Mechanistic study of manganese-substituted glycerol dehydrogenase using a kinetic and thermodynamic analysis.

PubMed

Fang, Baishan; Niu, Jin; Ren, Hong; Guo, Yingxia; Wang, Shizhen

2014-01-01

Mechanistic insights regarding the activity enhancement of dehydrogenase by metal ion substitution were investigated by a simple method using a kinetic and thermodynamic analysis. By profiling the binding energy of both the substrate and product, the metal ion's role in catalysis enhancement was revealed. Glycerol dehydrogenase (GDH) from Klebsiella pneumoniae sp., which demonstrated an improvement in activity by the substitution of a zinc ion with a manganese ion, was used as a model for the mechanistic study of metal ion substitution. A kinetic model based on an ordered Bi-Bi mechanism was proposed considering the noncompetitive product inhibition of dihydroxyacetone (DHA) and the competitive product inhibition of NADH. By obtaining preliminary kinetic parameters of substrate and product inhibition, the number of estimated parameters was reduced from 10 to 4 for a nonlinear regression-based kinetic parameter estimation. The simulated values of time-concentration curves fit the experimental values well, with an average relative error of 11.5% and 12.7% for Mn-GDH and GDH, respectively. A comparison of the binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicated that metal ion substitution accelerated the release of dioxyacetone. The metal ion's role in catalysis enhancement was explicated.

Comparative kinetic analysis on thermal degradation of some cephalosporins using TG and DSC data

PubMed Central

2013-01-01

Background The thermal decomposition of cephalexine, cefadroxil and cefoperazone under non-isothermal conditions using the TG, respectively DSC methods, was studied. In case of TG, a hyphenated technique, including EGA, was used. Results The kinetic analysis was performed using the TG and DSC data in air for the first step of cephalosporin’s decomposition at four heating rates. The both TG and DSC data were processed according to an appropriate strategy to the following kinetic methods: Kissinger-Akahira-Sunose, Friedman, and NPK, in order to obtain realistic kinetic parameters, even if the decomposition process is a complex one. The EGA data offer some valuable indications about a possible decomposition mechanism. The obtained data indicate a rather good agreement between the activation energy’s values obtained by different methods, whereas the EGA data and the chemical structures give a possible explanation of the observed differences on the thermal stability. A complete kinetic analysis needs a data processing strategy using two or more methods, but the kinetic methods must also be applied to the different types of experimental data (TG and DSC). Conclusion The simultaneous use of DSC and TG data for the kinetic analysis coupled with evolved gas analysis (EGA) provided us a more complete picture of the degradation of the three cephalosporins. It was possible to estimate kinetic parameters by using three different kinetic methods and this allowed us to compare the Ea values obtained from different experimental data, TG and DSC. The thermodegradation being a complex process, the both differential and integral methods based on the single step hypothesis are inadequate for obtaining believable kinetic parameters. Only the modified NPK method allowed an objective separation of the temperature, respective conversion influence on the reaction rate and in the same time to ascertain the existence of two simultaneous steps. PMID:23594763

Ab Initio-Based Kinetic Modeling for the Design of Molecular Catalysts: The Case of H 2 Production Electrocatalysts

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

Ho, Ming-Hsun; Rousseau, Roger; Roberts, John A. S.

2015-09-04

Design of fast, efficient electrocatalysts for energy production and energy utilization requires a systematic approach to predict and tune the energetics of reaction intermediates and the kinetic barriers between them as well as to tune reaction conditions (e.g., concentration of reactants, acidity of the reaction medium, and applied electric potential). Thermodynamics schemes based on the knowledge of pKa values, hydride donor ability, redox potentials, and other relevant thermodynamic properties have been demonstrated to be very effective for exploring possible reaction pathways. We seek to identify high-energy intermediates, which may represent a catalytic bottleneck, and low-energy intermediates, which may represent amore » thermodynamic sink. In this study, working on a well-established Ni-based bioinspired electrocatalyst for H2 production, we performed a detailed kinetic analysis of the catalytic pathways to assess the limitations of our current (standard state) thermodynamic analysis with respect to prediction of optimal catalyst performance. To this end, we developed a microkinetic model based on extensive ab initio simulations. The model was validated against available experimental data, and it reproduces remarkably well the observed turnover rate as a function of the acid concentration and catalytic conditions, providing valuable information on the main factors limiting catalysis. Using this kinetic analysis as a reference, we show that indeed a purely thermodynamic analysis of the possible reaction pathways provides us with valuable information, such as a qualitative picture of the species involved during catalysis, identification of the possible branching points, and the origin of the observed overpotential, which are critical insights for electrocatalyst design. However, a significant limitation of this approach is understanding how these insights relate to rate, which is an equally critical piece of information. Taking our analysis a step further, we show that the kinetic model can easily be extended to different catalytic conditions by using linear free energy relationships for activation barriers based on simple thermodynamics quantities, such as pKa values. We also outline a possible procedure to extend it to other catalytic platforms, making it a general and effective way to design catalysts with improved performance.« less

Mathematical Justification of Expression-Based Pathway Activation Scoring (PAS).

PubMed

Aliper, Alexander M; Korzinkin, Michael B; Kuzmina, Natalia B; Zenin, Alexander A; Venkova, Larisa S; Smirnov, Philip Yu; Zhavoronkov, Alex A; Buzdin, Anton A; Borisov, Nikolay M

2017-01-01

Although modeling of activation kinetics for various cell signaling pathways has reached a high grade of sophistication and thoroughness, most such kinetic models still remain of rather limited practical value for biomedicine. Nevertheless, recent advancements have been made in application of signaling pathway science for real needs of prescription of the most effective drugs for individual patients. The methods for such prescription evaluate the degree of pathological changes in the signaling machinery based on two types of data: first, on the results of high-throughput gene expression profiling, and second, on the molecular pathway graphs that reflect interactions between the pathway members. For example, our algorithm OncoFinder evaluates the activation of molecular pathways on the basis of gene/protein expression data in the objects of the interest.Yet, the question of assessment of the relative importance for each gene product in a molecular pathway remains unclear unless one call for the methods of parameter sensitivity /stiffness analysis in the interactomic kinetic models of signaling pathway activation in terms of total concentrations of each gene product.Here we show two principal points: 1. First, the importance coefficients for each gene in pathways that were obtained using the extremely time- and labor-consuming stiffness analysis of full-scaled kinetic models generally differ from much easier-to-calculate expression-based pathway activation score (PAS) not more than by 30%, so the concept of PAS is kinetically justified. 2. Second, the use of pathway-based approach instead of distinct gene analysis, due to the law of large numbers, allows restoring the correlation between the similar samples that were examined using different transcriptome investigation techniques.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

NASA Astrophysics Data System (ADS)

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-01

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

PubMed

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-07

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Quantitative Förster resonance energy transfer analysis for kinetic determinations of SUMO-specific protease.

PubMed

Liu, Yan; Song, Yang; Madahar, Vipul; Liao, Jiayu

2012-03-01

Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research, and it is a very powerful tool for elucidating protein interactions in either dynamic or steady state. SUMOylation (the process of SUMO [small ubiquitin-like modifier] conjugation to substrates) is an important posttranslational protein modification with critical roles in multiple biological processes. Conjugating SUMO to substrates requires an enzymatic cascade. Sentrin/SUMO-specific proteases (SENPs) act as an endopeptidase to process the pre-SUMO or as an isopeptidase to deconjugate SUMO from its substrate. To fully understand the roles of SENPs in the SUMOylation cycle, it is critical to understand their kinetics. Here, we report a novel development of a quantitative FRET-based protease assay for SENP1 kinetic parameter determination. The assay is based on the quantitative analysis of the FRET signal from the total fluorescent signal at acceptor emission wavelength, which consists of three components: donor (CyPet-SUMO1) emission, acceptor (YPet) emission, and FRET signal during the digestion process. Subsequently, we developed novel theoretical and experimental procedures to determine the kinetic parameters, k(cat), K(M), and catalytic efficiency (k(cat)/K(M)) of catalytic domain SENP1 toward pre-SUMO1. Importantly, the general principles of this quantitative FRET-based protease kinetic determination can be applied to other proteases. Copyright © 2011 Elsevier Inc. All rights reserved.

iSCHRUNK--In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks.

PubMed

Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily

2016-01-01

Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-based metabolic flux analysis contribute to improved understanding of steady-state properties of metabolism. However, knowledge about kinetics and enzyme activities though essential for quantitative understanding of metabolic dynamics remains scarce and involves uncertainty. Here, we present a computational methodology that allow us to determine and quantify the kinetic parameters that correspond to a certain physiology as it is described by a given metabolic flux profile and a given metabolite concentration vector. Though we initially determine kinetic parameters that involve a high degree of uncertainty, through the use of kinetic modeling and machine learning principles we are able to obtain more accurate ranges of kinetic parameters, and hence we are able to reduce the uncertainty in the model analysis. We computed the distribution of kinetic parameters for glucose-fed E. coli producing 1,4-butanediol and we discovered that the observed physiological state corresponds to a narrow range of kinetic parameters of only a few enzymes, whereas the kinetic parameters of other enzymes can vary widely. Furthermore, this analysis suggests which are the enzymes that should be manipulated in order to engineer the reference state of the cell in a desired way. The proposed approach also sets up the foundations of a novel type of approaches for efficient, non-asymptotic, uniform sampling of solution spaces. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Use of Ambient Ionization High-Resolution Mass Spectrometry for the Kinetic Analysis of Organic Surface Reactions.

PubMed

Sen, Rickdeb; Escorihuela, Jorge; Smulders, Maarten M J; Zuilhof, Han

2016-04-12

In contrast to homogeneous systems, studying the kinetics of organic reactions on solid surfaces remains a difficult task due to the limited availability of appropriate analysis techniques that are general, high-throughput, and capable of offering quantitative, structural surface information. Here, we demonstrate how direct analysis in real time mass spectrometry (DART-MS) complies with above considerations and can be used for determining interfacial kinetic parameters. The presented approach is based on the use of a MS tag that--in principle--allows application to other reactions. To show the potential of DART-MS, we selected the widely applied strain-promoted alkyne-azide cycloaddition (SPAAC) as a model reaction to elucidate the effects of the nanoenvironment on the interfacial reaction rate.

Thermogravimetric analysis for the determination of water release rate from microcrystalline cellulose dry powder and wet bead systems.

PubMed

Mayville, Francis C; Wigent, Rodney J; Schwartz, Joseph B

2006-01-01

The purpose of this work was to determine the total amount of water contained in dry powder and wet bead samples of microcrystalline cellulose, MCC, (Avicel PH-101), taken from various stages of the extrusion/marumerization process used to make beads and to determine the kinetic rates of water release from each sample. These samples were allowed to equilibrate in controlled humidity chambers at 25 degrees C. The total amount of water in each sample, after equilibration, was determined by thermogravimetric analysis (TGA) as a function of temperature. The rates of water release from these samples were determined by using isothermal gravimetric analysis (ITGA) as a function of time. Analysis of the results for these studies suggest that water was released from these systems by several different kinetic mechanisms. The water release mechanisms for these systems include: zero order, second order, and diffusion controlled kinetics. It is believed that all three kinetic mechanisms will occur at the same time, however; only one mechanism will be prominent. The prominent mechanism was based on the amount of water present in the sample.

Cloning of Trametes versicolar genes induced by nitrogen starvation

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

Trudel, P.; Courchesne, D.; Roy, C.

1988-06-01

We have screened a genomic library of Trametes versicolar for genes whose expression is associated with nitrogen starvation, which has been shown to induce ligninolytic activity. Using two different approaches based on differential expression, we isolated 29 clones. These were shown by restriction mapping and cross-hybridization to code for 11 distinct differentially expressed genes. Northern analysis of the kinetics of expression of these genes revealed that at least four of them have kinetics of induction that parallel kinetics of induction of ligninolytic activity.

Epithelial invasion outcompetes hypha development during Candida albicans infection as revealed by an image-based systems biology approach.

PubMed

Mech, Franziska; Wilson, Duncan; Lehnert, Teresa; Hube, Bernhard; Thilo Figge, Marc

2014-02-01

Candida albicans is the most common opportunistic fungal pathogen of the human mucosal flora, frequently causing infections. The fungus is responsible for invasive infections in immunocompromised patients that can lead to sepsis. The yeast to hypha transition and invasion of host-tissue represent major determinants in the switch from benign colonizer to invasive pathogen. A comprehensive understanding of the infection process requires analyses at the quantitative level. Utilizing fluorescence microscopy with differential staining, we obtained images of C. albicans undergoing epithelial invasion during a time course of 6 h. An image-based systems biology approach, combining image analysis and mathematical modeling, was applied to quantify the kinetics of hyphae development, hyphal elongation, and epithelial invasion. The automated image analysis facilitates high-throughput screening and provided quantities that allow for the time-resolved characterization of the morphological and invasive state of fungal cells. The interpretation of these data was supported by two mathematical models, a kinetic growth model and a kinetic transition model, that were developed using differential equations. The kinetic growth model describes the increase in hyphal length and revealed that hyphae undergo mass invasion of epithelial cells following primary hypha formation. We also provide evidence that epithelial cells stimulate the production of secondary hyphae by C. albicans. Based on the kinetic transition model, the route of invasion was quantified in the state space of non-invasive and invasive fungal cells depending on their number of hyphae. This analysis revealed that the initiation of hyphae formation represents an ultimate commitment to invasive growth and suggests that in vivo, the yeast to hypha transition must be under exquisitely tight negative regulation to avoid the transition from commensal to pathogen invading the epithelium. © 2013 International Society for Advancement of Cytometry.

On-Line Analysis and Kinetic Behavior of Arsenic Release during Coal Combustion and Pyrolysis.

PubMed

Shen, Fenghua; Liu, Jing; Zhang, Zhen; Dai, Jinxin

2015-11-17

The kinetic behavior of arsenic (As) release during coal combustion and pyrolysis in a fluidized bed was investigated by applying an on-line analysis system of trace elements in flue gas. This system, based on inductively coupled plasma optical emission spectroscopy (ICP-OES), was developed to measure trace elements concentrations in flue gas quantitatively and continuously. Obvious variations of arsenic concentration in flue gas were observed during coal combustion and pyrolysis, indicating strong influences of atmosphere and temperature on arsenic release behavior. Kinetic laws governing the arsenic release during coal combustion and pyrolysis were determined based on the results of instantaneous arsenic concentration in flue gas. A second-order kinetic law was determined for arsenic release during coal combustion, and the arsenic release during coal pyrolysis followed a fourth-order kinetic law. The results showed that the arsenic release rate during coal pyrolysis was faster than that during coal combustion. Thermodynamic calculations were carried out to identify the forms of arsenic in vapor and solid phases during coal combustion and pyrolysis, respectively. Ca3(AsO4)2 and Ca(AsO2)2 are the possible species resulting from As-Ca interaction during coal combustion. Ca(AsO2)2 is the most probable species during coal pyrolysis.

Oxidative desulfurization: kinetic modelling.

PubMed

Dhir, S; Uppaluri, R; Purkait, M K

2009-01-30

Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H(2)O(2) over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel.

Theoretical Analysis of Drug Dissolution: I. Solubility and Intrinsic Dissolution Rate.

PubMed

Shekunov, Boris; Montgomery, Eda Ross

2016-09-01

The first-principles approach presented in this work combines surface kinetics and convective diffusion modeling applied to compounds with pH-dependent solubility and in different dissolution media. This analysis is based on experimental data available for approximately 100 compounds of pharmaceutical interest. Overall, there is a linear relationship between the drug solubility and intrinsic dissolution rate expressed through the total kinetic coefficient of dissolution and dimensionless numbers defining the mass transfer regime. The contribution of surface kinetics appears to be significant constituting on average ∼20% resistance to the dissolution flux in the compendial rotating disk apparatus at 100 rpm. The surface kinetics contribution becomes more dominant under conditions of fast laminar or turbulent flows or in cases when the surface kinetic coefficient may decrease as a function of solution composition or pH. Limitations of the well-known convective diffusion equation for rotating disk by Levich are examined using direct computational modeling with simultaneous dissociation and acid-base reactions in which intrinsic dissolution rate is strongly dependent on pH profile and solution ionic strength. It is shown that concept of diffusion boundary layer does not strictly apply for reacting/interacting species and that thin-film diffusion models cannot be used quantitatively in general case. Copyright © 2016. Published by Elsevier Inc.

Generic Schemes for Single-Molecule Kinetics. 2: Information Content of the Poisson Indicator.

PubMed

Avila, Thomas R; Piephoff, D Evan; Cao, Jianshu

2017-08-24

Recently, we described a pathway analysis technique (paper 1) for analyzing generic schemes for single-molecule kinetics based upon the first-passage time distribution. Here, we employ this method to derive expressions for the Poisson indicator, a normalized measure of stochastic variation (essentially equivalent to the Fano factor and Mandel's Q parameter), for various renewal (i.e., memoryless) enzymatic reactions. We examine its dependence on substrate concentration, without assuming all steps follow Poissonian kinetics. Based upon fitting to the functional forms of the first two waiting time moments, we show that, to second order, the non-Poissonian kinetics are generally underdetermined but can be specified in certain scenarios. For an enzymatic reaction with an arbitrary intermediate topology, we identify a generic minimum of the Poisson indicator as a function of substrate concentration, which can be used to tune substrate concentration to the stochastic fluctuations and to estimate the largest number of underlying consecutive links in a turnover cycle. We identify a local maximum of the Poisson indicator (with respect to substrate concentration) for a renewal process as a signature of competitive binding, either between a substrate and an inhibitor or between multiple substrates. Our analysis explores the rich connections between Poisson indicator measurements and microscopic kinetic mechanisms.

Decay of Solar Wind Turbulence behind Interplanetary Shocks

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

Pitňa, Alexander; Šafránková, Jana; Němeček, Zdeněk

We investigate the decay of magnetic and kinetic energies behind IP shocks with motivation to find a relaxation time when downstream turbulence reaches a usual solar wind value. We start with a case study that introduces computation techniques and quantifies a contribution of kinetic fluctuations to the general energy balance. This part of the study is based on high-time (31 ms) resolution plasma data provided by the Spektr-R spacecraft. On the other hand, a statistical part is based on 92 s Wind plasma and magnetic data and its results confirm theoretically established decay laws for kinetic and magnetic energies. Wemore » observe the power-law behavior of the energy decay profiles and we estimated the power-law exponents of both kinetic and magnetic energy decay rates as −1.2. We found that the decay of MHD turbulence does not start immediately after the IP shock ramp and we suggest that the proper decay of turbulence begins when a contribution of the kinetic processes becomes negligible. We support this suggestion with a detailed analysis of the decay of turbulence at the kinetic scale.« less

Kinetics of the creatine kinase reaction in neonatal rabbit heart: An empirical analysis of the rate equation

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

McAuliffe, J.J.; Perry, S.B.; Brooks, E.E.

1991-03-12

Here the authors define the kinetics of the creatine kinase (CK) reaction in an intact mammalian heart containing the full rnage of CK isoenzymes. Previously derived kinetic constants were refit for the reaction occurring at 37C. Steady-state metabolite concentrations from {sup 31}P NMR and standard biochemical techniques were determined. {sup 31}P magnetization transfer data were obtained to determine unidirectional creatine kinase fluxes in hearts with differing total creatine contents and differing mitochondrial CK activities during KCl arrest and isovolumic work for both the forward reaction (MgATP synthesis) and reverse reaction (phosphocreatine synthesis). The NMR kinetic data and substrate concentrations datamore » were used in conjunction with a kinetic model based on MM-CK in solution to determine the applicability of the solution-based kinetic models to the CK kinetics of the intact heart. The results indicated that no single set of rate equation constants could describe both the KCl-arrested and working hearts. Analysis of the results indicated that the CK reaction is rate limited in the direction of ATP synthesis, the size of the guanidino substrate pool drives the measured CK flux in the intact heart, and during isovolumic work, the CK reaction operates under saturating conditions; that is, the substrate concentrations are at least 2-fold greater than the K{sub m} or K{sub im} for each substrate. However, during KCl arrest the reaction does not operate under saturating conditions and the CK reaction velocity is strongly influenced by the guanidino substrate pool size.« less

Kinetic analysis of reactions of Si-based epoxy resins by near-infrared spectroscopy, 13C NMR and soft-hard modelling.

PubMed

Garrido, Mariano; Larrechi, Maria Soledad; Rius, F Xavier; Mercado, Luis Adolfo; Galià, Marina

2007-02-05

Soft- and hard-modelling strategy was applied to near-infrared spectroscopy data obtained from monitoring the reaction between glycidyloxydimethylphenyl silane, a silicon-based epoxy monomer, and aniline. On the basis of the pure soft-modelling approach and previous chemical knowledge, a kinetic model for the reaction was proposed. Then, multivariate curve resolution-alternating least squares optimization was carried out under a hard constraint, that compels the concentration profiles to fulfil the proposed kinetic model at each iteration of the optimization process. In this way, the concentration profiles of each species and the corresponding kinetic rate constants of the reaction, unpublished until now, were obtained. The results obtained were contrasted with 13C NMR. The joint interval test of slope and intercept for detecting bias was not significant (alpha=5%).

Syntheses, structural, computational, and thermal analysis of acid-base complexes of picric acid with N-heterocyclic bases.

PubMed

Goel, Nidhi; Singh, Udai P

2013-10-10

Four new acid-base complexes using picric acid [(OH)(NO2)3C6H2] (PA) and N-heterocyclic bases (1,10-phenanthroline (phen)/2,2';6',2"-terpyridine (terpy)/hexamethylenetetramine (hmta)/2,4,6-tri(2-pyridyl)-1,3,5-triazine (tptz)) were prepared and characterized by elemental analysis, IR, NMR and X-ray crystallography. Crystal structures provide detailed information of the noncovalent interactions present in different complexes. The optimized structures of the complexes were calculated in terms of the density functional theory. The thermolysis of these complexes was investigated by TG-DSC and ignition delay measurements. The model-free isoconversional and model-fitting kinetic approaches have been applied to isothermal TG data for kinetics investigation of thermal decomposition of these complexes.

Influence of Proton Acceptors on the Proton-Coupled Electron Transfer Reaction Kinetics of a Ruthenium-Tyrosine Complex.

PubMed

Lennox, J Christian; Dempsey, Jillian L

2017-11-22

A polypyridyl ruthenium complex with fluorinated bipyridine ligands and a covalently bound tyrosine moiety was synthesized, and its photo-induced proton-coupled electron transfer (PCET) reactivity in acetonitrile was investigated with transient absorption spectroscopy. Using flash-quench methodology with methyl viologen as an oxidative quencher, a Ru 3+ species is generated that is capable of initiating the intramolecular PCET oxidation of the tyrosine moiety. Using a series of substituted pyridine bases, the reaction kinetics were found to vary as a function of proton acceptor concentration and identity, with no significant H/D kinetic isotope effect. Through analysis of the kinetics traces and comparison to a control complex without the tyrosine moiety, PCET reactivity was found to proceed through an equilibrium electron transfer followed by proton transfer (ET-PT) pathway in which irreversible deprotonation of the tyrosine radical cation shifts the ET equilibrium, conferring a base dependence on the reaction. Comprehensive kinetics modeling allowed for deconvolution of complex kinetics and determination of rate constants for each elementary step. Across the five pyridine bases explored, spanning a range of 4.2 pK a units, a linear free-energy relationship was found for the proton transfer rate constant with a slope of 0.32. These findings highlight the influence that proton transfer driving force exerts on PCET reaction kinetics.

Development of an ESI-LC-MS-based assay for kinetic evaluation of Mycobacterium tuberculosis shikimate kinase activity and inhibition.

PubMed

Simithy, Johayra; Gill, Gobind; Wang, Yu; Goodwin, Douglas C; Calderón, Angela I

2015-02-17

A simple and reliable liquid chromatography-mass spectrometry (LC-MS) assay has been developed and validated for the kinetic characterization and evaluation of inhibitors of shikimate kinase from Mycobacterium tuberculosis (MtSK), a potential target for the development of novel antitubercular drugs. This assay is based on the direct determination of the reaction product shikimate-3-phosphate (S3P) using electrospray ionization (ESI) and a quadrupole time-of-flight (Q-TOF) detector. A comparative analysis of the kinetic parameters of MtSK obtained by the LC-MS assay with those obtained by a conventional UV-assay was performed. Kinetic parameters determined by LC-MS were in excellent agreement with those obtained from the UV assay, demonstrating the accuracy, and reliability of this method. The validated assay was successfully applied to the kinetic characterization of a known inhibitor of shikimate kinase; inhibition constants and mode of inhibition were accurately delineated with LC-MS.

Validation of Bayesian analysis of compartmental kinetic models in medical imaging.

PubMed

Sitek, Arkadiusz; Li, Quanzheng; El Fakhri, Georges; Alpert, Nathaniel M

2016-10-01

Kinetic compartmental analysis is frequently used to compute physiologically relevant quantitative values from time series of images. In this paper, a new approach based on Bayesian analysis to obtain information about these parameters is presented and validated. The closed-form of the posterior distribution of kinetic parameters is derived with a hierarchical prior to model the standard deviation of normally distributed noise. Markov chain Monte Carlo methods are used for numerical estimation of the posterior distribution. Computer simulations of the kinetics of F18-fluorodeoxyglucose (FDG) are used to demonstrate drawing statistical inferences about kinetic parameters and to validate the theory and implementation. Additionally, point estimates of kinetic parameters and covariance of those estimates are determined using the classical non-linear least squares approach. Posteriors obtained using methods proposed in this work are accurate as no significant deviation from the expected shape of the posterior was found (one-sided P>0.08). It is demonstrated that the results obtained by the standard non-linear least-square methods fail to provide accurate estimation of uncertainty for the same data set (P<0.0001). The results of this work validate new methods for a computer simulations of FDG kinetics. Results show that in situations where the classical approach fails in accurate estimation of uncertainty, Bayesian estimation provides an accurate information about the uncertainties in the parameters. Although a particular example of FDG kinetics was used in the paper, the methods can be extended for different pharmaceuticals and imaging modalities. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Kinetic analysis of central ( sup 11 C)raclopride binding to D2-dopamine receptors studied by PET--a comparison to the equilibrium analysis

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

Farde, L.; Eriksson, L.; Blomquist, G.

1989-10-01

(11C)Raclopride binding to central D2-dopamine receptors in humans has previously been examined by positron emission tomography (PET). Based on the rapid occurrence of binding equilibrium, a saturation analysis has been developed for the determination of receptor density (Bmax) and affinity (Kd). For analysis of PET measurements obtained with other ligands, a kinetic three-compartment model has been used. In the present study, the brain uptake of (11C)raclopride was analyzed further by applying both a kinetic and an equilibrium analysis to data obtained from four PET experiments in each of three healthy subjects. First regional CBV was determined. In the second andmore » third experiment, (11C)-raclopride with high and low specific activity was used. In a fourth experiment, the (11C)raclopride enantiomer (11C)FLB472 was used to examine the concentration of free radioligand and nonspecific binding in brain. Radio-activity in arterial blood was measured using an automated blood sampling system. Bmax and Kd values for (11C)raclopride binding could be determined also with the kinetic analysis. As expected theoretically, those values were similar to those obtained with the equilibrium analysis. In addition, the kinetic analysis allowed separate determination of the association and dissociation rate constants, kon and koff, respectively. Examination of (11C)raclopride and (11C)FLB472 uptake in brain regions devoid of specific D2-dopamine receptor binding indicated a fourth compartment in which uptake was reversible, nonstereoselective, and nonsaturable in the dose range studied.« less

Fast Metabolic Response to Drug Intervention through Analysis on a Miniaturized, Highly Integrated Molecular Imaging System

PubMed Central

Wang, Jun; Hwang, Kiwook; Braas, Daniel; Dooraghi, Alex; Nathanson, David; Campbell, Dean O.; Gu, Yuchao; Sandberg, Troy; Mischel, Paul; Radu, Caius; Chatziioannou, Arion F.; Phelps, Michael E.; Christofk, Heather; Heath, James R.

2014-01-01

We report on a radiopharmaceutical imaging platform designed to capture the kinetics of cellular responses to drugs. Methods A portable in vitro molecular imaging system, comprised of a microchip and a beta-particle imaging camera, permits routine cell-based radioassays on small number of either suspension or adherent cells. We investigate the response kinetics of model lymphoma and glioblastoma cancer cell lines to [18F]fluorodeoxyglucose ([18F]FDG) uptake following drug exposure. Those responses are correlated with kinetic changes in the cell cycle, or with changes in receptor-tyrosine kinase signaling. Results The platform enables radioassays directly on multiple cell types, and yields results comparable to conventional approaches, but uses smaller sample sizes, permits a higher level of quantitation, and doesn’t require cell lysis. Conclusion The kinetic analysis enabled by the platform provides a rapid (~1 hour) drug screening assay. PMID:23978446

Estimation of beech pyrolysis kinetic parameters by Shuffled Complex Evolution.

PubMed

Ding, Yanming; Wang, Changjian; Chaos, Marcos; Chen, Ruiyu; Lu, Shouxiang

2016-01-01

The pyrolysis kinetics of a typical biomass energy feedstock, beech, was investigated based on thermogravimetric analysis over a wide heating rate range from 5K/min to 80K/min. A three-component (corresponding to hemicellulose, cellulose and lignin) parallel decomposition reaction scheme was applied to describe the experimental data. The resulting kinetic reaction model was coupled to an evolutionary optimization algorithm (Shuffled Complex Evolution, SCE) to obtain model parameters. To the authors' knowledge, this is the first study in which SCE has been used in the context of thermogravimetry. The kinetic parameters were simultaneously optimized against data for 10, 20 and 60K/min heating rates, providing excellent fits to experimental data. Furthermore, it was shown that the optimized parameters were applicable to heating rates (5 and 80K/min) beyond those used to generate them. Finally, the predicted results based on optimized parameters were contrasted with those based on the literature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Accounting for unintended binding events in the analysis of quartz crystal microbalance kinetic data.

PubMed

Heller, Gabriella T; Zwang, Theodore J; Sarapata, Elizabeth A; Haber, Michael A; Sazinsky, Matthew H; Radunskaya, Ami E; Johal, Malkiat S

2014-05-01

Previous methods for analyzing protein-ligand binding events using the quartz crystal microbalance with dissipation monitoring (QCM-D) fail to account for unintended binding that inevitably occurs during surface measurements and obscure kinetic information. In this article, we present a system of differential equations that accounts for both reversible and irreversible unintended interactions. This model is tested on three protein-ligand systems, each of which has different features, to establish the feasibility of using the QCM-D for protein binding analysis. Based on this analysis, we were able to obtain kinetic information for the intended interaction that is consistent with those obtained in literature via bulk-phase methods. In the appendix, we include a method for decoupling these from the intended binding events and extracting relevant affinity information. Copyright © 2014 Elsevier B.V. All rights reserved.

Relative effectiveness of kinetic analysis vs single point readings for classifying environmental samples based on community-level physiological profiles (CLPP)

NASA Technical Reports Server (NTRS)

Garland, J. L.; Mills, A. L.; Young, J. S.

2001-01-01

The relative effectiveness of average-well-color-development-normalized single-point absorbance readings (AWCD) vs the kinetic parameters mu(m), lambda, A, and integral (AREA) of the modified Gompertz equation fit to the color development curve resulting from reduction of a redox sensitive dye from microbial respiration of 95 separate sole carbon sources in microplate wells was compared for a dilution series of rhizosphere samples from hydroponically grown wheat and potato ranging in inoculum densities of 1 x 10(4)-4 x 10(6) cells ml-1. Patterns generated with each parameter were analyzed using principal component analysis (PCA) and discriminant function analysis (DFA) to test relative resolving power. Samples of equivalent cell density (undiluted samples) were correctly classified by rhizosphere type for all parameters based on DFA analysis of the first five PC scores. Analysis of undiluted and 1:4 diluted samples resulted in misclassification of at least two of the wheat samples for all parameters except the AWCD normalized (0.50 abs. units) data, and analysis of undiluted, 1:4, and 1:16 diluted samples resulted in misclassification for all parameter types. Ordination of samples along the first principal component (PC) was correlated to inoculum density in analyses performed on all of the kinetic parameters, but no such influence was seen for AWCD-derived results. The carbon sources responsible for classification differed among the variable types with the exception of AREA and A, which were strongly correlated. These results indicate that the use of kinetic parameters for pattern analysis in CLPP may provide some additional information, but only if the influence of inoculum density is carefully considered. c2001 Elsevier Science Ltd. All rights reserved.

Application of holographic sub-wavelength diffraction gratings for monitoring of kinetics of bioprocesses

NASA Astrophysics Data System (ADS)

Tamulevičius, Tomas; Šeperys, Rimas; Andrulevičius, Mindaugas; Kopustinskas, Vitoldas; Meškinis, Šarūnas; Tamulevičius, Sigitas; Mikalayeva, Valeryia; Daugelavičius, Rimantas

2012-09-01

In this work we present a refractive index (RI) sensor based on a sub-wavelength holographic diffraction grating. The sensor chip was fabricated by dry etching of the finely spaced (d = 428 nm) diffraction grating in SiOx doped diamond like carbon (DLC) film. It is shown that employing a fabricated sensor chip, and using the proposed method of analysis of data, one can inspect kinetics of processes in liquids occurring in the vicinity of the grating surface. The method is based on the spectral composition analysis of polarized polychromatic light reflected from the sub-wavelength diffraction grating. The RI measurement system was tested with different model liquid analytes including 25 wt.%, 50 wt.% sugar water solutions, 10 °C, 50 °C distilled water, also Gram-positive bacteria Bacillus subtilis interaction with ion-permeable channels forming antibiotic gramicidin D and a murolytic enzyme lysozyme. Analysis of the data set of specular reflection spectra enabled us to follow the kinetics of the RI changes in the analyte with millisecond resolution. Detectable changes in the effective RI were not worse than Δn = 10-4.

Mechanisms of starch digestion by α-amylase-Structural basis for kinetic properties.

PubMed

Dhital, Sushil; Warren, Frederick J; Butterworth, Peter J; Ellis, Peter R; Gidley, Michael J

2017-03-24

Recent studies of the mechanisms determining the rate and extent of starch digestion by α-amylase are reviewed in the light of current widely-used classifications for (a) the proportions of rapidly-digestible (RDS), slowly-digestible (SDS), and resistant starch (RS) based on in vitro digestibility, and (b) the types of resistant starch (RS 1,2,3,4…) based on physical and/or chemical form. Based on methodological advances and new mechanistic insights, it is proposed that both classification systems should be modified. Kinetic analysis of digestion profiles provides a robust set of parameters that should replace the classification of starch as a combination of RDS, SDS, and RS from a single enzyme digestion experiment. This should involve determination of the minimum number of kinetic processes needed to describe the full digestion profile, together with the proportion of starch involved in each process, and the kinetic properties of each process. The current classification of resistant starch types as RS1,2,3,4 should be replaced by one which recognizes the essential kinetic nature of RS (enzyme digestion rate vs. small intestinal passage rate), and that there are two fundamental origins for resistance based on (i) rate-determining access/binding of enzyme to substrate and (ii) rate-determining conversion of substrate to product once bound.

Dynamic PET of human liver inflammation: impact of kinetic modeling with optimization-derived dual-blood input function.

PubMed

Wang, Guobao; Corwin, Michael T; Olson, Kristin A; Badawi, Ramsey D; Sarkar, Souvik

2018-05-30

The hallmark of nonalcoholic steatohepatitis is hepatocellular inflammation and injury in the setting of hepatic steatosis. Recent work has indicated that dynamic 18F-FDG PET with kinetic modeling has the potential to assess hepatic inflammation noninvasively, while static FDG-PET did not show a promise. Because the liver has dual blood supplies, kinetic modeling of dynamic liver PET data is challenging in human studies. The objective of this study is to evaluate and identify a dual-input kinetic modeling approach for dynamic FDG-PET of human liver inflammation. Fourteen human patients with nonalcoholic fatty liver disease were included in the study. Each patient underwent one-hour dynamic FDG-PET/CT scan and had liver biopsy within six weeks. Three models were tested for kinetic analysis: traditional two-tissue compartmental model with an image-derived single-blood input function (SBIF), model with population-based dual-blood input function (DBIF), and modified model with optimization-derived DBIF through a joint estimation framework. The three models were compared using Akaike information criterion (AIC), F test and histopathologic inflammation reference. The results showed that the optimization-derived DBIF model improved the fitting of liver time activity curves and achieved lower AIC values and higher F values than the SBIF and population-based DBIF models in all patients. The optimization-derived model significantly increased FDG K1 estimates by 101% and 27% as compared with traditional SBIF and population-based DBIF. K1 by the optimization-derived model was significantly associated with histopathologic grades of liver inflammation while the other two models did not provide a statistical significance. In conclusion, modeling of DBIF is critical for kinetic analysis of dynamic liver FDG-PET data in human studies. The optimization-derived DBIF model is more appropriate than SBIF and population-based DBIF for dynamic FDG-PET of liver inflammation. © 2018 Institute of Physics and Engineering in Medicine.

Investigating High-School Chemical Kinetics: The Greek Chemistry Textbook and Students' Difficulties

ERIC Educational Resources Information Center

Gegios, Theodoros; Salta, Katerina; Koinis, Spyros

2017-01-01

In this study we present an analysis of how the structure and content of the Greek school textbook approaches the concepts of chemical kinetics, and an investigation of the difficulties that 11th grade Greek students face regarding these concepts. Based on the structure and content of the Greek textbook, a tool was developed and applied to…

Modeling the kinetics of survival of Staphylococcus aureus in regional yogurt from goat's milk.

PubMed

Bednarko-Młynarczyk, E; Szteyn, J; Białobrzewski, I; Wiszniewska-Łaszczych, A; Liedtke, K

2015-01-01

The aim of this study was to determine the kinetics of the survival of the test strain of Staphylococcus aureus in the product investigated. Yogurt samples were contaminated with S. aure to an initial level of 10(3)-10(4) cfu/g. The samples were then stored at four temperatures: 4, 6, 20, 22°C. During storage, the number of S. aureus forming colonies in a gram of yogurt was determined every two hours. Based on the results of the analysis culture the curves of survival were plotted. Three primary models were selected to describe the kinetics of changes in the count of bacteria: Cole's model, a modified model of Gompertz and the model of Baranyi and Roberts. Analysis of the model fit carried out based on the average values of Pearson's correlation coefficient, between the modeled and measured values, showed that the Cole's model had the worst fit. The modified Gompertz model showed the count of S. aureus as a negative value. These drawbacks were not observed in the model of Baranyi and Roberts. For this reason, this model best reflects the kinetics of changes in the number of staphylococci in yogurt.

Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

PubMed Central

2017-01-01

Large-scale kinetic models of metabolism are becoming increasingly comprehensive and accurate. A key challenge is to understand the biochemical basis of the dynamic properties of these models. Linear analysis methods are well-established as useful tools for characterizing the dynamic response of metabolic networks. Central to linear analysis methods are two key matrices: the Jacobian matrix (J) and the modal matrix (M-1) arising from its eigendecomposition. The modal matrix M-1 contains dynamically independent motions of the kinetic model near a reference state, and it is sparse in practice for metabolic networks. However, connecting the structure of M-1 to the kinetic properties of the underlying reactions is non-trivial. In this study, we analyze the relationship between J, M-1, and the kinetic properties of the underlying network for kinetic models of metabolism. Specifically, we describe the origin of mode sparsity structure based on features of the network stoichiometric matrix S and the reaction kinetic gradient matrix G. First, we show that due to the scaling of kinetic parameters in real networks, diagonal dominance occurs in a substantial fraction of the rows of J, resulting in simple modal structures with clear biological interpretations. Then, we show that more complicated modes originate from topologically-connected reactions that have similar reaction elasticities in G. These elasticities represent dynamic equilibrium balances within reactions and are key determinants of modal structure. The work presented should prove useful towards obtaining an understanding of the dynamics of kinetic models of metabolism, which are rooted in the network structure and the kinetic properties of reactions. PMID:29267329

Optimal bioprocess design through a gene regulatory network - growth kinetic hybrid model: Towards Replacing Monod kinetics.

PubMed

Tsipa, Argyro; Koutinas, Michalis; Usaku, Chonlatep; Mantalaris, Athanasios

2018-05-02

Currently, design and optimisation of biotechnological bioprocesses is performed either through exhaustive experimentation and/or with the use of empirical, unstructured growth kinetics models. Whereas, elaborate systems biology approaches have been recently explored, mixed-substrate utilisation is predominantly ignored despite its significance in enhancing bioprocess performance. Herein, bioprocess optimisation for an industrially-relevant bioremediation process involving a mixture of highly toxic substrates, m-xylene and toluene, was achieved through application of a novel experimental-modelling gene regulatory network - growth kinetic (GRN-GK) hybrid framework. The GRN model described the TOL and ortho-cleavage pathways in Pseudomonas putida mt-2 and captured the transcriptional kinetics expression patterns of the promoters. The GRN model informed the formulation of the growth kinetics model replacing the empirical and unstructured Monod kinetics. The GRN-GK framework's predictive capability and potential as a systematic optimal bioprocess design tool, was demonstrated by effectively predicting bioprocess performance, which was in agreement with experimental values, when compared to four commonly used models that deviated significantly from the experimental values. Significantly, a fed-batch biodegradation process was designed and optimised through the model-based control of TOL Pr promoter expression resulting in 61% and 60% enhanced pollutant removal and biomass formation, respectively, compared to the batch process. This provides strong evidence of model-based bioprocess optimisation at the gene level, rendering the GRN-GK framework as a novel and applicable approach to optimal bioprocess design. Finally, model analysis using global sensitivity analysis (GSA) suggests an alternative, systematic approach for model-driven strain modification for synthetic biology and metabolic engineering applications. Copyright © 2018. Published by Elsevier Inc.

Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

PubMed Central

Liu, Fei; Heiner, Monika; Yang, Ming

2016-01-01

Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information. PMID:26910830

Integrated Modeling of Time Evolving 3D Kinetic MHD Equilibria and NTV Torque

NASA Astrophysics Data System (ADS)

Logan, N. C.; Park, J.-K.; Grierson, B. A.; Haskey, S. R.; Nazikian, R.; Cui, L.; Smith, S. P.; Meneghini, O.

2016-10-01

New analysis tools and integrated modeling of plasma dynamics developed in the OMFIT framework are used to study kinetic MHD equilibria evolution on the transport time scale. The experimentally observed profile dynamics following the application of 3D error fields are described using a new OMFITprofiles workflow that directly addresses the need for rapid and comprehensive analysis of dynamic equilibria for next-step theory validation. The workflow treats all diagnostic data as fundamentally time dependent, provides physics-based manipulations such as ELM phase data selection, and is consistent across multiple machines - including DIII-D and NSTX-U. The seamless integration of tokamak data and simulation is demonstrated by using the self-consistent kinetic EFIT equilibria and profiles as input into 2D particle, momentum and energy transport calculations using TRANSP as well as 3D kinetic MHD equilibrium stability and neoclassical transport modeling using General Perturbed Equilibrium Code (GPEC). The result is a smooth kinetic stability and NTV torque evolution over transport time scales. Work supported by DE-AC02-09CH11466.

LSENS, The NASA Lewis Kinetics and Sensitivity Analysis Code

NASA Technical Reports Server (NTRS)

Radhakrishnan, K.

2000-01-01

A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS (the NASA Lewis kinetics and sensitivity analysis code), are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include: static system; steady, one-dimensional, inviscid flow; incident-shock initiated reaction in a shock tube; and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method (LSODE, the Livermore Solver for Ordinary Differential Equations), which works efficiently for the extremes of very fast and very slow reactions, is used to solve the "stiff" ordinary differential equation systems that arise in chemical kinetics. For static reactions, the code uses the decoupled direct method to calculate sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters. Solution methods for the equilibrium and post-shock conditions and for perfectly stirred reactor problems are either adapted from or based on the procedures built into the NASA code CEA (Chemical Equilibrium and Applications).

Virus Neutralisation: New Insights from Kinetic Neutralisation Curves

PubMed Central

Magnus, Carsten

2013-01-01

Antibodies binding to the surface of virions can lead to virus neutralisation. Different theories have been proposed to determine the number of antibodies that must bind to a virion for neutralisation. Early models are based on chemical binding kinetics. Applying these models lead to very low estimates of the number of antibodies needed for neutralisation. In contrast, according to the more conceptual approach of stoichiometries in virology a much higher number of antibodies is required for virus neutralisation by antibodies. Here, we combine chemical binding kinetics with (virological) stoichiometries to better explain virus neutralisation by antibody binding. This framework is in agreement with published data on the neutralisation of the human immunodeficiency virus. Knowing antibody reaction constants, our model allows us to estimate stoichiometrical parameters from kinetic neutralisation curves. In addition, we can identify important parameters that will make further analysis of kinetic neutralisation curves more valuable in the context of estimating stoichiometries. Our model gives a more subtle explanation of kinetic neutralisation curves in terms of single-hit and multi-hit kinetics. PMID:23468602

Reduction and Uncertainty Analysis of Chemical Mechanisms Based on Local and Global Sensitivities

NASA Astrophysics Data System (ADS)

Esposito, Gaetano

Numerical simulations of critical reacting flow phenomena in hypersonic propulsion devices require accurate representation of finite-rate chemical kinetics. The chemical kinetic models available for hydrocarbon fuel combustion are rather large, involving hundreds of species and thousands of reactions. As a consequence, they cannot be used in multi-dimensional computational fluid dynamic calculations in the foreseeable future due to the prohibitive computational cost. In addition to the computational difficulties, it is also known that some fundamental chemical kinetic parameters of detailed models have significant level of uncertainty due to limited experimental data available and to poor understanding of interactions among kinetic parameters. In the present investigation, local and global sensitivity analysis techniques are employed to develop a systematic approach of reducing and analyzing detailed chemical kinetic models. Unlike previous studies in which skeletal model reduction was based on the separate analysis of simple cases, in this work a novel strategy based on Principal Component Analysis of local sensitivity values is presented. This new approach is capable of simultaneously taking into account all the relevant canonical combustion configurations over different composition, temperature and pressure conditions. Moreover, the procedure developed in this work represents the first documented inclusion of non-premixed extinction phenomena, which is of great relevance in hypersonic combustors, in an automated reduction algorithm. The application of the skeletal reduction to a detailed kinetic model consisting of 111 species in 784 reactions is demonstrated. The resulting reduced skeletal model of 37--38 species showed that the global ignition/propagation/extinction phenomena of ethylene-air mixtures can be predicted within an accuracy of 2% of the full detailed model. The problems of both understanding non-linear interactions between kinetic parameters and identifying sources of uncertainty affecting relevant reaction pathways are usually addressed by resorting to Global Sensitivity Analysis (GSA) techniques. In particular, the most sensitive reactions controlling combustion phenomena are first identified using the Morris Method and then analyzed under the Random Sampling -- High Dimensional Model Representation (RS-HDMR) framework. The HDMR decomposition shows that 10% of the variance seen in the extinction strain rate of non-premixed flames is due to second-order effects between parameters, whereas the maximum concentration of acetylene, a key soot precursor, is affected by mostly only first-order contributions. Moreover, the analysis of the global sensitivity indices demonstrates that improving the accuracy of the reaction rates including the vinyl radical, C2H3, can drastically reduce the uncertainty of predicting targeted flame properties. Finally, the back-propagation of the experimental uncertainty of the extinction strain rate to the parameter space is also performed. This exercise, achieved by recycling the numerical solutions of the RS-HDMR, shows that some regions of the parameter space have a high probability of reproducing the experimental value of the extinction strain rate between its own uncertainty bounds. Therefore this study demonstrates that the uncertainty analysis of bulk flame properties can effectively provide information on relevant chemical reactions.

Membrane crystallization of lysozyme: kinetic aspects

NASA Astrophysics Data System (ADS)

Profio, Gianluca Di; Curcio, Efrem; Cassetta, Alberto; Lamba, Doriano; Drioli, Enrico

2003-10-01

The relevant kinetic aspects related to an innovative method of biological macromolecules crystallization based on microporous hydrophobic membranes, used both as active surfaces to promote heterogeneous nucleation and as a mass-transfer apparatus to concentrate macromolecular solutions by solvent removal in vapour phase, have been evaluated. Polypropylene membranes, supplied in the form of hollow fibres, have been aligned in a versatile system, designed for an on-line spectrophotometric monitoring of hen egg white lysozyme crystallizing solutions (experimental conditions: 0.1 M NaAc/HAc Buffer pH 4.6, 0.5-5.8% wt/vol NaCl, 20°C). The turbidity measurements have been exploited in order to follow: (i) the induction time of crystallization, (ii) the early stage nucleation kinetics based on the Rayleigh scattering theory, and (iii) the crystal growth rate (coupled with data evaluated from image-analysis carried out by optical microscopy) under a model hypothesis of exponential growth of clusters. The crystals have been qualitatively assessed by an X-ray crystallographic analysis carried out at the synchrotron light laboratory ELETTRA.

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

PubMed Central

Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.

2014-01-01

Computational strain design protocols aim at the system-wide identification of intervention strategies for the enhanced production of biochemicals in microorganisms. Existing approaches relying solely on stoichiometry and rudimentary constraint-based regulation overlook the effects of metabolite concentrations and substrate-level enzyme regulation while identifying metabolic interventions. In this paper, we introduce k-OptForce, which integrates the available kinetic descriptions of metabolic steps with stoichiometric models to sharpen the prediction of intervention strategies for improving the bio-production of a chemical of interest. It enables identification of a minimal set of interventions comprised of both enzymatic parameter changes (for reactions with available kinetics) and reaction flux changes (for reactions with only stoichiometric information). Application of k-OptForce to the overproduction of L-serine in E. coli and triacetic acid lactone (TAL) in S. cerevisiae revealed that the identified interventions tend to cause less dramatic rearrangements of the flux distribution so as not to violate concentration bounds. In some cases the incorporation of kinetic information leads to the need for additional interventions as kinetic expressions render stoichiometry-only derived interventions infeasible by violating concentration bounds, whereas in other cases the kinetic expressions impart flux changes that favor the overproduction of the target product thereby requiring fewer direct interventions. A sensitivity analysis on metabolite concentrations shows that the required number of interventions can be significantly affected by changing the imposed bounds on metabolite concentrations. Furthermore, k-OptForce was capable of finding non-intuitive interventions aiming at alleviating the substrate-level inhibition of key enzymes in order to enhance the flux towards the product of interest, which cannot be captured by stoichiometry-alone analysis. This study paves the way for the integrated analysis of kinetic and stoichiometric models and enables elucidating system-wide metabolic interventions while capturing regulatory and kinetic effects. PMID:24586136

Marigold (Calendula officinalis L.): an evidence-based systematic review by the Natural Standard Research Collaboration.

PubMed

Basch, Ethan; Bent, Steve; Foppa, Ivo; Haskmi, Sadaf; Kroll, David; Mele, Michelle; Szapary, Philippe; Ulbricht, Catherine; Vora, Mamta; Yong, Sophanna

2006-01-01

An evidence-based systematic review including written and statistical analysis of scientific literature, expert opinion, folkloric precedent, history, pharmacology, kinetics/dynamics, interactions, adverse effects, toxicology and dosing.

An evidence-based systematic review of saffron (Crocus sativus) by the Natural Standard Research Collaboration.

PubMed

Ulbricht, Catherine; Conquer, Julie; Costa, Dawn; Hollands, Whitney; Iannuzzi, Carmen; Isaac, Richard; Jordan, Joseph K; Ledesma, Natalie; Ostroff, Cathy; Serrano, Jill M Grimes; Shaffer, Michael D; Varghese, Minney

2011-03-01

An evidence-based systematic review including written and statistical analysis of scientific literature, expert opinion, folkloric precedent, history, pharmacology, kinetics/dynamics, interactions, adverse effects, toxicology, and dosing.

Evidence-based systematic review of saw palmetto by the Natural Standard Research Collaboration.

PubMed

Ulbricht, Catherine; Basch, Ethan; Bent, Steve; Boon, Heather; Corrado, Michelle; Foppa, Ivo; Hashmi, Sadaf; Hammerness, Paul; Kingsbury, Eileen; Smith, Michael; Szapary, Philippe; Vora, Mamta; Weissner, Wendy

2006-01-01

Here presented is an evidence-based systematic review including written and statistical analysis of scientific literature, expert opinion, folkloric precedent, history, pharmacology, kinetics/dynamics, interactions, adverse effects, toxicology, and dosing.

Multiplexed immunosensing and kinetics monitoring in nanofluidic devices with highly enhanced target capture efficiency

PubMed Central

Lin, Yii-Lih; Huang, Yen-Jun; Teerapanich, Pattamon; Leïchlé, Thierry

2016-01-01

Nanofluidic devices promise high reaction efficiency and fast kinetic responses due to the spatial constriction of transported biomolecules with confined molecular diffusion. However, parallel detection of multiple biomolecules, particularly proteins, in highly confined space remains challenging. This study integrates extended nanofluidics with embedded protein microarray to achieve multiplexed real-time biosensing and kinetics monitoring. Implementation of embedded standard-sized antibody microarray is attained by epoxy-silane surface modification and a room-temperature low-aspect-ratio bonding technique. An effective sample transport is achieved by electrokinetic pumping via electroosmotic flow. Through the nanoslit-based spatial confinement, the antigen-antibody binding reaction is enhanced with ∼100% efficiency and may be directly observed with fluorescence microscopy without the requirement of intermediate washing steps. The image-based data provide numerous spatially distributed reaction kinetic curves and are collectively modeled using a simple one-dimensional convection-reaction model. This study represents an integrated nanofluidic solution for real-time multiplexed immunosensing and kinetics monitoring, starting from device fabrication, protein immobilization, device bonding, sample transport, to data analysis at Péclet number less than 1. PMID:27375819

Visual evaluation of kinetic characteristics of PET probe for neuroreceptors using a two-phase graphic plot analysis.

PubMed

Ito, Hiroshi; Ikoma, Yoko; Seki, Chie; Kimura, Yasuyuki; Kawaguchi, Hiroshi; Takuwa, Hiroyuki; Ichise, Masanori; Suhara, Tetsuya; Kanno, Iwao

2017-05-01

Objectives In PET studies for neuroreceptors, tracer kinetics are described by the two-tissue compartment model (2-TCM), and binding parameters, including the total distribution volume (V T ), non-displaceable distribution volume (V ND ), and binding potential (BP ND ), can be determined from model parameters estimated by kinetic analysis. The stability of binding parameter estimates depends on the kinetic characteristics of radioligands. To describe these kinetic characteristics, we previously developed a two-phase graphic plot analysis in which V ND and V T can be estimated from the x-intercept of regression lines for early and delayed phases, respectively. In this study, we applied this graphic plot analysis to visual evaluation of the kinetic characteristics of radioligands for neuroreceptors, and investigated a relationship between the shape of these graphic plots and the stability of binding parameters estimated by the kinetic analysis with 2-TCM in simulated brain tissue time-activity curves (TACs) with various binding parameters. Methods 90-min TACs were generated with the arterial input function and assumed kinetic parameters according to 2-TCM. Graphic plot analysis was applied to these simulated TACs, and the curvature of the plot for each TAC was evaluated visually. TACs with several noise levels were also generated with various kinetic parameters, and the bias and variation of binding parameters estimated by kinetic analysis were calculated in each TAC. These bias and variation were compared with the shape of graphic plots. Results The graphic plots showed larger curvature for TACs with higher specific binding and slower dissociation of specific binding. The quartile deviations of V ND and BP ND determined by kinetic analysis were smaller for radioligands with slow dissociation. Conclusions The larger curvature of graphic plots for radioligands with slow dissociation might indicate a stable determination of V ND and BP ND by kinetic analysis. For investigation of the kinetics of radioligands, such kinetic characteristics should be considered.

Multivariate curve resolution of incomplete fused multiset data from chromatographic and spectrophotometric analyses for drug photostability studies.

PubMed

De Luca, Michele; Ragno, Gaetano; Ioele, Giuseppina; Tauler, Romà

2014-07-21

An advanced and powerful chemometric approach is proposed for the analysis of incomplete multiset data obtained by fusion of hyphenated liquid chromatographic DAD/MS data with UV spectrophotometric data from acid-base titration and kinetic degradation experiments. Column- and row-wise augmented data blocks were combined and simultaneously processed by means of a new version of the multivariate curve resolution-alternating least squares (MCR-ALS) technique, including the simultaneous analysis of incomplete multiset data from different instrumental techniques. The proposed procedure was applied to the detailed study of the kinetic photodegradation process of the amiloride (AML) drug. All chemical species involved in the degradation and equilibrium reactions were resolved and the pH dependent kinetic pathway described. Copyright © 2014 Elsevier B.V. All rights reserved.

Oxygen Diffusion and Reaction Kinetics in Continuous Fiber Ceramic Matrix Composites

NASA Technical Reports Server (NTRS)

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

1999-01-01

Previous stressed oxidation tests of C/SiC composites at elevated temperatures (350 C to 1500 C) and sustained stresses (69 MPa and 172 MPa) have led to the development of a finite difference cracked matrix model. The times to failure in the samples suggest oxidation occurred in two kinetic regimes defined by the rate controlling mechanisms (i.e. diffusion controlled and reaction controlled kinetics). Microstructural analysis revealed preferential oxidation along as-fabricated, matrix microcracks and also suggested two regimes of oxidation kinetics dependent on the oxidation temperature. Based on experimental results, observation, and theory, a finite difference model was developed. The model simulates the diffusion of oxygen into a matrix crack bridged by carbon fibers. The model facilitates the study of the relative importance of temperature, the reaction rate constant, and the diffusion coefficient on the overall oxidation kinetics.

On the complex interplay between learning and dynamics in life sciences. Comment on the paper "Collective learning modeling based on the kinetic theory of active particles" by Burini et al.

NASA Astrophysics Data System (ADS)

Bellomo, Nicola; Elaiw, Ahmed; Alghamdi, Mohamed Ali

2016-03-01

The paper by Burini, De Lillo, and Gibelli [8] presents an overview and critical analysis of the literature on the modeling of learning dynamics. The first reference is the celebrated paper by Cucker and Smale [9]. Then, the authors also propose their own approach, based on suitable development of methods of the kinetic theory [6] and theoretical tools of evolutionary game theory [12,13], recently developed on graphs [2].

TG study of the Li0.4Fe2.4Zn0.2O4 ferrite synthesis

NASA Astrophysics Data System (ADS)

Lysenko, E. N.; Nikolaev, E. V.; Surzhikov, A. P.

2016-02-01

In this paper, the kinetic analysis of Li-Zn ferrite synthesis was studied using thermogravimetry (TG) method through the simultaneous application of non-linear regression to several measurements run at different heating rates (multivariate non-linear regression). Using TG-curves obtained for the four heating rates and Netzsch Thermokinetics software package, the kinetic models with minimal adjustable parameters were selected to quantitatively describe the reaction of Li-Zn ferrite synthesis. It was shown that the experimental TG-curves clearly suggest a two-step process for the ferrite synthesis and therefore a model-fitting kinetic analysis based on multivariate non-linear regressions was conducted. The complex reaction was described by a two-step reaction scheme consisting of sequential reaction steps. It is established that the best results were obtained using the Yander three-dimensional diffusion model at the first stage and Ginstling-Bronstein model at the second step. The kinetic parameters for lithium-zinc ferrite synthesis reaction were found and discussed.

X-ray diffraction and TGA kinetic analyses for chemical looping combustion applications.

PubMed

Tijani, Mansour Mohammedramadan; Aqsha, Aqsha; Mahinpey, Nader

2018-04-01

Synthesis and characterization of supported metal-based oxygen carriers were carried out to provide information related to the use of oxygen carriers for chemical looping combustion processes. The Cu, Co, Fe, Ni metals supported with Al 2 O 3 , CeO 2 , TiO 2 , ZrO 2 were prepared using the wetness impregnation technique. Then, the X-ray Diffraction (XRD) characterization of oxidized and reduced samples was obtained and presented. The kinetic analysis using Thermogravimetric analyzer (TGA) of the synthesized samples was conducted. The kinetics of reduction reaction of all samples were estimated and explained.

Dynamic contrast-enhanced CT of head and neck tumors: perfusion measurements using a distributed-parameter tracer kinetic model. Initial results and comparison with deconvolution-based analysis

NASA Astrophysics Data System (ADS)

Bisdas, Sotirios; Konstantinou, George N.; Sherng Lee, Puor; Thng, Choon Hua; Wagenblast, Jens; Baghi, Mehran; San Koh, Tong

2007-10-01

The objective of this work was to evaluate the feasibility of a two-compartment distributed-parameter (DP) tracer kinetic model to generate functional images of several physiologic parameters from dynamic contrast-enhanced CT data obtained of patients with extracranial head and neck tumors and to compare the DP functional images to those obtained by deconvolution-based DCE-CT data analysis. We performed post-processing of DCE-CT studies, obtained from 15 patients with benign and malignant head and neck cancer. We introduced a DP model of the impulse residue function for a capillary-tissue exchange unit, which accounts for the processes of convective transport and capillary-tissue exchange. The calculated parametric maps represented blood flow (F), intravascular blood volume (v1), extravascular extracellular blood volume (v2), vascular transit time (t1), permeability-surface area product (PS), transfer ratios k12 and k21, and the fraction of extracted tracer (E). Based on the same regions of interest (ROI) analysis, we calculated the tumor blood flow (BF), blood volume (BV) and mean transit time (MTT) by using a modified deconvolution-based analysis taking into account the extravasation of the contrast agent for PS imaging. We compared the corresponding values by using Bland-Altman plot analysis. We outlined 73 ROIs including tumor sites, lymph nodes and normal tissue. The Bland-Altman plot analysis revealed that the two methods showed an accepted degree of agreement for blood flow, and, thus, can be used interchangeably for measuring this parameter. Slightly worse agreement was observed between v1 in the DP model and BV but even here the two tracer kinetic analyses can be used interchangeably. Under consideration of whether both techniques may be used interchangeably was the case of t1 and MTT, as well as for measurements of the PS values. The application of the proposed DP model is feasible in the clinical routine and it can be used interchangeably for measuring blood flow and vascular volume with the commercially available reference standard of the deconvolution-based approach. The lack of substantial agreement between the measurements of vascular transit time and permeability-surface area product may be attributed to the different tracer kinetic principles employed by both models and the detailed capillary tissue exchange physiological modeling of the DP technique.

Chemistry of Amadori rearrangement products: analysis, synthesis, kinetics, reactions, and spectroscopic properties.

PubMed

Yaylayan, V A; Huyghues-Despointes, A

1994-01-01

The chemistry of the key intermediate in the Maillard reaction, the Amadori rearrangements product, is reviewed covering the areas of synthesis, chromatographic analyses, chemical and spectroscopic methods of characterization, reactions, and kinetics. Synthetic strategies involving free and protected sugars are described in detail with specific synthetic procedures. GC- and HPLC-based separations of Amadori products are discussed in relation to the type of columns employed and methods of detection. Applications of infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy for structural elucidation of Amadori products are also reviewed. In addition, mass spectrometry of free, protected, and protein-bound Amadori products under different ionization conditions are presented. The mechanism of acid/base catalyzed thermal degradation reactions of Amadori compounds, as well as their kinetics of formation, are critically evaluated.

Self-consistent multidimensional electron kinetic model for inductively coupled plasma sources

NASA Astrophysics Data System (ADS)

Dai, Fa Foster

Inductively coupled plasma (ICP) sources have received increasing interest in microelectronics fabrication and lighting industry. In 2-D configuration space (r, z) and 2-D velocity domain (νθ,νz), a self- consistent electron kinetic analytic model is developed for various ICP sources. The electromagnetic (EM) model is established based on modal analysis, while the kinetic analysis gives the perturbed Maxwellian distribution of electrons by solving Boltzmann-Vlasov equation. The self- consistent algorithm combines the EM model and the kinetic analysis by updating their results consistently until the solution converges. The closed-form solutions in the analytical model provide rigorous and fast computing for the EM fields and the electron kinetic behavior. The kinetic analysis shows that the RF energy in an ICP source is extracted by a collisionless dissipation mechanism, if the electron thermovelocity is close to the RF phase velocities. A criterion for collisionless damping is thus given based on the analytic solutions. To achieve uniformly distributed plasma for plasma processing, we propose a novel discharge structure with both planar and vertical coil excitations. The theoretical results demonstrate improved uniformity for the excited azimuthal E-field in the chamber. Non-monotonic spatial decay in electric field and space current distributions was recently observed in weakly- collisional plasmas. The anomalous skin effect is found to be responsible for this phenomenon. The proposed model successfully models the non-monotonic spatial decay effect and achieves good agreements with the measurements for different applied RF powers. The proposed analytical model is compared with other theoretical models and different experimental measurements. The developed model is also applied to two kinds of ICP discharges used for electrodeless light sources. One structure uses a vertical internal coil antenna to excite plasmas and another has a metal shield to prevent the electromagnetic radiation. The theoretical results delivered by the proposed model agree quite well with the experimental measurements in many aspects. Therefore, the proposed self-consistent model provides an efficient and reliable means for designing ICP sources in various applications such as VLSI fabrication and electrodeless light sources.

Demon voltammetry and analysis software: Analysis of cocaine-induced alterations in dopamine signaling using multiple kinetic measures

PubMed Central

Yorgason, Jordan T.; España, Rodrigo A.; Jones, Sara R.

2011-01-01

The fast sampling rates of fast scan cyclic voltammetry make it a favorable method for measuring changes in brain monoamine release and uptake kinetics in slice, anesthetized, and freely moving preparations. The most common analysis technique for evaluating changes in dopamine signaling uses well-established Michaelis-Menten kinetic methods that can accurately model dopamine release and uptake parameters across multiple experimental conditions. Nevertheless, over the years, many researchers have turned to other measures to estimate changes in dopamine release and uptake, yet to our knowledge no systematic comparison amongst these measures has been conducted. To address this lack of uniformity in kinetic analyses, we have created the Demon Voltammetry and Analysis software suite, which is freely available to academic and non-profit institutions. Here we present an explanation of the Demon Acquisition and Analysis features, and demonstrate its utility for acquiring voltammetric data under in vitro, in vivo anesthetized, and freely moving conditions. Additionally, the software was used to compare the sensitivity of multiple kinetic measures of release and uptake to cocaine-induced changes in electrically evoked dopamine efflux in nucleus accumbens core slices. Specifically, we examined and compared tau, full width at half height, half-life, T20, T80, slope, peak height, calibrated peak dopamine concentration, and area under the curve to the well-characterized Michaelis-Menten parameters, dopamine per pulse, maximal uptake rate, and apparent affinity. Based on observed results we recommend tau for measuring dopamine uptake and calibrated peak dopamine concentration for measuring dopamine release. PMID:21392532

Molecular basis of HHQ biosynthesis: molecular dynamics simulations, enzyme kinetic and surface plasmon resonance studies

PubMed Central

2013-01-01

Background PQS (PseudomonasQuinolone Signal) and its precursor HHQ are signal molecules of the P. aeruginosa quorum sensing system. They explicate their role in mammalian pathogenicity by binding to the receptor PqsR that induces virulence factor production and biofilm formation. The enzyme PqsD catalyses the biosynthesis of HHQ. Results Enzyme kinetic analysis and surface plasmon resonance (SPR) biosensor experiments were used to determine mechanism and substrate order of the biosynthesis. Comparative analysis led to the identification of domains involved in functionality of PqsD. A kinetic cycle was set up and molecular dynamics (MD) simulations were used to study the molecular bases of the kinetics of PqsD. Trajectory analysis, pocket volume measurements, binding energy estimations and decompositions ensured insights into the binding mode of the substrates anthraniloyl-CoA and β-ketodecanoic acid. Conclusions Enzyme kinetics and SPR experiments hint at a ping-pong mechanism for PqsD with ACoA as first substrate. Trajectory analysis of different PqsD complexes evidenced ligand-dependent induced-fit motions affecting the modified ACoA funnel access to the exposure of a secondary channel. A tunnel-network is formed in which Ser317 plays an important role by binding to both substrates. Mutagenesis experiments resulting in the inactive S317F mutant confirmed the importance of this residue. Two binding modes for β-ketodecanoic acid were identified with distinct catalytic mechanism preferences. PMID:23916145

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

PubMed Central

2014-01-01

Background The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. Description KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data. KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. Conclusions KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects. The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org, along with its full documentation. PMID:25115331

Millisecond-Timescale Monitoring of PbS Nanoparticle Nucleation and Growth Using Droplet-Based Microfluidics.

PubMed

Lignos, Ioannis; Stavrakis, Stavros; Kilaj, Ardita; deMello, Andrew J

2015-08-26

The early-time kinetics (<1 s) of lead sulfide (PbS) quantum dot formation are probed using a novel droplet-based microfluidic platform, which allows for high-throughput and real-time optical analysis of the reactive process with millisecond time resolution. The reaction platform enables the concurrent investigation of the emission characteristics of PbS quantum dots and a real-time estimation of their size and concentration during nucleation and growth. These investigations reveal a two-stage mechanism for PbS nanoparticle formation. The first stage corresponds to the fast conversion of precursor species to PbS crystals, followed by the growth of the formed particles. The growth kinetics of the PbS nanoparticles follow the Lifshitz-Slyozov-Wagner model for Ostwald ripening, allowing direct estimation of the rate constants for the process. In addition, the extraction of absorption spectra of ultrasmall quantum dots is demonstrated for first time in an online manner. The droplet-based microfluidic platform integrated with online spectroscopic analysis provides a new tool for the quantitative extraction of high temperature kinetics for systems with rapid nucleation and growth stages. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism

PubMed Central

Fleming, R.M.T.; Thiele, I.; Provan, G.; Nasheuer, H.P.

2010-01-01

The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in E. coli and compare favourably with in silico prediction by flux balance analysis. PMID:20230840

General theory of the multistage geminate reactions of the isolated pairs of reactants. II. Detailed balance and universal asymptotes of kinetics.

PubMed

Kipriyanov, Alexey A; Doktorov, Alexander B

2014-10-14

The analysis of general (matrix) kinetic equations for the mean survival probabilities of any of the species in a sample (or mean concentrations) has been made for a wide class of the multistage geminate reactions of the isolated pairs. These kinetic equations (obtained in the frame of the kinetic approach based on the concept of "effective" particles in Paper I) take into account various possible elementary reactions (stages of a multistage reaction) excluding monomolecular, but including physical and chemical processes of the change in internal quantum states carried out with the isolated pairs of reactants (or isolated reactants). The general basic principles of total and detailed balance have been established. The behavior of the reacting system has been considered on macroscopic time scales, and the universal long-term kinetics has been determined.

Cold-start characteristics of polymer electrolyte fuel cells

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

Mishler, Jeff; Mukundan, Rangachary; Wang, Yun

2010-01-01

In this paper, we investigate the electrochemical reaction kinetics, species transport, and solid water dynamics in a polymer electrolyte fuel cell (PEFC) during cold start. A simplitied analysis is developed to enable the evaluation of the impact of ice volume fraction on cell performance during coldstart. Supporting neutron imaging data are also provided to reveal the real-time water evolution. Temperature-dependent voltage changes due to the reaction kinetics and ohmic loss are also analyzed based on the ionic conductivity of the membrane at subfreezing temperature. The analysis is valuable for the fundamental study of PEFC cold-start.

Jet-A reaction mechanism study for combustion application

NASA Technical Reports Server (NTRS)

Lee, Chi-Ming; Kundu, Krishna; Acosta, Waldo

1991-01-01

Simplified chemical kinetic reaction mechanisms for the combustion of Jet A fuel was studied. Initially, 40 reacting species and 118 elementary chemical reactions were chosen based on a literature review. Through a sensitivity analysis with the use of LSENS General Kinetics and Sensitivity Analysis Code, 16 species and 21 elementary chemical reactions were determined from this study. This mechanism is first justified by comparison of calculated ignition delay time with the available shock tube data, then it is validated by comparison of calculated emissions from the plug flow reactor code with in-house flame tube data.

Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA.

PubMed

Ren, Hang; Cheyne, Cameron G; Fleming, Aaron M; Burrows, Cynthia J; White, Henry S

2018-04-18

Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( k intra-extra ) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( k extra-intra ) remains unchanged. Both k intra-extra and k extra-intra are on the order of 1 × 10 -2 s -1 to 1 × 10 -1 s -1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H + into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for k intra-extra ( k H / k D ≈ 5) but a limited KIE for k extra-intra ( k H / k D ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.

Kinetic therapy in multiple trauma patients with severe blunt chest trauma: an analysis at a level-1 trauma center.

PubMed

Zeckey, C; Wendt, K; Mommsen, P; Winkelmann, M; Frömke, C; Weidemann, J; Stübig, T; Krettek, C; Hildebrand, F

2015-01-01

Chest trauma is a relevant risk factor for mortality after multiple trauma. Kinetic therapy (KT) represents a potential treatment option in order to restore pulmonary function. Decision criteria for performing kinetic therapy are not fully elucidated. The purpose of this study was to investigate the decision making process to initiate kinetic therapy in a well defined multiple trauma cohort. A retrospective analysis (2000-2009) of polytrauma patients (age > 16 years, ISS ⩾ 16) with severe chest trauma (AIS(Chest) ⩾ 3) was performed. Patients with AIS(Head) ⩾ 3 were excluded. Patients receiving either kinetic (KT+) or lung protective ventilation strategy (KT-) were compared. Chest trauma was classified according to the AIS(Chest), Pulmonary Contusion Score (PCS), Wagner Jamieson Score and Thoracic Trauma Severity Score (TTS). There were multiple outcome parameters investigated included mortality, posttraumatic complications and clinical data. A multivariate regression analysis was performed. Two hundred and eighty-three patients were included (KT+: n=160; KT-: n=123). AIS(Chest), age and gender were comparable in both groups. There were significant higher values of the ISS, PCS, Wagner Jamieson Score and TTS in group KT+. The incidence of posttraumatic complications and mortality was increased compared to group KT- (p< 0.05). Despite that, kinetic therapy failed to be an independent risk factor for mortality in multivariate logistic regression analysis. Kinetic therapy is an option in severely injured patients with severe chest trauma. Decision making is not only based on anatomical aspects such as the AIS(Chest), but on overall injury severity, pulmonary contusions and physiological deterioration. It could be assumed that the increased mortality in patients receiving KT is primarily caused by these factors and does not reflect an independent adverse effect of KT. Furthermore, KT was not shown to be an independent risk factor for mortality.

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.

Estimating the kinetic parameters of activated sludge storage using weighted non-linear least-squares and accelerating genetic algorithm.

PubMed

Fang, Fang; Ni, Bing-Jie; Yu, Han-Qing

2009-06-01

In this study, weighted non-linear least-squares analysis and accelerating genetic algorithm are integrated to estimate the kinetic parameters of substrate consumption and storage product formation of activated sludge. A storage product formation equation is developed and used to construct the objective function for the determination of its production kinetics. The weighted least-squares analysis is employed to calculate the differences in the storage product concentration between the model predictions and the experimental data as the sum of squared weighted errors. The kinetic parameters for the substrate consumption and the storage product formation are estimated to be the maximum heterotrophic growth rate of 0.121/h, the yield coefficient of 0.44 mg CODX/mg CODS (COD, chemical oxygen demand) and the substrate half saturation constant of 16.9 mg/L, respectively, by minimizing the objective function using a real-coding-based accelerating genetic algorithm. Also, the fraction of substrate electrons diverted to the storage product formation is estimated to be 0.43 mg CODSTO/mg CODS. The validity of our approach is confirmed by the results of independent tests and the kinetic parameter values reported in literature, suggesting that this approach could be useful to evaluate the product formation kinetics of mixed cultures like activated sludge. More importantly, as this integrated approach could estimate the kinetic parameters rapidly and accurately, it could be applied to other biological processes.

Understanding the effects of strain on morphological instabilities of a nanoscale island during heteroepitaxial growth

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

Feng, Lu; Wang, Jing; Wang, Shibin

A comprehensive morphological stability analysis of a nanoscale circular island during heteroepitaxial growth is presented based on continuum elasticity theory. The interplay between kinetic and thermodynamic mechanisms is revealed by including strain-related kinetic processes. In the kinetic regime, the Burton-Cabrera-Frank model is adopted to describe the growth front of the island. Together with kinetic boundary conditions, various kinetic processes including deposition flow, adatom diffusion, attachment-detachment kinetics, and the Ehrlich-Schwoebel barrier can be taken into account at the same time. In the thermodynamic regime, line tension, surface energy, and elastic energy are considered. As the strain relief in the early stagesmore » of heteroepitaxy is more complicated than commonly suggested by simple consideration of lattice mismatch, we also investigate the effects of external applied strain and elastic response due to perturbations on the island shape evolution. The analytical expressions for elastic fields induced by mismatch strain, external applied strain, and relaxation strain are presented. A systematic approach is developed to solve the system via a perturbation analysis which yields the conditions of film morphological instabilities. Consistent with previous experimental and theoretical work, parametric studies show the kinetic evolution of elastic relaxation, island morphology, and film composition under various conditions. Our present work offers an effective theoretical approach to get a comprehensive understanding of the interplay between different growth mechanisms and how to tailor the growth mode by controlling the nature of the crucial factors.« less

Electronic and structural aspects of p450-mediated drug metabolism.

PubMed

Lewis, David F V; Ito, Yuko; Lake, Brian G

2009-04-01

From a consideration of first principles for enzymes kinetics, we have employed theoretical methods which enable one to analyse the kinetics of cytochrome P450-mediated reactions which have been based on the known physicochemical principles underlying the majority of chemical or enzymatic reactions. A comparison is made between the correlation equations produced from the QSAR analysis of experimental P450 reaction rate data and those obtained from first principles, where there appears to be a generally satisfactory concordance between the two procedures. In this respect, we have developed expressions based on standard reaction kinetics theory which incorporate the Eyring and Marcus relationships. The analysis of P450-catalyzed reaction rates is elaborated to encompass a treatment of metabolic clearance, and satisfactory correlations are obtained with literature values for both intrinsic clearance and whole body clearance in terms of compound lipophilicity derived from log P data, where P is the octanol/water partition coefficient. The importance of ionization potential as a factor in the overall catalytic turnover of P450-mediated reactions is noted, especially in combination with the lipophilicity parameter, log P.

Transient-state kinetic approach to mechanisms of enzymatic catalysis.

PubMed

Fisher, Harvey F

2005-03-01

Transient-state kinetics by its inherent nature can potentially provide more directly observed detailed resolution of discrete events in the mechanistic time courses of enzyme-catalyzed reactions than its more widely used steady-state counterpart. The use of the transient-state approach, however, has been severely limited by the lack of any theoretically sound and applicable basis of interpreting the virtual cornucopia of time and signal-dependent phenomena that it provides. This Account describes the basic kinetic behavior of the transient state, critically examines some currently used analytic methods, discusses the application of a new and more soundly based "resolved component transient-state time-course method" to the L-glutamate-dehydrogenase reaction, and establishes new approaches for the analysis of both single- and multiple-step substituted transient-state kinetic isotope effects.

Influence of porogen nature on the kinetic and potential efficiencies of divinylbenzene-based monolithic sorbents in gas chromatography

NASA Astrophysics Data System (ADS)

Korolev, A. A.; Shiryaeva, V. E.; Popova, T. P.; Kanat'eva, A. Yu.; Kurganov, A. A.

2015-02-01

It has been shown that using Poppe curves for characterization of monolithic sorbents makes it possible to optimize conditions for both the synthesis of monoliths intended for high-speed analysis and achievement of the best separation efficiency. The influence of the nature of a porogen on the kinetic efficiency of monolithic sorbents in high-pressure gas chromatography has been considered. It has been found that the nature of the porogen alcohol determines to a considerable extent the structure of the monolith and its kinetic efficiency. The sorbents prepared with the use of octanol-1 and dodecanol-1 have shown the best kinetic characteristics; however, minimal HETP values have been observed for the columns prepared using hexanol-1 as a porogen.

The fractal architecture of cytoplasmic organization: scaling, kinetics and emergence in metabolic networks.

PubMed

Aon, Miguel Antonio; O'Rourke, Brian; Cortassa, Sonia

2004-01-01

In this work, we highlight the links between fractals and scaling in cells and explore the kinetic consequences for biochemical reactions operating in fractal media. Based on the proposal that the cytoskeletal architecture is organized as a percolation lattice, with clusters emerging as fractal forms, the analysis of kinetics in percolation clusters is especially emphasized. A key consequence of this spatiotemporal cytoplasmic organization is that enzyme reactions following Michaelis-Menten or allosteric type kinetics exhibit higher rates in fractal media (for short times and at lower substrate concentrations) at the percolation threshold than in Euclidean media. As a result, considerably faster and higher amplification of enzymatic activity is obtained. Finally, we describe some of the properties bestowed by cytoskeletal organization and dynamics on metabolic networks.

Dissociative adsorption of O2 on unreconstructed metal (100) surfaces: Pathways, energetics, and sticking kinetics

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

Liu, Da-Jiang; Evans, James W.

An accurate description of oxygen dissociation pathways and kinetics for various local adlayer environments is key for an understanding not just of the coverage dependence of oxygen sticking, but also of reactive steady states in oxidation reactions. Density functional theory analysis for M(100) surfaces with M=Pd, Rh, and Ni, where O prefers the fourfold hollow adsorption site, does not support the traditional Brundle-Behm-Barker picture of dissociative adsorption onto second-nearest-neighbor hollow sites with an additional blocking constraint. Rather adsorption via neighboring vicinal bridge sites dominates, although other pathways can be active. The same conclusion also applies for M=Pt and Ir, wheremore » oxygen prefers the bridge adsorption site. Statistical mechanical analysis is performed based on kinetic Monte Carlo simulation of a multisite lattice-gas model consistent with our revised picture of adsorption. This analysis determines the coverage and temperature dependence of sticking for a realistic treatment of the oxygen adlayer structure.« less

Detectable states, cycle fluxes, and motility scaling of molecular motor kinesin: An integrative kinetic graph theory analysis

NASA Astrophysics Data System (ADS)

Ren, Jie

2017-12-01

The process by which a kinesin motor couples its ATPase activity with concerted mechanical hand-over-hand steps is a foremost topic of molecular motor physics. Two major routes toward elucidating kinesin mechanisms are the motility performance characterization of velocity and run length, and single-molecular state detection experiments. However, these two sets of experimental approaches are largely uncoupled to date. Here, we introduce an integrative motility state analysis based on a theorized kinetic graph theory for kinesin, which, on one hand, is validated by a wealth of accumulated motility data, and, on the other hand, allows for rigorous quantification of state occurrences and chemomechanical cycling probabilities. An interesting linear scaling for kinesin motility performance across species is discussed as well. An integrative kinetic graph theory analysis provides a powerful tool to bridge motility and state characterization experiments, so as to forge a unified effort for the elucidation of the working mechanisms of molecular motors.

Kinetic parameters of grinding media in ball mills with various liner design and mill speed based on DEM modeling

NASA Astrophysics Data System (ADS)

Khakhalev, P. A.; Bogdanov, VS; Kovshechenko, V. M.

2018-03-01

The article presents analysis of the experiments in the ball mill of 0.5x0.3 m with four different liner types based on DEM modeling. The numerical experiment always complements laboratory research and allow obtaining high accuracy output data. An important property of the numerical experiment is the possibility of visualization of the results. The EDEM software allows calculating trajectory of the grinding bodies and kinetic parameters of each ball for the relative mill speed and the different types of mill’s liners.

In situ synchrotron investigation of grain growth behavior of nano-grained UO 2

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

Miao, Yinbin; Yao, Tiankai; Lian, Jie

Here, we report on the study of grain growth kinetics in nano-grained UO 2 samples. Dense nano-grained UO 2 samples with well-controlled stoichiometry and grain size were fabricated using the spark plasma sintering technique. To determine the grain growth kinetics at elevated temperatures, a synchrotron wide-angle X-ray scattering (WAXS) study was performed in situ to measure the real-time grain size evolution based on the modified Williamson-Hall analysis. The unique grain growth kinetics of nanocrystalline UO 2 at 730 °C and 820 °C were observed and explained by the difference in mobility of various grain boundaries.

In situ synchrotron investigation of grain growth behavior of nano-grained UO 2

DOE PAGES

Miao, Yinbin; Yao, Tiankai; Lian, Jie; ...

2017-01-09

Here, we report on the study of grain growth kinetics in nano-grained UO 2 samples. Dense nano-grained UO 2 samples with well-controlled stoichiometry and grain size were fabricated using the spark plasma sintering technique. To determine the grain growth kinetics at elevated temperatures, a synchrotron wide-angle X-ray scattering (WAXS) study was performed in situ to measure the real-time grain size evolution based on the modified Williamson-Hall analysis. The unique grain growth kinetics of nanocrystalline UO 2 at 730 °C and 820 °C were observed and explained by the difference in mobility of various grain boundaries.

An evidence-based systematic review of gymnema (Gymnema sylvestre R. Br.) by the Natural Standard Research Collaboration.

PubMed

Ulbricht, Catherine; Abrams, Tracee Rae; Basch, Ethan; Davies-Heerema, Theresa; Foppa, Ivo; Hammerness, Paul; Rusie, Erica; Tanguay-Colucci, Shaina; Taylor, Sarah; Ulbricht, Catherine; Varghese, Minney; Weissner, Wendy; Woods, Jen

2011-09-01

An evidence-based systematic review of gymnema (Gymnema sylvestre R. Br.), including written and statistical analysis of scientific literature, expert opinion, folkloric precedent, history, pharmacology, kinetics/dynamics, interactions, adverse effects, toxicology, and dosing.

Stochastic effects in a discretized kinetic model of economic exchange

NASA Astrophysics Data System (ADS)

Bertotti, M. L.; Chattopadhyay, A. K.; Modanese, G.

2017-04-01

Linear stochastic models and discretized kinetic theory are two complementary analytical techniques used for the investigation of complex systems of economic interactions. The former employ Langevin equations, with an emphasis on stock trade; the latter is based on systems of ordinary differential equations and is better suited for the description of binary interactions, taxation and welfare redistribution. We propose a new framework which establishes a connection between the two approaches by introducing random fluctuations into the kinetic model based on Langevin and Fokker-Planck formalisms. Numerical simulations of the resulting model indicate positive correlations between the Gini index and the total wealth, that suggest a growing inequality with increasing income. Further analysis shows, in the presence of a conserved total wealth, a simultaneous decrease in inequality as social mobility increases, in conformity with economic data.

On the thermodynamic and kinetic investigations of a [c2]daisy chain polymer

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

Hmadeh, Mohamad; Fang, Lei; Trabolsi, Ali

2010-01-01

We report a variety of [c2]daisy chain molecules which undergo quantitative, efficient, and fully reversible molecular movements upon the addition of base/acid in organic solvents. Such externally triggered molecular movements can induce the contraction and extension of the [c2]daisy chain molecule as a whole. A linear polymer of such a bistable [c2]daisy chain exerts similar types of movements and can be looked upon as a candidate for the development of artificial muscles. The spectrophotometric investigations of both the monomeric and polymeric bistable [c2]daisy chains, as well as the corresponding model compounds, were performed in MeCN at room temperature, in ordermore » to obtain the thermodynamic parameters for these mechanically interlocked molecules. Based on their spectrophotometric and thermodynamic characteristics, kinetic analysis of the acid/base-induced contraction and extension of the [c2]daisy chain monomer and polymer were conducted by employing a stopped-flow technique. These kinetic data suggest that the rates of contraction and extension for these [c2]daisy chain molecules are determined by the thermodynamic stabilities of the corresponding kinetic intermediates. Faster switching rates for both the contraction and extension processes of the polymeric [c2]daisy chain were observed when compared to those of its monomeric counterpart. These kinetic and thermodynamic investigations on [c2]daisy chain-based muscle-like compounds provide important information for those seeking an understanding of the mechanisms of actuation in mechanically interlocked macromolecules.« less

Derringer desirability and kinetic plot LC-column comparison approach for MS-compatible lipopeptide analysis.

PubMed

D'Hondt, Matthias; Verbeke, Frederick; Stalmans, Sofie; Gevaert, Bert; Wynendaele, Evelien; De Spiegeleer, Bart

2014-06-01

Lipopeptides are currently re-emerging as an interesting subgroup in the peptide research field, having historical applications as antibacterial and antifungal agents and new potential applications as antiviral, antitumor, immune-modulating and cell-penetrating compounds. However, due to their specific structure, chromatographic analysis often requires special buffer systems or the use of trifluoroacetic acid, limiting mass spectrometry detection. Therefore, we used a traditional aqueous/acetonitrile based gradient system, containing 0.1% (m/v) formic acid, to separate four pharmaceutically relevant lipopeptides (polymyxin B 1 , caspofungin, daptomycin and gramicidin A 1 ), which were selected based upon hierarchical cluster analysis (HCA) and principal component analysis (PCA). In total, the performance of four different C18 columns, including one UPLC column, were evaluated using two parallel approaches. First, a Derringer desirability function was used, whereby six single and multiple chromatographic response values were rescaled into one overall D -value per column. Using this approach, the YMC Pack Pro C18 column was ranked as the best column for general MS-compatible lipopeptide separation. Secondly, the kinetic plot approach was used to compare the different columns at different flow rate ranges. As the optimal kinetic column performance is obtained at its maximal pressure, the length elongation factor λ ( P max / P exp ) was used to transform the obtained experimental data (retention times and peak capacities) and construct kinetic performance limit (KPL) curves, allowing a direct visual and unbiased comparison of the selected columns, whereby the YMC Triart C18 UPLC and ACE C18 columns performed as best. Finally, differences in column performance and the (dis)advantages of both approaches are discussed.

A possible mechanism of metabolic regulation in Gibberella fujikuroi using a mixed carbon source of glucose and corn oil inferred from analysis of the kinetics data obtained in a stirrer tank bioreactor.

PubMed

Rios-Iribe, Erika Y; Hernández-Calderón, Oscar M; Reyes-Moreno, C; Contreras-Andrade, I; Flores-Cotera, Luis B; Escamilla-Silva, Eleazar M

2013-01-01

A nonstructured model was used to study the dynamics of gibberellic acid production in a stirred tank bioreactor. Experimental data were obtained from submerged batch cultures of Gibberella fujikuroi (CDBB H-984) grown in varying ratios of glucose-corn oil as the carbon source. The nitrogen depletion effect was included in mathematical model by considering the specific kinetic constants as a linear function of the normalized nitrogen consumption rate. The kinetics of biomass growth and consumption of phosphate and nitrogen were based on the logistic model. The traditional first-order kinetic model was used to describe the specific consumption of glucose and corn oil. The nitrogen effect was solely included in the phosphate and corn oil consumption and biomass growth. The model fit was satisfactory, revealing the dependence of the kinetics with respect to the nitrogen assimilation rate. Through simulations, it was possible to make diagrams of specific growth rate and specific rate of substrate consumptions, which was a powerful tool for understanding the metabolic interactions that occurred during the various stages of fermentation process. This kinetic analysis provided the proposal of a possible mechanism of regulation on growth, substrate consumptions, and production of gibberellic acid (GA3 ) in G. fujikuroi. © 2013 American Institute of Chemical Engineers.

Kinetics and Mechanisms of γ′ Reprecipitation in a Ni-based Superalloy

PubMed Central

Masoumi, F.; Shahriari, D.; Jahazi, M.; Cormier, J.; Devaux, A.

2016-01-01

The reprecipitation mechanisms and kinetics of γ′ particles during cooling from supersolvus and subsolvus temperatures were studied in AD730TM Ni-based superalloy using Differential Thermal Analysis (DTA). The evolution in the morphology and distribution of reprecipitated γ′ particles was investigated using Field Emission Gun Scanning Electron Microscopy (FEG-SEM). Depending on the cooling rate, γ′ particles showed multi or monomodal distribution. The irregularity growth characteristics observed at lower cooling rates were analyzed in the context of Mullins and Sekerka theory, and allowed the determination of a critical size of γ′ particles above which morphological instability appears. Precipitation kinetics parameters were determined using a non-isothermal JMA model and DTA data. The Avrami exponent was determined to be in the 1.5–2.3 range, suggesting spherical or irregular growth. A methodology was developed to take into account the temperature dependence of the rate coefficient k(T) in the non-isothermal JMA equation. In that regard, a function for k(T) was developed. Based on the results obtained, reprecipitation kinetics models for low and high cooling rates are proposed to quantify and predict the volume fraction of reprecipitated γ′ particles during the cooling process. PMID:27338868

Chemical kinetics of Cs species in an alkali-activated municipal solid waste incineration fly ash and pyrophyllite-based system using Cs K-edge in situ X-ray absorption fine structure analysis

NASA Astrophysics Data System (ADS)

Shiota, Kenji; Nakamura, Takafumi; Takaoka, Masaki; Nitta, Kiyofumi; Oshita, Kazuyuki; Fujimori, Takashi; Ina, Toshiaki

2017-05-01

We conducted in situ X-ray absorption fine structure (in situ XAFS) analysis at the Cs K-edge to investigate the chemical kinetics of Cs species during reaction in an alkali-activated municipal solid waste incineration fly ash (MSWIFA) and pyrophyllite-based system. Understanding the kinetics of Cs is essential to the design of appropriate conditions for Cs stabilization. In situ XAFS analysis of four pastes, prepared from NaOHaq, sodium silicate solution, pyrophyllite, and MSWIFA with the addition of CsCl, was conducted in custom-built reaction cells at four curing temperatures (room temperature, 60 °C, 80 °C, 105 °C) for approximately 34 h. The results indicated that the change in Cs species during reaction at room temperature was small, while changes at higher temperatures were faster and more extreme, with the fastest conversion to pollucite occurring at 105 °C. Further analysis using a leaching test and a simple reaction model for Cs species during reaction showed that the pollucite formation rate was dependent on the curing temperature and had a significant negative correlation with Cs leaching. The activation energy of pollucite formation was estimated to be 31.5 kJ/mol. These results revealed that an important change in the chemical state of Cs occurs during reaction in the system.

Analysis of mutagenic DNA repair in a thermoconditional mutant of Saccharomyces cerevisiae. III. Dose-response pattern of mutation induction in UV-irradiated rev2ts cells.

PubMed

Siede, W; Eckardt, F

1986-01-01

Recent studies regarding the influence of cycloheximide on the temperature-dependent increase in survival and mutation frequencies of a thermoconditional rev2 mutant lead to the suggestion that the REV2-coded mutagenic repair function is UV-inducible. In the present study we show that stationary-phase rev2ts cells are characterized by a biphasic linear-quadratic dose-dependence of mutation induction ("mutation kinetics") of ochre alleles at 23 degrees C (permissive temperature) but linear kinetics at the restrictive temperature of 36 degrees C. Mathematical analysis using a model based on Poisson statistics and a further mathematical procedure, the calculation of "apparent survival", support the assumption that the quadratic component of the reverse mutation kinetics investigated can be attributed to a UV-inducible component of mutagenic DNA repair controlled by the REV2 gene.

Web-based applications for building, managing and analysing kinetic models of biological systems.

PubMed

Lee, Dong-Yup; Saha, Rajib; Yusufi, Faraaz Noor Khan; Park, Wonjun; Karimi, Iftekhar A

2009-01-01

Mathematical modelling and computational analysis play an essential role in improving our capability to elucidate the functions and characteristics of complex biological systems such as metabolic, regulatory and cell signalling pathways. The modelling and concomitant simulation render it possible to predict the cellular behaviour of systems under various genetically and/or environmentally perturbed conditions. This motivates systems biologists/bioengineers/bioinformaticians to develop new tools and applications, allowing non-experts to easily conduct such modelling and analysis. However, among a multitude of systems biology tools developed to date, only a handful of projects have adopted a web-based approach to kinetic modelling. In this report, we evaluate the capabilities and characteristics of current web-based tools in systems biology and identify desirable features, limitations and bottlenecks for further improvements in terms of usability and functionality. A short discussion on software architecture issues involved in web-based applications and the approaches taken by existing tools is included for those interested in developing their own simulation applications.

Integrated software environment based on COMKAT for analyzing tracer pharmacokinetics with molecular imaging.

PubMed

Fang, Yu-Hua Dean; Asthana, Pravesh; Salinas, Cristian; Huang, Hsuan-Ming; Muzic, Raymond F

2010-01-01

An integrated software package, Compartment Model Kinetic Analysis Tool (COMKAT), is presented in this report. COMKAT is an open-source software package with many functions for incorporating pharmacokinetic analysis in molecular imaging research and has both command-line and graphical user interfaces. With COMKAT, users may load and display images, draw regions of interest, load input functions, select kinetic models from a predefined list, or create a novel model and perform parameter estimation, all without having to write any computer code. For image analysis, COMKAT image tool supports multiple image file formats, including the Digital Imaging and Communications in Medicine (DICOM) standard. Image contrast, zoom, reslicing, display color table, and frame summation can be adjusted in COMKAT image tool. It also displays and automatically registers images from 2 modalities. Parametric imaging capability is provided and can be combined with the distributed computing support to enhance computation speeds. For users without MATLAB licenses, a compiled, executable version of COMKAT is available, although it currently has only a subset of the full COMKAT capability. Both the compiled and the noncompiled versions of COMKAT are free for academic research use. Extensive documentation, examples, and COMKAT itself are available on its wiki-based Web site, http://comkat.case.edu. Users are encouraged to contribute, sharing their experience, examples, and extensions of COMKAT. With integrated functionality specifically designed for imaging and kinetic modeling analysis, COMKAT can be used as a software environment for molecular imaging and pharmacokinetic analysis.

Determination of in vivo regulation kinetics of small non-coding RNA in bacteria

NASA Astrophysics Data System (ADS)

Fei, Jingyi

Small RNAs (sRNAs) play important roles in regulating gene expression through a variety of mechanisms. As one of the most common strategies, sRNA induced target messenger RNA (mRNA) includes two major steps: target search by base-pairing interactions with the and downstream execution by modulating translation or the stability of the mRNA. Here we describe a new imaging and analysis platform based on super-resolution fluorescence microscopy, which enabled the first in vivo kinetic measurement of sRNA-mediated gene regulation. Specifically, this platform was used to investigate a sugar-phosphate stress-induced bacterial sRNA that induces the degradation of target mRNAs. The data reveal that the sRNA binds to a primary target mRNA in a reversible and dynamic fashion, and that formation of the sRNA-mRNA complexes is the rate-limiting step, dictating the overall efficiency of regulation in vivo; whereas the downstream co-degradation of sRNA-mRNA complex can kinetically compete with the fast complex disassembly. Examination of a secondary target of this sRNA indicated that differences in the target search kinetics contribute to setting the regulation priority among different target mRNAs. This super-resolution imaging and analysis approach provides a conceptual framework that can be generalized to other sRNA systems and other target search processes.

Quantitative Evaluation of the Total Magnetic Moments of Colloidal Magnetic Nanoparticles: A Kinetics-based Method.

PubMed

Liu, Haiyi; Sun, Jianfei; Wang, Haoyao; Wang, Peng; Song, Lina; Li, Yang; Chen, Bo; Zhang, Yu; Gu, Ning

2015-06-08

A kinetics-based method is proposed to quantitatively characterize the collective magnetization of colloidal magnetic nanoparticles. The method is based on the relationship between the magnetic force on a colloidal droplet and the movement of the droplet under a gradient magnetic field. Through computational analysis of the kinetic parameters, such as displacement, velocity, and acceleration, the magnetization of colloidal magnetic nanoparticles can be calculated. In our experiments, the values measured by using our method exhibited a better linear correlation with magnetothermal heating, than those obtained by using a vibrating sample magnetometer and magnetic balance. This finding indicates that this method may be more suitable to evaluate the collective magnetism of colloidal magnetic nanoparticles under low magnetic fields than the commonly used methods. Accurate evaluation of the magnetic properties of colloidal nanoparticles is of great importance for the standardization of magnetic nanomaterials and for their practical application in biomedicine. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microfluidic Dynamic Interfacial Tensiometry (μDIT).

PubMed

Brosseau, Quentin; Vrignon, Jérémy; Baret, Jean-Christophe

2014-05-07

We designed, developed and characterized a microfluidic method for the measurement of surfactant adsorption kinetics via interfacial tensiometry on a microfluidic chip. The principle of the measurement is based on the deformability of droplets as a response to hydrodynamic forcing through a series of microfluidic expansions. We focus our analysis on one perfluoro surfactant molecule of practical interest for droplet-based microfluidic applications. We show that although the adsorption kinetics is much faster than the kinetics of the corresponding pendant drop experiment, our droplet-based microfluidic system has a sufficient time resolution to obtain quantitative measurement at the sub-second time-scale on nanoliter droplet volumes, leading to both a gain by a factor of ∼10 in time resolution and a downscaling of the measurement volumes by a factor of ∼1000 compared to standard techniques. Our approach provides new insight into the adsorption of surfactant molecules at liquid-liquid interfaces in a confined environment, relevant to emulsification, encapsulation and foaming, and the ability to measure adsorption and desorption rate constants.

Swelling-induced optical anisotropy of thermoresponsive hydrogels based on poly(2-(2-methoxyethoxy)ethyl methacrylate): deswelling kinetics probed by quantitative Mueller matrix polarimetry.

PubMed

Patil, Nagaraj; Soni, Jalpa; Ghosh, Nirmalya; De, Priyadarsi

2012-11-29

Thermodynamically favored polymer-water interactions below the lower critical solution temperature (LCST) caused swelling-induced optical anisotropy (linear retardance) of thermoresponsive hydrogels based on poly(2-(2-methoxyethoxy)ethyl methacrylate). This was exploited to study the macroscopic deswelling kinetics quantitatively by a generalized polarimetry analysis method, based on measurement of the Mueller matrix and its subsequent inverse analysis via the polar decomposition approach. The derived medium polarization parameters, namely, linear retardance (δ), diattenuation (d), and depolarization coefficient (Δ), of the hydrogels showed interesting differences between the gels prepared by conventional free radical polymerization (FRP) and reversible addition-fragmentation chain transfer polymerization (RAFT) and also between dry and swollen state. The effect of temperature, cross-linking density, and polymerization technique employed to synthesize hydrogel on deswelling kinetics was systematically studied via conventional gravimetry and corroborated further with the corresponding Mueller matrix derived quantitative polarimetry characteristics (δ, d, and Δ). The RAFT gels exhibited higher swelling ratio and swelling-induced optical anisotropy compared to FRP gels and also deswelled faster at 30 °C. On the contrary, at 45 °C, deswelling was significantly retarded for the RAFT gels due to formation of a skin layer, which was confirmed and quantified via the enhanced diattenuation and depolarization parameters.

Acid-base equilibrium in aqueous solutions of 1,3-dimethylbarbituric acid as studied by 13C NMR spectroscopy

NASA Astrophysics Data System (ADS)

Gryff-Keller, A.; Kraska-Dziadecka, A.

2011-12-01

13C NMR spectra of 1,3-dimethylbarbituric acid in aqueous solutions of various acidities and for various solute concentrations have been recorded and interpreted. The spectra recorded at pH = 2 and below contain the signals of the neutral solute molecule exclusively, while the ones recorded at pH = 7 and above only the signals of the appropriate anion, which has been confirmed by theoretical GIAO-DFT calculations. The signals in the spectra recorded for solutions of pH < 7 show dynamic broadenings. The lineshape analysis of these signals has provided information on the kinetics of the processes running in the dynamic acid-base equilibrium. The kinetic data determined this way have been used to clarify the mechanisms of these processes. The numerical analysis has shown that under the investigated conditions deprotonation of the neutral solute molecules undergoes not only via a simple transfer of the C-H proton to water molecules but also through a process with participation of the barbiturate anions. Moreover, the importance of tautomerism, or association, or both these phenomena for the kinetics of the acid-base transformations in the investigated system has been shown. Qualitatively similar changes of 13C NMR spectra with the solution pH variation have been observed for the parent barbituric acid.

Raman-based noninvasive metabolic profile evaluation of in vitro bovine embryos

NASA Astrophysics Data System (ADS)

dos Santos, Érika Cristina; Martinho, Herculano; Annes, Kelly; da Silva, Thais; Soares, Carlos Alexandre; Leite, Roberta Ferreira; Milazzotto, Marcella Pecora

2016-07-01

The timing of the first embryonic cell divisions may predict the ability of an embryo to establish pregnancy. Similarly, metabolic profiles may be markers of embryonic viability. However, in bovine, data about the metabolomics profile of these embryos are still not available. In the present work, we describe Raman-based metabolomic profiles of culture media of bovine embryos with different developmental kinetics (fast x slow) throughout the in vitro culture. The principal component analysis enabled us to classify embryos with different developmental kinetics since they presented specific spectroscopic profiles for each evaluated time point. We noticed that bands at 1076 cm-1 (lipids), 1300 cm-1 (Amide III), and 2719 cm-1 (DNA nitrogen bases) gave the most relevant spectral features, enabling the separation between fast and slow groups. Bands at 1001 cm-1 (phenylalanine) and 2892 cm-1 (methylene group of the polymethylene chain) presented specific patterns related to embryonic stage and can be considered as biomarkers of embryonic development by Raman spectroscopy. The culture media analysis by Raman spectroscopy proved to be a simple and sensitive technique that can be applied with high efficiency to characterize the profiles of in vitro produced bovine embryos with different development kinetics and different stages of development.

Effect of ball milling on the physicochemical properties of atorvastatin calcium sesquihydrate: the dissolution kinetic behaviours of milled amorphous solids.

PubMed

Kobayashi, Makiko; Hattori, Yusuke; Sasaki, Tetsuo; Otsuka, Makoto

2017-01-01

The purposes of this study were to clarify the amorphization by ball milling of atorvastatin calcium sesquihydrate (AT) and to analyse the change in dissolution kinetics. The amorphous AT was prepared from crystal AT by ball milling and analysed in terms of the changes of its physicochemical properties by powder X-ray diffraction analysis (XRD), thermal analysis and infrared spectroscopy (IR). Moreover, to evaluate the usefulness of the amorphous form for pharmaceutical development, intrinsic solubility of the ground product was evaluated using a dissolution kinetic method. The XRD results indicated that crystalline AT was transformed into amorphous solids by more than 30-min milling. The thermal analysis result suggested that chemical potential of the ground AT are changed significantly by milling. The IR spectra of the AT showed the band shift from the amide group at 3406 cm -1 with an intermolecular hydrogen bond to a free amide group at 3365 cm -1 by milling. The dissolution of amorphous AT follows a dissolution kinetic model involving phase transformation. The initial dissolution rate of the ground product increased with the increase in milling time to reflect the increase in the intrinsic solubility based on the amorphous state. © 2016 Royal Pharmaceutical Society.

Precise non-steady-state characterization of solid active materials with no preliminary mechanistic assumptions

DOE PAGES

Constales, Denis; Yablonsky, Gregory S.; Wang, Lucun; ...

2017-04-25

This paper presents a straightforward and user-friendly procedure for extracting a reactivity characterization of catalytic reactions on solid materials under non-steady-state conditions, particularly in temporal analysis of products (TAP) experiments. The kinetic parameters derived by this procedure can help with the development of detailed mechanistic understanding. The procedure consists of the following two major steps: 1) Three “Laplace reactivities” are first determined based on the moments of the exit flow pulse response data; 2) Depending on a select kinetic model, kinetic constants of elementary reaction steps can then be expressed as a function of reactivities and determined accordingly. In particular,more » we distinguish two calculation methods based on the availability and reliability of reactant and product data. The theoretical results are illustrated using a reverse example with given parameters as well as an experimental example of CO oxidation over a supported Au/SiO 2 catalyst. The procedure presented here provides an efficient tool for kinetic characterization of many complex chemical reactions.« less

Analyte discrimination from chemiresistor response kinetics.

PubMed

Read, Douglas H; Martin, James E

2010-08-15

Chemiresistors are polymer-based sensors that transduce the sorption of a volatile organic compound into a resistance change. Like other polymer-based gas sensors that function through sorption, chemiresistors can be selective for analytes on the basis of the affinity of the analyte for the polymer. However, a single sensor cannot, in and of itself, discriminate between analytes, since a small concentration of an analyte that has a high affinity for the polymer might give the same response as a high concentration of another analyte with a low affinity. In this paper we use a field-structured chemiresistor to demonstrate that its response kinetics can be used to discriminate between analytes, even between those that have identical chemical affinities for the polymer phase of the sensor. The response kinetics is shown to be independent of the analyte concentration, and thus the magnitude of the sensor response, but is found to vary inversely with the analyte's saturation vapor pressure. Saturation vapor pressures often vary greatly from analyte to analyte, so analysis of the response kinetics offers a powerful method for obtaining analyte discrimination from a single sensor.

Kinetic Risk Factors of Running-Related Injuries in Female Recreational Runners.

PubMed

Napier, Christopher; MacLean, Christopher L; Maurer, Jessica; Taunton, Jack E; Hunt, Michael A

2018-05-30

Our objective was to prospectively investigate the association of kinetic variables with running-related injury (RRI) risk. Seventy-four healthy female recreational runners ran on an instrumented treadmill while 3D kinetic and kinematic data were collected. Kinetic outcomes were vertical impact transient, average vertical loading rate, instantaneous vertical loading rate, active peak, vertical impulse, and peak braking force (PBF). Participants followed a 15-week half-marathon training program. Exposure time (hours of running) was calculated from start of program until onset of injury, loss to follow-up, or end of program. After converting kinetic variables from continuous to ordinal variables based on tertiles, Cox proportional hazard models with competing risks were fit for each variable independently, before analysis in a forward stepwise multivariable model. Sixty-five participants were included in the final analysis, with a 33.8% injury rate. PBF was the only kinetic variable that was a significant predictor of RRI. Runners in the highest tertile (PBF <-0.27 BW) were injured at 5.08 times the rate of those in the middle tertile and 7.98 times the rate of those in the lowest tertile. When analyzed in the multivariable model, no kinetic variables made a significant contribution to predicting injury beyond what had already been accounted for by PBF alone. Findings from this study suggest PBF is associated with a significantly higher injury hazard ratio in female recreational runners and should be considered as a target for gait retraining interventions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

An HMM-based algorithm for evaluating rates of receptor–ligand binding kinetics from thermal fluctuation data

PubMed Central

Ju, Lining; Wang, Yijie Dylan; Hung, Ying; Wu, Chien-Fu Jeff; Zhu, Cheng

2013-01-01

Motivation: Abrupt reduction/resumption of thermal fluctuations of a force probe has been used to identify association/dissociation events of protein–ligand bonds. We show that off-rate of molecular dissociation can be estimated by the analysis of the bond lifetime, while the on-rate of molecular association can be estimated by the analysis of the waiting time between two neighboring bond events. However, the analysis relies heavily on subjective judgments and is time-consuming. To automate the process of mapping out bond events from thermal fluctuation data, we develop a hidden Markov model (HMM)-based method. Results: The HMM method represents the bond state by a hidden variable with two values: bound and unbound. The bond association/dissociation is visualized and pinpointed. We apply the method to analyze a key receptor–ligand interaction in the early stage of hemostasis and thrombosis: the von Willebrand factor (VWF) binding to platelet glycoprotein Ibα (GPIbα). The numbers of bond lifetime and waiting time events estimated by the HMM are much more than those estimated by a descriptive statistical method from the same set of raw data. The kinetic parameters estimated by the HMM are in excellent agreement with those by a descriptive statistical analysis, but have much smaller errors for both wild-type and two mutant VWF-A1 domains. Thus, the computerized analysis allows us to speed up the analysis and improve the quality of estimates of receptor–ligand binding kinetics. Contact: jeffwu@isye.gatech.edu or cheng.zhu@bme.gatech.edu PMID:23599504

Real-Time Probing of Nanowire Assembly Kinetics at the Air-Water Interface by In Situ Synchrotron X-Ray Scattering.

PubMed

He, Zhen; Jiang, Hui-Jun; Wu, Long-Long; Liu, Jian-Wei; Wang, Geng; Wang, Xiao; Wang, Jin-Long; Hou, Zhong-Huai; Chen, Gang; Yu, Shu-Hong

2018-07-02

Although many assembly strategies have been used to successfully construct well-aligned nanowire (NW) assemblies, the understanding of their assembly kinetics has remained elusive, which restricts the development of NW-based device and circuit fabrication. Now a versatile strategy that combines interfacial assembly and synchrotron-based grazing-incidence small-angle X-ray scattering (GISAXS) is presented to track the assembly evolution of the NWs in real time. During the interface assembly process, the randomly dispersed NWs gradually aggregate to form small ordered NW-blocks and finally are constructed into well-defined NW monolayer driven by the conformation entropy. The NW assembly mechanism can be well revealed by the thermodynamic analysis and large-scale molecular dynamics theoretical evaluation. These findings point to new opportunities for understanding NW assembly kinetics and manipulating NW assembled structures by bottom-up strategy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of correlated parameters and uncertainty in electronic-structure-based chemical kinetic modelling

NASA Astrophysics Data System (ADS)

Sutton, Jonathan E.; Guo, Wei; Katsoulakis, Markos A.; Vlachos, Dionisios G.

2016-04-01

Kinetic models based on first principles are becoming common place in heterogeneous catalysis because of their ability to interpret experimental data, identify the rate-controlling step, guide experiments and predict novel materials. To overcome the tremendous computational cost of estimating parameters of complex networks on metal catalysts, approximate quantum mechanical calculations are employed that render models potentially inaccurate. Here, by introducing correlative global sensitivity analysis and uncertainty quantification, we show that neglecting correlations in the energies of species and reactions can lead to an incorrect identification of influential parameters and key reaction intermediates and reactions. We rationalize why models often underpredict reaction rates and show that, despite the uncertainty being large, the method can, in conjunction with experimental data, identify influential missing reaction pathways and provide insights into the catalyst active site and the kinetic reliability of a model. The method is demonstrated in ethanol steam reforming for hydrogen production for fuel cells.

Kinetic Simulations of Type II Radio Burst Emission Processes

NASA Astrophysics Data System (ADS)

Ganse, U.; Spanier, F. A.; Vainio, R. O.

2011-12-01

The fundamental emission process of Type II Radio Bursts has been under discussion for many decades. While analytic deliberations point to three wave interaction as the source for fundamental and harmonic radio emissions, sparse in-situ observational data and high computational demands for kinetic simulations have not allowed for a definite conclusion to be reached. A popular model puts the radio emission into the foreshock region of a coronal mass ejection's shock front, where shock drift acceleration can create eletrcon beam populations in the otherwise quiescent foreshock plasma. Beam-driven instabilities are then assumed to create waves, forming the starting point of three wave interaction processes. Using our kinetic particle-in-cell code, we have studied a number of emission scenarios based on electron beam populations in a CME foreshock, with focus on wave-interaction microphysics on kinetic scales. The self-consistent, fully kinetic simulations with completely physical mass-ratio show fundamental and harmonic emission of transverse electromagnetic waves and allow for detailled statistical analysis of all contributing wavemodes and their couplings.

Modeling of kinetic, ionospheric and auroral contributions to the 557.7-nm nightglow

NASA Astrophysics Data System (ADS)

Campbell, L.; Brunger, M. J.

2010-11-01

Emission of 557.7-nm radiation from the Earth's upper atmosphere is produced by kinetic, ionospheric and auroral excitation of oxygen atoms. The mechanisms and hence the relative contributions of these three sources are not fully understood. A ground-based mid-latitude recording of the 557.7-nm emissions over the previous solar cycle facilitates a comparison of measurements with theoretical predictions. In this paper the predicted kinetic and ionospheric contributions are simulated and compared with the observations. Semi-quantitative agreement is found between the kinetic contribution and the observations, particularly in the presence of annual, semi-annual and solar cycle variations. An observed enhancement in the emissions in the years following solar maximum is not predicted by the kinetic model. However, correlation analysis reveals a component in the observed values that is related to the auroral hemispheric power. When this extra component is included, a better fit to the pre-midnight observations over the full solar cycle is found.

Simulation of the effects of sub-breakdown electric fields on the chemical kinetics in nonpremixed counterflow methane/air flames

NASA Astrophysics Data System (ADS)

Belhi, Memdouh; Im, Hong; Computational Reacting Flows Laboratory, Clean Combustion Research Center Team

2017-11-01

The effects of an electric field on the combustion kinetics in nonpremixed counterflow methane/air flames were investigated via one-dimensional numerical simulations. A classical fluid model coupling Poison's equation with transport equations for combustion species and electric field-induced particles was used. A methane-air reaction mechanism accounting for the natural ionization in flames was combined with a set of reactions that describe the formation of active particles induced by the electric field. Kinetic parameters for electron-impact reactions and transport coefficients of electrons were modeled as functions of reduced electric field via solutions to the Boltzmann kinetic equation using the BOLSIG code. Mobility of ions was computed based on the (n,6,4) and coulomb interaction potentials, while the diffusion coefficient was approximated from the mobility using Einstein relation. Contributions of electron dissociation, excitation and ionization processes were characterized quantitatively. An analysis to identify the plasma regime where the electric field can alter the combustion kinetic was proposed.

Design research of nanopositioner based on SPM and its simulation of FEM

NASA Astrophysics Data System (ADS)

Zhang, Zhenyu; Li, Hongqi; Zhou, Hongxiu; Li, Linan; Liu, Xiangjun

2006-01-01

A novel nanopositioning stage was designed according to the scanning property of SPM with flexure hinge as kinematic structure and piezoelectric ceramic as actuator. Kinetic precision and X directional area of nanopositioner are 1.55nm and 26.4 micron, respectively, which is demonstrated by kinetic analysis and finite element method FEM simulation. Designed nanopositioner based on SPM moves at 3 dimensions with nanometer scale and its motion of X, Y, and Z directions is decoupled and isotropic. Furthermore, frame of nanopositioner is simple and manufacturing is convenient, which will have broad prospect in the field of nanopositioning and nanotracing.

A prospectus on kinetic heliophysics

NASA Astrophysics Data System (ADS)

Howes, Gregory G.

2017-05-01

Under the low density and high temperature conditions typical of heliospheric plasmas, the macroscopic evolution of the heliosphere is strongly affected by the kinetic plasma physics governing fundamental microphysical mechanisms. Kinetic turbulence, collisionless magnetic reconnection, particle acceleration, and kinetic instabilities are four poorly understood, grand-challenge problems that lie at the new frontier of kinetic heliophysics. The increasing availability of high cadence and high phase-space resolution measurements of particle velocity distributions by current and upcoming spacecraft missions and of massively parallel nonlinear kinetic simulations of weakly collisional heliospheric plasmas provides the opportunity to transform our understanding of these kinetic mechanisms through the full utilization of the information contained in the particle velocity distributions. Several major considerations for future investigations of kinetic heliophysics are examined. Turbulent dissipation followed by particle heating is highlighted as an inherently two-step process in weakly collisional plasmas, distinct from the more familiar case in fluid theory. Concerted efforts must be made to tackle the big-data challenge of visualizing the high-dimensional (3D-3V) phase space of kinetic plasma theory through physics-based reductions. Furthermore, the development of innovative analysis methods that utilize full velocity-space measurements, such as the field-particle correlation technique, will enable us to gain deeper insight into these four grand-challenge problems of kinetic heliophysics. A systems approach to tackle the multi-scale problem of heliophysics through a rigorous connection between the kinetic physics at microscales and the self-consistent evolution of the heliosphere at macroscales will propel the field of kinetic heliophysics into the future.

A prospectus on kinetic heliophysics

PubMed Central

2017-01-01

Under the low density and high temperature conditions typical of heliospheric plasmas, the macroscopic evolution of the heliosphere is strongly affected by the kinetic plasma physics governing fundamental microphysical mechanisms. Kinetic turbulence, collisionless magnetic reconnection, particle acceleration, and kinetic instabilities are four poorly understood, grand-challenge problems that lie at the new frontier of kinetic heliophysics. The increasing availability of high cadence and high phase-space resolution measurements of particle velocity distributions by current and upcoming spacecraft missions and of massively parallel nonlinear kinetic simulations of weakly collisional heliospheric plasmas provides the opportunity to transform our understanding of these kinetic mechanisms through the full utilization of the information contained in the particle velocity distributions. Several major considerations for future investigations of kinetic heliophysics are examined. Turbulent dissipation followed by particle heating is highlighted as an inherently two-step process in weakly collisional plasmas, distinct from the more familiar case in fluid theory. Concerted efforts must be made to tackle the big-data challenge of visualizing the high-dimensional (3D-3V) phase space of kinetic plasma theory through physics-based reductions. Furthermore, the development of innovative analysis methods that utilize full velocity-space measurements, such as the field-particle correlation technique, will enable us to gain deeper insight into these four grand-challenge problems of kinetic heliophysics. A systems approach to tackle the multi-scale problem of heliophysics through a rigorous connection between the kinetic physics at microscales and the self-consistent evolution of the heliosphere at macroscales will propel the field of kinetic heliophysics into the future. PMID:29104421

Simultaneous determination of thermodynamic and kinetic parameters of aminopolycarbonate complexes of cobalt(II) and nickel(II) based on isothermal titration calorimetry data.

PubMed

Tesmar, Aleksandra; Wyrzykowski, Dariusz; Muñoz, Eva; Pilarski, Bogusław; Pranczk, Joanna; Jacewicz, Dagmara; Chmurzyński, Lech

2017-04-01

The influence of the different side chain residues on the thermodynamic and kinetic parameters for complexation reactions of the Co 2 + and Ni 2 + ions has been investigated by using the isothermal titration calorimetry (ITC) technique supported by potentiometric titration data. The study was concerned with the 2 common tripodal aminocarboxylate ligands, namely, nitrilotriacetic acid and N-(2-hydroxyethyl) iminodiacetic acid. Calorimetric measurements (ITC) were run in the 2-(N-morpholino)ethanesulfonic acid hydrate (2-(N-morpholino) ethanesulfonic acid), piperazine-N,N'-bis(2-ethanesulfonic acid), and dimethylarsenic acid buffers (0.1 mol L -1 , pH 6) at 298.15 K. The quantification of the metal-buffer interactions and their incorporation into the ITC data analysis enabled to obtain the pH-independent and buffer-independent thermodynamic parameters (K, ΔG, ΔH, and ΔS) for the reactions under study. Furthermore, the kinITC method was applied to obtain kinetic information on complexation reactions from the ITC data. Correlations, based on kinetic and thermodynamic data, between the kinetics of formation of Co 2 + and Ni 2 + complexes and their thermodynamic stabilities are discussed. Copyright © 2016 John Wiley & Sons, Ltd.

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

PubMed Central

Munir, Ahsan; Waseem, Hassan; Williams, Maggie R.; Stedtfeld, Robert D.; Gulari, Erdogan; Tiedje, James M.; Hashsham, Syed A.

2017-01-01

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131). PMID:28555058

Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB.

PubMed

Munir, Ahsan; Waseem, Hassan; Williams, Maggie R; Stedtfeld, Robert D; Gulari, Erdogan; Tiedje, James M; Hashsham, Syed A

2017-05-29

Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R² = 0.8131).

Physico-Geometrical Kinetics of Solid-State Reactions in an Undergraduate Thermal Analysis Laboratory

ERIC Educational Resources Information Center

Koga, Nobuyoshi; Goshi, Yuri; Yoshikawa, Masahiro; Tatsuoka, Tomoyuki

2014-01-01

An undergraduate kinetic experiment of the thermal decomposition of solids by microscopic observation and thermal analysis was developed by investigating a suitable reaction, applicable techniques of thermal analysis and microscopic observation, and a reliable kinetic calculation method. The thermal decomposition of sodium hydrogen carbonate is…

Integrated analysis of dynamic FET PET/CT parameters, histology, and methylation profiling of 44 gliomas.

PubMed

Röhrich, Manuel; Huang, Kristin; Schrimpf, Daniel; Albert, Nathalie L; Hielscher, Thomas; von Deimling, Andreas; Schüller, Ulrich; Dimitrakopoulou-Strauss, Antonia; Haberkorn, Uwe

2018-05-07

Dynamic 18 F-FET PET/CT is a powerful tool for the diagnosis of gliomas. 18 F-FET PET time-activity curves (TAC) allow differentiation between histological low-grade gliomas (LGG) and high-grade gliomas (HGG). Molecular methods such as epigenetic profiling are of rising importance for glioma grading and subclassification. Here, we analysed dynamic 18 F-FET PET data, and the histological and epigenetic features of 44 gliomas. Dynamic 18 F-FET PET was performed in 44 patients with newly diagnosed, untreated glioma: 10 WHO grade II glioma, 13 WHO grade III glioma and 21 glioblastoma (GBM). All patients underwent stereotactic biopsy or tumour resection after 18 F-FET PET imaging. As well as histological analysis of tissue samples, DNA was subjected to epigenetic analysis using the Illumina 850 K methylation array. TACs, standardized uptake values corrected for background uptake in healthy tissue (SUVmax/BG), time to peak (TTP) and kinetic modelling parameters were correlated with histological diagnoses and with epigenetic signatures. Multivariate analyses were performed to evaluate the diagnostic accuracy of 18 F-FET PET in relation to the tumour groups identified by histological and methylation-based analysis. Epigenetic profiling led to substantial tumour reclassification, with six grade II/III gliomas reclassified as GBM. Overlap of HGG-typical TACs and LGG-typical TACs was dramatically reduced when tumours were clustered on the basis of their methylation profile. SUVmax/BG values of GBM were higher than those of LGGs following both histological diagnosis and methylation-based diagnosis. The differences in TTP between GBMs and grade II/III gliomas were greater following methylation-based diagnosis than following histological diagnosis. Kinetic modeling showed that relative K1 and fractal dimension (FD) values significantly differed in histology- and methylation-based GBM and grade II/III glioma between those diagnosed histologically and those diagnosed by methylation analysis. Multivariate analysis revealed slightly greater diagnostic accuracy with methylation-based diagnosis. IDH-mutant gliomas and GBM subgroups tended to differ in their 18 F-FET PET kinetics. The status of dynamic 18 F-FET PET as a biologically and clinically relevant imaging modality is confirmed in the context of molecular glioma diagnosis.

A novel fast and flexible technique of radical kinetic behaviour investigation based on pallet for plasma evaluation structure and numerical analysis

NASA Astrophysics Data System (ADS)

Malinowski, Arkadiusz; Takeuchi, Takuya; Chen, Shang; Suzuki, Toshiya; Ishikawa, Kenji; Sekine, Makoto; Hori, Masaru; Lukasiak, Lidia; Jakubowski, Andrzej

2013-07-01

This paper describes a new, fast, and case-independent technique for sticking coefficient (SC) estimation based on pallet for plasma evaluation (PAPE) structure and numerical analysis. Our approach does not require complicated structure, apparatus, or time-consuming measurements but offers high reliability of data and high flexibility. Thermal analysis is also possible. This technique has been successfully applied to estimation of very low value of SC of hydrogen radicals on chemically amplified ArF 193 nm photoresist (the main goal of this study). Upper bound of our technique has been determined by investigation of SC of fluorine radical on polysilicon (in elevated temperature). Sources of estimation error and ways of its reduction have been also discussed. Results of this study give an insight into the process kinetics, and not only they are helpful in better process understanding but additionally they may serve as parameters in a phenomenological model development for predictive modelling of etching for ultimate CMOS topography simulation.

Assessment of bioethanol yield by S. cerevisiae grown on oil palm residues: Monte Carlo simulation and sensitivity analysis.

PubMed

Samsudin, Mohd Dinie Muhaimin; Mat Don, Mashitah

2015-01-01

Oil palm trunk (OPT) sap was utilized for growth and bioethanol production by Saccharomycescerevisiae with addition of palm oil mill effluent (POME) as nutrients supplier. Maximum yield (YP/S) was attained at 0.464g bioethanol/g glucose presence in the OPT sap-POME-based media. However, OPT sap and POME are heterogeneous in properties and fermentation performance might change if it is repeated. Contribution of parametric uncertainty analysis on bioethanol fermentation performance was then assessed using Monte Carlo simulation (stochastic variable) to determine probability distributions due to fluctuation and variation of kinetic model parameters. Results showed that based on 100,000 samples tested, the yield (YP/S) ranged 0.423-0.501g/g. Sensitivity analysis was also done to evaluate the impact of each kinetic parameter on the fermentation performance. It is found that bioethanol fermentation highly depend on growth of the tested yeast. Copyright © 2014 Elsevier Ltd. All rights reserved.

Non-Markovian closure kinetics of flexible polymers with hydrodynamic interactions.

PubMed

Levernier, N; Dolgushev, M; Bénichou, O; Blumen, A; Guérin, T; Voituriez, R

2015-11-28

This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete nonlinear dynamics. It is found that Markovian treatments based on a Wilemski-Fixman approximation significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects in the dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size N and capture radius b, which are identical in both Markovian and non-Markovian approaches. In particular, it is found that the scaling of the MFCT for large N is given by T ∼ N(3/2)ln(N/b(2)), which differs from the case of the Rouse dynamics where T ∼ N(2). The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented.

Steady state phosphorus mass balance model during hemodialysis based on a pseudo one-compartment kinetic model.

PubMed

Leypoldt, John K; Agar, Baris U; Akonur, Alp; Gellens, Mary E; Culleton, Bruce F

2012-11-01

Mathematical models of phosphorus kinetics and mass balance during hemodialysis are in early development. We describe a theoretical phosphorus steady state mass balance model during hemodialysis based on a novel pseudo one-compartment kinetic model. The steady state mass balance model accounted for net intestinal absorption of phosphorus and phosphorus removal by both dialysis and residual kidney function. Analytical mathematical solutions were derived to describe time-dependent intradialytic and interdialytic serum phosphorus concentrations assuming hemodialysis treatments were performed symmetrically throughout a week. Results from the steady state phosphorus mass balance model are described for thrice weekly hemodialysis treatment prescriptions only. The analysis predicts 1) a minimal impact of dialyzer phosphorus clearance on predialysis serum phosphorus concentration using modern, conventional hemodialysis technology, 2) variability in the postdialysis-to-predialysis phosphorus concentration ratio due to differences in patient-specific phosphorus mobilization, and 3) the importance of treatment time in determining the predialysis serum phosphorus concentration. We conclude that a steady state phosphorus mass balance model can be developed based on a pseudo one-compartment kinetic model and that predictions from this model are consistent with previous clinical observations. The predictions from this mass balance model are theoretical and hypothesis-generating only; additional prospective clinical studies will be required for model confirmation.

Kinetics of Forming Aldehydes in Frying Oils and Their Distribution in French Fries Revealed by LC-MS-Based Chemometrics.

PubMed

Wang, Lei; Csallany, A Saari; Kerr, Brian J; Shurson, Gerald C; Chen, Chi

2016-05-18

In this study, the kinetics of aldehyde formation in heated frying oils was characterized by 2-hydrazinoquinoline derivatization, liquid chromatography-mass spectrometry (LC-MS) analysis, principal component analysis (PCA), and hierarchical cluster analysis (HCA). The aldehydes contributing to time-dependent separation of heated soybean oil (HSO) in a PCA model were grouped by the HCA into three clusters (A1, A2, and B) on the basis of their kinetics and fatty acid precursors. The increases of 4-hydroxynonenal (4-HNE) and the A2-to-B ratio in HSO were well-correlated with the duration of thermal stress. Chemometric and quantitative analysis of three frying oils (soybean, corn, and canola oils) and French fry extracts further supported the associations between aldehyde profiles and fatty acid precursors and also revealed that the concentrations of pentanal, hexanal, acrolein, and the A2-to-B ratio in French fry extracts were more comparable to their values in the frying oils than other unsaturated aldehydes. All of these results suggest the roles of specific aldehydes or aldehyde clusters as novel markers of the lipid oxidation status for frying oils or fried foods.

Temporal measurements and kinetics of selenium release during coal combustion and gasification in a fluidized bed.

PubMed

Shen, Fenghua; Liu, Jing; Zhang, Zhen; Yang, Yingju

2016-06-05

The temporal release of selenium from coal during combustion and gasification in a fluidized bed was measured in situ by an on-line analysis system of trace elements in flue gas. The on-line analysis system is based on an inductively coupled plasma optical emission spectroscopy (ICP-OES), and can measure concentrations of trace elements in flue gas quantitatively and continuously. The results of on-line analysis suggest that the concentration of selenium in flue gas during coal gasification is higher than that during coal combustion. Based on the results of on-line analysis, a second-order kinetic law r(x)=0.94e(-26.58/RT)(-0.56 x(2) -0.51 x+1.05) was determined for selenium release during coal combustion, and r(x)=11.96e(-45.03/RT)(-0.53 x(2) -0.56 x+1.09) for selenium release during coal gasification. These two kinetic laws can predict respectively the temporal release of selenium during coal combustion and gasification with an acceptable accuracy. Thermodynamic calculations were conducted to predict selenium species during coal combustion and gasification. The speciation of selenium in flue gas during coal combustion differs from that during coal gasification, indicating that selenium volatilization is different. The gaseous selenium species can react with CaO during coal combustion, but it is not likely to interact with mineral during coal gasification. Copyright © 2016 Elsevier B.V. All rights reserved.

Number and brightness image analysis reveals ATF-induced dimerization kinetics of uPAR in the cell membrane

PubMed Central

Hellriegel, Christian; Caiolfa, Valeria R.; Corti, Valeria; Sidenius, Nicolai; Zamai, Moreno

2011-01-01

We studied the molecular forms of the GPI-anchored urokinase plasminogen activator receptor (uPAR-mEGFP) in the human embryo kidney (HEK293) cell membrane and demonstrated that the binding of the amino-terminal fragment (ATF) of urokinase plasminogen activator is sufficient to induce the dimerization of the receptor. We followed the association kinetics and determined precisely the dimeric stoichiometry of uPAR-mEGFP complexes by applying number and brightness (N&B) image analysis. N&B is a novel fluctuation-based approach for measuring the molecular brightness of fluorophores in an image time sequence in live cells. Because N&B is very sensitive to long-term temporal fluctuations and photobleaching, we have introduced a filtering protocol that corrects for these important sources of error. Critical experimental parameters in N&B analysis are illustrated and analyzed by simulation studies. Control experiments are based on mEGFP-GPI, mEGFP-mEGFP-GPI, and mCherry-GPI, expressed in HEK293. This work provides a first direct demonstration of the dimerization of uPAR in live cells. We also provide the first methodological guide on N&B to discern minor changes in molecular composition such as those due to dimerization events, which are involved in fundamental cell signaling mechanisms.—Hellriegel, C., Caiolfa, V. R., Corti, V., Sidenius, N., Zamai, M. Number and brightness image analysis reveals ATF-induced dimerization kinetics of uPAR in the cell membrane. PMID:21602447

Database-Centric Method for Automated High-Throughput Deconvolution and Analysis of Kinetic Antibody Screening Data.

PubMed

Nobrega, R Paul; Brown, Michael; Williams, Cody; Sumner, Chris; Estep, Patricia; Caffry, Isabelle; Yu, Yao; Lynaugh, Heather; Burnina, Irina; Lilov, Asparouh; Desroches, Jordan; Bukowski, John; Sun, Tingwan; Belk, Jonathan P; Johnson, Kirt; Xu, Yingda

2017-10-01

The state-of-the-art industrial drug discovery approach is the empirical interrogation of a library of drug candidates against a target molecule. The advantage of high-throughput kinetic measurements over equilibrium assessments is the ability to measure each of the kinetic components of binding affinity. Although high-throughput capabilities have improved with advances in instrument hardware, three bottlenecks in data processing remain: (1) intrinsic molecular properties that lead to poor biophysical quality in vitro are not accounted for in commercially available analysis models, (2) processing data through a user interface is time-consuming and not amenable to parallelized data collection, and (3) a commercial solution that includes historical kinetic data in the analysis of kinetic competition data does not exist. Herein, we describe a generally applicable method for the automated analysis, storage, and retrieval of kinetic binding data. This analysis can deconvolve poor quality data on-the-fly and store and organize historical data in a queryable format for use in future analyses. Such database-centric strategies afford greater insight into the molecular mechanisms of kinetic competition, allowing for the rapid identification of allosteric effectors and the presentation of kinetic competition data in absolute terms of percent bound to antigen on the biosensor.

Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA

NASA Astrophysics Data System (ADS)

Fujita, Keisuke; Iwaki, Mitsuhiro; Yanagida, Toshio

2016-12-01

Cell-to-cell variability plays a critical role in cellular responses and decision-making in a population, and transcriptional bursting has been broadly studied by experimental and theoretical approaches as the potential source of cell-to-cell variability. Although molecular mechanisms of transcriptional bursting have been proposed, there is little consensus. An unsolved key question is whether transcriptional bursting is intertwined with many transcriptional regulatory factors or is an intrinsic characteristic of RNA polymerase on DNA. Here we design an in vitro single-molecule measurement system to analyse the kinetics of transcriptional bursting. The results indicate that transcriptional bursting is caused by interplay between RNA polymerases on DNA. The kinetics of in vitro transcriptional bursting is quantitatively consistent with the gene-nonspecific kinetics previously observed in noisy gene expression in vivo. Our kinetic analysis based on a cellular automaton model confirms that arrest and rescue by trailing RNA polymerase intrinsically causes transcriptional bursting.

Removal Rate of Organic Matter Using Natural Cellulose via Adsorption Isotherm and Kinetic Studies.

PubMed

Din, Mohd Fadhil Md; Ponraj, Mohanadoss; Low, Wen-Pei; Fulazzaky, Mohamad Ali; Iwao, Kenzo; Songip, Ahmad Rahman; Chelliapan, Shreeshivadasan; Ismail, Zulhilmi; Jamal, Mohamad Hidayat

2016-02-01

In this study, the removal of natural organic matter (NOM) using coconut fiber (CF) and palm oil fiber (POF) was investigated. Preliminary analysis was performed using a jar test for the selection of optimal medium before the fabricated column model experiment. The equilibrium studies on isotherms and kinetic models for NOM adsorption were analyzed using linearized correlation coefficient. Results showed that the equilibrium data were fitted to Langmuir isotherm model for both CF and POF. The most suitable adsorption model was the pseudo-first-order kinetic model for POF and pseudo-second-order kinetic model for CF. The adsorption capacities achieved by the CF and POF were 15.67 and 30.8 mg/g respectively. Based on this investigation, it can be concluded that the POF is the most suitable material for the removal of NOM in semi polluted river water.

Thermal Stability and Kinetic Study of Fluvoxamine Stability in Binary Samples with Lactose.

PubMed

Ghaderi, Faranak; Nemati, Mahboob; Siahi-Shadbad, Mohammad Reza; Valizadeh, Hadi; Monajjemzadeh, Farnaz

2017-04-01

Purpose: In the present study the incompatibility of FLM (fluvoxamine) with lactose in solid state mixtures was investigated. The compatibility was evaluated using different physicochemical methods such as differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) spectroscopy and mass spectrometry. Methods: Non-Isothermally stressed physical mixtures were used to calculate the solid-state kinetic parameters. Different thermal models such as Friedman, Flynn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS) were used for the characterization of the drug-excipient interaction. Results: Overall, the incompatibility of FLM with lactose as a reducing carbohydrate was successfully evaluated and the activation energy of this interaction was calculated. Conclusion: In this research the lactose and FLM Maillard interaction was proved using physicochemical techniques including DSC and FTIR. It was shown that DSC- based kinetic analysis provides fast and versatile kinetic comparison of Arrhenius activation energies for different pharmaceutical samples.

Thermal Stability and Kinetic Study of Fluvoxamine Stability in Binary Samples with Lactose

PubMed Central

Ghaderi, Faranak; Nemati, Mahboob; Siahi-Shadbad, Mohammad Reza; Valizadeh, Hadi; Monajjemzadeh, Farnaz

2017-01-01

Purpose: In the present study the incompatibility of FLM (fluvoxamine) with lactose in solid state mixtures was investigated. The compatibility was evaluated using different physicochemical methods such as differential scanning calorimetry (DSC), Fourier-transform infrared (FTIR) spectroscopy and mass spectrometry. Methods: Non-Isothermally stressed physical mixtures were used to calculate the solid–state kinetic parameters. Different thermal models such as Friedman, Flynn–Wall–Ozawa (FWO) and Kissinger–Akahira–Sunose (KAS) were used for the characterization of the drug-excipient interaction. Results: Overall, the incompatibility of FLM with lactose as a reducing carbohydrate was successfully evaluated and the activation energy of this interaction was calculated. Conclusion: In this research the lactose and FLM Maillard interaction was proved using physicochemical techniques including DSC and FTIR. It was shown that DSC- based kinetic analysis provides fast and versatile kinetic comparison of Arrhenius activation energies for different pharmaceutical samples. PMID:28507936

Kinetically Controlled Lifetimes in Redox-Responsive Transient Supramolecular Hydrogels.

PubMed

Wojciechowski, Jonathan P; Martin, Adam D; Thordarson, Pall

2018-02-28

It remains challenging to program soft materials to show dynamic, tunable time-dependent properties. In this work, we report a strategy to design transient supramolecular hydrogels based on kinetic control of competing reactions. Specifically, the pH-triggered self-assembly of a redox-active supramolecular gelator, N,N'-dibenzoyl-l-cystine (DBC) in the presence of a reducing agent, which acts to disassemble the system. The lifetimes of the transient hydrogels can be tuned simply by pH or reducing agent concentration. We find through kinetic analysis that gel formation hinders the ability of the reducing agent and enables longer transient hydrogel lifetimes than would be predicted. The transient hydrogels undergo clean cycles, with no kinetically trapped aggregates observed. As a result, multiple transient hydrogel cycles are demonstrated and can be predicted. This work contributes to our understanding of designing transient assemblies with tunable temporal control.

A Kinetic Model Describing Injury-Burden in Team Sports.

PubMed

Fuller, Colin W

2017-12-01

Injuries in team sports are normally characterised by the incidence, severity, and location and type of injuries sustained: these measures, however, do not provide an insight into the variable injury-burden experienced during a season. Injury burden varies according to the team's match and training loads, the rate at which injuries are sustained and the time taken for these injuries to resolve. At the present time, this time-based variation of injury burden has not been modelled. To develop a kinetic model describing the time-based injury burden experienced by teams in elite team sports and to demonstrate the model's utility. Rates of injury were quantified using a large eight-season database of rugby injuries (5253) and exposure (60,085 player-match-hours) in English professional rugby. Rates of recovery from injury were quantified using time-to-recovery analysis of the injuries. The kinetic model proposed for predicting a team's time-based injury burden is based on a composite rate equation developed from the incidence of injury, a first-order rate of recovery from injury and the team's playing load. The utility of the model was demonstrated by examining common scenarios encountered in elite rugby. The kinetic model developed describes and predicts the variable injury-burden arising from match play during a season of rugby union based on the incidence of match injuries, the rate of recovery from injury and the playing load. The model is equally applicable to other team sports and other scenarios.

Fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics.

PubMed

Pujol-Vila, F; Vigués, N; Díaz-González, M; Muñoz-Berbel, X; Mas, J

2015-05-15

Global urban and industrial growth, with the associated environmental contamination, is promoting the development of rapid and inexpensive general toxicity methods. Current microbial methodologies for general toxicity determination rely on either bioluminescent bacteria and specific medium solution (i.e. Microtox(®)) or low sensitivity and diffusion limited protocols (i.e. amperometric microbial respirometry). In this work, fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics is presented, using Escherichia coli as a bacterial model. Ferricyanide reduction kinetic analysis (variation of ferricyanide absorption with time), much more sensitive than single absorbance measurements, allowed for direct and fast toxicity determination without pre-incubation steps (assay time=10 min) and minimizing biomass interference. Dual wavelength analysis at 405 (ferricyanide and biomass) and 550 nm (biomass), allowed for ferricyanide monitoring without interference of biomass scattering. On the other hand, refractive index (RI) matching with saccharose reduced bacterial light scattering around 50%, expanding the analytical linear range in the determination of absorbent molecules. With this method, different toxicants such as metals and organic compounds were analyzed with good sensitivities. Half maximal effective concentrations (EC50) obtained after 10 min bioassay, 2.9, 1.0, 0.7 and 18.3 mg L(-1) for copper, zinc, acetic acid and 2-phenylethanol respectively, were in agreement with previously reported values for longer bioassays (around 60 min). This method represents a promising alternative for fast and sensitive water toxicity monitoring, opening the possibility of quick in situ analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Kinetic Modeling of a Silicon Refining Process in a Moist Hydrogen Atmosphere

NASA Astrophysics Data System (ADS)

Chen, Zhiyuan; Morita, Kazuki

2018-03-01

We developed a kinetic model that considers both silicon loss and boron removal in a metallurgical grade silicon refining process. This model was based on the hypotheses of reversible reactions. The reaction rate coefficient kept the same form but error of terminal boron concentration could be introduced when relating irreversible reactions. Experimental data from published studies were used to develop a model that fit the existing data. At 1500 °C, our kinetic analysis suggested that refining silicon in a moist hydrogen atmosphere generates several primary volatile species, including SiO, SiH, HBO, and HBO2. Using the experimental data and the kinetic analysis of volatile species, we developed a model that predicts a linear relationship between the reaction rate coefficient k and both the quadratic function of p(H2O) and the square root of p(H2). Moreover, the model predicted the partial pressure values for the predominant volatile species and the prediction was confirmed by the thermodynamic calculations, indicating the reliability of the model. We believe this model provides a foundation for designing a silicon refining process with a fast boron removal rate and low silicon loss.

Automated analysis of non-mass-enhancing lesions in breast MRI based on morphological, kinetic, and spatio-temporal moments and joint segmentation-motion compensation technique

NASA Astrophysics Data System (ADS)

Hoffmann, Sebastian; Shutler, Jamie D.; Lobbes, Marc; Burgeth, Bernhard; Meyer-Bäse, Anke

2013-12-01

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) represents an established method for the detection and diagnosis of breast lesions. While mass-like enhancing lesions can be easily categorized according to the Breast Imaging Reporting and Data System (BI-RADS) MRI lexicon, a majority of diagnostically challenging lesions, the so called non-mass-like enhancing lesions, remain both qualitatively as well as quantitatively difficult to analyze. Thus, the evaluation of kinetic and/or morphological characteristics of non-masses represents a challenging task for an automated analysis and is of crucial importance for advancing current computer-aided diagnosis (CAD) systems. Compared to the well-characterized mass-enhancing lesions, non-masses have no well-defined and blurred tumor borders and a kinetic behavior that is not easily generalizable and thus discriminative for malignant and benign non-masses. To overcome these difficulties and pave the way for novel CAD systems for non-masses, we will evaluate several kinetic and morphological descriptors separately and a novel technique, the Zernike velocity moments, to capture the joint spatio-temporal behavior of these lesions, and additionally consider the impact of non-rigid motion compensation on a correct diagnosis.

Kinetic Modeling of a Silicon Refining Process in a Moist Hydrogen Atmosphere

NASA Astrophysics Data System (ADS)

Chen, Zhiyuan; Morita, Kazuki

2018-06-01

We developed a kinetic model that considers both silicon loss and boron removal in a metallurgical grade silicon refining process. This model was based on the hypotheses of reversible reactions. The reaction rate coefficient kept the same form but error of terminal boron concentration could be introduced when relating irreversible reactions. Experimental data from published studies were used to develop a model that fit the existing data. At 1500 °C, our kinetic analysis suggested that refining silicon in a moist hydrogen atmosphere generates several primary volatile species, including SiO, SiH, HBO, and HBO2. Using the experimental data and the kinetic analysis of volatile species, we developed a model that predicts a linear relationship between the reaction rate coefficient k and both the quadratic function of p(H2O) and the square root of p(H2). Moreover, the model predicted the partial pressure values for the predominant volatile species and the prediction was confirmed by the thermodynamic calculations, indicating the reliability of the model. We believe this model provides a foundation for designing a silicon refining process with a fast boron removal rate and low silicon loss.

Thermodynamic Analysis of Chemically Reacting Mixtures-Comparison of First and Second Order Models.

PubMed

Pekař, Miloslav

2018-01-01

Recently, a method based on non-equilibrium continuum thermodynamics which derives thermodynamically consistent reaction rate models together with thermodynamic constraints on their parameters was analyzed using a triangular reaction scheme. The scheme was kinetically of the first order. Here, the analysis is further developed for several first and second order schemes to gain a deeper insight into the thermodynamic consistency of rate equations and relationships between chemical thermodynamic and kinetics. It is shown that the thermodynamic constraints on the so-called proper rate coefficient are usually simple sign restrictions consistent with the supposed reaction directions. Constraints on the so-called coupling rate coefficients are more complex and weaker. This means more freedom in kinetic coupling between reaction steps in a scheme, i.e., in the kinetic effects of other reactions on the rate of some reaction in a reacting system. When compared with traditional mass-action rate equations, the method allows a reduction in the number of traditional rate constants to be evaluated from data, i.e., a reduction in the dimensionality of the parameter estimation problem. This is due to identifying relationships between mass-action rate constants (relationships which also include thermodynamic equilibrium constants) which have so far been unknown.

Exact and approximate solutions for the decades-old Michaelis-Menten equation: Progress-curve analysis through integrated rate equations.

PubMed

Goličnik, Marko

2011-01-01

The Michaelis-Menten rate equation can be found in most general biochemistry textbooks, where the time derivative of the substrate is a hyperbolic function of two kinetic parameters (the limiting rate V, and the Michaelis constant K(M) ) and the amount of substrate. However, fundamental concepts of enzyme kinetics can be difficult to understand fully, or can even be misunderstood, by students when based only on the differential form of the Michaelis-Menten equation, and the variety of methods available to calculate the kinetic constants from rate versus substrate concentration "textbook data." Consequently, enzyme kinetics can be confusing if an analytical solution of the Michaelis-Menten equation is not available. Therefore, the still rarely known exact solution to the Michaelis-Menten equation is presented here through the explicit closed-form equation in terms of the Lambert W(x) function. Unfortunately, as the W(x) is not available in standard curve-fitting computer programs, the practical use of this direct solution is limited for most life-science students. Thus, the purpose of this article is to provide analytical approximations to the equation for modeling Michaelis-Menten kinetics. The elementary and explicit nature of these approximations can provide students with direct and simple estimations of kinetic parameters from raw experimental time-course data. The Michaelis-Menten kinetics studied in the latter context can provide an ideal alternative to the 100-year-old problems of data transformation, graphical visualization, and data analysis of enzyme-catalyzed reactions. Hence, the content of the course presented here could gradually become an important component of the modern biochemistry curriculum in the 21st century. Copyright © 2011 Wiley Periodicals, Inc.

A Price To Pay for Relaxed Substrate Specificity: A Comparative Kinetic Analysis of the Class II Lanthipeptide Synthetases ProcM and HalM2

PubMed Central

2015-01-01

Lanthipeptides are a class of ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs) that typically harbor multiple intramolecular thioether linkages. For class II lanthipeptides, these cross-links are installed in a multistep reaction pathway by a single enzyme (LanM). The multifunctional nature of LanMs and the manipulability of their genetically encoded peptide substrates (LanAs) make LanM/LanA systems promising targets for the engineering of new antibacterial compounds. Here, we report the development of a semiquantitative mass spectrometry-based assay for kinetic characterization of LanM-catalyzed reactions. The assay was used to conduct a comparative kinetic analysis of two LanM enzymes (HalM2 and ProcM) that exhibit drastically different substrate selectivity. Numerical simulation of the kinetic data was used to develop models for the multistep HalM2- and ProcM-catalyzed reactions. These models illustrate that HalM2 and ProcM have markedly different catalytic efficiencies for the various reactions they catalyze. HalM2, which is responsible for the biosynthesis of a single compound (the Halβ subunit of the lantibiotic haloduracin), catalyzes reactions with higher catalytic efficiency than ProcM, which modifies 29 different ProcA precursor peptides during prochlorosin biosynthesis. In particular, the rates of thioether ring formation are drastically reduced in ProcM, likely because this enzyme is charged with installing a variety of lanthipeptide ring architectures in its prochlorosin products. Thus, ProcM appears to pay a kinetic price for its relaxed substrate specificity. In addition, our kinetic models suggest that conformational sampling of the LanM/LanA Michaelis complex could play an important role in the kinetics of LanA maturation. PMID:25409537

Oxidation characteristics of gasoline direct-injection (GDI) engine soot: Catalytic effects of ash and modified kinetic correlation

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

Choi, Seungmok; Seong, Heeje

In this paper, experimental analyses are conducted into the GDI soot oxidation characteristics as dependent on engine operating conditions. Soot is sampled at various engine operating conditions of a commercial 2.4 L GDI engine with a naturally aspirated, homogeneous, and stoichiometric operation strategy. The oxidation reactivity, ash composition, and carbon nanostructure of the GDI soot samples are analyzed using thermogravimetric analysis (TGA), scanning electron microscope–energy-dispersive spectroscopy (SEM-EDS), high-resolution transmission electron microscopy (HR-TEM), and Raman spectroscopy. Based on the analyses, a global GDI soot oxidation mechanism is proposed which includes the effects of soluble organic fractions (SOF)/weakly bonded carbon (WBC), andmore » three types of ash on GDI soot oxidation. The results show that GDI soot contains an order of magnitude higher ash fraction than does conventional diesel soot, and oxidation reactivity is significantly enhanced by the catalytic effects of ash, as a function of ash content in soot. A modified empirical kinetic correlation for GDI soot oxidation is suggested on the basis of the results, and the modified kinetic correlation predicts the GDI soot oxidation rate accurately for various engine operation points at wide ranges of soot conversion and temperature without modifying kinetic parameters. The kinetic parameters are determined from isothermal and non-isothermal thremogravimetric analysis (TGA) soot oxidation tests; the methods are elucidated in detail.« less

Oxidation characteristics of gasoline direct-injection (GDI) engine soot: Catalytic effects of ash and modified kinetic correlation

DOE PAGES

Choi, Seungmok; Seong, Heeje

2015-03-02

In this paper, experimental analyses are conducted into the GDI soot oxidation characteristics as dependent on engine operating conditions. Soot is sampled at various engine operating conditions of a commercial 2.4 L GDI engine with a naturally aspirated, homogeneous, and stoichiometric operation strategy. The oxidation reactivity, ash composition, and carbon nanostructure of the GDI soot samples are analyzed using thermogravimetric analysis (TGA), scanning electron microscope–energy-dispersive spectroscopy (SEM-EDS), high-resolution transmission electron microscopy (HR-TEM), and Raman spectroscopy. Based on the analyses, a global GDI soot oxidation mechanism is proposed which includes the effects of soluble organic fractions (SOF)/weakly bonded carbon (WBC), andmore » three types of ash on GDI soot oxidation. The results show that GDI soot contains an order of magnitude higher ash fraction than does conventional diesel soot, and oxidation reactivity is significantly enhanced by the catalytic effects of ash, as a function of ash content in soot. A modified empirical kinetic correlation for GDI soot oxidation is suggested on the basis of the results, and the modified kinetic correlation predicts the GDI soot oxidation rate accurately for various engine operation points at wide ranges of soot conversion and temperature without modifying kinetic parameters. The kinetic parameters are determined from isothermal and non-isothermal thremogravimetric analysis (TGA) soot oxidation tests; the methods are elucidated in detail.« less

Metabolic control analysis using transient metabolite concentrations. Determination of metabolite concentration control coefficients.

PubMed Central

Delgado, J; Liao, J C

1992-01-01

The methodology previously developed for determining the Flux Control Coefficients [Delgado & Liao (1992) Biochem. J. 282, 919-927] is extended to the calculation of metabolite Concentration Control Coefficients. It is shown that the transient metabolite concentrations are related by a few algebraic equations, attributed to mass balance, stoichiometric constraints, quasi-equilibrium or quasi-steady states, and kinetic regulations. The coefficients in these relations can be estimated using linear regression, and can be used to calculate the Control Coefficients. The theoretical basis and two examples are discussed. Although the methodology is derived based on the linear approximation of enzyme kinetics, it yields reasonably good estimates of the Control Coefficients for systems with non-linear kinetics. PMID:1497632

The Synergy Between Total Scattering and Advanced Simulation Techniques: Quantifying Geopolymer Gel Evolution

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

White, Claire; Bloomer, Breaunnah E.; Provis, John L.

2012-05-16

With the ever increasing demands for technologically advanced structural materials, together with emerging environmental consciousness due to climate change, geopolymer cement is fast becoming a viable alternative to traditional cements due to proven mechanical engineering characteristics and the reduction in CO2 emitted (approximately 80% less CO2 emitted compared to ordinary Portland cement). Nevertheless, much remains unknown regarding the kinetics of the molecular changes responsible for nanostructural evolution during the geopolymerization process. Here, in-situ total scattering measurements in the form of X-ray pair distribution function (PDF) analysis are used to quantify the extent of reaction of metakaolin/slag alkali-activated geopolymer binders, includingmore » the effects of various activators (alkali hydroxide/silicate) on the kinetics of the geopolymerization reaction. Restricting quantification of the kinetics to the initial ten hours of reaction does not enable elucidation of the true extent of the reaction, but using X-ray PDF data obtained after 128 days of reaction enables more accurate determination of the initial extent of reaction. The synergies between the in-situ X-ray PDF data and simulations conducted by multiscale density functional theory-based coarse-grained Monte Carlo analysis are outlined, particularly with regard to the potential for the X-ray data to provide a time scale for kinetic analysis of the extent of reaction obtained from the multiscale simulation methodology.« less

Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

PubMed Central

2011-01-01

In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison. PMID:21989173

Quantitative Analysis of Microstructural Constituents in Welded Transformation-Induced-Plasticity Steels

NASA Astrophysics Data System (ADS)

Amirthalingam, M.; Hermans, M. J. M.; Zhao, L.; Richardson, I. M.

2010-02-01

A quantitative analysis of retained austenite and nonmetallic inclusions in gas tungsten arc (GTA)-welded aluminum-containing transformation-induced-plasticity (TRIP) steels is presented. The amount of retained austenite in the heat-affected and fusion zones of welded aluminum-containing TRIP steel with different base metal austenite fractions has been measured by magnetic saturation measurements, to study the effect of weld thermal cycles on the stabilization of austenite. It is found that for base metals containing 3 to 14 pct of austenite, 4 to 13 pct of austenite is found in the heat-affected zones and 6 to 10 pct in the fusion zones. The decomposition kinetics of retained austenite in the base metal and welded samples was also studied by thermomagnetic measurements. The decomposition kinetics of the austenite in the fusion zone is found to be slower compared to that in the base metal. Thermomagnetic measurements indicated the formation of ferromagnetic ɛ carbides above 290 °C and paramagnetic η( ɛ') transient iron carbides at approximately 400 °C due to the decomposition of austenite during heating.

Kinetic modeling and fitting software for interconnected reaction schemes: VisKin.

PubMed

Zhang, Xuan; Andrews, Jared N; Pedersen, Steen E

2007-02-15

Reaction kinetics for complex, highly interconnected kinetic schemes are modeled using analytical solutions to a system of ordinary differential equations. The algorithm employs standard linear algebra methods that are implemented using MatLab functions in a Visual Basic interface. A graphical user interface for simple entry of reaction schemes facilitates comparison of a variety of reaction schemes. To ensure microscopic balance, graph theory algorithms are used to determine violations of thermodynamic cycle constraints. Analytical solutions based on linear differential equations result in fast comparisons of first order kinetic rates and amplitudes as a function of changing ligand concentrations. For analysis of higher order kinetics, we also implemented a solution using numerical integration. To determine rate constants from experimental data, fitting algorithms that adjust rate constants to fit the model to imported data were implemented using the Levenberg-Marquardt algorithm or using Broyden-Fletcher-Goldfarb-Shanno methods. We have included the ability to carry out global fitting of data sets obtained at varying ligand concentrations. These tools are combined in a single package, which we have dubbed VisKin, to guide and analyze kinetic experiments. The software is available online for use on PCs.

A numerical study of attraction/repulsion collective behavior models: 3D particle analyses and 1D kinetic simulations

NASA Astrophysics Data System (ADS)

Vecil, Francesco; Lafitte, Pauline; Rosado Linares, Jesús

2013-10-01

We study at particle and kinetic level a collective behavior model based on three phenomena: self-propulsion, friction (Rayleigh effect) and an attractive/repulsive (Morse) potential rescaled so that the total mass of the system remains constant independently of the number of particles N. In the first part of the paper, we introduce the particle model: the agents are numbered and described by their position and velocity. We identify five parameters that govern the possible asymptotic states for this system (clumps, spheres, dispersion, mills, rigid-body rotation, flocks) and perform a numerical analysis on the 3D setting. Then, in the second part of the paper, we describe the kinetic system derived as the limit from the particle model as N tends to infinity; we propose, in 1D, a numerical scheme for the simulations, and perform a numerical analysis devoted to trying to recover asymptotically patterns similar to those emerging for the equivalent particle systems, when particles originally evolved on a circle.

Combustion and kinetic parameters estimation of torrefied pine, acacia and Miscanthus giganteus using experimental and modelling techniques.

PubMed

Wilk, Małgorzata; Magdziarz, Aneta; Gajek, Marcin; Zajemska, Monika; Jayaraman, Kandasamy; Gokalp, Iskender

2017-11-01

A novel approach, linking both experiments and modelling, was applied to obtain a better understanding of combustion characteristics of torrefied biomass. Therefore, Pine, Acacia and Miscanthus giganteus have been investigated under 260°C, 1h residence time and argon atmosphere. A higher heating value and carbon content corresponding to a higher fixed carbon, lower volatile matter, moisture content, and ratio O/C were obtained for all torrefied biomass. TGA analysis was used in order to proceed with the kinetics study and Chemkin calculations. The kinetics analysis demonstrated that the torrefaction process led to a decrease in Ea compared to raw biomass. The average Ea of pine using the KAS method changed from 169.42 to 122.88kJ/mol. The changes in gaseous products of combustion were calculated by Chemkin, which corresponded with the TGA results. The general conclusion based on these investigations is that torrefaction improves the physical and chemical properties of biomass. Copyright © 2017 Elsevier Ltd. All rights reserved.

A study of hydriding kinetics of metal hydrides using a physically based model

NASA Astrophysics Data System (ADS)

Voskuilen, Tyler G.

The reaction of hydrogen with metals to form metal hydrides has numerous potential energy storage and management applications. The metal hydrogen system has a high volumetric energy density and is often reversible with a high cycle life. The stored hydrogen can be used to produce energy through combustion, reaction in a fuel cell, or electrochemically in metal hydride batteries. The high enthalpy of the metal-hydrogen reaction can also be used for rapid heat removal or delivery. However, improving the often poor gravimetric performance of such systems through the use of lightweight metals usually comes at the cost of reduced reaction rates or the requirement of pressure and temperature conditions far from the desired operating conditions. In this work, a 700 bar Sievert system was developed at the Purdue Hydrogen Systems Laboratory to study the kinetic and thermodynamic behavior of high pressure hydrogen absorption under near-ambient temperatures. This system was used to determine the kinetic and thermodynamic properties of TiCrMn, an intermetallic metal hydride of interest due to its ambient temperature performance for vehicular applications. A commonly studied intermetallic hydride, LaNi5, was also characterized as a base case for the phase field model. The analysis of the data obtained from such a system necessitate the use of specialized techniques to decouple the measured reaction rates from experimental conditions. These techniques were also developed as a part of this work. Finally, a phase field model of metal hydride formation in mass-transport limited interstitial solute reactions based on the regular solution model was developed and compared with measured kinetics of LaNi5 and TiCrMn. This model aided in the identification of key reaction features and was used to verify the proposed technique for the analysis of gas-solid reaction rates determined volumetrically. Additionally, the phase field model provided detailed quantitative predictions of the effects of multidimensional phase growth and transitions between rate-limiting processes on the experimentally determined reaction rates. Unlike conventional solid state reaction analysis methods, this model relies fully on rate parameters based on the physical mechanisms occurring in the hydride reaction and can be extended to reactions in any dimension.

Thermodynamic properties and crystallization kinetics at high liquid undercooling

NASA Technical Reports Server (NTRS)

Fecht, Hans J.

1990-01-01

The heat capacities of liquid and crystalline Au-Pb-Sb alloys in the glass-forming composition range were measured with droplet emulsion and bulk samples. Based on the measured C(sub p) data, the entropy, enthalpy, and Gibbs free energy functions of the eutectic, solid mixture, and undercooled liquid were determined as a function of undercooling and compared with theoretical predictions. The results indicate an isentropic temperature at 313 + or - 5 K, which agrees well with experimental data for the glass transition. A kinetics analysis of the nucleation undercooling response suggests that the proper choice for the Gibbs free energy change during crystallization is most important in analyzing the nucleation kinetics. By classical nucleation theory, the prefactors obtained, based on a variety of theoretical predictions for the driving force, can differ by six orders of magnitude. If the nucleation rates are extrapolated to high undercooling, the extrapolations based on measured heat capacity data show agreement, whereas the predicted nucleation rates are inconsistent with results from drop tower experiments. The implications for microg experiments are discussed.

Co-pyrolysis characteristics of microalgae Isochrysis and Chlorella: Kinetics, biocrude yield and interaction.

PubMed

Zhao, Bingwei; Wang, Xin; Yang, Xiaoyi

2015-12-01

Co-pyrolysis characteristics of Isochrysis (high lipid) and Chlorella (high protein) were investigated qualitatively and quantitatively based on DTG curves, biocrude yield and composition by individual pyrolysis and co-pyrolysis. DTG curves in co-pyrolysis have been compared accurately with those in individual pyrolysis. An interaction has been detected at 475-500°C in co-pyrolysis based on biocrude yields, and co-pyrolysis reaction mechanism appear three-dimensional diffusion in comparison with random nucleation followed by growth in individual pyrolysis based on kinetic analysis. There is no obvious difference in the maximum biocrude yields for individual pyrolysis and co-pyrolysis, but carboxylic acids (IC21) decreased and N-heterocyclic compounds (IC12) increased in co-pyrolysis. Simulation results of biocrude yield by Components Biofuel Model and Kinetics Biofuel Model indicate that the processes of co-pyrolysis comply with those of individual pyrolysis in solid phase by and large. Variation of percentage content in co-pyrolysis and individual pyrolysis biocrude indicated interaction in gas phase. Copyright © 2015. Published by Elsevier Ltd.

Is case-based learning an effective teaching strategy to challenge students' alternative conceptions regarding chemical kinetics?

NASA Astrophysics Data System (ADS)

Yalçınkaya, Eylem; Taştan-Kırık, Özgecan; Boz, Yezdan; Yıldıran, Demet

2012-07-01

Background: Case-based learning (CBL) is simply teaching the concept to the students based on the cases. CBL involves a case, which is a scenario based on daily life, and study questions related to the case, which allows students to discuss their ideas. Chemical kinetics is one of the most difficult concepts for students in chemistry. Students have generally low levels of conceptual understanding and many alternative conceptions regarding it. Purpose: This study aimed to explore the effect of CBL on dealing with students' alternative conceptions about chemical kinetics. Sample: The sample consists of 53 high school students from one public high school in Turkey. Design and methods : Nonequivalent pre-test and post-test control group design was used. Reaction Rate Concept Test and semi-structured interviews were used for data collection. Convenience sampling technique was followed. For data analysis, the independent samples t-test and ANOVA was performed. Results : Both concept test and interview results showed that students instructed with cases had better understanding of core concepts of chemical kinetics and had less alternative conceptions related to the subject matter compared to the control group students, despite the fact that it was impossible to challenge all the alternative conceptions in the experimental group. Conclusions: CBL is an effective teaching method for challenging students' alternative conceptions in the context of chemical kinetics. Since using cases in small groups and whole class discussions has been found to be an effective way to cope with the alternative conceptions, it can be applied to other subjects and grade levels in high schools with a higher sample size. Furthermore, the effect of this method on academic achievement, motivation and critical thinking skills are other variables that can be investigated for future studies in the subject area of chemistry.

Methods for Kinetic and Thermodynamic Analysis of Aminoacyl-tRNA Synthetases

PubMed Central

Francklyn, Christopher S.; First, Eric A.; Perona, John J.; Hou, Ya-Ming

2008-01-01

The accuracy of protein synthesis relies on the ability of aminoacyl-tRNA synthetases (aaRSs) to discriminate among true and near cognate substrates. To date, analysis of aaRSs function, including identification of residues of aaRS participating in amino acid and tRNA discrimination, has largely relied on the steady state kinetic pyrophosphate exchange and aminoacylation assays. Pre-steady state kinetic studies investigating a more limited set of aaRS systems have also been undertaken to assess the energetic contributions of individual enzyme-substrate interactions, particularly in the adenylation half reaction. More recently, a renewed interest in the use of rapid kinetics approaches for aaRSs has led to their application to several new aaRS systems, resulting in the identification of mechanistic differences that distinguish the two structurally distinct aaRS classes. Here, we review the techniques for thermodynamic and kinetic analysis of aaRS function. Following a brief survey of methods for the preparation of materials and for steady state kinetic analysis, this review will describe pre-steady state kinetic methods employing rapid quench and stopped-flow fluorescence for analysis of the activation and aminoacyl transfer reactions. Application of these methods to any aaRS system allows the investigator to derive detailed kinetic mechanisms for the activation and aminoacyl transfer reactions, permitting issues of substrate specificity, stereochemical mechanism, and inhibitor interaction to be addressed in a rigorous and quantitative fashion. PMID:18241792

Direct Detection and Sequencing of Damaged DNA Bases

PubMed Central

2011-01-01

Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications. PMID:22185597

Direct detection and sequencing of damaged DNA bases.

PubMed

Clark, Tyson A; Spittle, Kristi E; Turner, Stephen W; Korlach, Jonas

2011-12-20

Products of various forms of DNA damage have been implicated in a variety of important biological processes, such as aging, neurodegenerative diseases, and cancer. Therefore, there exists great interest to develop methods for interrogating damaged DNA in the context of sequencing. Here, we demonstrate that single-molecule, real-time (SMRT®) DNA sequencing can directly detect damaged DNA bases in the DNA template - as a by-product of the sequencing method - through an analysis of the DNA polymerase kinetics that are altered by the presence of a modified base. We demonstrate the sequencing of several DNA templates containing products of DNA damage, including 8-oxoguanine, 8-oxoadenine, O6-methylguanine, 1-methyladenine, O4-methylthymine, 5-hydroxycytosine, 5-hydroxyuracil, 5-hydroxymethyluracil, or thymine dimers, and show that these base modifications can be readily detected with single-modification resolution and DNA strand specificity. We characterize the distinct kinetic signatures generated by these DNA base modifications.

Differential equation methods for simulation of GFP kinetics in non-steady state experiments.

PubMed

Phair, Robert D

2018-03-15

Genetically encoded fluorescent proteins, combined with fluorescence microscopy, are widely used in cell biology to collect kinetic data on intracellular trafficking. Methods for extraction of quantitative information from these data are based on the mathematics of diffusion and tracer kinetics. Current methods, although useful and powerful, depend on the assumption that the cellular system being studied is in a steady state, that is, the assumption that all the molecular concentrations and fluxes are constant for the duration of the experiment. Here, we derive new tracer kinetic analytical methods for non-steady state biological systems by constructing mechanistic nonlinear differential equation models of the underlying cell biological processes and linking them to a separate set of differential equations governing the kinetics of the fluorescent tracer. Linking the two sets of equations is based on a new application of the fundamental tracer principle of indistinguishability and, unlike current methods, supports correct dependence of tracer kinetics on cellular dynamics. This approach thus provides a general mathematical framework for applications of GFP fluorescence microscopy (including photobleaching [FRAP, FLIP] and photoactivation to frequently encountered experimental protocols involving physiological or pharmacological perturbations (e.g., growth factors, neurotransmitters, acute knockouts, inhibitors, hormones, cytokines, and metabolites) that initiate mechanistically informative intracellular transients. When a new steady state is achieved, these methods automatically reduce to classical steady state tracer kinetic analysis. © 2018 Phair. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Comparison of the performance of tracer kinetic model-driven registration for dynamic contrast enhanced MRI using different models of contrast enhancement.

PubMed

Buonaccorsi, Giovanni A; Roberts, Caleb; Cheung, Sue; Watson, Yvonne; O'Connor, James P B; Davies, Karen; Jackson, Alan; Jayson, Gordon C; Parker, Geoff J M

2006-09-01

The quantitative analysis of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) data is subject to model fitting errors caused by motion during the time-series data acquisition. However, the time-varying features that occur as a result of contrast enhancement can confound motion correction techniques based on conventional registration similarity measures. We have therefore developed a heuristic, locally controlled tracer kinetic model-driven registration procedure, in which the model accounts for contrast enhancement, and applied it to the registration of abdominal DCE-MRI data at high temporal resolution. Using severely motion-corrupted data sets that had been excluded from analysis in a clinical trial of an antiangiogenic agent, we compared the results obtained when using different models to drive the tracer kinetic model-driven registration with those obtained when using a conventional registration against the time series mean image volume. Using tracer kinetic model-driven registration, it was possible to improve model fitting by reducing the sum of squared errors but the improvement was only realized when using a model that adequately described the features of the time series data. The registration against the time series mean significantly distorted the time series data, as did tracer kinetic model-driven registration using a simpler model of contrast enhancement. When an appropriate model is used, tracer kinetic model-driven registration influences motion-corrupted model fit parameter estimates and provides significant improvements in localization in three-dimensional parameter maps. This has positive implications for the use of quantitative DCE-MRI for example in clinical trials of antiangiogenic or antivascular agents.

Effect of semen preparation on casa motility results in cryopreserved bull spermatozoa.

PubMed

Contri, Alberto; Valorz, Claudio; Faustini, Massimo; Wegher, Laura; Carluccio, Augusto

2010-08-01

Computer-assisted sperm analyzers (CASA) have become the standard tool for evaluating sperm motility and kinetic patterns because they provide objective data for thousands of sperm tracks. However, these devices are not ready-to-use and standardization of analytical practices is a fundamental requirement. In this study, we evaluated the effects of some settings, such as frame rate and frames per field, chamber and time of analysis, and samples preparations, including thawing temperature, sperm sample concentration, and media used for dilution, on the kinetic results of bovine frozen-thawed semen using a CASA. In Experiment 1, the frame rate (30-60 frame/s) significantly affected motility parameters, whereas the number of frames per field (30 or 45) did not seem to affect sperm kinetics. In Experiment 2, the thawing protocol affects sperm motility and kinetic parameters. Sperm sample concentration significantly limited the opportunity to perform the analysis and the kinetic results. A concentration of 100 and 50 x 10(6) sperm/mL limited the device's ability to perform the analysis or gave wrong results, whereas 5, 10, 20, and 30 x 10(6) sperm/mL concentrations allowed the analysis to be performed, but with different results (Experiment 3). The medium used for the dilution of the sample, which is fundamental for a correct sperm head detection, affects sperm motility results (Experiment 4). In this study, Makler and Leja chambers were used to perform the semen analysis with CASA devices. The chamber used significantly affected motility results (Experiment 5). The time between chamber loading and analysis affected sperm velocities, regardless of chamber used. Based on results recorded in this study, we propose that the CASA evaluation of motility of bovine frozen-thawed semen using Hamilton-Thorne IVOS 12.3 should be performed using a frame rate of 60 frame/s and 30 frames per field. Semen should be diluted at least at 20 x 10(6) sperm/mL using PBS. Furthermore, it is necessary to consider the type of chamber used and perform the analysis within 1 or 2 min, regardless of the chamber used. Copyright 2010 Elsevier Inc. All rights reserved.

Multi-fluid CFD analysis in Process Engineering

NASA Astrophysics Data System (ADS)

Hjertager, B. H.

2017-12-01

An overview of modelling and simulation of flow processes in gas/particle and gas/liquid systems are presented. Particular emphasis is given to computational fluid dynamics (CFD) models that use the multi-dimensional multi-fluid techniques. Turbulence modelling strategies for gas/particle flows based on the kinetic theory for granular flows are given. Sub models for the interfacial transfer processes and chemical kinetics modelling are presented. Examples are shown for some gas/particle systems including flow and chemical reaction in risers as well as gas/liquid systems including bubble columns and stirred tanks.

ITC Recommendations for Transporter Kinetic Parameter Estimation and Translational Modeling of Transport-Mediated PK and DDIs in Humans

PubMed Central

Zamek-Gliszczynski, MJ; Lee, CA; Poirier, A; Bentz, J; Chu, X; Ellens, H; Ishikawa, T; Jamei, M; Kalvass, JC; Nagar, S; Pang, KS; Korzekwa, K; Swaan, PW; Taub, ME; Zhao, P; Galetin, A

2013-01-01

This white paper provides a critical analysis of methods for estimating transporter kinetics and recommendations on proper parameter calculation in various experimental systems. Rational interpretation of transporter-knockout animal findings and application of static and dynamic physiologically based modeling approaches for prediction of human transporter-mediated pharmacokinetics and drug–drug interactions (DDIs) are presented. The objective is to provide appropriate guidance for the use of in vitro, in vivo, and modeling tools in translational transporter science. PMID:23588311

Accurate prediction of vaccine stability under real storage conditions and during temperature excursions.

PubMed

Clénet, Didier

2018-04-01

Due to their thermosensitivity, most vaccines must be kept refrigerated from production to use. To successfully carry out global immunization programs, ensuring the stability of vaccines is crucial. In this context, two important issues are critical, namely: (i) predicting vaccine stability and (ii) preventing product damage due to excessive temperature excursions outside of the recommended storage conditions (cold chain break). We applied a combination of advanced kinetics and statistical analyses on vaccine forced degradation data to accurately describe the loss of antigenicity for a multivalent freeze-dried inactivated virus vaccine containing three variants. The screening of large amounts of kinetic models combined with a statistical model selection approach resulted in the identification of two-step kinetic models. Predictions based on kinetic analysis and experimental stability data were in agreement, with approximately five percentage points difference from real values for long-term stability storage conditions, after excursions of temperature and during experimental shipments of freeze-dried products. Results showed that modeling a few months of forced degradation can be used to predict various time and temperature profiles endured by vaccines, i.e. long-term stability, short time excursions outside the labeled storage conditions or shipments at ambient temperature, with high accuracy. Pharmaceutical applications of the presented kinetics-based approach are discussed. Copyright © 2018 The Author. Published by Elsevier B.V. All rights reserved.

A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling

NASA Astrophysics Data System (ADS)

Shapiro, B.; Jin, Q.

2015-12-01

Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.

Ion kinetic effects on the ignition and burn of inertial confinement fusion targets: A multi-scale approach

NASA Astrophysics Data System (ADS)

Peigney, B. E.; Larroche, O.; Tikhonchuk, V.

2014-12-01

In this article, we study the hydrodynamics and burn of the thermonuclear fuel in inertial confinement fusion pellets at the ion kinetic level. The analysis is based on a two-velocity-scale Vlasov-Fokker-Planck kinetic model that is specially tailored to treat fusion products (suprathermal α-particles) in a self-consistent manner with the thermal bulk. The model assumes spherical symmetry in configuration space and axial symmetry in velocity space around the mean flow velocity. A typical hot-spot ignition design is considered. Compared with fluid simulations where a multi-group diffusion scheme is applied to model α transport, the full ion-kinetic approach reveals significant non-local effects on the transport of energetic α-particles. This has a direct impact on hydrodynamic spatial profiles during combustion: the hot spot reactivity is reduced, while the inner dense fuel layers are pre-heated by the escaping α-suprathermal particles, which are transported farther out of the hot spot. We show how the kinetic transport enhancement of fusion products leads to a significant reduction of the fusion yield.

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

PubMed Central

Schmidt, Michael W.; Ivanic, Joseph; Ruedenberg, Klaus

2014-01-01

An analysis based on the variation principle shows that in the molecules H2+, H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation. PMID:24880263

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion.

PubMed

Schmidt, Michael W; Ivanic, Joseph; Ruedenberg, Klaus

2014-05-28

An analysis based on the variation principle shows that in the molecules H2 (+), H2, B2, C2, N2, O2, F2, covalent bonding is driven by the attenuation of the kinetic energy that results from the delocalization of the electronic wave function. For molecular geometries around the equilibrium distance, two features of the wave function contribute to this delocalization: (i) Superposition of atomic orbitals extends the electronic wave function from one atom to two or more atoms; (ii) intra-atomic contraction of the atomic orbitals further increases the inter-atomic delocalization. The inter-atomic kinetic energy lowering that (perhaps counter-intuitively) is a consequence of the intra-atomic contractions drives these contractions (which per se would increase the energy). Since the contractions necessarily encompass both, the intra-atomic kinetic and potential energy changes (which add to a positive total), the fact that the intra-atomic potential energy change renders the total potential binding energy negative does not alter the fact that it is the kinetic delocalization energy that drives the bond formation.

Ion kinetic effects on the ignition and burn of inertial confinement fusion targets: A multi-scale approach

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

Peigney, B. E.; Larroche, O.; Tikhonchuk, V.

2014-12-15

In this article, we study the hydrodynamics and burn of the thermonuclear fuel in inertial confinement fusion pellets at the ion kinetic level. The analysis is based on a two-velocity-scale Vlasov-Fokker-Planck kinetic model that is specially tailored to treat fusion products (suprathermal α-particles) in a self-consistent manner with the thermal bulk. The model assumes spherical symmetry in configuration space and axial symmetry in velocity space around the mean flow velocity. A typical hot-spot ignition design is considered. Compared with fluid simulations where a multi-group diffusion scheme is applied to model α transport, the full ion-kinetic approach reveals significant non-local effectsmore » on the transport of energetic α-particles. This has a direct impact on hydrodynamic spatial profiles during combustion: the hot spot reactivity is reduced, while the inner dense fuel layers are pre-heated by the escaping α-suprathermal particles, which are transported farther out of the hot spot. We show how the kinetic transport enhancement of fusion products leads to a significant reduction of the fusion yield.« less

Using kinetic energy measurements from altimetry to detect shifts in the positions of fronts in the Southern Ocean

NASA Astrophysics Data System (ADS)

Chambers, Don P.

2018-02-01

A novel analysis is performed utilizing cross-track kinetic energy (CKE) computed from along-track sea surface height anomalies. The midpoint of enhanced kinetic energy averaged over 3-year periods from 1993 to 2016 is determined across the Southern Ocean and examined to detect shifts in frontal positions, based on previous observations that kinetic energy is high around fronts in the Antarctic Circumpolar Current system due to jet instabilities. It is demonstrated that although the CKE does not represent the full eddy kinetic energy (computed from crossovers), the shape of the enhanced regions along ground tracks is the same, and CKE has a much finer spatial sampling of 6.9 km. Results indicate no significant shift in the front positions across the Southern Ocean, on average, although there are some localized, large movements. This is consistent with other studies utilizing sea surface temperature gradients, the latitude of mean transport, and the probability of jet occurrence, but is inconsistent with studies utilizing the movement of contours of dynamic topography.

Algernon Wargame

DTIC Science & Technology

2008-06-01

Free Play Strategic Approaches Green/Red Base Case and Six Excursions...RED or GREEN sides should be able to win. Blue/RED Strategic Approach Free Play Popular Protracted Warfare Military Velvet Revolution Free Play Base...6 Kinetic 3 1 Non-Kinetic 5 4 2 Cases: • Base Case: Blue Free Play ; RED Free Play • Case 1: Blue Non Kinetic RED Velvet • Case 2: Blue Kinetic

Extracting a respiratory signal from raw dynamic PET data that contain tracer kinetics.

PubMed

Schleyer, P J; Thielemans, K; Marsden, P K

2014-08-07

Data driven gating (DDG) methods provide an alternative to hardware based respiratory gating for PET imaging. Several existing DDG approaches obtain a respiratory signal by observing the change in PET-counts within specific regions of acquired PET data. Currently, these methods do not allow for tracer kinetics which can interfere with the respiratory signal and introduce error. In this work, we produced a DDG method for dynamic PET studies that exhibit tracer kinetics. Our method is based on an existing approach that uses frequency-domain analysis to locate regions within raw PET data that are subject to respiratory motion. In the new approach, an optimised non-stationary short-time Fourier transform was used to create a time-varying 4D map of motion affected regions. Additional processing was required to ensure that the relationship between the sign of the respiratory signal and the physical direction of movement remained consistent for each temporal segment of the 4D map. The change in PET-counts within the 4D map during the PET acquisition was then used to generate a respiratory curve. Using 26 min dynamic cardiac NH3 PET acquisitions which included a hardware derived respiratory measurement, we show that tracer kinetics can severely degrade the respiratory signal generated by the original DDG method. In some cases, the transition of tracer from the liver to the lungs caused the respiratory signal to invert. The new approach successfully compensated for tracer kinetics and improved the correlation between the data-driven and hardware based signals. On average, good correlation was maintained throughout the PET acquisitions.

Combustor kinetic energy efficiency analysis of the hypersonic research engine data

NASA Astrophysics Data System (ADS)

Hoose, K. V.

1993-11-01

A one-dimensional method for measuring combustor performance is needed to facilitate design and development scramjet engines. A one-dimensional kinetic energy efficiency method is used for measuring inlet and nozzle performance. The objective of this investigation was to assess the use of kinetic energy efficiency as an indicator for scramjet combustor performance. A combustor kinetic energy efficiency analysis was performed on the Hypersonic Research Engine (HRE) data. The HRE data was chosen for this analysis due to its thorough documentation and availability. The combustor, inlet, and nozzle kinetic energy efficiency values were utilized to determine an overall engine kinetic energy efficiency. Finally, a kinetic energy effectiveness method was developed to eliminate thermochemical losses from the combustion of fuel and air. All calculated values exhibit consistency over the flight speed range. Effects from fuel injection, altitude, angle of attack, subsonic-supersonic combustion transition, and inlet spike position are shown and discussed. The results of analyzing the HRE data indicate that the kinetic energy efficiency method is effective as a measure of scramjet combustor performance.

Influence of Prolonged Spaceflight on Heart Rate and Oxygen Uptake Kinetics

NASA Astrophysics Data System (ADS)

Hoffmann, U.; Moore, A.; Drescher, U.

2013-02-01

During prolonged spaceflight, physical training is used to minimize cardiovascular deconditioning. Measurement of the kinetics of cardiorespiratory parameters, in particular the kinetic analysis of heart rate, respiratory and muscular oxygen uptake, provides useful information with regard to the efficiency and regulation of the cardiorespiratory system. Practically, oxygen uptake kinetics can only be measured at the lung site (V’O2 resp). The dynamics of V’O2 resp, however, is not identical with the dynamics at the site of interest: skeletal muscle. Eight Astronauts were tested pre- and post-flight using pseudo random binary workload changes between 30 and 80 W. Their kinetic responses of heart rate, respiratory as well as muscular V’O2 kinetics were estimated by using time-series analysis. Statistical analysis revealed that the kinetic responses of respiratory as well as muscular V’O2 kinetics are slowed post-flight than pre-flight. Heart rate seems not to be influenced following flight. The influence of other factors (e. g. astronauts’ exercise training) may impact these parameters and is an area for future studies.

New strategy to identify radicals in a time evolving EPR data set by multivariate curve resolution-alternating least squares.

PubMed

Fadel, Maya Abou; de Juan, Anna; Vezin, Hervé; Duponchel, Ludovic

2016-12-01

Electron paramagnetic resonance (EPR) spectroscopy is a powerful technique that is able to characterize radicals formed in kinetic reactions. However, spectral characterization of individual chemical species is often limited or even unmanageable due to the severe kinetic and spectral overlap among species in kinetic processes. Therefore, we applied, for the first time, multivariate curve resolution-alternating least squares (MCR-ALS) method to EPR time evolving data sets to model and characterize the different constituents in a kinetic reaction. Here we demonstrate the advantage of multivariate analysis in the investigation of radicals formed along the kinetic process of hydroxycoumarin in alkaline medium. Multiset analysis of several EPR-monitored kinetic experiments performed in different conditions revealed the individual paramagnetic centres as well as their kinetic profiles. The results obtained by MCR-ALS method demonstrate its prominent potential in analysis of EPR time evolved spectra. Copyright © 2016 Elsevier B.V. All rights reserved.

Ground Vibration Test Planning and Pre-Test Analysis for the X-33 Vehicle

NASA Technical Reports Server (NTRS)

Bedrossian, Herand; Tinker, Michael L.; Hidalgo, Homero

2000-01-01

This paper describes the results of the modal test planning and the pre-test analysis for the X-33 vehicle. The pre-test analysis included the selection of the target modes, selection of the sensor and shaker locations and the development of an accurate Test Analysis Model (TAM). For target mode selection, four techniques were considered, one based on the Modal Cost technique, one based on Balanced Singular Value technique, a technique known as the Root Sum Squared (RSS) method, and a Modal Kinetic Energy (MKE) approach. For selecting sensor locations, four techniques were also considered; one based on the Weighted Average Kinetic Energy (WAKE), one based on Guyan Reduction (GR), one emphasizing engineering judgment, and one based on an optimum sensor selection technique using Genetic Algorithm (GA) search technique combined with a criteria based on Hankel Singular Values (HSV's). For selecting shaker locations, four techniques were also considered; one based on the Weighted Average Driving Point Residue (WADPR), one based on engineering judgment and accessibility considerations, a frequency response method, and an optimum shaker location selection based on a GA search technique combined with a criteria based on HSV's. To evaluate the effectiveness of the proposed sensor and shaker locations for exciting the target modes, extensive numerical simulations were performed. Multivariate Mode Indicator Function (MMIF) was used to evaluate the effectiveness of each sensor & shaker set with respect to modal parameter identification. Several TAM reduction techniques were considered including, Guyan, IRS, Modal, and Hybrid. Based on a pre-test cross-orthogonality checks using various reduction techniques, a Hybrid TAM reduction technique was selected and was used for all three vehicle fuel level configurations.

Unifying model of carpal mechanics based on computationally derived isometric constraints and rules-based motion - the stable central column theory.

PubMed

Sandow, M J; Fisher, T J; Howard, C Q; Papas, S

2014-05-01

This study was part of a larger project to develop a (kinetic) theory of carpal motion based on computationally derived isometric constraints. Three-dimensional models were created from computed tomography scans of the wrists of ten normal subjects and carpal spatial relationships at physiological motion extremes were assessed. Specific points on the surface of the various carpal bones and the radius that remained isometric through range of movement were identified. Analysis of the isometric constraints and intercarpal motion suggests that the carpus functions as a stable central column (lunate-capitate-hamate-trapezoid-trapezium) with a supporting lateral column (scaphoid), which behaves as a 'two gear four bar linkage'. The triquetrum functions as an ulnar translation restraint, as well as controlling lunate flexion. The 'trapezoid'-shaped trapezoid places the trapezium anterior to the transverse plane of the radius and ulna, and thus rotates the principal axis of the central column to correspond to that used in the 'dart thrower's motion'. This study presents a forward kinematic analysis of the carpus that provides the basis for the development of a unifying kinetic theory of wrist motion based on isometric constraints and rules-based motion.

Single-Molecule Counting of Point Mutations by Transient DNA Binding

NASA Astrophysics Data System (ADS)

Su, Xin; Li, Lidan; Wang, Shanshan; Hao, Dandan; Wang, Lei; Yu, Changyuan

2017-03-01

High-confidence detection of point mutations is important for disease diagnosis and clinical practice. Hybridization probes are extensively used, but are hindered by their poor single-nucleotide selectivity. Shortening the length of DNA hybridization probes weakens the stability of the probe-target duplex, leading to transient binding between complementary sequences. The kinetics of probe-target binding events are highly dependent on the number of complementary base pairs. Here, we present a single-molecule assay for point mutation detection based on transient DNA binding and use of total internal reflection fluorescence microscopy. Statistical analysis of single-molecule kinetics enabled us to effectively discriminate between wild type DNA sequences and single-nucleotide variants at the single-molecule level. A higher single-nucleotide discrimination is achieved than in our previous work by optimizing the assay conditions, which is guided by statistical modeling of kinetics with a gamma distribution. The KRAS c.34 A mutation can be clearly differentiated from the wild type sequence (KRAS c.34 G) at a relative abundance as low as 0.01% mutant to WT. To demonstrate the feasibility of this method for analysis of clinically relevant biological samples, we used this technology to detect mutations in single-stranded DNA generated from asymmetric RT-PCR of mRNA from two cancer cell lines.

Structure/function analysis of cotton-based peptide-cellulose conjugates: spatiotemporal/kinetic assessment of protease aerogels compared to nanocrystalline and paper cellulose

USDA-ARS?s Scientific Manuscript database

The growing incidence of chronic wounds in the world population has prompted increased interest in chronic wound dressings with protease-modulating activity and protease point of care sensors to treat and enable monitoring of elevated protease-based wound pathology. However, the overall design featu...

Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations

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

Arampatzis, Georgios, E-mail: garab@math.uoc.gr; Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003; Katsoulakis, Markos A., E-mail: markos@math.umass.edu

2014-03-28

In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-“coupled”- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that themore » new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz–Kalos–Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary MATLAB source code.« less

From kinetic-structure analysis to engineering crystalline fiber networks in soft materials.

PubMed

Wang, Rong-Yao; Wang, Peng; Li, Jing-Liang; Yuan, Bing; Liu, Yu; Li, Li; Liu, Xiang-Yang

2013-03-07

Understanding the role of kinetics in fiber network microstructure formation is of considerable importance in engineering gel materials to achieve their optimized performances/functionalities. In this work, we present a new approach for kinetic-structure analysis for fibrous gel materials. In this method, kinetic data is acquired using a rheology technique and is analyzed in terms of an extended Dickinson model in which the scaling behaviors of dynamic rheological properties in the gelation process are taken into account. It enables us to extract the structural parameter, i.e. the fractal dimension, of a fibrous gel from the dynamic rheological measurement of the gelation process, and to establish the kinetic-structure relationship suitable for both dilute and concentrated gelling systems. In comparison to the fractal analysis method reported in a previous study, our method is advantageous due to its general validity for a wide range of fractal structures of fibrous gels, from a highly compact network of the spherulitic domains to an open fibrous network structure. With such a kinetic-structure analysis, we can gain a quantitative understanding of the role of kinetic control in engineering the microstructure of the fiber network in gel materials.

Kinetics of (3-aminopropyl)triethoxylsilane (APTES) silanization of superparamagnetic iron oxide nanoparticles.

PubMed

Liu, Yue; Li, Yueming; Li, Xue-Mei; He, Tao

2013-12-10

Silanization of magnetic ironoxide nanoparticles with (3-aminopropyl)triethoxylsilane (APTES) is reported. The kinetics of silanization toward saturation was investigated using different solvents including water, water/ethanol (1/1), and toluene/methanol (1/1) at different reaction temperature with different APTES loading. The nanoparticles were characterized by Fourier transform infrared spectroscopy, vibrating sample magnetometry, transmission electron microscopy, and thermal gravimetric analysis (TGA). Grafting density data based on TGA were used for the kinetic modeling. It is shown that initial silanization takes place very fast but the progress toward saturation is very slow, and the mechanism may involve adsorption, chemical sorption, and chemical diffusion processes. The highest equilibrium grafting density of 301 mg/g was yielded when using toluene/methanol mixture as the solvent at a reaction temperature of 70 °C.

Kinetic modeling in PET imaging of hypoxia

PubMed Central

Li, Fan; Joergensen, Jesper T; Hansen, Anders E; Kjaer, Andreas

2014-01-01

Tumor hypoxia is associated with increased therapeutic resistance leading to poor treatment outcome. Therefore the ability to detect and quantify intratumoral oxygenation could play an important role in future individual personalized treatment strategies. Positron Emission Tomography (PET) can be used for non-invasive mapping of tissue oxygenation in vivo and several hypoxia specific PET tracers have been developed. Evaluation of PET data in the clinic is commonly based on visual assessment together with semiquantitative measurements e.g. standard uptake value (SUV). However, dynamic PET contains additional valuable information on the temporal changes in tracer distribution. Kinetic modeling can be used to extract relevant pharmacokinetic parameters of tracer behavior in vivo that reflects relevant physiological processes. In this paper, we review the potential contribution of kinetic analysis for PET imaging of hypoxia. PMID:25250200

Chaperonin-based biolayer interferometry to assess the kinetic stability of metastable, aggregation-prone proteins

PubMed Central

Lea, Wendy A.; Naik, Subhashchandra; Chaudhri, Tapan; Machen, Alexandra J.; O’Neil, Pierce T.; McGinn-Straub, Wesley; Tischer, Alexander; Auton, Matthew T.; Burns, Joshua R.; Baldwin, Michael R.; Khar, Karen R.; Karanicolas, John; Fisher, Mark T.

2017-01-01

Stabilizing the folded state of metastable and/or aggregation-prone proteins through exogenous ligand binding is an appealing strategy to decrease disease pathologies brought on by protein folding defects or deleterious kinetic transitions. Current methods of examining ligand binding to these marginally stable native states are limited, because protein aggregation typically interferes with analysis. Here, we describe a rapid method for assessing the kinetic stability of folded proteins and monitoring the effects of ligand stabilization for both intrinsically stable proteins (monomers, oligomers, multi-domain) and metastable proteins (e.g. low Tm) that uses a new GroEL chaperonin-based biolayer interferometry (BLI) denaturant-pulse platform. A kinetically controlled denaturation isotherm is generated by exposing a target protein immobilized on a BLI biosensor to increasing denaturant concentrations (urea or GnHCl) in a pulsatile manner to induce partial or complete unfolding of the attached protein population. Following the rapid removal of the denaturant, the extent of hydrophobic unfolded/partially folded species that remain is detected by increased GroEL binding. Since this kinetic denaturant pulse is brief, the amplitude of the GroEL binding to the immobilized protein depends on the duration of exposure to denaturant, the concentration of denaturant, wash times, and the underlying protein unfolding/refolding kinetics; fixing all other parameters and plotting GroEL binding amplitude versus denaturant pulse concentration results in a kinetically controlled denaturation isotherm. When folding osmolytes or stabilizing ligands are added to the immobilized target proteins before and during the denaturant pulse, the diminished population of unfolded/partially folded protein is manifested by a decreased GroEL binding and/or a marked shift in these kinetically controlled denaturation profiles to higher denaturant concentrations. This particular platform approach can be used to identify small molecules/solution conditions that can stabilize or destabilize thermally stable proteins, multi-domain proteins, oligomeric proteins, and most importantly, aggregation prone metastable proteins. PMID:27505032

Understanding the kinetic mechanism of RNA single base pair formation

PubMed Central

Xu, Xiaojun; Yu, Tao; Chen, Shi-Jie

2016-01-01

RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model. PMID:26699466

In vitro kinetics of P700+ reduction of Thermosynechococcus elongatus trimeric Photosystem I complexes by recombinant cytochrome c 6 using a Joliot-type LED spectrophotometer.

PubMed

Nguyen, Khoa; Vaughn, Michael; Frymier, Paul; Bruce, Barry D

2017-01-01

The reduction rate of photo-oxidized Photosystem I (PSI) with various natural and artificial electron donors have been well studied by transient absorption spectroscopy. The electron transfer rate from various donors to P 700 + has been measured for a wide range of photosynthetic organisms encompassing cyanobacteria, algae, and plants. PSI can be a limiting component due to tedious extraction and purification methods required for this membrane protein. In this report, we have determined the in vivo, intracellular cytochrome c 6 (cyt c 6 )/PSI ratio in Thermosynechococcus elongatus (T.e.) using quantitative Western blot analysis. This information permitted the determination of P 700 + reduction kinetics via recombinant cyt c 6 in a physiologically relevant ratio (cyt c 6 : PSI) with a Joliot-type, LED-driven, pump-probe spectrophotometer. Dilute PSI samples were tested under varying cyt c 6 concentration, temperature, pH, and ionic strength, each of which shows similar trends to the reported literature utilizing much higher PSI concentrations with laser-based spectrophotometer. Our results do however indicate kinetic differences between actinic light sources (laser vs. LED), and we have attempted to resolve these effects by varying our LED light intensity and duration. The standardized configuration of this spectrophotometer will also allow a more uniform kinetic analysis of samples in different laboratories. We can conclude that our findings from the LED-based system display an added total protein concentration effect due to multiple turnover events of P 700 + reduction by cyt c 6 during the longer illumination regime.

Kinetic analysis of a Michaelis-Menten mechanism in which the enzyme is unstable.

PubMed Central

Garrido-del Solo, C; García-Cánovas, F; Havsteen, B H; Varón-Castellanos, R

1993-01-01

A kinetic analysis of the Michaelis-Menten mechanism is made for the cases in which the free enzyme, or the enzyme-substrate complex, or both, are unstable, either spontaneously or as a result of the addition of a reagent. The explicit time-course equations of all of the species involved has been derived under conditions of limiting enzyme concentration. The validity of these equations has been checked by using numerical simulations. An experimental design and a kinetic data analysis allowing the evaluation of the parameters and kinetic constants are recommended. PMID:8373361

Oxidation kinetics of the combustible fraction of construction and demolition wastes.

PubMed

Chang, N B; Lin, K S; Sun, Y P; Wang, H P

2001-01-01

Proper disposal of construction and demolition wastes (CDW) has received wide attention recently due to significantly large quantities of waste streams collected from razed or retrofitted buildings in many metropolitan regions. Burning the combustible fractions of CDW (CCDW) and possibly recovering part of the heat content for economic uses could be valuable for energy conservation. This paper explores the oxidation kinetics of CCDW associated with its ash characterization. Kinetic parameters for the oxidation of CCDW were numerically calculated using thermal gravimetric analysis (TGA) and the resultant rate equations were therefore developed for illustrating the oxidation processes of CCDW simultaneously. Based on three designated heating rates, each of the oxidation processes can be featured distinctively with five different stages according to the rate of weight change at the temperature between 300 K and 923 K. In addition, Fourier transform infrared (FTIR) spectroscopy was employed, associated with a lab-scale fixed-bed incinerator for monitoring the composition of flue gas. Carbon dioxide (CO2) was found as a major component in the flue gas. The fuel analysis also included an ash composition analysis via the use of X-ray powder diffraction (XRD), atomic absorption (AA) spectroscopy, inductively coupled plasma-atomic emission spectroscopy (ICP-AES), and scanning electron microscopy-energy dispersive spectroscopy (SEM-EDX). The ash streams were identified as nonhazardous materials based on the toxicity characteristic leaching procedure (TCLP). Overall, the scientific findings gained in this study will be helpful for supporting a sound engineering design of real-world CCDW incineration systems.

Variability of Grip Kinetics during Adult Signature Writing

PubMed Central

Ghali, Bassma; Thalanki Anantha, Nayanashri; Chan, Jennifer; Chau, Tom

2013-01-01

Grip kinetics and their variation are emerging as important considerations in the clinical assessment of handwriting pathologies, fine motor rehabilitation, biometrics, forensics and ergonomic pen design. This study evaluated the intra- and inter-participant variability of grip shape kinetics in adults during signature writing. Twenty (20) adult participants wrote on a digitizing tablet using an instrumented pen that measured the forces exerted on its barrel. Signature samples were collected over 10 days, 3 times a day, to capture temporal variations in grip shape kinetics. A kinetic topography (i.e., grip shape image) was derived per signature by time-averaging the measured force at each of 32 locations around the pen barrel. The normalized cross correlations (NCC) of grip shape images were calculated within- and between-participants. Several classification algorithms were implemented to gauge the error rate of participant discrimination based on grip shape kinetics. Four different grip shapes emerged and several participants made grip adjustments (change in grip shape or grip height) or rotated the pen during writing. Nonetheless, intra-participant variation in grip kinetics was generally much smaller than inter-participant force variations. Using the entire grip shape images as a 32-dimensional input feature vector, a K-nearest neighbor classifier achieved an error rate of % in discriminating among participants. These results indicate that writers had unique grip shape kinetics that were repeatable over time but distinct from those of other participants. The topographic analysis of grip kinetics may inform the development of personalized interventions or customizable grips in clinical and industrial applications, respectively. PMID:23658812

Variability of grip kinetics during adult signature writing.

PubMed

Ghali, Bassma; Thalanki Anantha, Nayanashri; Chan, Jennifer; Chau, Tom

2013-01-01

Grip kinetics and their variation are emerging as important considerations in the clinical assessment of handwriting pathologies, fine motor rehabilitation, biometrics, forensics and ergonomic pen design. This study evaluated the intra- and inter-participant variability of grip shape kinetics in adults during signature writing. Twenty (20) adult participants wrote on a digitizing tablet using an instrumented pen that measured the forces exerted on its barrel. Signature samples were collected over 10 days, 3 times a day, to capture temporal variations in grip shape kinetics. A kinetic topography (i.e., grip shape image) was derived per signature by time-averaging the measured force at each of 32 locations around the pen barrel. The normalized cross correlations (NCC) of grip shape images were calculated within- and between-participants. Several classification algorithms were implemented to gauge the error rate of participant discrimination based on grip shape kinetics. Four different grip shapes emerged and several participants made grip adjustments (change in grip shape or grip height) or rotated the pen during writing. Nonetheless, intra-participant variation in grip kinetics was generally much smaller than inter-participant force variations. Using the entire grip shape images as a 32-dimensional input feature vector, a K-nearest neighbor classifier achieved an error rate of 1.2±0.4% in discriminating among participants. These results indicate that writers had unique grip shape kinetics that were repeatable over time but distinct from those of other participants. The topographic analysis of grip kinetics may inform the development of personalized interventions or customizable grips in clinical and industrial applications, respectively.

Kinetic release of hydrogen peroxide from different whitening products.

PubMed

da Silva Marques, Duarte Nuno; Silveira, Joao Miguel; Marques, Joana Rita; Amaral, Joao Almeida; Guilherme, Nuno Marques; da Mata, António Duarte

2012-01-01

The objective of this in vitro study was to evaluate the kinetics of hydrogen peroxide (HP) release from five different bleaching products: VivaStyle® 10% fitted tray gel, VivaStyle® 30% in-office bleaching gel, VivaStyle® Paint-On Plus paint-on bleaching varnish, Opalescence PF® 10% carbamide peroxide gel and Trèswhite Supreme™ 10% HP gel. Each product was firstly titrated for its HP content by a described method. HP release kinetics was assessed by a modified spectrophotometric technique. One sample t test was performed to test for differences between the manufacturers' claimed HP concentrations and the titrated HP content in the whitening products. Analysis of variance plus Tamhane's post hoc tests and Pearson correlation analysis were used as appropriate. Values of P < 0.05 were taken as significant. Titrated HP revealed an increased content when compared to the manufacturer's specifications for all the products tested (P < 0.05), although only products from one manufacturer produced significantly higher results. All products presented a significant (P < 0.05) and sustained release of HP. However, the product with paint-on cellulose-based matrix resulted in significantly (P < 0.05) faster kinetics when compared to other products tested. These results are consistent with manufacturers' reduced recommended application times. The results of this study suggest that modifying the matrix composition may be a viable alternative to HP concentration increase, since this may result in faster release kinetics without exposure to high HP concentrations.

Comparing kinetic curves in liquid chromatography

NASA Astrophysics Data System (ADS)

Kurganov, A. A.; Kanat'eva, A. Yu.; Yakubenko, E. E.; Popova, T. P.; Shiryaeva, V. E.

2017-01-01

Five equations for kinetic curves which connect the number of theoretical plates N and time of analysis t 0 for five different versions of optimization, depending on the parameters being varied (e.g., mobile phase flow rate, pressure drop, sorbent grain size), are obtained by means of mathematical modeling. It is found that a method based on the optimization of a sorbent grain size at fixed pressure is most suitable for the optimization of rapid separations. It is noted that the advantages of the method are limited by an area of relatively low efficiency, and the advantage of optimization is transferred to a method based on the optimization of both the sorbent grain size and the drop in pressure across a column in the area of high efficiency.

Hot prominence detected in the core of a coronal mass ejection. II. Analysis of the C III line detected by SOHO/UVCS

NASA Astrophysics Data System (ADS)

Jejčič, S.; Susino, R.; Heinzel, P.; Dzifčáková, E.; Bemporad, A.; Anzer, U.

2017-11-01

Context. We study the physics of erupting prominences in the core of coronal mass ejections (CMEs) and present a continuation of a previous analysis. Aims: We determine the kinetic temperature and microturbulent velocity of an erupting prominence embedded in the core of a CME that occurred on August 2, 2000 using the Ultraviolet Coronagraph and Spectrometer observations (UVCS) on board the Solar and Heliospheric Observatory (SOHO) simultaneously in the hydrogen Lα and C III lines. We develop the non-LTE (departures from the local thermodynamic equilibrium - LTE) spectral diagnostics based on Lα and Lβ measured integrated intensities to derive other physical quantities of the hot erupting prominence. Based on this, we synthesize the C III line intensity to compare it with observations. Methods: Our method is based on non-LTE modeling of eruptive prominences. We used a general non-LTE radiative-transfer code only for optically thin prominence points because optically thick points do not allow the direct determination of the kinetic temperature and microturbulence from the line profiles. The input parameters of the code were the kinetic temperature and microturbulent velocity derived from the Lα and C III line widths, as well as the integrated intensity of the Lα and Lβ lines. The code runs in three loops to compute the radial flow velocity, electron density, and effective thickness as the best fit to the Lα and Lβ integrated intensities within the accuracy defined by the absolute radiometric calibration of UVCS data. Results: We analyzed 39 observational points along the whole erupting prominence because for these points we found a solution for the kinetic temperature and microturbulent velocity. For these points we ran the non-LTE code to determine best-fit models. All models with τ0(Lα) ≤ 0.3 and τ0(C III) ≤ 0.3 were analyzed further, for which we computed the integrated intensity of the C III line using a two-level atom. The best agreement between computed and observed integrated intensity led to 30 optically thin points along the prominence. The results are presented as histograms of the kinetic temperature, microturbulent velocity, effective thickness, radial flow velocity, electron density, and gas pressure. We also show the relation between the microturbulence and kinetic temperature together with a scatter plot of computed versus observed C III integrated intensities and the ratio of the computed to observed C III integrated intensities versus kinetic temperature. Conclusions: The erupting prominence embedded in the CME is relatively hot with a low electron density, a wide range of effective thicknesses, a rather narrow range of radial flow velocities, and a microturbulence of about 25 km s-1. This analysis shows a disagreement between observed and synthetic intensities of the C III line, the reason for which most probably is that photoionization is neglected in calculations of the ionization equilibrium. Alternatively, the disagreement might be due to non-equilibrium processes.

Nonisothermal Carbothermal Reduction Kinetics of Titanium-Bearing Blast Furnace Slag

NASA Astrophysics Data System (ADS)

Hu, Mengjun; Wei, Ruirui; Hu, Meilong; Wen, Liangying; Ying, Fangqing

2018-05-01

The kinetics of carbothermal reduction of titanium-bearing blast furnace (BF) slag has been studied by thermogravimetric analysis and quadrupole mass spectrometry. The kinetic parameters (activation energy, preexponential factor, and reaction model function) were determined using the Flynn-Wall-Ozawa and Šatava-Šesták methods. The results indicated that reduction of titanium-bearing BF slag can be divided into two stages, namely reduction of phases containing iron and gasification of carbon (< 1095°C), followed by reduction of phases containing titanium (> 1095°C). CO2 was the main off-gas in the temperature range of 530-700°C, whereas CO became the main off-gas when the temperature was greater than 900°C. The activation energy calculated using the Flynn-Wall-Ozawa method was 221.2 kJ/mol. D4 is the mechanism function for carbothermal reduction of titanium-bearing BF slag. Meanwhile, a nonisothermal reduction model is proposed based on the obtained kinetic parameters.

EAST kinetic equilibrium reconstruction combining with Polarimeter-Interferometer internal measurement constraints

NASA Astrophysics Data System (ADS)

Lian, H.; Liu, H. Q.; Li, K.; Zou, Z. Y.; Qian, J. P.; Wu, M. Q.; Li, G. Q.; Zeng, L.; Zang, Q.; Lv, B.; Jie, Y. X.; EAST Team

2017-12-01

Plasma equilibrium reconstruction plays an important role in the tokamak plasma research. With a high temporal and spatial resolution, the POlarimeter-INTerferometer (POINT) system on EAST has provided effective measurements for 102s H-mode operation. Based on internal Faraday rotation measurements provided by the POINT system, the equilibrium reconstruction with a more accurate core current profile constraint has been demonstrated successfully on EAST. Combining other experimental diagnostics and external magnetic fields measurement, the kinetic equilibrium has also been reconstructed on EAST. Take the pressure and edge current information from kinetic EFIT into the equilibrium reconstruction with Faraday rotation constraint, the new equilibrium reconstruction not only provides a more accurate internal current profile but also contains edge current and pressure information. One time slice result using new kinetic equilibrium reconstruction with POINT data constraints is demonstrated in this paper and the result shows there is a reversed shear of q profile and the pressure profile is also contained. The new improved equilibrium reconstruction is greatly helpful to the future theoretical analysis.

Structural kinetic modeling of metabolic networks.

PubMed

Steuer, Ralf; Gross, Thilo; Selbig, Joachim; Blasius, Bernd

2006-08-08

To develop and investigate detailed mathematical models of metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, kinetic modeling is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a quantitative account of the dynamical capabilities of a metabolic system, without requiring any explicit information about the functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a statistical exploration of the comprehensive parameter space. The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.

Paralinear Oxidation of CVD SiC in Simulated Fuel-Rich Combustion

NASA Technical Reports Server (NTRS)

Fox, Dennis S.; Opila, Elizabeth J.; Hann, Raiford E.

2000-01-01

The oxidation kinetics of CVD SiC were measured by thermogravimetric analysis (TGA) in a 4H2 (central dot) 12H2O (central dot) 10CO (central dot) 7CO2 (central dot) 67N2 gas mixture flowing at 0.44 cm/s at temperatures between 1300 and 1450 C in fused quartz furnace tubes at I atm total pressure. The SiC was oxidized to form solid SiO2. At less than or = 1350 C, the SiO2 was in turn volatilized. Volatilization kinetics were consistent with the thermodynamic predictions based on SiO formation. These two simultaneous reactions resulted in overall paralinear kinetics. A curve fitting technique was used to determine the linear and parabolic rate constants from the paralinear kinetic data. Volatilization of the protective SiO2 scale resulted in accelerated consumption of SiC. Recession rates under conditions more representative of actual combustors were estimated from the furnace data.

The response of the HMX-based material PBXN-9 to thermal insults: thermal decomposition kinetics and morphological changes

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

Glascoe, E A; Hsu, P C; Springer, H K

PBXN-9, an HMX-formulation, is thermally damaged and thermally decomposed in order to determine the morphological changes and decomposition kinetics that occur in the material after mild to moderate heating. The material and its constituents were decomposed using standard thermal analysis techniques (DSC and TGA) and the decomposition kinetics are reported using different kinetic models. Pressed parts and prill were thermally damaged, i.e. heated to temperatures that resulted in material changes but did not result in significant decomposition or explosion, and analyzed. In general, the thermally damaged samples showed a significant increase in porosity and decrease in density and a smallmore » amount of weight loss. These PBXN-9 samples appear to sustain more thermal damage than similar HMX-Viton A formulations and the most likely reasons are the decomposition/evaporation of a volatile plasticizer and a polymorphic transition of the HMX from {beta} to {delta} phase.« less

Kinetic constrained optimization of the golf swing hub path.

PubMed

Nesbit, Steven M; McGinnis, Ryan S

2014-12-01

This study details an optimization of the golf swing, where the hand path and club angular trajectories are manipulated. The optimization goal was to maximize club head velocity at impact within the interaction kinetic limitations (force, torque, work, and power) of the golfer as determined through the analysis of a typical swing using a two-dimensional dynamic model. The study was applied to four subjects with diverse swing capabilities and styles. It was determined that it is possible for all subjects to increase their club head velocity at impact within their respective kinetic limitations through combined modifications to their respective hand path and club angular trajectories. The manner of the modifications, the degree of velocity improvement, the amount of kinetic reduction, and the associated kinetic limitation quantities were subject dependent. By artificially minimizing selected kinetic inputs within the optimization algorithm, it was possible to identify swing trajectory characteristics that indicated relative kinetic weaknesses of a subject. Practical implications are offered based upon the findings of the study. Key PointsThe hand path trajectory is an important characteristic of the golf swing and greatly affects club head velocity and golfer/club energy transfer.It is possible to increase the energy transfer from the golfer to the club by modifying the hand path and swing trajectories without increasing the kinetic output demands on the golfer.It is possible to identify relative kinetic output strengths and weakness of a golfer through assessment of the hand path and swing trajectories.Increasing any one of the kinetic outputs of the golfer can potentially increase the club head velocity at impact.The hand path trajectory has important influences over the club swing trajectory.

Kinetic Constrained Optimization of the Golf Swing Hub Path

PubMed Central

Nesbit, Steven M.; McGinnis, Ryan S.

2014-01-01

This study details an optimization of the golf swing, where the hand path and club angular trajectories are manipulated. The optimization goal was to maximize club head velocity at impact within the interaction kinetic limitations (force, torque, work, and power) of the golfer as determined through the analysis of a typical swing using a two-dimensional dynamic model. The study was applied to four subjects with diverse swing capabilities and styles. It was determined that it is possible for all subjects to increase their club head velocity at impact within their respective kinetic limitations through combined modifications to their respective hand path and club angular trajectories. The manner of the modifications, the degree of velocity improvement, the amount of kinetic reduction, and the associated kinetic limitation quantities were subject dependent. By artificially minimizing selected kinetic inputs within the optimization algorithm, it was possible to identify swing trajectory characteristics that indicated relative kinetic weaknesses of a subject. Practical implications are offered based upon the findings of the study. Key Points The hand path trajectory is an important characteristic of the golf swing and greatly affects club head velocity and golfer/club energy transfer. It is possible to increase the energy transfer from the golfer to the club by modifying the hand path and swing trajectories without increasing the kinetic output demands on the golfer. It is possible to identify relative kinetic output strengths and weakness of a golfer through assessment of the hand path and swing trajectories. Increasing any one of the kinetic outputs of the golfer can potentially increase the club head velocity at impact. The hand path trajectory has important influences over the club swing trajectory. PMID:25435779

Thermogravimetric analysis and kinetic modeling of low-transition-temperature mixtures pretreated oil palm empty fruit bunch for possible maximum yield of pyrolysis oil.

PubMed

Yiin, Chung Loong; Yusup, Suzana; Quitain, Armando T; Uemura, Yoshimitsu; Sasaki, Mitsuru; Kida, Tetsuya

2018-05-01

The impacts of low-transition-temperature mixtures (LTTMs) pretreatment on thermal decomposition and kinetics of empty fruit bunch (EFB) were investigated by thermogravimetric analysis. EFB was pretreated with the LTTMs under different duration of pretreatment which enabled various degrees of alteration to their structure. The TG-DTG curves showed that LTTMs pretreatment on EFB shifted the temperature and rate of decomposition to higher values. The EFB pretreated with sucrose and choline chloride-based LTTMs had attained the highest mass loss of volatile matter (78.69% and 75.71%) after 18 h of pretreatment. For monosodium glutamate-based LTTMs, the 24 h pretreated EFB had achieved the maximum mass loss (76.1%). Based on the Coats-Redfern integral method, the LTTMs pretreatment led to an increase in activation energy of the thermal decomposition of EFB from 80.00 to 82.82-94.80 kJ/mol. The activation energy was mainly affected by the demineralization and alteration in cellulose crystallinity after LTTMs pretreatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Modeling, simulation and optimization of a no-chamber solid oxide fuel cell operated with a flat-flame burner

NASA Astrophysics Data System (ADS)

Vogler, Marcel; Horiuchi, Michio; Bessler, Wolfgang G.

A detailed computational model of a direct-flame solid oxide fuel cell (DFFC) is presented. The DFFC is based on a fuel-rich methane-air flame stabilized on a flat-flame burner and coupled to a solid oxide fuel cell (SOFC). The model consists of an elementary kinetic description of the premixed methane-air flame, a stagnation-point flow description of the coupled heat and mass transport within the gas phase, an elementary kinetic description of the electrochemistry, as well as heat, mass and charge transport within the SOFC. Simulated current-voltage characteristics show excellent agreement with experimental data published earlier (Kronemayer et al., 2007 [10]). The model-based analysis of loss processes reveals that ohmic resistance in the current collection wires dominates polarization losses, while electronic loss currents in the mixed conducting electrolyte have only little influence on the polarized cell. The model was used to propose an optimized cell design. Based on this analysis, power densities of above 200 mW cm -2 can be expected.

Kinetic method for the large-scale analysis of the binding mechanism of histone deacetylase inhibitors.

PubMed

Meyners, Christian; Baud, Matthias G J; Fuchter, Matthew J; Meyer-Almes, Franz-Josef

2014-09-01

Performing kinetic studies on protein ligand interactions provides important information on complex formation and dissociation. Beside kinetic parameters such as association rates and residence times, kinetic experiments also reveal insights into reaction mechanisms. Exploiting intrinsic tryptophan fluorescence a parallelized high-throughput Förster resonance energy transfer (FRET)-based reporter displacement assay with very low protein consumption was developed to enable the large-scale kinetic characterization of the binding of ligands to recombinant human histone deacetylases (HDACs) and a bacterial histone deacetylase-like amidohydrolase (HDAH) from Bordetella/Alcaligenes. For the binding of trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), and two other SAHA derivatives to HDAH, two different modes of action, simple one-step binding and a two-step mechanism comprising initial binding and induced fit, were verified. In contrast to HDAH, all compounds bound to human HDAC1, HDAC6, and HDAC8 through a two-step mechanism. A quantitative view on the inhibitor-HDAC systems revealed two types of interaction, fast binding and slow dissociation. We provide arguments for the thesis that the relationship between quantitative kinetic and mechanistic information and chemical structures of compounds will serve as a valuable tool for drug optimization. Copyright © 2014 Elsevier Inc. All rights reserved.

On direct internal methane steam reforming kinetics in operating solid oxide fuel cells with nickel-ceria anodes

NASA Astrophysics Data System (ADS)

Thallam Thattai, A.; van Biert, L.; Aravind, P. V.

2017-12-01

Major operating challenges remain to safely operate methane fuelled solid oxide fuel cells due to undesirable temperature gradients across the porous anode and carbon deposition. This article presents an experimental study on methane steam reforming (MSR) global kinetics for single operating SOFCs with Ni-GDC (gadolinium doped ceria) anodes for low steam to carbon (S/C) ratios and moderate current densities. The study points out the hitherto insufficient research on MSR global and intrinsic kinetics for operating SOFCs with complete Ni-ceria anodes. Further, it emphasizes the need to develop readily applicable global kinetic models as a subsequent step from previously reported state-of-art and complex intrinsic models. Two rate expressions of the Power law (PL) and Langmuir-Hinshelwood (LH) type have been compared and based on the analysis, limitations of using previously proposed rate expressions for Ni catalytic beds to study MSR kinetics for complete cermet anodes have been identified. Firstly, it has been shown that methane reforming on metallic (Ni) current collectors may not be always negligible, contrary to literature reports. Both PL and LH kinetic models predict significantly different local MSR reaction rate and species partial pressure distributions along the normalized reactor length, indicating a strong need for further experimental verifications.

Development of an LC-MS based enzyme activity assay for MurC: application to evaluation of inhibitors and kinetic analysis.

PubMed

Deng, Gejing; Gu, Rong-Fang; Marmor, Stephen; Fisher, Stewart L; Jahic, Haris; Sanyal, Gautam

2004-06-29

An enzyme activity assay, based on mass spectrometric (MS) detection of specific reaction product following HPLC separation, has been developed to evaluate pharmaceutical hits identified from primary high throughput screening (HTS) against target enzyme Escherichia coli UDP-N-acetyl-muramyl-L-alanine ligase (MurC), an essential enzyme in the bacterial peptidoglycan biosynthetic pathway, and to study the kinetics of the enzyme. A comparative analysis of this new liquid chromatographic-MS (LC-MS) based assay with a conventional spectrophotometric Malachite Green (MG) assay, which detects phosphate produced in the reaction, was performed. The results demonstrated that the LC-MS assay, which determines specific ligase activity of MurC, offers several advantages including a lower background (0.2% versus 26%), higher sensitivity (> or = 10 fold), lower limit of quantitation (LOQ) (0.02 microM versus 1 microM) and wider linear dynamic range (> or = 4 fold) than the MG assay. Good precision for the LC-MS assay was demonstrated by the low intraday and interday coefficient of variation (CV) values (3 and 6%, respectively). The LC-MS assay, free of the artifacts often seen in the Malachite Green assay, offers a valuable secondary assay for hit evaluation in which the false positives from the primary high throughput screening can be eliminated. In addition, the applicability of this assay to the study of enzyme kinetics has also been demonstrated. Copyright 2004 Elsevier B.V.

pyJac: Analytical Jacobian generator for chemical kinetics

NASA Astrophysics Data System (ADS)

Niemeyer, Kyle E.; Curtis, Nicholas J.; Sung, Chih-Jen

2017-06-01

Accurate simulations of combustion phenomena require the use of detailed chemical kinetics in order to capture limit phenomena such as ignition and extinction as well as predict pollutant formation. However, the chemical kinetic models for hydrocarbon fuels of practical interest typically have large numbers of species and reactions and exhibit high levels of mathematical stiffness in the governing differential equations, particularly for larger fuel molecules. In order to integrate the stiff equations governing chemical kinetics, generally reactive-flow simulations rely on implicit algorithms that require frequent Jacobian matrix evaluations. Some in situ and a posteriori computational diagnostics methods also require accurate Jacobian matrices, including computational singular perturbation and chemical explosive mode analysis. Typically, finite differences numerically approximate these, but for larger chemical kinetic models this poses significant computational demands since the number of chemical source term evaluations scales with the square of species count. Furthermore, existing analytical Jacobian tools do not optimize evaluations or support emerging SIMD processors such as GPUs. Here we introduce pyJac, a Python-based open-source program that generates analytical Jacobian matrices for use in chemical kinetics modeling and analysis. In addition to producing the necessary customized source code for evaluating reaction rates (including all modern reaction rate formulations), the chemical source terms, and the Jacobian matrix, pyJac uses an optimized evaluation order to minimize computational and memory operations. As a demonstration, we first establish the correctness of the Jacobian matrices for kinetic models of hydrogen, methane, ethylene, and isopentanol oxidation (number of species ranging 13-360) by showing agreement within 0.001% of matrices obtained via automatic differentiation. We then demonstrate the performance achievable on CPUs and GPUs using pyJac via matrix evaluation timing comparisons; the routines produced by pyJac outperformed first-order finite differences by 3-7.5 times and the existing analytical Jacobian software TChem by 1.1-2.2 times on a single-threaded basis. It is noted that TChem is not thread-safe, while pyJac is easily parallelized, and hence can greatly outperform TChem on multicore CPUs. The Jacobian matrix generator we describe here will be useful for reducing the cost of integrating chemical source terms with implicit algorithms in particular and algorithms that require an accurate Jacobian matrix in general. Furthermore, the open-source release of the program and Python-based implementation will enable wide adoption.

Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

PubMed Central

Martí-Centelles, Vicente; Burguete, M. Isabel; Luis, Santiago V.

2012-01-01

Several kinetic models for the macrocyclization of a C2 pseudopeptide with a dihalide through a SN2 reaction have been developed. These models not only focus on the kinetic analysis of the main macrocyclization reaction, but also consider the competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes. PMID:22666148

Determination of cell metabolite VEGF₁₆₅ and dynamic analysis of protein-DNA interactions by combination of microfluidic technique and luminescent switch-on probe.

PubMed

Lin, Xuexia; Leung, Ka-Ho; Lin, Ling; Lin, Luyao; Lin, Sheng; Leung, Chung-Hang; Ma, Dik-Lung; Lin, Jin-Ming

2016-05-15

In this paper, we rationally design a novel G-quadruplex-selective luminescent iridium (III) complex for rapid detection of oligonucleotide and VEGF165 in microfluidics. This new probe is applied as a convenient biosensor for label-free quantitative analysis of VEGF165 protein from cell metabolism, as well as for studying the kinetics of the aptamer-protein interaction combination with a microfluidic platform. As a result, we have successfully established a quantitative analysis of VEGF165 from cell metabolism. Furthermore, based on the principles of hydrodynamic focusing and diffusive mixing, different transient states during kinetics process were monitored and recorded. Thus, the combination of microfluidic technique and G-quadruplex luminescent probe will be potentially applied in the studies of intramolecular interactions and molecule recognition in the future. Copyright © 2015 Elsevier B.V. All rights reserved.

The size effects upon shock plastic compression of nanocrystals

NASA Astrophysics Data System (ADS)

Malygin, G. A.; Klyavin, O. V.

2017-10-01

For the first time a theoretical analysis of scale effects upon the shock plastic compression of nanocrystals is implemented in the context of a dislocation kinetic approach based on the equations and relationships of dislocation kinetics. The yield point of crystals τy is established as a quantitative function of their cross-section size D and the rate of shock deformation as τy ɛ2/3 D. This dependence is valid in the case of elastic stress relaxation on account of emission of dislocations from single-pole Frank-Read sources near the crystal surface.

Units of analysis and kinetic structure of behavioral repertoires

PubMed Central

Thompson, Travis; Lubinski, David

1986-01-01

It is suggested that molar streams of behavior are constructed of various arrangements of three elementary constituents (elicited, evoked, and emitted response classes). An eight-cell taxonomy is elaborated as a framework for analyzing and synthesizing complex behavioral repertoires based on these functional units. It is proposed that the local force binding functional units into a smoothly articulated kinetic sequence arises from temporally arranged relative response probability relationships. Behavioral integration is thought to reflect the joint influence of the organism's hierarchy of relative response probabilities, fluctuating biological states, and the arrangement of environmental and behavioral events in time. PMID:16812461

Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

DOEpatents

Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

2010-05-04

A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

Rate-determining Step of Flap Endonuclease 1 (FEN1) Reflects a Kinetic Bias against Long Flaps and Trinucleotide Repeat Sequences.

PubMed

Tarantino, Mary E; Bilotti, Katharina; Huang, Ji; Delaney, Sarah

2015-08-21

Flap endonuclease 1 (FEN1) is a structure-specific nuclease responsible for removing 5'-flaps formed during Okazaki fragment maturation and long patch base excision repair. In this work, we use rapid quench flow techniques to examine the rates of 5'-flap removal on DNA substrates of varying length and sequence. Of particular interest are flaps containing trinucleotide repeats (TNR), which have been proposed to affect FEN1 activity and cause genetic instability. We report that FEN1 processes substrates containing flaps of 30 nucleotides or fewer at comparable single-turnover rates. However, for flaps longer than 30 nucleotides, FEN1 kinetically discriminates substrates based on flap length and flap sequence. In particular, FEN1 removes flaps containing TNR sequences at a rate slower than mixed sequence flaps of the same length. Furthermore, multiple-turnover kinetic analysis reveals that the rate-determining step of FEN1 switches as a function of flap length from product release to chemistry (or a step prior to chemistry). These results provide a kinetic perspective on the role of FEN1 in DNA replication and repair and contribute to our understanding of FEN1 in mediating genetic instability of TNR sequences. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Investigation of the kinetic mechanism of the demanganization reaction between carbon-saturated liquid iron and CaF2-CaO-SiO2-based slags

NASA Astrophysics Data System (ADS)

Duan, Sheng-chao; Li, Chuang; Guo, Han-jie; Guo, Jing; Han, Shao-wei; Yang, Wen-sheng

2018-04-01

The demanganization reaction kinetics of carbon-saturated liquid iron with an eight-component slag consisting of CaO-SiO2-MgO-FeO-MnO-Al2O3-TiO2-CaF2 was investigated at 1553, 1623, and 1673 K in this study. The rate-controlling step (RCS) for the demanganization reaction with regard to the hot metal pretreatment conditions was studied via kinetics analysis based on the fundamental equation of heterogeneous reaction kinetics. From the temperature dependence of the mass transfer coefficient of a transition-metal oxide (MnO), the apparent activation energy of the demanganization reaction was estimated to be 189.46 kJ·mol-1 in the current study, which indicated that the mass transfer of MnO in the molten slag controlled the overall rate of the demanganization reaction. The calculated apparent activation energy was slightly lower than the values reported in the literature for mass transfer in a slag phase. This difference was attributed to an increase in the "specific reaction interface" (SRI) value, either as a result of turbulence at the reaction interface or a decrease of the absolute amount of slag phase during sampling, and to the addition of calcium fluoride to the slag.

Kinetic and theoretical studies of novel biodegradable thermo-sensitive xerogels based on PEG/PVP/silica for sustained release of enrofloxacin

NASA Astrophysics Data System (ADS)

Ebadi, Azra; Rafati, Amir Abbas; Bavafa, Sadeghali; Mohammadi, Masoumah

2017-12-01

This study involves the synthesis of a new silica-based colloidal hybrid system. In this new hybrid system, poly (ethylene glycol) (PEG) and thermo-sensitive amphiphilic biocompatible poly (vinyl pyrrolidone) (PVP) were used to create suitable storage for hydrophobic drugs. The possibility of using variable PVP/PEG molar ratios to modulate drug release rate from silica nanoparticles was a primary goal of the current research. In addition, an investigation of the drug release kinetic was conducted. To achieve this, silica nanoparticles were synthesized in poly (ethylene glycol) (PEG) and poly (vinyl pyrrolidone) (PVP) solution incorporated with enrofloxacin (EFX) (as a model hydrophobic drug), using a simple synthetic strategy of hybrid materials which avoided waste and multi-step processes. The impacts of PVP/PEG molar ratios, temperature, and pH of the release medium on release kinetic were investigated. The physicochemical properties of the drug-loaded composites were studied by Fourier transform infrared (FT-IR) spectra, scanning electron microscopy (SEM), and thermogravimetric analysis (TGA). In vitro drug release studies demonstrated that the drug release rate, which was evaluated by analyzing the experimental data with seven kinetic models in a primarily non-Fickian diffusion-controlled process, aligned well with both Ritger-Peppas and Sahlin-Peppas equations.

Computer Series, 15: Bits and Pieces, 4.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1981-01-01

Supplies short descriptions of several computer applications in the college science classroom and laboratory, including: applications; interfacing and data collection with the TRS-80; programs for activity corrections in acid/base and precipitation titration curve calculations; computer-assisted data analysis of enzyme kinetics; and microcomputer…

Maximum likelihood-based analysis of single-molecule photon arrival trajectories

NASA Astrophysics Data System (ADS)

Hajdziona, Marta; Molski, Andrzej

2011-02-01

In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 103 photons. When the intensity levels are well-separated and 104 photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

Towards the identification of Idiopathic Parkinson’s Disease from the speech. New articulatory kinetic biomarkers

PubMed Central

Shattuck-Hufnagel, S.; Choi, J. Y.; Moro-Velázquez, L.; Gómez-García, J. A.

2017-01-01

Although a large amount of acoustic indicators have already been proposed in the literature to evaluate the hypokinetic dysarthria of people with Parkinson’s Disease, the goal of this work is to identify and interpret new reliable and complementary articulatory biomarkers that could be applied to predict/evaluate Parkinson’s Disease from a diadochokinetic test, contributing to the possibility of a further multidimensional analysis of the speech of parkinsonian patients. The new biomarkers proposed are based on the kinetic behaviour of the envelope trace, which is directly linked with the articulatory dysfunctions introduced by the disease since the early stages. The interest of these new articulatory indicators stands on their easiness of identification and interpretation, and their potential to be translated into computer based automatic methods to screen the disease from the speech. Throughout this paper, the accuracy provided by these acoustic kinetic biomarkers is compared with the one obtained with a baseline system based on speaker identification techniques. Results show accuracies around 85% that are in line with those obtained with the complex state of the art speaker recognition techniques, but with an easier physical interpretation, which open the possibility to be transferred to a clinical setting. PMID:29240814

Dynamic analysis of apoptosis using cyanine SYTO probes: From classical to microfluidic cytometry

PubMed Central

Wlodkowic, Donald; Skommer, Joanna; Faley, Shannon; Darzynkiewicz, Zbigniew; Cooper, Jonathan M.

2013-01-01

Cell death is a stochastic process, often initiated and/or executed in a multi-pathway/multi-organelle fashion. Therefore, high-throughput single-cell analysis platforms are required to provide detailed characterization of kinetics and mechanisms of cell death in heterogeneous cell populations. However, there is still a largely unmet need for inert fluorescent probes, suitable for prolonged kinetic studies. Here, we compare the use of innovative adaptation of unsymmetrical SYTO dyes for dynamic real-time analysis of apoptosis in conventional as well as microfluidic chip-based systems. We show that cyanine SYTO probes allow non-invasive tracking of intracellular events over extended time. Easy handling and “stain–no wash” protocols open up new opportunities for high-throughput analysis and live-cell sorting. Furthermore, SYTO probes are easily adaptable for detection of cell death using automated microfluidic chip-based cytometry. Overall, the combined use of SYTO probes and state-of-the-art Lab-on-a-Chip platform emerges as a cost effective solution for automated drug screening compared to conventional Annexin V or TUNEL assays. In particular, it should allow for dynamic analysis of samples where low cell number has so far been an obstacle, e.g. primary cancer stems cells or circulating minimal residual tumors. PMID:19298813

Kinetic and kinematic follow‐up gait analysis in Doberman Pinschers with cervical spondylomyelopathy treated medically and surgically

PubMed Central

Smith, Rebecca L.; da Costa, Ronaldo C.

2018-01-01

Background The efficacy of treatment of dogs with cervical spondylomyelopathy (CSM) is commonly based on the owner's and clinician's perception of the gait, which is highly subjective and suffers from observer bias. Hypothesis/Objectives To compare selected kinetic and kinematic parameters before and after treatments and to correlate the findings of gait analysis to clinical outcome. Animals Eight Doberman Pinschers with CSM confirmed by magnetic resonsance imaging. Methods Patients were prospectively studied and treated with either medical management (n = 5) or surgery (n = 3). Force plate analysis and 3‐D kinematic motion capture were performed at initial presentation and approximately 8 weeks later. Force plate parameters evaluated included peak vertical force (PVF). Kinematic parameters measured included number of pelvic limb strides, stifle flexion and extension, maximum and minimum thoracic limb distance, truncal sway, and thoracic limb stride duration. Results Kinematic analysis showed that deviation of the spine to the right (truncal sway) was significantly smaller (P < .001) and the degree of right stifle flexion was significantly larger (P = .029) after treatment. Force plate analysis indicated that PVF was significantly different after treatment (P = .049) and the difference of the PVF also was significantly larger (P = .027). However, no correlation was found with either method of gait analysis and clinical recovery. Conclusions and Clinical Importance Kinetic and kinematic gait analysis were able to detect differences in dogs with CSM before and after treatment. A correlation of gait analysis to clinical improvement could not be determined. PMID:29572944

Multi-technique approach for qualitative and quantitative characterization of furazidin degradation kinetics under alkaline conditions.

PubMed

Bērziņš, Kārlis; Kons, Artis; Grante, Ilze; Dzabijeva, Diana; Nakurte, Ilva; Actiņš, Andris

2016-09-10

Degradation of drug furazidin was studied under different conditions of environmental pH (11-13) and temperature (30-60°C). The novel approach of hybrid hard- and soft-multivariate curve resolution-alternating least squares (HS-MCR-ALS) method was applied to UV-vis spectral data to determine a valid kinetic model and kinetic parameters of the degradation process. The system was found to be comprised of three main species and best characterized by two consecutive first-order reactions. Furazidin degradation rate was found to be highly dependent on the applied environmental conditions, showing more prominent differences between both degradation steps towards higher pH and temperature. Complimentary qualitative analysis of the degradation process was carried out using HPLC-DAD-TOF-MS. Based on the obtained chromatographic and mass spectrometric results, as well as additional computational analysis of the species (theoretical UV-vis spectra calculations utilizing TD-DFT methodology), the operating degradation mechanism was proposed to include formation of a 5-hydroxyfuran derivative, followed by complete hydrolysis of furazidin hydantoin ring. Copyright © 2016 Elsevier B.V. All rights reserved.

Mechanistic Kinetic Modeling of Thiol-Michael Addition Photopolymerizations via Photocaged "Superbase" Generators: An Analytical Approach.

PubMed

Claudino, Mauro; Zhang, Xinpeng; Alim, Marvin D; Podgórski, Maciej; Bowman, Christopher N

2016-11-08

A kinetic mechanism and the accompanying mathematical framework are presented for base-mediated thiol-Michael photopolymerization kinetics involving a photobase generator. Here, model kinetic predictions demonstrate excellent agreement with a representative experimental system composed of 2-(2-nitrophenyl)propyloxycarbonyl-1,1,3,3-tetramethylguanidine (NPPOC-TMG) as a photobase generator that is used to initiate thiol-vinyl sulfone Michael addition reactions and polymerizations. Modeling equations derived from a basic mechanistic scheme indicate overall polymerization rates that follow a pseudo-first-order kinetic process in the base and coreactant concentrations, controlled by the ratio of the propagation to chain-transfer kinetic parameters ( k p / k CT ) which is dictated by the rate-limiting step and controls the time necessary to reach gelation. Gelation occurs earlier as the k p / k CT ratio reaches a critical value, wherefrom gel times become nearly independent of k p / k CT . The theoretical approach allowed determining the effect of induction time on the reaction kinetics due to initial acid-base neutralization for the photogenerated base caused by the presence of protic contaminants. Such inhibition kinetics may be challenging for reaction systems that require high curing rates but are relevant for chemical systems that need to remain kinetically dormant until activated although at the ultimate cost of lower polymerization rates. The pure step-growth character of this living polymerization and the exhibited kinetics provide unique potential for extended dark-cure reactions and uniform material properties. The general kinetic model is applicable to photobase initiators where photolysis follows a unimolecular cleavage process releasing a strong base catalyst without cogeneration of intermediate radical species.

Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases

PubMed Central

Su, Yan; Guengerich, F. Peter

2016-01-01

Pre-steady-state kinetic analysis is a powerful and widely used method to obtain multiple kinetic parameters. This protocol provides a step-by-step procedure for pre-steady-state kinetic analysis of single-nucleotide incorporation by a DNA polymerase. It describes the experimental details of DNA substrate annealing, reaction mixture preparation, handling of the RQF-3 rapid quench-flow instrument, denaturing polyacrylamide DNA gel preparation, electrophoresis, quantitation, and data analysis. The core and unique part of this protocol is the rationale for preparation of the reaction mixture (the ratio of the polymerase to the DNA substrate) and methods for conducting pre-steady-state assays on an RQF-3 rapid quench-flow instrument, as well as data interpretation after analysis. In addition, the methods for the DNA substrate annealing and DNA polyacrylamide gel preparation, electrophoresis, quantitation and analysis are suitable for use in other studies. PMID:27248785

Analyzing Students’ Level of Understanding on Kinetic Theory of Gases

NASA Astrophysics Data System (ADS)

Nurhuda, T.; Rusdiana, D.; Setiawan, W.

2017-02-01

The purpose of this research is to analysis students’ level of understanding on gas kinetic theory. The method used is descriptive analytic with 32 students at the 11th grade of one high school in Bandung city as a sample. The sample was taken using random sampling technique. Data collection tool used is an essay test with 23 questions. The instrument was used to identify students’ level of understanding and was judged by four expert judges before it was employed, from 27 questions become to 23 questions, for data collection. Questions used are the conceptual understanding including the competence to explain, extrapolate, translate and interpret. Kinetic theory of gases section that was tested includes ideal gas law, kinetic molecular theory and equipartition of energy. The result shows from 0-4 level of understanding, 19% of the students have partial understanding on the 3th level and 81% of them have partial understanding with a specific misconception on 2th level. For the future research, it is suggested to overcome these conceptual understanding with an Interactive Lecture Demonstrations teaching model and coupled with some teaching materials based on multi-visualization because kinetic theory of gases is a microscopic concept.

Measurement of the Turbulence Kinetic Energy Budget of a Turbulent Planar Wake Flow in Pressure Gradients

NASA Technical Reports Server (NTRS)

Liu, Xiao-Feng; Thomas, Flint O.; Nelson, Robert C.

2001-01-01

Turbulence kinetic energy (TKE) is a very important quantity for turbulence modeling and the budget of this quantity in its transport equation can provide insight into the flow physics. Turbulence kinetic energy budget measurements were conducted for a symmetric turbulent wake flow subjected to constant zero, favorable and adverse pressure gradients in year-three of research effort. The purpose of this study is to clarify the flow physics issues underlying the demonstrated influence of pressure gradient on wake development and provide experimental support for turbulence modeling. To ensure the reliability of these notoriously difficult measurements, the experimental procedure was carefully designed on the basis of an uncertainty analysis. Four different approaches, based on an isotropic turbulence assumption, a locally axisymmetric homogeneous turbulence assumption, a semi-isotropy assumption and a forced balance of the TKE equation, were applied for the estimate of the dissipation term. The pressure transport term is obtained from a forced balance of the turbulence kinetic energy equation. This report will present the results of the turbulence kinetic energy budget measurement and discuss their implication on the development of strained turbulent wakes.

[Prostate cancer. Part 1: Review of cell kinetics over the years 1966-2015 and future perspectives of the new grading of the International Society of Urological Pathology (ISUP)].

PubMed

Helpap, B; Bubendorf, L

2016-02-01

Using tritium-labeled thymidine histoautoradiography, the AgNOR staining technique and Ki67-MIB-1 immunohistochemistry to study cell kinetics, prostate cancer can be subdivided into slowly, moderately and rapidly proliferating tumors. These are important supplementary methods and prerequisites for a grading as low, intermediate and high-grade in addition to classical histology and cytology. Cytometry of DNA can confirm the cell kinetics of prostate cancer by detection of a predominance of diploid or aneuploid cell nuclei but should only be evaluated together with histological investigations. All histology-based analyses of cell kinetics encompass the classical highly and poorly differentiated glandular and cribriform patterns as well as solid undifferentiated structures and the various subcategories. The malignancy grading of prostate cancer can result from the summation of histological grading and cell kinetic analyses, as long as the named investigations are included. The future perspectives of individualized therapy options, including active surveillance in early low-grade and also for high-grade prostate cancer and new antihormonal treatment in advanced disease, may increasingly rely on tissue biomarkers and advanced technologies for whole genome analysis including next generation sequencing.

Preparation and thermoluminescent dosimetry features of high sensitivity LiF:Mg,Ce phosphor

NASA Astrophysics Data System (ADS)

Shoushtari, M. K.; Zahedifar, M.; Sadeghi, E.

2018-04-01

Thermoluminescence (TL) kinetics and dosimetry features of newly produced LiF doped with Mg and Ce were investigated. Different contents of Mg (0-1 mol%) and Ce (0-2 mol%) were introduced in host material by melting method. The most TL sensitivity of the fabricated phosphor was obtained at 0.7 and 0.05 mol% concentrations of Mg and Ce impurities, respectively. The optimum pre-irradiation annealing regime of the synthesized LiF-based material was found at 350 °C for 10 min. Kinetic parameters of LiF:Mg,Ce dosimeter were obtained using different methods of computerized glow curve deconvolution (CGCD), initial rise (IR) and isothermal decay (ID). A good conformity are observed between the results obtained from different kinetic analysis methods. Other TL features such as fading, dose response and reusability were also examined.

Biomechanical Analysis of the Closed Kinetic Chain Upper-Extremity Stability Test.

PubMed

Tucci, Helga T; Felicio, Lilian R; McQuade, Kevin J; Bevilaqua-Grossi, Debora; Camarini, Paula Maria Ferreira; Oliveira, Anamaria S

2017-01-01

The closed kinetic chain upper-extremity stability (CKCUES) test is a functional test for the upper extremity performed in the push-up position, where individuals support their body weight on 1 hand placed on the ground and swing the opposite hand until touching the hand on the ground, then switch hands and repeat the process as fast as possible for 15 s. To study scapular kinematic and kinetic measures during the CKCUES test for 3 different distances between hands. Experimental. Laboratory. 30 healthy individuals (15 male, 15 female). Participants performed 3 repetitions of the test at 3 distance conditions: original (36 in), interacromial, and 150% interacromial distance between hands. Participants completed a questionnaire on pain intensity and perceived exertion before and after the procedures. Scapular internal/external rotation, upward/downward rotation, and posterior/anterior tilting kinematics and kinetic data on maximum force and time to maximum force were measured bilaterally in all participants. Percentage of body weight on upper extremities was calculated. Data analyses were based on the total numbers of hand touches performed for each distance condition, and scapular kinematics and kinetic values were averaged over the 3 trials. Scapular kinematics, maximum force, and time to maximum force were compared for the 3 distance conditions within each gender. Significance level was set at α = .05. Scapular internal rotation, posterior tilting, and upward rotation were significantly greater in the dominant side for both genders. Scapular upward rotation was significantly greater in original distance than interacromial distance in swing phase. Time to maximum force in women was significantly greater in the dominant side. CKCUES test kinematic and kinetic measures were not different among 3 conditions based on distance between hands. However, the test might not be suitable for initial or mild-level rehabilitation due to its challenging requirements.

Prediagnostic prostate-specific antigen kinetics and the risk of biopsy progression in active surveillance patients.

PubMed

Iremashvili, Viacheslav; Barney, Shane L; Manoharan, Murugesan; Kava, Bruce R; Parekh, Dipen J; Punnen, Sanoj

2016-04-01

To analyze the association between prediagnostic prostate-specific antigen kinetics and the risk of biopsy progression in prostate cancer patients on active surveillance, and to study the effect of prediagnostic prostate-specific antigen values on the predictive performance of prostate-specific antigen velocity and prostate-specific antigen doubling time. The study included 137 active surveillance patients with two or more prediagnostic prostate-specific antigen levels measured over a period of at least 3 months. Two sets of analyses were carried out. First, the association between prostate-specific antigen kinetics calculated using only the prediagnostic prostate-specific antigen values and the risk of biopsy progression was studied. Second, using the same cohort of patients, the predictive value of prostate-specific antigen kinetics calculated using only post-diagnostic prostate-specific antigens and compared with that of prostate-specific antigen kinetics based on both pre- and post-diagnostic prostate-specific antigen levels was analyzed. Of 137 patients included in the analysis, 37 (27%) had biopsy progression over a median follow-up period of 3.2 years. Prediagnostic prostate-specific antigen velocity of more than 2 ng/mL/year and 3 ng/mL/year was statistically significantly associated with the risk of future biopsy progression. However, after adjustment for baseline prostate-specific antigen density, these associations were no longer significant. None of the tested prostate-specific antigen kinetics based on combined pre- and post-diagnostic prostate-specific antigen values were statistically significantly associated with the risk of biopsy progression. Historical prediagnostic prostate-specific antigens seems to be not clinically useful in patients diagnosed with low-risk prostate cancer on active surveillance. © 2016 The Japanese Urological Association.

Kinetic analysis of enzyme systems with suicide substrate in the presence of a reversible competitive inhibitor, tested by simulated progress curves.

PubMed

Moruno-Dávila, M A; Garrido-del Solo, C; García-Moreno, M; Havsteen, B H; Garcia-Sevilla, F; Garcia-Cánovas, F; Varón, R

2001-02-01

The use of suicide substrates remains a very important and useful method in enzymology for studying enzyme mechanisms and designing potential drugs. Suicide substrates act as modified substrates for the target enzymes and bind to the active site. Therefore the presence of a competitive reversible inhibitor decreases the rate of substrate-induced inactivation and protects the enzyme from this inactivation. This lowering on the inactivation rate has evident physiological advantages, since it allows the easy acquisition of experimental data and facilitates kinetic data analysis by providing another variable (inhibitor concentration). However despite the importance of the simultaneous action of a suicide substrate and a competitive reversible inhibition, to date no corresponding kinetic analysis has been carried out. Therefore we present a general kinetic analysis of a Michaelis-Menten reaction mechanism with double inhibition caused by both, a suicide substrate and a competitive reversible inhibitor. We assume rapid equilibrium of the reversible reaction steps involved, while the time course equations for the reaction product have been derived with the assumption of a limiting enzyme. The goodness of the analytical solutions has been tested by comparison with the simulated curves obtained by numerical integration. A kinetic data analysis to determine the corresponding kinetic parameters from the time progress curve of the product is suggested. In conclusion, we present a complete kinetic analysis of an enzyme reaction mechanism as described above in an attempt to fill a gap in the theoretical treatment of this type of system.

Applying an intelligent model and sensitivity analysis to inspect mass transfer kinetics, shrinkage and crust color changes of deep-fat fried ostrich meat cubes.

PubMed

Amiryousefi, Mohammad Reza; Mohebbi, Mohebbat; Khodaiyan, Faramarz

2014-01-01

The objectives of this study were to use image analysis and artificial neural network (ANN) to predict mass transfer kinetics as well as color changes and shrinkage of deep-fat fried ostrich meat cubes. Two generalized feedforward networks were separately developed by using the operation conditions as inputs. Results based on the highest numerical quantities of the correlation coefficients between the experimental versus predicted values, showed proper fitting. Sensitivity analysis results of selected ANNs showed that among the input variables, frying temperature was the most sensitive to moisture content (MC) and fat content (FC) compared to other variables. Sensitivity analysis results of selected ANNs showed that MC and FC were the most sensitive to frying temperature compared to other input variables. Similarly, for the second ANN architecture, microwave power density was the most impressive variable having the maximum influence on both shrinkage percentage and color changes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling

NASA Astrophysics Data System (ADS)

Núñez, M.; Robie, T.; Vlachos, D. G.

2017-10-01

Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis

DOE PAGES

Hoffmann, Max J.; Engelmann, Felix; Matera, Sebastian

2017-01-31

Lattice kinetic Monte Carlo simulations have become a vital tool for predictive quality atomistic understanding of complex surface chemical reaction kinetics over a wide range of reaction conditions. In order to expand their practical value in terms of giving guidelines for atomic level design of catalytic systems, it is very desirable to readily evaluate a sensitivity analysis for a given model. The result of such a sensitivity analysis quantitatively expresses the dependency of the turnover frequency, being the main output variable, on the rate constants entering the model. In the past the application of sensitivity analysis, such as Degree ofmore » Rate Control, has been hampered by its exuberant computational effort required to accurately sample numerical derivatives of a property that is obtained from a stochastic simulation method. Here in this study we present an efficient and robust three stage approach that is capable of reliably evaluating the sensitivity measures for stiff microkinetic models as we demonstrate using CO oxidation on RuO 2(110) as a prototypical reaction. In a first step, we utilize the Fisher Information Matrix for filtering out elementary processes which only yield negligible sensitivity. Then we employ an estimator based on linear response theory for calculating the sensitivity measure for non-critical conditions which covers the majority of cases. Finally we adopt a method for sampling coupled finite differences for evaluating the sensitivity measure of lattice based models. This allows efficient evaluation even in critical regions near a second order phase transition that are hitherto difficult to control. The combined approach leads to significant computational savings over straightforward numerical derivatives and should aid in accelerating the nano scale design of heterogeneous catalysts.« less

A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis.

PubMed

Hoffmann, Max J; Engelmann, Felix; Matera, Sebastian

2017-01-28

Lattice kinetic Monte Carlo simulations have become a vital tool for predictive quality atomistic understanding of complex surface chemical reaction kinetics over a wide range of reaction conditions. In order to expand their practical value in terms of giving guidelines for the atomic level design of catalytic systems, it is very desirable to readily evaluate a sensitivity analysis for a given model. The result of such a sensitivity analysis quantitatively expresses the dependency of the turnover frequency, being the main output variable, on the rate constants entering the model. In the past, the application of sensitivity analysis, such as degree of rate control, has been hampered by its exuberant computational effort required to accurately sample numerical derivatives of a property that is obtained from a stochastic simulation method. In this study, we present an efficient and robust three-stage approach that is capable of reliably evaluating the sensitivity measures for stiff microkinetic models as we demonstrate using the CO oxidation on RuO 2 (110) as a prototypical reaction. In the first step, we utilize the Fisher information matrix for filtering out elementary processes which only yield negligible sensitivity. Then we employ an estimator based on the linear response theory for calculating the sensitivity measure for non-critical conditions which covers the majority of cases. Finally, we adapt a method for sampling coupled finite differences for evaluating the sensitivity measure for lattice based models. This allows for an efficient evaluation even in critical regions near a second order phase transition that are hitherto difficult to control. The combined approach leads to significant computational savings over straightforward numerical derivatives and should aid in accelerating the nano-scale design of heterogeneous catalysts.

A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis

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

Hoffmann, Max J.; Engelmann, Felix; Matera, Sebastian

Lattice kinetic Monte Carlo simulations have become a vital tool for predictive quality atomistic understanding of complex surface chemical reaction kinetics over a wide range of reaction conditions. In order to expand their practical value in terms of giving guidelines for atomic level design of catalytic systems, it is very desirable to readily evaluate a sensitivity analysis for a given model. The result of such a sensitivity analysis quantitatively expresses the dependency of the turnover frequency, being the main output variable, on the rate constants entering the model. In the past the application of sensitivity analysis, such as Degree ofmore » Rate Control, has been hampered by its exuberant computational effort required to accurately sample numerical derivatives of a property that is obtained from a stochastic simulation method. Here in this study we present an efficient and robust three stage approach that is capable of reliably evaluating the sensitivity measures for stiff microkinetic models as we demonstrate using CO oxidation on RuO 2(110) as a prototypical reaction. In a first step, we utilize the Fisher Information Matrix for filtering out elementary processes which only yield negligible sensitivity. Then we employ an estimator based on linear response theory for calculating the sensitivity measure for non-critical conditions which covers the majority of cases. Finally we adopt a method for sampling coupled finite differences for evaluating the sensitivity measure of lattice based models. This allows efficient evaluation even in critical regions near a second order phase transition that are hitherto difficult to control. The combined approach leads to significant computational savings over straightforward numerical derivatives and should aid in accelerating the nano scale design of heterogeneous catalysts.« less

A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis

NASA Astrophysics Data System (ADS)

Hoffmann, Max J.; Engelmann, Felix; Matera, Sebastian

2017-01-01

Lattice kinetic Monte Carlo simulations have become a vital tool for predictive quality atomistic understanding of complex surface chemical reaction kinetics over a wide range of reaction conditions. In order to expand their practical value in terms of giving guidelines for the atomic level design of catalytic systems, it is very desirable to readily evaluate a sensitivity analysis for a given model. The result of such a sensitivity analysis quantitatively expresses the dependency of the turnover frequency, being the main output variable, on the rate constants entering the model. In the past, the application of sensitivity analysis, such as degree of rate control, has been hampered by its exuberant computational effort required to accurately sample numerical derivatives of a property that is obtained from a stochastic simulation method. In this study, we present an efficient and robust three-stage approach that is capable of reliably evaluating the sensitivity measures for stiff microkinetic models as we demonstrate using the CO oxidation on RuO2(110) as a prototypical reaction. In the first step, we utilize the Fisher information matrix for filtering out elementary processes which only yield negligible sensitivity. Then we employ an estimator based on the linear response theory for calculating the sensitivity measure for non-critical conditions which covers the majority of cases. Finally, we adapt a method for sampling coupled finite differences for evaluating the sensitivity measure for lattice based models. This allows for an efficient evaluation even in critical regions near a second order phase transition that are hitherto difficult to control. The combined approach leads to significant computational savings over straightforward numerical derivatives and should aid in accelerating the nano-scale design of heterogeneous catalysts.

Pyrolysis characteristics and kinetics of microalgae via thermogravimetric analysis (TGA): A state-of-the-art review.

PubMed

Bach, Quang-Vu; Chen, Wei-Hsin

2017-12-01

Pyrolysis is a promising route for biofuels production from microalgae at moderate temperatures (400-600°C) in an inert atmosphere. Depending on the operating conditions, pyrolysis can produce biochar and/or bio-oil. In practice, knowledge for thermal decomposition characteristics and kinetics of microalgae during pyrolysis is essential for pyrolyzer design and pyrolysis optimization. Recently, the pyrolysis kinetics of microalgae has become a crucial topic and received increasing interest from researchers. Thermogravimetric analysis (TGA) has been employed as a proven technique for studying microalgae pyrolysis in a kinetic control regime. In addition, a number of kinetic models have been applied to process the TGA data for kinetic evaluation and parameters estimation. This paper aims to provide a state-of-the art review on recent research activities in pyrolysis characteristics and kinetics of various microalgae. Common kinetic models predicting the thermal degradation of microalgae are examined and their pros and cons are illustrated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sex-Based Differences in Knee Kinetics With Anterior Cruciate Ligament Strain on Cadaveric Impact Simulations

PubMed Central

Schilaty, Nathan D.; Bates, Nathaniel A.; Nagelli, Christopher; Krych, Aaron J.; Hewett, Timothy E.

2018-01-01

Background: Females are at an increased risk of sustaining noncontact knee ligament injuries as compared with their male counterparts. The kinetics that load the anterior cruciate ligament (ACL) are still under dispute in the literature. Purpose/Hypothesis: The purpose of this study was to determine whether there are differences in knee kinetics between the sexes that lead to greater ACL strain in females when similar external loads are applied during a simulated drop vertical jump landing task. It was hypothesized that female limbs would demonstrate significant differences in knee abduction moment that predispose females to ACL injury when compared with males. Study Design: Controlled laboratory study. Methods: Motion analysis data of 67 athletes who performed a drop vertical jump were collected. The kinematic and kinetic data were used to categorize tertiles of relative risk, and these values were input into a cadaveric impact simulator to assess ligamentous loads during the simulated landing task. Uni- and multiaxial load cells and differential variable reluctance transducer strain sensors were utilized to collect kinetic data and maximum ACL strain for analysis. Conditions of external loads applied to the cadaveric limbs were systematically varied and randomized. Data were analyzed with 2-way repeated-measures analysis of variance and the Fisher exact test. Results: Five kinetic parameters were evaluated. Of the 5 kinetic variables, only knee abduction moment (KAM) demonstrated significant differences in females as compared with males (F 1,136 = 4.398, P = .038). When normalized to height and weight, this difference between males and females increased in significance (F 1,136 = 7.155, P = .008). Compared with males, females exhibited a 10.3-N·m increased knee abduction torque at 66 milliseconds postimpact and a 22.3-N·m increased abduction torque at 100 milliseconds postimpact. For loading condition, the condition of “maximum ACL strain” demonstrated a maximum difference of 54.3-N·m increased abduction torque and 74.5-N·m increased abduction torque at 66 milliseconds postimpact. Conclusion: Under the tested conditions, increased external loads led to increased medial knee translation force, knee abduction moment, and external knee moment. Females exhibited greater forces and moments at the knee, especially at KAM, when loaded in similar conditions. As these KAM loads are associated with increased load and strain on the ACL, the sex-based differences observed in the present study may account for a portion of the underlying mechanics that predispose females to ACL injury as compared with males in a controlled simulated athletic task. Clinical Relevance: KAM increases strain to the ACL under clinically representative loading. Additionally, this work establishes the biomechanical characteristics of knee loading between sexes. PMID:29568787

Sex-Based Differences in Knee Kinetics With Anterior Cruciate Ligament Strain on Cadaveric Impact Simulations.

PubMed

Schilaty, Nathan D; Bates, Nathaniel A; Nagelli, Christopher; Krych, Aaron J; Hewett, Timothy E

2018-03-01

Females are at an increased risk of sustaining noncontact knee ligament injuries as compared with their male counterparts. The kinetics that load the anterior cruciate ligament (ACL) are still under dispute in the literature. The purpose of this study was to determine whether there are differences in knee kinetics between the sexes that lead to greater ACL strain in females when similar external loads are applied during a simulated drop vertical jump landing task. It was hypothesized that female limbs would demonstrate significant differences in knee abduction moment that predispose females to ACL injury when compared with males. Controlled laboratory study. Motion analysis data of 67 athletes who performed a drop vertical jump were collected. The kinematic and kinetic data were used to categorize tertiles of relative risk, and these values were input into a cadaveric impact simulator to assess ligamentous loads during the simulated landing task. Uni- and multiaxial load cells and differential variable reluctance transducer strain sensors were utilized to collect kinetic data and maximum ACL strain for analysis. Conditions of external loads applied to the cadaveric limbs were systematically varied and randomized. Data were analyzed with 2-way repeated-measures analysis of variance and the Fisher exact test. Five kinetic parameters were evaluated. Of the 5 kinetic variables, only knee abduction moment (KAM) demonstrated significant differences in females as compared with males ( F 1,136 = 4.398, P = .038). When normalized to height and weight, this difference between males and females increased in significance ( F 1,136 = 7.155, P = .008). Compared with males, females exhibited a 10.3-N·m increased knee abduction torque at 66 milliseconds postimpact and a 22.3-N·m increased abduction torque at 100 milliseconds postimpact. For loading condition, the condition of "maximum ACL strain" demonstrated a maximum difference of 54.3-N·m increased abduction torque and 74.5-N·m increased abduction torque at 66 milliseconds postimpact. Under the tested conditions, increased external loads led to increased medial knee translation force, knee abduction moment, and external knee moment. Females exhibited greater forces and moments at the knee, especially at KAM, when loaded in similar conditions. As these KAM loads are associated with increased load and strain on the ACL, the sex-based differences observed in the present study may account for a portion of the underlying mechanics that predispose females to ACL injury as compared with males in a controlled simulated athletic task. KAM increases strain to the ACL under clinically representative loading. Additionally, this work establishes the biomechanical characteristics of knee loading between sexes.

Predicting axillary lymph node metastasis from kinetic statistics of DCE-MRI breast images

NASA Astrophysics Data System (ADS)

Ashraf, Ahmed B.; Lin, Lilie; Gavenonis, Sara C.; Mies, Carolyn; Xanthopoulos, Eric; Kontos, Despina

2012-03-01

The presence of axillary lymph node metastases is the most important prognostic factor in breast cancer and can influence the selection of adjuvant therapy, both chemotherapy and radiotherapy. In this work we present a set of kinetic statistics derived from DCE-MRI for predicting axillary node status. Breast DCE-MRI images from 69 women with known nodal status were analyzed retrospectively under HIPAA and IRB approval. Axillary lymph nodes were positive in 12 patients while 57 patients had no axillary lymph node involvement. Kinetic curves for each pixel were computed and a pixel-wise map of time-to-peak (TTP) was obtained. Pixels were first partitioned according to the similarity of their kinetic behavior, based on TTP values. For every kinetic curve, the following pixel-wise features were computed: peak enhancement (PE), wash-in-slope (WIS), wash-out-slope (WOS). Partition-wise statistics for every feature map were calculated, resulting in a total of 21 kinetic statistic features. ANOVA analysis was done to select features that differ significantly between node positive and node negative women. Using the computed kinetic statistic features a leave-one-out SVM classifier was learned that performs with AUC=0.77 under the ROC curve, outperforming the conventional kinetic measures, including maximum peak enhancement (MPE) and signal enhancement ratio (SER), (AUCs of 0.61 and 0.57 respectively). These findings suggest that our DCE-MRI kinetic statistic features can be used to improve the prediction of axillary node status in breast cancer patients. Such features could ultimately be used as imaging biomarkers to guide personalized treatment choices for women diagnosed with breast cancer.

A numerical investigation of the scale-up effects on flow, heat transfer, and kinetics processes of FCC units.

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

Chang, S. L.

1998-08-25

Fluid Catalytic Cracking (FCC) technology is the most important process used by the refinery industry to convert crude oil to valuable lighter products such as gasoline. Process development is generally very time consuming especially when a small pilot unit is being scaled-up to a large commercial unit because of the lack of information to aide in the design of scaled-up units. Such information can now be obtained by analysis based on the pilot scale measurements and computer simulation that includes controlling physics of the FCC system. A Computational fluid dynamic (CFD) code, ICRKFLO, has been developed at Argonne National Laboratorymore » (ANL) and has been successfully applied to the simulation of catalytic petroleum cracking risers. It employs hybrid hydrodynamic-chemical kinetic coupling techniques, enabling the analysis of an FCC unit with complex chemical reaction sets containing tens or hundreds of subspecies. The code has been continuously validated based on pilot-scale experimental data. It is now being used to investigate the effects of scaled-up FCC units. Among FCC operating conditions, the feed injection conditions are found to have a strong impact on the product yields of scaled-up FCC units. The feed injection conditions appear to affect flow and heat transfer patterns and the interaction of hydrodynamics and cracking kinetics causes the product yields to change accordingly.« less

Principal component analysis acceleration of rovibrational coarse-grain models for internal energy excitation and dissociation

NASA Astrophysics Data System (ADS)

Bellemans, Aurélie; Parente, Alessandro; Magin, Thierry

2018-04-01

The present work introduces a novel approach for obtaining reduced chemistry representations of large kinetic mechanisms in strong non-equilibrium conditions. The need for accurate reduced-order models arises from compression of large ab initio quantum chemistry databases for their use in fluid codes. The method presented in this paper builds on existing physics-based strategies and proposes a new approach based on the combination of a simple coarse grain model with Principal Component Analysis (PCA). The internal energy levels of the chemical species are regrouped in distinct energy groups with a uniform lumping technique. Following the philosophy of machine learning, PCA is applied on the training data provided by the coarse grain model to find an optimally reduced representation of the full kinetic mechanism. Compared to recently published complex lumping strategies, no expert judgment is required before the application of PCA. In this work, we will demonstrate the benefits of the combined approach, stressing its simplicity, reliability, and accuracy. The technique is demonstrated by reducing the complex quantum N2(g+1Σ) -N(S4u ) database for studying molecular dissociation and excitation in strong non-equilibrium. Starting from detailed kinetics, an accurate reduced model is developed and used to study non-equilibrium properties of the N2(g+1Σ) -N(S4u ) system in shock relaxation simulations.

Study of subgrid-scale velocity models for reacting and nonreacting flows

NASA Astrophysics Data System (ADS)

Langella, I.; Doan, N. A. K.; Swaminathan, N.; Pope, S. B.

2018-05-01

A study is conducted to identify advantages and limitations of existing large-eddy simulation (LES) closures for the subgrid-scale (SGS) kinetic energy using a database of direct numerical simulations (DNS). The analysis is conducted for both reacting and nonreacting flows, different turbulence conditions, and various filter sizes. A model, based on dissipation and diffusion of momentum (LD-D model), is proposed in this paper based on the observed behavior of four existing models. Our model shows the best overall agreements with DNS statistics. Two main investigations are conducted for both reacting and nonreacting flows: (i) an investigation on the robustness of the model constants, showing that commonly used constants lead to a severe underestimation of the SGS kinetic energy and enlightening their dependence on Reynolds number and filter size; and (ii) an investigation on the statistical behavior of the SGS closures, which suggests that the dissipation of momentum is the key parameter to be considered in such closures and that dilatation effect is important and must be captured correctly in reacting flows. Additional properties of SGS kinetic energy modeling are identified and discussed.

Crystallization processes in Ge{sub 2}Sb{sub 2}Se{sub 4}Te glass

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

Svoboda, Roman, E-mail: roman.svoboda@upce.cz; Bezdička, Petr; Gutwirth, Jan

2015-01-15

Highlights: • Crystallization kinetics of Ge{sub 2}Sb{sub 2}Se{sub 4}Te glass was studied in dependence on particle size by DSC. • All studied fractions were described in terms of the SB autocatalytic model. • Relatively high amount of Te enhances manifestation of bulk crystallization mechanisms. • XRD analysis of samples crystallized under different conditions showed correlation with DSC data. • XRD analysis revealed a new crystallization mechanism indistinguishable by DSC. - Abstract: Differential scanning calorimetry (DSC) and X-ray diffraction (XRD) analysis were used to study crystallization in Ge{sub 2}Sb{sub 2}Se{sub 4}Te glass under non-isothermal conditions as a function of the particlemore » size. The crystallization kinetics was described in terms of the autocatalytic Šesták–Berggren model. An extensive discussion of all aspects of a full-scale kinetic study of a crystallization process was undertaken. Dominance of the crystallization process originating from mechanically induced strains and heterogeneities was confirmed. Substitution of Se by Te was found to enhance the manifestation of the bulk crystallization mechanisms (at the expense of surface crystallization). The XRD analysis showed significant dependence of the crystalline structural parameters on the crystallization conditions (initial particle size of the glassy grains and applied heating rate). Based on this information, a new microstructural crystallization mechanism, indistinguishable by DSC, was proposed.« less

Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway.

PubMed

Dana, Saswati; Nakakuki, Takashi; Hatakeyama, Mariko; Kimura, Shuhei; Raha, Soumyendu

2011-01-01

Mutation and/or dysfunction of signaling proteins in the mitogen activated protein kinase (MAPK) signal transduction pathway are frequently observed in various kinds of human cancer. Consistent with this fact, in the present study, we experimentally observe that the epidermal growth factor (EGF) induced activation profile of MAP kinase signaling is not straightforward dose-dependent in the PC3 prostate cancer cells. To find out what parameters and reactions in the pathway are involved in this departure from the normal dose-dependency, a model-based pathway analysis is performed. The pathway is mathematically modeled with 28 rate equations yielding those many ordinary differential equations (ODE) with kinetic rate constants that have been reported to take random values in the existing literature. This has led to us treating the ODE model of the pathways kinetics as a random differential equations (RDE) system in which the parameters are random variables. We show that our RDE model captures the uncertainty in the kinetic rate constants as seen in the behavior of the experimental data and more importantly, upon simulation, exhibits the abnormal EGF dose-dependency of the activation profile of MAP kinase signaling in PC3 prostate cancer cells. The most likely set of values of the kinetic rate constants obtained from fitting the RDE model into the experimental data is then used in a direct transcription based dynamic optimization method for computing the changes needed in these kinetic rate constant values for the restoration of the normal EGF dose response. The last computation identifies the parameters, i.e., the kinetic rate constants in the RDE model, that are the most sensitive to the change in the EGF dose response behavior in the PC3 prostate cancer cells. The reactions in which these most sensitive parameters participate emerge as candidate drug targets on the signaling pathway. 2011 Elsevier Ireland Ltd. All rights reserved.

Synthetic spectral analysis of a kinetic model for slow-magnetosonic waves in solar corona

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

Ruan, Wenzhi; He, Jiansen; Tu, Chuanyi

We propose a kinetic model of slow-magnetosonic waves to explain various observational features associated with the propagating intensity disturbances (PIDs) occurring in the solar corona. The characteristics of slow mode waves, e.g, inphase oscillations of density, velocity, and thermal speed, are reproduced in this kinetic model. Moreover, the red-blue (R-B) asymmetry of the velocity distribution as self-consistently generated in the model is found to be contributed from the beam component, as a result of the competition between Landau resonance and Coulomb collisions. Furthermore, we synthesize the spectral lines and make the spectral analysis, based on the kinetic simulation data ofmore » the flux tube plasmas and the hypothesis of the surrounding background plasmas. It is found that the fluctuations of parameters of the synthetic spectral lines are basically consistent with the observations: (1) the line intensity, Doppler shift, and line width are fluctuating in phase; (2) the R-B asymmetry usually oscillate out of phase with the former three parameters; (3) the blueward asymmetry is more evident than the redward asymmetry in the R-B fluctuations. The oscillations of line parameters become weakened for the case with denser surrounding background plasmas. Similar to the observations, there is no doubled-frequency oscillation of the line width for the case with flux-tube plasmas flowing bulkly upward among the static background plasmas. Therefore, we suggest that the “wave + beam flow” kinetic model may be a viable interpretation for the PIDs observed in the solar corona.« less

Physical stability and recrystallization kinetics of amorphous ibipinabant drug product by fourier transform raman spectroscopy.

PubMed

Sinclair, Wayne; Leane, Michael; Clarke, Graham; Dennis, Andrew; Tobyn, Mike; Timmins, Peter

2011-11-01

The solid-state physical stability and recrystallization kinetics during storage stability are described for an amorphous solid dispersed drug substance, ibipinabant, at a low concentration (1.0%, w/w) in a solid oral dosage form (tablet). The recrystallization behavior of the amorphous ibipinabant-polyvinylpyrrolidone solid dispersion in the tablet product was characterized by Fourier transform (FT) Raman spectroscopy. A partial least-square analysis used for multivariate calibration based on Raman spectra was developed and validated to detect less than 5% (w/w) of the crystalline form (equivalent to less than 0.05% of the total mass of the tablet). The method provided reliable and highly accurate predictive crystallinity assessments after exposure to a variety of stability storage conditions. It was determined that exposure to moisture had a significant impact on the crystallinity of amorphous ibipinabant. The information provided by the method has potential utility for predictive physical stability assessments. Dissolution testing demonstrated that the predicted crystallinity had a direct correlation with this physical property of the drug product. Recrystallization kinetics was measured using FT Raman spectroscopy for the solid dispersion from the tablet product stored at controlled temperature and relative humidity. The measurements were evaluated by application of the Johnson-Mehl-Avrami (JMA) kinetic model to determine recrystallization rate constants and Avrami exponent (n = 2). The analysis showed that the JMA equation could describe the process very well, and indicated that the recrystallization kinetics observed was a two-step process with an induction period (nucleation) followed by rod-like crystal growth. Copyright © 2011 Wiley-Liss, Inc.

Hafnium-Based Bulk Metallic Glasses for Kinetic Energy Penetrators

DTIC Science & Technology

2004-12-01

uranium -based (DU) and tungsten- nickel -iron (W-Ni-Fe) composite kinetic energy (KE) munitions is primarily ascribed to their high densities (U: ρ...based on an invariant point identified in the hafnium- copper- nickel ternary system. They are denser than zirconium-based glass-forming compositions...depleted- uranium penetrators. 1. INTRODUCTION 1.1 Criterion for Effective Kinetic Energy Penetrator Performance The lethality of depleted

Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution

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

Kim, Sun Mo, E-mail: Sunmo.Kim@rmp.uhn.on.ca; Haider, Masoom A.; Jaffray, David A.

Purpose: A previously proposed method to reduce radiation dose to patient in dynamic contrast-enhanced (DCE) CT is enhanced by principal component analysis (PCA) filtering which improves the signal-to-noise ratio (SNR) of time-concentration curves in the DCE-CT study. The efficacy of the combined method to maintain the accuracy of kinetic parameter estimates at low temporal resolution is investigated with pixel-by-pixel kinetic analysis of DCE-CT data. Methods: The method is based on DCE-CT scanning performed with low temporal resolution to reduce the radiation dose to the patient. The arterial input function (AIF) with high temporal resolution can be generated with a coarselymore » sampled AIF through a previously published method of AIF estimation. To increase the SNR of time-concentration curves (tissue curves), first, a region-of-interest is segmented into squares composed of 3 × 3 pixels in size. Subsequently, the PCA filtering combined with a fraction of residual information criterion is applied to all the segmented squares for further improvement of their SNRs. The proposed method was applied to each DCE-CT data set of a cohort of 14 patients at varying levels of down-sampling. The kinetic analyses using the modified Tofts’ model and singular value decomposition method, then, were carried out for each of the down-sampling schemes between the intervals from 2 to 15 s. The results were compared with analyses done with the measured data in high temporal resolution (i.e., original scanning frequency) as the reference. Results: The patients’ AIFs were estimated to high accuracy based on the 11 orthonormal bases of arterial impulse responses established in the previous paper. In addition, noise in the images was effectively reduced by using five principal components of the tissue curves for filtering. Kinetic analyses using the proposed method showed superior results compared to those with down-sampling alone; they were able to maintain the accuracy in the quantitative histogram parameters of volume transfer constant [standard deviation (SD), 98th percentile, and range], rate constant (SD), blood volume fraction (mean, SD, 98th percentile, and range), and blood flow (mean, SD, median, 98th percentile, and range) for sampling intervals between 10 and 15 s. Conclusions: The proposed method of PCA filtering combined with the AIF estimation technique allows low frequency scanning for DCE-CT study to reduce patient radiation dose. The results indicate that the method is useful in pixel-by-pixel kinetic analysis of DCE-CT data for patients with cervical cancer.« less

Application of Petri net based analysis techniques to signal transduction pathways.

PubMed

Sackmann, Andrea; Heiner, Monika; Koch, Ina

2006-11-02

Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules.

Application of Petri net based analysis techniques to signal transduction pathways

PubMed Central

Sackmann, Andrea; Heiner, Monika; Koch, Ina

2006-01-01

Background Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. Methods We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. Results We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. Conclusion The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules. PMID:17081284

Nucleation and Growth Kinetics from LaMer Burst Data.

PubMed

Chu, Daniel B K; Owen, Jonathan S; Peters, Baron

2017-10-12

In LaMer burst nucleation, the individual nucleation events happen en masse, quasi-simultaneously, and at nearly identical homogeneous conditions. These properties make LaMer burst nucleation important for applications that require monodispersed particles and also for theoretical analyses. Sugimoto and co-workers predicted that the number of nuclei generated during a LaMer burst depends only on the solute supply rate and the growth rate, independent of the nucleation kinetics. Some experiments confirm that solute supply kinetics control the number of nuclei, but flaws in the original theoretical analysis raise questions about the predicted roles of growth and nucleation kinetics. We provide a rigorous analysis of the coupled equations that govern concentrations of nuclei and solutes. Our analysis confirms that the number of nuclei is largely determined by the solute supply and growth rates, but our predicted relationship differs from that of Sugimoto et al. Moreover, we find that additional nucleus size dependent corrections should emerge in systems with slow growth kinetics. Finally, we show how the nucleation kinetics determine the particle size distribution. We suggest that measured particle size distributions might therefore provide ways to test theoretical models of homogeneous nucleation kinetics.

Piezoresistive microcantilever aptasensor for ricin detection and kinetic analysis

NASA Astrophysics Data System (ADS)

Liu, Zhi-Wei; Tong, Zhao-Yang; Liu, Bing; Hao, Lan-Qun; Mu, Xi-Hui; Zhang, Jin-Ping; Gao, Chuan

2015-04-01

Up to now, there has been no report on target molecules detection by a piezoresistive microcantilever aptasensor. In order to evaluate the test performance and investigate the response dynamic characteristics of a piezoresistive microcantilever aptasensor, a novel method for ricin detection and kinetic analysis based on a piezoresistive microcantilever aptasensor was proposed, where ricin aptamer was immobilised on the microcantilever surface by biotin-avidin binding system. Results showed that the detection limit of ricin was 0.04μg L-1 (S/N ≥ 3). A linear relationship between the response voltage and the concentration of ricin in the range of 0.2μg L-1-40μg L-1 was obtained, with the linear regression equation of ΔUe = 0.904C + 5.852 (n = 5, R = 0.991, p < 0.001). The sensor showed no response for abrin, BSA, and could overcome the influence of complex environmental disruptors, indicating high specificity and good selectivity. Recovery and reproducibility in the result of simulated samples (simulated water, soil, and flour sample) determination met the analysis requirements, which was 90.5˜95.5% and 7.85%˜9.39%, respectively. On this basis, a reaction kinetic model based on ligand-receptor binding and the relationship with response voltage was established. The model could well reflect the dynamic response of the sensor. The correlation coefficient (R) was greater than or equal to 0.9456 (p < 0.001). Response voltage (ΔUe) and response time (t0) obtained from the fitting equation on different concentrations of ricin fitted well with the measured values.

Computerized breast parenchymal analysis on DCE-MRI

NASA Astrophysics Data System (ADS)

Li, Hui; Giger, Maryellen L.; Yuan, Yading; Jansen, Sanaz A.; Lan, Li; Bhooshan, Neha; Newstead, Gillian M.

2009-02-01

Breast density has been shown to be associated with the risk of developing breast cancer, and MRI has been recommended for high-risk women screening, however, it is still unknown how the breast parenchymal enhancement on DCE-MRI is associated with breast density and breast cancer risk. Ninety-two DCE-MRI exams of asymptomatic women with normal MR findings were included in this study. The 3D breast volume was automatically segmented using a volume-growing based algorithm. The extracted breast volume was classified into fibroglandular and fatty regions based on the discriminant analysis method. The parenchymal kinetic curves within the breast fibroglandular region were extracted and categorized by use of fuzzy c-means clustering, and various parenchymal kinetic characteristics were extracted from the most enhancing voxels. Correlation analysis between the computer-extracted percent dense measures and radiologist-noted BIRADS density ratings yielded a correlation coefficient of 0.76 (p<0.0001). From kinetic analyses, 70% (64/92) of most enhancing curves showed persistent curve type and reached peak parenchymal intensity at the last postcontrast time point; with 89% (82/92) of most enhancing curves reaching peak intensity at either 4th or 5th post-contrast time points. Women with dense breast (BIRADS 3 and 4) were found to have more parenchymal enhancement at their peak time point (Ep) with an average Ep of 116.5% while those women with fatty breasts (BIRADS 1 and 2) demonstrated an average Ep of 62.0%. In conclusion, breast parenchymal enhancement may be associated with breast density and may be potential useful as an additional characteristic for assessing breast cancer risk.

Sparger system for MMH-helium vents

NASA Technical Reports Server (NTRS)

Rakow, A.

1983-01-01

Based on a calculated vent flow rate and MMH concentration, a TI-59 program was run to determine total sparger hole area for a given sparger inlet pressure. Hole diameter is determined from a mass transfer analysis in the holding tank to achieve complete capture of MMH. In addition, based on oxidation kinetics and vapor pressure data, MMh atmospheric concentrations are determined 2 ft above the holding tank.

Utilization of physicochemical variables developed from changes in sensory attributes and consumer acceptability to predict the shelf life of fresh-cut mango fruit.

PubMed

Salinas-Hernández, Rosa María; González-Aguilar, Gustavo A; Tiznado-Hernández, Martín Ernesto

2015-01-01

Sensory evaluation is the ideal tool for shelf-life determination. With the objective to develop an easy shelf-life indicator, color (L*, a*, b*, chroma and hue angle), total soluble solids (TSS), firmness (F), pH, acidity, and the sensory attributes of appearance, brightness, browning, odor, flavor, texture, color, acidity and sweetness were evaluated in fresh cut mangoes (FCM) stored at 5, 10, 15 and 20 °C. Overall acceptability was evaluated by consumers. Correlation analysis between sensory attributes and physicochemical variables was carried out. Physicochemical cut-off points based on sensory attributes and consumer acceptability was obtained by regression analysis and utilized to estimate FCM shelf-life by kinetic models fitted to each variable. The validation of the model was done by comparing the shelf life estimated by kinetic models and consumers. It was recorded large correlations between appearance, brightness, and color with L*; appearance and color with chroma and hue angle; sweetness and flavor with TSS, and between F and texture. The shelf life estimated based on consumer using a 9 point hedonic scale was in the range of 10-12, 2.3-2.6, 1.3-1.5 and 1.0-1.1 days for 5, 10, 15 and 20 °C. It was recorded large correlation coefficients between the shelf life estimated by consumer acceptability scores and physicochemical variables. Kinetic models based on physicochemical variables showed a tendency to overestimate the shelf life as compared with the models bases on the sensory attributes. It was concluded that physicochemical variables can be used as a tool to estimate the FCM shelf life.

An analysis of OH excited state absorption lines in DR 21 and K3-50

NASA Astrophysics Data System (ADS)

Jones, K. N.; Doel, R. C.; Field, D.; Gray, M. D.; Walker, R. N. F.

1992-10-01

We present an analysis of the OH absorption line zones observed toward the compact H II regions DR 21 and K3-50. Using as parameters the kinetic and dust temperatures, the H2 number density and the ratio of OH-H2 number densities to the velocity gradient, the model quantitatively reproduces the absorption line data for the six main line transitions in 2 Pi3/2 J = 5/2, 7/2, and 9/2. Observed upper limits for the absorption or emission in the satellite lines of 2 Pi3/2 J = 5/2 are crucial in constraining the range of derived parameters. Physical conditions derived for DR 21 show that the kinetic temperature centers around 140 K, the H2 number density around 10 exp 7/cu cm, and that the OH column density in the excited state absorption zone lies between 1 x 10 exp 15/sq cm and 2 x 10 exp 15/sq cm. Including contributions from a J = 3/2 absorption zone, the total OH column density is more than a factor of 2 lower than estimates based upon LTE (Walmsley et al., 1986). The OH absorption zone in K3-50 tends toward higher density and displays a larger column density, while the kinetic temperature is similar. For both sources, the dust temperature is found to be significantly lower than the kinetic temperature.

Microstructure-Property Correlation in Magnesium-based Hydrogen Storage Systems: The Case for Ball-milled Magnesium Hydride Powder and Magnesium-based Multilayered Composites

NASA Astrophysics Data System (ADS)

Danaie, Mohsen

The main focus of this thesis is the characterization of defects and microstructure in high-energy ball milled magnesium hydride powder and magnesium-based multilayered composites. Enhancement in kinetics of hydrogen cycling in magnesium can be achieved by applying severe plastic deformation. A literature survey reveals that, due to extreme instability of alpha-MgH 2 in transmission electron microscope (TEM), the physical parameters that researchers have studied are limited to particle size and grain size. By utilizing a cryogenic TEM sample holder, we extended the stability time of the hydride phase during TEM characterization. Milling for only 30 minutes resulted in a significant enhancement in desorption kinetics. A subsequent annealing cycle under pressurized hydrogen reverted the kinetics to its initial sluggish state. Cryo-TEM analysis of the milled hydride revealed that mechanical milling induces deformation twinning in the hydride microstructure. Milling did not alter the thermodynamics of desorption. Twins can enhance the kinetics by acting as preferential locations for the heterogeneous nucleation of metallic magnesium. We also looked at the phase transformation characteristics of desorption in MgH2. By using energy-filtered TEM, we investigated the morphology of the phases in a partially desorbed state. Our observations prove that desorption phase transformation in MgH2 is of "nucleation and growth" type, with a substantial energy barrier for nucleation. This is contrary to the generally assumed "core-shell" structure in most of the simulation models for this system. We also tested the hydrogen storage cycling behavior of bulk centimeter-scale Mg-Ti and Mg-SS multilayer composites synthesized by accumulative roll-bonding. Addition of either phase (Ti or SS) allows the reversible hydrogen sorption at 350°C, whereas identically roll-bonded pure magnesium cannot be absorbed. In the composites the first cycle of absorption (also called "activation") kinetics improve with increased number of fold and roll (FR) operations. With increasing FR operations the distribution of the Ti phase is progressively refined, and the shape of the absorption curve no longer remains sigmoidal. Up to a point, increasing the loading amount of the second phase also accelerates the kinetics. Microscopy analysis performed on 1--2 wt.% hydrogen absorbed composites demonstrates that MgH 2 formed exclusively on various heterogeneous nucleation sites. During activation, MgH2 nucleation occurred at the Mg-hard phase interfaces. On the subsequent absorption cycles, heterogeneous nucleation primarily occurred in the vicinity of "internal" free surfaces such as cracks.

Kinetic energy budgets in areas of intense convection

NASA Technical Reports Server (NTRS)

Fuelberg, H. E.; Berecek, E. M.; Ebel, D. M.; Jedlovec, G. J.

1980-01-01

A kinetic energy budget analysis of the AVE-SESAME 1 period which coincided with the deadly Red River Valley tornado outbreak is presented. Horizontal flux convergence was found to be the major kinetic energy source to the region, while cross contour destruction was the major sink. Kinetic energy transformations were dominated by processes related to strong jet intrusion into the severe storm area. A kinetic energy budget of the AVE 6 period also is presented. The effects of inherent rawinsonde data errors on widely used basic kinematic parameters, including velocity divergence, vorticity advection, and kinematic vertical motion are described. In addition, an error analysis was performed in terms of the kinetic energy budget equation. Results obtained from downward integration of the continuity equation to obtain kinematic values of vertical motion are described. This alternate procedure shows promising results in severe storm situations.

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

Aghaei, Faranak; Tan, Maxine; Liu, Hong

Purpose: To identify a new clinical marker based on quantitative kinetic image features analysis and assess its feasibility to predict tumor response to neoadjuvant chemotherapy. Methods: The authors assembled a dataset involving breast MR images acquired from 68 cancer patients before undergoing neoadjuvant chemotherapy. Among them, 25 patients had complete response (CR) and 43 had partial and nonresponse (NR) to chemotherapy based on the response evaluation criteria in solid tumors. The authors developed a computer-aided detection scheme to segment breast areas and tumors depicted on the breast MR images and computed a total of 39 kinetic image features from bothmore » tumor and background parenchymal enhancement regions. The authors then applied and tested two approaches to classify between CR and NR cases. The first one analyzed each individual feature and applied a simple feature fusion method that combines classification results from multiple features. The second approach tested an attribute selected classifier that integrates an artificial neural network (ANN) with a wrapper subset evaluator, which was optimized using a leave-one-case-out validation method. Results: In the pool of 39 features, 10 yielded relatively higher classification performance with the areas under receiver operating characteristic curves (AUCs) ranging from 0.61 to 0.78 to classify between CR and NR cases. Using a feature fusion method, the maximum AUC = 0.85 ± 0.05. Using the ANN-based classifier, AUC value significantly increased to 0.96 ± 0.03 (p < 0.01). Conclusions: This study demonstrated that quantitative analysis of kinetic image features computed from breast MR images acquired prechemotherapy has potential to generate a useful clinical marker in predicting tumor response to chemotherapy.« less

Quantitative kinetic analysis of lung nodules by temporal subtraction technique in dynamic chest radiography with a flat panel detector

NASA Astrophysics Data System (ADS)

Tsuchiya, Yuichiro; Kodera, Yoshie; Tanaka, Rie; Sanada, Shigeru

2007-03-01

Early detection and treatment of lung cancer is one of the most effective means to reduce cancer mortality; chest X-ray radiography has been widely used as a screening examination or health checkup. The new examination method and the development of computer analysis system allow obtaining respiratory kinetics by the use of flat panel detector (FPD), which is the expanded method of chest X-ray radiography. Through such changes functional evaluation of respiratory kinetics in chest has become available. Its introduction into clinical practice is expected in the future. In this study, we developed the computer analysis algorithm for the purpose of detecting lung nodules and evaluating quantitative kinetics. Breathing chest radiograph obtained by modified FPD was converted into 4 static images drawing the feature, by sequential temporal subtraction processing, morphologic enhancement processing, kinetic visualization processing, and lung region detection processing, after the breath synchronization process utilizing the diaphragmatic analysis of the vector movement. The artificial neural network used to analyze the density patterns detected the true nodules by analyzing these static images, and drew their kinetic tracks. For the algorithm performance and the evaluation of clinical effectiveness with 7 normal patients and simulated nodules, both showed sufficient detecting capability and kinetic imaging function without statistically significant difference. Our technique can quantitatively evaluate the kinetic range of nodules, and is effective in detecting a nodule on a breathing chest radiograph. Moreover, the application of this technique is expected to extend computer-aided diagnosis systems and facilitate the development of an automatic planning system for radiation therapy.

How Kinetics within the Unfolded State Affects Protein Folding: an Analysis Based on Markov State Models and an Ultra-Long MD Trajectory

PubMed Central

Deng, Nan-jie; Dai, Wei

2013-01-01

Understanding how kinetics in the unfolded state affects protein folding is a fundamentally important yet less well-understood issue. Here we employ three different models to analyze the unfolded landscape and folding kinetics of the miniprotein Trp-cage. The first is a 208 μs explicit solvent molecular dynamics (MD) simulation from D. E. Shaw Research containing tens of folding events. The second is a Markov state model (MSM-MD) constructed from the same ultra-long MD simulation; MSM-MD can be used to generate thousands of folding events. The third is a Markov state model built from temperature replica exchange MD simulations in implicit solvent (MSM-REMD). All the models exhibit multiple folding pathways, and there is a good correspondence between the folding pathways from direct MD and those computed from the MSMs. The unfolded populations interconvert rapidly between extended and collapsed conformations on time scales ≤ 40 ns, compared with the folding time of ≈ 5 μs. The folding rates are independent of where the folding is initiated from within the unfolded ensemble. About 90 % of the unfolded states are sampled within the first 40 μs of the ultra-long MD trajectory, which on average explores ~27 % of the unfolded state ensemble between consecutive folding events. We clustered the folding pathways according to structural similarity into “tubes”, and kinetically partitioned the unfolded state into populations that fold along different tubes. From our analysis of the simulations and a simple kinetic model, we find that when the mixing within the unfolded state is comparable to or faster than folding, the folding waiting times for all the folding tubes are similar and the folding kinetics is essentially single exponential despite the presence of heterogeneous folding paths with non-uniform barriers. When the mixing is much slower than folding, different unfolded populations fold independently leading to non-exponential kinetics. A kinetic partition of the Trp-cage unfolded state is constructed which reveals that different unfolded populations have almost the same probability to fold along any of the multiple folding paths. We are investigating whether the results for the kinetics in the unfolded state of the twenty-residue Trp-cage is representative of larger single domain proteins. PMID:23705683

Quantifying heterogeneity of lesion uptake in dynamic contrast enhanced MRI for breast cancer diagnosis

NASA Astrophysics Data System (ADS)

Karahaliou, A.; Vassiou, K.; Skiadopoulos, S.; Kanavou, T.; Yiakoumelos, A.; Costaridou, L.

2009-07-01

The current study investigates whether texture features extracted from lesion kinetics feature maps can be used for breast cancer diagnosis. Fifty five women with 57 breast lesions (27 benign, 30 malignant) were subjected to dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) on 1.5T system. A linear-slope model was fitted pixel-wise to a representative lesion slice time series and fitted parameters were used to create three kinetic maps (wash out, time to peak enhancement and peak enhancement). 28 grey level co-occurrence matrices features were extracted from each lesion kinetic map. The ability of texture features per map in discriminating malignant from benign lesions was investigated using a Probabilistic Neural Network classifier. Additional classification was performed by combining classification outputs of most discriminating feature subsets from the three maps, via majority voting. The combined scheme outperformed classification based on individual maps achieving area under Receiver Operating Characteristics curve 0.960±0.029. Results suggest that heterogeneity of breast lesion kinetics, as quantified by texture analysis, may contribute to computer assisted tissue characterization in DCE-MRI.

Thermoluminescence glow curve deconvolution and trapping parameters determination of dysprosium doped magnesium borate glass

NASA Astrophysics Data System (ADS)

Salama, E.; Soliman, H. A.

2018-07-01

In this paper, thermoluminescence glow curves of gamma irradiated magnesium borate glass doped with dysprosium were studied. The number of interfering peaks and in turn the number of electron trap levels are determined using the Repeated Initial Rise (RIR) method. At different heating rates (β), the glow curves were deconvoluted into two interfering peaks based on the results of RIR method. Kinetic parameters such as trap depth, kinetic order (b) and frequency factor (s) for each electron trap level is determined using the Peak Shape (PS) method. The obtained results indicated that, the magnesium borate glass doped with dysprosium has two electron trap levels with the average depth energies of 0.63 and 0.79 eV respectively. These two traps have second order kinetic and are formed at low temperature region. The obtained results due to the glow curve analysis could be used to explain some observed properties such as, high thermal fading and light sensitivity for such thermoluminescence material. In this work, systematic procedures to determine the kinetic parameters of any thermoluminescence material are successfully introduced.

Kinetic study of nickel laterite reduction roasting by palm kernel shell charcoal

NASA Astrophysics Data System (ADS)

Sugiarto, E.; Putera, A. D. P.; Petrus, H. T. B. M.

2017-05-01

Demand to process nickel-bearing laterite ore increase as continuous depletion of high-grade nickel-bearing sulfide ore takes place. Due to its common nickel association with iron, processing nickel laterite ore into nickel pig iron (NPI) has been developed by some industries. However, to achieve satisfying nickel recoveries, the process needs massive high-grade metallurgical coke consumption. Concerning on the sustainability of coke supply and positive carbon emission, reduction of nickel laterite ore using biomass-based reductor was being studied.In this study, saprolitic nickel laterite ore was being reduced by palm kernel shell charcoal at several temperatures (800-1000 °C). Variation of biomass-laterite composition was also conducted to study the reduction mechanism. X-ray diffraction and gravimetry analysis were applied to justify the phenomenon and predict kinetic model of the reduction. Results of this study provide information that palm kernel shell charcoal has similar reducing result compared with the conventional method. Reduction, however, was carried out by carbon monoxide rather than solid carbon. Regarding kinetics, Ginstling-Brouhnstein kinetic model provides satisfying results to predict the reduction phenomenon.

Thermodynamics and kinetics of pack aluminide coating formation on IN-100

NASA Technical Reports Server (NTRS)

Levine, S. R.; Caves, R. M.

1973-01-01

An investigation of the effects of pack variables on the formation of aluminide coatings on nickel-base superalloy IN-100 was conducted. Also, the thermodynamics and kinetics of coating formation were analyzed. Observed coating weights were in good agreement with predictions made from the analysis. Pack temperature rather than pack aluminum activity controls the principal coating phase formed. In 1 weight percent aluminum packs, aluminum weight gains were related to the halide pack activator. Solid-state nickel diffusion controlled coating formation from sodium fluoride and chloride and ammonium fluoride activated packs. In other ammonium and sodium halide activated 1 weight percent aluminum packs, gaseous diffusion controlled coating formation.

Magnetic dynamo action at low magnetic Prandtl numbers.

PubMed

Malyshkin, Leonid M; Boldyrev, Stanislav

2010-11-19

Amplification of magnetic field due to kinematic turbulent dynamo action is studied in the regime of small magnetic Prandtl numbers. Such a regime is relevant for planets and stars interiors, as well as for liquid-metal laboratory experiments. A comprehensive analysis based on the Kazantsev-Kraichnan model is reported, which establishes the dynamo threshold and the dynamo growth rates for varying kinetic helicity of turbulent fluctuations. It is proposed that in contrast with the case of large magnetic Prandtl numbers, the kinematic dynamo action at small magnetic Prandtl numbers is significantly affected by kinetic helicity, and it can be made quite efficient with an appropriate choice of the helicity spectrum.

Improving formaldehyde consumption drives methanol assimilation in engineered E. coli.

PubMed

Woolston, Benjamin M; King, Jason R; Reiter, Michael; Van Hove, Bob; Stephanopoulos, Gregory

2018-06-19

Due to volatile sugar prices, the food vs fuel debate, and recent increases in the supply of natural gas, methanol has emerged as a promising feedstock for the bio-based economy. However, attempts to engineer Escherichia coli to metabolize methanol have achieved limited success. Here, we provide a rigorous systematic analysis of several potential pathway bottlenecks. We show that regeneration of ribulose 5-phosphate in E. coli is insufficient to sustain methanol assimilation, and overcome this by activating the sedoheptulose bisphosphatase variant of the ribulose monophosphate pathway. By leveraging the kinetic isotope effect associated with deuterated methanol as a chemical probe, we further demonstrate that under these conditions overall pathway flux is kinetically limited by methanol dehydrogenase. Finally, we identify NADH as a potent kinetic inhibitor of this enzyme. These results provide direction for future engineering strategies to improve methanol utilization, and underscore the value of chemical biology methodologies in metabolic engineering.

Recent advances in parametric neuroreceptor mapping with dynamic PET: basic concepts and graphical analyses.

PubMed

Seo, Seongho; Kim, Su Jin; Lee, Dong Soo; Lee, Jae Sung

2014-10-01

Tracer kinetic modeling in dynamic positron emission tomography (PET) has been widely used to investigate the characteristic distribution patterns or dysfunctions of neuroreceptors in brain diseases. Its practical goal has progressed from regional data quantification to parametric mapping that produces images of kinetic-model parameters by fully exploiting the spatiotemporal information in dynamic PET data. Graphical analysis (GA) is a major parametric mapping technique that is independent on any compartmental model configuration, robust to noise, and computationally efficient. In this paper, we provide an overview of recent advances in the parametric mapping of neuroreceptor binding based on GA methods. The associated basic concepts in tracer kinetic modeling are presented, including commonly-used compartment models and major parameters of interest. Technical details of GA approaches for reversible and irreversible radioligands are described, considering both plasma input and reference tissue input models. Their statistical properties are discussed in view of parametric imaging.

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.

Observation and analysis of tidal and residual current in the North Yellow Sea in the spring

NASA Astrophysics Data System (ADS)

Miao, Qingsheng; Yang, Jinkun; Yang, Yang; Wan, Fangfang; Yu, Jia

2018-02-01

In order to study the current characteristics of the North Yellow Sea (NYS), 4 moored ADCPs (Acoustic Doppler Current Profilers) were deployed and Current characteristics were analyzed based on the observations. Results show that tidal current is the dominant and M2 is the main constituent. Shallow water constituents are obvious in the near-shore area, and tidal current ellipses directions have relations with topography. Residual currents in the Bohai Strait point to the Bohai Sea interior and the magnitude have a connection with terrain. Residual current in south NYS can be divided into two layers, and energy of residual current only accounts for about 13% of the total energy. Barotropic eddy kinetic energy plays a major role and the average in NYS accounts for 87%, baroclinic mean kinetic energy is larger in north NYS, in other regions barotropic mean kinetic energy take the leading position.

History and Philosophy of Science through Models: The Case of Chemical Kinetics

NASA Astrophysics Data System (ADS)

Justi, Rosária; Gilbert, John K.

The case for a greater role for the history and philosophy of science in science education is reviewed. It is argued that such a role can only be realised if it is based on both a credible analytical approach to the history and philosophy of science and if the evolution of a sufficient number of major themes in science is known in suitable detail. Adopting Lakatos' Theory of Scientific Research Programmes as the analytical approach, it is proposed that the development, use, and replacement, of specific models forms the core of such programmes.Chemical kinetics was selected as an exemplar major topic in chemistry. Eight models which have played a central role in the evolution of the study of chemical kinetics were identified by an analysis of the literature. The implications that these models have for the teaching and learning of chemistry today are discussed.

Analytical solution of Luedeking-Piret equation for a batch fermentation obeying Monod growth kinetics.

PubMed

Garnier, Alain; Gaillet, Bruno

2015-12-01

Not so many fermentation mathematical models allow analytical solutions of batch process dynamics. The most widely used is the combination of the logistic microbial growth kinetics with Luedeking-Piret bioproduct synthesis relation. However, the logistic equation is principally based on formalistic similarities and only fits a limited range of fermentation types. In this article, we have developed an analytical solution for the combination of Monod growth kinetics with Luedeking-Piret relation, which can be identified by linear regression and used to simulate batch fermentation evolution. Two classical examples are used to show the quality of fit and the simplicity of the method proposed. A solution for the combination of Haldane substrate-limited growth model combined with Luedeking-Piret relation is also provided. These models could prove useful for the analysis of fermentation data in industry as well as academia. © 2015 Wiley Periodicals, Inc.

Linear prediction and single-channel recording.

PubMed

Carter, A A; Oswald, R E

1995-08-01

The measurement of individual single-channel events arising from the gating of ion channels provides a detailed data set from which the kinetic mechanism of a channel can be deduced. In many cases, the pattern of dwells in the open and closed states is very complex, and the kinetic mechanism and parameters are not easily determined. Assuming a Markov model for channel kinetics, the probability density function for open and closed time dwells should consist of a sum of decaying exponentials. One method of approaching the kinetic analysis of such a system is to determine the number of exponentials and the corresponding parameters which comprise the open and closed dwell time distributions. These can then be compared to the relaxations predicted from the kinetic model to determine, where possible, the kinetic constants. We report here the use of a linear technique, linear prediction/singular value decomposition, to determine the number of exponentials and the exponential parameters. Using simulated distributions and comparing with standard maximum-likelihood analysis, the singular value decomposition techniques provide advantages in some situations and are a useful adjunct to other single-channel analysis techniques.

Quantitative analysis of protein-ligand interactions by NMR.

PubMed

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used to analyze population-averaged NMR quantities. Essentially, to apply NMR successfully, both the type of experiment and equation to fit the data must be carefully and specifically chosen for the protein-ligand interaction under analysis. In this review, we first explain the exchange regimes and kinetic models of protein-ligand interactions, and then describe the NMR methods that quantitatively analyze these specific interactions. Copyright © 2016 Elsevier B.V. All rights reserved.

A burnout prediction model based around char morphology

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

Tao Wu; Edward Lester; Michael Cloke

Several combustion models have been developed that can make predictions about coal burnout and burnout potential. Most of these kinetic models require standard parameters such as volatile content and particle size to make a burnout prediction. This article presents a new model called the char burnout (ChB) model, which also uses detailed information about char morphology in its prediction. The input data to the model is based on information derived from two different image analysis techniques. One technique generates characterization data from real char samples, and the other predicts char types based on characterization data from image analysis of coalmore » particles. The pyrolyzed chars in this study were created in a drop tube furnace operating at 1300{sup o}C, 200 ms, and 1% oxygen. Modeling results were compared with a different carbon burnout kinetic model as well as the actual burnout data from refiring the same chars in a drop tube furnace operating at 1300{sup o}C, 5% oxygen, and residence times of 200, 400, and 600 ms. A good agreement between ChB model and experimental data indicates that the inclusion of char morphology in combustion models could well improve model predictions. 38 refs., 5 figs., 6 tabs.« less

Evolutions and equilibrium parameters of foam films from individual solutions of Bovine serum albumin, n-dodecyl-β-D-maltoside and from their mixed solutions

NASA Astrophysics Data System (ADS)

Gerasimova, Anelia Tsvetanova; Angarska, Jana Krumova; Tachev, Krasimir Dimov

2017-03-01

The evolutions of thinning of films from individual solutions of BSA, C12G2 and from their mixed solutions with molar ratios 1:1, 1:7.5, 1:50 and 1:100 with pH = 4.9 were recorded by modified (with video camera) interferometric method. Based on them the stages through which the film goes from its formation to the equilibrium state were distinguished. It was shown that: (i) the difference between the kinetic of drainage of films stabilized by high and low molecular surfactants is drastic; (ii) only the change of the pH solution under or above isoelectric point strongly retards the film drainage; (iii) the transition of the kinetic of thinning of films from mixed solutions from a kinetic typical for high molecular substances towards a kinetic for low substances depends on the molar ratio between the components in the solution. From the picture of film corresponding to its equilibrium state the type of film was determined. From the analysis of this picture the equilibrium thickness and contact angle were calculated. It was found that the criterion for Newtonium black films (based on the values of film thickness and contact angle) is not directly applicable for films from protein solutions or mixed solutions with the participation of proteins.

Structure/Function Analysis of Cotton-Based Peptide-Cellulose Conjugates: Spatiotemporal/Kinetic Assessment of Protease Aerogels Compared to Nanocrystalline and Paper Cellulose

PubMed Central

Edwards, J. Vincent; Fontenot, Krystal; Liebner, Falk; Pircher, Nicole Doyle nee; French, Alfred D.; Condon, Brian D.

2018-01-01

Nanocellulose has high specific surface area, hydration properties, and ease of derivatization to prepare protease sensors. A Human Neutrophil Elastase sensor designed with a nanocellulose aerogel transducer surface derived from cotton is compared with cotton filter paper, and nanocrystalline cellulose versions of the sensor. X-ray crystallography was employed along with Michaelis–Menten enzyme kinetics, and circular dichroism to contrast the structure/function relations of the peptide-cellulose conjugate conformation to enzyme/substrate binding and turnover rates. The nanocellulosic aerogel was found to have a cellulose II structure. The spatiotemporal relation of crystallite surface to peptide-cellulose conformation is discussed in light of observed enzyme kinetics. A higher substrate binding affinity (Km) of elastase was observed with the nanocellulose aerogel and nanocrystalline peptide-cellulose conjugates than with the solution-based elastase substrate. An increased Km observed for the nanocellulosic aerogel sensor yields a higher enzyme efficiency (kcat/Km), attributable to binding of the serine protease to the negatively charged cellulose surface. The effect of crystallite size and β-turn peptide conformation are related to the peptide-cellulose kinetics. Models demonstrating the orientation of cellulose to peptide O6-hydroxymethyl rotamers of the conjugates at the surface of the cellulose crystal suggest the relative accessibility of the peptide-cellulose conjugates for enzyme active site binding. PMID:29534033

Quantitative evaluation of dual-flip-angle T1 mapping on DCE-MRI kinetic parameter estimation in head and neck

PubMed Central

Chow, Steven Kwok Keung; Yeung, David Ka Wai; Ahuja, Anil T; King, Ann D

2012-01-01

Purpose To quantitatively evaluate the kinetic parameter estimation for head and neck (HN) dynamic contrast-enhanced (DCE) MRI with dual-flip-angle (DFA) T1 mapping. Materials and methods Clinical DCE-MRI datasets of 23 patients with HN tumors were included in this study. T1 maps were generated based on multiple-flip-angle (MFA) method and different DFA combinations. Tofts model parameter maps of kep, Ktrans and vp based on MFA and DFAs were calculated and compared. Fitted parameter by MFA and DFAs were quantitatively evaluated in primary tumor, salivary gland and muscle. Results T1 mapping deviations by DFAs produced remarkable kinetic parameter estimation deviations in head and neck tissues. In particular, the DFA of [2º, 7º] overestimated, while [7º, 12º] and [7º, 15º] underestimated Ktrans and vp, significantly (P<0.01). [2º, 15º] achieved the smallest but still statistically significant overestimation for Ktrans and vp in primary tumors, 32.1% and 16.2% respectively. kep fitting results by DFAs were relatively close to the MFA reference compared to Ktrans and vp. Conclusions T1 deviations induced by DFA could result in significant errors in kinetic parameter estimation, particularly Ktrans and vp, through Tofts model fitting. MFA method should be more reliable and robust for accurate quantitative pharmacokinetic analysis in head and neck. PMID:23289084

Structure/Function Analysis of Cotton-Based Peptide-Cellulose Conjugates: Spatiotemporal/Kinetic Assessment of Protease Aerogels Compared to Nanocrystalline and Paper Cellulose.

PubMed

Edwards, J Vincent; Fontenot, Krystal; Liebner, Falk; Pircher, Nicole Doyle Nee; French, Alfred D; Condon, Brian D

2018-03-13

Nanocellulose has high specific surface area, hydration properties, and ease of derivatization to prepare protease sensors. A Human Neutrophil Elastase sensor designed with a nanocellulose aerogel transducer surface derived from cotton is compared with cotton filter paper, and nanocrystalline cellulose versions of the sensor. X-ray crystallography was employed along with Michaelis-Menten enzyme kinetics, and circular dichroism to contrast the structure/function relations of the peptide-cellulose conjugate conformation to enzyme/substrate binding and turnover rates. The nanocellulosic aerogel was found to have a cellulose II structure. The spatiotemporal relation of crystallite surface to peptide-cellulose conformation is discussed in light of observed enzyme kinetics. A higher substrate binding affinity ( K m ) of elastase was observed with the nanocellulose aerogel and nanocrystalline peptide-cellulose conjugates than with the solution-based elastase substrate. An increased K m observed for the nanocellulosic aerogel sensor yields a higher enzyme efficiency ( k cat / K m ), attributable to binding of the serine protease to the negatively charged cellulose surface. The effect of crystallite size and β-turn peptide conformation are related to the peptide-cellulose kinetics. Models demonstrating the orientation of cellulose to peptide O6-hydroxymethyl rotamers of the conjugates at the surface of the cellulose crystal suggest the relative accessibility of the peptide-cellulose conjugates for enzyme active site binding.

Time-Temperature Indicator Based on Enzymatic Degradation of Dye-Loaded Polyhydroxybutyrate.

PubMed

Anbukarasu, Preetam; Sauvageau, Dominic; Elias, Anastasia L

2017-09-01

An enzyme activated time-temperature indicator (TTI) which produces a direct colour change concomitant to variations in integrated time and temperature conditions is described. This direct colour change is realised by degrading a dye-loaded polyhydroxybutyrate (PHB) film by a depolymerase enzyme. The degradation of the PHB film by the enzyme causes the release of the dye in solution, which in turn undergoes an optical transition from clear to coloured with elapsing time. Macroscopic and microscopic optical observations confirms the uniform distribution of the dye in the PHB film. The dye release kinetics, mediated by the enzymatic reaction, are tested at different temperatures ranging from 4 to 37 °C, and are used to determine the suitability of a dye-loaded PHB as a time-temperature indicator for fresh food products based on kinetic parameters previously reported. The kinetic analysis shows that the activation energy of the dye release process is 74 kJ mol -1 , and that, at 37 °C, the dye would be totally released within 6 h. However, when incubated at 4 °C, the TTI requires in the range of 168 h (7 days) to release all the dye. These kinetics values highlight the potential of the TTI for monitoring fresh food products that have optimum shelf life around 4 °C. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Plate with decentralised velocity feedback loops: Power absorption and kinetic energy considerations

NASA Astrophysics Data System (ADS)

Gardonio, P.; Miani, S.; Blanchini, F.; Casagrande, D.; Elliott, S. J.

2012-04-01

This paper is focused on the vibration effects produced by an array of decentralised velocity feedback loops that are evenly distributed over a rectangular thin plate to minimise its flexural response. The velocity feedback loops are formed by collocated ideal velocity sensor and point force actuator pairs, which are unconditionally stable and produce 'sky-hook' damping on the plate. The study compares how the overall flexural vibration of the plate and the local absorption of vibration power by the feedback loops vary with the control gains. The analysis is carried out both considering a typical frequency-domain formulation based on kinetic energy and structural power physical quantities, which is normally used to study vibration and noise problems, and a time-domain formulation also based on kinetic energy and structural power, which is usually implemented to investigate control problems. The time-domain formulation shows to be much more computationally efficient and robust with reference to truncation errors. Thus it has been used to perform a parametric study to assess if, and under which conditions, the minimum of the kinetic energy and the maximum of the absorbed power cost functions match with reference to: (a) the number of feedback control loops, (b) the structural damping in the plate, (c) the mutual distance of a pair of control loops and (d) the mutual gains implemented in a pair of feedback loops.

Kinetic Analysis of Competitive Electrocatalytic Pathways: New Insights into Hydrogen Production with Nickel Electrocatalysts

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

Wiedner, Eric S.; Brown, Houston J.; Helm, Monte L.

2016-01-20

The hydrogen production electrocatalyst Ni(PPh2NPh2)22+ (1) is capable of traversing multiple electrocatalytic pathways. When using dimethylformamidium, DMF(H)+, the mechanism of formation of H2 catalyzed by 1 changes from an ECEC to an EECC mechanism as the potential approaches the Ni(I/0) couple. Two recent electrochemical methods, current-potential analysis and foot-of-the-wave analysis (FOWA), were performed on 1 to measure the detailed chemical kinetics of the competing ECEC and EECC pathways. A sensitivity analysis was performed on the electrochemical methods using digital simulations to gain a better understanding of their strengths and limitations. Notably, chemical rate constants were significantly underestimated when not accountingmore » for electron transfer kinetics, even when electron transfer was fast enough to afford a reversible non-catalytic wave. The EECC pathway of 1 was found to be faster than the ECEC pathway under all conditions studied. Using buffered DMF: DMF(H)+ mixtures led to an increase in the catalytic rate constant (kobs) of the EECC pathway, but kobs for the ECEC pathway did not change when using buffered acid. Further kinetic analysis of the ECEC path revealed that added base increases the rate of isomerization of the exo-protonated Ni(0) isomers to the catalytically active endo-isomers, but decreases the net rate of protonation of Ni(I). FOWA on 1 did not provide accurate rate constants due to incomplete reduction of the exo-protonated Ni(I) intermediate at the foot of the wave, but FOWA could be used to estimate the reduction potential of this previously undetected intermediate. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Combined TGA-MS kinetic analysis of multistep processes. Thermal decomposition and ceramification of polysilazane and polysiloxane preceramic polymers.

PubMed

García-Garrido, C; Sánchez-Jiménez, P E; Pérez-Maqueda, L A; Perejón, A; Criado, José M

2016-10-26

The polymer-to-ceramic transformation kinetics of two widely employed ceramic precursors, 1,3,5,7-tetramethyl-1,3,5,7-tetravinylcyclotetrasiloxane (TTCS) and polyureamethylvinylsilazane (CERASET), have been investigated using coupled thermogravimetry and mass spectrometry (TG-MS), Raman, XRD and FTIR. The thermally induced decomposition of the pre-ceramic polymer is the critical step in the synthesis of polymer derived ceramics (PDCs) and accurate kinetic modeling is key to attaining a complete understanding of the underlying process and to attempt any behavior predictions. However, obtaining a precise kinetic description of processes of such complexity, consisting of several largely overlapping physico-chemical processes comprising the cleavage of the starting polymeric network and the release of organic moieties, is extremely difficult. Here, by using the evolved gases detected by MS as a guide it has been possible to determine the number of steps that compose the overall process, which was subsequently resolved using a semiempirical deconvolution method based on the Frasier-Suzuki function. Such a function is more appropriate that the more usual Gaussian or Lorentzian functions since it takes into account the intrinsic asymmetry of kinetic curves. Then, the kinetic parameters of each constituent step were independently determined using both model-free and model-fitting procedures, and it was found that the processes obey mostly diffusion models which can be attributed to the diffusion of the released gases through the solid matrix. The validity of the obtained kinetic parameters was tested not only by the successful reconstruction of the original experimental curves, but also by predicting the kinetic curves of the overall processes yielded by different thermal schedules and by a mixed TTCS-CERASET precursor.

In-depth investigation on the pyrolysis kinetics of raw biomass. Part I: kinetic analysis for the drying and devolatilization stages.

PubMed

Chen, Dengyu; Zheng, Yan; Zhu, Xifeng

2013-03-01

An in-depth investigation was conducted on the kinetic analysis of raw biomass using thermogravimetric analysis (TGA), from which the activation energy distribution of the whole pyrolysis process was obtained. Two different stages, namely, drying stage (Stage I) and devolatilization stage (Stage II), were shown in the pyrolysis process in which the activation energy values changed with conversion. The activation energy at low conversions (below 0.15) in the drying stage ranged from 10 to 30 kJ/mol. Such energy was calculated using the nonisothermal Page model, known as the best model to describe the drying kinetics. Kinetic analysis was performed using the distributed activation energy model in a wide range of conversions (0.15-0.95) in the devolatilization stage. The activation energy first ranged from 178.23 to 245.58 kJ/mol and from 159.66 to 210.76 kJ/mol for corn straw and wheat straw, respectively, then increasing remarkably with an irregular trend. Copyright © 2012 Elsevier Ltd. All rights reserved.

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks.

PubMed

Ruppin, Eytan; Papin, Jason A; de Figueiredo, Luis F; Schuster, Stefan

2010-08-01

With the advent of modern omics technologies, it has become feasible to reconstruct (quasi-) whole-cell metabolic networks and characterize them in more and more detail. Computer simulations of the dynamic behavior of such networks are difficult due to a lack of kinetic data and to computational limitations. In contrast, network analysis based on appropriate constraints such as the steady-state condition (constraint-based analysis) is feasible and allows one to derive conclusions about the system's metabolic capabilities. Here, we review methods for the reconstruction of metabolic networks, modeling techniques such as flux balance analysis and elementary flux modes and current progress in their development and applications. Game-theoretical methods for studying metabolic networks are discussed as well. Copyright © 2010 Elsevier Ltd. All rights reserved.

Kinetic theory of pattern formation in mixtures of microtubules and molecular motors

NASA Astrophysics Data System (ADS)

Maryshev, Ivan; Marenduzzo, Davide; Goryachev, Andrew B.; Morozov, Alexander

2018-02-01

In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous work by Aranson and Tsimring [Phys. Rev. E 74, 031915 (2006), 10.1103/PhysRevE.74.031915] we model the motor-induced reorientation of microtubules as collision rules, and devise a semianalytical method to calculate the corresponding interaction integrals. This procedure yields an infinite hierarchy of kinetic equations that we terminate by employing a well-established closure strategy, developed in the pattern-formation community and based on a power-counting argument. We thus arrive at a closed set of coupled equations for slowly varying local density and orientation of the microtubules, and study its behavior by performing a linear stability analysis and direct numerical simulations. By comparing our method with the work of Aranson and Tsimring, we assess the validity of the assumptions required to derive their and our theories. We demonstrate that our approximation-free evaluation of the interaction integrals and our choice of a systematic closure strategy result in a rather different dynamical behavior than was previously reported. Based on our theory, we discuss the ensuing phase diagram and the patterns observed.

Assessing Consequential Scenarios in a Complex Operational Environment Using Agent Based Simulation

DTIC Science & Technology

2017-03-16

RWISE) 93 5.1.5 Conflict Modeling, Planning, and Outcomes Experimentation Program (COMPOEX) 94 5.1.6 Joint Non -Kinetic Effects Model (JNEM)/Athena... experimental design and testing. 4.3.8 Types and Attributes of Agent-Based Model Design Patterns Using the aforementioned ABM flowchart design methodology ...speed, or flexibility during tactical US Army wargaming. The report considers methodologies to improve analysis of the human domain, identifies

An evidence-based systematic review of elderberry and elderflower (Sambucus nigra) by the Natural Standard Research Collaboration.

PubMed

Ulbricht, Catherine; Basch, Ethan; Cheung, Lisa; Goldberg, Harley; Hammerness, Paul; Isaac, Richard; Khalsa, Karta Purkh Singh; Romm, Aviva; Rychlik, Idalia; Varghese, Minney; Weissner, Wendy; Windsor, Regina C; Wortley, Jayme

2014-03-01

An evidence-based systematic review of elderberry and elderflower (Sambucus nigra) by the Natural Standard Research Collaboration consolidates the safety and efficacy data available in the scientific literature using a validated, reproducible grading rationale. This article includes written and statistical analysis of clinical trials, plus a compilation of expert opinion, folkloric precedent, history, pharmacology, kinetics/dynamics, interactions, adverse effects, toxicology, and dosing.

Formal reasoning about systems biology using theorem proving

PubMed Central

Hasan, Osman; Siddique, Umair; Tahar, Sofiène

2017-01-01

System biology provides the basis to understand the behavioral properties of complex biological organisms at different levels of abstraction. Traditionally, analysing systems biology based models of various diseases have been carried out by paper-and-pencil based proofs and simulations. However, these methods cannot provide an accurate analysis, which is a serious drawback for the safety-critical domain of human medicine. In order to overcome these limitations, we propose a framework to formally analyze biological networks and pathways. In particular, we formalize the notion of reaction kinetics in higher-order logic and formally verify some of the commonly used reaction based models of biological networks using the HOL Light theorem prover. Furthermore, we have ported our earlier formalization of Zsyntax, i.e., a deductive language for reasoning about biological networks and pathways, from HOL4 to the HOL Light theorem prover to make it compatible with the above-mentioned formalization of reaction kinetics. To illustrate the usefulness of the proposed framework, we present the formal analysis of three case studies, i.e., the pathway leading to TP53 Phosphorylation, the pathway leading to the death of cancer stem cells and the tumor growth based on cancer stem cells, which is used for the prognosis and future drug designs to treat cancer patients. PMID:28671950

Improved hydrogen absorption and desorption kinetics of magnesium-based alloy via addition of yttrium

NASA Astrophysics Data System (ADS)

Yang, Tai; Li, Qiang; Liu, Ning; Liang, Chunyong; Yin, Fuxing; Zhang, Yanghuan

2018-02-01

Yttrium (Y) is selected to modify the microstructure of magnesium (Mg) to improve the hydrogen storage performance. Thereby, binary alloys with the nominal compositions of Mg24Yx (x = 1-5) are fabricated by inexpensive casting technique. Their microstructure and phase transformation during hydriding and dehydriding process are characterized by using X-ray diffraction, scanning electron microscopy, and high-resolution transmission electron microscopy analysis. The isothermal hydrogen absorption and desorption kinetics are also measured by a Sievert's-type apparatus at various temperatures. Typical multiphase structures of binary alloy can be clearly observed. All of these alloys can reversibly absorb and desorb large amount of hydrogen at proper temperatures. The addition of Y markedly promotes the hydrogen absorption kinetics. However, it results in a reduction of reversible hydrogen storage capacity. A maximum value of dehydrogenation rate is observed with the increase of Y content. The Mg24Y3 alloy has the optimal desorption kinetic performance, and it can desorb about 5.4 wt% of hydrogen at 380 °C within 12 min. Combining Johnson-Mehl-Avrami kinetic model and Arrhenius equation, the dehydrogenation activation energy of the alloys are evaluated. The Mg24Y3 alloy also has the lowest dehydrogenation activation energy (119 kJ mol-1).

[Complex formation between alpha-chymotrypsin and block copolymers based on ethylene and propylene oxide, induced by high pressure].

PubMed

Topchieva, I N; Sorokina, E M; Kurganov, B I; Zhulin, V M; Makarova, Z G

1996-06-01

A new method of formation of non-covalent adducts based on an amphiphilic diblock copolymer of ethylene and propylene oxides with molecular mass of 2 kDa and alpha-chymotrypsin (ChT) under high pressure, has been developed. The composition of the complexes corresponds to seven polymer molecules per one ChT molecule in the pressure range of 1.1 to 400 MPa. The complexes fully retain the catalytic activity. Kinetic constants (Km and kcat) for enzymatic hydrolysis of N-benzoyl-L-tyrosine ethyl ester catalyzed by the complexes are identical with the corresponding values for native ChT. Analysis of kinetics of thermal inactivation of the complexes revealed that the constant of the rate of the slow inactivation step is markedly lower than for ChT.

Kinetic Studies with Ion Selective Electrodes: Determination of Creatinine in Urine with a Picrate Ion Selective Electrode: A Laboratory Experiment.

ERIC Educational Resources Information Center

Diamandis, E. P.; And Others

1983-01-01

The kinetic of the Jaffe reaction with picrate ion selective electrode (ISE) and a kinetic method for determining creatinine in urine is presented. The experiment could be used to familarize students with the application of ISE in kinetic studies and chemical analysis. (Author/JN)

Design Principles of DNA Enzyme-Based Walkers: Translocation Kinetics and Photoregulation.

PubMed

Cha, Tae-Gon; Pan, Jing; Chen, Haorong; Robinson, Heather N; Li, Xiang; Mao, Chengde; Choi, Jong Hyun

2015-07-29

Dynamic DNA enzyme-based walkers complete their stepwise movements along the prescribed track through a series of reactions, including hybridization, enzymatic cleavage, and strand displacement; however, their overall translocation kinetics is not well understood. Here, we perform mechanistic studies to elucidate several key parameters that govern the kinetics and processivity of DNA enzyme-based walkers. These parameters include DNA enzyme core type and structure, upper and lower recognition arm lengths, and divalent metal cation species and concentration. A theoretical model is developed within the framework of single-molecule kinetics to describe overall translocation kinetics as well as each reaction step. A better understanding of kinetics and design parameters enables us to demonstrate a walker movement near 5 μm at an average speed of ∼1 nm s(-1). We also show that the translocation kinetics of DNA walkers can be effectively controlled by external light stimuli using photoisomerizable azobenzene moieties. A 2-fold increase in the cleavage reaction is observed when the hairpin stems of enzyme catalytic cores are open under UV irradiation. This study provides general design guidelines to construct highly processive, autonomous DNA walker systems and to regulate their translocation kinetics, which would facilitate the development of functional DNA walkers.

Kinetics and thermodynamic analysis in one-pot pyrolysis of rice hull using renewable calcium oxide based catalysts.

PubMed

Gan, Darren Kin Wai; Loy, Adrian Chun Minh; Chin, Bridgid Lai Fui; Yusup, Suzana; Unrean, Pornkamol; Rianawati, Elisabeth; Acda, Menandro N

2018-06-06

Thermodynamic and kinetic parameters of catalytic pyrolysis of rice hull (RH) pyrolysis using two different types of renewable catalysts namely natural limestone (LS) and eggshells (ES) using thermogravimetric analysis (TG) approach at different heating rates of 10-100 K min -1 in temperature range of 323-1173 K are investigated. Catalytic pyrolysis mechanism of both catalysts had shown significant effect on the degradation of RH. Model free kinetic of iso-conversional method (Flynn-Wall-Ozawa) and multi-step reaction model (Distributed Activation Energy Model) were employed into present study. The average activation energy was found in the range of 175.4-177.7 kJ mol -1 (RH), 123.3-132.5 kJ mol -1 (RH-LS), and 96.1-100.4 kJ mol -1 (RH-ES) respectively. The syngas composition had increased from 60.05 wt% to 63.1 wt% (RH-LS) and 63.4 wt% (RH-ES). However, the CO 2 content had decreased from 24.1 wt% (RH) to 20.8 wt% (RH-LS) and 19.9 wt% (RH-ES). Copyright © 2018 Elsevier Ltd. All rights reserved.

Ultrasound assisted, thermally activated persulfate oxidation of coal tar DNAPLs.

PubMed

Peng, Libin; Wang, Li; Hu, Xingting; Wu, Peihui; Wang, Xueqing; Huang, Chumei; Wang, Xiangyang; Deng, Dayi

2016-11-15

The feasibility of ultrasound assisted, thermally activated persulfate for effective oxidation of twenty 2-6 ringed coal tar PAHs in a biphasic tar/water system and a triphasic tar/soil/water system were investigated and established. The results indicate that ultrasonic assistance, persulfate and elevated reaction temperature are all required to achieve effective oxidation of coal tar PAHs, while the heating needed can be provided by ultrasonic induced heating as well. Further kinetic analysis reveals that the oxidation of individual PAH in the biphasic tar/water system follows the first-order kinetics, and individual PAH oxidation rate is primary determined by the mass transfer coefficients, tar/water interfacial areas, the aqueous solubility of individual PAH and its concentration in coal tar. Based on the kinetic analysis and experimental results, the contributions of ultrasound, persulfate and elevated reaction temperature to PAHs oxidation were characterized, and the effects of ultrasonic intensity and oxidant dosage on PAHs oxidation efficiency were investigated. In addition, the results indicate that individual PAH degradability is closely related to its reactivity as well, and the high reactivity of 4-6 ringed PAHs substantially improves their degradability. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis, characterization and in vitro cytotoxicity analysis of a novel cellulose based drug carrier for the controlled delivery of 5-fluorouracil, an anticancer drug

NASA Astrophysics Data System (ADS)

Anirudhan, Thayyath S.; Nima, Jayachandran; Divya, Peethambaran L.

2015-11-01

The present investigation concerns the development and evaluation of a novel drug delivery system, aminated-glycidylmethacrylate grafted cellulose-grafted polymethacrylic acid-succinyl cyclodextrin (Cell-g-(GMA/en)-PMA-SCD) for the controlled release of 5-Fluorouracil, an anticancer drug. The prepared drug carrier was characterized by FT-IR, XRD and SEM techniques. Binding kinetics and isotherm studies of 5-FU onto Cell-g-(GMA/en)-PMA-SCD were found to follow pseudo-second-order and Langmuir model respectively. Maximum binding capacity of drug carrier was found to be 149.09 mg g-1 at 37 °C. Swelling studies, in vitro release kinetics, drug loading efficiency and encapsulation efficiency of Cell-g-(GMA/en)-PMA-SCD were studied. The release kinetics was analyzed using Ritger-Peppas equation at pH 7.4. Cytotoxicity analysis on MCF-7 (human breast carcinoma) cells indicated that the drug carrier shows sustained and controlled release of drug to the target site. Hence, it is evident from this investigation that Cell-g-(GMA/en)-PMA-SCD could be a promising carrier for 5-FU.

Cr(VI) sorption by free and immobilised chromate-reducing bacterial cells in PVA-alginate matrix: equilibrium isotherms and kinetic studies.

PubMed

Rawat, Monica; Rawat, A P; Giri, Krishna; Rai, J P N

2013-08-01

Chromate-resistant bacterial strain isolated from the soil of tannery was studied for Cr(VI) bioaccumulation in free and immobilised cells to evaluate its applicability in chromium removal from aqueous solution. Based on the comparative analysis of the 16S rRNA gene, and phenotypic and biochemical characterization, this strain was identified as Paenibacillus xylanilyticus MR12. Mechanism of Cr adsorption was also ascertained by chemical modifications of the bacterial biomass followed by Fourier transform infrared spectroscopy analysis of the cell wall constituents. The equilibrium biosorption analysed using isotherms (Langmuir, Freundlich and Dubinin-Redushkevich) and kinetics models (pseudo-first-order, second-order and Weber-Morris) revealed that the Langmuir model best correlated to experimental data, and Weber-Morris equation well described Cr(VI) biosorption kinetics. Polyvinyl alcohol alginate immobilised cells had the highest Cr(VI) removal efficiency than that of free cells and could also be reused four times for Cr(VI) removal. Complete reduction of chromate in simulated effluent containing Cu(2+), Mg(2+), Mn(2+) and Zn(2+) by immobilised cells, demonstrated potential applications of a novel immobilised bacterial strain MR12, as a vital bioresource in Cr(VI) bioremediation technology.

Kinetics of Some Metal Atom and Metal Fluoride Oxidation Reactions Relevant to Air Force Technology Development

DTIC Science & Technology

1981-03-01

Products and Chemicals , Inc ., supplied a complete analysis with each cylinder. Initial measurements with the original batch (cylinder 1) were considered...NF 3] in this limited tempera- ture range. The NFs used in these experiments was made available by Kelly Air Force Base. The manufacturer, Air

Maximum likelihood-based analysis of single-molecule photon arrival trajectories.

PubMed

Hajdziona, Marta; Molski, Andrzej

2011-02-07

In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 10(3) photons. When the intensity levels are well-separated and 10(4) photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

Critical evaluation of Jet-A spray combustion using propane chemical kinetics in gas turbine combustion simulated by KIVA-2

NASA Technical Reports Server (NTRS)

Nguyen, H. L.; Ying, S.-J.

1990-01-01

Jet-A spray combustion has been evaluated in gas turbine combustion with the use of propane chemical kinetics as the first approximation for the chemical reactions. Here, the numerical solutions are obtained by using the KIVA-2 computer code. The KIVA-2 code is the most developed of the available multidimensional combustion computer programs for application of the in-cylinder combustion dynamics of internal combustion engines. The released version of KIVA-2 assumes that 12 chemical species are present; the code uses an Arrhenius kinetic-controlled combustion model governed by a four-step global chemical reaction and six equilibrium reactions. Researchers efforts involve the addition of Jet-A thermophysical properties and the implementation of detailed reaction mechanisms for propane oxidation. Three different detailed reaction mechanism models are considered. The first model consists of 131 reactions and 45 species. This is considered as the full mechanism which is developed through the study of chemical kinetics of propane combustion in an enclosed chamber. The full mechanism is evaluated by comparing calculated ignition delay times with available shock tube data. However, these detailed reactions occupy too much computer memory and CPU time for the computation. Therefore, it only serves as a benchmark case by which to evaluate other simplified models. Two possible simplified models were tested in the existing computer code KIVA-2 for the same conditions as used with the full mechanism. One model is obtained through a sensitivity analysis using LSENS, the general kinetics and sensitivity analysis program code of D. A. Bittker and K. Radhakrishnan. This model consists of 45 chemical reactions and 27 species. The other model is based on the work published by C. K. Westbrook and F. L. Dryer.

A Three-Dimensional Kinematic and Kinetic Study of the College-Level Female Softball Swing

PubMed Central

Milanovich, Monica; Nesbit, Steven M.

2014-01-01

This paper quantifies and discusses the three-dimensional kinematic and kinetic characteristics of the female softball swing as performed by fourteen female collegiate amateur subjects. The analyses were performed using a three-dimensional computer model. The model was driven kinematically from subject swings data that were recorded with a multi-camera motion analysis system. Each subject used two distinct bats with significantly different inertial properties. Model output included bat trajectories, subject/bat interaction forces and torques, work, and power. These data formed the basis for a detailed analysis and description of fundamental swing kinematic and kinetic quantities. The analyses revealed that the softball swing is a highly coordinated and individual three-dimensional motion and subject-to-subject variations were significant in all kinematic and kinetic quantities. In addition, the potential effects of bat properties on swing mechanics are discussed. The paths of the hands and the centre-of-curvature of the bat relative to the horizontal plane appear to be important trajectory characteristics of the swing. Descriptions of the swing mechanics and practical implications are offered based upon these findings. Key Points The female softball swing is a highly coordinated and individual three-dimensional motion and subject-to-subject variations were significant in all kinematic and kinetic quantities. The paths of the grip point, bat centre-of-curvature, CG, and COP are complex yet reveal consistent patterns among subjects indicating that these patterns are fundamental components of the swing. The most important mechanical quantity relative to generating bat speed is the total work applied to the bat from the batter. Computer modeling of the softball swing is a viable means for study of the fundamental mechanics of the swing motion, the interactions between the batter and the bat, and the energy transfers between the two. PMID:24570623

Monochloramine Disinfection Kinetics of Nitrosomonas europaea by Propidium Monoazide Quantitative PCR and Live/Dead BacLight Methods▿

PubMed Central

Wahman, David G.; Wulfeck-Kleier, Karen A.; Pressman, Jonathan G.

2009-01-01

Monochloramine disinfection kinetics were determined for the pure-culture ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) by two culture-independent methods, namely, Live/Dead BacLight (LD) and propidium monoazide quantitative PCR (PMA-qPCR). Both methods were first verified with mixtures of heat-killed (nonviable) and non-heat-killed (viable) cells before a series of batch disinfection experiments with stationary-phase cultures (batch grown for 7 days) at pH 8.0, 25°C, and 5, 10, and 20 mg Cl2/liter monochloramine. Two data sets were generated based on the viability method used, either (i) LD or (ii) PMA-qPCR. These two data sets were used to estimate kinetic parameters for the delayed Chick-Watson disinfection model through a Bayesian analysis implemented in WinBUGS. This analysis provided parameter estimates of 490 mg Cl2-min/liter for the lag coefficient (b) and 1.6 × 10−3 to 4.0 × 10−3 liter/mg Cl2-min for the Chick-Watson disinfection rate constant (k). While estimates of b were similar for both data sets, the LD data set resulted in a greater k estimate than that obtained with the PMA-qPCR data set, implying that the PMA-qPCR viability measure was more conservative than LD. For N. europaea, the lag phase was not previously reported for culture-independent methods and may have implications for nitrification in drinking water distribution systems. This is the first published application of a PMA-qPCR method for disinfection kinetic model parameter estimation as well as its application to N. europaea or monochloramine. Ultimately, this PMA-qPCR method will allow evaluation of monochloramine disinfection kinetics for mixed-culture bacteria in drinking water distribution systems. PMID:19561179

A three-dimensional kinematic and kinetic study of the college-level female softball swing.

PubMed

Milanovich, Monica; Nesbit, Steven M

2014-01-01

This paper quantifies and discusses the three-dimensional kinematic and kinetic characteristics of the female softball swing as performed by fourteen female collegiate amateur subjects. The analyses were performed using a three-dimensional computer model. The model was driven kinematically from subject swings data that were recorded with a multi-camera motion analysis system. Each subject used two distinct bats with significantly different inertial properties. Model output included bat trajectories, subject/bat interaction forces and torques, work, and power. These data formed the basis for a detailed analysis and description of fundamental swing kinematic and kinetic quantities. The analyses revealed that the softball swing is a highly coordinated and individual three-dimensional motion and subject-to-subject variations were significant in all kinematic and kinetic quantities. In addition, the potential effects of bat properties on swing mechanics are discussed. The paths of the hands and the centre-of-curvature of the bat relative to the horizontal plane appear to be important trajectory characteristics of the swing. Descriptions of the swing mechanics and practical implications are offered based upon these findings. Key PointsThe female softball swing is a highly coordinated and individual three-dimensional motion and subject-to-subject variations were significant in all kinematic and kinetic quantities.The paths of the grip point, bat centre-of-curvature, CG, and COP are complex yet reveal consistent patterns among subjects indicating that these patterns are fundamental components of the swing.The most important mechanical quantity relative to generating bat speed is the total work applied to the bat from the batter.Computer modeling of the softball swing is a viable means for study of the fundamental mechanics of the swing motion, the interactions between the batter and the bat, and the energy transfers between the two.

Biodegradable polymer based ternary blends for removal of trace metals from simulated industrial wastewater.

PubMed

Prakash, N; Arungalai Vendan, S

2016-02-01

The ternary blends consisting of Chitosan (CS), Nylon 6 (Ny 6) and Montmorillonite clay (MM clay) were prepared by the solution blending method with glutaraldehyde. The prepared ternary blends were characterization by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Thermo gravimetric analysis (TGA), Differential scanning calorimetry (DSC) and Scanning electron microscope (SEM). The FTIR results showed that the strong intermolecular hydrogen bondings were established between chitosan, nylon 6 and montmorillonite clay. TGA showed the thermal stability of the blend is enhanced by glutaraldehyde as Crosslink agent. Results of XRD indicated that the relative crystalline of the pure chitosan film was reduced when the polymeric network was reticulated by glutaraldehyde. Finally, the results of scanning electron microscopy (SEM) indicated that the morphology of the blend was rough and heterogenous. Further, it confirms the interaction between the functional groups of the blend components. The extent of removal of the trace metals was found to be almost the same. The removal of these metals at different pH was also done and the maximum removal of the metals was observed at pH 4.5 for both trace metals. Adsorption studies and kinetic analysis have also been made. Moreover, the protonation of amine groups is induced an electrostatic repulsion of cations. When the pH of the solution was more than 5.5, the sorption rate began to decrease. Besides, the quantity of adsorbate on absorbent was fitted as a function in Langmuir and Freundlich isotherm. The sorption kinetics was tested for pseudo first order and pseudo second order reaction. The kinetic experimental data correlated with the second order kinetic model and rate constants of sorption for kinetic models were calculated and accordingly, the correlation coefficients were obtained. Copyright © 2016. Published by Elsevier B.V.

Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

DTIC Science & Technology

2015-03-16

sensitivity value was the maximum uncertainty in that value estimated by the Sobol method. 2.4. Global Sensitivity Analysis of the Reduced Order Coagulation...sensitivity analysis, using the variance-based method of Sobol , to estimate which parameters controlled the performance of the reduced order model [69]. We...Environment. Comput. Sci. Eng. 2007, 9, 90–95. 69. Sobol , I. Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates

3D Material Response Analysis of PICA Pyrolysis Experiments

NASA Technical Reports Server (NTRS)

Oliver, A. Brandon

2017-01-01

The PICA decomposition experiments of Bessire and Minton are investigated using 3D material response analysis. The steady thermoelectric equations have been added to the CHAR code to enable analysis of the Joule-heated experiments and the DAKOTA optimization code is used to define the voltage boundary condition that yields the experimentally observed temperature response. This analysis has identified a potential spatial non-uniformity in the PICA sample temperature driven by the cooled copper electrodes and thermal radiation from the surface of the test article (Figure 1). The non-uniformity leads to a variable heating rate throughout the sample volume that has an effect on the quantitative results of the experiment. Averaging the results of integrating a kinetic reaction mechanism with the heating rates seen across the sample volume yield a shift of peak species production to lower temperatures that is more significant for higher heating rates (Figure 2) when compared to integrating the same mechanism at the reported heating rate. The analysis supporting these conclusions will be presented along with a proposed analysis procedure that permits quantitative use of the existing data. Time permitting, a status on the in-development kinetic decomposition mechanism based on this data will be presented as well.

A Physiologically-Based Description of the Inhalation Pharmacokinetics of Styrene in Rats and Humans

DTIC Science & Technology

1983-01-01

model for rat were scaled to give a description of human kinetics and the predictions agreed closely with available data from the literature (Fig. 4...for predicting human kinetics from a data base in other mammalian species. The ability to anticipate kinetic behavior in humans could very much improve

Exploring Secondary Students' Understanding of Chemical Kinetics through Inquiry-Based Learning Activities

ERIC Educational Resources Information Center

Chairam, Sanoe; Klahan, Nutsuda; Coll, Richard K.

2015-01-01

This research is trying to evaluate the feedback of Thai secondary school students to inquiry-based teaching and learning methods, exemplified by the study of chemical kinetics. This work used the multiple-choice questions, scientifically practical diagram and questionnaire to assess students' understanding of chemical kinetics. The findings…

Model free approach to kinetic analysis of real-time hyperpolarized 13C magnetic resonance spectroscopy data.

PubMed

Hill, Deborah K; Orton, Matthew R; Mariotti, Erika; Boult, Jessica K R; Panek, Rafal; Jafar, Maysam; Parkes, Harold G; Jamin, Yann; Miniotis, Maria Falck; Al-Saffar, Nada M S; Beloueche-Babari, Mounia; Robinson, Simon P; Leach, Martin O; Chung, Yuen-Li; Eykyn, Thomas R

2013-01-01

Real-time detection of the rates of metabolic flux, or exchange rates of endogenous enzymatic reactions, is now feasible in biological systems using Dynamic Nuclear Polarization Magnetic Resonance. Derivation of reaction rate kinetics from this technique typically requires multi-compartmental modeling of dynamic data, and results are therefore model-dependent and prone to misinterpretation. We present a model-free formulism based on the ratio of total areas under the curve (AUC) of the injected and product metabolite, for example pyruvate and lactate. A theoretical framework to support this novel analysis approach is described, and demonstrates that the AUC ratio is proportional to the forward rate constant k. We show that the model-free approach strongly correlates with k for whole cell in vitro experiments across a range of cancer cell lines, and detects response in cells treated with the pan-class I PI3K inhibitor GDC-0941 with comparable or greater sensitivity. The same result is seen in vivo with tumor xenograft-bearing mice, in control tumors and following drug treatment with dichloroacetate. An important finding is that the area under the curve is independent of both the input function and of any other metabolic pathways arising from the injected metabolite. This model-free approach provides a robust and clinically relevant alternative to kinetic model-based rate measurements in the clinical translation of hyperpolarized (13)C metabolic imaging in humans, where measurement of the input function can be problematic.

Model Free Approach to Kinetic Analysis of Real-Time Hyperpolarized 13C Magnetic Resonance Spectroscopy Data

PubMed Central

Mariotti, Erika; Boult, Jessica K. R.; Panek, Rafal; Jafar, Maysam; Parkes, Harold G.; Jamin, Yann; Miniotis, Maria Falck; Al-Saffar, Nada M. S.; Beloueche-Babari, Mounia; Robinson, Simon P.; Leach, Martin O.; Chung, Yuen-Li; Eykyn, Thomas R.

2013-01-01

Real-time detection of the rates of metabolic flux, or exchange rates of endogenous enzymatic reactions, is now feasible in biological systems using Dynamic Nuclear Polarization Magnetic Resonance. Derivation of reaction rate kinetics from this technique typically requires multi-compartmental modeling of dynamic data, and results are therefore model-dependent and prone to misinterpretation. We present a model-free formulism based on the ratio of total areas under the curve (AUC) of the injected and product metabolite, for example pyruvate and lactate. A theoretical framework to support this novel analysis approach is described, and demonstrates that the AUC ratio is proportional to the forward rate constant k. We show that the model-free approach strongly correlates with k for whole cell in vitro experiments across a range of cancer cell lines, and detects response in cells treated with the pan-class I PI3K inhibitor GDC-0941 with comparable or greater sensitivity. The same result is seen in vivo with tumor xenograft-bearing mice, in control tumors and following drug treatment with dichloroacetate. An important finding is that the area under the curve is independent of both the input function and of any other metabolic pathways arising from the injected metabolite. This model-free approach provides a robust and clinically relevant alternative to kinetic model-based rate measurements in the clinical translation of hyperpolarized 13C metabolic imaging in humans, where measurement of the input function can be problematic. PMID:24023724

Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

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

Dash, Satyakam; Khodayari, Ali; Zhou, Jilai

Background. Clostridium thermocellum is a Gram-positive anaerobe with the ability to hydrolyze and metabolize cellulose into biofuels such as ethanol, making it an attractive candidate for consolidated bioprocessing (CBP). At present, metabolic engineering in C. thermocellum is hindered due to the incomplete description of its metabolic repertoire and regulation within a predictive metabolic model. Genome-scale metabolic (GSM) models augmented with kinetic models of metabolism have been shown to be effective at recapitulating perturbed metabolic phenotypes. Results. In this effort, we first update a second-generation genome-scale metabolic model (iCth446) for C. thermocellum by correcting cofactor dependencies, restoring elemental and charge balances,more » and updating GAM and NGAM values to improve phenotype predictions. The iCth446 model is next used as a scaffold to develop a core kinetic model (k-ctherm118) of the C. thermocellum central metabolism using the Ensemble Modeling (EM) paradigm. Model parameterization is carried out by simultaneously imposing fermentation yield data in lactate, malate, acetate, and hydrogen production pathways for 19 measured metabolites spanning a library of 19 distinct single and multiple gene knockout mutants along with 18 intracellular metabolite concentration data for a Δgldh mutant and ten experimentally measured Michaelis–Menten kinetic parameters. Conclusions. The k-ctherm118 model captures significant metabolic changes caused by (1) nitrogen limitation leading to increased yields for lactate, pyruvate, and amino acids, and (2) ethanol stress causing an increase in intracellular sugar phosphate concentrations (~1.5-fold) due to upregulation of cofactor pools. Robustness analysis of k-ctherm118 alludes to the presence of a secondary activity of ketol-acid reductoisomerase and possible regulation by valine and/or leucine pool levels. In addition, cross-validation and robustness analysis allude to missing elements in k-ctherm118 and suggest additional experiments to improve kinetic model prediction fidelity. Overall, the study quantitatively assesses the advantages of EM-based kinetic modeling towards improved prediction of C. thermocellum metabolism and develops a predictive kinetic model which can be used to design biofuel-overproducing strains.« less

Photo-Darkening Kinetics and Structural Anisotropic Modifications in the Chalcogenide Glass Arsenic Trisulfide: a Study of Kinetic X-Ray Absorption Spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Jay Min

1990-08-01

The purpose of the study is to investigate the mechanisms involved with photo-induced atomic structural modifications in the chalcogenide glass As_2 S_3. This glass exhibits the reversible effects of photo-darkening followed by thermal bleaching. We observed the time behavior of photo-induced properties under the influence of linearly polarized band -gap light. In a macroscopic optical investigation, we monitor optical changes in the photo-darkening process, and in a local structural probe we study kinetic (or time -resolved dispersive) x-ray absorption spectroscopy. Our observations center on kinetic phenomena and structural modifications induced by polarized excitation of lone-pair orbitals in the chalcogenide glass. Experimental results include the following observations: (i) The polarity of the optically induced anisotropy is critically dependent on the intensity and the polarization of the band-gap irradiation beam. (ii) The near edge peak height in x-ray absorption spectra shows subtle but sensitive change during the photo-darkening process. (iii) Photon intensity dependent dichroic kinetics reflect a connection between the optically probed macroscopic property and the x-ray probed local anisotropic structure. Analysis of the x-ray absorption results includes a computer simulation of the polarized absorption spectra. These results suggest that specific structural units tend to orient themselves with respect to the photon polarization. A substantial part of the analysis involves a major effort in dealing with the x-ray kinetic data manipulation and the experimental difficulties caused by a synchrotron instability problem. Based on our observations, we propose a possible mechanism for the observed photo-structural modifications. Through a model of computer relaxed photo-darkening kinetics, we support the notion that a twisting of a specific intermediate range order structure is responsible for local directional variations and global network distortions. In the course of this study, we refine knowledge of intermediate range order structural configurations and the bistabilities related to these configurations. The importance of the lone-pair orbital interactions in the chalcogenide glassy network is underscored.

Development of a core Clostridium thermocellum kinetic metabolic model consistent with multiple genetic perturbations

DOE PAGES

Dash, Satyakam; Khodayari, Ali; Zhou, Jilai; ...

2017-05-02

Background. Clostridium thermocellum is a Gram-positive anaerobe with the ability to hydrolyze and metabolize cellulose into biofuels such as ethanol, making it an attractive candidate for consolidated bioprocessing (CBP). At present, metabolic engineering in C. thermocellum is hindered due to the incomplete description of its metabolic repertoire and regulation within a predictive metabolic model. Genome-scale metabolic (GSM) models augmented with kinetic models of metabolism have been shown to be effective at recapitulating perturbed metabolic phenotypes. Results. In this effort, we first update a second-generation genome-scale metabolic model (iCth446) for C. thermocellum by correcting cofactor dependencies, restoring elemental and charge balances,more » and updating GAM and NGAM values to improve phenotype predictions. The iCth446 model is next used as a scaffold to develop a core kinetic model (k-ctherm118) of the C. thermocellum central metabolism using the Ensemble Modeling (EM) paradigm. Model parameterization is carried out by simultaneously imposing fermentation yield data in lactate, malate, acetate, and hydrogen production pathways for 19 measured metabolites spanning a library of 19 distinct single and multiple gene knockout mutants along with 18 intracellular metabolite concentration data for a Δgldh mutant and ten experimentally measured Michaelis–Menten kinetic parameters. Conclusions. The k-ctherm118 model captures significant metabolic changes caused by (1) nitrogen limitation leading to increased yields for lactate, pyruvate, and amino acids, and (2) ethanol stress causing an increase in intracellular sugar phosphate concentrations (~1.5-fold) due to upregulation of cofactor pools. Robustness analysis of k-ctherm118 alludes to the presence of a secondary activity of ketol-acid reductoisomerase and possible regulation by valine and/or leucine pool levels. In addition, cross-validation and robustness analysis allude to missing elements in k-ctherm118 and suggest additional experiments to improve kinetic model prediction fidelity. Overall, the study quantitatively assesses the advantages of EM-based kinetic modeling towards improved prediction of C. thermocellum metabolism and develops a predictive kinetic model which can be used to design biofuel-overproducing strains.« less

Deformable image registration as a tool to improve survival prediction after neoadjuvant chemotherapy for breast cancer: results from the ACRIN 6657/I-SPY-1 trial

NASA Astrophysics Data System (ADS)

Jahani, Nariman; Cohen, Eric; Hsieh, Meng-Kang; Weinstein, Susan P.; Pantalone, Lauren; Davatzikos, Christos; Kontos, Despina

2018-02-01

We examined the ability of DCE-MRI longitudinal features to give early prediction of recurrence-free survival (RFS) in women undergoing neoadjuvant chemotherapy for breast cancer, in a retrospective analysis of 106 women from the ISPY 1 cohort. These features were based on the voxel-wise changes seen in registered images taken before treatment and after the first round of chemotherapy. We computed the transformation field using a robust deformable image registration technique to match breast images from these two visits. Using the deformation field, parametric response maps (PRM) — a voxel-based feature analysis of longitudinal changes in images between visits — was computed for maps of four kinetic features (signal enhancement ratio, peak enhancement, and wash-in/wash-out slopes). A two-level discrete wavelet transform was applied to these PRMs to extract heterogeneity information about tumor change between visits. To estimate survival, a Cox proportional hazard model was applied with the C statistic as the measure of success in predicting RFS. The best PRM feature (as determined by C statistic in univariable analysis) was determined for each of the four kinetic features. The baseline model, incorporating functional tumor volume, age, race, and hormone response status, had a C statistic of 0.70 in predicting RFS. The model augmented with the four PRM features had a C statistic of 0.76. Thus, our results suggest that adding information on the texture of voxel-level changes in tumor kinetic response between registered images of first and second visits could improve early RFS prediction in breast cancer after neoadjuvant chemotherapy.

Comparative testing of disinfectant efficacy on planktonic bacteria and bacterial biofilms using a new assay based on kinetic analysis of metabolic activity.

PubMed

Günther, F; Scherrer, M; Kaiser, S J; DeRosa, A; Mutters, N T

2017-03-01

The aim of our study was to develop a new reproducible method for disinfectant efficacy testing on bacterial biofilms and to evaluate the efficacy of different disinfectants against biofilms. Clinical multidrug-resistant strains were chosen as test isolates to ensure practical relevance. We compared the standard qualitative suspension assay for disinfectant testing, which does not take into account biofilm formation, to the new biofilm viability assay that uses kinetic analysis of metabolic activity in biofilms after disinfectant exposure to evaluate disinfectant efficacy. In addition, the efficacy of four standard disinfectants to clinical isolates was tested using both methods. All tested disinfectants were effective against test isolates when in planktonic state using the standard qualitative suspension assay, while disinfectants were only weakly effective against bacteria in biofilms. Disinfectant efficacy testing on planktonic organisms ignores biofilms and overestimates disinfectant susceptibility of bacteria. However, biofilm forming, e.g. on medical devices or hospital surfaces, is the natural state of bacterial living and needs to be considered in disinfectant testing. Although bacterial biofilms are the predominant manner of bacterial colonization, most standard procedures for antimicrobial susceptibility testing and efficacy testing of disinfectants are adapted for application to planktonic bacteria. To our knowledge, this is the first study to use a newly developed microplate-based biofilm test system that uses kinetic analysis of the metabolic activity in biofilms, after disinfectant exposure, to evaluate disinfectant efficacy. Our study shows that findings obtained from disinfectant efficacy testing on planktonic bacteria cannot be extrapolated to predict disinfectant efficacy on bacterial biofilms of clinically relevant multidrug-resistant organisms. © 2016 The Society for Applied Microbiology.

The logic of kinetic regulation in the thioredoxin system

PubMed Central

2011-01-01

Background The thioredoxin system consisting of NADP(H), thioredoxin reductase and thioredoxin provides reducing equivalents to a large and diverse array of cellular processes. Despite a great deal of information on the kinetics of individual thioredoxin-dependent reactions, the kinetic regulation of this system as an integrated whole is not known. We address this by using kinetic modeling to identify and describe kinetic behavioral motifs found within the system. Results Analysis of a realistic computational model of the Escherichia coli thioredoxin system revealed several modes of kinetic regulation in the system. In keeping with published findings, the model showed that thioredoxin-dependent reactions were adaptable (i.e. changes to the thioredoxin system affected the kinetic profiles of these reactions). Further and in contrast to other systems-level descriptions, analysis of the model showed that apparently unrelated thioredoxin oxidation reactions can affect each other via their combined effects on the thioredoxin redox cycle. However, the scale of these effects depended on the kinetics of the individual thioredoxin oxidation reactions with some reactions more sensitive to changes in the thioredoxin cycle and others, such as the Tpx-dependent reduction of hydrogen peroxide, less sensitive to these changes. The coupling of the thioredoxin and Tpx redox cycles also allowed for ultrasensitive changes in the thioredoxin concentration in response to changes in the thioredoxin reductase concentration. We were able to describe the kinetic mechanisms underlying these behaviors precisely with analytical solutions and core models. Conclusions Using kinetic modeling we have revealed the logic that underlies the functional organization and kinetic behavior of the thioredoxin system. The thioredoxin redox cycle and associated reactions allows for a system that is adaptable, interconnected and able to display differential sensitivities to changes in this redox cycle. This work provides a theoretical, systems-biological basis for an experimental analysis of the thioredoxin system and its associated reactions. PMID:21266044

Evaluation of the cure kinetics of the wood/pMDI bondline

Treesearch

David P. Harper; Michael P. Wolcott; Timothy G. Rials

2001-01-01

Micro-dielectric analysis (µDEA) and differentia1 scanning calorimetry (DSC) were used to monitor cure of polymeric diphenyl-methane diisocyanate (pMDI) resin with wood strands in a saturated steam environment. A first-order autocatalyzed kinetic model was employed to determine kinetic parameters. The kinetics were found to follow an Arrhenius relation. A single ramp...

Gait Analysis Using Wearable Sensors

PubMed Central

Tao, Weijun; Liu, Tao; Zheng, Rencheng; Feng, Hutian

2012-01-01

Gait analysis using wearable sensors is an inexpensive, convenient, and efficient manner of providing useful information for multiple health-related applications. As a clinical tool applied in the rehabilitation and diagnosis of medical conditions and sport activities, gait analysis using wearable sensors shows great prospects. The current paper reviews available wearable sensors and ambulatory gait analysis methods based on the various wearable sensors. After an introduction of the gait phases, the principles and features of wearable sensors used in gait analysis are provided. The gait analysis methods based on wearable sensors is divided into gait kinematics, gait kinetics, and electromyography. Studies on the current methods are reviewed, and applications in sports, rehabilitation, and clinical diagnosis are summarized separately. With the development of sensor technology and the analysis method, gait analysis using wearable sensors is expected to play an increasingly important role in clinical applications. PMID:22438763

Kinetic-limited etching of magnesium doping nitrogen polar GaN in potassium hydroxide solution

NASA Astrophysics Data System (ADS)

Jiang, Junyan; Zhang, Yuantao; Chi, Chen; Yang, Fan; Li, Pengchong; Zhao, Degang; Zhang, Baolin; Du, Guotong

2016-01-01

KOH based wet etchings were performed on both undoped and Mg-doped N-polar GaN films grown by metal-organic chemical vapor deposition. It is found that the etching rate for Mg-doped N-polar GaN gets slow obviously compared with undoped N-polar GaN. X-ray photoelectron spectroscopy analysis proved that Mg oxide formed on N-polar GaN surface is insoluble in KOH solution so that kinetic-limited etching occurs as the etching process goes on. The etching process model of Mg-doped N-polar GaN in KOH solution is tentatively purposed using a simplified ideal atomic configuration. Raman spectroscopy analysis reveals that Mg doping can induce tensile strain in N-polar GaN films. Meanwhile, p-type N-polar GaN film with a hole concentration of 2.4 ÿ 1017 cm⿿3 was obtained by optimizing bis-cyclopentadienyl magnesium flow rates.

Direct optical detection of protein-ligand interactions.

PubMed

Gesellchen, Frank; Zimmermann, Bastian; Herberg, Friedrich W

2005-01-01

Direct optical detection provides an excellent means to investigate interactions of molecules in biological systems. The dynamic equilibria inherent to these systems can be described in greater detail by recording the kinetics of a biomolecular interaction. Optical biosensors allow direct detection of interaction patterns without the need for labeling. An overview covering several commercially available biosensors is given, with a focus on instruments based on surface plasmon resonance (SPR) and reflectometric interference spectroscopy (RIFS). Potential assay formats and experimental design, appropriate controls, and calibration procedures, especially when handling low molecular weight substances, are discussed. The single steps of an interaction analysis combined with practical tips for evaluation, data processing, and interpretation of kinetic data are described in detail. In a practical example, a step-by-step procedure for the analysis of a low molecular weight compound interaction with serum protein, determined on a commercial SPR sensor, is presented.

Multi-scale modeling of irradiation effects in spallation neutron source materials

NASA Astrophysics Data System (ADS)

Yoshiie, T.; Ito, T.; Iwase, H.; Kaneko, Y.; Kawai, M.; Kishida, I.; Kunieda, S.; Sato, K.; Shimakawa, S.; Shimizu, F.; Hashimoto, S.; Hashimoto, N.; Fukahori, T.; Watanabe, Y.; Xu, Q.; Ishino, S.

2011-07-01

Changes in mechanical property of Ni under irradiation by 3 GeV protons were estimated by multi-scale modeling. The code consisted of four parts. The first part was based on the Particle and Heavy-Ion Transport code System (PHITS) code for nuclear reactions, and modeled the interactions between high energy protons and nuclei in the target. The second part covered atomic collisions by particles without nuclear reactions. Because the energy of the particles was high, subcascade analysis was employed. The direct formation of clusters and the number of mobile defects were estimated using molecular dynamics (MD) and kinetic Monte-Carlo (kMC) methods in each subcascade. The third part considered damage structural evolutions estimated by reaction kinetic analysis. The fourth part involved the estimation of mechanical property change using three-dimensional discrete dislocation dynamics (DDD). Using the above four part code, stress-strain curves for high energy proton irradiated Ni were obtained.

Analysis of thickness dependent on crystallization kinetics in thin isotactic-polysterene films

NASA Astrophysics Data System (ADS)

Khairuddin

2016-11-01

Crystalliaztion kinetics of thin film of Isotactic Polysterene (it-PS) films has been studied. Thin PET films having thickness of 338, 533, 712, 1096, 1473, and 2185 A° were prepared by using spin-cast technique. The it-PS crystals were grown on Linkam-hostage in the temperature range 130-240°C with an interval of 10°C. The crystal growths are measured by optical microscopy in lateral direction. It was found that a substantial thickness dependence on crystallisation rate. The analysis using fitting technique based on theory crystal growth of Lauritzen-Hoffman showed that the fitting technique could not resolve to predict the mechanism controlling the thickness dependence on the rate of crystallisation. The possible reasons were due to the crystallisation rate varies with the type of crystals (smooth, rough, overgrowth terrace), and the crystallisation rate changes with the time of crystallisation.

Process characteristics for microwave assisted hydrothermal carbonization of cellulose.

PubMed

Zhang, Junting; An, Ying; Borrion, Aiduan; He, Wenzhi; Wang, Nan; Chen, Yirong; Li, Guangming

2018-07-01

The process characteristics of microwave assisted hydrothermal carbonization of cellulose was investigated and a first order kinetics model based on carbon concentration was developed. Chemical properties analysis showed that comparing to conventional hydrothermal carbonization, hydrochar with comparable energy properties can be obtained with 5-10 times decrease in reaction time with assistance of microwave heating. Results from kinetics study was in great agreement with experimental analysis, that they both illustrated the predominant mechanism of the reaction depend on variations in the reaction rates of two co-existent pathways. Particularly, the pyrolysis-like intramolecular dehydration reaction was proved to be the predominant mechanism for hydrochar generation under high temperatures. Finally, the enhancement effects of microwave heating were reflected under both soluble and solid pathways in this research, suggesting microwave-assisted hydrothermal carbonization as a more attracting method for carbon-enriched hydrochar recovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

Complexity analysis and mathematical tools towards the modelling of living systems.

PubMed

Bellomo, N; Bianca, C; Delitala, M

2009-09-01

This paper is a review and critical analysis of the mathematical kinetic theory of active particles applied to the modelling of large living systems made up of interacting entities. The first part of the paper is focused on a general presentation of the mathematical tools of the kinetic theory of active particles. The second part provides a review of a variety of mathematical models in life sciences, namely complex social systems, opinion formation, evolution of epidemics with virus mutations, and vehicular traffic, crowds and swarms. All the applications are technically related to the mathematical structures reviewed in the first part of the paper. The overall contents are based on the concept that living systems, unlike the inert matter, have the ability to develop behaviour geared towards their survival, or simply to improve the quality of their life. In some cases, the behaviour evolves in time and generates destructive and/or proliferative events.

Growth kinetic and fuel quality parameters as selective criterion for screening biodiesel producing cyanobacterial strains.

PubMed

Gayathri, Manickam; Shunmugam, Sumathy; Mugasundari, Arumugam Vanmathi; Rahman, Pattanathu K S M; Muralitharan, Gangatharan

2018-01-01

The efficiency of cyanobacterial strains as biodiesel feedstock varies with the dwelling habitat. Fourteen indigenous heterocystous cyanobacterial strains from rice field ecosystem were screened based on growth kinetic and fuel parameters. The highest biomass productivity was obtained in Nostoc punctiforme MBDU 621 (19.22mg/L/day) followed by Calothrix sp. MBDU 701 (13.43mg/L/day). While lipid productivity and lipid content was highest in Nostoc spongiaeforme MBDU 704 (4.45mg/L/day and 22.5%dwt) followed by Calothrix sp. MBDU 701 (1.54mg/L/day and 10.75%dwt). Among the tested strains, Nostoc spongiaeforme MBDU 704 and Nostoc punctiforme MBDU 621 were selected as promising strains for good quality biodiesel production by Preference Ranking Organization Method for Enrichment Evaluation (PROMETHEE) and Graphical Analysis for Interactive Assistance (GAIA) analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simplification and analysis of models of calcium dynamics based on IP3-sensitive calcium channel kinetics.

PubMed

Tang, Y; Stephenson, J L; Othmer, H G

1996-01-01

We study the models for calcium (Ca) dynamics developed in earlier studies, in each of which the key component is the kinetics of intracellular inositol-1,4,5-trisphosphate-sensitive Ca channels. After rapidly equilibrating steps are eliminated, the channel kinetics in these models are represented by a single differential equation that is linear in the state of the channel. In the reduced kinetic model, the graph of the steady-state fraction of conducting channels as a function of log10(Ca) is a bell-shaped curve. Dynamically, a step increase in inositol-1,4,5-trisphosphate induces an incremental increase in the fraction of conducting channels, whereas a step increase in Ca can either potentiate or inhibit channel activation, depending on the Ca level before and after the increase. The relationships among these models are discussed, and experimental tests to distinguish between them are given. Under certain conditions the models for intracellular calcium dynamics are reduced to the singular perturbed form epsilon dx/d tau = f(x, y, p), dy/d tau = g(x, y, p). Phase-plane analysis is applied to a generic form of these simplified models to show how different types of Ca response, such as excitability, oscillations, and a sustained elevation of Ca, can arise. The generic model can also be used to study frequency encoding of hormonal stimuli, to determine the conditions for stable traveling Ca waves, and to understand the effect of channel properties on the wave speed.

Structure and Kinetic Analysis of H2S Production by Human Mercaptopyruvate Sulfurtransferase*

PubMed Central

Yadav, Pramod Kumar; Yamada, Kazuhiro; Chiku, Taurai; Koutmos, Markos; Banerjee, Ruma

2013-01-01

Mercaptopyruvate sulfurtransferase (MST) is a source of endogenous H2S, a gaseous signaling molecule implicated in a wide range of physiological processes. The contribution of MST versus the other two H2S generators, cystathionine β-synthase and γ-cystathionase, has been difficult to evaluate because many studies on MST have been conducted at high pH and have used varied reaction conditions. In this study, we have expressed, purified, and crystallized human MST in the presence of the substrate 3-mercaptopyruvate (3-MP). The kinetics of H2S production by MST from 3-MP was studied at pH 7.4 in the presence of various physiological persulfide acceptors: cysteine, dihydrolipoic acid, glutathione, homocysteine, and thioredoxin, and in the presence of cyanide. The crystal structure of MST reveals a mixture of the product complex containing pyruvate and an active site cysteine persulfide (Cys248-SSH) and a nonproductive intermediate in which 3-MP is covalently linked via a disulfide bond to an active site cysteine. The crystal structure analysis allows us to propose a detailed mechanism for MST in which an Asp-His-Ser catalytic triad is positioned to activate the nucleophilic cysteine residue and participate in general acid-base chemistry, whereas our kinetic analysis indicates that thioredoxin is likely to be the major physiological persulfide acceptor for MST. PMID:23698001

Rapid freezing of water under dynamic compression

NASA Astrophysics Data System (ADS)

Myint, Philip C.; Belof, Jonathan L.

2018-06-01

Understanding the behavior of materials at extreme pressures is a central issue in fields like aerodynamics, astronomy, and geology, as well as for advancing technological grand challenges such as inertial confinement fusion. Dynamic compression experiments to probe high-pressure states often encounter rapid phase transitions that may cause the materials to behave in unexpected ways, and understanding the kinetics of these phase transitions remains an area of great interest. In this review, we examine experimental and theoretical/computational efforts to study the freezing kinetics of water to a high-pressure solid phase known as ice VII. We first present a detailed analysis of dynamic compression experiments in which water has been observed to freeze on sub-microsecond time scales to ice VII. This is followed by a discussion of the limitations of currently available molecular and continuum simulation methods in modeling these experiments. We then describe how our phase transition kinetics models, which are based on classical nucleation theory, provide a more physics-based framework that overcomes some of these limitations. Finally, we give suggestions on future experimental and modeling work on the liquid–ice VII transition, including an outline of the development of a predictive multiscale model in which molecular and continuum simulations are intimately coupled.

Kinetics of Static Strain Aging in Polycrystalline NiAl-based Alloys

NASA Technical Reports Server (NTRS)

Weaver, M. L.; Kaufman, M. J.; Noebe, R. D.

1996-01-01

The kinetics of yield point return have been studied in two NiAl-based alloys as a function of aging time at temperatures between 300 and 700 K. The results indicate that the upper yield stress increment, Delta sigma(sub u) (i.e., stress difference between the upper yield point and the final flow stress achieved during prestraining), in conventional purity (CP-NiAl) and in high purity carbon-doped (NiAl-C) material first increased with a t(exp 2/3) relationship before reaching a plateau. This behavior suggests that a Cottrell locking mechanism is the cause for yield points in NiAl. In addition, positive y-axis intercepts were observed in plots of Delta sigma(sub u) versus t(exp 2/3) suggesting the operation of a Snoek mechanism. Analysis according to the Cottrell Bilby model of atmosphere formation around dislocations yields an activation energy for yield point return in the range 70 to 76 kJ/mol which is comparable to the activation energy for diffusion of interstitial impurities in bcc metals. It is, thus, concluded that the kinetics of static strain aging in NiAl are controlled by the locking of dislocations by Cottrell atmospheres of carbon atoms around dislocations.

Measurements of cloud condensation nuclei activity and droplet activation kinetics of fresh unprocessed regional dust samples and minerals

NASA Astrophysics Data System (ADS)

Kumar, P.; Sokolik, I. N.; Nenes, A.

2011-04-01

This study reports laboratory measurements of cloud condensation nuclei (CCN) activity and droplet activation kinetics of aerosols dry generated from clays, calcite, quartz, and desert soil samples from Northern Africa, East Asia/China, and Northern America. Based on the observed dependence of critical supersaturation, sc, with particle dry diameter, Ddry, we found that FHH (Frenkel, Halsey and Hill) adsorption activation theory is a far more suitable framework for describing fresh dust CCN activity than Köhler theory. One set of FHH parameters (AFHH ∼ 2.25 ± 0.75, BFHH ∼ 1.20 ± 0.10) can adequately reproduce the measured CCN activity for all species considered, and also explains the large range of hygroscopicities reported in the literature. Based on a threshold droplet growth analysis, mineral dust aerosols were found to display retarded activation kinetics compared to ammonium sulfate. Comprehensive simulations of mineral dust activation and growth in the CCN instrument suggest that this retardation is equivalent to a reduction of the water vapor uptake coefficient (relative to that for calibration ammonium sulfate aerosol) by 30-80%. These results suggest that dust particles do not require deliquescent material to act as CCN in the atmosphere.

Measurements of cloud condensation nuclei activity and droplet activation kinetics of fresh unprocessed regional dust samples and minerals

NASA Astrophysics Data System (ADS)

Kumar, P.; Sokolik, I. N.; Nenes, A.

2010-12-01

This study reports laboratory measurements of cloud condensation nuclei (CCN) activity and droplet activation kinetics of aerosols dry-generated from clays, calcite, quartz, and desert soil samples from Northern Africa, East Asia/China, and Northern America. Based on the observed dependence of critical supersaturation, sc, with particle dry diameter, Ddry, we find that FHH adsorption activation theory is a far more suitable framework for describing fresh dust CCN activity than Köhler theory. One set of FHH parameters (AFFH ~ 2.25 ± 0.75, BFFH ~ 1.20 ± 0.10) can adequately reproduce the measured CCN activity for all species considered, and also explains the large range of hygroscopicities reported in the literature. Based on threshold droplet growth analysis, mineral dust aerosols were found to display retarded activation kinetics compared to ammonium sulfate. Comprehensive simulations of mineral dust activation and growth in the CCN instrument suggest that this retardation is equivalent to a reduction of the water vapor uptake coefficient (relative to that for calibration ammonium sulfate aerosol) by 30-80%. These results suggest that dust particles do not require deliquescent material to act as CCN in the atmosphere.

Preparation of nano-TiO2/diatomite-based porous ceramics and their photocatalytic kinetics for formaldehyde degradation

NASA Astrophysics Data System (ADS)

Gao, Ru-qin; Sun, Qian; Fang, Zhi; Li, Guo-ting; Jia, Meng-zhe; Hou, Xin-mei

2018-01-01

Diatomite-based porous ceramics were adopted as carriers to immobilize nano-TiO2 via a hydrolysis-deposition technique. The thermal degradation of as-prepared composites was investigated using thermogravimetric-differential thermal analysis, and the phase and microstructure were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, and transmission electron microscopy. The results indicated that the carriers were encapsulated by nano-TiO2 with a thickness of 300-450 nm. The main crystalline phase of TiO2 calcined at 650°C was anatase, and the average grain size was 8.3 nm. The FT-IR absorption bands at 955.38 cm-1 suggested that new chemical bonds among Ti, O, and Si had formed in the composites. The photocatalytic (PC) activity of the composites was investigated under UV irradiation. Furthermore, the photodegradation kinetics of formaldehyde was investigated using the composites as the cores of an air cleaner. A kinetics study showed that the reaction rate constants of the gas-phase PC reaction of formaldehyde were κ = 0.576 mg·m-3·min-1 and K = 0.048 m3/mg.

Rapid freezing of water under dynamic compression.

PubMed

Myint, Philip C; Belof, Jonathan L

2018-06-13

Understanding the behavior of materials at extreme pressures is a central issue in fields like aerodynamics, astronomy, and geology, as well as for advancing technological grand challenges such as inertial confinement fusion. Dynamic compression experiments to probe high-pressure states often encounter rapid phase transitions that may cause the materials to behave in unexpected ways, and understanding the kinetics of these phase transitions remains an area of great interest. In this review, we examine experimental and theoretical/computational efforts to study the freezing kinetics of water to a high-pressure solid phase known as ice VII. We first present a detailed analysis of dynamic compression experiments in which water has been observed to freeze on sub-microsecond time scales to ice VII. This is followed by a discussion of the limitations of currently available molecular and continuum simulation methods in modeling these experiments. We then describe how our phase transition kinetics models, which are based on classical nucleation theory, provide a more physics-based framework that overcomes some of these limitations. Finally, we give suggestions on future experimental and modeling work on the liquid-ice VII transition, including an outline of the development of a predictive multiscale model in which molecular and continuum simulations are intimately coupled.

Spatio-temporal diffusion of dynamic PET images

NASA Astrophysics Data System (ADS)

Tauber, C.; Stute, S.; Chau, M.; Spiteri, P.; Chalon, S.; Guilloteau, D.; Buvat, I.

2011-10-01

Positron emission tomography (PET) images are corrupted by noise. This is especially true in dynamic PET imaging where short frames are required to capture the peak of activity concentration after the radiotracer injection. High noise results in a possible bias in quantification, as the compartmental models used to estimate the kinetic parameters are sensitive to noise. This paper describes a new post-reconstruction filter to increase the signal-to-noise ratio in dynamic PET imaging. It consists in a spatio-temporal robust diffusion of the 4D image based on the time activity curve (TAC) in each voxel. It reduces the noise in homogeneous areas while preserving the distinct kinetics in regions of interest corresponding to different underlying physiological processes. Neither anatomical priors nor the kinetic model are required. We propose an automatic selection of the scale parameter involved in the diffusion process based on a robust statistical analysis of the distances between TACs. The method is evaluated using Monte Carlo simulations of brain activity distributions. We demonstrate the usefulness of the method and its superior performance over two other post-reconstruction spatial and temporal filters. Our simulations suggest that the proposed method can be used to significantly increase the signal-to-noise ratio in dynamic PET imaging.

Removal of free fatty acid in Azadirachta indica (Neem) seed oil using phosphoric acid modified mordenite for biodiesel production.

PubMed

SathyaSelvabala, Vasanthakumar; Varathachary, Thiruvengadaravi Kadathur; Selvaraj, Dinesh Kirupha; Ponnusamy, Vijayalakshmi; Subramanian, Sivanesan

2010-08-01

In this study free fatty acids present in Azadirachta indica (Neem) oil were esterified with our synthesized phosphoric acid modified catalyst. During the esterification, the acid value was reduced from 24.4 to 1.8 mg KOH/g oil. Synthesized catalyst was characterized by NH(3) TPD, XRD, SEM, FTIR and TGA analysis. During phosphoric acid modification hydrophobic character and weak acid sites of the mordenite were increased, which lead to better esterification when compared to H-mordenite. A kinetic study demonstrates that the esterification reaction followed pseudo-first order kinetics. Thermodynamic studies were also done based on the Arrhenius model. (c) 2010 Elsevier Ltd. All rights reserved.

Kinetics of biological decolorisation of anthraquinone based Reactive Blue 19 using an isolated strain of Enterobacter sp.F NCIM 5545.

PubMed

Holkar, Chandrakant R; Pandit, Aniruddha B; Pinjari, Dipak V

2014-12-01

In the present study, an attempt was made to evaluate the bacterial decolorisation of Reactive Blue 19 by an Enterobacter sp.F which was isolated from a mixed culture from anaerobic digester for biogas production. Phenotypic characterization and phylogenetic analysis based on DNA sequencing comparisons indicate that Enterobacter sp.F was 99.7% similar to Enterobacter cloacae ATCC13047. The kinetics of Reactive Blue 19 dye decolorisation by bacterium had been estimated. Effects of substrate concentration, oxygen, temperature, pH, glucose and glucose to microbe weight ratio on the rate of decolorisation were investigated to understand key factor that determines the performance of dye decolorisation. The maximum decolorisation efficiency of Reactive Blue 19 was 90% over period of 24 h for optimized parameter. To the best of our knowledge, this research study is the report where Enterobacter sp.F has been reported with about 90% decolorizing ability against anthraquinone based Reactive Blue 19 dye. Copyright © 2014 Elsevier Ltd. All rights reserved.

Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks.

PubMed

Deng, De-Ming; Chang, Cheng-Hung

2015-05-14

Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal the same experimentally measured fluctuating behaviors and unique fluctuation related physical properties. To clarify these questions, we introduce stochasticity into the traditional lumping analysis, generalize it from rate equations to chemical master equations and stochastic differential equations, and extract the fluctuation relations between kinetically and thermodynamically equivalent networks under intrinsic and extrinsic noises. The results provide a theoretical basis for the legitimate use of low-dimensional models in the studies of macromolecular fluctuations and, more generally, for exploring stochastic features in different levels of contracted networks in chemical and biological kinetic systems.

NASA upper atmosphere research program: Research summaries, 1990 - 1991. Report to the Congress and the Environmental Protection Agency

NASA Technical Reports Server (NTRS)

1992-01-01

The objectives, status, and accomplishments of the research tasks supported under the NASA Upper Atmosphere Research Program (UARP) are presented. The topics covered include the following: balloon-borne in situ measurements; balloon-borne remote measurements; ground-based measurements; aircraft-borne measurements; rocket-borne measurements; instrument development; reaction kinetics and photochemistry; spectroscopy; stratospheric dynamics and related analysis; stratospheric chemistry, analysis, and related modeling; and global chemical modeling.

New insight in quantitative analysis of vascular permeability during immune reaction (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kalchenko, Vyacheslav; Molodij, Guillaume; Kuznetsov, Yuri; Smolyakov, Yuri; Israeli, David; Meglinski, Igor; Harmelin, Alon

2016-03-01

The use of fluorescence imaging of vascular permeability becomes a golden standard for assessing the inflammation process during experimental immune response in vivo. The use of the optical fluorescence imaging provides a very useful and simple tool to reach this purpose. The motivation comes from the necessity of a robust and simple quantification and data presentation of inflammation based on a vascular permeability. Changes of the fluorescent intensity, as a function of time is a widely accepted method to assess the vascular permeability during inflammation related to the immune response. In the present study we propose to bring a new dimension by applying a more sophisticated approach to the analysis of vascular reaction by using a quantitative analysis based on methods derived from astronomical observations, in particular by using a space-time Fourier filtering analysis followed by a polynomial orthogonal modes decomposition. We demonstrate that temporal evolution of the fluorescent intensity observed at certain pixels correlates quantitatively to the blood flow circulation at normal conditions. The approach allows to determine the regions of permeability and monitor both the fast kinetics related to the contrast material distribution in the circulatory system and slow kinetics associated with extravasation of the contrast material. Thus, we introduce a simple and convenient method for fast quantitative visualization of the leakage related to the inflammatory (immune) reaction in vivo.

Cysteine-Functionalized Chitosan Magnetic Nano-Based Particles for the Recovery of Light and Heavy Rare Earth Metals: Uptake Kinetics and Sorption Isotherms

PubMed Central

Galhoum, Ahmed A.; Mafhouz, Mohammad G.; Abdel-Rehem, Sayed T.; Gomaa, Nabawia A.; Atia, Asem A.; Vincent, Thierry; Guibal, Eric

2015-01-01

Cysteine-functionalized chitosan magnetic nano-based particles were synthesized for the sorption of light and heavy rare earth (RE) metal ions (La(III), Nd(III) and Yb(III)). The structural, surface, and magnetic properties of nano-sized sorbent were investigated by elemental analysis, FTIR, XRD, TEM and VSM (vibrating sample magnetometry). Experimental data show that the pseudo second-order rate equation fits the kinetic profiles well, while sorption isotherms are described by the Langmuir model. Thermodynamic constants (ΔG°, ΔH°) demonstrate the spontaneous and endothermic nature of sorption. Yb(III) (heavy RE) was selectively sorbed while light RE metal ions La(III) and Nd(III) were concentrated/enriched in the solution. Cationic species RE(III) in aqueous solution can be adsorbed by the combination of chelating and anion-exchange mechanisms. The sorbent can be efficiently regenerated using acidified thiourea. PMID:28347004

Atmospheric Transformation of Volatile Organic Compounds

DTIC Science & Technology

2008-03-01

Study Analysis Reactant mixtures and standards from product identification experiments were sampled by exposing a 100% polydimethylsiloxane solid...later using the DNPH derivatization method described above and confirmed against a commercial standard. HPLC analysis of the DNPH cartridges also...reaction mixture for a combined total photolysis time ofapproximately 50 seconds. 2.3. Kinetic Study Analysis Samples from kinetic studies were

Use of Physicochemical Parameters to Assess the Environmental Fate of Organic Pollutants: The Fugacity Model

ERIC Educational Resources Information Center

Domenech, Xavier; Ayllon, Jose Antonio; Peral, Jose

2006-01-01

The environmental fate and behavior of different organic pollutants based on the qualitative analysis of thermodynamic and kinetic data is presented. The Fugacity model allows the use of different partition constants in an easy way, to determine the distribution of chemical between different phases in equilibrium of an environmental system.

Dynamic determination of kinetic parameters and computer simulation of growth of Clostridium perfringens in cooked beef

USDA-ARS?s Scientific Manuscript database

The objective of this research was to develop a new one-step methodology that uses a dynamic approach to directly construct a tertiary model for prediction of the growth of C. perfringens in cooked beef. This methodology was based on numerical analysis and optimization of both primary and secondary...

Impact of Temperature and Non-Gaussian Statistics on Electron Transfer in Donor-Bridge-Acceptor Molecules.

PubMed

Waskasi, Morteza M; Newton, Marshall D; Matyushov, Dmitry V

2017-03-30

A combination of experimental data and theoretical analysis provides evidence of a bell-shaped kinetics of electron transfer in the Arrhenius coordinates ln k vs 1/T. This kinetic law is a temperature analogue of the familiar Marcus bell-shaped dependence based on ln k vs the reaction free energy. These results were obtained for reactions of intramolecular charge shift between the donor and acceptor separated by a rigid spacer studied experimentally by Miller and co-workers. The non-Arrhenius kinetic law is a direct consequence of the solvent reorganization energy and reaction driving force changing approximately as hyperbolic functions with temperature. The reorganization energy decreases and the driving force increases when temperature is increased. The point of equality between them marks the maximum of the activationless reaction rate. Reaching the consistency between the kinetic and thermodynamic experimental data requires the non-Gaussian statistics of the donor-acceptor energy gap described by the Q-model of electron transfer. The theoretical formalism combines the vibrational envelope of quantum vibronic transitions with the Q-model describing the classical component of the Franck-Condon factor and a microscopic solvation model of the solvent reorganization energy and the reaction free energy.

Evaluation of a non-Arrhenius model for therapeutic monoclonal antibody aggregation.

PubMed

Kayser, Veysel; Chennamsetty, Naresh; Voynov, Vladimir; Helk, Bernhard; Forrer, Kurt; Trout, Bernhardt L

2011-07-01

Understanding antibody aggregation is of great significance for the pharmaceutical industry. We studied the aggregation of five different therapeutic monoclonal antibodies (mAbs) with size-exclusion chromatography-high-performance liquid chromatography (SEC-HPLC), fluorescence spectroscopy, electron microscopy, and light scattering methods at various temperatures with the aim of gaining insight into the aggregation process and developing models of it. In particular, we find that the kinetics can be described by a second-order model and are non-Arrhenius. Thus, we develop a non-Arrhenius model to connect accelerated aggregation experiments at high temperature to long-term storage experiments at low temperature. We evaluate our model by predicting mAb aggregation and comparing it with long-term behavior. Our results suggest that the number of monomers and mAb conformations within aggregates vary with the size and age of the aggregates, and that only certain sizes of aggregates are populated in the solution. We also propose a kinetic model based on conformational changes of proteins and monomer peak loss kinetics from SEC-HPLC. This model could be employed for a detail analysis of mAb aggregation kinetics. Copyright © 2011 Wiley-Liss, Inc. and the American Pharmacists Association

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

Waskasi, Morteza M.; Newton, Marshall D.; Matyushov, Dmitry V.

A combination of experimental data and theoretical analysis provides evidence of a bell-shaped kinetics of electron transfer in the Arrhenius coordinates ln k vs 1/T . This kinetic law is a temperature analog of the familiar Marcus bell-shaped dependence based on ln k vs the reaction free energy. These results were obtained for reactions of intramolecular charge shift between the donor and acceptor separated by a rigid spacer studied experimentally by Miller and co-workers. The non-Arrhenius kinetic law is a direct consequence of the solvent reorganization energy and reaction driving force changing approximately as hyperbolic functions with temperature. The reorganizationmore » energy decreases and the driving force increases when temperature is increased. The point of equality between them marks the maximum of the activationless reaction rate. Reaching the consistency between the kinetic and thermodynamic experimental data requires the non-Gaussian statistics of the donor-acceptor energy gap described by the Q-model of electron transfer. Furthermore, the theoretical formalism combines the vibrational envelope of quantum vibronic transitions with the Q-model describing the classical component of the Franck-Condon factor and a microscopic solvation model of the solvent reorganization energy and the reaction free energy.« less

Transport in semiconductor nanowire superlattices described by coupled quantum mechanical and kinetic models.

PubMed

Alvaro, M; Bonilla, L L; Carretero, M; Melnik, R V N; Prabhakar, S

2013-08-21

In this paper we develop a kinetic model for the analysis of semiconductor superlattices, accounting for quantum effects. The model consists of a Boltzmann-Poisson type system of equations with simplified Bhatnagar-Gross-Krook collisions, obtained from the general time-dependent Schrödinger-Poisson model using Wigner functions. This system for superlattice transport is supplemented by the quantum mechanical part of the model based on the Ben-Daniel-Duke form of the Schrödinger equation for a cylindrical superlattice of finite radius. The resulting energy spectrum is used to characterize the Fermi-Dirac distribution that appears in the Bhatnagar-Gross-Krook collision, thereby coupling the quantum mechanical and kinetic parts of the model. The kinetic model uses the dispersion relation obtained by the generalized Kronig-Penney method, and allows us to estimate radii of quantum wire superlattices that have the same miniband widths as in experiments. It also allows us to determine more accurately the time-dependent characteristics of superlattices, in particular their current density. Results, for several experimentally grown superlattices, are discussed in the context of self-sustained coherent oscillations of the current density which are important in an increasing range of current and potential applications.

Kinetic parameters and structural variations in Cu-Al-Mn and Cu-Al-Mn-Mg shape memory alloys

NASA Astrophysics Data System (ADS)

Canbay, Canan Aksu

2017-02-01

In this work polycrystalline Cu-Al-Mn and Cu-Al-Mn-Mg SMAs were fabricated by arc melting. The thermal analysis was made to determine the characteristic transformation temperatures of the samples and kinetic parameters. Also the effect of Mg on transformation temperatures and kinetic parameters detected. The structural analysis was made to designate the diffraction planes of martensite phase at room temperature and this was supported by optical measurement observations.

[Progress in Raman spectroscopic measurement of methane hydrate].

PubMed

Xu, Feng; Zhu, Li-hua; Wu, Qiang; Xu, Long-jun

2009-09-01

Complex thermodynamics and kinetics problems are involved in the methane hydrate formation and decomposition, and these problems are crucial to understanding the mechanisms of hydrate formation and hydrate decomposition. However, it was difficult to accurately obtain such information due to the difficulty of measurement since methane hydrate is only stable under low temperature and high pressure condition, and until recent years, methane hydrate has been measured in situ using Raman spectroscopy. Raman spectroscopy, a non-destructive and non-invasive technique, is used to study vibrational modes of molecules. Studies of methane hydrate using Raman spectroscopy have been developed over the last decade. The Raman spectra of CH4 in vapor phase and in hydrate phase are presented in this paper. The progress in the research on methane hydrate formation thermodynamics, formation kinetics, decomposition kinetics and decomposition mechanism based on Raman spectroscopic measurements in the laboratory and deep sea are reviewed. Formation thermodynamic studies, including in situ observation of formation condition of methane hydrate, analysis of structure, and determination of hydrate cage occupancy and hydration numbers by using Raman spectroscopy, are emphasized. In the aspect of formation kinetics, research on variation in hydrate cage amount and methane concentration in water during the growth of hydrate using Raman spectroscopy is also introduced. For the methane hydrate decomposition, the investigation associated with decomposition mechanism, the mutative law of cage occupancy ratio and the formulation of decomposition rate in porous media are described. The important aspects for future hydrate research based on Raman spectroscopy are discussed.

Quantitative pharmacological analysis of antagonist binding kinetics at CRF1 receptors in vitro and in vivo

PubMed Central

Ramsey, Simeon J; Attkins, Neil J; Fish, Rebecca; van der Graaf, Piet H

2011-01-01

BACKGROUND AND PURPOSE A series of novel non-peptide corticotropin releasing factor type-1 receptor (CRF1) antagonists were found to display varying degrees of insurmountable and non-competitive behaviour in functional in vitro assays. We describe how we attempted to relate this behaviour to ligand receptor-binding kinetics in a quantitative manner and how this resulted in the development and implementation of an efficient pharmacological screening method based on principles described by Motulsky and Mahan. EXPERIMENTAL APPROACH A non-equilibrium binding kinetic assay was developed to determine the receptor binding kinetics of non-peptide CRF1 antagonists. Nonlinear, mixed-effects modelling was used to obtain estimates of the compounds association and dissociation rates. We present an integrated pharmacokinetic–pharmacodynamic (PKPD) approach, whereby the time course of in vivo CRF1 receptor binding of novel compounds can be predicted on the basis of in vitro assays. KEY RESULTS The non-competitive antagonist behaviour appeared to be correlated to the CRF1 receptor off-rate kinetics. The integrated PKPD model suggested that, at least in a qualitative manner, the in vitro assay can be used to triage and select compounds for further in vivo investigations. CONCLUSIONS AND IMPLICATIONS This study provides evidence for a link between ligand offset kinetics and insurmountable/non-competitive antagonism at the CRF1 receptor. The exact molecular pharmacological nature of this association remains to be determined. In addition, we have developed a quantitative framework to study and integrate in vitro and in vivo receptor binding kinetic behaviour of CRF1 receptor antagonists in an efficient manner in a drug discovery setting. PMID:21449919

Theoretical study of the kinetics of reactions of the monohalogenated methanes with atomic chlorine.

PubMed

Brudnik, Katarzyna; Twarda, Maria; Sarzyński, Dariusz; Jodkowski, Jerzy T

2013-04-01

Ab initio calculations at the G2 level were used in a theoretical description of the kinetics and mechanism of the hydrogen abstraction reactions from fluoro-, chloro- and bromomethane by chlorine atoms. The profiles of the potential energy surfaces show that mechanism of the reactions under investigation is complex and consists of two - in the case of CH3F+Cl - and of three elementary steps for CH3Cl+Cl and CH3Br+Cl. The heights of the energy barrier related to the H-abstraction are of 8-10 kJ mol(-1), the lowest value corresponds to CH3Cl+Cl and the highest one to CH3F+Cl. The rate constants were calculated using the theoretical method based on the RRKM theory and the simplified version of the statistical adiabatic channel model. The kinetic equations derived in this study[Formula: see text]and[Formula: see text]allow a description of the kinetics of the reactions under investigation in the temperature range of 200-3000 K. The kinetics of reactions of the entirely deuterated reactants were also included in the kinetic analysis. Results of ab initio calculations show that D-abstraction process is related with the energy barrier of 5 kJ mol(-1) higher than the H-abstraction from the corresponding non-deuterated reactant molecule. The derived analytical equations for the reactions, CD3X+Cl, CH2X+HCl and CD2X+DCl (X = F, Cl and Br) are a substantial supplement of the kinetic data necessary for the description and modeling of the processes of importance in the atmospheric chemistry.

Low Temperature Kinetics of the First Steps of Water Cluster Formation

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

Bourgalais, J.; Roussel, V.; Capron, M.

2016-03-01

We present a combined experimental and theoretical low temperature kinetic study of water cluster formation. Water cluster growth takes place in low temperature (23-69 K) supersonic flows. The observed kinetics of formation of water clusters are reproduced with a kinetic model based on theoretical predictions for the first steps of clusterization. The temperature-and pressure-dependent association and dissociation rate coefficients are predicted with an ab initio transition state theory based master equation approach over a wide range of temperatures (20-100 K) and pressures (10(-6) - 10 bar).

Structural investigation of oxovanadium(IV) Schiff base complexes: X-ray crystallography, electrochemistry and kinetic of thermal decomposition.

PubMed

Asadi, Mozaffar; Asadi, Zahra; Savaripoor, Nooshin; Dusek, Michal; Eigner, Vaclav; Shorkaei, Mohammad Ranjkesh; Sedaghat, Moslem

2015-02-05

A series of new VO(IV) complexes of tetradentate N2O2 Schiff base ligands (L(1)-L(4)), were synthesized and characterized by FT-IR, UV-vis and elemental analysis. The structure of the complex VOL(1)⋅DMF was also investigated by X-ray crystallography which revealed a vanadyl center with distorted octahedral coordination where the 2-aza and 2-oxo coordinating sites of the ligand were perpendicular to the "-yl" oxygen. The electrochemical properties of the vanadyl complexes were investigated by cyclic voltammetry. A good correlation was observed between the oxidation potentials and the electron withdrawing character of the substituents on the Schiff base ligands, showing the following trend: MeO5-H>5-Br>5-Cl. Furthermore, the kinetic parameters of thermal decomposition were calculated by using the Coats-Redfern equation. According to the Coats-Redfern plots the kinetics of thermal decomposition of studied complexes is of the first-order in all stages, the free energy of activation for each following stage is larger than the previous one and the complexes have good thermal stability. The preparation of VOL(1)⋅DMF yielded also another compound, one kind of vanadium oxide [VO]X, with different habitus of crystals, (platelet instead of prisma) and without L(1) ligand, consisting of a V10O28 cage, diaminium moiety and dimethylamonium as a counter ions. Because its crystal structure was also new, we reported it along with the targeted complex. Copyright © 2014 Elsevier B.V. All rights reserved.

Inverse modeling approach for evaluation of kinetic parameters of a biofilm reactor using tabu search.

PubMed

Kumar, B Shiva; Venkateswarlu, Ch

2014-08-01

The complex nature of biological reactions in biofilm reactors often poses difficulties in analyzing such reactors experimentally. Mathematical models could be very useful for their design and analysis. However, application of biofilm reactor models to practical problems proves somewhat ineffective due to the lack of knowledge of accurate kinetic models and uncertainty in model parameters. In this work, we propose an inverse modeling approach based on tabu search (TS) to estimate the parameters of kinetic and film thickness models. TS is used to estimate these parameters as a consequence of the validation of the mathematical models of the process with the aid of measured data obtained from an experimental fixed-bed anaerobic biofilm reactor involving the treatment of pharmaceutical industry wastewater. The results evaluated for different modeling configurations of varying degrees of complexity illustrate the effectiveness of TS for accurate estimation of kinetic and film thickness model parameters of the biofilm process. The results show that the two-dimensional mathematical model with Edward kinetics (with its optimum parameters as mu(max)rho(s)/Y = 24.57, Ks = 1.352 and Ki = 102.36) and three-parameter film thickness expression (with its estimated parameters as a = 0.289 x 10(-5), b = 1.55 x 10(-4) and c = 15.2 x 10(-6)) better describes the biofilm reactor treating the industry wastewater.

Application of the kinetic and isotherm models for better understanding of the behaviors of silver nanoparticles adsorption onto different adsorbents.

PubMed

Syafiuddin, Achmad; Salmiati, Salmiati; Jonbi, Jonbi; Fulazzaky, Mohamad Ali

2018-07-15

It is the first time to do investigation the reliability and validity of thirty kinetic and isotherm models for describing the behaviors of adsorption of silver nanoparticles (AgNPs) onto different adsorbents. The purpose of this study is therefore to assess the most reliable models for the adsorption of AgNPs onto feasibility of an adsorbent. The fifteen kinetic models and fifteen isotherm models were used to test secondary data of AgNPs adsorption collected from the various data sources. The rankings of arithmetic mean were estimated based on the six statistical analysis methods of using a dedicated software of the MATLAB Optimization Toolbox with a least square curve fitting function. The use of fractal-like mixed 1, 2-order model for describing the adsorption kinetics and that of Fritz-Schlunder and Baudu models for describing the adsorption isotherms can be recommended as the most reliable models for AgNPs adsorption onto the natural and synthetic adsorbent materials. The application of thirty models have been identified for the adsorption of AgNPs to clarify the usefulness of both groups of the kinetic and isotherm equations in the rank order of the levels of accuracy, and this significantly contributes to understandability and usability of the proper models and makes to knowledge beyond the existing literatures. Copyright © 2018 Elsevier Ltd. All rights reserved.

Compartmental Modeling and Dosimetry of in Vivo Metabolic Studies of Leucine and Three Secretory Proteins in Humans Using Radioactive Tracers

NASA Astrophysics Data System (ADS)

Venkatakrishnan, Vaidehi

1995-01-01

Physical and mathematical models provide a systematic means of looking at biological systems. Radioactive tracer kinetic studies open a unique window to study complex tracee systems such as protein metabolism in humans. This research deals with compartmental modeling of tracer kinetic data on leucine and apolipoprotein metabolism obtained using an endogenous tritiated leucine tracer administered as a bolus, and application of compartmental modeling techniques for dosimetric evaluation of metabolic studies of radioiodinated apolipoproteins. Dr. Waldo R. Fisher, Department of Medicine, was the coordinating research supervisor and the work was carried out in his laboratory. A compartmental model for leucine kinetics in humans has been developed that emphasizes its recycling pathways which were examined over two weeks. This model builds on a previously published model of Cobelli et al, that analyzed leucine kinetic data up to only eight hours. The proposed model includes different routes for re-entry of leucine from protein breakdown into plasma accounting for proteins which turn over at different rates. This new model successfully incorporates published models of three secretory proteins: albumin, apoA-I, and VLDL apoB, in toto thus increasing its validity and utility. The published model of apoA-I, based on an exogenous radioiodinated tracer, was examined with data obtained using an endogenous leucine tracer using compartmental techniques. The analysis concludes that the major portion of apoA-I enters plasma by a fast pathway but the major fraction of apoA-I in plasma resides with a second slow pathway; further the study is suggestive of a precursor-product relationship between the two plasma apoA-I pools. The possible relevance of the latter suggestion to the aberrant kinetics of apoA-I in Tangier disease is discussed. The analysis of apoA-II data resulted in similar conclusions. A methodology for evaluating the dosimetry of radioiodinated apolipoproteins by combining kinetic models of iodine and apolipoprotein metabolism has been developed. Residence times for source organs, whole body, thyroid, bladder, and red bone marrow obtained with this analysis, were used to calculate the cumulated activities and thus doses arising from these organs. The influence of the duration of the thyroid blocking period using stable iodine on the dose to the thyroid has been demonstrated.

Model-based metabolism design: constraints for kinetic and stoichiometric models

PubMed Central

Stalidzans, Egils; Seiman, Andrus; Peebo, Karl; Komasilovs, Vitalijs; Pentjuss, Agris

2018-01-01

The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms. Some constraints (mass balance, energy balance, and steady-state assumption) serve as a basis for many modelling approaches. There are others (total enzyme activity constraint and homeostatic constraint) proposed decades ago, but which are frequently ignored in design development. Several new approaches of cellular analysis have made possible the application of constraints like cell size, surface, and resource balance. Constraints for kinetic and stoichiometric models are grouped according to their applicability preconditions in (1) general constraints, (2) organism-level constraints, and (3) experiment-level constraints. General constraints are universal and are applicable for any system. Organism-level constraints are applicable for biological systems and usually are organism-specific, but these constraints can be applied without information about experimental conditions. To apply experimental-level constraints, peculiarities of the organism and the experimental set-up have to be taken into account to calculate the values of constraints. The limitations of applicability of particular constraints for kinetic and stoichiometric models are addressed. PMID:29472367

A [32P]-NAD+-based method to identify and quantitate long residence time enoyl-ACP reductase inhibitors

PubMed Central

Yu, Weixuan; Neckles, Carla; Chang, Andrew; Bommineni, Gopal Reddy; Spagnuolo, Lauren; Zhang, Zhuo; Liu, Nina; Lai, Christina; Truglio, James; Tonge, Peter J.

2015-01-01

The classical methods for quantifying drug-target residence time (tR) use loss or regain of enzyme activity in progress curve kinetic assays. However, such methods become imprecise at very long residence times, mitigating the use of alternative strategies. Using the NAD(P)H-dependent FabI enoyl-ACP reductase as a model system, we developed a Penefsky column-based method for direct measurement of tR, where the off-rate of the drug was determined with radiolabeled [adenylate-32P] NAD(P+) cofactor. Twenty-three FabI inhibitors were analyzed and a mathematical model was used to estimate limits to the tR values of each inhibitor based on percent drug-target complex recovery following gel filtration. In general, this method showed good agreement with the classical steady state kinetic methods for compounds with tR values of 10-100 min. In addition, we were able to identify seven long tR inhibitors (100-1500 min) and to accurately determine their tR values. The method was then used to measure tR as a function of temperature, an analysis not previously possible using the standard kinetic approach due to decreased NAD(P)H stability at elevated temperatures. In general, a 4-fold difference in tR was observed when the temperature was increased from 25 °C to 37 °C . PMID:25684450

Kinetics and Thermodynamics of DNA Processing by Wild Type DNA-Glycosylase Endo III and Its Catalytically Inactive Mutant Forms.

PubMed

Kladova, Olga A; Krasnoperov, Lev N; Kuznetsov, Nikita A; Fedorova, Olga S

2018-03-30

Endonuclease III (Endo III or Nth) is one of the key enzymes responsible for initiating the base excision repair of oxidized or reduced pyrimidine bases in DNA. In this study, a thermodynamic analysis of structural rearrangements of the specific and nonspecific DNA-duplexes during their interaction with Endo III is performed based on stopped-flow kinetic data. 1,3-diaza-2-oxophenoxazine (tC O ), a fluorescent analog of the natural nucleobase cytosine, is used to record multistep DNA binding and lesion recognition within a temperature range (5-37 °C). Standard Gibbs energy, enthalpy, and entropy of the specific steps are derived from kinetic data using Van't Hoff plots. The data suggest that enthalpy-driven exothermic 5,6-dihydrouracil (DHU) recognition and desolvation-accompanied entropy-driven adjustment of the enzyme-substrate complex into a catalytically active state play equally important parts in the overall process. The roles of catalytically significant amino acids Lys120 and Asp138 in the DNA lesion recognition and catalysis are identified. Lys120 participates not only in the catalytic steps but also in the processes of local duplex distortion, whereas substitution Asp138Ala leads to a complete loss of the ability of Endo III to distort a DNA double chain during enzyme-DNA complex formation.

Kinetic and morphology study of alginate-vineyard pruning waste biocomposite vs. non modified vineyard pruning waste for dye removal.

PubMed

Vecino, Xanel; Devesa-Rey, Rosa; Villagrasa, Salvador; Cruz, Jose M; Moldes, Ana B

2015-12-01

In this work a comparative bioadsorption study between a biocomposite consisting of hydrolysed vineyard pruning waste entrapped in calcium alginate spheres and non entrapped vineyard residue was carried out. Results have demonstrated that the biocomposite based on lignocellulose-calcium alginate spheres removed 77.3% of dyes, while non entrapped lignocellulose eliminated only removed 27.8% of colour compounds. The experimental data were fitted to several kinetic models (pseudo-first order, pseudo-second order, Chien-Clayton model, intraparticle diffusion model and Bangham model); being pseudo-second order the kinetic model that better described the adsorption of dyes onto both bioadsorbents. In addition, a morphological study (roughness and shape) of alginate-vineyard biocomposite was established under extreme conditions, observing significant differences between hydrated and dehydrated alginate-vineyard biocomposite. The techniques used to carry out this morphological study consisted of scanning electron microscopy (SEM), perfilometry and 3D surface analysis. Copyright © 2015. Published by Elsevier B.V.

Utilization of integrated Michaelis-Menten equations for enzyme inhibition diagnosis and determination of kinetic constants using Solver supplement of Microsoft Office Excel.

PubMed

Bezerra, Rui M F; Fraga, Irene; Dias, Albino A

2013-01-01

Enzyme kinetic parameters are usually determined from initial rates nevertheless, laboratory instruments only measure substrate or product concentration versus reaction time (progress curves). To overcome this problem we present a methodology which uses integrated models based on Michaelis-Menten equation. The most severe practical limitation of progress curve analysis occurs when the enzyme shows a loss of activity under the chosen assay conditions. To avoid this problem it is possible to work with the same experimental points utilized for initial rates determination. This methodology is illustrated by the use of integrated kinetic equations with the well-known reaction catalyzed by alkaline phosphatase enzyme. In this work nonlinear regression was performed with the Solver supplement (Microsoft Office Excel). It is easy to work with and track graphically the convergence of SSE (sum of square errors). The diagnosis of enzyme inhibition was performed according to Akaike information criterion. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Hyperbolic scaling and computing in social crowds: Comment on "Human behaviours in evacuation crowd dynamics: From modelling to "big data" toward crisis management" by Nicola Bellomo et al.

NASA Astrophysics Data System (ADS)

Outada, Nisrine

2016-09-01

I have read with great interest the paper [5] where the authors present an overview and critical analysis of the literature on the modeling of the crowd dynamics with special attention to evacuation dynamics. The approach developed is based on suitable development of methods of the kinetic theory. Interactions, which lead to the decision choice, are modeled by theoretical tools of stochastic evolutionary game theory [11,12]. However, the paper [5] provides not only a survey focused on topics of great interest for our society, but also it looks ahead to a variety of interesting and challenging mathematical problems. Specifically, I am interested in the derivation of macroscopic (hydrodynamic) models from the underlying description given from the kinetic theory approach, more specifically by the kinetic theory for active particles [8]. A general reference on crowd modeling is the recently published book [10].

Kinetics of antigen binding to arrays of antibodies in different sized spots

NASA Technical Reports Server (NTRS)

Sapsford, K. E.; Liron, Z.; Shubin, Y. S.; Ligler, F. S.

2001-01-01

A fluorescence-based array biosensor has been developed which can measure the binding kinetics of an antigen to an immobilized antibody in real time. A patterned array of antibodies immobilized on the surface of a planar waveguide was used to capture a Cy5-labeled antigen present in a solution that was continuously flowed over the surface. The CCD image of the waveguide was monitored continuously for 25 min. The resulting exponential rise in fluorescence signal was determined by image analysis software and fitted to a reaction-limited kinetics model, giving a kf of 3.6 x 10(5) M(-1) s(-1). Different spot sizes were then patterned on the surface of the waveguide using either a PDMS flow cell or laser exposure, producing width sizes ranging from 80 to 1145 microm. It was demonstrated that under flow conditions, the reduction of spot size did not alter the association rate of the antigen with immobilized antibody; however, as the spot width decreased to < 200 nm, the signal intensity also decreased.

Core Physics and Kinetics Calculations for the Fissioning Plasma Core Reactor

NASA Technical Reports Server (NTRS)

Butler, C.; Albright, D.

2007-01-01

Highly efficient, compact nuclear reactors would provide high specific impulse spacecraft propulsion. This analysis and numerical simulation effort has focused on the technical feasibility issues related to the nuclear design characteristics of a novel reactor design. The Fissioning Plasma Core Reactor (FPCR) is a shockwave-driven gaseous-core nuclear reactor, which uses Magneto Hydrodynamic effects to generate electric power to be used for propulsion. The nuclear design of the system depends on two major calculations: core physics calculations and kinetics calculations. Presently, core physics calculations have concentrated on the use of the MCNP4C code. However, initial results from other codes such as COMBINE/VENTURE and SCALE4a. are also shown. Several significant modifications were made to the ISR-developed QCALC1 kinetics analysis code. These modifications include testing the state of the core materials, an improvement to the calculation of the material properties of the core, the addition of an adiabatic core temperature model and improvement of the first order reactivity correction model. The accuracy of these modifications has been verified, and the accuracy of the point-core kinetics model used by the QCALC1 code has also been validated. Previously calculated kinetics results for the FPCR were described in the ISR report, "QCALC1: A code for FPCR Kinetics Model Feasibility Analysis" dated June 1, 2002.

Metastable Solution Thermodynamic Properties and Crystal Growth Kinetics

NASA Technical Reports Server (NTRS)

Kim, Soojin; Myerson, Allan S.

1996-01-01

The crystal growth rates of NH4H2PO4, KH2PO4, (NH4)2SO4, KAl(SO4)2 central dot 12H2O, NaCl, and glycine and the nucleation rates of KBr, KCl, NaBr central dot 2H2O, (NH4)2Cl, and (NH4)2SO4 were expressed in terms of the fundamental driving force of crystallization calculated from the activity of supersaturated solutions. The kinetic parameters were compared with those from the commonly used kinetic expression based on the concentration difference. From the viewpoint of thermodynamics, rate expressions based on the chemical potential difference provide accurate kinetic representation over a broad range of supersaturation. The rates estimated using the expression based on the concentration difference coincide with the true rates of crystallization only in the concentration range of low supersaturation and deviate from the true kinetics as the supersaturation increases.

An Evidence-Based Systematic Review of Beta-Sitosterol, Sitosterol (22,23- dihydrostigmasterol, 24-ethylcholesterol) by the Natural Standard Research Collaboration.

PubMed

Ulbricht, Catherine E

2016-01-01

An evidence-based systematic review of beta-sitosterol, sitosterol (22,23-dihydrostigmasterol, 24-ethylcholesterol) by the Natural Standard Research Collaboration consolidates the safety and efficacy data available in the scientific literature using a validated, reproducible grading rationale. This article includes written and statistical analysis of clinical trials, plus a compilation of expert opinion, folkloric precedent, history, pharmacology, kinetics/dynamics, interactions, adverse effects, toxicology, and dosing.

Lipid-associated Oral Delivery: Mechanisms and Analysis of Oral Absorption Enhancement

PubMed Central

Rezhdo, Oljora; Speciner, Lauren; Carrier, Rebecca L.

2016-01-01

The majority of newly discovered oral drugs are poorly water soluble, and co-administration with lipids has proven effective in significantly enhancing bioavailability of some compounds with low aqueous solubility. Yet, lipid-based delivery technologies have not been widely employed in commercial oral products. Lipids can impact drug transport and fate in the gastrointestinal (GI) tract through multiple mechanisms including enhancement of solubility and dissolution kinetics, enhancement of permeation through the intestinal mucosa, and triggering drug precipitation upon lipid emulsion depletion (e.g., by digestion). The effect of lipids on drug absorption is currently not quantitatively predictable, in part due to the multiple complex dynamic processes that can be impacted by lipids. Quantitative mechanistic analysis of the processes significant to lipid system function and overall impact on drug absorption can aid understanding of drug-lipid interactions in the GI tract and exploitation of such interactions to achieve optimal lipid-based drug delivery. In this review, we discuss the impact of co-delivered lipids and lipid digestion on drug dissolution, partitioning, and absorption in the context of the experimental tools and associated kinetic expressions used to study and model these processes. The potential benefit of a systems-based consideration of the concurrent multiple dynamic processes occurring upon co-dosing lipids and drugs to predict the impact of lipids on drug absorption and enable rational design of lipid-based delivery systems is presented. PMID:27520734

Dynamic identification of growth and survival kinetic parameters of microorganisms in foods

USDA-ARS?s Scientific Manuscript database

Inverse analysis is a mathematical method used in predictive microbiology to determine the kinetic parameters of microbial growth and survival in foods. The traditional approach in inverse analysis relies on isothermal experiments that are time-consuming and labor-intensive, and errors are accumula...

Kinetic Study of Acetone-Butanol-Ethanol Fermentation in Continuous Culture

PubMed Central

Buehler, Edward A.; Mesbah, Ali

2016-01-01

Acetone-butanol-ethanol (ABE) fermentation by clostridia has shown promise for industrial-scale production of biobutanol. However, the continuous ABE fermentation suffers from low product yield, titer, and productivity. Systems analysis of the continuous ABE fermentation will offer insights into its metabolic pathway as well as into optimal fermentation design and operation. For the ABE fermentation in continuous Clostridium acetobutylicum culture, this paper presents a kinetic model that includes the effects of key metabolic intermediates and enzymes as well as culture pH, product inhibition, and glucose inhibition. The kinetic model is used for elucidating the behavior of the ABE fermentation under the conditions that are most relevant to continuous cultures. To this end, dynamic sensitivity analysis is performed to systematically investigate the effects of culture conditions, reaction kinetics, and enzymes on the dynamics of the ABE production pathway. The analysis provides guidance for future metabolic engineering and fermentation optimization studies. PMID:27486663

Free Radical Addition Polymerization Kinetics without Steady-State Approximations: A Numerical Analysis for the Polymer, Physical, or Advanced Organic Chemistry Course

ERIC Educational Resources Information Center

Iler, H. Darrell; Brown, Amber; Landis, Amanda; Schimke, Greg; Peters, George

2014-01-01

A numerical analysis of the free radical addition polymerization system is described that provides those teaching polymer, physical, or advanced organic chemistry courses the opportunity to introduce students to numerical methods in the context of a simple but mathematically stiff chemical kinetic system. Numerical analysis can lead students to an…

SVD-aided pseudo principal-component analysis: A new method to speed up and improve determination of the optimum kinetic model from time-resolved data

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

Oang, Key Young; Yang, Cheolhee; Muniyappan, Srinivasan

Determination of the optimum kinetic model is an essential prerequisite for characterizing dynamics and mechanism of a reaction. Here, we propose a simple method, termed as singular value decomposition-aided pseudo principal-component analysis (SAPPA), to facilitate determination of the optimum kinetic model from time-resolved data by bypassing any need to examine candidate kinetic models. We demonstrate the wide applicability of SAPPA by examining three different sets of experimental time-resolved data and show that SAPPA can efficiently determine the optimum kinetic model. In addition, the results of SAPPA for both time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) data of themore » same protein reveal that global structural changes of protein, which is probed by TRXSS, may occur more slowly than local structural changes around the chromophore, which is probed by TA spectroscopy.« less

A comparison of region-based and pixel-based CEUS kinetics parameters in the assessment of arthritis

NASA Astrophysics Data System (ADS)

Grisan, E.; Raffeiner, B.; Coran, A.; Rizzo, G.; Ciprian, L.; Stramare, R.

2014-03-01

Inflammatory rheumatic diseases are leading causes of disability and constitute a frequent medical disorder, leading to inability to work, high comorbidity and increased mortality. The gold-standard for diagnosing and differentiating arthritis is based on patient conditions and radiographic findings, as joint erosions or decalcification. However, early signs of arthritis are joint effusion, hypervascularization and synovial hypertrophy. In particular, vascularization has been shown to correlate with arthritis' destructive behavior, more than clinical assessment. Contrast Enhanced Ultrasound (CEUS) examination of the small joints is emerging as a sensitive tool for assessing vascularization and disease activity. The evaluation of perfusion pattern rely on subjective semi-quantitative scales, that are able to capture the macroscopic degree of vascularization, but are unable to detect the subtler differences in kinetics perfusion parameters that might lead to a deeper understanding of disease progression and a better management of patients. Quantitative assessment is mostly performed by means of the Qontrast software package, that requires the user to define a region of interest, whose mean intensity curve is fitted with an exponential function. We show that using a more physiologically motivated perfusion curve, and by estimating the kinetics parameters separately pixel per pixel, the quantitative information gathered is able to differentiate more effectively different perfusion patterns. In particular, we will show that a pixel-based analysis is able to provide significant markers differentiating rheumatoid arthritis from simil-rheumatoid psoriatic arthritis, that have non-significant differences in clinical evaluation (DAS28), serological markers, or region-based parameters.

Upper limb joint kinetic analysis during tennis serve: Assessment of competitive level on efficiency and injury risks.

PubMed

Martin, C; Bideau, B; Ropars, M; Delamarche, P; Kulpa, R

2014-08-01

The aim of this work was to compare the joint kinetics and stroke production efficiency for the shoulder, elbow, and wrist during the serve between professionals and advanced tennis players and to discuss their potential relationship with given overuse injuries. Eleven professional and seven advanced tennis players were studied with an optoelectronic motion analysis system while performing serves. Normalized peak kinetic values of the shoulder, elbow, and wrist joints were calculated using inverse dynamics. To measure serve efficiency, all normalized peak kinetic values were divided by ball velocity. t-tests were used to determine significant differences between the resultant joint kinetics and efficiency values in both groups (advanced vs professional). Shoulder inferior force, shoulder anterior force, shoulder horizontal abduction torque, and elbow medial force were significantly higher in advanced players. Professional players were more efficient than advanced players, as they maximize ball velocity with lower joint kinetics. Since advanced players are subjected to higher joint kinetics, the results suggest that they appeared more susceptible to high risk of shoulder and elbow injuries than professionals, especially during the cocking and deceleration phases of the serve. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Analysis of transient fission gas behaviour in oxide fuel using BISON and TRANSURANUS

NASA Astrophysics Data System (ADS)

Barani, T.; Bruschi, E.; Pizzocri, D.; Pastore, G.; Van Uffelen, P.; Williamson, R. L.; Luzzi, L.

2017-04-01

The modelling of fission gas behaviour is a crucial aspect of nuclear fuel performance analysis in view of the related effects on the thermo-mechanical performance of the fuel rod, which can be particularly significant during transients. In particular, experimental observations indicate that substantial fission gas release (FGR) can occur on a small time scale during transients (burst release). To accurately reproduce the rapid kinetics of the burst release process in fuel performance calculations, a model that accounts for non-diffusional mechanisms such as fuel micro-cracking is needed. In this work, we present and assess a model for transient fission gas behaviour in oxide fuel, which is applied as an extension of conventional diffusion-based models to introduce the burst release effect. The concept and governing equations of the model are presented, and the sensitivity of results to the newly introduced parameters is evaluated through an analytic sensitivity analysis. The model is assessed for application to integral fuel rod analysis by implementation in two structurally different fuel performance codes: BISON (multi-dimensional finite element code) and TRANSURANUS (1.5D code). Model assessment is based on the analysis of 19 light water reactor fuel rod irradiation experiments from the OECD/NEA IFPE (International Fuel Performance Experiments) database, all of which are simulated with both codes. The results point out an improvement in both the quantitative predictions of integral fuel rod FGR and the qualitative representation of the FGR kinetics with the transient model relative to the canonical, purely diffusion-based models of the codes. The overall quantitative improvement of the integral FGR predictions in the two codes is comparable. Moreover, calculated radial profiles of xenon concentration after irradiation are investigated and compared to experimental data, illustrating the underlying representation of the physical mechanisms of burst release.

A novel microfluidic mixer based on dual-hydrodynamic focusing for interrogating the kinetics of DNA-protein interaction.

PubMed

Li, Ying; Xu, Fei; Liu, Chao; Xu, Youzhi; Feng, Xiaojun; Liu, Bi-Feng

2013-08-21

Kinetic measurement of biomacromolecular interaction plays a significant role in revealing the underlying mechanisms of cellular activities. Due to the small diffusion coefficient of biomacromolecules, it is difficult to resolve the rapid kinetic process with traditional analytical methods such as stopped-flow or laminar mixers. Here, we demonstrated a unique continuous-flow laminar mixer based on microfluidic dual-hydrodynamic focusing to characterize the kinetics of DNA-protein interactions. The time window of this mixer for kinetics observation could cover from sub-milliseconds to seconds, which made it possible to capture the folding process with a wide dynamic range. Moreover, the sample consumption was remarkably reduced to <0.55 μL min⁻¹, over 1000-fold saving in comparison to those reported previously. We further interrogated the interaction kinetics of G-quadruplex and the single-stranded DNA binding protein, indicating that this novel micromixer would be a useful approach for analyzing the interaction kinetics of biomacromolecules.

A Rational Reconstruction of the Kinetic Molecular Theory of Gases Based on History and Philosophy of Science and Its Implications for Chemistry Textbooks.

ERIC Educational Resources Information Center

Niaz, Mansoor

2000-01-01

Describes a study that was designed to develop a framework for examining the way in which chemistry textbooks describe the kinetic theory and related issues. The framework was developed by a rational reconstruction of the kinetic molecular theory of gases based on historians and philosophers of science. (Contains 102 references.)(Author/LRW)

Correlation between lifetime heterogeneity and kinetics heterogeneity during chlorophyll fluorescence induction in leaves: 2. Multi-frequency phase and modulation analysis evidences a loosely connected PSII pigment-protein complex.

PubMed

Moise, Nicolae; Moya, Ismaël

2004-06-28

We report the first direct decomposition of the fluorescence lifetime heterogeneity during multiphasic fluorescence induction in dark-adapted leaves by multi-frequency phase and modulation fluorometry (PMF). A very fast component, assigned to photosystem I (PSI), was found to be constant in lifetime and yield, whereas the two slow components, which are strongly affected by the closure of the reaction centers by light, were assigned to PSII. Based on a modified "reversible radical pair" kinetic model with three compartments, we showed that a loosely connected pigment complex, which is assumed to be the CP47 complex, plays a specific role with respect to the structure and function of the PSII: (i) it explains the heterogeneity of PSII fluorescence lifetime as a compartmentation of excitation energy in the antenna, (ii) it is the site of a conformational change in the first second of illumination, and (iii) it is involved in the mechanisms of nonphotochemical quenching (NPQ). On the basis of the multi-frequency PMF analysis, we reconciled two apparently antagonistic aspects of chlorophyll a fluorescence in vivo: it is heterogeneous with respect to the kinetic structure (several lifetime components) and homogeneous with respect to average quantities (quasi-linear mean tau-Phi relationship).

Studies of the di-iron(VI) Intermediate in ferrate-dependent oxygen evolution from water.

PubMed

Sarma, Rupam; Angeles-Boza, Alfredo M; Brinkley, David W; Roth, Justine P

2012-09-19

Molecular oxygen is produced from water via the following reaction of potassium ferrate (K(2)FeO(4)) in acidic solution: 4[H(3)Fe(VI)O(4)](+) + 8H(3)O(+) → 4Fe(3+) + 3O(2) + 18H(2)O. This study focuses upon the mechanism by which the O-O bond is formed. Stopped-flow kinetics at variable acidities in H(2)O and D(2)O are used to complement the analysis of competitive oxygen-18 kinetic isotope effects ((18)O KIEs) upon consumption of natural abundance water. The derived (18)O KIEs provide insights concerning the identity of the transition state. Water attack (WA) and oxo-coupling (OC) transition states were evaluated for various reactions of monomeric and dimeric ferrates using a calibrated density functional theory protocol. Vibrational frequencies from optimized isotopic structures are used here to predict (18)O KIEs for comparison to experimental values determined using an established competitive isotope-fractionation method. The high level of agreement between experimental and theoretic isotope effects points to an intramolecular OC mechanism within a di-iron(VI) intermediate, consistent with the analysis of the reaction kinetics. Alternative mechanisms are excluded based on insurmountably high free energy barriers and disagreement with calculated (18)O KIEs.

Arcjet thruster research and technology, phase 1

NASA Technical Reports Server (NTRS)

Knowles, Steven C.

1987-01-01

The objectives of Phase 1 were to evaluate analytically and experimentally the operation, performance, and lifetime of arcjet thrusters operating between 0.5 and 3.0 kW with catalytically decomposed hydrazine (N2H4) and to begin development of the requisite power control unit (PCU) technology. Fundamental analyses were performed of the arcjet nozzle, the gas kinetic reaction effects, the thermal environment, and the arc stabilizing vortex. The VNAP2 flow code was used to analyze arcjet nozzle performance with non-uniform entrance profiles. Viscous losses become dominant beyond expansion ratios of 50:1 because of the low Reynolds numbers. A survey of vortex phenomena and analysis techniques identified viscous dissipation and vortex breakdown as two flow instabilities that could affect arcjet operation. The gas kinetics code CREK1D was used to study the gas kinetics of high temperature N2H4 decomposition products. The arc/gas energy transfer is a non-equilibrium process because of the reaction rate constants and the short gas residence times. A thermal analysis code was used to guide design work and to provide a means to back out power losses at the anode fall based on test thermocouple data. The low flow rate and large thermal masses made optimization of a regenerative heating scheme unnecessary.

Automated region selection for analysis of dynamic cardiac SPECT data

NASA Astrophysics Data System (ADS)

Di Bella, E. V. R.; Gullberg, G. T.; Barclay, A. B.; Eisner, R. L.

1997-06-01

Dynamic cardiac SPECT using Tc-99m labeled teboroxime can provide kinetic parameters (washin, washout) indicative of myocardial blood flow. A time-consuming and subjective step of the data analysis is drawing regions of interest to delineate blood pool and myocardial tissue regions. The time-activity curves of the regions are then used to estimate local kinetic parameters. In this work, the appropriate regions are found automatically, in a manner similar to that used for calculating maximum count circumferential profiles in conventional static cardiac studies. The drawbacks to applying standard static circumferential profile methods are the high noise level and high liver uptake common in dynamic teboroxime studies. Searching along each ray for maxima to locate the myocardium does not typically provide useful information. Here we propose an iterative scheme in which constraints are imposed on the radii searched along each ray. The constraints are based on the shape of the time-activity curves of the circumferential profile members and on an assumption that the short axis slices are approximately circular. The constraints eliminate outliers and help to reduce the effects of noise and liver activity. Kinetic parameter estimates from the automatically generated regions were comparable to estimates from manually selected regions in dynamic canine teboroxime studies.

Characterization of the Microchemical Structure of Seed Endosperm within a Cellular Dimension among Six Barley Varieties with Distinct Degradation Kinetics, Using Ultraspatially Resolved Synchrotron-Based Infrared Synchrotron-Based Infrared

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

Liu, N.; Yu, P

2010-01-01

Barley varieties have similar chemical composition but exhibit different rumen degradation kinetics and nutrient availability. These biological differences may be related to molecular, structural, and chemical makeup among the seed endosperm tissue. No detailed study was carried out. The objectives of this study were: (1) to use a molecular spectroscopy technique, synchrotron-based Fourier transform infrared microspectroscopy (SFTIRM), to determine the microchemical-structural features in seed endosperm tissue of six developed barley varieties; (2) to study the relationship among molecular-structural characteristics, degradation kinetics, and nutrient availability in six genotypes of barley. The results showed that inherent microchemical-structural differences in the endosperm amongmore » the six barley varieties were detected by the synchrotron-based analytical technique, SFTIRM, with the univariate molecular spectral analysis. The SFTIRM spectral profiles differed (P < 0.05) among the barley samples in terms of the peak ratio and peak area and height intensities of amides I (ca. 1650 cm{sup -1}) and II (ca. 1550 cm{sup -1}), cellulosic compounds (ca. 1240 cm{sup -1}), CHO component peaks (the first peak at the region ca. 1184-1132 cm{sup -1}, the second peak at ca. 1132-1066 cm{sup -1}, and the third peak at ca. 1066-950 cm{sup -1}). With the SFTIRM technique, the structural characteristics of the cereal seeds were illuminated among different cultivars at an ultraspatial resolution. The structural differences of barley seeds may be one reason for the various digestive behaviors and nutritive values in ruminants. The results show weak correlations between the functional groups spectral data (peak area, height intensities, and ratios) and rumen biodegradation kinetics (rate and extent of nutrient degradation). Weak correlations may indicate that limited variations of these six barley varieties might not be sufficient to interpret the relationship between spectroscopic information and the nutrient value of barley grain, although significant differences in biodegradation kinetics were observed. In conclusion, the studies demonstrated the potential of ultraspatially resolved synchrotron based technology (SFTIRM) to reveal the structural and chemical makeup within cellular and subcellular dimensions without destruction of the inherent structure of cereal grain tissue.« less

Physics of spacecraft-based interplanetary dust collection by impact into low-density media

NASA Technical Reports Server (NTRS)

Anderson, William W.; Ahrens, T. J.

1994-01-01

A spacecraft encountering an interplanetary dust particle (IDP) at a relative velocity of several kilometers per second may be used to capture that particle for in situ analysis or for analysis upon Earth return. In this paper we study the impact of a dust particle into a low-density medium (i.e., a foam) such that the foam dissipates the kinetic energy of impact over a sufficient distance to stop the particle without destroying it.

Data Capture and Analysis Using the BBC Microcomputer--an Interfacing Project Applied to Enzyme Kinetics.

ERIC Educational Resources Information Center

Jones, Lawrence; Graham, Ian

1986-01-01

Reviews the main principles of interfacing and discusses the software developed to perform kinetic data capture and analysis with a BBC microcomputer linked to a recording spectrophotometer. Focuses on the steps in software development. Includes results of a lactate dehydrogenase assay. (ML)

Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction.

PubMed

Monge-Palacios, M; Rangel, C; Espinosa-Garcia, J

2013-02-28

A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200-2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.

STATIC AND KINETIC SITE-SPECIFIC PROTEIN-DNA PHOTOCROSSLINKING: ANALYSIS OF BACTERIAL TRANSCRIPTION INITIATION COMPLEXES

PubMed Central

Naryshkin, Nikolai; Druzhinin, Sergei; Revyakin, Andrei; Kim, Younggyu; Mekler, Vladimir; Ebright, Richard H.

2009-01-01

Static site-specific protein-DNA photocrosslinking permits identification of protein-DNA interactions within multiprotein-DNA complexes. Kinetic site-specific protein-DNA photocrosslinking--involving rapid-quench-flow mixing and pulsed-laser irradiation--permits elucidation of pathways and kinetics of formation of protein-DNA interactions within multiprotein-DNA complexes. We present detailed protocols for application of static and kinetic site-specific protein-DNA photocrosslinking to bacterial transcription initiation complexes. PMID:19378179

Modeling of uncertainties in biochemical reactions.

PubMed

Mišković, Ljubiša; Hatzimanikatis, Vassily

2011-02-01

Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and measurement methods. In this contribution, we propose a novel way to model the uncertainty in the enzyme kinetics and to predict quantitatively the responses of metabolic reactions to the changes in enzyme activities under uncertainty. The proposed methodology accounts explicitly for mechanistic properties of enzymes and physico-chemical and thermodynamic constraints, and is based on formalism from systems theory and metabolic control analysis. We achieve this by observing that kinetic responses of metabolic reactions depend: (i) on the distribution of the enzymes among their free form and all reactive states; (ii) on the equilibrium displacements of the overall reaction and that of the individual enzymatic steps; and (iii) on the net fluxes through the enzyme. Relying on this observation, we develop a novel, efficient Monte Carlo sampling procedure to generate all states within a metabolic reaction that satisfy imposed constrains. Thus, we derive the statistics of the expected responses of the metabolic reactions to changes in enzyme levels and activities, in the levels of metabolites, and in the values of the kinetic parameters. We present aspects of the proposed framework through an example of the fundamental three-step reversible enzymatic reaction mechanism. We demonstrate that the equilibrium displacements of the individual enzymatic steps have an important influence on kinetic responses of the enzyme. Furthermore, we derive the conditions that must be satisfied by a reversible three-step enzymatic reaction operating far away from the equilibrium in order to respond to changes in metabolite levels according to the irreversible Michelis-Menten kinetics. The efficient sampling procedure allows easy, scalable, implementation of this methodology to modeling of large-scale biochemical networks. © 2010 Wiley Periodicals, Inc.

Global sensitivity analysis in stochastic simulators of uncertain reaction networks.

PubMed

Navarro Jimenez, M; Le Maître, O P; Knio, O M

2016-12-28

Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol's decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes that the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. A sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.

Global sensitivity analysis in stochastic simulators of uncertain reaction networks

DOE PAGES

Navarro Jimenez, M.; Le Maître, O. P.; Knio, O. M.

2016-12-23

Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol’s decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes thatmore » the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. Here, a sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.« less

Global sensitivity analysis in stochastic simulators of uncertain reaction networks

NASA Astrophysics Data System (ADS)

Navarro Jimenez, M.; Le Maître, O. P.; Knio, O. M.

2016-12-01

Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol's decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes that the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. A sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.

Nonparametric Residue Analysis of Dynamic PET Data With Application to Cerebral FDG Studies in Normals.

PubMed

O'Sullivan, Finbarr; Muzi, Mark; Spence, Alexander M; Mankoff, David M; O'Sullivan, Janet N; Fitzgerald, Niall; Newman, George C; Krohn, Kenneth A

2009-06-01

Kinetic analysis is used to extract metabolic information from dynamic positron emission tomography (PET) uptake data. The theory of indicator dilutions, developed in the seminal work of Meier and Zierler (1954), provides a probabilistic framework for representation of PET tracer uptake data in terms of a convolution between an arterial input function and a tissue residue. The residue is a scaled survival function associated with tracer residence in the tissue. Nonparametric inference for the residue, a deconvolution problem, provides a novel approach to kinetic analysis-critically one that is not reliant on specific compartmental modeling assumptions. A practical computational technique based on regularized cubic B-spline approximation of the residence time distribution is proposed. Nonparametric residue analysis allows formal statistical evaluation of specific parametric models to be considered. This analysis needs to properly account for the increased flexibility of the nonparametric estimator. The methodology is illustrated using data from a series of cerebral studies with PET and fluorodeoxyglucose (FDG) in normal subjects. Comparisons are made between key functionals of the residue, tracer flux, flow, etc., resulting from a parametric (the standard two-compartment of Phelps et al. 1979) and a nonparametric analysis. Strong statistical evidence against the compartment model is found. Primarily these differences relate to the representation of the early temporal structure of the tracer residence-largely a function of the vascular supply network. There are convincing physiological arguments against the representations implied by the compartmental approach but this is the first time that a rigorous statistical confirmation using PET data has been reported. The compartmental analysis produces suspect values for flow but, notably, the impact on the metabolic flux, though statistically significant, is limited to deviations on the order of 3%-4%. The general advantage of the nonparametric residue analysis is the ability to provide a valid kinetic quantitation in the context of studies where there may be heterogeneity or other uncertainty about the accuracy of a compartmental model approximation of the tissue residue.

Temporal dissociation between muscle and pulmonary oxygen uptake kinetics: influences of perfusion dynamics and arteriovenous oxygen concentration differences in muscles and lungs.

PubMed

Drescher, U; Koschate, J; Thieschäfer, L; Schneider, S; Hoffmann, U

2018-06-22

The aim of the study was to test whether or not the arteriovenous oxygen concentration difference (avDO 2 ) kinetics at the pulmonary (avDO 2 pulm) and muscle (avDO 2 musc) levels is significantly different during dynamic exercise. A re-analysis involving six publications dealing with kinetic analysis was utilized with an overall sample size of 69 participants. All studies comprised an identical pseudorandom binary sequence work rate (WR) protocol-WR changes between 30 and 80 W-to analyze the kinetic responses of pulmonary ([Formula: see text]) and muscle ([Formula: see text]) oxygen uptake kinetics as well as those of avDO 2 pulm and avDO 2 musc. A significant difference between [Formula: see text] (0.395 ± 0.079) and [Formula: see text] kinetics (0.330 ± 0.078) was observed (p < 0.001), where the variables showed a significant relationship (r SP  = 0.744, p < 0.001). There were no significant differences between avDO 2 musc (0.446 ± 0.077) and avDO 2 pulm kinetics (0.451 ± 0.075), which are highly correlated (r = 0.929, p < 0.001). It is suggested that neither avDO 2 pulm nor avDO 2 musc kinetic responses seem to be responsible for the differences between estimated [Formula: see text] and measured [Formula: see text] kinetics. Obviously, the conflation of avDO 2 and perfusion ([Formula: see text] ) at different points in time and at different physiological levels drive potential differences in [Formula: see text] and [Formula: see text] kinetics. Therefore, [Formula: see text] should, in general, be considered whenever oxygen uptake kinetics are analyzed or discussed.

Experiments on Nucleation in Different Flow Regimes

NASA Technical Reports Server (NTRS)

Bayuzick, R. J.; Hofmeister, W. H.; Morton, C. M.; Robinson, M. B.

1998-01-01

The vast majority of metallic engineering materials are solidified from the liquid phase. Understanding the solidification process is essential to control microstructure, which in turn, determines the properties of materials. The genesis of solidification is nucleation, where the first stable solid forms from the liquid phase. Nucleation kinetics determine the degree of undercooling and phase selection. As such, it is important to understand nucleation phenomena in order to control solidification or glass formation in metals and alloys. Early experiments in nucleation kinetics were accomplished by droplet dispersion methods. Dilitometry was used by Turnbull and others, and more recently differential thermal analysis and differential scanning calorimetry have been used for kinetic studies. These techniques have enjoyed success; however, there are difficulties with these experiments. Since materials are dispersed in a medium, the character of the emulsion/metal interface affects the nucleation behavior. Statistics are derived from the large number of particles observed in a single experiment, but dispersions have a finite size distribution which adds to the uncertainty of the kinetic determinations. Even though temperature can be controlled quite well before the onset of nucleation, the release of the latent heat of fusion during nucleation of particles complicates the assumption of isothermality during these experiments. Containerless processing has enabled another approach to the study of nucleation kinetics. With levitation techniques it is possible to undercool one sample to nucleation repeatedly in a controlled manner, such that the statistics of the nucleation process can be derived from multiple experiments on a single sample. The authors have fully developed the analysis of nucleation experiments on single samples following the suggestions of Skripov. The advantage of these experiments is that the samples are directly observable. The nucleation temperature can be measured by noncontact optical pyrometry, the mass of the sample is known, and post-processing analysis can be conducted on the sample. The disadvantages are that temperature measurement must have exceptionally high precision, and it is not possible to isolate specific heterogeneous sites as in droplet dispersions. Levitation processing of refractory materials in ultra high vacuum provides an avenue to conduct these kinetic studies on single samples. Two experimental methods have been identified where ultra high vacuum experiments are possible; electrostatic levitation in ground-based experiments and electromagnetic processing in low earth orbit on TEMPUS. Such experiments, reported here, were conducted on zirconium. Liquid zirconium is an excellent solvent and has a high solubility for contaminants contained in the bulk material as well as those contaminants found in the vacuum environment. Oxides, nitrides, and carbides do not exist in the melt, and do not form on the surface of molten zirconium, for the materials and vacuum levels used in this study. Ground-based experiments with electrostatic levitation have shown that the statistical nucleation kinetic experiments are viable and yield results which are consistent with classical nucleation theory. The advantage of low earth orbit experiments is the ability to vary the flow conditions in the liquid prior to nucleation. The put-pose of nucleation experiments in TEMPUS was to examine.

Kinetic characteristics of the luminescence decay for industrial yttrium-gadolinium-aluminium garnet based phosphors

NASA Astrophysics Data System (ADS)

Lisitsyn, V. M.; Stepanov, S. A.; Valiev, D. T.; Vishnyakova, E. A.; Abdullin, H. A.; Marhabaeva, A. A.; Tulegenova, A. T.

2016-02-01

The spectral and decay kinetic characteristics of pulse cathodoluminescence and photoluminescence of phosphors based on yttrium-gadolinium-aluminum garnet were investigated using pulsed optical time resolved spectroscopy.

Effects of particle reinforcement and ECAP on the precipitation kinetics of an Al-Cu alloy

NASA Astrophysics Data System (ADS)

Härtel, M.; Wagner, S.; Frint, P.; F-X Wagner, M.

2014-08-01

The precipitation kinetics of Al-Cu alloys have recently been revisited in various studies, considering either the effect of severe plastic deformation (e.g., by equal-channel angular pressing - ECAP), or the effect of particle reinforcements. However, it is not clear how these effects interact when ECAP is performed on particle-reinforced alloys. In this study, we analyze how a combination of particle reinforcement and ECAP affects precipitation kinetics. After solution annealing, an AA2017 alloy (initial state: base material without particle reinforcement); AA2017 + 10 vol.-% Al2O3; and AA2017 + 10 vol.-% SiC were deformed in one pass in a 120° ECAP tool at a temperature of 140°C. Systematic differential scanning calorimetry (DSC) measurements of each condition were carried out. TEM specimens were prepared out of samples from additional DSC measurements, where the samples were immediately quenched in liquid nitrogen after reaching carefully selected temperatures. TEM analysis was performed to characterize the morphology of the different types of precipitates, and to directly relate microstructural information to the endo- and exothermic peaks in our DSC data. Our results show that both ECAP and particle reinforcement are associated with a shift of exothermic precipitation peaks towards lower temperatures. This effect is even more pronounced when ECAP and particle reinforcement are combined. The DSC data agrees well with our TEM observations of nucleation and morphology of different precipitates, indicating that DSC measurements are an appropriate tool for the analysis of how severe plastic deformation and particle reinforcement affect precipitation kinetics in Al-Cu alloys.

Quantum theory of atoms in molecules: results for the SR-ZORA Hamiltonian.

PubMed

Anderson, James S M; Ayers, Paul W

2011-11-17

The quantum theory of atoms in molecules (QTAIM) is generalized to include relativistic effects using the popular scalar-relativistic zeroth-order regular approximation (SR-ZORA). It is usually assumed that the definition of the atom as a volume bounded by a zero-flux surface of the electron density is closely linked to the form of the kinetic energy, so it is somewhat surprising that the atoms corresponding to the relativistic kinetic-energy operator in the SR-ZORA Hamiltonian are also bounded by zero-flux surfaces. The SR-ZORA Hamiltonian should be sufficient for qualitative descriptions of molecular electronic structure across the periodic table, which suggests that QTAIM-based analysis can be useful for molecules and solids containing heavy atoms.

Theoretical Study of the Oxidation Behavior of Precipitation Hardening Steel

NASA Astrophysics Data System (ADS)

Pistofidis, N.; Vourlias, G.; Psyllaki, P.; Chrissafis, K.

2010-01-01

The oxidation of precipitation hardening (PH) steels is a rather unexplored area. In the present work an attempt is made is made to estimate the kinetics of a PH steel. For this purpose specimens of the material under examination were isothermally heated at 850, 900 and 950° C for 15 hr. Kinetics was based on TGA results. During heating a thick scale is formed on the substrate surface, which is composed by different oxides. The layer close to the substrate is compact and as a result it impedes corrosion. The mathematical analysis of the collected data shows that the change of the mass of the substrate per unit area versus time is described by a parabolic law.

Line shape analysis of the K β transition in muonic hydrogen

NASA Astrophysics Data System (ADS)

Covita, Daniel S.; Anagnostopoulos, Dimitrios F.; Fuhrmann, Hermann; Gorke, Hubert; Gotta, Detlev; Gruber, Alexander; Hirtl, Albert; Ishiwatari, Tomoichi; Indelicato, Paul; Jensen, Thomas S.; Le Bigot, Eric-Olivier; Markushin, Valeri E.; Nekipelov, Michael; Pomerantsev, Vladimir N.; Popov, Vladimir P.; dos Santos, Joaquim M. F.; Schmid, Philipp; Simons, Leopold M.; Theisen, Marian; Trassinelli, Martino; Veloso, Joao F. C. A.; Zmeskal, Johann

2018-04-01

The K β transition in muonic hydrogen was measured with a high-resolution crystal spectrometer. The spectrum is shown to be sensitive to the ground-state hyperfine splitting, the corresponding triplet-to-singlet ratio, and the kinetic energy distribution in the 3 p state. The hyperfine splitting and triplet-to-singlet ratio are found to be consistent with the values expected from theoretical and experimental investigations and, therefore, were fixed accordingly in order to reduce the uncertainties in the further reconstruction of the kinetic energy distribution. The presence of high-energetic components was established and quantified in both a phenomenological, i.e. cascade-model-free fit, and in a direct deconvolution of the Doppler broadening based on the Bayesian method.

Kinetics of propagation of the lattice excitation in a swift heavy ion track

NASA Astrophysics Data System (ADS)

Lipp, V. P.; Volkov, A. E.; Sorokin, M. V.; Rethfeld, B.

2011-05-01

In this research we verify the applicability of the temperature and heat diffusion conceptions for the description of subpicosecond lattice excitations in nanometric tracks of swift heavy ions (SHI) decelerated in solids in the electronic stopping regime. The method is based on the molecular dynamics (MD) analysis of temporal evolutions of the local kinetic and configurational temperatures of a lattice. We used solid argon as the model system. MD simulations demonstrated that in a SHI track (a) thermalization of lattice excitations takes time of several picoseconds, and (b) application of the parabolic heat diffusion equations for the description of spatial and temporal propagation of lattice excitations is questionable at least up to 10 ps after the ion passage.

How to Run FAST Simulations.

PubMed

Zimmerman, M I; Bowman, G R

2016-01-01

Molecular dynamics (MD) simulations are a powerful tool for understanding enzymes' structures and functions with full atomistic detail. These physics-based simulations model the dynamics of a protein in solution and store snapshots of its atomic coordinates at discrete time intervals. Analysis of the snapshots from these trajectories provides thermodynamic and kinetic properties such as conformational free energies, binding free energies, and transition times. Unfortunately, simulating biologically relevant timescales with brute force MD simulations requires enormous computing resources. In this chapter we detail a goal-oriented sampling algorithm, called fluctuation amplification of specific traits, that quickly generates pertinent thermodynamic and kinetic information by using an iterative series of short MD simulations to explore the vast depths of conformational space. © 2016 Elsevier Inc. All rights reserved.

Use of force plate analysis to evaluate the efficacy of external beam radiation to alleviate osteosarcoma pain.

PubMed

Weinstein, Jeff I; Payne, Sarah; Poulson, Jean M; Azuma, Chieko

2009-01-01

A standard of therapy for osteosarcoma includes amputation with or without adjuvant chemotherapy. There is a subset of dogs with osteosarcoma that are unsuitable for amputation. We evaluated kinetic variables in dogs with appendicular osteosarcoma treated with a single 8 Gy dose of radiation. Eighteen pet dogs with appendicular osteosarcoma received one 8 Gy fraction of palliative radiation on day 0. Force plate measurements and clinical assessments were made on days 0, 7, 14, and 21. Peak vertical forces (Fz) were recorded for each limb and a symmetric index (SI) was calculated. There were no significant changes in kinetic parameters after one 8 Gy dose of radiation therapy. Nine of these 18 dogs exhibited increased limb function at day 21 based on force plate analysis. Significant factors affecting Fz included gender and tumor location. There was a significant correlation between Fz and response to therapy based on SI at day 21. SI seems to be useful to objectively assess response in this mixed population of dogs. One 8 Gy fraction of radiation therapy alone did not reduce lameness associated with appendicular osteosarcoma, but a subset of dogs did have improved limb function after a single dose.

Drug Delivery and Transport into the Central Circulation: An Example of Zero-Order In vivo Absorption of Rotigotine from a Transdermal Patch Formulation.

PubMed

Cawello, Willi; Braun, Marina; Andreas, Jens-Otto

2018-01-13

Pharmacokinetic studies using deconvolution methods and non-compartmental analysis to model clinical absorption of drugs are not well represented in the literature. The purpose of this research was (1) to define the system of equations for description of rotigotine (a dopamine receptor agonist delivered via a transdermal patch) absorption based on a pharmacokinetic model and (2) to describe the kinetics of rotigotine disposition after single and multiple dosing. The kinetics of drug disposition was evaluated based on rotigotine plasma concentration data from three phase 1 trials. In two trials, rotigotine was administered via a single patch over 24 h in healthy subjects. In a third trial, rotigotine was administered once daily over 1 month in subjects with early-stage Parkinson's disease (PD). A pharmacokinetic model utilizing deconvolution methods was developed to describe the relationship between drug release from the patch and plasma concentrations. Plasma-concentration over time profiles were modeled based on a one-compartment model with a time lag, a zero-order input (describing a constant absorption via skin into central circulation) and first-order elimination. Corresponding mathematical models for single- and multiple-dose administration were developed. After single-dose administration of rotigotine patches (using 2, 4 or 8 mg/day) in healthy subjects, a constant in vivo absorption was present after a minor time lag (2-3 h). On days 27 and 30 of the multiple-dose study in patients with PD, absorption was constant during patch-on periods and resembled zero-order kinetics. Deconvolution based on rotigotine pharmacokinetic profiles after single- or multiple-dose administration of the once-daily patch demonstrated that in vivo absorption of rotigotine showed constant input through the skin into the central circulation (resembling zero-order kinetics). Continuous absorption through the skin is a basis for stable drug exposure.

Real-time cell toxicity profiling of Tox21 10K compounds reveals cytotoxicity dependent toxicity pathway linkage

PubMed Central

Huang, Ruili; Lin, Ja-An; Sedykh, Alexander; Zhao, Jinghua; Tice, Raymond R.; Paules, Richard S.; Xia, Menghang; Auerbach, Scott S.

2017-01-01

Cytotoxicity is a commonly used in vitro endpoint for evaluating chemical toxicity. In support of the U.S. Tox21 screening program, the cytotoxicity of ~10K chemicals was interrogated at 0, 8, 16, 24, 32, & 40 hours of exposure in a concentration dependent fashion in two cell lines (HEK293, HepG2) using two multiplexed, real-time assay technologies. One technology measures the metabolic activity of cells (i.e., cell viability, glo) while the other evaluates cell membrane integrity (i.e., cell death, flor). Using glo technology, more actives and greater temporal variations were seen in HEK293 cells, while results for the flor technology were more similar across the two cell types. Chemicals were grouped into classes based on their cytotoxicity kinetics profiles and these classes were evaluated for their associations with activity in the Tox21 nuclear receptor and stress response pathway assays. Some pathways, such as the activation of H2AX, were associated with the fast-responding cytotoxicity classes, while others, such as activation of TP53, were associated with the slow-responding cytotoxicity classes. By clustering pathways based on their degree of association to the different cytotoxicity kinetics labels, we identified clusters of pathways where active chemicals presented similar kinetics of cytotoxicity. Such linkages could be due to shared underlying biological processes between pathways, for example, activation of H2AX and heat shock factor. Others involving nuclear receptor activity are likely due to shared chemical structures rather than pathway level interactions. Based on the linkage between androgen receptor antagonism and Nrf2 activity, we surmise that a subclass of androgen receptor antagonists cause cytotoxicity via oxidative stress that is associated with Nrf2 activation. In summary, the real-time cytotoxicity screen provides informative chemical cytotoxicity kinetics data related to their cytotoxicity mechanisms, and with our analysis, it is possible to formulate mechanism-based hypotheses on the cytotoxic properties of the tested chemicals. PMID:28531190

Quantitative analysis of immobilized penicillinase using enzyme-modified AlGaN/GaN field-effect transistors.

PubMed

Müntze, Gesche Mareike; Baur, Barbara; Schäfer, Wladimir; Sasse, Alexander; Howgate, John; Röth, Kai; Eickhoff, Martin

2015-02-15

Penicillinase-modified AlGaN/GaN field-effect transistors (PenFETs) are utilized to systematically investigate the covalently immobilized enzyme penicillinase under different experimental conditions. We demonstrate quantitative evaluation of covalently immobilized penicillinase layers on pH-sensitive field-effect transistors (FETs) using an analytical kinetic PenFET model. This kinetic model is explicitly suited for devices with thin enzyme layers that are not diffusion-limited, as it is the case for the PenFETs discussed here. By means of the kinetic model it was possible to extract the Michaelis constant of covalently immobilized penicillinase as well as relative transport coefficients of the different species associated with the enzymatic reaction which, exempli gratia, give information about the permeability of the enzymatic layer. Based on this analysis we quantify the reproducibility and the stability of the analyzed PenFETs over the course of 33 days as well as the influence of pH and buffer concentration on the properties of the enzymatic layer. Thereby the stability measurements reveal a Michalis constant KM of (67 ± 13)μM while the chronological development of the relative transport coefficients suggests a detachment of physisorbed penicillinase during the first two weeks since production. Our results show that AlGaN/GaN PenFETs prepared by covalent immobilization of a penicillinase enzyme layer present a powerful tool for quantitative analysis of enzyme functionality. Copyright © 2014 Elsevier B.V. All rights reserved.

Kinetic and Kinematic Analysis for Assessing the Differences in Countermovement Jump Performance in Rugby Players.

PubMed

Floría, Pablo; Gómez-Landero, Luis A; Suárez-Arrones, Luis; Harrison, Andrew J

2016-09-01

Floría, P, Gómez-Landero, LA, Suárez-Arrones, L, and Harrison, AJ. Kinetic and kinematic analysis for assessing the differences in countermovement jump performance in rugby players. J Strength Cond Res 30(9): 2533-2539, 2016-The aim of this study was to ascertain the differences in kinetic and kinematic profiles between better and poorer performers of the vertical jump within a homogeneous group of trained adults. Fifty rugby players were divided into low scoring (LOW) and high scoring (HIGH) groups based on their performance in the vertical jump. The force, velocity, displacement, and rate of force development (RFD)-time curves were analyzed to determine the differences between groups. The analysis of the data showed differences in all the patterns of the ensemble mean curves of the HIGH and LOW groups. During the eccentric phase, the differences in the HIGH group with respect to the LOW group were lower crouch position, higher downward velocity, and higher force and RFD during the braking of the downward movement. During the concentric phase, the HIGH group achieved higher upward velocity, higher force at the end of phase, and a higher position at takeoff. The higher jump performances seem to be related to a more effective stretch-shortening cycle function that is characterized by a deeper and faster countermovement with higher eccentric forces being applied to decelerate the downward movement leading to enhanced force generation during the concentric phase.

Base-Catalyzed Linkage Isomerization: An Undergraduate Inorganic Kinetics Experiment.

ERIC Educational Resources Information Center

Jackson, W. G.; And Others

1981-01-01

Describes kinetics experiments completed in a single two-hour laboratory period at 25 degrees Centigrade of nitrito to nitro rearrangement, based on the recently discovered base-catalysis path. Includes information on synthesis and characterization of linkage isomers, spectrophotometric techniques, and experimental procedures. (SK)

PET brain kinetics studies of 11C-ITMM and 11C-ITDM,radioprobes for metabotropic glutamate receptor type 1, in a nonhuman primate

PubMed Central

Yamasaki, Tomoteru; Maeda, Jun; Fujinaga, Masayuki; Nagai, Yuji; Hatori, Akiko; Yui, Joji; Xie, Lin; Nengaki, Nobuki; Zhang, Ming-Rong

2014-01-01

The metabotropic glutamate receptor type 1 (mGluR1) is a novel target protein for the development of new drugs against central nervous system disorders. Recently, we have developed 11C-labeled PET probes 11C-ITMM and 11C-ITDM, which demonstrate similar profiles, for imaging of mGluR1. In the present study, we compared 11C-ITMM and 11C-ITDM PET imaging and quantitative analysis in the monkey brain. Respective PET images showed similar distribution of uptake in the cerebellum, thalamus, and cingulate cortex. Slightly higher uptake was detected with 11C-ITDM than with 11C-ITMM. For the kinetic analysis using the two-tissue compartment model (2-TCM), the distribution volume (VT) in the cerebellum, an mGluR1-rich region in the brain, was 2.5 mL∙cm-3 for 11C-ITMM and 3.6 mL∙cm-3 for 11C-ITDM. By contrast, the VT in the pons, a region with negligible mGluR1 expression, was similarly low for both radiopharmaceuticals. Based on these results, we performed noninvasive PET quantitative analysis with general reference tissue models using the time-activity curve of the pons as a reference region. We confirmed the relationship and differences between the reference tissue models and 2-TCM using correlational scatter plots and Bland-Altman plots analyses. Although the scattergrams of both radiopharmaceuticals showed over- or underestimations of reference tissue model-based the binding potentials against 2-TCM, there were no significant differences between the two kinetic analysis models. In conclusion, we first demonstrated the potentials of 11C-ITMM and 11C-ITDM for noninvasive PET quantitative analysis using reference tissue models. In addition, our findings suggest that 11C-ITDM may be superior to 11C-ITMM as a PET probe for imaging of mGluR1, because regional VT values in PET with 11C-ITDM were higher than those of 11C-ITMM. Clinical studies of 11C-ITDM in humans will be necessary in the future. PMID:24795840

PET brain kinetics studies of (11)C-ITMM and (11)C-ITDM,radioprobes for metabotropic glutamate receptor type 1, in a nonhuman primate.

PubMed

Yamasaki, Tomoteru; Maeda, Jun; Fujinaga, Masayuki; Nagai, Yuji; Hatori, Akiko; Yui, Joji; Xie, Lin; Nengaki, Nobuki; Zhang, Ming-Rong

2014-01-01

The metabotropic glutamate receptor type 1 (mGluR1) is a novel target protein for the development of new drugs against central nervous system disorders. Recently, we have developed (11)C-labeled PET probes (11)C-ITMM and (11)C-ITDM, which demonstrate similar profiles, for imaging of mGluR1. In the present study, we compared (11)C-ITMM and (11)C-ITDM PET imaging and quantitative analysis in the monkey brain. Respective PET images showed similar distribution of uptake in the cerebellum, thalamus, and cingulate cortex. Slightly higher uptake was detected with (11)C-ITDM than with (11)C-ITMM. For the kinetic analysis using the two-tissue compartment model (2-TCM), the distribution volume (VT) in the cerebellum, an mGluR1-rich region in the brain, was 2.5 mL∙cm(-3) for (11)C-ITMM and 3.6 mL∙cm(-3) for (11)C-ITDM. By contrast, the VT in the pons, a region with negligible mGluR1 expression, was similarly low for both radiopharmaceuticals. Based on these results, we performed noninvasive PET quantitative analysis with general reference tissue models using the time-activity curve of the pons as a reference region. We confirmed the relationship and differences between the reference tissue models and 2-TCM using correlational scatter plots and Bland-Altman plots analyses. Although the scattergrams of both radiopharmaceuticals showed over- or underestimations of reference tissue model-based the binding potentials against 2-TCM, there were no significant differences between the two kinetic analysis models. In conclusion, we first demonstrated the potentials of (11)C-ITMM and (11)C-ITDM for noninvasive PET quantitative analysis using reference tissue models. In addition, our findings suggest that (11)C-ITDM may be superior to (11)C-ITMM as a PET probe for imaging of mGluR1, because regional VT values in PET with (11)C-ITDM were higher than those of (11)C-ITMM. Clinical studies of (11)C-ITDM in humans will be necessary in the future.

Kinetic analysis of inhibition of glucoamylase and active site mutants via chemoselective oxime immobilization of acarbose on SPR chip surfaces.

PubMed

Sauer, Jørgen; Abou Hachem, Maher; Svensson, Birte; Jensen, Knud J; Thygesen, Mikkel B

2013-06-28

We here report a quantitative study on the binding kinetics of inhibition of the enzyme glucoamylase and how individual active site amino acid mutations influence kinetics. To address this challenge, we have developed a fast and efficient method for anchoring native acarbose to gold chip surfaces for surface plasmon resonance studies employing wild type glucoamylase and active site mutants, Y175F, E180Q, and R54L, as analytes. The key method was the chemoselective and protecting group-free oxime functionalization of the pseudo-tetrasaccharide-based inhibitor acarbose. By using this technique we have shown that at pH 7.0 the association and dissociation rate constants for the acarbose-glucoamylase interaction are 10(4)M(-1)s(-1) and 10(3)s(-1), respectively, and that the conformational change to a tight enzyme-inhibitor complex affects the dissociation rate constant by a factor of 10(2)s(-1). Additionally, the acarbose-presenting SPR surfaces could be used as a glucoamylase sensor that allowed rapid, label-free affinity screening of small carbohydrate-based inhibitors in solution, which is otherwise difficult with immobilized enzymes or other proteins. Copyright © 2013 Elsevier Ltd. All rights reserved.

Forced unfolding of single-chain polymeric nanoparticles.

PubMed

Hosono, Nobuhiko; Kushner, Aaron M; Chung, Jaeyoon; Palmans, Anja R A; Guan, Zhibin; Meijer, E W

2015-06-03

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is applied to single-chain polymeric nanoparticles (SCPNs) to acquire information about the internal folding structure of SCPNs and inherent kinetic parameters of supramolecular self-assembling motifs embedded into the SCPNs. The SCPNs used here are polyacrylate-based polymers carrying 2-ureido-4-[1H]-pyrimidinone (UPy) or benzene-1,3,5-tricarboxamide (BTA) pendants that induce an intramolecular chain collapse into nanoparticles consisting of one polymer chain only via internal supramolecular cross-linking. The SCPN is stretched by an AFM cantilever to unfold mechanically, which allows measuring of force-extension profiles of the SCPNs. Consecutive peaks observed in the force profiles are attributed to rupture events of self-assembled UPy/BTA units in the SCPNs. The force profiles have been analyzed statistically for a series of polymers with different UPy/BTA incorporation densities. The results provide insights into the internal conformation of SCPNs, where the folding structure can be changed with the incorporation density of UPy/BTA. In addition, dynamic loading rate analysis allows the determination of kinetic parameters of BTA self-assembly, which has not been accessible by any other method. This study offers a rational tool for understanding the folding structure, kinetics, and pathway of two series of SCPNs.

1D kinetic simulations of a short glow discharge in helium

NASA Astrophysics Data System (ADS)

Yuan, Chengxun; Bogdanov, E. A.; Eliseev, S. I.; Kudryavtsev, A. A.

2017-07-01

This paper presents a 1D model of a direct current glow discharge based on the solution of the kinetic Boltzmann equation in the two-term approximation. The model takes into account electron-electron coulomb collisions, the corresponding collision integral is written in both detailed and simplified forms. The Boltzmann equation for electrons is coupled with continuity equations for ions and metastable atoms and the Poisson equation for electric potential. Simulations are carried out self-consistently for the whole length of discharge in helium (from cathode to anode) for cases p = 1 Torr, L = 3.6 cm and p = 20 Torr, L = 1.8 mm, so that pL = 3.6 cm.Torr in both cases. It is shown that simulations based on the kinetic approach give lower values of electron temperature in plasma than fluid simulations. Peaks in spatial differential flux corresponding to the electrons originating from superelastic collisions and Penning ionization were observed in simulations. Different approaches of taking coulomb collisions into account give significantly different values of electron density and electron temperature in plasma. Analysis showed that using a simplified approach gives a non-zero contribution to the electron energy balance, which is comparable to energy losses on elastic and inelastic collisions and leads to significant errors and thus is not recommended.

Hybrid Parallelization of Adaptive MHD-Kinetic Module in Multi-Scale Fluid-Kinetic Simulation Suite

DOE PAGES

Borovikov, Sergey; Heerikhuisen, Jacob; Pogorelov, Nikolai

2013-04-01

The Multi-Scale Fluid-Kinetic Simulation Suite has a computational tool set for solving partially ionized flows. In this paper we focus on recent developments of the kinetic module which solves the Boltzmann equation using the Monte-Carlo method. The module has been recently redesigned to utilize intra-node hybrid parallelization. We describe in detail the redesign process, implementation issues, and modifications made to the code. Finally, we conduct a performance analysis.

Kinetic magnetic resonance imaging analysis of abnormal segmental motion of the functional spine unit.

PubMed

Kong, Min Ho; Hymanson, Henry J; Song, Kwan Young; Chin, Dong Kyu; Cho, Yong Eun; Yoon, Do Heum; Wang, Jeffrey C

2009-04-01

The authors conducted a retrospective observational study using kinetic MR imaging to investigate the relationship between instability, abnormal sagittal segmental motion, and radiographic variables consisting of intervertebral disc degeneration, facet joint osteoarthritis (FJO), degeneration of the interspinous ligaments, ligamentum flavum hypertrophy (LFH), and the status of the paraspinal muscles. Abnormal segmental motion, defined as > 10 degrees angulation and > 3 mm of translation in the sagittal plane, was investigated in 1575 functional spine units (315 patients) in flexion, neutral, and extension postures using kinetic MR imaging. Each segment was assessed based on the extent of disc degeneration (Grades I-V), FJO (Grades 1-4), interspinous ligament degeneration (Grades 1-4), presence of LFH, and paraspinal muscle fatty infiltration observed on kinetic MR imaging. These factors are often noted in patients with degenerative disease, and there are grading systems to describe these changes. For the first time, the authors attempted to address the relationship between these radiographic observations and the effects on the motion and instability of the functional spine unit. The prevalence of abnormal translational motion was significantly higher in patients with Grade IV degenerative discs and Grade 3 arthritic facet joints (p < 0.05). In patients with advanced disc degeneration and FJO, there was a lesser amount of motion in both segmental translation and angulation when compared with lower grades of degeneration, and this difference was statistically significant for angular motion (p < 0.05). Patients with advanced degenerative Grade 4 facet joint arthritis had a significantly lower percentage of abnormal angular motion compared to patients with normal facet joints (p < 0.001). The presence of LFH was strongly associated with abnormal translational and angular motion. Grade 4 interspinous ligament degeneration and the presence of paraspinal muscle fatty infiltration were both significantly associated with excessive abnormal angular motion (p < 0.05). This kinetic MR imaging analysis showed that the lumbar functional unit with more disc degeneration, FJO, and LFH had abnormal sagittal plane translation and angulation. These findings suggest that abnormal segmental motion noted on kinetic MR images is closely associated with disc degeneration, FJO, and the pathological characteristics of interspinous ligaments, ligamentum flavum, and paraspinal muscles. Kinetic MR imaging in patients with mechanical back pain may prove a valuable source of information about the stability of the functional spine unit by measuring abnormal segmental motion and grading of radiographic parameters simultaneously.

A combined kinematic and kinetic analysis at the residuum/socket interface of a knee-disarticulation amputee.

PubMed

Tang, Jinghua; McGrath, Michael; Hale, Nick; Jiang, Liudi; Bader, Dan; Laszczak, Piotr; Moser, David; Zahedi, Saeed

2017-11-01

The bespoke interface between a lower limb residuum and a prosthetic socket is critical for an amputee's comfort and overall rehabilitation outcomes. Analysis of interface kinematics and kinetics is important to gain full understanding of the interface biomechanics, which could aid clinical socket fit, rehabilitation and amputee care. This pilot study aims to investigate the dynamic correlation between kinematic movement and kinetic stresses at the interface during walking tests on different terrains. One male, knee disarticulation amputee participated in the study. He was asked to walk on both a level surface and a 5° ramped surface. The movement between the residuum and the socket was evaluated by the angular and axial couplings, based on the outputs from a 3D motion capture system. The corresponding kinetic stresses at anterior-proximal (AP), posterior-proximal (PP) and anterior-distal (AD) locations of the residuum were measured, using individual stress sensors. Approximately 8° of angular coupling and up to 32 mm of axial coupling were measured when walking on different terrains. The direction of the angular coupling shows strong correlation with the pressure difference between the PP and AP sensors. Higher pressure was obtained at the PP location than the AP location during stance phase, associated with the direction of the angular coupling. A strong correlation between axial coupling length, L, and longitudinal shear was also evident at the PP and AD locations i.e. the shortening of L corresponds to the increase of shear in the proximal direction. Although different terrains did not affect these correlations in principle, interface kinematic and kinetic values suggested that gait changes can induce modifications to the interface biomechanics. It is envisaged that the reported techniques could be potentially used to provide combined kinematics and kinetics for the understanding of biomechanics at the residuum/socket interface, which may play an important role in the clinical assessment of prosthetic component settings, including socket fit quality. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Pyrolysis kinetics and combustion of thin wood using advanced cone calorimetry test method

Treesearch

Mark A. Dietenberger

2011-01-01

Mechanistic pyrolysis kinetics analysis of extractives, holocellulose, and lignin in solid wood over entire heating regime was possible using specialized cone calorimeter test and new mathematical analysis tools. Added hardware components include: modified sample holder for thin specimen with tiny thermocouples, methane ring burner with stainless steel mesh above cone...

Direct dynamic kinetic analysis and computer simulation of growth of Clostridium perfringens in cooked turkey during cooling

USDA-ARS?s Scientific Manuscript database

This research applied a new one-step methodology to directly construct a tertiary model for describing the growth of C. perfringens in cooked turkey meat under dynamically cooling conditions. The kinetic parameters of the growth models were determined by numerical analysis and optimization using mu...

A biomechanical analysis of upper extremity kinetics in children with cerebral palsy using anterior and posterior walkers.

PubMed

Konop, Katherine A; Strifling, Kelly M B; Wang, Mei; Cao, Kevin; Schwab, Jeffrey P; Eastwood, Daniel; Jackson, Scott; Ackman, Jeffrey D; Harris, Gerald F

2009-10-01

Upper extremity (UE) joint kinetics during aided ambulation is an area of research that is not well characterized in the current literature. Biped UE joints are not anatomically designed to be weight bearing, therefore it is important to quantify UE kinetics during assisted gait. This will help to better understand the biomechanical implications of UE weight bearing, and enable physicians to prescribe more effective methods for treatment and therapy, perhaps minimizing excessive loads and torques. To address this challenge, an UE model that incorporates both kinematics and kinetics has been developed for use with walkers instrumented with load cells. In this study, the UE joint kinetics are calculated for 10 children with cerebral palsy using both anterior and posterior walkers. Three-dimensional joint reaction forces and moments are fully characterized for the wrist, elbow, and shoulder (glenohumeral) joints for both walker types. Statistical analysis methods are used to quantify the differences in forces or moments between the two walker types. Comparisons showed no significant differences in kinetic joint parameters between walker types. Results from a power analysis of the current data are provided which may be useful for planning longer term clinical studies. If risk factors for UE joint pathology can be identified early, perhaps a change in gait training routine, walker prescription, or walker design could prevent further harm.

Analysis of a kinetic multi-segment foot model part II: kinetics and clinical implications.

PubMed

Bruening, Dustin A; Cooney, Kevin M; Buczek, Frank L

2012-04-01

Kinematic multi-segment foot models have seen increased use in clinical and research settings, but the addition of kinetics has been limited and hampered by measurement limitations and modeling assumptions. In this second of two companion papers, we complete the presentation and analysis of a three segment kinetic foot model by incorporating kinetic parameters and calculating joint moments and powers. The model was tested on 17 pediatric subjects (ages 7-18 years) during normal gait. Ground reaction forces were measured using two adjacent force platforms, requiring targeted walking and the creation of two sub-models to analyze ankle, midtarsal, and 1st metatarsophalangeal joints. Targeted walking resulted in only minimal kinematic and kinetic differences compared with walking at self selected speeds. Joint moments and powers were calculated and ensemble averages are presented as a normative database for comparison purposes. Ankle joint powers are shown to be overestimated when using a traditional single-segment foot model, as substantial angular velocities are attributed to the mid-tarsal joint. Power transfer is apparent between the 1st metatarsophalangeal and mid-tarsal joints in terminal stance/pre-swing. While the measurement approach presented here is limited to clinical populations with only minimal impairments, some elements of the model can also be incorporated into routine clinical gait analysis. Copyright © 2011 Elsevier B.V. All rights reserved.

ROCKETSHIP: a flexible and modular software tool for the planning, processing and analysis of dynamic MRI studies.

PubMed

Barnes, Samuel R; Ng, Thomas S C; Santa-Maria, Naomi; Montagne, Axel; Zlokovic, Berislav V; Jacobs, Russell E

2015-06-16

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a promising technique to characterize pathology and evaluate treatment response. However, analysis of DCE-MRI data is complex and benefits from concurrent analysis of multiple kinetic models and parameters. Few software tools are currently available that specifically focuses on DCE-MRI analysis with multiple kinetic models. Here, we developed ROCKETSHIP, an open-source, flexible and modular software for DCE-MRI analysis. ROCKETSHIP incorporates analyses with multiple kinetic models, including data-driven nested model analysis. ROCKETSHIP was implemented using the MATLAB programming language. Robustness of the software to provide reliable fits using multiple kinetic models is demonstrated using simulated data. Simulations also demonstrate the utility of the data-driven nested model analysis. Applicability of ROCKETSHIP for both preclinical and clinical studies is shown using DCE-MRI studies of the human brain and a murine tumor model. A DCE-MRI software suite was implemented and tested using simulations. Its applicability to both preclinical and clinical datasets is shown. ROCKETSHIP was designed to be easily accessible for the beginner, but flexible enough for changes or additions to be made by the advanced user as well. The availability of a flexible analysis tool will aid future studies using DCE-MRI. A public release of ROCKETSHIP is available at https://github.com/petmri/ROCKETSHIP .

Biosorption of copper ions from dilute aqueous solutions on base treated rubber (Hevea brasiliensis) leaves powder: kinetics, isotherm, and biosorption mechanisms.

PubMed

Wan Ngah, W S; Hanafiah, M A K M

2008-01-01

The efficiency of sodium hydroxide treated rubber (Hevea brasiliensis) leaves powder (NHBL) for removing copper ions from aqueous solutions has been investigated. The effects of physicochemical parameters on biosorption capacities such as stirring speed, pH, biosorbent dose, initial concentrations of copper, and ionic strength were studied. The biosorption capacities of NHBL increased with increase in pH, stirring speed and copper concentration but decreased with increase in biosorbent dose and ionic strength. The isotherm study indicated that NHBL fitted well with Langmuir model compared to Freundlich and Dubinin-Radushkevich models. The maximum biosorption capacity determined from Langmuir isotherm was 14.97 mg/g at 27 degrees C. The kinetic study revealed that pseudosecond order model fitted well the kinetic data, while Boyd kinetic model indicated that film diffusion was the main rate determining step in biosorption process. Based on surface area analysis, NHBL has low surface area and categorized as macroporous. Fourier transform infrared (FT-IR) analyses revealed that hydroxyl, carboxyl, and amino are the main functional groups involved in the binding of copper ions. Complexation was one of the main mechanisms for the removal of copper ions as indicated by FT-IR spectra. Ion exchange was another possible mechanism since the ratio of adsorbed cations (Cu2+ and H+) to the released cations (Na+, Ca2+, and Mg2+) from NHBL was almost unity. Copper ions bound on NHBL were able to be desorbed at > 99% using 0.05 mol/L HCl, 0.01 mol/L HNO3, and 0.01 mol/L EDTA solutions.

Rapid quantification and sex determination of forensic evidence materials.

PubMed

Andréasson, Hanna; Allen, Marie

2003-11-01

DNA quantification of forensic evidence is very valuable for an optimal use of the available biological material. Moreover, sex determination is of great importance as additional information in criminal investigations as well as in identification of missing persons, no suspect cases, and ancient DNA studies. While routine forensic DNA analysis based on short tandem repeat markers includes a marker for sex determination, analysis of samples containing scarce amounts of DNA is often based on mitochondrial DNA, and sex determination is not performed. In order to allow quantification and simultaneous sex determination on minute amounts of DNA, an assay based on real-time PCR analysis of a marker within the human amelogenin gene has been developed. The sex determination is based on melting curve analysis, while an externally standardized kinetic analysis allows quantification of the nuclear DNA copy number in the sample. This real-time DNA quantification assay has proven to be highly sensitive, enabling quantification of single DNA copies. Although certain limitations were apparent, the system is a rapid, cost-effective, and flexible assay for analysis of forensic casework samples.

Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize.

PubMed

Majeran, Wojciech; Friso, Giulia; Ponnala, Lalit; Connolly, Brian; Huang, Mingshu; Reidel, Edwin; Zhang, Cankui; Asakura, Yukari; Bhuiyan, Nazmul H; Sun, Qi; Turgeon, Robert; van Wijk, Klaas J

2010-11-01

C(4) grasses, such as maize (Zea mays), have high photosynthetic efficiency through combined biochemical and structural adaptations. C(4) photosynthesis is established along the developmental axis of the leaf blade, leading from an undifferentiated leaf base just above the ligule into highly specialized mesophyll cells (MCs) and bundle sheath cells (BSCs) at the tip. To resolve the kinetics of maize leaf development and C(4) differentiation and to obtain a systems-level understanding of maize leaf formation, the accumulation profiles of proteomes of the leaf and the isolated BSCs with their vascular bundle along the developmental gradient were determined using large-scale mass spectrometry. This was complemented by extensive qualitative and quantitative microscopy analysis of structural features (e.g., Kranz anatomy, plasmodesmata, cell wall, and organelles). More than 4300 proteins were identified and functionally annotated. Developmental protein accumulation profiles and hierarchical cluster analysis then determined the kinetics of organelle biogenesis, formation of cellular structures, metabolism, and coexpression patterns. Two main expression clusters were observed, each divided in subclusters, suggesting that a limited number of developmental regulatory networks organize concerted protein accumulation along the leaf gradient. The coexpression with BSC and MC markers provided strong candidates for further analysis of C(4) specialization, in particular transporters and biogenesis factors. Based on the integrated information, we describe five developmental transitions that provide a conceptual and practical template for further analysis. An online protein expression viewer is provided through the Plant Proteome Database.

Radiolysis Model Sensitivity Analysis for a Used Fuel Storage Canister

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

Wittman, Richard S.

2013-09-20

This report fulfills the M3 milestone (M3FT-13PN0810027) to report on a radiolysis computer model analysis that estimates the generation of radiolytic products for a storage canister. The analysis considers radiolysis outside storage canister walls and within the canister fill gas over a possible 300-year lifetime. Previous work relied on estimates based directly on a water radiolysis G-value. This work also includes that effect with the addition of coupled kinetics for 111 reactions for 40 gas species to account for radiolytic-induced chemistry, which includes water recombination and reactions with air.

Characterization of breast lesion using T1-perfusion magnetic resonance imaging: Qualitative vs. quantitative analysis.

PubMed

Thakran, S; Gupta, P K; Kabra, V; Saha, I; Jain, P; Gupta, R K; Singh, A

2018-06-14

The objective of this study was to quantify the hemodynamic parameters using first pass analysis of T 1 -perfusion magnetic resonance imaging (MRI) data of human breast and to compare these parameters with the existing tracer kinetic parameters, semi-quantitative and qualitative T 1 -perfusion analysis in terms of lesion characterization. MRI of the breast was performed in 50 women (mean age, 44±11 [SD] years; range: 26-75) years with a total of 15 benign and 35 malignant breast lesions. After pre-processing, T 1 -perfusion MRI data was analyzed using qualitative approach by two radiologists (visual inspection of the kinetic curve into types I, II or III), semi-quantitative (characterization of kinetic curve types using empirical parameters), generalized-tracer-kinetic-model (tracer kinetic parameters) and first pass analysis (hemodynamic-parameters). Chi-squared test, t-test, one-way analysis-of-variance (ANOVA) using Bonferroni post-hoc test and receiver-operating-characteristic (ROC) curve were used for statistical analysis. All quantitative parameters except leakage volume (Ve), qualitative (type-I and III) and semi-quantitative curves (type-I and III) provided significant differences (P<0.05) between benign and malignant lesions. Kinetic parameters, particularly volume transfer coefficient (K trans ) provided a significant difference (P<0.05) between all grades except grade-II vs III. The hemodynamic parameter (relative-leakage-corrected-breast-blood-volume [rBBVcorr) provided a statistically significant difference (P<0.05) between all grades. It also provided highest sensitivity and specificity among all parameters in differentiation between different grades of malignant breast lesions. Quantitative parameters, particularly rBBVcorr and K trans provided similar sensitivity and specificity in differentiating benign from malignant breast lesions for this cohort. Moreover, rBBVcorr provided better differentiation between different grades of malignant breast lesions among all the parameters. Copyright © 2018. Published by Elsevier Masson SAS.

qPIPSA: Relating enzymatic kinetic parameters and interaction fields

PubMed Central

Gabdoulline, Razif R; Stein, Matthias; Wade, Rebecca C

2007-01-01

Background The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. Results We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure. Conclusion Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism. PMID:17919319

Spectator Ions ARE Important! A Kinetic Study of the Copper-Aluminum Displacement Reaction

ERIC Educational Resources Information Center

Sobel, Sabrina G.; Cohen, Skyler

2010-01-01

Surprisingly, spectator ions are responsible for unexpected kinetics in the biphasic copper(II)-aluminum displacement reaction, with the rate of reaction dependent on the identity of the otherwise ignored spectator ions. Application of a published kinetic analysis developed for a reaction between a rotating Al disk and a Cu(II) ion solution to the…

Kinetic concepts of thermally stimulated reactions in solids

NASA Astrophysics Data System (ADS)

Vyazovkin, Sergey

Historical analysis suggests that the basic kinetic concepts of reactions in solids were inherited from homogeneous kinetics. These concepts rest upon the assumption of a single-step reaction that disagrees with the multiple-step nature of solid-state processes. The inadequate concepts inspire such unjustified anticipations of kinetic analysis as evaluating constant activation energy and/or deriving a single-step reaction mechanism for the overall process. A more adequate concept is that of the effective activation energy, which may vary with temperature and extent of conversion. The adequacy of this concept is illustrated by literature data as well as by experimental data on the thermal dehydration of calcium oxalate monohydrate and thermal decomposition of calcium carbonate, ammonium nitrate and 1,3,5,7- tetranitro-1,3,5,7-tetrazocine.

A study of the liquid-vapor phase change of mercury based on irreversible thermodynamics.

NASA Technical Reports Server (NTRS)

Adt, R. R., Jr.; Hatsopoulos, G. N.; Bornhorst, W. J.

1972-01-01

The object of this work is to determine the transport coefficients which appear in linear irreversible-thermodynamic rate equations of a phase change. An experiment which involves the steady-state evaporation of mercury was performed to measure the principal transport coefficient appearing in the mass-rate equation and the coupling transport coefficient appearing in both the mass-rate equation and the energy-rate equation. The principal transport coefficient sigma, usually termed the 'condensation' or 'evaporation' coefficient, is found to be approximately 0.9, which is higher than that measured previously in condensation-of-mercury experiments. The experimental value of the coupling coefficient K does not agree with the value predicted from Schrage's kinetic analysis of the phase change. A modified kinetic analysis in which the Onsager reciprocal law and the conservation laws are invoked is presented which removes this discrepancy but which shows that the use of Schrage's equation for predicting mass rates of phase change is a good approximation.

Whole-Body Human Inverse Dynamics with Distributed Micro-Accelerometers, Gyros and Force Sensing †

PubMed Central

Latella, Claudia; Kuppuswamy, Naveen; Romano, Francesco; Traversaro, Silvio; Nori, Francesco

2016-01-01

Human motion tracking is a powerful tool used in a large range of applications that require human movement analysis. Although it is a well-established technique, its main limitation is the lack of estimation of real-time kinetics information such as forces and torques during the motion capture. In this paper, we present a novel approach for a human soft wearable force tracking for the simultaneous estimation of whole-body forces along with the motion. The early stage of our framework encompasses traditional passive marker based methods, inertial and contact force sensor modalities and harnesses a probabilistic computational technique for estimating dynamic quantities, originally proposed in the domain of humanoid robot control. We present experimental analysis on subjects performing a two degrees-of-freedom bowing task, and we estimate the motion and kinetics quantities. The results demonstrate the validity of the proposed method. We discuss the possible use of this technique in the design of a novel soft wearable force tracking device and its potential applications. PMID:27213394

Analysis of monoclonal antibodies reactive with molecules upregulated or expressed only on activated lymphocytes.

PubMed

Davis, W C; Naessens, J; Brown, W C; Ellis, J A; Hamilton, M J; Cantor, G H; Barbosa, J I; Ferens, W; Bohach, G A

1996-08-01

Monoclonal antibodies potentially specific for antigens expressed or upregulated on activated leukocytes were selected for further analysis from the panel submitted to the third international workshop on ruminant leukocyte antigens. The kinetics of expression of these activation antigens on resting peripheral mononuclear cells (PBMC) and PBMC stimulated with concanavalin A or staphylococcal superantigen SECI for 4, 24 or 96 h were compared, as well as their appearance on various subsets of cells. For some of them, a molecular mass could be determined after immunoprecipitation from radio-labeled, lectin-stimulated cells. Based on the results from the clustering, kinetic studies and biochemical data, evidence was gathered for assigning two additional mAbs to cluster BoCD25 (IL-2 receptor) and two mAbs to cluster BoCD71 (transferrin receptor). Four mAbs recognized an early activation antigen predominantly expressed on gamma delta T cells in short-term cultures. A number of other activation antigens were further characterized.

Identification of synergistic impacts during anaerobic co-digestion of organic wastes.

PubMed

Astals, S; Batstone, D J; Mata-Alvarez, J; Jensen, P D

2014-10-01

Anaerobic co-digestion has been widely investigated, but there is limited analysis of interaction between substrates. The objective of this work was to assess the role of carbohydrates, protein and lipids in co-digestion behaviour separately, and together. Two sets of batch tests were done, each set consisting of the mono-digestion of three substrates, and the co-digestion of seven mixtures. The first was done with pure substrates--cellulose, casein and olive oil--while in the second slaughterhouse waste--paunch, blood and fat--were used as carbohydrate, protein and lipid sources, respectively. Synergistic effects were mainly improvement of process kinetics without a significant change in biodegradability. Kinetics improvement was linked to the mitigation of inhibitory compounds, particularly fats dilution. The exception was co-digestion of paunch with lipids, which resulted in an improved final yield with model based analysis indicating the presence of paunch improved degradability of the fatty feed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Transient-Free Operations With Physics-Based Real-time Analysis and Control

NASA Astrophysics Data System (ADS)

Kolemen, Egemen; Burrell, Keith; Eggert, William; Eldon, David; Ferron, John; Glasser, Alex; Humphreys, David

2016-10-01

In order to understand and predict disruptions, the two most common methods currently employed in tokamak analysis are the time-consuming ``kinetic EFITs,'' which are done offline with significant human involvement, and the search for correlations with global precursors using various parameterization techniques. We are developing automated ``kinetic EFITs'' at DIII-D to enable calculation of the stability as the plasma evolves close to the disruption. This allows us to quantify the probabilistic nature of the stability calculations and provides a stability metric for all possible linear perturbations to the plasma. This study also provides insight into how the control system can avoid the unstable operating space, which is critical for high-performance operations close to stability thresholds at ITER. A novel, efficient ideal stability calculation method and new real-time CER acquisition system are being developed, and a new 77-core server has been installed on the DIII-D PCS to enable experimental use. Sponsored by US DOE under DE-SC0015878 and DE-FC02-04ER54698.

Surface analysis of mixed-conducting ferrite membranes by the conversion-electron Mössbauer spectroscopy

NASA Astrophysics Data System (ADS)

Waerenborgh, J. C.; Tsipis, E. V.; Yaremchenko, A. A.; Kharton, V. V.

2011-09-01

Conversion-electron Mössbauer spectroscopy analysis of iron surface states in the dense ceramic membranes made of 57Fe-enriched SrFe 0.7Al 0.3O 3- δ perovskite, shows no traces of reductive decomposition or carbide formation in the interfacial layers after operation under air/CH 4 gradient at 1173 K, within the limits of experimental uncertainty. The predominant trivalent state of iron cations at the membrane permeate-side surface exposed to flowing dry methane provides evidence of the kinetic stabilization mechanism, which is only possible due to slow oxygen-exchange kinetics and enables long-term operation of the ferrite-based ceramic reactors for natural gas conversion. At the membrane feed-side surface exposed to air, the fractions of Fe 4+ and Fe 3+ are close to those in the powder equilibrated at atmospheric oxygen pressure, suggesting that the exchange limitations to oxygen transport are essentially localized at the partially reduced surface.

Homogeneous crystal nucleation in Ni droplets

NASA Astrophysics Data System (ADS)

Kožíšek, Zdeněk; Demo, Pavel

2017-10-01

Crystal nucleation kinetics is often represented by induction times or metastable zone widths (Kulkarni et al., 2013; Bokeloh et al., 2011). Repeating measurements of supercooling or time delay, at which phase transition is detected, are statistically processed to determine the so-called survivorship function, from which nucleation rate is computed. The size distribution of nuclei is difficult to measure near the critical size directly, and it is not clear which amount of nuclei is formed at the moment when the phase transition is detected. In the present paper, kinetic nucleation equations are solved for the crystal nucleation in Ni liquid droplet to determine the number of nuclei formed within a considered system. Analysis of supercooling experimental data, based on the classical nucleation theory CNT), computes appropriate values of the nucleation rate. However, CNT underestimates the number of nuclei F (F ≪ 1 for supercritical sizes). Taking into account the dependence of the surface energy on nucleus size to data analysis overcomes this discrepancy and leads to reasonable values of the size distribution of nuclei.

Descriptive analysis of kinematics and kinetics of catchers throwing to second base from their knees.

PubMed

Plummer, Hillary A; Oliver, Gretchen D

2016-08-01

In order to decrease the amount of time that it takes the catcher to throw the ball, a catcher may chose to throw from the knees. Upper extremity kinematics may play a significant role in the kinetics about the elbow observed in catchers throwing from the knees. If relationships between kinematics and kinetics exist then the development of training and coaching instruction may help in reduced upper extremity injury risk. Twenty-two baseball and softball catchers (14.36±3.86years; 165.11±17.54cm; 65.67±20.60kg) volunteered. The catchers exhibited a less trunk rotation (5.6±16.2°), greater elbow flexion (87.9±21.4°) and decreased humeral elevation (71.1±12.3°) at the event of maximum shoulder external rotation as compared to what has previously reported in catchers. These variables are important, as they have previously been established as potential injury risk factors in pitchers, however it is not yet clear the role these variables play in catchers' risk of injury. A positive relationship between elbow varus torque during the deceleration phase and elbow flexion at MIR was observed (r=0.609; p=0.003). Throwing from the knees reduces a catcher's ability to utilize the proximal kinetic chain and this may help to explain why their kinematics and kinetics differ from what has previously been presented in the literature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impact of Temperature and Non-Gaussian Statistics on Electron Transfer in Donor–Bridge–Acceptor Molecules

DOE PAGES

Waskasi, Morteza M.; Newton, Marshall D.; Matyushov, Dmitry V.

2017-03-16

A combination of experimental data and theoretical analysis provides evidence of a bell-shaped kinetics of electron transfer in the Arrhenius coordinates ln k vs 1/T . This kinetic law is a temperature analog of the familiar Marcus bell-shaped dependence based on ln k vs the reaction free energy. These results were obtained for reactions of intramolecular charge shift between the donor and acceptor separated by a rigid spacer studied experimentally by Miller and co-workers. The non-Arrhenius kinetic law is a direct consequence of the solvent reorganization energy and reaction driving force changing approximately as hyperbolic functions with temperature. The reorganizationmore » energy decreases and the driving force increases when temperature is increased. The point of equality between them marks the maximum of the activationless reaction rate. Reaching the consistency between the kinetic and thermodynamic experimental data requires the non-Gaussian statistics of the donor-acceptor energy gap described by the Q-model of electron transfer. Furthermore, the theoretical formalism combines the vibrational envelope of quantum vibronic transitions with the Q-model describing the classical component of the Franck-Condon factor and a microscopic solvation model of the solvent reorganization energy and the reaction free energy.« less

Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation cycle in extremely thermoacidophilic archaea

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

Loder, Andrew J.; Han, Yejun; Hawkins, Aaron B.

Here, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO 2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35%–65% split of carbon flux throughmore » the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO 2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxyproprionate.« less

Evidence for Alkene cis-Aminocupration, an Aminooxygenation Case Study: Kinetics, EPR Spectroscopy, and DFT Calculations

PubMed Central

Paderes, Monissa C.; Belding, Lee; Fanovic, Branden; Dudding, Travis; Keister, Jerome B.

2012-01-01

Alkene difunctionalization reactions are important in organic synthesis. We have recently shown that copper(II) complexes can promote and catalyze intramolecular alkene aminooxygenation, carboamination, and diamination reactions. In this contribution, we report a combined experimental and theoretical examination of the mechanism of the copper(II)-promoted olefin aminooxygenation reaction. Kinetics experiments revealed a mechanistic pathway involving an equilibrium reaction between a copper(II) carboxylate complex and the γ-alkenyl sulfonamide substrate and a rate-limiting intramolecular cis-addition of N–Cu across the olefin. Kinetic isotope effect studies support that the cis-aminocupration is the rate-determining step. UV/Vis spectra support a role for the base in the break-up of copper(II) carboxylate dimer to monomeric species. Electron paramagnetic resonance (EPR) spectra provide evidence for a kinetically competent N–Cu intermediate with a CuII oxidation state. Due to the highly similar stereochemical and reactivity trends among the CuII-promoted and catalyzed alkene difunctionalization reactions we have developed, the cis-aminocupration mechanism can reasonably be generalized across the reaction class. The methods and findings disclosed in this report should also prove valuable to the mechanism analysis and optimization of other copper(-II) carboxylate promoted reactions, especially those that take place in aprotic organic solvents. PMID:22237868

Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation cycle in extremely thermoacidophilic archaea

DOE PAGES

Loder, Andrew J.; Han, Yejun; Hawkins, Aaron B.; ...

2016-10-19

Here, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO 2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35%–65% split of carbon flux throughmore » the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO 2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxyproprionate.« less

A Native Threonine Coordinates Ordered Water to Tune Light-Oxygen-Voltage (LOV) Domain Photocycle Kinetics and Osmotic Stress Signaling in Trichoderma reesei ENVOY.

PubMed

Lokhandwala, Jameela; Silverman Y de la Vega, Rafael I; Hopkins, Hilary C; Britton, Collin W; Rodriguez-Iglesias, Aroa; Bogomolni, Roberto; Schmoll, Monika; Zoltowski, Brian D

2016-07-08

Light-oxygen-voltage (LOV) domain-containing proteins function as small light-activated modules capable of imparting blue light control of biological processes. Their small modular nature has made them model proteins for allosteric signal transduction and optogenetic devices. Despite intense research, key aspects of their signal transduction mechanisms and photochemistry remain poorly understood. In particular, ordered water has been identified as a possible key mediator of photocycle kinetics, despite the lack of ordered water in the LOV active site. Herein, we use recent crystal structures of a fungal LOV protein ENVOY to interrogate the role of Thr(101) in recruiting water to the flavin active site where it can function as an intrinsic base to accelerate photocycle kinetics. Kinetic and molecular dynamic simulations confirm a role in solvent recruitment to the active site and identify structural changes that correlate with solvent recruitment. In vivo analysis of T101I indicates a direct role of the Thr(101) position in mediating adaptation to osmotic stress, thereby verifying biological relevance of ordered water in LOV signaling. The combined studies identify position 101 as a mediator of both allostery and photocycle catalysis that can impact organism physiology. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Detailed kinetics and regulation of mammalian 2-oxoglutarate dehydrogenase

PubMed Central

2011-01-01

Background Mitochondrial 2-oxoglutarate (α-ketoglutarate) dehydrogenase complex (OGDHC), a key regulatory point of tricarboxylic acid (TCA) cycle, plays vital roles in multiple pathways of energy metabolism and biosynthesis. The catalytic mechanism and allosteric regulation of this large enzyme complex are not fully understood. Here computer simulation is used to test possible catalytic mechanisms and mechanisms of allosteric regulation of the enzyme by nucleotides (ATP, ADP), pH, and metal ion cofactors (Ca2+ and Mg2+). Results A model was developed based on an ordered ter-ter enzyme kinetic mechanism combined with con-formational changes that involve rotation of one lipoic acid between three catalytic sites inside the enzyme complex. The model was parameterized using a large number of kinetic data sets on the activity of OGDHC, and validated by comparison of model predictions to independent data. Conclusions The developed model suggests a hybrid rapid-equilibrium ping-pong random mechanism for the kinetics of OGDHC, consistent with previously reported mechanisms, and accurately describes the experimentally observed regulatory effects of cofactors on the OGDHC activity. This analysis provides a single consistent theoretical explanation for a number of apparently contradictory results on the roles of phosphorylation potential, NAD (H) oxidation-reduction state ratio, as well as the regulatory effects of metal ions on ODGHC function. PMID:21943256

Microsecond Unfolding Kinetics of Sheep Prion Protein Reveals an Intermediate that Correlates with Susceptibility to Classical Scrapie

PubMed Central

Chen, Kai-Chun; Xu, Ming; Wedemeyer, William J.; Roder, Heinrich

2011-01-01

The microsecond folding and unfolding kinetics of ovine prion proteins (ovPrP) were measured under various solution conditions. A fragment comprising residues 94–233 of the full-length ovPrP was studied for four variants with differing susceptibilities to classical scrapie in sheep. The observed biexponential unfolding kinetics of ovPrP provides evidence for an intermediate species. However, in contrast to previous results for human PrP, there is no evidence for an intermediate under refolding conditions. Global analysis of the kinetic data, based on a sequential three-state mechanism, quantitatively accounts for all folding and unfolding data as a function of denaturant concentration. The simulations predict that an intermediate accumulates under both folding and unfolding conditions, but is observable only in unfolding experiments because the intermediate is optically indistinguishable from the native state. The relative population of intermediates in two ovPrP variants, both transiently and under destabilizing equilibrium conditions, correlates with their propensities for classical scrapie. The variant susceptible to classical scrapie has a larger population of the intermediate state than the resistant variant. Thus, the susceptible variant should be favored to undergo the PrPC to PrPSc conversion and oligomerization. PMID:21889460

Kinetics of the reduction of bushveld complex chromite ore at 1416 °C

NASA Astrophysics Data System (ADS)

Soykan, O.; Eric, R. H.; King, R. P.

1991-12-01

The kinetics of the reduction of chromite ore from the LG-6 layer of the Bushveld Complex of the Transvaal in South Africa were studied at 1416 °C by the thermogravimetric analysis (TGA) technique. Spectroscopic graphite powder was employed as the reductant. The aim of this article is to present a kinetic model that satisfactorily describes the solid-state carbothermic reduction of chromite. A generalized rate model based on an ionic diffusion mechanism was developed. The model included the contribution of the interfacial area between partially reduced and unreduced zones in chromite particles and diffusion. The kinetic model described the process for degrees of reduction from 10 to 75 pet satisfactorily. It was observed that at a given particle size, the rate of reduction was controlled mainly by interfacial area up to about 40 pet reduction, after which the rate was dominated by diffusion. On the other hand, for a given degree of reduction, the contribution of the interfacial area to the rate increased, while that of diffusion decreased, with a decrease in the particle size. The value of the diffusion coefficient for the Fe2+ species at 1416 °C was calculated to be 2.63 x 10-2 cm2/s.

Substrate and Enzyme Specificity of the Kinetic Isotope Effects Associated with the Dioxygenation of Nitroaromatic Contaminants.

PubMed

Pati, Sarah G; Kohler, Hans-Peter E; Pabis, Anna; Paneth, Piotr; Parales, Rebecca E; Hofstetter, Thomas B

2016-07-05

Compound-specific isotope analysis (CSIA) is a promising approach for tracking biotransformation of organic pollutants, but isotope fractionation associated with aromatic oxygenations is only poorly understood. We investigated the dioxygenation of a series of nitroaromatic compounds to the corresponding catechols by two enzymes, namely, nitrobenzene and 2-nitrotoluene dioxygenase (NBDO and 2NTDO) to elucidate the enzyme- and substrate-specificity of C and H isotope fractionation. While the apparent (13)C- and (2)H-kinetic isotope effects of nitrobenzene, nitrotoluene isomers, 2,6-dinitrotoluene, and naphthalene dioxygenation by NBDO varied considerably, the correlation of C and H isotope fractionation revealed a common mechanism for nitrobenzene and nitrotoluenes. Similar observations were made for the dioxygenation of these substrates by 2NTDO. Evaluation of reaction kinetics, isotope effects, and commitment-to-catalysis based on experiment and theory showed that rates of dioxygenation are determined by the enzymatic O2 activation and aromatic C oxygenation. The contribution of enzymatic O2 activation to the reaction rate varies for different nitroaromatic substrates of NBDO and 2NTDO. Because aromatic dioxygenation by nonheme iron dioxygenases is frequently the initial step of biodegradation, O2 activation kinetics may also have been responsible for the minor isotope fractionation reported for the oxygenation of other aromatic contaminants.

Evaluation and linking of effective parameters in particle-based models and continuum models for mixing-limited bimolecular reactions

NASA Astrophysics Data System (ADS)

Zhang, Yong; Papelis, Charalambos; Sun, Pengtao; Yu, Zhongbo

2013-08-01

Particle-based models and continuum models have been developed to quantify mixing-limited bimolecular reactions for decades. Effective model parameters control reaction kinetics, but the relationship between the particle-based model parameter (such as the interaction radius R) and the continuum model parameter (i.e., the effective rate coefficient Kf) remains obscure. This study attempts to evaluate and link R and Kf for the second-order bimolecular reaction in both the bulk and the sharp-concentration-gradient (SCG) systems. First, in the bulk system, the agent-based method reveals that R remains constant for irreversible reactions and decreases nonlinearly in time for a reversible reaction, while mathematical analysis shows that Kf transitions from an exponential to a power-law function. Qualitative link between R and Kf can then be built for the irreversible reaction with equal initial reactant concentrations. Second, in the SCG system with a reaction interface, numerical experiments show that when R and Kf decline as t-1/2 (for example, to account for the reactant front expansion), the two models capture the transient power-law growth of product mass, and their effective parameters have the same functional form. Finally, revisiting of laboratory experiments further shows that the best fit factor in R and Kf is on the same order, and both models can efficiently describe chemical kinetics observed in the SCG system. Effective model parameters used to describe reaction kinetics therefore may be linked directly, where the exact linkage may depend on the chemical and physical properties of the system.

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

PubMed Central

Chylek, Lily A.; Harris, Leonard A.; Tung, Chang-Shung; Faeder, James R.; Lopez, Carlos F.

2013-01-01

Rule-based modeling was developed to address the limitations of traditional approaches for modeling chemical kinetics in cell signaling systems. These systems consist of multiple interacting biomolecules (e.g., proteins), which themselves consist of multiple parts (e.g., domains, linear motifs, and sites of phosphorylation). Consequently, biomolecules that mediate information processing generally have the potential to interact in multiple ways, with the number of possible complexes and post-translational modification states tending to grow exponentially with the number of binary interactions considered. As a result, only large reaction networks capture all possible consequences of the molecular interactions that occur in a cell signaling system, which is problematic because traditional modeling approaches for chemical kinetics (e.g., ordinary differential equations) require explicit network specification. This problem is circumvented through representation of interactions in terms of local rules. With this approach, network specification is implicit and model specification is concise. Concise representation results in a coarse graining of chemical kinetics, which is introduced because all reactions implied by a rule inherit the rate law associated with that rule. Coarse graining can be appropriate if interactions are modular, and the coarseness of a model can be adjusted as needed. Rules can be specified using specialized model-specification languages, and recently developed tools designed for specification of rule-based models allow one to leverage powerful software engineering capabilities. A rule-based model comprises a set of rules, which can be processed by general-purpose simulation and analysis tools to achieve different objectives (e.g., to perform either a deterministic or stochastic simulation). PMID:24123887

A numerical analysis of heat and mass transfer during the steam reforming process of ethane

NASA Astrophysics Data System (ADS)

Tomiczek, Marcin; Kaczmarczyk, Robert; Mozdzierz, Marcin; Brus, Grzegorz

2017-11-01

This paper presents a numerical analysis of heat and mass transfer during the steam reforming of ethane. From a chemical point of view, the reforming process of heavy hydrocarbons, such as ethane, is complex. One of the main issue is a set of undesired chemical reactions that causes the deposition of solid carbon and consequently blocks the catalytic property of a reactor. In the literature a carbon deposition regime is selected by thermodynamical analysis to design safe operation conditions. In the case of Computational Fluid Dynamic (CFD, hereafter) models each control volume should be investigated to determinate if carbon deposition is thermodynamically favourable. In this paper the authors combine equilibrium and kinetics analysis to simulate the steam reforming of methane-ethane rich fuel. The results of the computations were juxtaposed with experimental data for methane steam reforming, and good agreement was found. An analysis based on the kinetics of reactions was conducted to predict the influence of temperature drop and non-equilibrium composition on solid carbon deposition. It was found that strong non-uniform temperature distribution in the reactor causes conditions favourable for carbon deposition at the inlet of the reformer. It was shown that equilibrium calculations, often used in the literature, are insufficient.

The reliability of an instrumented start block analysis system.

PubMed

Tor, Elaine; Pease, David L; Ball, Kevin A

2015-02-01

The swimming start is highly influential to overall competition performance. Therefore, it is paramount to develop reliable methods to perform accurate biomechanical analysis of start performance for training and research. The Wetplate Analysis System is a custom-made force plate system developed by the Australian Institute of Sport--Aquatic Testing, Training and Research Unit (AIS ATTRU). This sophisticated system combines both force data and 2D digitization to measure a number of kinetic and kinematic parameter values in an attempt to evaluate start performance. Fourteen elite swimmers performed two maximal effort dives (performance was defined as time from start signal to 15 m) over two separate testing sessions. Intraclass correlation coefficients (ICC) were used to determine each parameter's reliability. The kinetic parameters all had ICC greater than 0.9 except the time of peak vertical force (0.742). This may have been due to variations in movement initiation after the starting signal between trials. The kinematic and time parameters also had ICC greater than 0.9 apart from for the time of maximum depth (0.719). This parameter was lower due to the swimmers varying their depth between trials. Based on the high ICC scores for all parameters, the Wetplate Analysis System is suitable for biomechanical analysis of swimming starts.

CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.

PubMed

Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J; Hasenauer, Jan

2016-01-01

Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/.

LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 3: Illustrative test problems

NASA Technical Reports Server (NTRS)

Bittker, David A.; Radhakrishnan, Krishnan

1994-01-01

LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 3 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 3 explains the kinetics and kinetics-plus-sensitivity analysis problems supplied with LSENS and presents sample results. These problems illustrate the various capabilities of, and reaction models that can be solved by, the code and may provide a convenient starting point for the user to construct the problem data file required to execute LSENS. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

PubMed Central

Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J.; Hasenauer, Jan

2016-01-01

Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/. PMID:26807911

Determining Kinetic Parameters for Isothermal Crystallization of Glasses

NASA Technical Reports Server (NTRS)

Ray, C. S.; Zhang, T.; Reis, S. T.; Brow, R. K.

2006-01-01

Non-isothermal crystallization techniques are frequently used to determine the kinetic parameters for crystallization in glasses. These techniques are experimentally simple and quick compared to the isothermal techniques. However, the analytical models used for non-isothermal data analysis, originally developed for describing isothermal transformation kinetics, are fundamentally flawed. The present paper describes a technique for determining the kinetic parameters for isothermal crystallization in glasses, which eliminates most of the common problems that generally make the studies of isothermal crystallization laborious and time consuming. In this technique, the volume fraction of glass that is crystallized as a function of time during an isothermal hold was determined using differential thermal analysis (DTA). The crystallization parameters for the lithium-disilicate (Li2O.2SiO2) model glass were first determined and compared to the same parameters determined by other techniques to establish the accuracy and usefulness of the present technique. This technique was then used to describe the crystallization kinetics of a complex Ca-Sr-Zn-silicate glass developed for sealing solid oxide fuel cells.

"Batch" kinetics in flow: online IR analysis and continuous control.

PubMed

Moore, Jason S; Jensen, Klavs F

2014-01-07

Currently, kinetic data is either collected under steady-state conditions in flow or by generating time-series data in batch. Batch experiments are generally considered to be more suitable for the generation of kinetic data because of the ability to collect data from many time points in a single experiment. Now, a method that rapidly generates time-series reaction data from flow reactors by continuously manipulating the flow rate and reaction temperature has been developed. This approach makes use of inline IR analysis and an automated microreactor system, which allowed for rapid and tight control of the operating conditions. The conversion/residence time profiles at several temperatures were used to fit parameters to a kinetic model. This method requires significantly less time and a smaller amount of starting material compared to one-at-a-time flow experiments, and thus allows for the rapid generation of kinetic data. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Are We There Yet? Applying Thermodynamic and Kinetic Profiling on Embryonic Ectoderm Development (EED) Hit-to-Lead Program.

PubMed

Wang, Ying; Edalji, Rohinton P; Panchal, Sanjay C; Sun, Chaohong; Djuric, Stevan W; Vasudevan, Anil

2017-10-26

It is advocated that kinetic and thermodynamic profiling of bioactive compounds should be incorporated and utilized as complementary tools for hit and lead optimizations in drug discovery. To assess their applications in the EED hit-to-lead optimization process, large amount of thermodynamic and kinetic data were collected and analyzed via isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR), respectively. Slower dissociation rates (k off ) of the lead compounds were observed as the program progressed. Analysis of the kinetic data indicated that compound cellular activity correlated with both K i and k off . Our analysis revealed that ITC data should be interpreted in the context of chiral purity of the compounds. The thermodynamic signatures of the EED aminopyrrolidine compounds were found to be mainly enthalpy driven with improved enthalpic contributions as the program progressed. Our study also demonstrated that significant challenges still exist in utilizing kinetic and thermodynamic parameters for hit selection.

Force Plate Gait Analysis in Doberman Pinschers with and without Cervical Spondylomyelopathy

PubMed Central

Foss, K.; da Costa, R.C.; Rajala-Shultz, P.J.; Allen, M.J.

2014-01-01

Background The most accepted means of evaluating the response of a patient with cervical spondylomyelopathy (CSM) to treatment is subjective and based on the owner and clinician's perception of the gait. Objective To establish and compare kinetic parameters based on force plate gait analysis between normal and CSM-affected Dobermans. Animals Nineteen Doberman Pinschers: 10 clinically normal and 9 with CSM. Methods Force plate analysis was prospectively performed in all dogs. At least 4 runs of ipsilateral limbs were collected from each dog. Eight force platform parameters were evaluated, including peak vertical force (PVF) and peak vertical impulse (PVI), peak mediolateral force (PMLF) and peak mediolateral impulse, peak braking force and peak braking impulse, and peak propulsive force (PPF) and peak propulsive impulse. In addition, the coefficient of variation (CV) for each limb was calculated for each parameter. Data analysis was performed by a repeated measures approach. Results PMLF (P = .0062), PVI (P = .0225), and PPF (P = .0408) were found to be lower in CSM-affected dogs compared with normal dogs. Analysis by CV as the outcome indicated more variability in PVF in CSM-affected dogs (P = 0.0045). The largest difference in the CV of PVF was seen in the thoracic limbs of affected dogs when compared with the thoracic limbs of normal dogs (P = 0.0019). Conclusions and Clinical Importance The CV of PVF in all 4 limbs, especially the thoracic limbs, distinguished clinically normal Dobermans from those with CSM. Other kinetic parameters less reliably distinguished CSM-affected from clinically normal Dobermans. PMID:23278957

The Effect of Temperature on Kinetics and Diffusion Coefficients of Metallocene Derivatives in Polyol-Based Deep Eutectic Solvents

PubMed Central

Bahadori, Laleh; Chakrabarti, Mohammed Harun; Manan, Ninie Suhana Abdul; Hashim, Mohd Ali; Mjalli, Farouq Sabri; AlNashef, Inas Muen; Brandon, Nigel

2015-01-01

The temperature dependence of the density, dynamic viscosity and ionic conductivity of several deep eutectic solvents (DESs) containing ammonium-based salts and hydrogen bond donvnors (polyol type) are investigated. The temperature-dependent electrolyte viscosity as a function of molar conductivity is correlated by means of Walden’s rule. The oxidation of ferrocene (Fc/Fc+) and reduction of cobaltocenium (Cc+/Cc) at different temperatures are studied by cyclic voltammetry and potential-step chronoamperometry in DESs. For most DESs, chronoamperometric transients are demonstrated to fit an Arrhenius-type relation to give activation energies for the diffusion of redox couples at different temperatures. The temperature dependence of the measured conductivities of DES1 and DES2 are better correlated with the Vogel-Tamman-Fulcher equation. The kinetics of the Fc/Fc+ and Cc+/Cc electrochemical systems have been investigated over a temperature range from 298 to 338 K. The heterogeneous electron transfer rate constant is then calculated at different temperatures by means of a logarithmic analysis. The glycerol-based DES (DES5) appears suitable for further testing in electrochemical energy storage devices. PMID:26642045

Program Helps To Determine Chemical-Reaction Mechanisms

NASA Technical Reports Server (NTRS)

Bittker, D. A.; Radhakrishnan, K.

1995-01-01

General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code developed for use in solving complex, homogeneous, gas-phase, chemical-kinetics problems. Provides for efficient and accurate chemical-kinetics computations and provides for sensitivity analysis for variety of problems, including problems involving honisothermal conditions. Incorporates mathematical models for static system, steady one-dimensional inviscid flow, reaction behind incident shock wave (with boundary-layer correction), and perfectly stirred reactor. Computations of equilibrium properties performed for following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. Written in FORTRAN 77 with exception of NAMELIST extensions used for input.

Increased robustness of single-molecule counting with microfluidics, digital isothermal amplification, and a mobile phone versus real-time kinetic measurements.

PubMed

Selck, David A; Karymov, Mikhail A; Sun, Bing; Ismagilov, Rustem F

2013-11-19

Quantitative bioanalytical measurements are commonly performed in a kinetic format and are known to not be robust to perturbation that affects the kinetics itself or the measurement of kinetics. We hypothesized that the same measurements performed in a "digital" (single-molecule) format would show increased robustness to such perturbations. Here, we investigated the robustness of an amplification reaction (reverse-transcription loop-mediated amplification, RT-LAMP) in the context of fluctuations in temperature and time when this reaction is used for quantitative measurements of HIV-1 RNA molecules under limited-resource settings (LRS). The digital format that counts molecules using dRT-LAMP chemistry detected a 2-fold change in concentration of HIV-1 RNA despite a 6 °C temperature variation (p-value = 6.7 × 10(-7)), whereas the traditional kinetic (real-time) format did not (p-value = 0.25). Digital analysis was also robust to a 20 min change in reaction time, to poor imaging conditions obtained with a consumer cell-phone camera, and to automated cloud-based processing of these images (R(2) = 0.9997 vs true counts over a 100-fold dynamic range). Fluorescent output of multiplexed PCR amplification could also be imaged with the cell phone camera using flash as the excitation source. Many nonlinear amplification schemes based on organic, inorganic, and biochemical reactions have been developed, but their robustness is not well understood. This work implies that these chemistries may be significantly more robust in the digital, rather than kinetic, format. It also calls for theoretical studies to predict robustness of these chemistries and, more generally, to design robust reaction architectures. The SlipChip that we used here and other digital microfluidic technologies already exist to enable testing of these predictions. Such work may lead to identification or creation of robust amplification chemistries that enable rapid and precise quantitative molecular measurements under LRS. Furthermore, it may provide more general principles describing robustness of chemical and biological networks in digital formats.

The Impact of ENSO on Extratropical Low Frequency Noise in Seasonal Forecasts

NASA Technical Reports Server (NTRS)

Schubert, Siegfried D.; Suarez, Max J.; Chang, Yehui; Branstator, Grant

2000-01-01

This study examines the uncertainty in forecasts of the January-February-March (JFM) mean extratropical circulation, and how that uncertainty is modulated by the El Nino/Southern Oscillation (ENSO). The analysis is based on ensembles of hindcasts made with an Atmospheric General Circulation Model (AGCM) forced with sea surface temperatures observed during; the 1983 El Nino and 1989 La Nina events. The AGCM produces pronounced interannual differences in the magnitude of the extratropical seasonal mean noise (intra-ensemble variability). The North Pacific, in particular, shows extensive regions where the 1989 seasonal mean noise kinetic energy (SKE), which is dominated by a "PNA-like" spatial structure, is more than twice that of the 1983 forecasts. The larger SKE in 1989 is associated with a larger than normal barotropic conversion of kinetic energy from the mean Pacific jet to the seasonal mean noise. The generation of SKE due to sub-monthly transients also shows substantial interannual differences, though these are much smaller than the differences in the mean flow conversions. An analysis of the Generation of monthly mean noise kinetic energy (NIKE) and its variability suggests that the seasonal mean noise is predominantly a statistical residue of variability resulting from dynamical processes operating on monthly and shorter times scales. A stochastically-forced barotropic model (linearized about the AGCM's 1983 and 1989 base states) is used to further assess the role of the basic state, submonthly transients, and tropical forcing, in modulating the uncertainties in the seasonal AGCM forecasts. When forced globally with spatially-white noise, the linear model generates much larger variance for the 1989 base state, consistent with the AGCM results. The extratropical variability for the 1989 base state is dominanted by a single eigenmode, and is strongly coupled with forcing over tropical western Pacific and the Indian Ocean, again consistent with the AGCM results. Linear calculations that include forcing from the AGCM variance of the tropical forcing and submonthly transients show a small impact on the variability over the Pacific/North American region compared with that of the base state differences.

Some fundamental questions concerning the kinetic theory of electrons in molecular gases and the e H2 vibrational cross section controversy

NASA Astrophysics Data System (ADS)

Robson, R. E.; White, R. D.; Morrison, Michael A.

2003-10-01

We commence a fundamental re-examination of the kinetic theory of charged particle swarms in molecular gases, focusing on collisional excitation of molecular rotational and ro-vibrational states by electrons. Modern day analysis of electron swarms has been based upon the kinetic equation of Wang-Chang et al, which simply treats all processes as scalar energy excitations, and ignores angular momentum conservation and the vector dynamics associated with rotational excitation. It is pointed out that there is no alternative, more exact kinetic equation readily available for electrons which enables one to directly ascertain the degree of error introduced by this approximation. Thus in this preliminary study, we approach the problem indirectly, from the standpoint of the neutral molecules, using the Waldmann-Snider quantum kinetic equation, and insist that an electron-molecule collision must look the same from the perspective of both electron and molecule. We give a formula for quantitatively assessing the importance of scalar versus vectorial treatments of rotational excitation by looking at the post-collisional 'echo' produced by an electron swarm as it passes through the gas. It is then pointed out that in order to remedy any deficiency, it will be necessary to introduce a kinetic collisional operator non-local in space to properly account for angular momentum conservation, as has long been established in the literature. This is a major exercise and given the preliminary nature of this study, we consider the inclusion of such effects from a formal point of view only. In particular we show how non-local effects lead to a spatially dependent 'source' term in the equation of continuity, and hence to corrections for both drift velocity and diffusion coefficients. The magnitude of these corrections has yet to be established.

Effects of CO addition on the characteristics of laminar premixed CH{sub 4}/air opposed-jet flames

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

Wu, C.-Y.; Chao, Y.-C.; Chen, C.-P.

2009-02-15

The effects of CO addition on the characteristics of premixed CH{sub 4}/air opposed-jet flames are investigated experimentally and numerically. Experimental measurements and numerical simulations of the flame front position, temperature, and velocity are performed in stoichiometric CH{sub 4}/CO/air opposed-jet flames with various CO contents in the fuel. Thermocouple is used for the determination of flame temperature, velocity measurement is made using particle image velocimetry (PIV), and the flame front position is measured by direct photograph as well as with laser-induced predissociative fluorescence (LIPF) of OH imaging techniques. The laminar burning velocity is calculated using the PREMIX code of Chemkin collectionmore » 3.5. The flame structures of the premixed stoichiometric CH{sub 4}/CO/air opposed-jet flames are simulated using the OPPDIF package with GRI-Mech 3.0 chemical kinetic mechanisms and detailed transport properties. The measured flame front position, temperature, and velocity of the stoichiometric CH{sub 4}/CO/air flames are closely predicted by the numerical calculations. Detailed analysis of the calculated chemical kinetic structures reveals that as the CO content in the fuel is increased from 0% to 80%, CO oxidation (R99) increases significantly and contributes to a significant level of heat-release rate. It is also shown that the laminar burning velocity reaches a maximum value (57.5 cm/s) at the condition of 80% of CO in the fuel. Based on the results of sensitivity analysis, the chemistry of CO consumption shifts to the dry oxidation kinetics when CO content is further increased over 80%. Comparison between the results of computed laminar burning velocity, flame temperature, CO consumption rate, and sensitivity analysis reveals that the effect of CO addition on the laminar burning velocity of the stoichiometric CH{sub 4}/CO/air flames is due mostly to the transition of the dominant chemical kinetic steps. (author)« less

Tunneling Kinetics and Nonadiabatic Proton-Coupled Electron Transfer in Proteins: The Effect of Electric Fields and Anharmonic Donor-Acceptor Interactions.

PubMed

Salna, Bridget; Benabbas, Abdelkrim; Russo, Douglas; Champion, Paul M

2017-07-20

A proper description of proton donor-acceptor (D-A) distance fluctuations is crucial for understanding tunneling in proton-coupled electron transport (PCET). The typical harmonic approximation for the D-A potential results in a Gaussian probability distribution, which does not appropriately reflect the electronic repulsion forces that increase the energetic cost of sampling shorter D-A distances. Because these shorter distances are the primary channel for thermally activated tunneling, the analysis of tunneling kinetics depends sensitively on the inherently anharmonic nature of the D-A interaction. Thus, we have used quantum chemical calculations to account for the D-A interaction and developed an improved model for the analysis of experimental tunneling kinetics. Strong internal electric fields are also considered and found to contribute significantly to the compressive forces when the D-A distance distribution is positioned below the van der Waals contact distance. This model is applied to recent experiments on the wild type (WT) and a double mutant (DM) of soybean lipoxygenase-1 (SLO). The compressive force necessary to prepare the tunneling-active distribution in WT SLO is found to fall in the ∼ nN range, which greatly exceeds the measured values of molecular motor and protein unfolding forces. This indicates that ∼60-100 MV/cm electric fields, aligned along the D-A bond axis, must be generated by an enzyme conformational interconversion that facilitates the PCET tunneling reaction. Based on the absolute value of the measured tunneling rate, and using previously calculated values of the electronic matrix element, the population of this tunneling-active conformation is found to lie in the range 10 -5 -10 -7 , indicating this is a rare structural fluctuation that falls well below the detection threshold of recent ENDOR experiments. Additional analysis of the DM tunneling kinetics leads to a proposal that a disordered (high entropy) conformation could be tunneling-active due to its broad range of sampled D-A distances.

Pyrolysis kinetics and combustion of thin wood by an advanced cone caorimetry test method

Treesearch

Mark Dietenberger

2012-01-01

Pyrolysis kinetics analysis of extractives, holocellulose, and lignin in the solid redwood over the entire heating regime was possible by specialized cone calorimeter test and new mathematical analysis tools. Added hardware components include: modified sample holder for the thin specimen with tiny thermocouples, the methane ring burner with stainless-steel mesh above...

Kinetic Resolution of Secondary Alcohols Using Amidine-Based Catalysts

PubMed Central

Li, Ximin; Jiang, Hui; Uffman, Eric W.; Guo, Lei; Zhang, Yuhua; Yang, Xing; Birman, Vladimir B.

2012-01-01

Kinetic resolution of racemic alcohols has been traditionally achieved via enzymatic enantioselective esterification and ester hydrolysis. However, there has long been considerable interest in devising nonenzymatic alternative methods for this transformation. Amidine-Based Catalysts (ABCs), a new class of enantioselective acyl transfer catalysts developed in our group, have demonstrated, inter alia, high efficacy in the kinetic resolution of benzylic, allylic and propargylic secondary alcohols and 2-substituted cycloalkanols, and thus provide a viable alternative to enzymes. PMID:22283696

Iron oxide nanoparticle-based magnetic resonance method to monitor release kinetics from polymeric particles with high resolution.

PubMed

Chan, Minnie; Schopf, Eric; Sankaranarayanan, Jagadis; Almutairi, Adah

2012-09-18

A new method to precisely monitor rapid release kinetics from polymeric particles using super paramagnetic iron oxide nanoparticles, specifically by measuring spin-spin relaxation time (T(2)), is reported. Previously, we have published the formulation of logic gate particles from an acid-sensitive poly-β-aminoester ketal-2 polymer. Here, a series of poly-β-aminoester ketal-2 polymers with varying hydrophobicities were synthesized and used to formulate particles. We attempted to measure fluorescence of released Nile red to determine whether the structural adjustments could finely tune the release kinetics in the range of minutes to hours; however, this standard technique did not differentiate each release rate of our series. Thus, a new method based on encapsulation of iron oxide nanoparticles was developed, which enabled us to resolve the release kinetics of our particles. Moreover, the kinetics matched the relative hydrophobicity order determined by octanol-water partition coefficients. To the best of our knowledge, this method provides the highest resolution of release kinetics to date.

Lipid-associated oral delivery: Mechanisms and analysis of oral absorption enhancement.

PubMed

Rezhdo, Oljora; Speciner, Lauren; Carrier, Rebecca

2016-10-28

The majority of newly discovered oral drugs are poorly water soluble, and co-administration with lipids has proven effective in significantly enhancing bioavailability of some compounds with low aqueous solubility. Yet, lipid-based delivery technologies have not been widely employed in commercial oral products. Lipids can impact drug transport and fate in the gastrointestinal (GI) tract through multiple mechanisms including enhancement of solubility and dissolution kinetics, enhancement of permeation through the intestinal mucosa, and triggering drug precipitation upon lipid emulsion depletion (e.g., by digestion). The effect of lipids on drug absorption is currently not quantitatively predictable, in part due to the multiple complex dynamic processes that can be impacted by lipids. Quantitative mechanistic analysis of the processes significant to lipid system function and overall impact on drug absorption can aid in the understanding of drug-lipid interactions in the GI tract and exploitation of such interactions to achieve optimal lipid-based drug delivery. In this review, we discuss the impact of co-delivered lipids and lipid digestion on drug dissolution, partitioning, and absorption in the context of the experimental tools and associated kinetic expressions used to study and model these processes. The potential benefit of a systems-based consideration of the concurrent multiple dynamic processes occurring upon co-dosing lipids and drugs to predict the impact of lipids on drug absorption and enable rational design of lipid-based delivery systems is presented. Copyright © 2016 Elsevier B.V. All rights reserved.

High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single nucleotide polymorphisms.

PubMed

Tong, Steven Y C; Xie, Shirley; Richardson, Leisha J; Ballard, Susan A; Dakh, Farshid; Grabsch, Elizabeth A; Grayson, M Lindsay; Howden, Benjamin P; Johnson, Paul D R; Giffard, Philip M

2011-01-01

We have developed a single nucleotide polymorphism (SNP) nucleated high-resolution melting (HRM) technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST) database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the results with MLST, pulsed-field gel electrophoresis (PFGE) and an allele specific real-time PCR (AS kinetic PCR) SNP typing method. In silico analysis based on predicted HRM curves according to the G+C content of each fragment for all 567 sequence types (STs) in the MLST database together with empiric data from the 85 isolates demonstrated that HRM analysis resolves E. faecium into 231 "melting types" (MelTs) and provides a Simpson's Index of Diversity (D) of 0.991 with respect to MLST. This is a significant improvement on the AS kinetic PCR SNP typing scheme that resolves 61 SNP types with D of 0.95. The MelTs were concordant with the known ST of the isolates. For the 85 isolates, there were 13 PFGE patterns, 17 STs, 14 MelTs and eight SNP types. There was excellent concordance between PFGE, MLST and MelTs with Adjusted Rand Indices of PFGE to MelT 0.936 and ST to MelT 0.973. In conclusion, this HRM based method appears rapid and reproducible. The results are concordant with MLST and the MLST based population structure.

Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

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

Parker, Stephen S.; White, Josh; Hosemann, Peter

High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. We measured the oxidation kinetic constant (k) as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3–5 orders of magnitude lower across the experimental temperature range. Our results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

DOE PAGES

Parker, Stephen S.; White, Josh; Hosemann, Peter; ...

2017-11-03

High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. We measured the oxidation kinetic constant (k) as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3–5 orders of magnitude lower across the experimental temperature range. Our results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

NASA Astrophysics Data System (ADS)

Parker, Stephen S.; White, Josh; Hosemann, Peter; Nelson, Andrew

2018-02-01

High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. The oxidation kinetic constant ( k) was measured as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3-5 orders of magnitude lower across the experimental temperature range. The results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

Reproducibility of Quantitative Brain Imaging Using a PET-Only and a Combined PET/MR System

PubMed Central

Lassen, Martin L.; Muzik, Otto; Beyer, Thomas; Hacker, Marcus; Ladefoged, Claes Nøhr; Cal-González, Jacobo; Wadsak, Wolfgang; Rausch, Ivo; Langer, Oliver; Bauer, Martin

2017-01-01

The purpose of this study was to test the feasibility of migrating a quantitative brain imaging protocol from a positron emission tomography (PET)-only system to an integrated PET/MR system. Potential differences in both absolute radiotracer concentration as well as in the derived kinetic parameters as a function of PET system choice have been investigated. Five healthy volunteers underwent dynamic (R)-[11C]verapamil imaging on the same day using a GE-Advance (PET-only) and a Siemens Biograph mMR system (PET/MR). PET-emission data were reconstructed using a transmission-based attenuation correction (AC) map (PET-only), whereas a standard MR-DIXON as well as a low-dose CT AC map was applied to PET/MR emission data. Kinetic modeling based on arterial blood sampling was performed using a 1-tissue-2-rate constant compartment model, yielding kinetic parameters (K1 and k2) and distribution volume (VT). Differences for parametric values obtained in the PET-only and the PET/MR systems were analyzed using a 2-way Analysis of Variance (ANOVA). Comparison of DIXON-based AC (PET/MR) with emission data derived from the PET-only system revealed average inter-system differences of −33 ± 14% (p < 0.05) for the K1 parameter and −19 ± 9% (p < 0.05) for k2. Using a CT-based AC for PET/MR resulted in slightly lower systematic differences of −16 ± 18% for K1 and −9 ± 10% for k2. The average differences in VT were −18 ± 10% (p < 0.05) for DIXON- and −8 ± 13% for CT-based AC. Significant systematic differences were observed for kinetic parameters derived from emission data obtained from PET/MR and PET-only imaging due to different standard AC methods employed. Therefore, a transfer of imaging protocols from PET-only to PET/MR systems is not straightforward without application of proper correction methods. Clinical Trial Registration: www.clinicaltrialsregister.eu, identifier 2013-001724-19 PMID:28769742

Enzyme Kinetics Experiment with the Multienzyme Complex Viscozyme L and Two Substrates for the Accurate Determination of Michaelian Parameters

ERIC Educational Resources Information Center

Guerra, Nelson Pérez

2017-01-01

A laboratory experiment in which students study the kinetics of the Viscozyme-L-catalyzed hydrolysis of cellulose and starch comparatively was designed for an upper-division biochemistry laboratory. The main objective of this experiment was to provide an opportunity to perform enhanced enzyme kinetics data analysis using appropriate informatics…

Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease.

PubMed

Walkenhorst, W F; Green, S M; Roder, H

1997-05-13

The complex kinetic behavior commonly observed in protein folding studies suggests that a heterogeneous population of molecules exists in solution and that a number of discrete steps are involved in the conversion of unfolded molecules to the fully native form. A central issue in protein folding is whether any of these kinetic events represent conformational steps important for efficient folding rather than side reactions caused by slow steps such as proline isomerization or misfolding of the polypeptide chain. In order to address this question, we used stopped-flow fluorescence techniques to characterize the kinetic mechanism of folding and unfolding for a Pro- variant of SNase in which all six proline residues were replaced by glycines or alanines. Compared to the wild-type protein, which exhibits a series of proline-dependent slow folding phases, the folding kinetics of Pro- SNase were much simpler, which made quantitative kinetic analysis possible. Despite the absence of prolines or other complicating factors, the folding kinetics still contain several phases and exhibit a complex denaturant dependence. The GuHCl dependence of the major observable folding phase and a distinct lag in the appearance of the native state provide clear evidence for an early folding intermediate. The fluorescence of Trp140 in the alpha-helical domain is insensitive to the formation of this early intermediate, which is consistent with a partially folded state with a stable beta-domain and a largely disordered alpha-helical region. A second intermediate is required to model the kinetics of unfolding for the Pro- variant, which shows evidence for a denaturant-induced change in the rate-limiting unfolding step. With the inclusion of these two intermediates, we are able to completely model the major phase(s) in both folding and unfolding across a wide range of denaturant concentrations using a sequential four-state folding mechanism. In order to model the minor slow phase observed for the Pro- mutant, a six-state scheme containing a parallel pathway originating from a distinct unfolded state was required. The properties of this alternate unfolded conformation are consistent with those expected due to the presence of a non-prolyl cis peptide bond. To test the kinetic model, we used simulations based on the six-state scheme and were able to completely reproduce the folding kinetics for Pro- SNase across a range of denaturant concentrations.

WAKES: Wavelet Adaptive Kinetic Evolution Solvers

NASA Astrophysics Data System (ADS)

Mardirian, Marine; Afeyan, Bedros; Larson, David

2016-10-01

We are developing a general capability to adaptively solve phase space evolution equations mixing particle and continuum techniques in an adaptive manner. The multi-scale approach is achieved using wavelet decompositions which allow phase space density estimation to occur with scale dependent increased accuracy and variable time stepping. Possible improvements on the SFK method of Larson are discussed, including the use of multiresolution analysis based Richardson-Lucy Iteration, adaptive step size control in explicit vs implicit approaches. Examples will be shown with KEEN waves and KEEPN (Kinetic Electrostatic Electron Positron Nonlinear) waves, which are the pair plasma generalization of the former, and have a much richer span of dynamical behavior. WAKES techniques are well suited for the study of driven and released nonlinear, non-stationary, self-organized structures in phase space which have no fluid, limit nor a linear limit, and yet remain undamped and coherent well past the drive period. The work reported here is based on the Vlasov-Poisson model of plasma dynamics. Work supported by a Grant from the AFOSR.

Tracking of cell nuclei for assessment of in vitro uptake kinetics in ultrasound-mediated drug delivery using fibered confocal fluorescence microscopy.

PubMed

Derieppe, Marc; de Senneville, Baudouin Denis; Kuijf, Hugo; Moonen, Chrit; Bos, Clemens

2014-10-01

Previously, we demonstrated the feasibility to monitor ultrasound-mediated uptake of a cell-impermeable model drug in real time with fibered confocal fluorescence microscopy. Here, we present a complete post-processing methodology, which corrects for cell displacements, to improve the accuracy of pharmacokinetic parameter estimation. Nucleus detection was performed based on the radial symmetry transform algorithm. Cell tracking used an iterative closest point approach. Pharmacokinetic parameters were calculated by fitting a two-compartment model to the time-intensity curves of individual cells. Cells were tracked successfully, improving time-intensity curve accuracy and pharmacokinetic parameter estimation. With tracking, 93 % of the 370 nuclei showed a fluorescence signal variation that was well-described by a two-compartment model. In addition, parameter distributions were narrower, thus increasing precision. Dedicated image analysis was implemented and enabled studying ultrasound-mediated model drug uptake kinetics in hundreds of cells per experiment, using fiber-based confocal fluorescence microscopy.

Analysis of Electromagnetic Wave Propagation in a Magnetized Re-Entry Plasma Sheath Via the Kinetic Equation

NASA Technical Reports Server (NTRS)

Manning, Robert M.

2009-01-01

Based on a theoretical model of the propagation of electromagnetic waves through a hypersonically induced plasma, it has been demonstrated that the classical radiofrequency communications blackout that is experienced during atmospheric reentry can be mitigated through the appropriate control of an external magnetic field of nominal magnitude. The model is based on the kinetic equation treatment of Vlasov and involves an analytical solution for the electric and magnetic fields within the plasma allowing for a description of the attendant transmission, reflection and absorption coefficients. The ability to transmit through the magnetized plasma is due to the magnetic windows that are created within the plasma via the well-known whistler modes of propagation. The case of 2 GHz transmission through a re-entry plasma is considered. The coefficients are found to be highly sensitive to the prevailing electron density and will thus require a dynamic control mechanism to vary the magnetic field as the plasma evolves through the re-entry phase.

Ozone decomposition

PubMed Central

Batakliev, Todor; Georgiev, Vladimir; Anachkov, Metody; Rakovsky, Slavcho

2014-01-01

Catalytic ozone decomposition is of great significance because ozone is a toxic substance commonly found or generated in human environments (aircraft cabins, offices with photocopiers, laser printers, sterilizers). Considerable work has been done on ozone decomposition reported in the literature. This review provides a comprehensive summary of the literature, concentrating on analysis of the physico-chemical properties, synthesis and catalytic decomposition of ozone. This is supplemented by a review on kinetics and catalyst characterization which ties together the previously reported results. Noble metals and oxides of transition metals have been found to be the most active substances for ozone decomposition. The high price of precious metals stimulated the use of metal oxide catalysts and particularly the catalysts based on manganese oxide. It has been determined that the kinetics of ozone decomposition is of first order importance. A mechanism of the reaction of catalytic ozone decomposition is discussed, based on detailed spectroscopic investigations of the catalytic surface, showing the existence of peroxide and superoxide surface intermediates. PMID:26109880

Transient performance analysis of the master cylinder hydraulic system of a 6.3 MN fineblanking press

NASA Astrophysics Data System (ADS)

Yi, Guodong; Li, Jin

2018-03-01

The master cylinder hydraulic system is the core component of the fineblanking press that seriously affects the machine performance. A key issue in the design of the master cylinder hydraulic system is dealing with the heavy shock loads in the fineblanking process. In this paper, an equivalent model of the master cylinder hydraulic system is established based on typical process parameters for practical fineblanking; then, the response characteristics of the master cylinder slider to the step changes in the load and control current are analyzed, and lastly, control strategies for the proportional valve are studied based on the impact of the control parameters on the kinetic stability of the slider. The results show that the kinetic stability of the slider is significantly affected by the step change of the control current, while it is slightly affected by the step change of the system load, which can be improved by adjusting the flow rate and opening time of the proportional valve.

Dynamic biogas upgrading based on the Sabatier process: thermodynamic and dynamic process simulation.

PubMed

Jürgensen, Lars; Ehimen, Ehiaze Augustine; Born, Jens; Holm-Nielsen, Jens Bo

2015-02-01

This study aimed to investigate the feasibility of substitute natural gas (SNG) generation using biogas from anaerobic digestion and hydrogen from renewable energy systems. Using thermodynamic equilibrium analysis, kinetic reactor modeling and transient simulation, an integrated approach for the operation of a biogas-based Sabatier process was put forward, which was then verified using a lab scale heterogenous methanation reactor. The process simulation using a kinetic reactor model demonstrated the feasibility of the production of SNG at gas grid standards using a single reactor setup. The Wobbe index, CO2 content and calorific value were found to be controllable by the H2/CO2 ratio fed the methanation reactor. An optimal H2/CO2 ratio of 3.45-3.7 was seen to result in a product gas with high calorific value and Wobbe index. The dynamic reactor simulation verified that the process start-up was feasible within several minutes to facilitate surplus electricity use from renewable energy systems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Distribution of apparent activation energy counterparts during thermo - And thermo-oxidative degradation of Aronia melanocarpa (black chokeberry).

PubMed

Janković, Bojan; Marinović-Cincović, Milena; Janković, Marija

2017-09-01

Kinetics of degradation for Aronia melanocarpa fresh fruits in argon and air atmospheres were investigated. The investigation was based on probability distributions of apparent activation energy of counterparts (ε a ). Isoconversional analysis results indicated that the degradation process in an inert atmosphere was governed by decomposition reactions of esterified compounds. Also, based on same kinetics approach, it was assumed that in an air atmosphere, the primary compound in degradation pathways could be anthocyanins, which undergo rapid chemical reactions. A new model of reactivity demonstrated that, under inert atmospheres, expectation values for ε a occured at levels of statistical probability. These values corresponded to decomposition processes in which polyphenolic compounds might be involved. ε a values obeyed laws of binomial distribution. It was established that, for thermo-oxidative degradation, Poisson distribution represented a very successful approximation for ε a values where there was additional mechanistic complexity and the binomial distribution was no longer valid. Copyright © 2017 Elsevier Ltd. All rights reserved.

Theoretical analysis of factors controlling the nonalternating CO/C(2)H(4) copolymerization.

PubMed

Haras, Alicja; Michalak, Artur; Rieger, Bernhard; Ziegler, Tom

2005-06-22

A [P-O]Pd catalyst based on o-alkoxy derivatives of diphenylphosphinobenzene sulfonic acid (I) has recently been shown by Drent et al. to perform nonalternating CO/C(2)H(4) copolymerization with subsequent incorporation of ethylene units into the polyketone chain. The origin of the nonalternation is investigated in a theoretical study of I, where calculated activation barriers and reaction heats of all involved elementary steps are used to generate a complete kinetic model. The kinetic model is able to account for the observed productivity and degree of nonalternation as a function of temperature. Consistent with the energy changes obtained for the real catalyst model, the selectivity toward a nonalternating distribution of both comonomers appears to be mainly a result of a strong destabilization of the Pd-acyl complex.

Modeling Photo-Bleaching Kinetics to Create High Resolution Maps of Rod Rhodopsin in the Human Retina

PubMed Central

Ehler, Martin; Dobrosotskaya, Julia; Cunningham, Denise; Wong, Wai T.; Chew, Emily Y.; Czaja, Wojtek; Bonner, Robert F.

2015-01-01

We introduce and describe a novel non-invasive in-vivo method for mapping local rod rhodopsin distribution in the human retina over a 30-degree field. Our approach is based on analyzing the brightening of detected lipofuscin autofluorescence within small pixel clusters in registered imaging sequences taken with a commercial 488nm confocal scanning laser ophthalmoscope (cSLO) over a 1 minute period. We modeled the kinetics of rhodopsin bleaching by applying variational optimization techniques from applied mathematics. The physical model and the numerical analysis with its implementation are outlined in detail. This new technique enables the creation of spatial maps of the retinal rhodopsin and retinal pigment epithelium (RPE) bisretinoid distribution with an ≈ 50μm resolution. PMID:26196397

Gyrokinetic-water-bag modeling of low-frequency instabilities in a laboratory magnetized plasma column

NASA Astrophysics Data System (ADS)

Gravier, E.; Klein, R.; Morel, P.; Besse, N.; Bertrand, P.

2008-12-01

A new model is presented, named collisional-gyro-water-bag (CGWB), which describes the collisional drift waves and ion-temperature-gradient (ITG) instabilities in a plasma column. This model is based on the kinetic gyro-water-bag approach recently developed [P. Morel et al., Phys. Plasmas 14, 112109 (2007)] to investigate ion-temperature-gradient modes. In CGWB electron-neutral collisions have been introduced and are now taken into account. The model has been validated by comparing CGWB linear analysis with other models previously proposed and experimental results as well. Kinetic effects on collisional drift waves are investigated, resulting in a less effective growth rate, and the transition from collisional drift waves to ITG instability depending on the ion temperature gradient is studied.

Feasibility of Traveling Wave Direct Energy Conversion of Fission Reaction Fragments

NASA Technical Reports Server (NTRS)

Tarditi, A. G.; George, J. A.; Miley, G. H.; Scott, J. H.

2013-01-01

Fission fragment direct energy conversion has been considered in the past for the purpose of increasing nuclear power plant efficiency and for advanced space propulsion. Since the fragments carry electric charge (typically in the order of 20 e) and have 100 MeV-range kinetic energy, techniques utilizing very high-voltage DC electrodes have been considered. This study is focused on a different approach: the kinetic energy of the charged fission fragments is converted into alternating current by means of a traveling wave coupling scheme (Traveling Wave Direct Energy Converter, TWDEC), thereby not requiring the utilization of high voltage technology. A preliminary feasibility analysis of the concept is introduced based on a conceptual level study and on a particle simulation model of the beam dynamics.

Kinetic Limitations of Cooperativity-Based Drug Delivery Systems

NASA Astrophysics Data System (ADS)

Licata, Nicholas A.; Tkachenko, Alexei V.

2008-04-01

We study theoretically a novel drug delivery system that utilizes the overexpression of certain proteins in cancerous cells for cell-specific chemotherapy. The system consists of dendrimers conjugated with “keys” (ex: folic acid) which “key-lock” bind to particular cell-membrane proteins (ex: folate receptor). The increased concentration of “locks” on the surface leads to a longer residence time for the dendrimer and greater incorporation into the cell. Cooperative binding of the nanocomplexes leads to an enhancement of cell specificity. However, both our theory and detailed analysis of in vitro experiments indicate that the degree of cooperativity is kinetically limited. We demonstrate that cooperativity and hence the specificity to particular cell type can be increased by making the strength of individual bonds weaker, and suggest a particular implementation of this idea.

Comparing kinetic profiles between bifunctional and binary type of Zn(salen)-based catalysts for organic carbonate formation

PubMed Central

Martín, Carmen

2014-01-01

Summary Zn(salen) complexes have been employed as active catalysts for the formation of cyclic carbonates from epoxides and CO2. A series of kinetic experiments was carried out to obtain information about the mechanism for this process catalyzed by these complexes and in particular about the order-dependence in catalyst. A comparative analysis was done between the binary catalyst system Zn(salphen)/NBu4I and a bifunctional system Zn(salpyr)·MeI with a built-in nucleophile. The latter system demonstrates an apparent second-order dependence on the bifunctional catalyst concentration and thus follows a different, bimetallic mechanism as opposed to the binary catalyst that is connected with a first-order dependence on the catalyst concentration and a monometallic mechanism. PMID:25161742

Automated Voxel-Based Analysis of Volumetric Dynamic Contrast-Enhanced CT Data Improves Measurement of Serial Changes in Tumor Vascular Biomarkers

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

Coolens, Catherine, E-mail: catherine.coolens@rmp.uhn.on.ca; Department of Radiation Oncology, University of Toronto, Toronto, Ontario; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario

2015-01-01

Objectives: Development of perfusion imaging as a biomarker requires more robust methodologies for quantification of tumor physiology that allow assessment of volumetric tumor heterogeneity over time. This study proposes a parametric method for automatically analyzing perfused tissue from volumetric dynamic contrast-enhanced (DCE) computed tomography (CT) scans and assesses whether this 4-dimensional (4D) DCE approach is more robust and accurate than conventional, region-of-interest (ROI)-based CT methods in quantifying tumor perfusion with preliminary evaluation in metastatic brain cancer. Methods and Materials: Functional parameter reproducibility and analysis of sensitivity to imaging resolution and arterial input function were evaluated in image sets acquired from amore » 320-slice CT with a controlled flow phantom and patients with brain metastases, whose treatments were planned for stereotactic radiation surgery and who consented to a research ethics board-approved prospective imaging biomarker study. A voxel-based temporal dynamic analysis (TDA) methodology was used at baseline, at day 7, and at day 20 after treatment. The ability to detect changes in kinetic parameter maps in clinical data sets was investigated for both 4D TDA and conventional 2D ROI-based analysis methods. Results: A total of 7 brain metastases in 3 patients were evaluated over the 3 time points. The 4D TDA method showed improved spatial efficacy and accuracy of perfusion parameters compared to ROI-based DCE analysis (P<.005), with a reproducibility error of less than 2% when tested with DCE phantom data. Clinically, changes in transfer constant from the blood plasma into the extracellular extravascular space (K{sub trans}) were seen when using TDA, with substantially smaller errors than the 2D method on both day 7 post radiation surgery (±13%; P<.05) and by day 20 (±12%; P<.04). Standard methods showed a decrease in K{sub trans} but with large uncertainty (111.6 ± 150.5) %. Conclusions: Parametric voxel-based analysis of 4D DCE CT data resulted in greater accuracy and reliability in measuring changes in perfusion CT-based kinetic metrics, which have the potential to be used as biomarkers in patients with metastatic brain cancer.« less

Screening based approach and dehydrogenation kinetics for MgH2: Guide to find suitable dopant using first-principles approach.

PubMed

Kumar, E Mathan; Rajkamal, A; Thapa, Ranjit

2017-11-14

First-principles based calculations are performed to investigate the dehydrogenation kinetics considering doping at various layers of MgH 2 (110) surface. Doping at first and second layer of MgH 2 (110) has a significant role in lowering the H 2 desorption (from surface) barrier energy, whereas the doping at third layer has no impact on the barrier energy. Molecular dynamics calculations are also performed to check the bonding strength, clusterization, and system stability. We study in details about the influence of doping on dehydrogenation, considering the screening factors such as formation enthalpy, bulk modulus, and gravimetric density. Screening based approach assist in finding Al and Sc as the best possible dopant in lowering of desorption temperature, while preserving similar gravimetric density and Bulk modulus as of pure MgH 2 system. The electron localization function plot and population analysis illustrate that the bond between Dopant-Hydrogen is mainly covalent, which weaken the Mg-Hydrogen bonds. Overall we observed that Al as dopant is suitable and surface doping can help in lowering the desorption temperature. So layer dependent doping studies can help to find the best possible reversible hydride based hydrogen storage materials.

Modeling Dynamic Contrast-Enhanced MRI Data with a Constrained Local AIF.

PubMed

Duan, Chong; Kallehauge, Jesper F; Pérez-Torres, Carlos J; Bretthorst, G Larry; Beeman, Scott C; Tanderup, Kari; Ackerman, Joseph J H; Garbow, Joel R

2018-02-01

This study aims to develop a constrained local arterial input function (cL-AIF) to improve quantitative analysis of dynamic contrast-enhanced (DCE)-magnetic resonance imaging (MRI) data by accounting for the contrast-agent bolus amplitude error in the voxel-specific AIF. Bayesian probability theory-based parameter estimation and model selection were used to compare tracer kinetic modeling employing either the measured remote-AIF (R-AIF, i.e., the traditional approach) or an inferred cL-AIF against both in silico DCE-MRI data and clinical, cervical cancer DCE-MRI data. When the data model included the cL-AIF, tracer kinetic parameters were correctly estimated from in silico data under contrast-to-noise conditions typical of clinical DCE-MRI experiments. Considering the clinical cervical cancer data, Bayesian model selection was performed for all tumor voxels of the 16 patients (35,602 voxels in total). Among those voxels, a tracer kinetic model that employed the voxel-specific cL-AIF was preferred (i.e., had a higher posterior probability) in 80 % of the voxels compared to the direct use of a single R-AIF. Maps of spatial variation in voxel-specific AIF bolus amplitude and arrival time for heterogeneous tissues, such as cervical cancer, are accessible with the cL-AIF approach. The cL-AIF method, which estimates unique local-AIF amplitude and arrival time for each voxel within the tissue of interest, provides better modeling of DCE-MRI data than the use of a single, measured R-AIF. The Bayesian-based data analysis described herein affords estimates of uncertainties for each model parameter, via posterior probability density functions, and voxel-wise comparison across methods/models, via model selection in data modeling.

Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB

NASA Astrophysics Data System (ADS)

Liu, Hao; Guo, Xiang; Han, Jingcheng; Luo, Ray; Chen, Hai-Feng

2018-06-01

Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved. In this study, molecular dynamics (MD) simulations were used to study the order-to-disorder transition kinetics of KID based on the good agreement with the experiment on its disordered-state properties. Specifically, we tested four force fields, ff99SBildn, ff99IDPs, ff14IDPSFF, and ff14IDPs in the simulations of KID and found that ff14IDPSFF can generate more diversified disordered conformers and also reproduce more accurate experimental secondary chemical shifts. Kinetics analysis of MD simulations demonstrates that the order-disorder transition of KID obeys the first-order kinetics, and the transition nucleus is I127/L128/L141. The possible transition pathways from the nucleus to the last folded residues were identified as I127-R125-L138-L141-S143-A145 and L128-R125-L138-L141-S143-A145 based on a residue-level dynamical network analysis. These computational studies not only provide testable prediction/hypothesis on the order-disorder transition of KID but also confirm that the ff14IDPSFF force field can be used to explore the correlation between the structure and function of IDPs.

Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay

PubMed Central

Prasanphanich, Adam F.; White, Douglas E.; Gran, Margaret A.

2016-01-01

The side population (SP) assay, a technique used in cancer and stem cell research, assesses the activity of ABC transporters on Hoechst staining in the presence and absence of transporter inhibition, identifying SP and non-SP cell (NSP) subpopulations by differential staining intensity. The interpretation of the assay is complicated because the transporter-mediated mechanisms fail to account for cell-to-cell variability within a population or adequately control the direct role of transporter activity on staining intensity. We hypothesized that differences in dye kinetics at the single-cell level, such as ABCG2 transporter-mediated efflux and DNA binding, are responsible for the differential cell staining that demarcates SP/NSP identity. We report changes in A549 phenotype during time in culture and with TGFβ treatment that correlate with SP size. Clonal expansion of individually sorted cells re-established both SP and NSPs, indicating that SP membership is dynamic. To assess the validity of a purely kinetics-based interpretation of SP/NSP identity, we developed a computational approach that simulated cell staining within a heterogeneous cell population; this exercise allowed for the direct inference of the role of transporter activity and inhibition on cell staining. Our simulated SP assay yielded appropriate SP responses for kinetic scenarios in which high transporter activity existed in a portion of the cells and little differential staining occurred in the majority of the population. With our approach for single-cell analysis, we observed SP and NSP cells at both ends of a transporter activity continuum, demonstrating that features of transporter activity as well as DNA content are determinants of SP/NSP identity. PMID:27851764