods were successfully applied to the assay of sodium valproate in tablets and oral solution dosage forms with good accuracy and precision. Assay results were statistically compared to a reference pharmacopoeial HPLC method where no significant differences were observed between the proposed methods and reference method.

Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.

PubMed

Schaff, James C; Gao, Fei; Li, Ye; Novak, Igor L; Slepchenko, Boris M

2016-12-01

Hybrid deterministic-stochastic methods provide an efficient alternative to a fully stochastic treatment of models which include components with disparate levels of stochasticity. However, general-purpose hybrid solvers for spatially resolved simulations of reaction-diffusion systems are not widely available. Here we describe fundamentals of a general-purpose spatial hybrid method. The method generates realizations of a spatially inhomogeneous hybrid system by appropriately integrating capabilities of a deterministic partial differential equation solver with a popular particle-based stochastic simulator, Smoldyn. Rigorous validation of the algorithm is detailed, using a simple model of calcium 'sparks' as a testbed. The solver is then applied to a deterministic-stochastic model of spontaneous emergence of cell polarity. The approach is general enough to be implemented within biologist-friendly software frameworks such as Virtual Cell.

Detailed surface reaction mechanism in a three-way catalyst.

PubMed

Chatterjee, D; Deutschmann, O; Warnatz, J

2001-01-01

Monolithic three-way catalysts are applied to reduce the emission of combustion engines. The design of such a catalytic converter is a complex process involving the optimization of different physical and chemical parameters (in the simplest case, e.g., length, cell densities or metal coverage of the catalyst). Numerical simulation can be used as an effective tool for the investigation of the catalytic properties of a catalytic converter and for the prediction of the performance of the catalyst. To attain this goal, a two-dimensional flow-field description is coupled with a detailed surface reaction model (gas-phase reactions can be neglected in three-way catalysts). This surface reaction mechanism (with C3H6 taken as representative of unburnt hydrocarbons) was developed using sub-mechanisms recently developed for hydrogen, carbon monoxide and methane oxidation, literature values for C3H6 oxidation, and estimates for the remaining unknown reactions. Results of the simulation of a monolithic single channel are used to validate the surface reaction mechanism. The performance of the catalyst was simulated under lean, nearly stoichiometric and rich conditions. For these characteristic conditions, the oxidation of propene and carbon monoxide and the reduction of NO on a typical Pt/Rh coated three-way catalyst were simulated as a function of temperature. The numerically predicted conversion data are compared with experimentally measured data. The simulation further reveals the coupling between chemical reactions and transport processes within the monolithic channel.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2011-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2010-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier.Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Update of the Polar SWIFT model for polar stratospheric ozone loss (Polar SWIFT version 2)

NASA Astrophysics Data System (ADS)

Wohltmann, Ingo; Lehmann, Ralph; Rex, Markus

2017-07-01

The Polar SWIFT model is a fast scheme for calculating the chemistry of stratospheric ozone depletion in polar winter. It is intended for use in global climate models (GCMs) and Earth system models (ESMs) to enable the simulation of mutual interactions between the ozone layer and climate. To date, climate models often use prescribed ozone fields, since a full stratospheric chemistry scheme is computationally very expensive. Polar SWIFT is based on a set of coupled differential equations, which simulate the polar vortex-averaged mixing ratios of the key species involved in polar ozone depletion on a given vertical level. These species are O3, chemically active chlorine (ClOx), HCl, ClONO2 and HNO3. The only external input parameters that drive the model are the fraction of the polar vortex in sunlight and the fraction of the polar vortex below the temperatures necessary for the formation of polar stratospheric clouds. Here, we present an update of the Polar SWIFT model introducing several improvements over the original model formulation. In particular, the model is now trained on vortex-averaged reaction rates of the ATLAS Chemistry and Transport Model, which enables a detailed look at individual processes and an independent validation of the different parameterizations contained in the differential equations. The training of the original Polar SWIFT model was based on fitting complete model runs to satellite observations and did not allow for this. A revised formulation of the system of differential equations is developed, which closely fits vortex-averaged reaction rates from ATLAS that represent the main chemical processes influencing ozone. In addition, a parameterization for the HNO3 change by denitrification is included. The rates of change of the concentrations of the chemical species of the Polar SWIFT model are purely chemical rates of change in the new version, whereas in the original Polar SWIFT model, they included a transport effect caused by the original training on satellite data. Hence, the new version allows for an implementation into climate models in combination with an existing stratospheric transport scheme. Finally, the model is now formulated on several vertical levels encompassing the vertical range in which polar ozone depletion is observed. The results of the Polar SWIFT model are validated with independent Microwave Limb Sounder (MLS) satellite observations and output from the original detailed chemistry model of ATLAS.

A Computational Fluid Dynamic Model for a Novel Flash Ironmaking Process

NASA Astrophysics Data System (ADS)

Perez-Fontes, Silvia E.; Sohn, Hong Yong; Olivas-Martinez, Miguel

A computational fluid dynamic model for a novel flash ironmaking process based on the direct gaseous reduction of iron oxide concentrates is presented. The model solves the three-dimensional governing equations including both gas-phase and gas-solid reaction kinetics. The turbulence-chemistry interaction in the gas-phase is modeled by the eddy dissipation concept incorporating chemical kinetics. The particle cloud model is used to track the particle phase in a Lagrangian framework. A nucleation and growth kinetics rate expression is adopted to calculate the reduction rate of magnetite concentrate particles. Benchmark experiments reported in the literature for a nonreacting swirling gas jet and a nonpremixed hydrogen jet flame were simulated for validation. The model predictions showed good agreement with measurements in terms of gas velocity, gas temperature and species concentrations. The relevance of the computational model for the analysis of a bench reactor operation and the design of an industrial-pilot plant is discussed.