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.

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...

From thermometric to spectrophotometric kinetic-catalytic methods of analysis. A review.

PubMed

Cerdà, Víctor; González, Alba; Danchana, Kaewta

2017-05-15

Kinetic-catalytic analytical methods have proved to be very easy and highly sensitive strategies for chemical analysis, that rely on simple instrumentation [1,2]. Molecular absorption spectrophotometry is commonly used as the detection technique. However, other detection systems, like electrochemical or thermometric ones, offer some interesting possibilities since they are not affected by the color or turbidity of the samples. In this review some initial experience with thermometric kinetic-catalytic methods is described, up to our current experience exploiting spectrophotometric flow techniques to automate this kind of reactions, including the use of integrated chips. Procedures for determination of inorganic and organic species in organic and inorganic matrices are presented. Copyright © 2017 Elsevier B.V. All rights reserved.

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

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).

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.

Study of strength kinetics of sand concrete system of accelerated hardening

NASA Astrophysics Data System (ADS)

Sharanova, A. V.; Lenkova, D. A.; Panfilova, A. D.

2018-04-01

Methods of calorimetric analysis are used to study the dynamics of the hydration processes of concretes with different accelerator contents. The efficiency of the isothermal calorimetry method is shown for study of strength kinetics of concrete mixtures of accelerated hardening, promising for additive technologies in civil engineering.

Kinetics and mechanism of the oxidation process of two-component Fe-Al alloys

NASA Technical Reports Server (NTRS)

Przewlocka, H.; Siedlecka, J.

1982-01-01

The oxidation process of two-component Fe-Al alloys containing up to 7.2% Al and from 18 to 30% Al was studied. Kinetic measurements were conducted using the isothermal gravimetric method in the range of 1073-1223 K and 1073-1373 K for 50 hours. The methods used in studies of the mechanism of oxidation included: X-ray microanalysis, X-ray structural analysis, metallographic analysis and marker tests.

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…

"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.

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...

Critical Evaluation of Kinetic Method Measurements: Possible Origins of Nonlinear Effects

NASA Astrophysics Data System (ADS)

Bourgoin-Voillard, Sandrine; Afonso, Carlos; Lesage, Denis; Zins, Emilie-Laure; Tabet, Jean-Claude; Armentrout, P. B.

2013-03-01

The kinetic method is a widely used approach for the determination of thermochemical data such as proton affinities (PA) and gas-phase acidities ( ΔH° acid ). These data are easily obtained from decompositions of noncovalent heterodimers if care is taken in the choice of the method, references used, and experimental conditions. Previously, several papers have focused on theoretical considerations concerning the nature of the references. Few investigations have been devoted to conditions required to validate the quality of the experimental results. In the present work, we are interested in rationalizing the origin of nonlinear effects that can be obtained with the kinetic method. It is shown that such deviations result from intrinsic properties of the systems investigated but can also be enhanced by artifacts resulting from experimental issues. Overall, it is shown that orthogonal distance regression (ODR) analysis of kinetic method data provides the optimum way of acquiring accurate thermodynamic information.

An Automated Method of Scanning Probe Microscopy (SPM) Data Analysis and Reactive Site Tracking for Mineral-Water Interface Reactions Observed at the Nanometer Scale

NASA Astrophysics Data System (ADS)

Campbell, B. D.; Higgins, S. R.

2008-12-01

Developing a method for bridging the gap between macroscopic and microscopic measurements of reaction kinetics at the mineral-water interface has important implications in geological and chemical fields. Investigating these reactions on the nanometer scale with SPM is often limited by image analysis and data extraction due to the large quantity of data usually obtained in SPM experiments. Here we present a computer algorithm for automated analysis of mineral-water interface reactions. This algorithm automates the analysis of sequential SPM images by identifying the kinetically active surface sites (i.e., step edges), and by tracking the displacement of these sites from image to image. The step edge positions in each image are readily identified and tracked through time by a standard edge detection algorithm followed by statistical analysis on the Hough Transform of the edge-mapped image. By quantifying this displacement as a function of time, the rate of step edge displacement is determined. Furthermore, the total edge length, also determined from analysis of the Hough Transform, combined with the computed step speed, yields the surface area normalized rate of the reaction. The algorithm was applied to a study of the spiral growth of the calcite(104) surface from supersaturated solutions, yielding results almost 20 times faster than performing this analysis by hand, with results being statistically similar for both analysis methods. This advance in analysis of kinetic data from SPM images will facilitate the building of experimental databases on the microscopic kinetics of mineral-water interface reactions.

Extraction kinetic modelling of total polyphenols and total anthocyanins from saffron floral bio-residues: Comparison of extraction methods.

PubMed

Da Porto, Carla; Natolino, Andrea

2018-08-30

Analysis of the extraction kinetic modelling for natural compounds is essential for industrial application. The second order rate model was applied to estimate the extraction kinetics of conventional solid-liquid extraction (CSLE), ultrasound-assisted extraction (UAE) and microwave-assisted extraction (MAE) of total polyphenols (TPC) from saffron floral bio-residues at different solid-to-liquid ratios (R S/L )(1:10, 1:20, 1:30, 1:50 g ml -1 ), ethanol 59% as solvent and 66 °C temperature. The optimum solid-to-liquid ratios for TPC kinetics were 1:20 for CLSE, 1:30 for UAE and 1:50 for MAE. The kinetics of total anthocyanins (TA) and antioxidant activity (AA) were investigated for the optimum R S/L for each method. The results showed a good prediction of the model for extraction kinetics in all experiments (R 2  > 0.99; NRMS 0.65-3.35%). The kinetic parameters were calculated and discussed. UAE, compared with the other methods, had the greater efficiency for TPC, TA and AA. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pseudo-second order models for the adsorption of safranin onto activated carbon: comparison of linear and non-linear regression methods.

PubMed

Kumar, K Vasanth

2007-04-02

Kinetic experiments were carried out for the sorption of safranin onto activated carbon particles. The kinetic data were fitted to pseudo-second order model of Ho, Sobkowsk and Czerwinski, Blanchard et al. and Ritchie by linear and non-linear regression methods. Non-linear method was found to be a better way of obtaining the parameters involved in the second order rate kinetic expressions. Both linear and non-linear regression showed that the Sobkowsk and Czerwinski and Ritchie's pseudo-second order models were the same. Non-linear regression analysis showed that both Blanchard et al. and Ho have similar ideas on the pseudo-second order model but with different assumptions. The best fit of experimental data in Ho's pseudo-second order expression by linear and non-linear regression method showed that Ho pseudo-second order model was a better kinetic expression when compared to other pseudo-second order kinetic expressions.

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...

Adaptive Nodal Transport Methods for Reactor Transient Analysis

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

Thomas Downar; E. Lewis

2005-08-31

Develop methods for adaptively treating the angular, spatial, and time dependence of the neutron flux in reactor transient analysis. These methods were demonstrated in the DOE transport nodal code VARIANT and the US NRC spatial kinetics code, PARCS.

Linear stability analysis of detonations via numerical computation and dynamic mode decomposition

NASA Astrophysics Data System (ADS)

Kabanov, Dmitry I.; Kasimov, Aslan R.

2018-03-01

We introduce a new method to investigate linear stability of gaseous detonations that is based on an accurate shock-fitting numerical integration of the linearized reactive Euler equations with a subsequent analysis of the computed solution via the dynamic mode decomposition. The method is applied to the detonation models based on both the standard one-step Arrhenius kinetics and two-step exothermic-endothermic reaction kinetics. Stability spectra for all cases are computed and analyzed. The new approach is shown to be a viable alternative to the traditional normal-mode analysis used in detonation theory.

Microgravimetric Analysis Method for Activation-Energy Extraction from Trace-Amount Molecule Adsorption.

PubMed

Xu, Pengcheng; Yu, Haitao; Li, Xinxin

2016-05-03

Activation-energy (Ea) value for trace-amount adsorption of gas molecules on material is rapidly and inexpensively obtained, for the first time, from a microgravimetric analysis experiment. With the material loaded, a resonant microcantilever is used to record in real time the adsorption process at two temperatures. The kinetic parameter Ea is thereby extracted by solving the Arrhenius equation. As an example, two CO2 capture nanomaterials are examined by the Ea extracting method for evaluation/optimization and, thereby, demonstrating the applicability of the microgravimetric analysis method. The achievement helps to solve the absence in rapid quantitative characterization of sorption kinetics and opens a new route to investigate molecule adsorption processes and materials.

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.

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.

Pyrolytic Characteristics and Kinetics of Phragmites australis

PubMed Central

Zhao, Hui; Yan, Huaxiao; Zhang, Congwang; Liu, Xiaodong; Xue, Yanhui; Qiao, Yingyun; Tian, Yuanyu; Qin, Song

2011-01-01

The pyrolytic kinetics of Phragmites australis was investigated using thermogravimetric analysis (TGA) method with linear temperature programming process under an inert atmosphere. Kinetic expressions for the degradation rate in devolatilization and combustion steps have been obtained for P. australis with Dollimore method. The values of apparent activation energy, the most probable mechanism functions, and the corresponding preexponential factor were determined. The results show that the model agrees well with the experimental data and provide useful information for the design of pyrolytic processing system using P. australis as feedstock to produce biofuel. PMID:22007256

Redefining the utility of the three-isotope method

NASA Astrophysics Data System (ADS)

Cao, Xiaobin; Bao, Huiming

2017-09-01

The equilibrium isotope fractionation factor αeq is a fundamental parameter in the study of stable isotope effects. Experimentally, it has been difficult to establish that a system has attained equilibrium. The three-isotope method, using the initial trajectory of changing isotope ratios (e.g. 16O, 17O, and 18O) to deduce the final equilibrium point of isotope exchange, has long been hailed as the most rigorous experimental approach. However, over the years some researchers have cautioned on the limitations of this method, but the foundation of three-isotope method has not been properly examined and the method is still widely used in calibrating αeq for both traditional and increasingly non-traditional isotope systems today. Here, using water-water and dissolved CO2-water oxygen exchange as model systems, we conduct an isotopologues-specific kinetic analysis of the exchange processes and explore the underlying assumptions and validity of the three-isotope method. We demonstrate that without knowing the detailed exchange kinetics a priori the three-isotope method cannot lead to a reliable αeq. For a two-reservoir exchanging system, α determined by this method may be αeq, kinetic isotope effect, or apparent kinetic isotope effect, which can all bear different values. When multiple reservoirs exist during exchange, the evolving trajectory can be complex and hard to predict. Instead of being a tool for αeq determination, three-isotope method should be used as a tool for studying kinetic isotope effect, apparent kinetic isotope effect, and detailed exchange kinetics in diverse systems.

Dehydration of detomidine hydrochloride monohydrate.

PubMed

Veldre, K; Actiņš, A; Jaunbergs, J

2011-10-09

The thermodynamic stability of detomidine hydrochloride monohydrate has been evaluated on the basis of phase transition kinetics in solid state. A method free of empirical models was used for the treatment of kinetic data, and compared to several known solid state kinetic data processing methods. Phase transitions were monitored by powder X-ray diffraction (PXRD) and thermal analysis. Full PXRD profiles were used for determining the phase content instead of single reflex intensity measurements, in order to minimize the influence of particle texture. We compared the applicability of isothermal and nonisothermal methods to our investigation of detomidine hydrochlorine monohydrate dehydration. Copyright © 2011 Elsevier B.V. All rights reserved.

Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

PubMed Central

Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

2012-01-01

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

PubMed

Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

2012-07-03

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

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

Peptide kinetics from picoseconds to microseconds using boxed molecular dynamics: Power law rate coefficients in cyclisation reactions

NASA Astrophysics Data System (ADS)

Shalashilin, Dmitrii V.; Beddard, Godfrey S.; Paci, Emanuele; Glowacki, David R.

2012-10-01

Molecular dynamics (MD) methods are increasingly widespread, but simulation of rare events in complex molecular systems remains a challenge. We recently introduced the boxed molecular dynamics (BXD) method, which accelerates rare events, and simultaneously provides both kinetic and thermodynamic information. We illustrate how the BXD method may be used to obtain high-resolution kinetic data from explicit MD simulations, spanning picoseconds to microseconds. The method is applied to investigate the loop formation dynamics and kinetics of cyclisation for a range of polypeptides, and recovers a power law dependence of the instantaneous rate coefficient over six orders of magnitude in time, in good agreement with experimental observations. Analysis of our BXD results shows that this power law behaviour arises when there is a broad and nearly uniform spectrum of reaction rate coefficients. For the systems investigated in this work, where the free energy surfaces have relatively small barriers, the kinetics is very sensitive to the initial conditions: strongly non-equilibrium conditions give rise to power law kinetics, while equilibrium initial conditions result in a rate coefficient with only a weak dependence on time. These results suggest that BXD may offer us a powerful and general algorithm for describing kinetics and thermodynamics in chemical and biochemical systems.

Binding kinetics of five drugs to beta2-adrenoceptor using peak profiling method and nonlinear chromatography.

PubMed

Liang, Yuan; Wang, Jing; Fei, Fuhuan; Sun, Huanmei; Liu, Ting; Li, Qian; Zhao, Xinfeng; Zheng, Xiaohui

2018-02-23

Investigations of drug-protein interactions have advanced our knowledge of ways to design more rational drugs. In addition to extensive thermodynamic studies, ongoing works are needed to enhance the exploration of drug-protein binding kinetics. In this work, the beta2-adrenoceptor (β 2 -AR) was immobilized on N, N'-carbonyldiimidazole activated amino polystyrene microspheres to prepare an affinity column (4.6 mm × 5.0 cm, 8 μm). The β 2 -AR column was utilized to determine the binding kinetics of five drugs to the receptor. Introducing peak profiling method into this receptor chromatographic analysis, we determined the dissociation rate constants (k d ) of salbutamol, terbutaline, methoxyphenamine, isoprenaline hydrochloride and ephedrine hydrochloride to β 2 -AR to be 15 (±1), 22 (±1), 3.3 (±0.2), 2.3 (±0.2) and 2.1 (±0.1) s -1 , respectively. The employment of nonlinear chromatography (NLC) in this case exhibited the same rank order of k d values for the five drugs bound to β 2 -AR. We confirmed that both the peak profiling method and NLC were capable of routine measurement of receptor-drug binding kinetics. Compared with the peak profiling method, NLC was advantageous in the simultaneous assessment of the kinetic and apparent thermodynamic parameters. It will become a powerful method for high throughput drug-receptor interaction analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

ESR Analysis of Polymer Photo-Oxidation

NASA Technical Reports Server (NTRS)

Kim, Soon Sam; Liang, Ranty Hing; Tsay, Fun-Dow; Gupta, Amitave

1987-01-01

Electron-spin resonance identifies polymer-degradation reactions and their kinetics. New technique enables derivation of kinetic model of specific chemical reactions involved in degradation of particular polymer. Detailed information provided by new method enables prediction of aging characteristics long before manifestation of macroscopic mechanical properties.

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.

Sum over Histories Representation for Kinetic Sensitivity Analysis: How Chemical Pathways Change When Reaction Rate Coefficients Are Varied

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

Bai, Shirong; Davis, Michael J.; Skodje, Rex T.

2015-11-12

The sensitivity of kinetic observables is analyzed using a newly developed sum over histories representation of chemical kinetics. In the sum over histories representation, the concentrations of the chemical species are decomposed into the sum of probabilities for chemical pathways that follow molecules from reactants to products or intermediates. Unlike static flux methods for reaction path analysis, the sum over histories approach includes the explicit time dependence of the pathway probabilities. Using the sum over histories representation, the sensitivity of an observable with respect to a kinetic parameter such as a rate coefficient is then analyzed in terms of howmore » that parameter affects the chemical pathway probabilities. The method is illustrated for species concentration target functions in H-2 combustion where the rate coefficients are allowed to vary over their associated uncertainty ranges. It is found that large sensitivities are often associated with rate limiting steps along important chemical pathways or by reactions that control the branching of reactive flux« less

The art of maturity modeling. Part 2. Alternative models and sensitivity analysis

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

Waples, D.W.; Suizu, Masahiro; Kamata, Hiromi

1992-01-01

The sensitivity of exploration decisions to variations in several input parameters for maturity modeling was examined for the MITI Rumoi well, Hokkaido, Japan. Decisions were almost completely insensitive to uncertainties about formation age and erosional removal across some unconformities, but were more sensitive to changes in removal during unconformities which occurred near maximum paleotemperatures. Exploration decisions were not very sensitive to the choice of a particular kinetic model for hydrocarbon generation. Uncertainties in kerogen type and the kinetics of different kerogen types are more serious than differences among the various kinetic models. Results of modeling using the TTI method weremore » unsatisfactory. Thermal history and timing and amount of hydrocarbon generation estimated or calculated using the TTI method were greatly different from those obtained using a purely kinetic model. The authors strongly recommend use of the kinetic R{sub o} method instead of the TTI method. If they had lacked measured R{sub o} data, subsurface temperature data, or both, their confidence in the modeling results would have been sharply reduced. Conceptual models for predicting heat flow and thermal conductivity are simply too weak at present to allow one to carry out highly meaningful modeling unless the input is constrained by measured data. Maturity modeling therefore requires the use of more, not fewer, measured temperature and maturity data. The use of sensitivity analysis in maturity modeling is very important for understanding the geologic system, for knowing what level of confidence to place on the results, and for determining what new types of data would be most necessary to improve confidence. Sensitivity analysis can be carried out easily using a rapid, interactive maturity-modeling program.« less

Effect of pre-heating on the thermal decomposition kinetics of cotton

USDA-ARS?s Scientific Manuscript database

The effect of pre-heating at low temperatures (160-280°C) on the thermal decomposition kinetics of scoured cotton fabrics was investigated by thermogravimetric analysis under nonisothermal conditions. Isoconversional methods were used to calculate the activation energies for the pyrolysis after one-...

INFLUENCE OF PEAT ON FENTON OXIDATION

EPA Science Inventory

A diagnostic probe was used to estimate the activity of Fenton-derived hydroxyl radicals (@OH), reaction kinetics, and oxidation efficiency in batch suspensions comprised of silica sand, crushed goethite ("-FeOOH) ore, peat, and H2O2 (0.13 mM). A simple method of kinetic analysi...

Permeabilization Activated Reduction in Fluorescence (PARF): a novel method to measure kinetics of protein interactions with intracellular structures

PubMed Central

Singh, Pali P.; Hawthorne, Jenci L.; Davis, Christie A.; Quintero, Omar A.

2016-01-01

Understanding kinetic information is fundamental in understanding biological function. Advanced imaging technologies have fostered the development of kinetic analyses in cells. We have developed Permeabilization Activated Reduction in Fluorescence (PARF) analysis for determination of apparent t1/2 and immobile fraction, describing the dissociation of a protein of interest from intracellular structures. To create conditions where dissociation events are observable, cells expressing a fluorescently-tagged protein are permeabilized with digitonin, diluting the unbound protein into the extracellular media. As the media volume is much larger than the cytosolic volume, the concentration of the unbound pool decreases drastically, shifting the system out of equilibrium--favoring dissociation events. Loss of bound protein is observed as loss of fluorescence from intracellular structures and can be fit to an exponential decay. We compared PARF dissociation kinetics with previously published equilibrium kinetics as determined by FRAP. PARF dissociation rates agreed with the equilibrium-based FRAP analysis predictions of the magnitude of those rates. When used to investigate binding kinetics of a panel of cytoskeletal proteins, PARF analysis revealed that filament stabilization resulted in slower fluorescence loss. Additionally, commonly used “general” F-actin labels display differences in kinetic properties, suggesting that not all fluorescently-tagged actin labels interact with the actin network in the same way. We also observed differential dissociation kinetics for GFP-VASP depending on which cellular structure was being labeled. These results demonstrate that PARF analysis of non-equilibrium systems reveals kinetic information without the infrastructure investment required for other quantitative approaches such as FRAP, photoactivation, or in vitro reconstitution assays. PMID:27126922

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

Kinetic compensation effect in logistic distributed activation energy model for lignocellulosic biomass pyrolysis.

PubMed

Xu, Di; Chai, Meiyun; Dong, Zhujun; Rahman, Md Maksudur; Yu, Xi; Cai, Junmeng

2018-06-04

The kinetic compensation effect in the logistic distributed activation energy model (DAEM) for lignocellulosic biomass pyrolysis was investigated. The sum of square error (SSE) surface tool was used to analyze two theoretically simulated logistic DAEM processes for cellulose and xylan pyrolysis. The logistic DAEM coupled with the pattern search method for parameter estimation was used to analyze the experimental data of cellulose pyrolysis. The results showed that many parameter sets of the logistic DAEM could fit the data at different heating rates very well for both simulated and experimental processes, and a perfect linear relationship between the logarithm of the frequency factor and the mean value of the activation energy distribution was found. The parameters of the logistic DAEM can be estimated by coupling the optimization method and isoconversional kinetic methods. The results would be helpful for chemical kinetic analysis using DAEM. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Wheelchair pushrim kinetics measurement: A method to cancel inaccuracies due to pushrim weight and wheel camber.

PubMed

Chénier, Félix; Aissaoui, Rachid; Gauthier, Cindy; Gagnon, Dany H

2017-02-01

The commercially available SmartWheel TM is largely used in research and increasingly used in clinical practice to measure the forces and moments applied on the wheelchair pushrims by the user. However, in some situations (i.e. cambered wheels or increased pushrim weight), the recorded kinetics may include dynamic offsets that affect the accuracy of the measurements. In this work, an automatic method to identify and cancel these offsets is proposed and tested. First, the method was tested on an experimental bench with different cambers and pushrim weights. Then, the method was generalized to wheelchair propulsion. Nine experienced wheelchair users propelled their own wheelchairs instrumented with two SmartWheels with anti-slip pushrim covers. The dynamic offsets were correctly identified using the propulsion acquisition, without needing a separate baseline acquisition. A kinetic analysis was performed with and without dynamic offset cancellation using the proposed method. The most altered kinetic variables during propulsion were the vertical and total forces, with errors of up to 9N (p<0.001, large effect size of 5). This method is simple to implement, fully automatic and requires no further acquisitions. Therefore, we advise to use it systematically to enhance the accuracy of existing and future kinetic measurements. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

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.

Pseudo second order kinetics and pseudo isotherms for malachite green onto activated carbon: comparison of linear and non-linear regression methods.

PubMed

Kumar, K Vasanth; Sivanesan, S

2006-08-25

Pseudo second order kinetic expressions of Ho, Sobkowsk and Czerwinski, Blanachard et al. and Ritchie were fitted to the experimental kinetic data of malachite green onto activated carbon by non-linear and linear method. Non-linear method was found to be a better way of obtaining the parameters involved in the second order rate kinetic expressions. Both linear and non-linear regression showed that the Sobkowsk and Czerwinski and Ritchie's pseudo second order model were the same. Non-linear regression analysis showed that both Blanachard et al. and Ho have similar ideas on the pseudo second order model but with different assumptions. The best fit of experimental data in Ho's pseudo second order expression by linear and non-linear regression method showed that Ho pseudo second order model was a better kinetic expression when compared to other pseudo second order kinetic expressions. The amount of dye adsorbed at equilibrium, q(e), was predicted from Ho pseudo second order expression and were fitted to the Langmuir, Freundlich and Redlich Peterson expressions by both linear and non-linear method to obtain the pseudo isotherms. The best fitting pseudo isotherm was found to be the Langmuir and Redlich Peterson isotherm. Redlich Peterson is a special case of Langmuir when the constant g equals unity.

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.

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 among Reconstruction Algorithms for Quantitative Analysis of 11C-Acetate Cardiac PET Imaging.

PubMed

Shi, Ximin; Li, Nan; Ding, Haiyan; Dang, Yonghong; Hu, Guilan; Liu, Shuai; Cui, Jie; Zhang, Yue; Li, Fang; Zhang, Hui; Huo, Li

2018-01-01

Kinetic modeling of dynamic 11 C-acetate PET imaging provides quantitative information for myocardium assessment. The quality and quantitation of PET images are known to be dependent on PET reconstruction methods. This study aims to investigate the impacts of reconstruction algorithms on the quantitative analysis of dynamic 11 C-acetate cardiac PET imaging. Suspected alcoholic cardiomyopathy patients ( N = 24) underwent 11 C-acetate dynamic PET imaging after low dose CT scan. PET images were reconstructed using four algorithms: filtered backprojection (FBP), ordered subsets expectation maximization (OSEM), OSEM with time-of-flight (TOF), and OSEM with both time-of-flight and point-spread-function (TPSF). Standardized uptake values (SUVs) at different time points were compared among images reconstructed using the four algorithms. Time-activity curves (TACs) in myocardium and blood pools of ventricles were generated from the dynamic image series. Kinetic parameters K 1 and k 2 were derived using a 1-tissue-compartment model for kinetic modeling of cardiac flow from 11 C-acetate PET images. Significant image quality improvement was found in the images reconstructed using iterative OSEM-type algorithms (OSME, TOF, and TPSF) compared with FBP. However, no statistical differences in SUVs were observed among the four reconstruction methods at the selected time points. Kinetic parameters K 1 and k 2 also exhibited no statistical difference among the four reconstruction algorithms in terms of mean value and standard deviation. However, for the correlation analysis, OSEM reconstruction presented relatively higher residual in correlation with FBP reconstruction compared with TOF and TPSF reconstruction, and TOF and TPSF reconstruction were highly correlated with each other. All the tested reconstruction algorithms performed similarly for quantitative analysis of 11 C-acetate cardiac PET imaging. TOF and TPSF yielded highly consistent kinetic parameter results with superior image quality compared with FBP. OSEM was relatively less reliable. Both TOF and TPSF were recommended for cardiac 11 C-acetate kinetic analysis.

Enzymatic Spectrophotometric Reaction Rate Determination of Glucose in Fruit Drinks and Carbonated Beverages. An Analytical Chemistry Laboratory Experiment for Food Science-Oriented Students

NASA Astrophysics Data System (ADS)

Vasilarou, Argyro-Maria G.; Georgiou, Constantinos A.

2000-10-01

The glucose oxidase-horseradish peroxidase coupled reaction using phenol and 4-aminoantipyrine is used for the kinetic determination of glucose in drinks and beverages. This laboratory experiment demonstrates the implementation of reaction rate kinetic methods of analysis, the use of enzymes as selective analytical reagents for the determination of substrates, the kinetic masking of ascorbic acid interference, and the analysis of glucose in drinks and beverages. The method is optimized for student use in the temperature range of 18-28 °C and can be used in low-budget laboratories equipped with an inexpensive visible photometer. The mixed enzyme-chromogen solution that is used is stable for two months. Precision ranged from 5.1 to 12% RSD for analyses conducted during a period of two months by 48 students.

Evaluation of the Kinetic Property of Single-Molecule Junctions by Tunneling Current Measurements.

PubMed

Harashima, Takanori; Hasegawa, Yusuke; Kiguchi, Manabu; Nishino, Tomoaki

2018-01-01

We investigated the formation and breaking of single-molecule junctions of two kinds of dithiol molecules by time-resolved tunneling current measurements in a metal nanogap. The resulting current trajectory was statistically analyzed to determine the single-molecule conductance and, more importantly, to reveal the kinetic property of the single-molecular junction. These results suggested that combining a measurement of the single-molecule conductance and statistical analysis is a promising method to uncover the kinetic properties of the single-molecule junction.

Statistical inference in single molecule measurements of protein adsorption

NASA Astrophysics Data System (ADS)

Armstrong, Megan J.; Tsitkov, Stanislav; Hess, Henry

2018-02-01

Significant effort has been invested into understanding the dynamics of protein adsorption on surfaces, in particular to predict protein behavior at the specialized surfaces of biomedical technologies like hydrogels, nanoparticles, and biosensors. Recently, the application of fluorescent single molecule imaging to this field has permitted the tracking of individual proteins and their stochastic contribution to the aggregate dynamics of adsorption. However, the interpretation of these results is complicated by (1) the finite time available to observe effectively infinite adsorption timescales and (2) the contribution of photobleaching kinetics to adsorption kinetics. Here, we perform a protein adsorption simulation to introduce specific survival analysis methods that overcome the first complication. Additionally, we collect single molecule residence time data from the adsorption of fibrinogen to glass and use survival analysis to distinguish photobleaching kinetics from protein adsorption kinetics.

Analysis of senior high school student understanding on gas kinetic theory material

NASA Astrophysics Data System (ADS)

Anri, Y.; Maknun, J.; Chandra, D. T.

2018-05-01

The purpose of this research conducted to find out student understanding profile about gas kinetic theory. Particularly, on ideal gas law material, ideal gas equations and kinetic energy of ideal gas. This research was conducted on student of class XII in one of the schools in Bandung. This research is a descriptive research. The data of this research collected by using test instrument which was the essay that has been developed by the researcher based on Bloom’s Taxonomy revised. Based on the analysis result to student answer, this research discovered that whole student has low understanding in the material of gas kinetic theory. This low understanding caused of the misconception of the student, student attitude on physic subjects, and teacher teaching method who are less helpful in obtaining clear pictures in material being taught.

An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking

PubMed Central

Hoffman, Elizabeth A.; Zaidi, Hussain; Shetty, Savera J.; Bekiranov, Stefan; Auble, David T.

2018-01-01

Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that are typically made do not provide unambiguous information about the dynamic properties of these interactions. We have developed a method to estimate binding kinetic parameters from time-dependent formaldehyde crosslinking data, called crosslinking kinetics (CLK) analysis. Cultures of yeast cells are crosslinked with formaldehyde for various periods of time, yielding the relative ChIP signal at particular loci. We fit the data using the mass-action CLK model to extract kinetic parameters of the TF-chromatin interaction, including the on- and off-rates and crosslinking rate. From the on- and off-rate we obtain the occupancy and residence time. The following protocol is the second iteration of this method, CLKv2, updated with improved crosslinking and quenching conditions, more information about crosslinking rates, and systematic procedures for modeling the observed kinetic regimes. CLKv2 analysis has been applied to investigate the binding behavior of the TATA-binding protein (TBP), and a selected subset of other TFs. The protocol was developed using yeast cells, but may be applicable to cells from other organisms as well. PMID:29682595

Analyzing bean extracts using time-dependent SDS trapping to quantify the kinetic stability of phaseolin proteins.

PubMed

Thibeault, Jane; Church, Jennifer; Ortiz-Perez, Brian; Addo, Samuel; Hill, Shakeema; Khalil, Areeg; Young, Malaney; Xia, Ke; Colón, Wilfredo

2017-09-30

In common beans and lima bean, the storage protein phaseolin is difficult to degrade and SDS-resistant, a sign of kinetic stability. Kinetically stable proteins (KSPs) are characterized by having a high-energy barrier between the native and denatured states that results in very slow unfolding. Such proteins are resistant to proteolytic degradation and detergents, such as SDS. Here the method SDS-Trapping of Proteins (S-TraP) is applied directly on bean extracts to quantify the kinetic stability of phaseolin in lima bean and several common beans, including black bean, navy bean, and small red bean. The bean extracts were incubated in SDS at various temperatures (60-75 °C) for different time periods, followed by SDS-PAGE analysis at room temperature, and subsequent band quantification to determine the kinetics of phaseolin unfolding. Eyring plot analysis showed that the phaseolin from each bean has high kinetic stability, with an SDS-trapping (i.e. unfolding) half-life ranging from about 20-100 years at 24 °C and 2-7 years at 37 °C. The remarkably high kinetic stability of these phaseolin proteins is consistent with the low digestibility of common beans and lima bean, as well as their relatively high germination temperatures. From a practical perspective, this work exemplifies that S-TraP is a useful and cost-effective method for quantifying the kinetic stability of proteins in biological extracts or lysates. Depending on the protein to be studied and its abundance, S-TraP may be performed directly on the extract without need for protein purification. Copyright © 2017 Elsevier Inc. 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

Determination of Kinetic Parameters for the Thermal Decomposition of Parthenium hysterophorus

NASA Astrophysics Data System (ADS)

Dhaundiyal, Alok; Singh, Suraj B.; Hanon, Muammel M.; Rawat, Rekha

2018-02-01

A kinetic study of pyrolysis process of Parthenium hysterophorous is carried out by using thermogravimetric analysis (TGA) equipment. The present study investigates the thermal degradation and determination of the kinetic parameters such as activation E and the frequency factor A using model-free methods given by Flynn Wall and Ozawa (FWO), Kissinger-Akahira-Sonuse (KAS) and Kissinger, and model-fitting (Coats Redfern). The results derived from thermal decomposition process demarcate decomposition of Parthenium hysterophorous among the three main stages, such as dehydration, active and passive pyrolysis. It is shown through DTG thermograms that the increase in the heating rate caused temperature peaks at maximum weight loss rate to shift towards higher temperature regime. The results are compared with Coats Redfern (Integral method) and experimental results have shown that values of kinetic parameters obtained from model-free methods are in good agreement. Whereas the results obtained through Coats Redfern model at different heating rates are not promising, however, the diffusion models provided the good fitting with the experimental data.

The moisture outgassing kinetics of a silica reinforced polydimethylsiloxane

NASA Astrophysics Data System (ADS)

Sharma, H. N.; McLean, W.; Maxwell, R. S.; Dinh, L. N.

2016-09-01

A silica-filled polydimethylsiloxane (PDMS) composite M9787 was investigated for potential outgassing in a vacuum/dry environment with the temperature programmed desorption/reaction method. The outgassing kinetics of 463 K vacuum heat-treated samples, vacuum heat-treated samples which were subsequently re-exposed to moisture, and untreated samples were extracted using the isoconversional and constrained iterative regression methods in a complementary fashion. Density functional theory (DFT) calculations of water interactions with a silica surface were also performed to provide insight into the structural motifs leading to the obtained kinetic parameters. Kinetic analysis/model revealed that no outgassing occurs from the vacuum heat-treated samples in subsequent vacuum/dry environment applications at room temperature (˜300 K). The main effect of re-exposure of the vacuum heat-treated samples to a glove box condition (˜30 ppm by volume of H2O) for even a couple of days was the formation, on the silica surface fillers, of ˜60 ppm by weight of physisorbed and loosely bonded moisture, which subsequently outgasses at room temperature in a vacuum/dry environment in a time span of 10 yr. However, without any vacuum heat treatment and even after 1 h of vacuum pump down, about 300 ppm by weight of H2O would be released from the PDMS in the next few hours. Thereafter the outgassing rate slows down substantially. The presented methodology of using the isoconversional kinetic analysis results and some appropriate nature of the reaction as the constraints for more accurate iterative regression analysis/deconvolution of complex kinetic spectra, and of checking the so-obtained results with first principle calculations such as DFT can serve as a template for treating other complex physical/chemical processes as well.

The moisture outgassing kinetics of a silica reinforced polydimethylsiloxane

DOE PAGES

Sharma, H. N.; McLean, W.; Maxwell, R. S.; ...

2016-09-21

We investigated a silica-filled polydimethylsiloxane (PDMS) composite M9787 for potential outgassing in a vacuum/dry environment with the temperature programmed desorption/reaction method. The outgassing kinetics of 463 K vacuum heat-treated samples, vacuum heat-treated samples which were subsequently re-exposed to moisture, and untreated samples were extracted using the isoconversional and constrained iterative regression methods in a complementary fashion. Density functional theory (DFT) calculations of water interactions with a silica surface were also performed to provide insight into the structural motifs leading to the obtained kinetic parameters. Kinetic analysis/model revealed that no outgassing occurs from the vacuum heat-treated samples in subsequent vacuum/dry environmentmore » applications at room temperature (~300 K). Moreover, the main effect of re-exposure of the vacuum heat-treated samples to a glove box condition (~30 ppm by volume of H 2O) for even a couple of days was the formation, on the silica surface fillers, of ~60 ppm by weight of physisorbed and loosely bonded moisture, which subsequently outgasses at room temperature in a vacuum/dry environment in a time span of 10 yr. However, without any vacuum heat treatment and even after 1 h of vacuum pump down, about 300 ppm by weight of H 2O would be released from the PDMS in the next few hours. Thereafter the outgassing rate slows down substantially. Our presented methodology of using the isoconversional kinetic analysis results and some appropriate nature of the reaction as the constraints for more accurate iterative regression analysis/deconvolution of complex kinetic spectra, and of checking the so-obtained results with first principle calculations such as DFT can serve as a template for treating other complex physical/chemical processes as well.« less

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.

Investigating Uranium Concentrations in Groundwaters in the State of Idaho Using Kinetic Phosphorescence Analysis and Inductively Coupled Plasma Mass Spectrometry.

PubMed

Tkavadze, Levan; Dunker, Roy E; Brey, Richard R; Dudgeon, John

2016-11-01

The determination of uranium concentrations in natural water samples is of great interest due to the environmental consequences of this radionuclide. In this study, 380 groundwater samples from various locations within the state of Idaho were analyzed using two different techniques. The first method was Kinetic Phosphorescence Analysis (KPA), which gives the total uranium concentrations in water samples. The second analysis method was inductively coupled plasma mass spectrometry (ICP- MS). This method determines the total uranium concentration as well as the separate isotope concentrations of uranium. The U/U isotopic ratio was also measured for each sample to confirm that there was no depleted or enriched uranium present. The results were compared and mapped separately from each other. The study also found that in some areas of the state, natural uranium concentrations are relatively high.

Breakdown parameter for kinetic modeling of multiscale gas flows.

PubMed

Meng, Jianping; Dongari, Nishanth; Reese, Jason M; Zhang, Yonghao

2014-06-01

Multiscale methods built purely on the kinetic theory of gases provide information about the molecular velocity distribution function. It is therefore both important and feasible to establish new breakdown parameters for assessing the appropriateness of a fluid description at the continuum level by utilizing kinetic information rather than macroscopic flow quantities alone. We propose a new kinetic criterion to indirectly assess the errors introduced by a continuum-level description of the gas flow. The analysis, which includes numerical demonstrations, focuses on the validity of the Navier-Stokes-Fourier equations and corresponding kinetic models and reveals that the new criterion can consistently indicate the validity of continuum-level modeling in both low-speed and high-speed flows at different Knudsen numbers.

Automatic network coupling analysis for dynamical systems based on detailed kinetic models.

PubMed

Lebiedz, Dirk; Kammerer, Julia; Brandt-Pollmann, Ulrich

2005-10-01

We introduce a numerical complexity reduction method for the automatic identification and analysis of dynamic network decompositions in (bio)chemical kinetics based on error-controlled computation of a minimal model dimension represented by the number of (locally) active dynamical modes. Our algorithm exploits a generalized sensitivity analysis along state trajectories and subsequent singular value decomposition of sensitivity matrices for the identification of these dominant dynamical modes. It allows for a dynamic coupling analysis of (bio)chemical species in kinetic models that can be exploited for the piecewise computation of a minimal model on small time intervals and offers valuable functional insight into highly nonlinear reaction mechanisms and network dynamics. We present results for the identification of network decompositions in a simple oscillatory chemical reaction, time scale separation based model reduction in a Michaelis-Menten enzyme system and network decomposition of a detailed model for the oscillatory peroxidase-oxidase enzyme system.

Sensitivity analysis of a coupled hydrodynamic-vegetation model using the effectively subsampled quadratures method

USGS Publications Warehouse

Kalra, Tarandeep S.; Aretxabaleta, Alfredo; Seshadri, Pranay; Ganju, Neil K.; Beudin, Alexis

2017-01-01

Coastal hydrodynamics can be greatly affected by the presence of submerged aquatic vegetation. The effect of vegetation has been incorporated into the Coupled-Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Modeling System. The vegetation implementation includes the plant-induced three-dimensional drag, in-canopy wave-induced streaming, and the production of turbulent kinetic energy by the presence of vegetation. In this study, we evaluate the sensitivity of the flow and wave dynamics to vegetation parameters using Sobol' indices and a least squares polynomial approach referred to as Effective Quadratures method. This method reduces the number of simulations needed for evaluating Sobol' indices and provides a robust, practical, and efficient approach for the parameter sensitivity analysis. The evaluation of Sobol' indices shows that kinetic energy, turbulent kinetic energy, and water level changes are affected by plant density, height, and to a certain degree, diameter. Wave dissipation is mostly dependent on the variation in plant density. Performing sensitivity analyses for the vegetation module in COAWST provides guidance for future observational and modeling work to optimize efforts and reduce exploration of parameter space.

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.

Detection of kinetic change points in piece-wise linear single molecule motion

NASA Astrophysics Data System (ADS)

Hill, Flynn R.; van Oijen, Antoine M.; Duderstadt, Karl E.

2018-03-01

Single-molecule approaches present a powerful way to obtain detailed kinetic information at the molecular level. However, the identification of small rate changes is often hindered by the considerable noise present in such single-molecule kinetic data. We present a general method to detect such kinetic change points in trajectories of motion of processive single molecules having Gaussian noise, with a minimum number of parameters and without the need of an assumed kinetic model beyond piece-wise linearity of motion. Kinetic change points are detected using a likelihood ratio test in which the probability of no change is compared to the probability of a change occurring, given the experimental noise. A predetermined confidence interval minimizes the occurrence of false detections. Applying the method recursively to all sub-regions of a single molecule trajectory ensures that all kinetic change points are located. The algorithm presented allows rigorous and quantitative determination of kinetic change points in noisy single molecule observations without the need for filtering or binning, which reduce temporal resolution and obscure dynamics. The statistical framework for the approach and implementation details are discussed. The detection power of the algorithm is assessed using simulations with both single kinetic changes and multiple kinetic changes that typically arise in observations of single-molecule DNA-replication reactions. Implementations of the algorithm are provided in ImageJ plugin format written in Java and in the Julia language for numeric computing, with accompanying Jupyter Notebooks to allow reproduction of the analysis presented here.

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

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.

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

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.

Purification of SUMO conjugating enzymes and kinetic analysis of substrate conjugation

PubMed Central

Yunus, Ali A.; Lima, Christopher D.

2009-01-01

SUMO conjugation to protein substrates requires the concerted action of a dedicated E2 ubiquitin conjugation enzyme (Ubc9) and associated E3 ligases. Although Ubc9 can directly recognize and modify substrate lysine residues that occur within a consensus site for SUMO modification, E3 ligases can redirect specificity and enhance conjugation rates during SUMO conjugation in vitro and in vivo. In this chapter, we will describe methods utilized to purify SUMO conjugating enzymes and model substrates which can be used for analysis of SUMO conjugation in vitro. We will also describe methods to extract kinetic parameters during E3-dependent or E3-independent substrate conjugation. PMID:19107417

Advances in electron kinetics and theory of gas discharges

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

Kolobov, Vladimir I.; The University of Alabama in Huntsville, Huntsville, Alabama 35899

2013-10-15

“Electrons, like people, are fertile and infertile: high-energy electrons are fertile and able to reproduce.”—Lev TsendinModern physics of gas discharges increasingly uses physical kinetics for analysis of non-equilibrium plasmas. The description of underlying physics at the kinetic level appears to be important for plasma applications in modern technologies. In this paper, we attempt to grasp the legacy of Professor Lev Tsendin, who advocated the use of the kinetic approach for understanding fundamental problems of gas discharges. We outline the fundamentals of electron kinetics in low-temperature plasmas, describe elements of the modern kinetic theory of gas discharges, and show examples ofmore » the theoretical approach to gas discharge problems used by Lev Tsendin. Important connections between electron kinetics in gas discharges and semiconductors are also discussed. Using several examples, we illustrate how Tsendin's ideas and methods are currently being developed for the implementation of next generation computational tools for adaptive kinetic-fluid simulations of gas discharges used in modern technologies.« less

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

PubMed

Cotten, Cameron; Reed, Jennifer L

2013-01-30

Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

PubMed Central

2013-01-01

Background Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. Results In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. Conclusions This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets. PMID:23360254

Quantitation of TGF-beta1 mRNA in porcine mesangial cells by comparative kinetic RT/PCR: comparison with ribonuclease protection assay and in situ hybridization.

PubMed

Ceol, M; Forino, M; Gambaro, G; Sauer, U; Schleicher, E D; D'Angelo, A; Anglani, F

2001-01-01

Gene expression can be examined with different techniques including ribonuclease protection assay (RPA), in situ hybridisation (ISH), and quantitative reverse transcription-polymerase chain reaction (RT/PCR). These methods differ considerably in their sensitivity and precision in detecting and quantifying low abundance mRNA. Although there is evidence that RT/PCR can be performed in a quantitative manner, the quantitative capacity of this method is generally underestimated. To demonstrate that the comparative kinetic RT/PCR strategy-which uses a housekeeping gene as internal standard-is a quantitative method to detect significant differences in mRNA levels between different samples, the inhibitory effect of heparin on phorbol 12-myristate 13-acetate (PMA)-induced-TGF-beta1 mRNA expression was evaluated by RT/PCR and RPA, the standard method of mRNA quantification, and the results were compared. The reproducibility of RT/PCR amplification was calculated by comparing the quantity of G3PDH and TGF-beta1 PCR products, generated during the exponential phases, estimated from two different RT/PCR (G3PDH, r = 0.968, P = 0.0000; TGF-beta1, r = 0.966, P = 0.0000). The quantitative capacity of comparative kinetic RT/PCR was demonstrated by comparing the results obtained from RPA and RT/PCR using linear regression analysis. Starting from the same RNA extraction, but using only 1% of the RNA for the RT/PCR compared to RPA, significant correlation was observed (r = 0.984, P = 0.0004). Moreover the morphometric analysis of ISH signal was applied for the semi-quantitative evaluation of the expression and localisation of TGF-beta1 mRNA in the entire cell population. Our results demonstrate the close similarity of the RT/PCR and RPA methods in giving quantitative information on mRNA expression and indicate the possibility to adopt the comparative kinetic RT/PCR as reliable quantitative method of mRNA analysis. Copyright 2001 Wiley-Liss, Inc.

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.

General Methods for Analysis of Sequential “n-step” Kinetic Mechanisms: Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding

PubMed Central

Lucius, Aaron L.; Maluf, Nasib K.; Fischer, Christopher J.; Lohman, Timothy M.

2003-01-01

Helicase-catalyzed DNA unwinding is often studied using “all or none” assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using “n-step” sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the “kinetic step size”, m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using “n-step” sequential mechanisms has previously been limited by an inability to float the number of “unwinding steps”, n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, fss(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain fss(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation. PMID:14507688

General methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding.

PubMed

Lucius, Aaron L; Maluf, Nasib K; Fischer, Christopher J; Lohman, Timothy M

2003-10-01

Helicase-catalyzed DNA unwinding is often studied using "all or none" assays that detect only the final product of fully unwound DNA. Even using these assays, quantitative analysis of DNA unwinding time courses for DNA duplexes of different lengths, L, using "n-step" sequential mechanisms, can reveal information about the number of intermediates in the unwinding reaction and the "kinetic step size", m, defined as the average number of basepairs unwound between two successive rate limiting steps in the unwinding cycle. Simultaneous nonlinear least-squares analysis using "n-step" sequential mechanisms has previously been limited by an inability to float the number of "unwinding steps", n, and m, in the fitting algorithm. Here we discuss the behavior of single turnover DNA unwinding time courses and describe novel methods for nonlinear least-squares analysis that overcome these problems. Analytic expressions for the time courses, f(ss)(t), when obtainable, can be written using gamma and incomplete gamma functions. When analytic expressions are not obtainable, the numerical solution of the inverse Laplace transform can be used to obtain f(ss)(t). Both methods allow n and m to be continuous fitting parameters. These approaches are generally applicable to enzymes that translocate along a lattice or require repetition of a series of steps before product formation.

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.

Development of kinetic analysis technique for PACS management and a screening examination in dynamic radiography

NASA Astrophysics Data System (ADS)

Tsuchiya, Yuichiro; Kodera, Yoshie

2005-04-01

The purpose of this study was to develop of kinetic analysis method for PACS management and computer-aided diagnosis. We obtained dynamic chest radiographs (512x512, 8bit, 4fps, and 1344x1344, 12bit, 3fps) of five healthy volunteers during respiration using an I.I. system twice, and one healthy volunteer using dynamic FPD system. Optical flows of images were obtained using customized block matching technique, and were divided into a direction, and transformed into the RGB color. Density was determined by the sum pixel length of movement during respiration phase. The made new static image was defined as the "kinetic map". The evaluation of patient's collation was performed with a template matching to the three colors. The same person's each correlation value and similar-coefficient which is defined in this study were statistically significant high (P<0.01). We used the artificial neural network (ANN) for the judgment of the same person. Five volunteers were divided into two groups, three volunteers and two volunteers became a training signal and unknown signal. Correlation value and similar-coefficient was used for the input signal, and ANN was designed so that the same person's probability might be outputted. The average of the specificity of the unknown signal obtained 98.2%. The kinetic map including the imitation tumor was used for the simulation. The tumor was detected by temporal subtraction of kinetic map, and then the superior sensitivity was obtained. Our analysis method was useful in risk management and computer-aided diagnosis.

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

Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

PubMed

Markin, Craig J; Spyracopoulos, Leo

2012-12-01

NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements from NMR-monitored chemical shift titrations, for which the dependence of K ( D ) on the chemical shift difference (Δω) between free and bound states is extrapolated to Δω = 0. The demonstrated accuracy and precision for k ( off ) will be valuable for the interpretation of biological kinetics in weakly interacting protein-protein networks, where a small change in the magnitude of the underlying kinetics of a given pathway may lead to large changes in the associated downstream signaling cascade.

Differential RPA-1 and RAD-51 recruitment in vivo throughout the C. elegans germline, as revealed by laser microirradiation.

PubMed

Koury, Emily; Harrell, Kailey; Smolikove, Sarit

2018-01-25

Studies of the repair pathways associated with DNA double strand breaks (DSBs) are numerous, and provide evidence for cell-cycle specific regulation of homologous recombination (HR) by the regulation of its associated proteins. Laser microirradiation is a well-established method to examine in vitro kinetics of repair and allows for live-imaging of DSB repair from the moment of induction. Here we apply this method to whole, live organisms, introducing an effective system to analyze exogenous, microirradiation-induced breaks in the Caenorhabditis elegans germline. Through this method we observed the sequential kinetics of the recruitment of ssDNA binding proteins RPA-1 and RAD-51 in vivo. We analyze these kinetics throughout different regions of the germline, and thus throughout a range of developmental stages of mitotic and meiotic nuclei. Our analysis demonstrates a largely conserved timing of recruitment of ssDNA binding proteins to DSBs throughout the germline, with a delay of RAD-51 recruitment at mid-pachytene nuclei. Microirradiated nuclei are viable and undergo a slow kinetics of resolution. We observe RPA-1 and RAD-51 colocalization for hours post-microirradiation throughout the germline, suggesting that there are mixed RPA-1/RAD-51 filaments. Finally, through live imaging analysis we observed RAD-51 foci movement with low frequency of coalescence. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Differential RPA-1 and RAD-51 recruitment in vivo throughout the C. elegans germline, as revealed by laser microirradiation

PubMed Central

Koury, Emily; Harrell, Kailey

2018-01-01

Abstract Studies of the repair pathways associated with DNA double strand breaks (DSBs) are numerous, and provide evidence for cell-cycle specific regulation of homologous recombination (HR) by the regulation of its associated proteins. Laser microirradiation is a well-established method to examine in vitro kinetics of repair and allows for live-imaging of DSB repair from the moment of induction. Here we apply this method to whole, live organisms, introducing an effective system to analyze exogenous, microirradiation-induced breaks in the Caenorhabditis elegans germline. Through this method we observed the sequential kinetics of the recruitment of ssDNA binding proteins RPA-1 and RAD-51 in vivo. We analyze these kinetics throughout different regions of the germline, and thus throughout a range of developmental stages of mitotic and meiotic nuclei. Our analysis demonstrates a largely conserved timing of recruitment of ssDNA binding proteins to DSBs throughout the germline, with a delay of RAD-51 recruitment at mid-pachytene nuclei. Microirradiated nuclei are viable and undergo a slow kinetics of resolution. We observe RPA-1 and RAD-51 colocalization for hours post-microirradiation throughout the germline, suggesting that there are mixed RPA-1/RAD-51 filaments. Finally, through live imaging analysis we observed RAD-51 foci movement with low frequency of coalescence. PMID:29244155

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 teacher-developed inquiry model to teach the molecular basis of hyperbolic kinetics in biological membrane transport.

PubMed

Marcus, Leanne; Plumeri, Julia; Baker, Gary M; Miller, Jon S

2013-06-01

A previously published classroom teaching method for helping students visualize and understand Michaelis-Menten kinetics (19) was used as an anticipatory set with high school and middle school science teachers in an Illinois Math and Science Partnership Program. As part of the activity, the teachers were asked to collect data by replicating the method and to analyze and report the data. All concluded that the rate data they had collected were hyperbolic. As part of a guided inquiry plan, teachers were then prompted to reexamine the method and evaluate its efficacy as a teaching strategy for developing specific kinetic concepts. After further data collection and analysis, the teachers discovered that their data trends were not, in fact, hyperbolic, which led to several teacher-developed revisions aimed at obtaining a true hyperbolic outcome. This article outlines the inquiry process that led to these revisions and illustrates their alignment with several key concepts, such as rapid equilibrium kinetics. Instructional decisions were necessary at several key points, and these are discussed.

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.

Evaluation of agricultural residues pyrolysis under non-isothermal conditions: Thermal behaviors, kinetics, and thermodynamics.

PubMed

Chen, Jianbiao; Wang, Yanhong; Lang, Xuemei; Ren, Xiu'e; Fan, Shuanshi

2017-10-01

The thermal conversion characteristics, kinetics, and thermodynamics of agricultural residues, rape straw (RS) and wheat bran (WB), were investigated under non-isothermal conditions. TGA experiments showed that the pyrolysis characteristics of RS were quite different from those of WB. As reflected by the comprehensive devolatilization index, when the heating rate increased from 10 to 30Kmin -1 , the pyrolysis performance of RS and WB were improved 5.27 and 5.96 times, respectively. The kinetic triplets of the main pyrolysis process of agricultural residues were calculated by the Starink method and the integral master-plots method. Kinetic analysis results indicated that the most potential kinetic models for the pyrolysis of RS and WB were D 2 and F 2.7 , respectively. The thermodynamic parameters (ΔH, ΔG, and ΔS) were determined by the activated complex theory. The positive ΔH, positive ΔG, and negative ΔS at characteristic temperatures validated that the pyrolysis of agricultural residues was endothermic and non-spontaneous. Copyright © 2017 Elsevier Ltd. 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.

The kinetic energy spectrum of protons produced by the dissociative ionization of H2 by electron impact

NASA Technical Reports Server (NTRS)

Khakoo, M. A.; Srivastava, S. K.

1985-01-01

The kinetic energy spectra of protons resulting from the dissociative ionization of H2 by electron impact have been measured for electron impact energies from threshold (approximately 17 eV) to 160 eV at 90 deg and 30 deg detection angles, using a crossed-beam experimental arrangement. To check reliability, two separate proton energy analysis methods have been employed, i.e., a time-of-flight proton energy analysis and an electrostatic hemispherical energy analyzer. The present results are compared with previous measurements.

Kinetic and Mechanism Study of Vanadium Acid Leaching from Black Shale Using Microwave Heating Method

NASA Astrophysics Data System (ADS)

Wang, Jing-peng; Zhang, Yi-min; Huang, Jing; Liu, Tao

2018-04-01

The leaching kinetics of the vanadium leaching process were investigated by the comparison of microwave heating and conventional heating methods. Microwave heating with CaF2 had a synergistic effect and improved the vanadium leaching efficiency. In contrast to conventional heating leaching, microwave heating accelerated the vanadium leaching rate by approximately 1-3% and by approximately 15% when CaF2 was also used. The kinetics analysis showed that the calculated activation energy decreased in the microwave heating method in the presence and absence of CaF2. The control procedure of leaching also changed from a chemical reaction control step to a mixed chemical diffusion control step upon the addition of CaF2. Microwave heating was shown to be suitable for leaching systems with diffusion or mixed chemical diffusion control steps when the target mineral does not have a microwave absorbing ability.

Kinetic and Mechanism Study of Vanadium Acid Leaching from Black Shale Using Microwave Heating Method

NASA Astrophysics Data System (ADS)

Wang, Jing-peng; Zhang, Yi-min; Huang, Jing; Liu, Tao

2018-06-01

The leaching kinetics of the vanadium leaching process were investigated by the comparison of microwave heating and conventional heating methods. Microwave heating with CaF2 had a synergistic effect and improved the vanadium leaching efficiency. In contrast to conventional heating leaching, microwave heating accelerated the vanadium leaching rate by approximately 1-3% and by approximately 15% when CaF2 was also used. The kinetics analysis showed that the calculated activation energy decreased in the microwave heating method in the presence and absence of CaF2. The control procedure of leaching also changed from a chemical reaction control step to a mixed chemical diffusion control step upon the addition of CaF2. Microwave heating was shown to be suitable for leaching systems with diffusion or mixed chemical diffusion control steps when the target mineral does not have a microwave absorbing ability.

The study of zinc ions binding to casein.

PubMed

Pomastowski, P; Sprynskyy, M; Buszewski, B

2014-08-01

The presented research was focused on physicochemical study of casein properties and the kinetics of zinc ions binding to the protein. Moreover, a fast and simple method of casein extraction from cow's milk has been proposed. Casein isoforms, zeta potential (ζ) and particle size of the separated caseins were characterized with the use of capillary electrophoresis, zeta potential analysis and field flow fractionation (FFF) technique, respectively. The kinetics of the metal-binding process was investigated in batch adsorption experiments. Intraparticle diffusion model, first-order and zero-order kinetic models were applied to test the kinetic experimental data. Analysis of changes in infrared bands registered for casein before and after zinc binding was also performed. The obtained results showed that the kinetic process of zinc binding to casein is not homogeneous but is expressed with an initial rapid stage with about 70% of zinc ions immobilized by casein and with a much slower second step. Maximum amount of bound zinc in the experimental conditions was 30.04mgZn/g casein. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Kinetic Analysis of the Main Temperature Stage of Fast Pyrolysis

NASA Astrophysics Data System (ADS)

Yang, Xiaoxiao; Zhao, Yuying; Xu, Lanshu; Li, Rui

2017-10-01

Kinetics of the thermal decomposition of eucalyptus chips was evaluated using a high-rate thermogravimetric analyzer (BL-TGA) designed by our research group. The experiments were carried out under non-isothermal condition in order to determine the fast pyrolysis behavior of the main temperature stage (350-540ºC) at heating rates of 60, 120, 180, and 360ºC min-1. The Coats-Redfern integral method and four different reaction mechanism models were adopted to calculate the kinetic parameters including apparent activation energy and pre-exponential factor, and the Flynn-Wall-Ozawa method was employed to testify apparent activation energy. The results showed that estimation value was consistent with the values obtained by linear fitting equations, and the best-fit model for fast pyrolysis was found.

Sensitivity analysis of a coupled hydrodynamic-vegetation model using the effectively subsampled quadratures method (ESQM v5.2)

NASA Astrophysics Data System (ADS)

Kalra, Tarandeep S.; Aretxabaleta, Alfredo; Seshadri, Pranay; Ganju, Neil K.; Beudin, Alexis

2017-12-01

Coastal hydrodynamics can be greatly affected by the presence of submerged aquatic vegetation. The effect of vegetation has been incorporated into the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) modeling system. The vegetation implementation includes the plant-induced three-dimensional drag, in-canopy wave-induced streaming, and the production of turbulent kinetic energy by the presence of vegetation. In this study, we evaluate the sensitivity of the flow and wave dynamics to vegetation parameters using Sobol' indices and a least squares polynomial approach referred to as the Effective Quadratures method. This method reduces the number of simulations needed for evaluating Sobol' indices and provides a robust, practical, and efficient approach for the parameter sensitivity analysis. The evaluation of Sobol' indices shows that kinetic energy, turbulent kinetic energy, and water level changes are affected by plant stem density, height, and, to a lesser degree, diameter. Wave dissipation is mostly dependent on the variation in plant stem density. Performing sensitivity analyses for the vegetation module in COAWST provides guidance to optimize efforts and reduce exploration of parameter space for future observational and modeling work.

An investigation about the structures, thermodynamics and kinetics of the formic acid involved molecular clusters

NASA Astrophysics Data System (ADS)

Zhang, Rui; Jiang, Shuai; Liu, Yi-Rong; Wen, Hui; Feng, Ya-Juan; Huang, Teng; Huang, Wei

2018-05-01

Despite the very important role of atmospheric aerosol nucleation in climate change and air quality, the detailed aerosol nucleation mechanism is still unclear. Here we investigated the formic acid (FA) involved multicomponent nucleation molecular clusters including sulfuric acid (SA), dimethylamine (DMA) and water (W) through a quantum chemical method. The thermodynamics and kinetics analysis was based on the global minima given by Basin-Hopping (BH) algorithm coupled with Density Functional Theory (DFT) and subsequent benchmarked calculations. Then the interaction analysis based on ElectroStatic Potential (ESP), Topological and Atomic Charges analysis was made to characterize the binding features of the clusters. The results show that FA binds weakly with the other molecules in the cluster while W binds more weakly. Further kinetic analysis about the time evolution of the clusters show that even though the formic acid's weak interaction with other nucleation precursors, its effect on sulfuric acid dimer steady state concentration cannot be neglected due to its high concentration in the atmosphere.

Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

PubMed Central

2012-01-01

Background Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illuminated by an intense laser pulse, while images are taken with reduced laser power with a time lag between the bleaches. Despite its popularity, tools are lacking for quantitative analysis of FLIP experiments. Typically, the user defines regions of interest (ROIs) for further analysis which is subjective and does not allow for comparing different cells and experimental settings. Results We present two complementary methods to detect and quantify protein transport and aggregation in living cells from FLIP image series. In the first approach, a stretched exponential (StrExp) function is fitted to fluorescence loss (FL) inside and outside the bleached region. We show by reaction–diffusion simulations, that the StrExp function can describe both, binding/barrier–limited and diffusion-limited FL kinetics. By pixel-wise regression of that function to FL kinetics of enhanced green fluorescent protein (eGFP), we determined in a user-unbiased manner from which cellular regions eGFP can be replenished in the bleached area. Spatial variation in the parameters calculated from the StrExp function allow for detecting diffusion barriers for eGFP in the nucleus and cytoplasm of living cells. Polyglutamine (polyQ) disease proteins like mutant huntingtin (mtHtt) can form large aggregates called inclusion bodies (IB’s). The second method combines single particle tracking with multi-compartment modelling of FL kinetics in moving IB’s to determine exchange rates of eGFP-tagged mtHtt protein (eGFP-mtHtt) between aggregates and the cytoplasm. This method is self-calibrating since it relates the FL inside and outside the bleached regions. It makes it therefore possible to compare release kinetics of eGFP-mtHtt between different cells and experiments. Conclusions We present two complementary methods for quantitative analysis of FLIP experiments in living cells. They provide spatial maps of exchange dynamics and absolute binding parameters of fluorescent molecules to moving intracellular entities, respectively. Our methods should be of great value for quantitative studies of intracellular transport. PMID:23148417

Kinetic Modeling of PET Data Without Blood Sampling

NASA Astrophysics Data System (ADS)

Bentourkia, M.

2005-06-01

In positron emission tomography (PET) imaging, application of kinetic modeling always requires an input curve (IC) together with the PET data. The IC can be obtained by means of external blood sampling or, in the case of cardiac studies, by means of a region-of-interest (ROI) drawn on the blood pool. It is, however, very unsuitable to withdraw and to analyze blood samples, and in small animals, these operations become difficult, while ICs determined from ROIs are generally contaminated by emissions from neighboring sites, or they are underestimated because of partial volume effect. In this paper, we report a new method to extract kinetic parameters from dynamic PET studies without a priori knowledge of the IC. The method is applied in human brain data measured with fluorodeoxyglucose (FDG) human-brain and in cardiac-rat perfusion studies with /sup 13/N-ammonia and /sup 11/C-acetate. The tissue blood volume (TBV), usually fitted together with the rate constants, is extracted simultaneously with the tissue time activity curves for cardiac studies, while for brain gray matter, TBV is known to be about 4% to 7%. The shape of IC is obtained by means of factor analysis from an ROI drawn around a cardiac tissue or a brain artery. The results show a good correlation (p<0.05) between the cerebral metabolic rate of glucose, myocardial blood flow, and oxygen consumption obtained with the new method in comparison to the usual method. In conclusion, it is possible to apply kinetic modeling without any blood sampling, which significantly simplifies PET acquisition and data analysis.

Determination of urea kinetics by isotope dilution with [13C]urea and gas chromatography-isotope ratio mass spectrometry (GC-IRMS) analysis.

PubMed

Kloppenburg, W D; Wolthers, B G; Stellaard, F; Elzinga, H; Tepper, T; de Jong, P E; Huisman, R M

1997-07-01

1. Stable urea isotopes can be used to study urea kinetics in humans. The use of stable urea isotopes for studying urea kinetic parameters in humans on a large scale is hampered by the high costs of the labelled material. We devised a urea dilution for measurement of the distribution volume, production rate and clearance of urea in healthy subjects and renal failure patients using the inexpensive single labelled [13C]urea isotope with subsequent analysis by headspace chromatography-isotope ratio MS (GC-IRMS) of the [13C]urea enrichment. 2. The method involves measurement of the molar percentage excess of [13C]urea in plasma samples taken over a 4 h period after an intravenous bolus injection of [13C]urea. During the sample processing procedure, the plasma samples together with calibration samples containing a known molar percentage excess of [13C]urea are acidified with phosphoric acid to remove endogenous CO2, and are subsequently incubated with urease to convert the urea present in the plasma samples into CO2. The 13C enrichment of the generated CO2 is analysed by means of GC-IRMS. This method allows measurement of the molar percentage excess of [13C]urea to an accuracy of 0.02%. 3. Reproducibility studies showed that the sample processing procedure [within-run coefficient of variation (CV) < 2.8% and between-run CV < 8.8%] and the GC-IRMS analysis (within-day CV < 1.3% and between-day CV < 1.3%) could be repeated with good reproducibility. 4. In clinical urea kinetic studies in a healthy subject and in a renal failure patient without residual renal function, reproducible values of the distribution volume, production rate and clearance of urea were determined using minimal amounts of [13C]urea (25-50 mg). 5. Because only low [13C]urea enrichments are needed in this urea dilution method using GC-IRMS analysis, the costs of urea kinetic studies are reduced considerably, especially in patients with renal failure.

Chloroquine transport in Plasmodium falciparum. 1. Influx and efflux kinetics for live trophozoite parasites using a novel fluorescent chloroquine probe.

PubMed

Cabrera, Mynthia; Natarajan, Jayakumar; Paguio, Michelle F; Wolf, Christian; Urbach, Jeffrey S; Roepe, Paul D

2009-10-13

Several models for how amino acid substitutions in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) confer resistance to chloroquine (CQ) and other antimalarial drugs have been proposed. Distinguishing between these models requires detailed analysis of high-resolution CQ transport data that is unfortunately impossible to obtain with traditional radio-tracer methods. Thus, we have designed and synthesized fluorescent CQ analogues for drug transport studies. One probe places a NBD (6-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)hexanoic acid) group at the tertiary aliphatic N of CQ, via a flexible 6 C amide linker. This probe localizes to the malarial parasite digestive vacuole (DV) during initial perfusion under physiologic conditions and exhibits similar pharmacology relative to CQ, vs both CQ-sensitive (CQS) and CQ-resistant (CQR) parasites. Using live, synchronized intraerythrocytic parasites under continuous perfusion, we define NBD-CQ influx and efflux kinetics for CQS vs CQR parasites. Since this fluorescence approach provides data at much higher kinetic resolution relative to fast-filtration methods using (3)H-CQ, rate constants vs linear initial rates for CQ probe flux can be analyzed in detail. Importantly, we find that CQR parasites have a decreased rate constant for CQ influx into the DV and that this is due to mutation of PfCRT. Analysis of zero trans efflux for CQS and CQR parasites suggests that distinguishing between bound vs free pools of intra-DV drug probe is essential for proper kinetic analysis of efflux. The accompanying paper (DOI 10.1021/bi901035j ) further probes efflux kinetics for proteoliposomes containing purified, reconstituted PfCRT.

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

Sharma, H. N.; McLean, W.; Maxwell, R. S.

We investigated a silica-filled polydimethylsiloxane (PDMS) composite M9787 for potential outgassing in a vacuum/dry environment with the temperature programmed desorption/reaction method. The outgassing kinetics of 463 K vacuum heat-treated samples, vacuum heat-treated samples which were subsequently re-exposed to moisture, and untreated samples were extracted using the isoconversional and constrained iterative regression methods in a complementary fashion. Density functional theory (DFT) calculations of water interactions with a silica surface were also performed to provide insight into the structural motifs leading to the obtained kinetic parameters. Kinetic analysis/model revealed that no outgassing occurs from the vacuum heat-treated samples in subsequent vacuum/dry environmentmore » applications at room temperature (~300 K). Moreover, the main effect of re-exposure of the vacuum heat-treated samples to a glove box condition (~30 ppm by volume of H 2O) for even a couple of days was the formation, on the silica surface fillers, of ~60 ppm by weight of physisorbed and loosely bonded moisture, which subsequently outgasses at room temperature in a vacuum/dry environment in a time span of 10 yr. However, without any vacuum heat treatment and even after 1 h of vacuum pump down, about 300 ppm by weight of H 2O would be released from the PDMS in the next few hours. Thereafter the outgassing rate slows down substantially. Our presented methodology of using the isoconversional kinetic analysis results and some appropriate nature of the reaction as the constraints for more accurate iterative regression analysis/deconvolution of complex kinetic spectra, and of checking the so-obtained results with first principle calculations such as DFT can serve as a template for treating other complex physical/chemical processes as well.« 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.

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

Edgue, E.

The point kinetics approach is a classical useful method for a reactor transient analysis. It is helpful to known, however, when a more elaborate transient analysis, involving the space-dependence change of the flux through a given transient, should be considered. In this paper, the authors present a rather elegant and quick method to check the need for a space-dependent flux analysis through a control rod transient in a given nuclear reactor. The method is applied to a series of rod ejection experiments in the TRIGA MARK-II reactor of Istanbul Technical University (ITU).

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.

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.

A normalized plot as a novel and time-saving tool in complex enzyme kinetic analysis.

PubMed

Bravo, I G; Busto, F; De Arriaga, D; Ferrero, M A; Rodríguez-Aparicio, L B; Martínez-Blanco, H; Reglero, A

2001-09-15

A new data treatment is described for designing kinetic experiments and analysing kinetic results for multi-substrate enzymes. Normalized velocities are plotted against normalized substrate concentrations. Data are grouped into n + 1 families across the range of substrate or product tested, n being the number of substrates plus products assayed. It has the following advantages over traditional methods: (1) it reduces to less than a half the amount of data necessary for a proper description of the system; (2) it introduces a self-consistency checking parameter that ensures the 'scientific reliability' of the mathematical output; (3) it eliminates the need for a prior knowledge of Vmax; (4) the normalization of data allows the use of robust and fuzzy methods suitable for managing really 'noisy' data; (5) it is appropriate for analysing complex systems, as the complete general equation is used, and the actual influence of effectors can be typified; (6) it is amenable to being implemented as a software that incorporates testing and electing among rival kinetic models.

Kinetic study of the thermal decomposition of uranium metaphosphate, U(PO3)4, into uranium pyrophosphate, UP2O7

NASA Astrophysics Data System (ADS)

Yang, Hee-Chul; Kim, Hyung-Ju; Lee, Si-Young; Yang, In-Hwan; Chung, Dong-Yong

2017-06-01

The thermochemical properties of uranium compounds have attracted much interest in relation to thermochemical treatments and the safe disposal of radioactive waste bearing uranium compounds. The characteristics of the thermal decomposition of uranium metaphosphate, U(PO3)4, into uranium pyrophosphate, UP2O7, have been studied from the view point of reaction kinetics and acting mechanisms. A mixture of U(PO3)4 and UP2O7 was prepared from the pyrolysis residue of uranium-bearing spent TBP. A kinetic analysis of the reaction of U(PO3)4 into UP2O7 was conducted using an isoconversional method and a master plot method on the basis of data from a non-isothermal thermogravimetric analysis. The thermal decomposition of U(PO3)4 into UP2O7 followed a single-step reaction with an activation energy of 175.29 ± 1.58 kJ mol-1. The most probable kinetic model was determined as a type of nucleation and nuclei-growth models, the Avrami-Erofeev model (A3), which describes that there are certain restrictions on nuclei growth of UP2O7 during the solid-state decomposition of U(PO3)4.

Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection.

PubMed

Liu, Yang; Wilson, W David

2010-01-01

Surface plasmon resonance (SPR) technology with biosensor surfaces has become a widely-used tool for the study of nucleic acid interactions without any labeling requirements. The method provides simultaneous kinetic and equilibrium characterization of the interactions of biomolecules as well as small molecule-biopolymer binding. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetic methods for systems with strong binding coupled to small spectroscopic signals and/or reaction heats. A detailed and practical guide for nucleic acid interaction analysis using SPR-biosensor methods is presented. Details of the SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples, as well as extensive information on experimental design, quantitative and qualitative data analysis and presentation. A specific example of the interaction of a minor-groove-binding agent with DNA is evaluated by both kinetic and steady-state SPR methods to illustrate the technique. Since the molecules that bind cooperatively to specific DNA sequences are attractive for many applications, a cooperative small molecule-DNA interaction is also presented.

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.

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.

Chiral Analysis by Tandem Mass Spectrometry Using the Kinetic Method, by Polarimetry, and by [Superscript 1]H NMR Spectroscopy

ERIC Educational Resources Information Center

Fedick, Patrick W.; Bain, Ryan M.; Bain, Kinsey; Cooks, R. Graham

2017-01-01

The goal of this laboratory exercise was for students to understand the concept of chirality and how enantiomeric excess (ee) is experimentally determined using the analysis of ibuprofen as an example. Students determined the enantiomeric excess of the analyte by three different instrumental methods: mass spectrometry, nuclear magnetic resonance…

Incorporation of MRI-AIF Information For Improved Kinetic Modelling of Dynamic PET Data

NASA Astrophysics Data System (ADS)

Sari, Hasan; Erlandsson, Kjell; Thielemans, Kris; Atkinson, David; Ourselin, Sebastien; Arridge, Simon; Hutton, Brian F.

2015-06-01

In the analysis of dynamic PET data, compartmental kinetic analysis methods require an accurate knowledge of the arterial input function (AIF). Although arterial blood sampling is the gold standard of the methods used to measure the AIF, it is usually not preferred as it is an invasive method. An alternative method is the simultaneous estimation method (SIME), where physiological parameters and the AIF are estimated together, using information from different anatomical regions. Due to the large number of parameters to estimate in its optimisation, SIME is a computationally complex method and may sometimes fail to give accurate estimates. In this work, we try to improve SIME by utilising an input function derived from a simultaneously obtained DSC-MRI scan. With the assumption that the true value of one of the six parameter PET-AIF model can be derived from an MRI-AIF, the method is tested using simulated data. The results indicate that SIME can yield more robust results when the MRI information is included with a significant reduction in absolute bias of Ki estimates.

Mode Reduction and Upscaling of Reactive Transport Under Incomplete Mixing

NASA Astrophysics Data System (ADS)

Lester, D. R.; Bandopadhyay, A.; Dentz, M.; Le Borgne, T.

2016-12-01

Upscaling of chemical reactions in partially-mixed fluid environments is a challenging problem due to the detailed interactions between inherently nonlinear reaction kinetics and complex spatio-temporal concentration distributions under incomplete mixing. We address this challenge via the development of an order reduction method for the advection-diffusion-reaction equation (ADRE) via projection of the reaction kinetics onto a small number N of leading eigenmodes of the advection-diffusion operator (the so-called "strange eigenmodes" of the flow) as an N-by-N nonlinear system, whilst mixing dynamics only are projected onto the remaining modes. For simple kinetics and moderate Péclet and Damkhöler numbers, this approach yields analytic solutions for the concentration mean, evolving spatio-temporal distribution and PDF in terms of the well-mixed reaction kinetics and mixing dynamics. For more complex kinetics or large Péclet or Damkhöler numbers only a small number of modes are required to accurately quantify the mixing and reaction dynamics in terms of the concentration field and PDF, facilitating greatly simplified approximation and analysis of reactive transport. Approximate solutions of this low-order nonlinear system provide quantiative predictions of the evolving concentration PDF. We demonstrate application of this method to a simple random flow and various mass-action reaction kinetics.

Modeling and analysis of the effect of training on V O2 kinetics and anaerobic capacity.

PubMed

Stirling, J R; Zakynthinaki, M S; Billat, V

2008-07-01

In this paper, we present an application of a number of tools and concepts for modeling and analyzing raw, unaveraged, and unedited breath-by-breath oxygen uptake data. A method for calculating anaerobic capacity is used together with a model, in the form of a set of coupled nonlinear ordinary differential equations to make predictions of the VO(2) kinetics, the time to achieve a percentage of a certain constant oxygen demand, and the time limit to exhaustion at intensities other than those in which we have data. Speeded oxygen kinetics and increased time limit to exhaustion are also investigated using the eigenvalues of the fixed points of our model. We also use a way of analyzing the oxygen uptake kinetics using a plot of V O(2)(t) vs V O(2)(t) which allows one to observe both the fixed point solutions and also the presence of speeded oxygen kinetics following training. A method of plotting the eigenvalue versus oxygen demand is also used which allows one to observe where the maximum amplitude of the so-called slow component will be and also how training has changed the oxygen uptake kinetics by changing the strength of the attracting fixed point for a particular demand.

Preparation, non-isothermal decomposition kinetics, heat capacity and adiabatic time-to-explosion of NTOxDNAZ.

PubMed

Ma, Haixia; Yan, Biao; Li, Zhaona; Guan, Yulei; Song, Jirong; Xu, Kangzhen; Hu, Rongzu

2009-09-30

NTOxDNAZ was prepared by mixing 3,3-dinitroazetidine (DNAZ) and 3-nitro-1,2,4-triazol-5-one (NTO) in ethanol solution. The thermal behavior of the title compound was studied under a non-isothermal condition by DSC and TG/DTG methods. The kinetic parameters were obtained from analysis of the DSC and TG/DTG curves by Kissinger method, Ozawa method, the differential method and the integral method. The main exothermic decomposition reaction mechanism of NTOxDNAZ is classified as chemical reaction, and the kinetic parameters of the reaction are E(a)=149.68 kJ mol(-1) and A=10(15.81)s(-1). The specific heat capacity of the title compound was determined with continuous C(p) mode of microcalorimeter. The standard mole specific heat capacity of NTOxDNAZ was 352.56 J mol(-1)K(-1) in 298.15K. Using the relationship between C(p) and T and the thermal decomposition parameters, the time of the thermal decomposition from initialization to thermal explosion (adiabatic time-to-explosion) was obtained.

Phenytoin crystal growth rates in the presence of phosphate and chloride ions

NASA Astrophysics Data System (ADS)

Zipp, G. L.; Rodríguez-Hornedo, N.

1992-09-01

Phenytoin crystal growth kinetics have been measured as a function of supersaturation in pH 2.2 phosphoric acid and pH 2.2 hydrochloric acid solutions. Two different methods were used for the kinetic analysis. The first involved a zone-sensing device which provided an analysis of the distribution of crystals in a batch crystallizer. Crystal growth rates were calculated from the increase in the size of the distribution with time. In the second method, growth rates were evaluated from the change in size with time of individual crystals observed under an inverted microscope. The results from each method compare favorably. The use of both techniques provides an excellent opportunity to exploit the strengths of each: an average growth rate from a population of crystals from batch crystallization and insight into the effect of growth on the morphology of the crystals from the individual crystal measurements.

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.

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.

Molecular mechanisms of protein aggregation from global fitting of kinetic models.

PubMed

Meisl, Georg; Kirkegaard, Julius B; Arosio, Paolo; Michaels, Thomas C T; Vendruscolo, Michele; Dobson, Christopher M; Linse, Sara; Knowles, Tuomas P J

2016-02-01

The elucidation of the molecular mechanisms by which soluble proteins convert into their amyloid forms is a fundamental prerequisite for understanding and controlling disorders that are linked to protein aggregation, such as Alzheimer's and Parkinson's diseases. However, because of the complexity associated with aggregation reaction networks, the analysis of kinetic data of protein aggregation to obtain the underlying mechanisms represents a complex task. Here we describe a framework, using quantitative kinetic assays and global fitting, to determine and to verify a molecular mechanism for aggregation reactions that is compatible with experimental kinetic data. We implement this approach in a web-based software, AmyloFit. Our procedure starts from the results of kinetic experiments that measure the concentration of aggregate mass as a function of time. We illustrate the approach with results from the aggregation of the β-amyloid (Aβ) peptides measured using thioflavin T, but the method is suitable for data from any similar kinetic experiment measuring the accumulation of aggregate mass as a function of time; the input data are in the form of a tab-separated text file. We also outline general experimental strategies and practical considerations for obtaining kinetic data of sufficient quality to draw detailed mechanistic conclusions, and the procedure starts with instructions for extensive data quality control. For the core part of the analysis, we provide an online platform (http://www.amylofit.ch.cam.ac.uk) that enables robust global analysis of kinetic data without the need for extensive programming or detailed mathematical knowledge. The software automates repetitive tasks and guides users through the key steps of kinetic analysis: determination of constraints to be placed on the aggregation mechanism based on the concentration dependence of the aggregation reaction, choosing from several fundamental models describing assembly into linear aggregates and fitting the chosen models using an advanced minimization algorithm to yield the reaction orders and rate constants. Finally, we outline how to use this approach to investigate which targets potential inhibitors of amyloid formation bind to and where in the reaction mechanism they act. The protocol, from processing data to determining mechanisms, can be completed in <1 d.

Kinetics analysis and quantitative calculations for the successive radioactive decay process

NASA Astrophysics Data System (ADS)

Zhou, Zhiping; Yan, Deyue; Zhao, Yuliang; Chai, Zhifang

2015-01-01

The general radioactive decay kinetics equations with branching were developed and the analytical solutions were derived by Laplace transform method. The time dependence of all the nuclide concentrations can be easily obtained by applying the equations to any known radioactive decay series. Taking the example of thorium radioactive decay series, the concentration evolution over time of various nuclide members in the family has been given by the quantitative numerical calculations with a computer. The method can be applied to the quantitative prediction and analysis for the daughter nuclides in the successive decay with branching of the complicated radioactive processes, such as the natural radioactive decay series, nuclear reactor, nuclear waste disposal, nuclear spallation, synthesis and identification of superheavy nuclides, radioactive ion beam physics and chemistry, etc.

Kinetic analysis of non-isothermal solid-state reactions: multi-stage modeling without assumptions in the reaction mechanism.

PubMed

Pomerantsev, Alexey L; Kutsenova, Alla V; Rodionova, Oxana Ye

2017-02-01

A novel non-linear regression method for modeling non-isothermal thermogravimetric data is proposed. Experiments for several heating rates are analyzed simultaneously. The method is applicable to complex multi-stage processes when the number of stages is unknown. Prior knowledge of the type of kinetics is not required. The main idea is a consequent estimation of parameters when the overall model is successively changed from one level of modeling to another. At the first level, the Avrami-Erofeev functions are used. At the second level, the Sestak-Berggren functions are employed with the goal to broaden the overall model. The method is tested using both simulated and real-world data. A comparison of the proposed method with a recently published 'model-free' deconvolution method is presented.

Thermal decomposition and kinetics of coal and fermented cornstalk using thermogravimetric analysis.

PubMed

He, Yuyuan; Chang, Chun; Li, Pan; Han, Xiuli; Li, Hongliang; Fang, Shuqi; Chen, Junying; Ma, Xiaojian

2018-07-01

The thermal behavior and kinetics of Yiluo coal (YC) and the residues of fermented cornstalk (FC) were investigated in this study. The Kissinger-Akahira-Sunose (KAS) and Flynn-Wall-Ozawa (FWO) methods were used for the kinetic analysis of the pyrolysis process. The results showed that the activation energy (E α ) was increased with the increase of the thermal conversion rate (α), and the average values of E α of YC, FC and the blend (m YC /m FC  = 6/4) were 304.26, 224.94 and 233.46 kJ/mol, respectively. The order reaction model function for the blend was also developed by the master-plots method. By comparing the E a and the enthalpy, it was found that the blend was favored to format activated complex due to the lower potential energy barrier. Meanwhile, the average value of Gibbs free energy of the blend was 169.83 kJ/mol, and the changes of entropies indicated that the pyrolysis process was evolved from ordered-state to disordered-state. Copyright © 2018 Elsevier Ltd. All rights reserved.

In vitro dissolution kinetic study of theophylline from hydrophilic and hydrophobic matrices.

PubMed

Maswadeh, Hamzah M; Semreen, Mohammad H; Abdulhalim, Abdulatif A

2006-01-01

Oral dosage forms containing 300 mg theophylline in matrix type tablets, were prepared by direct compression method using two kinds of matrices, glycerylbehenate (hydrophobic), and (hydroxypropyl)methyl cellulose (hydrophilic). The in vitro release kinetics of these formulations were studied at pH 6.8 using the USP dissolution apparatus with the paddle assemble. The kinetics of the dissolution process were studied by analyzing the dissolution data using four kinetic equations, the zero-order equation, the first-order equation, the Higuchi square root equation and the Hixson-Crowell cube root law. The analysis of the dissolution kinetic data for the theophylline preparations in this study shows that it follows the first order kinetics and the release process involves erosion / diffusion and an alteration in the surface area and diameter of the matrix system, as well as in the diffusion path length from the matrix drug load during the dissolution process. This relation is best described by the use of both the first-order equation and the Hixson-Crowell cube root law.

A Lattice Kinetic Monte Carlo Solver for First-Principles Microkinetic Trend Studies

DOE PAGES

Hoffmann, Max J.; Bligaard, Thomas

2018-01-22

Here, mean-field microkinetic models in combination with Brønsted–Evans–Polanyi like scaling relations have proven highly successful in identifying catalyst materials with good or promising reactivity and selectivity. Analysis of the microkinetic model by means of lattice kinetic Monte Carlo promises a faithful description of a range of atomistic features involving short-range ordering of species in the vicinity of an active site. In this paper, we use the “fruit fly” example reaction of CO oxidation on fcc(111) transition and coinage metals to motivate and develop a lattice kinetic Monte Carlo solver suitable for the numerically challenging case of vastly disparate rate constants.more » As a result, we show that for the case of infinitely fast diffusion and absence of adsorbate-adsorbate interaction it is, in fact, possible to match the prediction of the mean-field-theory method and the lattice kinetic Monte Carlo method. As a corollary, we conclude that lattice kinetic Monte Carlo simulations of surface chemical reactions are most likely to provide additional insight over mean-field simulations if diffusion limitations or adsorbate–adsorbate interactions have a significant influence on the mixing of the adsorbates.« less

A Lattice Kinetic Monte Carlo Solver for First-Principles Microkinetic Trend Studies

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

Hoffmann, Max J.; Bligaard, Thomas

Here, mean-field microkinetic models in combination with Brønsted–Evans–Polanyi like scaling relations have proven highly successful in identifying catalyst materials with good or promising reactivity and selectivity. Analysis of the microkinetic model by means of lattice kinetic Monte Carlo promises a faithful description of a range of atomistic features involving short-range ordering of species in the vicinity of an active site. In this paper, we use the “fruit fly” example reaction of CO oxidation on fcc(111) transition and coinage metals to motivate and develop a lattice kinetic Monte Carlo solver suitable for the numerically challenging case of vastly disparate rate constants.more » As a result, we show that for the case of infinitely fast diffusion and absence of adsorbate-adsorbate interaction it is, in fact, possible to match the prediction of the mean-field-theory method and the lattice kinetic Monte Carlo method. As a corollary, we conclude that lattice kinetic Monte Carlo simulations of surface chemical reactions are most likely to provide additional insight over mean-field simulations if diffusion limitations or adsorbate–adsorbate interactions have a significant influence on the mixing of the adsorbates.« less

Steam Hydrocarbon Cracking and Reforming

ERIC Educational Resources Information Center

Golombok, Michael

2004-01-01

The interactive methods of steam hydrocarbon reforming and cracking of the oil and chemical industries are scrutinized, with special focus on their resemblance and variations. The two methods are illustrations of equilibrium-controlled and kinetically-controlled processes, the analysis of which involves theories, which overlap and balance each…

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

The correlation between proprioception and handwriting legibility in children

PubMed Central

Hong, So Young; Jung, Nam-Hae; Kim, Kyeong Mi

2016-01-01

[Purpose] This study investigated the association between proprioception, including joint position sense and kinetic sense, and handwriting legibility in healthy children. [Subjects and Methods] Assessment of joint position sense, kinetic sense, and handwriting legibility was conducted for 19 healthy children. Joint position sense was assessed by asking the children to flex their right elbow between 30° to 110° while blindfolded. The range of elbow movement was analyzed with Compact Measuring System 10 for 3D motion Analysis. Kinetic sense was assessed using the Sensory Integration and Praxis Test. The children were directed to write 30 words from the Korean alphabet, and the legibility of their handwriting was scored for form, alignment, space, size, and shape. To analyze the data, descriptive statistics and Spearman correlation analysis were conducted using IBM SPSS Statistics 20.0. [Results] There was significant negative correlation between handwriting legibility and Kinetic sense. A significant correlation between handwriting legibility and Joint position sense was not found. [Conclusion] This study showed that a higher Kinetic sense was associated with better legibility of handwriting. Further work is needed to determine the association of handwriting legibility and speed with Joint position sense of the elbow, wrist, and fingers. PMID:27821948

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

PubMed Central

Whitford, Paul C.; Blanchard, Scott C.; Cate, Jamie H. D.; Sanbonmatsu, Karissa Y.

2013-01-01

Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states. PMID:23555233

Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.

PubMed

Whitford, Paul C; Blanchard, Scott C; Cate, Jamie H D; Sanbonmatsu, Karissa Y

2013-01-01

Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds) to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.

Large-scale kinetic energy spectra from Eulerian analysis of EOLE wind data

NASA Technical Reports Server (NTRS)

Desbois, M.

1975-01-01

A data set of 56,000 winds determined from the horizontal displacements of EOLE balloons at the 200 mb level in the Southern Hemisphere during the period October 1971-February 1972 is utilized for the computation of planetary- and synoptic-scale kinetic energy space spectra. However, the random distribution of measurements in space and time presents some problems for the spectral analysis. Two different approaches are used, i.e., a harmonic analysis of daily wind values at equi-distant points obtained by space-time interpolation of the data, and a correlation method using the direct measurements. Both methods give similar results for small wavenumbers, but the second is more accurate for higher wavenumbers (k above or equal to 10). The spectra show a maximum at wavenumbers 5 and 6 due to baroclinic instability and then decrease for high wavenumbers up to wavenumber 35 (which is the limit of the analysis), according to the inverse power law k to the negative p, with p close to 3.

Kinetic analysis of hyperpolarized data with minimum a priori knowledge: Hybrid maximum entropy and nonlinear least squares method (MEM/NLS).

PubMed

Mariotti, Erika; Veronese, Mattia; Dunn, Joel T; Southworth, Richard; Eykyn, Thomas R

2015-06-01

To assess the feasibility of using a hybrid Maximum-Entropy/Nonlinear Least Squares (MEM/NLS) method for analyzing the kinetics of hyperpolarized dynamic data with minimum a priori knowledge. A continuous distribution of rates obtained through the Laplace inversion of the data is used as a constraint on the NLS fitting to derive a discrete spectrum of rates. Performance of the MEM/NLS algorithm was assessed through Monte Carlo simulations and validated by fitting the longitudinal relaxation time curves of hyperpolarized [1-(13) C] pyruvate acquired at 9.4 Tesla and at three different flip angles. The method was further used to assess the kinetics of hyperpolarized pyruvate-lactate exchange acquired in vitro in whole blood and to re-analyze the previously published in vitro reaction of hyperpolarized (15) N choline with choline kinase. The MEM/NLS method was found to be adequate for the kinetic characterization of hyperpolarized in vitro time-series. Additional insights were obtained from experimental data in blood as well as from previously published (15) N choline experimental data. The proposed method informs on the compartmental model that best approximate the biological system observed using hyperpolarized (13) C MR especially when the metabolic pathway assessed is complex or a new hyperpolarized probe is used. © 2014 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc.

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

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).

Second-order kinetic model for the sorption of cadmium onto tree fern: a comparison of linear and non-linear methods.

PubMed

Ho, Yuh-Shan

2006-01-01

A comparison was made of the linear least-squares method and a trial-and-error non-linear method of the widely used pseudo-second-order kinetic model for the sorption of cadmium onto ground-up tree fern. Four pseudo-second-order kinetic linear equations are discussed. Kinetic parameters obtained from the four kinetic linear equations using the linear method differed but they were the same when using the non-linear method. A type 1 pseudo-second-order linear kinetic model has the highest coefficient of determination. Results show that the non-linear method may be a better way to obtain the desired parameters.

Validation of Non-Invasive Tracer Kinetic Analysis of 18F-Florbetaben PET Using a Dual Time-Window Acquisition Protocol.

PubMed

Bullich, Santiago; Barthel, Henryk; Koglin, Norman; Becker, Georg A; De Santi, Susan; Jovalekic, Aleksandar; Stephens, Andrew W; Sabri, Osama

2017-11-24

Accurate amyloid PET quantification is necessary for monitoring amyloid-beta accumulation and response to therapy. Currently, most of the studies are analyzed using the static standardized uptake value ratio (SUVR) approach because of its simplicity. However, this approach may be influenced by changes in cerebral blood flow (CBF) or radiotracer clearance. Full tracer kinetic models require arterial blood sampling and dynamic image acquisition. The objectives of this work were: (1) to validate a non-invasive kinetic modeling approach for 18 F-florbetaben PET using an acquisition protocol with the best compromise between quantification accuracy and simplicity and (2) to assess the impact of CBF changes and radiotracer clearance on SUVRs and non-invasive kinetic modeling data in 18 F-florbetaben PET. Methods: Data from twenty subjects (10 patients with probable Alzheimer's dementia/ 10 healthy volunteers) were used to compare the binding potential (BP ND ) obtained from the full kinetic analysis to the SUVR and to non-invasive tracer kinetic methods (simplified reference tissue model (SRTM), and multilinear reference tissue model 2 (MRTM2)). Different approaches using shortened or interrupted acquisitions were compared to the results of the full acquisition (0-140 min). Simulations were carried out to assess the effect of CBF and radiotracer clearance changes on SUVRs and non-invasive kinetic modeling outputs. Results: A 0-30 and 120-140 min dual time-window acquisition protocol using appropriate interpolation of the missing time points provided the best compromise between patient comfort and quantification accuracy. Excellent agreement was found between BP ND obtained using full and dual time-window (2TW) acquisition protocols (BP ND,2TW =0.01+ 1.00 BP ND,FULL , R2=0.97 (MRTM2); BP ND,2TW = 0.05+ 0.92·BP ND,FULL , R2=0.93 (SRTM)). Simulations showed a limited impact of CBF and radiotracer clearance changes on MRTM parameters and SUVRs. Conclusion: This study demonstrates accurate non-invasive kinetic modeling of 18 F-florbetaben PET data using a dual time-window acquisition protocol, thus providing a good compromise between quantification accuracy, scan duration and patient burden. The influence of CBF and radiotracer clearance changes on amyloid-beta load estimates was small. For most clinical research applications, the SUVR approach is appropriate. However, for longitudinal studies in which a maximum quantification accuracy is desired, this non-invasive dual time-window acquisition protocol and kinetic analysis is recommended. Copyright © 2017 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data.

PubMed

Emami, Fereshteh; Maeder, Marcel; Abdollahi, Hamid

2015-05-07

Thermodynamic studies of equilibrium chemical reactions linked with kinetic procedures are mostly impossible by traditional approaches. In this work, the new concept of generalized kinetic study of thermodynamic parameters is introduced for dynamic data. The examples of equilibria intertwined with kinetic chemical mechanisms include molecular charge transfer complex formation reactions, pH-dependent degradation of chemical compounds and tautomerization kinetics in micellar solutions. Model-based global analysis with the possibility of calculating and embedding the equilibrium and kinetic parameters into the fitting algorithm has allowed the complete analysis of the complex reaction mechanisms. After the fitting process, the optimal equilibrium and kinetic parameters together with an estimate of their standard deviations have been obtained. This work opens up a promising new avenue for obtaining equilibrium constants through the kinetic data analysis for the kinetic reactions that involve equilibrium processes.

ASTM E 1559 method for measuring material outgassing/deposition kinetics has applications to aerospace, electronics, and semiconductor industries

NASA Technical Reports Server (NTRS)

Garrett, J. W.; Glassford, A. P. M.; Steakley, J. M.

1994-01-01

The American Society for Testing and Materials has published a new standard test method for characterizing time and temperature-dependence of material outgassing kinetics and the deposition kinetics of outgassed species on surfaces at various temperatures. This new ASTM standard, E 1559(1), uses the quartz crystal microbalance (QCM) collection measurement approach. The test method was originally developed under a program sponsored by the United States Air Force Materials Laboratory (AFML) to create a standard test method for obtaining outgassing and deposition kinetics data for spacecraft materials. Standardization by ASTM recognizes that the method has applications beyond aerospace. In particular, the method will provide data of use to the electronics, semiconductor, and high vacuum industries. In ASTM E 1559 the material sample is held in vacuum in a temperature-controlled effusion cell, while its outgassing flux impinges on several QCM's which view the orifice of the effusion cell. Sample isothermal total mass loss (TML) is measured as a function of time from the mass collected on one of the QCM's which is cooled by liquid nitrogen, and the view factor from this QCM to the cell. The amount of outgassed volatile condensable material (VCM) on surfaces at higher temperatures is measured as a function of time during the isothermal outgassing test by controlling the temperatures of the remaining QCM's to selected values. The VCM on surfaces at temperatures in between those of the collector QCM's is determined at the end of the isothermal test by heating the QCM's at a controlled rate and measuring the mass loss from the end of the QCM's as a function of time and temperature. This reevaporation of the deposit collected on the QCM's is referred to as QCM thermogravimetric analysis. Isothermal outgassing and deposition rates can be determined by differentiating the isothermal TML and VCM data, respectively, while the evaporation rates of the species can be obtained as a function of temperature by differentiating the QCM thermogravimetric analysis data.

Photocatalytic characteristic and photodegradation kinetics of toluene using N-doped TiO2 modified by radio frequency plasma.

PubMed

Shie, Je-Lueng; Lee, Chiu-Hsuan; Chiou, Chyow-San; Chen, Yi-Hung; Chang, Ching-Yuan

2014-01-01

This study investigates the feasibility of applications of the plasma surface modification of photocatalysts and the removal of toluene from indoor environments. N-doped TiO2 is prepared by precipitation methods and calcined using a muffle furnace (MF) and modified by radio frequency plasma (RF) at different temperatures with light sources from a visible light lamp (VLL), a white light-emitting diode (WLED) and an ultraviolet light-emitting diode (UVLED). The operation parameters and influential factors are addressed and prepared for characteristic analysis and photo-decomposition examination. Furthermore, related kinetic models are established and used to simulate the experimental data. The characteristic analysis results show that the RF plasma-calcination method enhanced the Brunauer Emmett Teller surface area of the modified photocatalysts effectively. For the elemental analysis, the mass percentages of N for the RF-modified photocatalyst are larger than those of MF by six times. The aerodynamic diameters of the RF-modifiedphotocatalyst are all smaller than those of MF. Photocatalytic decompositions of toluene are elucidated according to the Langmuir-Hinshelwood model. Decomposition efficiencies (eta) of toluene for RF-calcined methods are all higher than those of commercial TiO2 (P25). Reaction kinetics ofphoto-decomposition reactions using RF-calcined methods with WLED are proposed. A comparison of the simulation results with experimental data is also made and indicates good agreement. All the results provide useful information and design specifications. Thus, this study shows the feasibility and potential use of plasma modification via LED in photocatalysis.

Chapter 5: Modulation Excitation Spectroscopy with Phase-Sensitive Detection for Surface Analysis

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

Shulda, Sarah; Richards, Ryan M.

Advancements in in situ spectroscopic techniques have led to significant progress being made in elucidating heterogeneous reaction mechanisms. The potential of these progressive methods is often limited only by the complexity of the system and noise in the data. Short-lived intermediates can be challenging, if not impossible, to identify with conventional spectra analysis means. Often equally difficult is separating signals that arise from active and inactive species. Modulation excitation spectroscopy combined with phase-sensitive detection analysis is a powerful tool for removing noise from the data while simultaneously revealing the underlying kinetics of the reaction. A stimulus is applied at amore » constant frequency to the reaction system, for example, a reactant cycled with an inert phase. Through mathematical manipulation of the data, any signal contributing to the overall spectra but not oscillating with the same frequency as the stimulus will be dampened or removed. With phase-sensitive detection, signals oscillating with the stimulus frequency but with various lag times are amplified providing valuable kinetic information. In this chapter, some examples are provided from the literature that have successfully used modulation excitation spectroscopy with phase-sensitive detection to uncover previously unobserved reaction intermediates and kinetics. Examples from a broad range of spectroscopic methods are included to provide perspective to the reader.« 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.

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.

The mechanism of interactions between tea polyphenols and porcine pancreatic alpha‐amylase: Analysis by inhibition kinetics, fluorescence quenching, differential scanning calorimetry and isothermal titration calorimetry

PubMed Central

Sun, Lijun; Gidley, Michael J.

2017-01-01

Scope This study aims to use a combination of biochemical and biophysical methods to derive greater mechanistic understanding of the interactions between tea polyphenols and porcine pancreatic α‐amylase (PPA). Methods and results The interaction mechanism was studied through fluorescence quenching (FQ), differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC) and compared with inhibition kinetics. The results showed that a higher quenching effect of polyphenols corresponded to a stronger inhibitory activity against PPA. The red‐shift of maximum emission wavelength of PPA bound with some polyphenols indicated a potential structural unfolding of PPA. This was also suggested by the decreased thermostability of PPA with these polyphenols in DSC thermograms. Through thermodynamic binding analysis of ITC and inhibition kinetics, the equilibrium of competitive inhibition was shown to result from the binding of particularly galloylated polyphenols with specific sites on PPA. There were positive linear correlations between the reciprocal of competitive inhibition constant (1/K ic), quenching constant (K FQ) and binding constant (K itc). Conclusion The combination of inhibition kinetics, FQ, DSC and ITC can reasonably characterize the interactions between tea polyphenols and PPA. The galloyl moiety is an important group in catechins and theaflavins in terms of binding with and inhibiting the activity of PPA. PMID:28618113

Analysis of transformations of the ultrafast electron transfer photoreaction mechanism in liquid solutions by the rate distribution approach.

PubMed

Kuzmin, Michael G; Soboleva, Irina V

2014-05-01

Representation of the experimental reaction kinetics in the form of rate distribution is shown to be an effective method for the analysis of the mechanisms of these reactions and for comparisons of the kinetics with QC calculations, as well as with the experimental data on the medium mobility. The rate constant distribution function P(k) can be obtained directly from the experimental kinetics N(t) by an inverse Laplace transform. The application of this approach to kinetic data for several excited-state electron transfer reactions reveals the transformations of their rate control factors in the time domain of 1-1000 ps. In neat electron donating solvents two components are observed. The fastest component (k > 1 ps(-1)) was found to be controlled by the fluctuations of the overall electronic coupling matrix element, involving all the reactant molecules, located inside the interior of the solvent shell, rather than for specific pairs of reactant molecules. The slower component (1 > k > 0.1 ps(-1)) is controlled by the medium reorganization (longitudinal relaxation times, τL). A substantial contribution from the non-stationary diffusion controlled reaction is observed in diluted solutions ([Q] < 1 M). No contribution from the long-distance electron transfer (electron tunneling) proposed earlier for the excited-state electron transfer between perylene and tetracyanoethylene in acetonitrile is observed. The rate distribution approach provides a simple and efficient method for the quantitative analysis of the reaction mechanism and transformation of the rate control factors in the course of the reactions.

Immersed boundary method for Boltzmann model kinetic equations

NASA Astrophysics Data System (ADS)

Pekardan, Cem; Chigullapalli, Sruti; Sun, Lin; Alexeenko, Alina

2012-11-01

Three different immersed boundary method formulations are presented for Boltzmann model kinetic equations such as Bhatnagar-Gross-Krook (BGK) and Ellipsoidal statistical Bhatnagar-Gross-Krook (ESBGK) model equations. 1D unsteady IBM solution for a moving piston is compared with the DSMC results and 2D quasi-steady microscale gas damping solutions are verified by a conformal finite volume method solver. Transient analysis for a sinusoidally moving beam is also carried out for the different pressure conditions (1 atm, 0.1 atm and 0.01 atm) corresponding to Kn=0.05,0.5 and 5. Interrelaxation method (Method 2) is shown to provide a faster convergence as compared to the traditional interpolation scheme used in continuum IBM formulations. Unsteady damping in rarefied regime is characterized by a significant phase-lag which is not captured by quasi-steady approximations.

A simple and inexpensive image analysis technique to study the effect of disintegrants concentration and diluents type on disintegration.

PubMed

Berardi, Alberto; Bisharat, Lorina; Blaibleh, Anaheed; Pavoni, Lucia; Cespi, Marco

2018-06-20

Tablets disintegration is often the result of a size expansion of the tablets. In this study, we quantified the extent and direction of size expansion of tablets during disintegration, using readily available techniques, i.e. a digital camera and a public domain image analysis software. After validating the method, the influence of disintegrants concentration and diluents type on kinetics and mechanisms of disintegration were studied. Tablets containing diluent, disintegrant (sodium starch glycolate-SSG, crospovidone-PVPP or croscarmellose sodium-CCS) and lubricant were prepared by direct compression. Projected area and aspect ratio of the tablets were monitored using image analysis techniques. The developed method could describe the kinetics and mechanisms of disintegration qualitatively and quantitatively. SSG and PVPP acted purely by swelling and shape recovery mechanisms. Instead, CCS worked by a combination of both mechanisms, the extent of which changed depending on its concentration and the diluent type. We anticipate that the method described here could provide a framework for the routine screening of tablets disintegration using readily available equipment. Copyright © 2018. Published by Elsevier Inc.

Proceedings of the 6. international conference on stability and handling of liquid fuels. Volume 2

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

Giles, H.N.

Volume 2 of these proceedings contain 42 papers arranged under the following topical sections: Fuel blending and compatibility; Middle distillates; Microbiology; Alternative fuels; General topics (analytical methods, tank remediation, fuel additives, storage stability); and Poster presentations (analysis methods, oxidation kinetics, health problems).

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.

Fluxgate magnetorelaxometry for characterization of hydrogel polymerization kinetics and physical entrapment capacity.

PubMed

Heim, E; Harling, S; Ludwig, F; Menzel, H; Schilling, M

2008-05-21

Hydrogels have the potential for providing drug delivery systems with long release rates. The polymerization kinetics and the physical entrapment capacity of photo-cross-linked hydroxyethyl methacrylate hydroxyethylstarch hydrogels are investigated with a non-destructive method. For this purpose, superparamagnetic nanoparticles as replacements for biomolecules are used as probes. By analyzing their magnetic relaxation behavior, the amounts of physically entrapped and mobile nanoparticles can be determined. The hydrogels were loaded with five different concentrations of nanoparticles. Different methods of analysis of the relaxation curves and the influence of the microviscosity are discussed. This investigation allows one to optimize the UV light irradiation time and to determine the amount of physically entrapped nanoparticles in the hydrogel network. It was found that the polymerization kinetics is faster for decreasing nanoparticle concentration but not all nanoparticles can be physically entrapped in the network.

The Harrison Diffusion Kinetics Regimes in Solute Grain Boundary Diffusion

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

Belova, Irina; Fiedler, T; Kulkarni, Nagraj S

2012-01-01

Knowledge of the limits of the principal Harrison kinetics regimes (Type-A, B and C) for grain boundary diffusion is very important for the correct analysis of the depth profiles in a tracer diffusion experiment. These regimes for self-diffusion have been extensively studied in the past by making use of the phenomenological Lattice Monte Carlo (LMC) method with the result that the limits are now well established. The relationship of those self-diffusion limits to the corresponding ones for solute diffusion in the presence of solute segregation to the grain boundaries remains unclear. In the present study, the influence of solute segregationmore » on the limits is investigated with the LMC method for the well-known parallel grain boundary slab model by showing the equivalence of two diffusion models. It is shown which diffusion parameters are useful for identifying the limits of the Harrison kinetics regimes for solute grain boundary diffusion. It is also shown how the measured segregation factor from the diffusion experiment in the Harrison Type-B kinetics regime may differ from the global segregation factor.« less

A kinetic study of struvite precipitation recycling technology with NaOH/Mg(OH)2 addition.

PubMed

Yu, Rongtai; Ren, Hongqiang; Wang, Yanru; Ding, Lili; Geng, Jingji; Xu, Ke; Zhang, Yan

2013-09-01

Struvite precipitation recycling technology is received wide attention in removal ammonium and phosphate out of wastewater. While past study focused on process efficiency, and less on kinetics. The kinetic study is essential for the design and optimization in the application of struvite precipitation recycling technology. The kinetics of struvite with NaOH/Mg(OH)2 addition were studied by thermogravimetry analysis with three rates (5, 10, 20 °C/min), using Friedman method and Ozawa-Flynn-Wall method, respectively. Degradation process of struvite with NaOH/Mg(OH)2 addition was three steps. The stripping of ammonia from struvite was mainly occurred at the first step. In the first step, the activation energy was about 70 kJ/mol, which has gradually declined as the reaction progress. By model fitting studies, the proper mechanism function for struvite decomposition process with NaOH/Mg(OH)2 addition was revealed. The mechanism function was f(α)=α(α)-(1-α)(n), a Prout-Tompkins nth order (Bna) model. Copyright © 2013 Elsevier Ltd. All rights reserved.

An analysis of artificial viscosity effects on reacting flows using a spectral multi-domain technique

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.; Streett, C. L.; Hussaini, M. Y.

1987-01-01

Standard techniques used to model chemically-reacting flows require an artificial viscosity for stability in the presence of strong shocks. The resulting shock is smeared over at least three computational cells, so that the thickness of the shock is dictated by the structure of the overall mesh and not the shock physics. A gas passing through a strong shock is thrown into a nonequilibrium state and subsequently relaxes down over some finite distance to an equilibrium end state. The artificial smearing of the shock envelops this relaxation zone which causes the chemical kinetics of the flow to be altered. A method is presented which can investigate these issues by following the chemical kinetics and flow kinetics of a gas passing through a fully resolved shock wave at hypersonic Mach numbers. A nonequilibrium chemistry model for air is incorporated into a spectral multidomain Navier-Stokes solution method. Since no artificial viscosity is needed for stability of the multidomain technique, the precise effect of this artifice on the chemical kinetics and relevant flow features can be determined.

LSENS, a general chemical kinetics and sensitivity analysis code for gas-phase reactions: User's guide

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; Bittker, David A.

1993-01-01

A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS, are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include static system, steady, one-dimensional, inviscid flow, shock initiated reaction, and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method, which works efficiently for the extremes of very fast and very slow reaction, is used for solving the 'stiff' differential equation systems that arise in chemical kinetics. For static reactions, sensitivity coefficients of all dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters can be computed. This paper presents descriptions of the code and its usage, and includes several illustrative example problems.

Study on reaction mechanism by analysis of kinetic energy spectra of light particles and formation of final products

NASA Astrophysics Data System (ADS)

Giardina, G.; Mandaglio, G.; Nasirov, A. K.; Anastasi, A.; Curciarello, F.; Fazio, G.

2018-05-01

The sensitivity of reaction mechanism in the formation of compound nucleus (CN) by the analysis of kinetic energy spectra of light particles and of reaction products are shown. The dependence of the P CN fusion probability of reactants and W sur survival probability of CN against fission at its deexcitation on the mass and charge symmetries in the entrance channel of heavy-ion collisions, as well as on the neutron numbers is discussed. The possibility of conducting a complex program of investigations of the complete fusion by reliable ways depends on the detailed and refined methods of experimental and theoretical analyses.

Potential and kinetic energetic analysis of phonon modes in varied molecular solids

NASA Astrophysics Data System (ADS)

Kraczek, Brent

2015-03-01

We calculate partitioned kinetic and potential energies of the phonon modes in molecular solids to illuminate the dynamical behavior of the constituent molecules. This enables analysis of the relationship between the characteristics of sets of phonon modes, molecular structure and chemical reactivity by partitioning the kinetic energy into the translational, rotational and vibrational motions of groups of atoms (including molecules), and the potential energy into the energy contained within interatomic interactions. We consider three solids of differing size and rigidity: naphthalene (C1 0 H6), nitromethane (CH3NO2)andα-HMX(C4H8N8O8). Naphthalene and nitromethane mostly act in the semi-rigid manner often expected in molecular solids. HMX exhibits behavior that is significantly less-rigid. While there are definite correlations between the kinetic and potential energetic analyses, there are also differences, particularly in the excitation of chemical bonds by low-frequency lattice modes. This suggests that in many cases computational and experimental methods dependent on atomic displacements may not identify phonon modes active in chemical reactivity.

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.

Measuring kinetics of complex single ion channel data using mean-variance histograms.

PubMed

Patlak, J B

1993-07-01

The measurement of single ion channel kinetics is difficult when those channels exhibit subconductance events. When the kinetics are fast, and when the current magnitudes are small, as is the case for Na+, Ca2+, and some K+ channels, these difficulties can lead to serious errors in the estimation of channel kinetics. I present here a method, based on the construction and analysis of mean-variance histograms, that can overcome these problems. A mean-variance histogram is constructed by calculating the mean current and the current variance within a brief "window" (a set of N consecutive data samples) superimposed on the digitized raw channel data. Systematic movement of this window over the data produces large numbers of mean-variance pairs which can be assembled into a two-dimensional histogram. Defined current levels (open, closed, or sublevel) appear in such plots as low variance regions. The total number of events in such low variance regions is estimated by curve fitting and plotted as a function of window width. This function decreases with the same time constants as the original dwell time probability distribution for each of the regions. The method can therefore be used: 1) to present a qualitative summary of the single channel data from which the signal-to-noise ratio, open channel noise, steadiness of the baseline, and number of conductance levels can be quickly determined; 2) to quantify the dwell time distribution in each of the levels exhibited. In this paper I present the analysis of a Na+ channel recording that had a number of complexities. The signal-to-noise ratio was only about 8 for the main open state, open channel noise, and fast flickers to other states were present, as were a substantial number of subconductance states. "Standard" half-amplitude threshold analysis of these data produce open and closed time histograms that were well fitted by the sum of two exponentials, but with apparently erroneous time constants, whereas the mean-variance histogram technique provided a more credible analysis of the open, closed, and subconductance times for the patch. I also show that the method produces accurate results on simulated data in a wide variety of conditions, whereas the half-amplitude method, when applied to complex simulated data shows the same errors as were apparent in the real data. The utility and the limitations of this new method are discussed.

Reticulation of Aqueous Polyurethane Systems Controlled by DSC Method

PubMed Central

Cakic, Suzana; Lacnjevac, Caslav; Rajkovic, Milos B.; Raskovic, Ljiljana; Stamenkovic, Jakov

2006-01-01

The DSC method has been employed to monitor the kinetics of reticulation of aqueous polyurethane systems without catalysts, and with the commercial catalyst of zirconium (CAT®XC-6212) and the highly selective manganese catalyst, the complex Mn(III)-diacetylacetonemaleinate (MAM). Among the polyol components, the acrylic emulsions were used for reticulation in this research, and as suitable reticulation agents the water emulsible aliphatic polyisocyanates based on hexamethylendoisocyanate with the different contents of NCO-groups were employed. On the basis of DSC analysis, applying the methods of Kissinger, Freeman-Carroll and Crane-Ellerstein the pseudo kinetic parameters of the reticulation reaction of aqueous systems were determined. The temperature of the examination ranged from 50°C to 450°C with the heat rate of 0.5°C/min. The reduction of the activation energy and the increase of the standard deviation indicate the catalytic action of the selective catalysts of zirconium and manganese. The impact of the catalysts on the reduction of the activation energy is the strongest when using the catalysts of manganese and applying all the three afore-said methods. The least aberrations among the stated methods in defining the kinetic parameters were obtained by using the manganese catalyst.

Microwave-assisted synthesis of carbon supported metal/metal oxide nanocomposites and their application in water purification

NASA Astrophysics Data System (ADS)

Gunawan, Gunawan

A novel, easy, and cost effective method for synthesizing carbon supported metal/metal oxide nanocomposites has been studied. Carbon supported metal/metal oxide nanocomposites have niche applications in the area of catalysis, fuel cells, electrodes, and more. The method utilizes a commercial microwave and features the addition of a developed graphite-jacket technique with renewable carbon resources, tannin and lignin. The method has been successfully used to synthesize carbon/nickel, carbon/iron oxide, and carbon/nickel phosphide nanocomposites. The method has shown its versatility in the synthesis of carbon nanocomposites. The process is much simpler when compared with the available methods for synthesizing carbon nanocomposites. The synthesized nanocomposites were classified using several characterization techniques, such as electron microscopy, X-ray powder diffraction, surface area analysis, thermogravimetric analysis, and spectrophotometric studies. One application of the carbon nanocomposite is in wastewater remediation. The synthesized carbon/iron oxide nanocomposite was noted as being useful for removing arsenic (As) and phosphorus (P) from contaminated water. The adsorption process of the nanocomposite was critically studied in order to understand the process of removing pollutants from contaminated water. The study shows that the nanocomposites are capable of removing As and P from contaminated water. Kinetic and adsorption isotherm studies were applied to understand the adsorption of As and P onto the adsorbent. Several methods, such as pseudo-first and second order kinetic models, Elovich's equation, and the Weber-Morris intraparticle diffusion model were used to explain the kinetic aspects of the adsorption process. For the adsorption isotherm study, Langmuir and Freundlich isotherm models were applied.

Optimization of magnetization transfer measurements: statistical analysis by stochastic simulation. Application to creatine kinase kinetics.

PubMed

Rydzy, M; Deslauriers, R; Smith, I C; Saunders, J K

1990-08-01

A systematic study was performed to optimize the accuracy of kinetic parameters derived from magnetization transfer measurements. Three techniques were investigated: time-dependent saturation transfer (TDST), saturation recovery (SRS), and inversion recovery (IRS). In the last two methods, one of the resonances undergoing exchange is saturated throughout the experiment. The three techniques were compared with respect to the accuracy of the kinetic parameters derived from experiments performed in a given, fixed, amount of time. Stochastic simulation of magnetization transfer experiments was performed to optimize experimental design. General formulas for the relative accuracies of the unidirectional rate constant (k) were derived for each of the three experimental methods. It was calculated that for k values between 0.1 and 1.0 s-1, T1 values between 1 and 10 s, and relaxation delays appropriate for the creatine kinase reaction, the SRS method yields more accurate values of k than does the IRS method. The TDST method is more accurate than the SRS method for reactions where T1 is long and k is large, within the range of k and T1 values examined. Experimental verification of the method was carried out on a solution in which the forward (PCr----ATP) rate constant (kf) of the creatine kinase reaction was measured.

A mathematical analysis to address the 6 degree-of-freedom segmental power imbalance.

PubMed

Ebrahimi, Anahid; Collins, John D; Kepple, Thomas M; Takahashi, Kota Z; Higginson, Jill S; Stanhope, Steven J

2018-01-03

Segmental power is used in human movement analyses to indicate the source and net rate of energy transfer between the rigid bodies of biomechanical models. Segmental power calculations are performed using segment endpoint dynamics (kinetic method). A theoretically equivalent method is to measure the rate of change in a segment's mechanical energy state (kinematic method). However, these two methods have not produced experimentally equivalent results for segments proximal to the foot, with the difference in methods deemed the "power imbalance." In a 6 degree-of-freedom model, segments move independently, resulting in relative segment endpoint displacement and non-equivalent segment endpoint velocities at a joint. In the kinetic method, a segment's distal end translational velocity may be defined either at the anatomical end of the segment or at the location of the joint center (defined here as the proximal end of the adjacent distal segment). Our mathematical derivations revealed the power imbalance between the kinetic method using the anatomical definition and the kinematic method can be explained by power due to relative segment endpoint displacement. In this study, we tested this analytical prediction through experimental gait data from nine healthy subjects walking at a typical speed. The average absolute segmental power imbalance was reduced from 0.023 to 0.046 W/kg using the anatomical definition to ≤0.001 W/kg using the joint center definition in the kinetic method (95.56-98.39% reduction). Power due to relative segment endpoint displacement in segmental power analyses is substantial and should be considered in analyzing energetic flow into and between segments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

NASA Astrophysics Data System (ADS)

Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

2010-10-01

In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters of biomolecular interaction by using Newton Iteration Method and Least Squares Method. First, the pseudo first order kinetic model of biomolecular interaction was established. Then the data of molecular interaction of HBsAg and HBsAb was obtained by bioanalyzer. Finally, we used the optical SPR bioanalyzer software which was written by ourselves to make nonlinear fit about the association and dissociation curves. The correlation coefficient R-squared is 0.99229 and 0.99593, respectively. Furthermore, the kinetic parameters and affinity constants were evaluated using the obtained data from the fitting results.

Comparative Solid-State Stability of Perindopril Active Substance vs. Pharmaceutical Formulation

PubMed Central

Buda, Valentina; Andor, Minodora; Ledeti, Adriana; Ledeti, Ionut; Vlase, Gabriela; Vlase, Titus; Cristescu, Carmen; Voicu, Mirela; Suciu, Liana; Tomescu, Mirela Cleopatra

2017-01-01

This paper presents the results obtained after studying the thermal stability and decomposition kinetics of perindopril erbumine as a pure active pharmaceutical ingredient as well as a solid pharmaceutical formulation containing the same active pharmaceutical ingredient (API). Since no data were found in the literature regarding the spectroscopic description, thermal behavior, or decomposition kinetics of perindopril, our goal was the evaluation of the compatibility of this antihypertensive agent with the excipients in the tablet under ambient conditions and to study the effect of thermal treatment on the stability of perindopril erbumine. ATR-FTIR (Attenuated Total Reflectance Fourier Transform Infrared) spectroscopy, thermal analysis (thermogravimetric mass curve (TG—thermogravimetry), derivative thermogravimetric mass curve (DTG), and heat flow (HF)) and model-free kinetics were chosen as investigational tools. Since thermal behavior is a simplistic approach in evaluating the thermal stability of pharmaceuticals, in-depth kinetic studies were carried out by classical kinetic methods (Kissinger and ASTM E698) and later with the isoconversional methods of Friedman, Kissinger-Akahira-Sunose and Flynn-Wall-Ozawa. It was shown that the main thermal degradation step of perindopril erbumine is characterized by activation energy between 59 and 69 kJ/mol (depending on the method used), while for the tablet, the values were around 170 kJ/mol. The used excipients (anhydrous colloidal silica, microcrystalline cellulose, lactose, and magnesium stearate) should be used in newly-developed generic solid pharmaceutical formulations, since they contribute to an increased thermal stability of perindopril erbumine. PMID:28098840

Analysis of the interaction between membrane proteins and soluble binding partners by surface plasmon resonance.

PubMed

Wu, Zht Cheng; de Keyzer, Jeanine; Kusters, Ilja; Driessen, Arnold J M

2013-01-01

The interaction between membrane proteins and their (protein) ligands is conventionally investigated by nonequilibrium methods such as co-sedimentation or pull-down assays. Surface Plasmon Resonance can be used to monitor such binding events in real-time using isolated membranes immobilized to a surface providing insights in the kinetics of binding under equilibrium conditions. This application provides a fast, automated way to detect interacting species and to determine the kinetics and affinity (Kd) of the interaction.

Adjusting the surface areal density of click-reactive azide groups by kinetic control of the azide substitution reaction on bromine-functional SAMs.

PubMed

Zhang, Shuo; Maidenberg, Yanir; Luo, Kai; Koberstein, Jeffrey T

2014-06-03

Azide-alkyne click chemistry has emerged as an important and versatile means for tethering a wide variety of guest molecules to virtually any substrate. In many of these applications, it is important to exercise control over the areal density of surface functional groups to achieve a desired areal density of the tethered guest molecule of interest. We demonstrate herein that the areal density of surface azide groups on flat germanium surfaces and nanoparticle substrates (silica and iron oxide) can be controlled kinetically by appropriately timed quenching of the S(N)2 substitution reaction of bromo-alkane-silane monolayers induced by the addition of sodium azide. The kinetics of the azide substitution reaction on monolayers formed on flat Ge substrates, determined by attenuated total reflection infrared spectroscopy (ATR-IR), are found to be identical to those for monolayers formed on both silica and iron oxide nanoparticles, the latter determined by transmission infrared spectroscopy. To validate the method, the percentages of surface bromine groups converted to azide groups after various reaction times were measured by quenching the S(N)2 reaction followed by analysis with ATR-IR (for Ge) and thermogravimetric analysis (after a subsequent click reaction with an alkyne-terminal polymer) for the nanoparticle substrates. The conversions found after quenching agree well with those expected from the standard kinetic curves. The latter result suggests that the kinetic method for the control of azide group areal density is a versatile means for functionalizing substrates with a prescribed areal density of azide groups for subsequent click reactions, and that the method is universal for any substrate, flat or nanoparticle, that can be modified with bromo-alkane-silane monolayers. Regardless of the surface geometry, we find that the azide substitution reaction is complete within 2-3 h, in sharp contrast to previous reports that indicate times of 48-60 h required for completion of the reaction.

In vitro evaluation of flow patterns and turbulent kinetic energy in trans-catheter aortic valve prostheses.

PubMed

Giese, Daniel; Weiss, Kilian; Baeßler, Bettina; Madershahian, Navid; Choi, Yeong-Hoon; Maintz, David; Bunck, Alexander C

2018-02-01

The objective of the current work was to evaluate flow and turbulent kinetic energy in different transcatheter aortic valve implants using highly undersampled time-resolved multi-point 3-directional phase-contrast measurements (4D Flow MRI) in an in vitro setup. A pulsatile flow setup was used with a compliant tubing mimicking a stiff left ventricular outflow tract and ascending aorta. Five different implants were measured using a highly undersampled multi-point 4D Flow MRI sequence. Velocities and turbulent kinetic energy values were analysed and compared. Strong variations of turbulent kinetic energy distributions between the valves were observed. Maximum turbulent kinetic energy values ranged from 100 to over 500 J/m 3 while through-plane velocities were similar between all valves. Highly accelerated 4D Flow MRI for the measurement of velocities and turbulent kinetic energy values allowed for the assessment of hemodynamic parameters in five different implant models. The presented setup, measurement protocol and analysis methods provides an efficient approach to compare different valve implants and could aid future novel valve designs.

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.

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

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.

TU-C-12A-11: Comparisons Between Cu-ATSM PET and DCE-CT Kinetic Parameters in Canine Sinonasal Tumors

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

La Fontaine, M; Bradshaw, T; Kubicek, L

2014-06-15

Purpose: Regions of poor perfusion within tumors may be associated with higher hypoxic levels. This study aimed to test this hypothesis by comparing measurements of hypoxia from Cu-ATSM PET to vasculature kinetic parameters from DCE-CT kinetic analysis. Methods: Ten canine patients with sinonasal tumors received one Cu-ATSM PET/CT scan and three DCE-CT scans prior to treatment. Cu-ATSM PET/CT and DCE-CT scans were registered and resampled to matching voxel dimensions. Kinetic analysis was performed on DCE-CT scans and for each patient, the resulting kinetic parameter values from the three DCE-CT scans were averaged together. Cu-ATSM SUVs were spatially correlated (r{sub spatial})more » on a voxel-to-voxel basis against the following DCE-CT kinetic parameters: transit time (t{sub 1}), blood flow (F), vasculature fraction (v{sub 1}), and permeability (PS). In addition, whole-tumor comparisons were performed by correlating (r{sub ROI}) the mean Cu-ATSM SUV (SUV{sub mean}) with median kinetic parameter values. Results: The spatial correlations (r{sub spatial}) were poor and ranged from -0.04 to 0.21 for all kinetic parameters. These low spatial correlations may be due to high variability in the DCE-CT kinetic parameter voxel values between scans. In our hypothesis, t{sub 1} was expected to have a positive correlation, while F was expected to have a negative correlation to hypoxia. However, in wholetumor analysis the opposite was found for both t{sub 1} (r{sub ROI} = -0.25) and F (r{sub ROI} = 0.56). PS and v{sub 1} may depict angiogenic responses to hypoxia and found positive correlations to Cu-ATSM SUV for PS (r{sub ROI} = 0.41), and v{sub 1} (r{sub ROI} = 0.57). Conclusion: Low spatial correlations were found between Cu-ATSM uptake and DCE-CT vasculature parameters, implying that poor perfusion is not associated with higher hypoxic regions. Across patients, the most hypoxic tumors tended to have higher blood flow values, which is contrary to our initial hypothesis. Funding: R01 CA136927.« less

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.

Combustion and Magnetohydrodynamic Processes in Advanced Pulse Detonation Rocket Engines

DTIC Science & Technology

2012-10-01

use of high-order numerical methods can also be a powerful tool in the analysis of such complex flows, but we need to understand the interaction of...computational physics, 43(2):357372, 1981. [47] B. Einfeldt. On godunov-type methods for gas dynamics . SIAM Journal on Numerical Analysis , pages 294...dimensional effects with complex reaction kinetics, the simple one-dimensional detonation structure provides a rich spectrum of dynamical features which are

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

Respiratory motion compensation algorithm of ultrasound hepatic perfusion data acquired in free-breathing

NASA Astrophysics Data System (ADS)

Wu, Kaizhi; Zhang, Xuming; Chen, Guangxie; Weng, Fei; Ding, Mingyue

2013-10-01

Images acquired in free breathing using contrast enhanced ultrasound exhibit a periodic motion that needs to be compensated for if a further accurate quantification of the hepatic perfusion analysis is to be executed. In this work, we present an algorithm to compensate the respiratory motion by effectively combining the PCA (Principal Component Analysis) method and block matching method. The respiratory kinetics of the ultrasound hepatic perfusion image sequences was firstly extracted using the PCA method. Then, the optimal phase of the obtained respiratory kinetics was detected after normalizing the motion amplitude and determining the image subsequences of the original image sequences. The image subsequences were registered by the block matching method using cross-correlation as the similarity. Finally, the motion-compensated contrast images can be acquired by using the position mapping and the algorithm was evaluated by comparing the TICs extracted from the original image sequences and compensated image subsequences. Quantitative comparisons demonstrated that the average fitting error estimated of ROIs (region of interest) was reduced from 10.9278 +/- 6.2756 to 5.1644 +/- 3.3431 after compensating.

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

Kinetics of Hypotension during 50 Sessions of Resistance and Aerobic Training in Hypertensive Patients: a Randomized Clinical Trial

PubMed Central

Damorim, Igor Rodrigues; Santos, Tony Meireles; Barros, Gustavo Willames Pimentel; Carvalho, Paulo Roberto Cavalcanti

2017-01-01

Background Resistance and aerobic training are recommended as an adjunctive treatment for hypertension. However, the number of sessions required until the hypotensive effect of the exercise has stabilized has not been clearly established. Objective To establish the adaptive kinetics of the blood pressure (BP) responses as a function of time and type of training in hypertensive patients. Methods We recruited 69 patients with a mean age of 63.4 ± 2.1 years, randomized into one group of resistance training (n = 32) and another of aerobic training (n = 32). Anthropometric measurements were obtained, and one repetition maximum (1RM) testing was performed. BP was measured before each training session with a digital BP arm monitor. The 50 training sessions were categorized into quintiles. To compare the effect of BP reduction with both training methods, we used two-way analysis of covariance (ANCOVA) adjusted for the BP values obtained before the interventions. The differences between the moments were established by one-way analysis of variance (ANOVA). Results The reductions in systolic (SBP) and diastolic BP (DBP) were 6.9 mmHg and 5.3 mmHg, respectively, with resistance training and 16.5 mmHg and 11.6 mmHg, respectively, with aerobic training. The kinetics of the hypotensive response of the SBP showed significant reductions until the 20th session in both groups. Stabilization of the DBP occurred in the 20th session of resistance training and in the 10th session of aerobic training. Conclusion A total of 20 sessions of resistance or aerobic training are required to achieve the maximum benefits of BP reduction. The methods investigated yielded distinct adaptive kinetic patterns along the 50 sessions. PMID:28380132

Simultaneous kinetic spectrometric determination of three flavonoid antioxidants in fruit with the aid of chemometrics

NASA Astrophysics Data System (ADS)

Sun, Ruiling; Wang, Yong; Ni, Yongnian; Kokot, Serge

2014-03-01

A simple, inexpensive and sensitive kinetic spectrophotometric method was developed for the simultaneous determination of three anti-carcinogenic flavonoids: catechin, quercetin and naringenin, in fruit samples. A yellow chelate product was produced in the presence neocuproine and Cu(I) - a reduction product of the reaction between the flavonoids with Cu(II), and this enabled the quantitative measurements with UV-vis spectrophotometry. The overlapping spectra obtained, were resolved with chemometrics calibration models, and the best performing method was the fast independent component analysis (fast-ICA/PCR (Principal component regression)); the limits of detection were 0.075, 0.057 and 0.063 mg L-1 for catechin, quercetin and naringenin, respectively. The novel method was found to outperform significantly the common HPLC procedure.

Kinetic determinations of accurate relative oxidation potentials of amines with reactive radical cations.

PubMed

Gould, Ian R; Wosinska, Zofia M; Farid, Samir

2006-01-01

Accurate oxidation potentials for organic compounds are critical for the evaluation of thermodynamic and kinetic properties of their radical cations. Except when using a specialized apparatus, electrochemical oxidation of molecules with reactive radical cations is usually an irreversible process, providing peak potentials, E(p), rather than thermodynamically meaningful oxidation potentials, E(ox). In a previous study on amines with radical cations that underwent rapid decarboxylation, we estimated E(ox) by correcting the E(p) from cyclic voltammetry with rate constants for decarboxylation obtained using laser flash photolysis. Here we use redox equilibration experiments to determine accurate relative oxidation potentials for the same amines. We also describe an extension of these experiments to show how relative oxidation potentials can be obtained in the absence of equilibrium, from a complete kinetic analysis of the reversible redox kinetics. The results provide support for the previous cyclic voltammetry/laser flash photolysis method for determining oxidation potentials.

Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica

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

Oboh, I., E-mail: innocentoboh@uniuyo.edu.ng; Aluyor, E.; Audu, T.

The biosorption of Zinc (II) ions onto a biomaterial - Luffa cylindrica has been studied. This biomaterial was characterized by elemental analysis, surface area, pore size distribution, scanning electron microscopy, and the biomaterial before and after sorption, was characterized by Fourier Transform Infra Red (FTIR) spectrometer. The kinetic nonlinear models fitted were Pseudo-first order, Pseudo-second order and Intra-particle diffusion. A comparison of non-linear regression method in selecting the kinetic model was made. Four error functions, namely coefficient of determination (R{sup 2}), hybrid fractional error function (HYBRID), average relative error (ARE), and sum of the errors squared (ERRSQ), were used tomore » predict the parameters of the kinetic models. The strength of this study is that a biomaterial with wide distribution particularly in the tropical world and which occurs as waste material could be put into effective utilization as a biosorbent to address a crucial environmental problem.« less

Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica

NASA Astrophysics Data System (ADS)

Oboh, I.; Aluyor, E.; Audu, T.

2015-03-01

The biosorption of Zinc (II) ions onto a biomaterial - Luffa cylindrica has been studied. This biomaterial was characterized by elemental analysis, surface area, pore size distribution, scanning electron microscopy, and the biomaterial before and after sorption, was characterized by Fourier Transform Infra Red (FTIR) spectrometer. The kinetic nonlinear models fitted were Pseudo-first order, Pseudo-second order and Intra-particle diffusion. A comparison of non-linear regression method in selecting the kinetic model was made. Four error functions, namely coefficient of determination (R2), hybrid fractional error function (HYBRID), average relative error (ARE), and sum of the errors squared (ERRSQ), were used to predict the parameters of the kinetic models. The strength of this study is that a biomaterial with wide distribution particularly in the tropical world and which occurs as waste material could be put into effective utilization as a biosorbent to address a crucial environmental problem.

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

Technical note: An inverse method to relate organic carbon reactivity to isotope composition from serial oxidation

NASA Astrophysics Data System (ADS)

Hemingway, Jordon D.; Rothman, Daniel H.; Rosengard, Sarah Z.; Galy, Valier V.

2017-11-01

Serial oxidation coupled with stable carbon and radiocarbon analysis of sequentially evolved CO2 is a promising method to characterize the relationship between organic carbon (OC) chemical composition, source, and residence time in the environment. However, observed decay profiles depend on experimental conditions and oxidation pathway. It is therefore necessary to properly assess serial oxidation kinetics before utilizing decay profiles as a measure of OC reactivity. We present a regularized inverse method to estimate the distribution of OC activation energy (E), a proxy for bond strength, using serial oxidation. Here, we apply this method to ramped temperature pyrolysis or oxidation (RPO) analysis but note that this approach is broadly applicable to any serial oxidation technique. RPO analysis directly compares thermal reactivity to isotope composition by determining the E range for OC decaying within each temperature interval over which CO2 is collected. By analyzing a decarbonated test sample at multiple masses and oven ramp rates, we show that OC decay during RPO analysis follows a superposition of parallel first-order kinetics and that resulting E distributions are independent of experimental conditions. We therefore propose the E distribution as a novel proxy to describe OC thermal reactivity and suggest that E vs. isotope relationships can provide new insight into the compositional controls on OC source and residence time.

Removal of Rhodamine B from aqueous solution using magnetic NiFe nanoparticles.

PubMed

Liu, Yan; Liu, Kaige; Zhang, Lin; Zhang, Zhaowen

2015-01-01

Surface-modified magnetic nano alloy particles Ni2.33Fe were prepared using a hydrothermal method and they were utilized for removing Rhodamine B (RhB) from aqueous solution. The magnetic nanoparticles were characterized by X-ray diffraction, scanning electron microscopy, thermogravimetric analysis and Fourier transform infrared spectroscopy, which confirmed that the surface of the magnetic product with a face-centered cubic-type structure was successfully modified by sodium citrate. Kinetics studies were conducted. The pseudo-second-order kinetic model was used for fitting the kinetic data successfully. The Freundlich and Langmuir adsorption models were employed for the mathematical description of adsorption equilibrium. It was found that the adsorption isotherm can be very satisfactorily fitted by the Freundlich model.

Electrochemical Behavior of Sulfur in Aqueous Alkaline Solutions

NASA Astrophysics Data System (ADS)

Mamyrbekova, Aigul; Mamitova, A. D.; Mamyrbekova, Aizhan

2018-03-01

The kinetics and mechanism of the electrode oxidation-reduction of sulfur on an electrically conductive sulfur-graphite electrode in an alkaline solution was studied by the potentiodynamic method. To examine the mechanism of electrode processes occurring during AC polarization on a sulfur-graphite electrode, the cyclic polarization in both directions and anodic polarization curves were recorded. The kinetic parameters: charge transfer coefficients (α), diffusion coefficients ( D), heterogeneous rate constants of electrode process ( k s), and effective activation energies of the process ( E a) were calculated from the results of polarization measurements. An analysis of the results and calculated kinetic parameters of electrode processes showed that discharge ionization of sulfur in alkaline solutions occurs as a sequence of two stages and is a quasireversible process.

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

Mechanics and pathomechanics in the overhead athlete.

PubMed

Kibler, W Ben; Wilkes, Trevor; Sciascia, Aaron

2013-10-01

Optimal performance of the overhead throwing task requires precise mechanics that involve coordinated kinetic and kinematic chains to develop, transfer, and regulate the forces the body needs to withstand the inherent demands of the task and to allow optimal performance. These chains have been evaluated and the basic components, called nodes, have been identified. Impaired performance and/or injury, the DTS, is associated with alterations in the mechanics that are called pathomechanics. They can occur at multiple locations throughout the kinetic chain. They must be evaluated and treated as part of the overall problem. Observational analysis of the mechanics and pathomechanics using the node analysis method can be useful in highlighting areas of alteration that can be evaluated for anatomic injury or altered physiology. The comprehensive kinetic chain examination can evaluate sites of kinetic chain breakage, and a detailed shoulder examination can assess joint internal derangement of altered physiology that may contribute to the pathomechanics. Treatment of the DTS should be comprehensive, directed toward restoring physiology and mechanics and optimizing anatomy. This maximizes the body’s ability to develop normal mechanics to accomplish the overhead throwing task. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

A Sensitive and Robust Enzyme Kinetic Experiment Using Microplates and Fluorogenic Ester Substrates

ERIC Educational Resources Information Center

Johnson, R. Jeremy; Hoops, Geoffrey C.; Savas, Christopher J.; Kartje, Zachary; Lavis, Luke D.

2015-01-01

Enzyme kinetics measurements are a standard component of undergraduate biochemistry laboratories. The combination of serine hydrolases and fluorogenic enzyme substrates provides a rapid, sensitive, and general method for measuring enzyme kinetics in an undergraduate biochemistry laboratory. In this method, the kinetic activity of multiple protein…

Optimization of deflection of a big NEO through impact with a small one.

PubMed

Zhu, Kaijian; Huang, Weiping; Wang, Yuncai; Niu, Wei; Wu, Gongyou

2014-01-01

Using a small near-Earth object (NEO) to impact a larger and potentially threatening NEO has been suggested as an effective method to avert a collision with Earth. This paper develops a procedure for analysis of the technique for specific NEOs. First, an optimization method is used to select a proper small body from the database. Some principles of optimality are achieved with the optimization process. Then, the orbit of the small body is changed to guarantee that it flies toward and impacts the big threatening NEO. Kinetic impact by a spacecraft is chosen as the strategy of deflecting the small body. The efficiency of this method is compared with that of a direct kinetic impact to the big NEO by a spacecraft. Finally, a case study is performed for the deflection of the Apophis NEO, and the efficiency of the method is assessed.

Optimization of Deflection of a Big NEO through Impact with a Small One

PubMed Central

Zhu, Kaijian; Huang, Weiping; Wang, Yuncai; Niu, Wei; Wu, Gongyou

2014-01-01

Using a small near-Earth object (NEO) to impact a larger and potentially threatening NEO has been suggested as an effective method to avert a collision with Earth. This paper develops a procedure for analysis of the technique for specific NEOs. First, an optimization method is used to select a proper small body from the database. Some principles of optimality are achieved with the optimization process. Then, the orbit of the small body is changed to guarantee that it flies toward and impacts the big threatening NEO. Kinetic impact by a spacecraft is chosen as the strategy of deflecting the small body. The efficiency of this method is compared with that of a direct kinetic impact to the big NEO by a spacecraft. Finally, a case study is performed for the deflection of the Apophis NEO, and the efficiency of the method is assessed. PMID:25525627

A new method to characterize the kinetics of cholinesterases inhibited by carbamates.

PubMed

Xiao, Qiaoling; Zhou, Huimin; Wei, Hong; Du, Huaqiao; Tan, Wen; Zhan, Yiyi; Pistolozzi, Marco

2017-09-10

The inhibition of cholinesterases (ChEs) by carbamates includes a carbamylation (inhibition) step, in which the drug transfers its carbamate moiety to the active site of the enzyme and a decarbamylation (activity recovery) step, in which the carbamyl group is hydrolyzed from the enzyme. The carbamylation and decarbamylation kinetics decide the extent and the duration of the inhibition, thus the full characterization of candidate carbamate inhibitors requires the measurement of the kinetic constants describing both steps. Carbamylation and decarbamylation rate constants are traditionally measured by two separate set of experiments, thus making the full characterization of candidate inhibitors time-consuming. In this communication we show that by the analysis of the area under the inhibition-time curve of cholinesterases inhibited by carbamates it is possible to calculate the decarbamylation rate constant from the same data traditionally used to characterize only the carbamylation kinetics, therefore it is possible to obtain a full characterization of the inhibition with a single set of experiments. The characterization of the inhibition kinetics of human and dog plasma butyrylcholinesterase and of human acetylcholinesterase by bambuterol and bambuterol monocarbamate enantiomers was used to demonstrate the validity of the approach. The results showed that the proposed method provides reliable estimations of carbamylation and decarbamylation rate constants thus representing a simple and useful approach to reduce the time required for the characterization of carbamate inhibitors. Copyright © 2017 Elsevier B.V. All rights reserved.

Harmonic force spectroscopy measures load-dependent kinetics of individual human β-cardiac myosin molecules.

PubMed

Sung, Jongmin; Nag, Suman; Mortensen, Kim I; Vestergaard, Christian L; Sutton, Shirley; Ruppel, Kathleen; Flyvbjerg, Henrik; Spudich, James A

2015-08-04

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using 'harmonic force spectroscopy'. In this method, harmonic oscillation of the sample stage of a laser trap immediately, automatically and randomly applies sinusoidally varying loads to a single motor molecule interacting with a single track along which it moves. The experimental protocol and the data analysis are simple, fast and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human β-cardiac myosin molecules interacting with an actin filament at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load, in qualitative agreement with cardiac muscle, which contracts with a velocity inversely proportional to external load.

Harmonic force spectroscopy measures load-dependent kinetics of individual human β-cardiac myosin molecules

PubMed Central

Sung, Jongmin; Nag, Suman; Mortensen, Kim I.; Vestergaard, Christian L.; Sutton, Shirley; Ruppel, Kathleen; Flyvbjerg, Henrik; Spudich, James A.

2015-01-01

Molecular motors are responsible for numerous cellular processes from cargo transport to heart contraction. Their interactions with other cellular components are often transient and exhibit kinetics that depend on load. Here, we measure such interactions using ‘harmonic force spectroscopy'. In this method, harmonic oscillation of the sample stage of a laser trap immediately, automatically and randomly applies sinusoidally varying loads to a single motor molecule interacting with a single track along which it moves. The experimental protocol and the data analysis are simple, fast and efficient. The protocol accumulates statistics fast enough to deliver single-molecule results from single-molecule experiments. We demonstrate the method's performance by measuring the force-dependent kinetics of individual human β-cardiac myosin molecules interacting with an actin filament at physiological ATP concentration. We show that a molecule's ADP release rate depends exponentially on the applied load, in qualitative agreement with cardiac muscle, which contracts with a velocity inversely proportional to external load. PMID:26239258

Kinetic Analysis of Weakly ionized Plasmas in presence of collecting walls

NASA Astrophysics Data System (ADS)

Gonzalez, J.; Donoso, J. M.

2018-02-01

Description of plasmas in contact with a wall able to collecting or emitting charged particles is a research topic of great importance. This situation arises in a great variety of phenomena such as the characterization of plasmas by means of electric probes, in the surface treatment of materials and in the service-life of coatings in electric thrusters. In particular, in this work we devote attention to the dynamics of an argon weakly ionized plasma in the presence of a collecting wall. It is proposed a kinetic model in a 1D1V planar phase-space geometry. The model accounts for the electric field coupled to the system by solving the associated Poisson’s equation. To solve numerically the resulting non-linear system of equations, the Propagator Integral Method is used in conjunction with a slabbing method. On each interrelating plasma slab the integral advancing scheme operates in velocity space, in such a way that the all the species dynamics dominating the system evolution are kinetically described.

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

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].

Kinetics of phase transformation in glass forming systems

NASA Technical Reports Server (NTRS)

Ray, Chandra S.

1994-01-01

The objectives of this research were to (1) develop computer models for realistic simulations of nucleation and crystal growth in glasses, which would also have the flexibility to accomodate the different variables related to sample characteristics and experimental conditions, and (2) design and perform nucleation and crystallization experiments using calorimetric measurements, such as differential scanning calorimetry (DSC) and differential thermal analysis (DTA) to verify these models. The variables related to sample characteristics mentioned in (1) above include size of the glass particles, nucleating agents, and the relative concentration of the surface and internal nuclei. A change in any of these variables changes the mode of the transformation (crystallization) kinetics. A variation in experimental conditions includes isothermal and nonisothermal DSC/DTA measurements. This research would lead to develop improved, more realistic methods for analysis of the DSC/DTA peak profiles to determine the kinetic parameters for nucleation and crystal growth as well as to assess the relative merits and demerits of the thermoanalytical models presently used to study the phase transformation in glasses.

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.

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.

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

The mathematical origins of the kinetic compensation effect: 2. The effect of systematic errors.

PubMed

Barrie, Patrick J

2012-01-07

The kinetic compensation effect states that there is a linear relationship between Arrhenius parameters ln A and E for a family of related processes. It is a widely observed phenomenon in many areas of science, notably heterogeneous catalysis. This paper explores mathematical, rather than physicochemical, explanations for the compensation effect in certain situations. Three different topics are covered theoretically and illustrated by examples. Firstly, the effect of systematic errors in experimental kinetic data is explored, and it is shown that these create apparent compensation effects. Secondly, analysis of kinetic data when the Arrhenius parameters depend on another parameter is examined. In the case of temperature programmed desorption (TPD) experiments when the activation energy depends on surface coverage, it is shown that a common analysis method induces a systematic error, causing an apparent compensation effect. Thirdly, the effect of analysing the temperature dependence of an overall rate of reaction, rather than a rate constant, is investigated. It is shown that this can create an apparent compensation effect, but only under some conditions. This result is illustrated by a case study for a unimolecular reaction on a catalyst surface. Overall, the work highlights the fact that, whenever a kinetic compensation effect is observed experimentally, the possibility of it having a mathematical origin should be carefully considered before any physicochemical conclusions are drawn.

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

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

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.

Electrochemistry at Nanometer-Scaled Electrodes

ERIC Educational Resources Information Center

Watkins, John J.; Bo Zhang; White, Henry S.

2005-01-01

Electrochemical studies using nanometer-scaled electrodes are leading to better insights into electrochemical kinetics, interfacial structure, and chemical analysis. Various methods of preparing electrodes of nanometer dimensions are discussed and a few examples of their behavior and applications in relatively simple electrochemical experiments…

Analysis of a boron-carbide-drum-controlled critical reactor experiment

NASA Technical Reports Server (NTRS)

Mayo, W. T.

1972-01-01

In order to validate methods and cross sections used in the neutronic design of compact fast-spectrum reactors for generating electric power in space, an analysis of a boron-carbide-drum-controlled critical reactor was made. For this reactor the transport analysis gave generally satisfactory results. The calculated multiplication factor for the most detailed calculation was only 0.7-percent Delta k too high. Calculated reactivity worth of the control drums was $11.61 compared to measurements of $11.58 by the inverse kinetics methods and $11.98 by the inverse counting method. Calculated radial and axial power distributions were in good agreement with experiment.

Measuring kinetics of complex single ion channel data using mean-variance histograms.

PubMed Central

Patlak, J B

1993-01-01

The measurement of single ion channel kinetics is difficult when those channels exhibit subconductance events. When the kinetics are fast, and when the current magnitudes are small, as is the case for Na+, Ca2+, and some K+ channels, these difficulties can lead to serious errors in the estimation of channel kinetics. I present here a method, based on the construction and analysis of mean-variance histograms, that can overcome these problems. A mean-variance histogram is constructed by calculating the mean current and the current variance within a brief "window" (a set of N consecutive data samples) superimposed on the digitized raw channel data. Systematic movement of this window over the data produces large numbers of mean-variance pairs which can be assembled into a two-dimensional histogram. Defined current levels (open, closed, or sublevel) appear in such plots as low variance regions. The total number of events in such low variance regions is estimated by curve fitting and plotted as a function of window width. This function decreases with the same time constants as the original dwell time probability distribution for each of the regions. The method can therefore be used: 1) to present a qualitative summary of the single channel data from which the signal-to-noise ratio, open channel noise, steadiness of the baseline, and number of conductance levels can be quickly determined; 2) to quantify the dwell time distribution in each of the levels exhibited. In this paper I present the analysis of a Na+ channel recording that had a number of complexities. The signal-to-noise ratio was only about 8 for the main open state, open channel noise, and fast flickers to other states were present, as were a substantial number of subconductance states. "Standard" half-amplitude threshold analysis of these data produce open and closed time histograms that were well fitted by the sum of two exponentials, but with apparently erroneous time constants, whereas the mean-variance histogram technique provided a more credible analysis of the open, closed, and subconductance times for the patch. I also show that the method produces accurate results on simulated data in a wide variety of conditions, whereas the half-amplitude method, when applied to complex simulated data shows the same errors as were apparent in the real data. The utility and the limitations of this new method are discussed. Images FIGURE 2 FIGURE 4 FIGURE 8 FIGURE 9 PMID:7690261

Chemical kinetic studies of atmospheric reactions using tunable diode laser spectroscopy

NASA Technical Reports Server (NTRS)

Worsnop, Douglas R.; Nelson, David D.; Zahniser, Mark S.

1993-01-01

IR absorption using tunable diode laser spectroscopy provides a sensitive and quantitative detection method for laboratory kinetic studies of atmospheric trace gases. Improvements in multipass cell design, real time signal processing, and computer controlled data acquisition and analysis have extended the applicability of the technique. We have developed several optical systems using off-axis resonator mirror designs which maximize path length while minimizing both the sample volume and the interference fringes inherent in conventional 'White' cells. Computerized signal processing using rapid scan (300 kHz), sweep integration with 100 percent duty cycle allows substantial noise reduction while retaining the advantages of using direct absorption for absolute absorbance measurements and simultaneous detection of multiple species. Peak heights and areas are determined by curve fitting using nonlinear least square methods. We have applied these techniques to measurements of: (1) heterogeneous uptake chemistry of atmospheric trace gases (HCl, H2O2, and N2O5) on aqueous and sulfuric acid droplets; (2) vapor pressure measurements of nitric acid and water over prototypical stratospheric aerosol (nitric acid trihydrate) surfaces; and (3) discharge flow tube kinetic studies of the HO2 radical using isotopic labeling for product channel and mechanistic analysis. Results from each of these areas demonstrate the versatility of TDL absorption spectroscopy for atmospheric chemistry applications.

Analysis of kinematic, kinetic and electromyographic patterns during root canal preparation with rotary and manual instruments

PubMed Central

PASTERNAK-JÚNIOR, Braulio; de SOUSA NETO, Manoel Damião; DIONÍSIO, Valdeci Carlos; PÉCORA, Jesus Djalma; SILVA, Ricardo Gariba

2012-01-01

Objective This study assessed the muscular activity during root canal preparation through kinematics, kinetics, and electromyography (EMG). Material and Methods The operators prepared one canal with RaCe rotary instruments and another with Flexo-files. The kinematics of the major joints was reconstructed using an optoelectronic system and electromyographic responses of the flexor carpi radialis, extensor carpi radialis, brachioradialis, biceps brachii, triceps brachii, middle deltoid, and upper trapezius were recorded. The joint torques of the shoulder, elbow and wrist were calculated using inverse dynamics. In the kinematic analysis, angular movements of the wrist and elbow were classified as low risk factors for work-related musculoskeletal disorders. With respect to the shoulder, the classification was medium-risk. Results There was no significant difference revealed by the kinetic reports. The EMG results showed that for the middle deltoid and upper trapezius the rotary instrumentation elicited higher values. The flexor carpi radialis and extensor carpi radialis, as well as the brachioradialis showed a higher value with the manual method. Conclusion The muscular recruitment for accomplishment of articular movements for root canal preparation with either the rotary or manual techniques is distinct. Nevertheless, the rotary instrument presented less difficulty in the generation of the joint torque in each articulation, thus, presenting a greater uniformity of joint torques. PMID:22437679

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

Global Energetics in Solar Flares and Coronal Mass Ejections

NASA Astrophysics Data System (ADS)

Aschwanden, Markus J.

2017-08-01

We present a statistical study of the energetics of coronal mass ejections (CME) and compare it with the magnetic, thermal, and nonthermal energy dissipated in flares. The physical parameters of CME speeds, mass, and kinetic energies are determined with two different independent methods, i.e., the traditional white-light scattering method using LASCO/SOHO data, and the EUV dimming method using AIA/SDO data. We analyze all 860 GOES M- and X-class flare events observed during the first 7 years (2010-2016) of the SDO mission. The new ingredients of our CME modeling includes: (1) CME geometry in terms of a self-similar adiabatic expansion, (2) DEM analysis of CME mass over entire coronal temperature range, (3) deceleration of CME due to gravity force which controls the kinetic and potentail CME energy as a function of time, (4) the critical speed that controls eruptive and confined CMEs, (5) the relationship between the center-of-mass motion during EUV dimming and the leading edge motion observed in white-light coronagraphs. Novel results are: (1) Physical parameters obtained from both the EUV dimming and white-light method can be reconciled; (2) the equi-partition of CME kinetic and thermal flare energy; (3) the Rosner-Tucker-Vaiana scaling law. We find that the two methods in EUV and white-light wavelengths are highly complementary and yield more complete models than each method alone.

[Analysis of hydrodynamics parameters of runoff erosion and sediment-yielding on unpaved road].

PubMed

Huang, Peng-Fei; Wang, Wen-Long; Luo, Ting; Wang, Zhen; Wang, Zheng-Li; Li, Ren

2013-02-01

By the method of field runoff washout experiment, a simulation study was conducted on the relationships between the soil detachment rate and the hydrodynamic parameters on unpaved road, and the related quantitative formulas were established. Under the conditions of different flow discharges and road gradients, the averaged soil detachment rate increased with increasing flow discharge and road gradient, and the relationships between them could be described by a power function. As compared with road gradient, flow discharge had greater effects on the soil detachment rate. The soil detachment rate had a power relation with water flow velocity and runoff kinetic energy, and the runoff kinetic energy was of importance to the soil detachment rate. The soil detachment rate was linearly correlated with the unit runoff kinetic energy. The averaged soil erodibility was 0.120 g m-1.J-F-1, and the averaged critical unit runoff kinetic energy was 2.875 g.m-1.J-1. Flow discharge, road gradient, and unit runoff kinetic energy could be used to accurately describe the soil erosion process and calculate the soil erosion rate on unpaved road.

Unique nucleation activity of inorganic fullerene-like WS2 nanoparticles in polyphenylene sulfide nanocomposites: isokinetic and isoconversional study of dynamic crystallization kinetics.

PubMed

Naffakh, Mohammed; Marco, Carlos; Gómez, Marián A; Jiménez, Ignacio

2009-05-21

The dynamic crystallization kinetics of polyphenylene sulfide (PPS) nanocomposites with inorganic fullerene WS2 nanopartices (IF-WS2) content varying from 0.05 to 8 wt % has been studied using differential scanning calorimetry (DSC). The analysis of the crystallization at different cooling rates demonstrates that the completely isokinetic description of the crystallization process is not possible. However, the isoconversional methods in combination with the JMAEK equation provide a better understanding of the kinetics of the dynamic crystallization process. The addition of IF-WS2 influences the crystallization kinetics of PPS but in ways unexpected for polymer nanocomposites. A drastic change from retardation to promotion of crystallization is observed with increasing nanoparticle content. In the same way, the results of the nucleation activity and the effective energy barrier confirmed the unique dependence of the crystallization behavior of PPS on composition. In addition, the morphological data obtained from the polarized optical microscopy (POM) and time-resolved synchrotron X-ray diffraction is consistent with results of the crystallization kinetics of PPS/IF-WS2 nanocomposites.

Kinetic study of an enzymic cycling system coupled to an enzymic step: determination of alkaline phosphatase activity.

PubMed Central

Valero, E; Varón, R; García-Carmona, F

1995-01-01

A kinetic study is made of a system consisting of a specific enzymic cycling assay coupled to an enzymic reaction. A kinetic analysis of this system is presented, and the accumulation of chromophore involved in the cycle is seen to be parabolic, i.e. the rate of the reaction increases continuously with constant acceleration. The system is illustrated by the measurement of alkaline phosphatase activity using beta-NADP+ as substrate. The enzymes alcohol dehydrogenase and diaphorase are used to cycle beta-NAD+ in the presence of ethanol and p-Iodonitrotetrazolium Violet. During each turn of the cycle, one molecule of the tetrazolium salt is reduced to an intensely coloured formazan. A simple procedure for evaluating the kinetic parameters involved in the system and for optimizing this cycling assay is described. The method is applicable to the measurement of any enzyme, and its amplification capacity as well as the simplicity of determining kinetic parameters enable it to be employed in enzyme immunoassays to increase the magnitude of the measured response. PMID:7619054

Automated Transition State Theory Calculations for High-Throughput Kinetics.

PubMed

Bhoorasingh, Pierre L; Slakman, Belinda L; Seyedzadeh Khanshan, Fariba; Cain, Jason Y; West, Richard H

2017-09-21

A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.

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

Arbitrary-order Hilbert Spectral Analysis and Intermittency in Solar Wind Density Fluctuations

NASA Astrophysics Data System (ADS)

Carbone, Francesco; Sorriso-Valvo, Luca; Alberti, Tommaso; Lepreti, Fabio; Chen, Christopher H. K.; Němeček, Zdenek; Šafránková, Jana

2018-05-01

The properties of inertial- and kinetic-range solar wind turbulence have been investigated with the arbitrary-order Hilbert spectral analysis method, applied to high-resolution density measurements. Due to the small sample size and to the presence of strong nonstationary behavior and large-scale structures, the classical analysis in terms of structure functions may prove to be unsuccessful in detecting the power-law behavior in the inertial range, and may underestimate the scaling exponents. However, the Hilbert spectral method provides an optimal estimation of the scaling exponents, which have been found to be close to those for velocity fluctuations in fully developed hydrodynamic turbulence. At smaller scales, below the proton gyroscale, the system loses its intermittent multiscaling properties and converges to a monofractal process. The resulting scaling exponents, obtained at small scales, are in good agreement with those of classical fractional Brownian motion, indicating a long-term memory in the process, and the absence of correlations around the spectral-break scale. These results provide important constraints on models of kinetic-range turbulence in the solar wind.

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

Solving complex photocycle kinetics. Theory and direct method.

PubMed Central

Nagle, J F

1991-01-01

A direct nonlinear least squares method is described that obtains the true kinetic rate constants and the temperature-independent spectra of n intermediates from spectroscopic data taken in the visible at three or more temperatures. A theoretical analysis, which is independent of implementation of the direct method, proves that well determined local solutions are not possible for fewer than three temperatures. This analysis also proves that measurements at more than n wavelengths are redundant, although the direct method indicates that convergence is faster if n + m wavelengths are measured, where m is of order one. This suggests that measurements should concentrate on high precision for a few measuring wavelengths, rather than lower precision for many wavelengths. Globally, false solutions occur, and the ability to reject these depends upon the precision of the data, as shown by explicit example. An optimized way to analyze vibrational spectroscopic data is also presented. Such data yield unique results, which are comparably accurate to those obtained from data taken in the visible with comparable noise. It is discussed how use of both kinds of data is advantageous if the data taken in the visible are significantly less noisy. PMID:2009362

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

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.

Signatures of van der Waals binding: A coupling-constant scaling analysis

NASA Astrophysics Data System (ADS)

Jiao, Yang; Schröder, Elsebeth; Hyldgaard, Per

2018-02-01

The van der Waals (vdW) density functional (vdW-DF) method [Rep. Prog. Phys. 78, 066501 (2015), 10.1088/0034-4885/78/6/066501] describes dispersion or vdW binding by tracking the effects of an electrodynamic coupling among pairs of electrons and their associated exchange-correlation holes. This is done in a nonlocal-correlation energy term Ecnl, which permits density functional theory calculation in the Kohn-Sham scheme. However, to map the nature of vdW forces in a fully interacting materials system, it is necessary to also account for associated kinetic-correlation energy effects. Here, we present a coupling-constant scaling analysis, which permits us to compute the kinetic-correlation energy Tcnl that is specific to the vdW-DF account of nonlocal correlations. We thus provide a more complete spatially resolved analysis of the electrodynamical-coupling nature of nonlocal-correlation binding, including vdW attraction, in both covalently and noncovalently bonded systems. We find that kinetic-correlation energy effects play a significant role in the account of vdW or dispersion interactions among molecules. Furthermore, our mapping shows that the total nonlocal-correlation binding is concentrated to pockets in the sparse electron distribution located between the material fragments.

Discussion of the Investigation Method on the Reaction Kinetics of Metallurgical Reaction Engineering

NASA Astrophysics Data System (ADS)

Du, Ruiling; Wu, Keng; Zhang, Jiazhi; Zhao, Yong

Reaction kinetics of metallurgical physical chemistry which was successfully applied in metallurgy (as ferrous metallurgy, non-ferrous metallurgy) became an important theoretical foundation for subject system of traditional metallurgy. Not only the research methods were very perfect, but also the independent structures and systems of it had been formed. One of the important tasks of metallurgical reaction engineering was the simulation of metallurgical process. And then, the mechanism of reaction process and the conversion time points of different control links should be obtained accurately. Therefore, the research methods and results of reaction kinetics in metallurgical physical chemistry were not very suitable for metallurgical reaction engineering. In order to provide the definite conditions of transmission, reaction kinetics parameters and the conversion time points of different control links for solving the transmission and reaction equations in metallurgical reaction engineering, a new method for researching kinetics mechanisms in metallurgical reaction engineering was proposed, which was named stepwise attempt method. Then the comparison of results between the two methods and the further development of stepwise attempt method were discussed in this paper. As a new research method for reaction kinetics in metallurgical reaction engineering, stepwise attempt method could not only satisfy the development of metallurgical reaction engineering, but also provide necessary guarantees for establishing its independent subject system.

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.

Validation of a thin-layer chromatography/densitometry method for the characterization of invertase activity.

PubMed

Ferey, Justine; Da Silva, David; Bravo-Veyrat, Sophie; Lafite, Pierre; Daniellou, Richard; Maunit, Benoît

2016-12-16

This paper presents a kinetic study of invertase, a specific fructofuranosidase cloned from the Leishmania major genome. The kinetic parameters of the β-d-fructofuranosidase from Leishmania major (BfrA) were determined using Thin-Layer Chromatography (TLC) and UV-densitometry (TLC@UV) specifically developed for the separation and detection of three carbohydrates namely sucrose, glucose and fructose. Separation was performed on TLC silica gel 60 F254 plates impregnated with sodium bisulphate and citrate and heated prior to development. This fast and easy separation was performed with two successive developments using ACN/H 2 O 80/20 (v/v) as mobile phase. Sensitive and repeatable derivatization of sugars was achieved by dipping the plates in a solution of 4-aminobenzoic acid. Quantification was performed by UV-detection. The method was validated according to ICH guidelines Q2(R1) in terms of specificity, limits of detection and quantification, precision and robustness (with n=3 replicates and CV ≤10%). The characterization of BfrA reaction kinetic was performed by monitoring the accumulation of either glucose or fructose detected by TLC@UV. Hydrolysis of sucrose was described by the Michaelis-Menten kinetic parameters (K M ; V max ) respectively equal to 63.09±7.590mM; 0.037±0.00094mM/min using glucose production and 83.01±14.39mM; 0.031±0.0021mM/min monitoring fructose. Hydrolyses of three alternative substrates, raffinose, stachyose and inulin, were also compared and the regiospecificity of the reaction was characterized. This TLC@UV method is shown to be suitable for the refined kinetic analysis of different reactions related to the hydrolysis of sugars. Copyright © 2016. Published by Elsevier B.V.

LSENS - GENERAL CHEMICAL KINETICS AND SENSITIVITY ANALYSIS CODE

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1994-01-01

LSENS has been developed for solving complex, homogeneous, gas-phase, chemical kinetics problems. The motivation for the development of this program is the continuing interest in developing detailed chemical reaction mechanisms for complex reactions such as the combustion of fuels and pollutant formation and destruction. A reaction mechanism is the set of all elementary chemical reactions that are required to describe the process of interest. Mathematical descriptions of chemical kinetics problems constitute sets of coupled, nonlinear, first-order ordinary differential equations (ODEs). The number of ODEs can be very large because of the numerous chemical species involved in the reaction mechanism. Further complicating the situation are the many simultaneous reactions needed to describe the chemical kinetics of practical fuels. For example, the mechanism describing the oxidation of the simplest hydrocarbon fuel, methane, involves over 25 species participating in nearly 100 elementary reaction steps. Validating a chemical reaction mechanism requires repetitive solutions of the governing ODEs for a variety of reaction conditions. Analytical solutions to the systems of ODEs describing chemistry are not possible, except for the simplest cases, which are of little or no practical value. Consequently, there is a need for fast and reliable numerical solution techniques for chemical kinetics problems. In addition to solving the ODEs describing chemical kinetics, it is often necessary to know what effects variations in either initial condition values or chemical reaction mechanism parameters have on the solution. Such a need arises in the development of reaction mechanisms from experimental data. The rate coefficients are often not known with great precision and in general, the experimental data are not sufficiently detailed to accurately estimate the rate coefficient parameters. The development of a reaction mechanism is facilitated by a systematic sensitivity analysis which provides the relationships between the predictions of a kinetics model and the input parameters of the problem. LSENS provides for efficient and accurate chemical kinetics computations and includes sensitivity analysis for a variety of problems, including nonisothermal conditions. LSENS replaces the previous NASA general chemical kinetics codes GCKP and GCKP84. LSENS is designed for flexibility, convenience and computational efficiency. A variety of chemical reaction models can be considered. The models include static system, steady one-dimensional inviscid flow, reaction behind an incident shock wave including boundary layer correction, and the perfectly stirred (highly backmixed) reactor. In addition, computations of equilibrium properties can be performed for the following assigned states, enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. For static problems LSENS computes sensitivity coefficients with respect to the initial values of the dependent variables and/or the three rates coefficient parameters of each chemical reaction. To integrate the ODEs describing chemical kinetics problems, LSENS uses the packaged code LSODE, the Livermore Solver for Ordinary Differential Equations, because it has been shown to be the most efficient and accurate code for solving such problems. The sensitivity analysis computations use the decoupled direct method, as implemented by Dunker and modified by Radhakrishnan. This method has shown greater efficiency and stability with equal or better accuracy than other methods of sensitivity analysis. LSENS is written in FORTRAN 77 with the exception of the NAMELIST extensions used for input. While this makes the code fairly machine independent, execution times on IBM PC compatibles would be unacceptable to most users. LSENS has been successfully implemented on a Sun4 running SunOS and a DEC VAX running VMS. With minor modifications, it should also be easily implemented on other platforms with FORTRAN compilers which support NAMELIST input. LSENS required 4Mb of RAM under SunOS 4.1.1 and 3.4Mb of RAM under VMS 5.5.1. The standard distribution medium for LSENS is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. It is also available on a 1600 BPI 9-track magnetic tape or a TK50 tape cartridge in DEC VAX BACKUP format. Alternate distribution media and formats are available upon request. LSENS was developed in 1992.

A gas-kinetic BGK scheme for the compressible Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Xu, Kun

2000-01-01

This paper presents an improved gas-kinetic scheme based on the Bhatnagar-Gross-Krook (BGK) model for the compressible Navier-Stokes equations. The current method extends the previous gas-kinetic Navier-Stokes solver developed by Xu and Prendergast by implementing a general nonequilibrium state to represent the gas distribution function at the beginning of each time step. As a result, the requirement in the previous scheme, such as the particle collision time being less than the time step for the validity of the BGK Navier-Stokes solution, is removed. Therefore, the applicable regime of the current method is much enlarged and the Navier-Stokes solution can be obtained accurately regardless of the ratio between the collision time and the time step. The gas-kinetic Navier-Stokes solver developed by Chou and Baganoff is the limiting case of the current method, and it is valid only under such a limiting condition. Also, in this paper, the appropriate implementation of boundary condition for the kinetic scheme, different kinetic limiting cases, and the Prandtl number fix are presented. The connection among artificial dissipative central schemes, Godunov-type schemes, and the gas-kinetic BGK method is discussed. Many numerical tests are included to validate the current method.

Impedance Analysis of Ion Transport Through Supported Lipid Membranes Doped with Ionophores: A New Kinetic Approach

PubMed Central

Alvarez, P. E.; Vallejo, A. E.

2008-01-01

Kinetics of facilitated ion transport through planar bilayer membranes are normally analyzed by electrical conductance methods. The additional use of electrical relaxation techniques, such as voltage jump, is necessary to evaluate individual rate constants. Although electrochemical impedance spectroscopy is recognized as the most powerful of the available electric relaxation techniques, it has rarely been used in connection with these kinetic studies. According to the new approach presented in this work, three steps were followed. First, a kinetic model was proposed that has the distinct quality of being general, i.e., it properly describes both carrier and channel mechanisms of ion transport. Second, the state equations for steady-state and for impedance experiments were derived, exhibiting the input–output representation pertaining to the model’s structure. With the application of a method based on the similarity transformation approach, it was possible to check that the proposed mechanism is distinguishable, i.e., no other model with a different structure exhibits the same input–output behavior for any input as the original. Additionally, the method allowed us to check whether the proposed model is globally identifiable (i.e., whether there is a single set of fit parameters for the model) when analyzed in terms of its impedance response. Thus, our model does not represent a theoretical interpretation of the experimental impedance but rather constitutes the prerequisite to select this type of experiment in order to obtain optimal kinetic identification of the system. Finally, impedance measurements were performed and the results were fitted to the proposed theoretical model in order to obtain the kinetic parameters of the system. The successful application of this approach is exemplified with results obtained for valinomycin–K+ in lipid bilayers supported onto gold substrates, i.e., an arrangement capable of emulating biological membranes. PMID:19669528

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

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.

Poster — Thur Eve — 44: Linearization of Compartmental Models for More Robust Estimates of Regional Hemodynamic, Metabolic and Functional Parameters using DCE-CT/PET Imaging

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

Blais, AR; Dekaban, M; Lee, T-Y

2014-08-15

Quantitative analysis of dynamic positron emission tomography (PET) data usually involves minimizing a cost function with nonlinear regression, wherein the choice of starting parameter values and the presence of local minima affect the bias and variability of the estimated kinetic parameters. These nonlinear methods can also require lengthy computation time, making them unsuitable for use in clinical settings. Kinetic modeling of PET aims to estimate the rate parameter k{sub 3}, which is the binding affinity of the tracer to a biological process of interest and is highly susceptible to noise inherent in PET image acquisition. We have developed linearized kineticmore » models for kinetic analysis of dynamic contrast enhanced computed tomography (DCE-CT)/PET imaging, including a 2-compartment model for DCE-CT and a 3-compartment model for PET. Use of kinetic parameters estimated from DCE-CT can stabilize the kinetic analysis of dynamic PET data, allowing for more robust estimation of k{sub 3}. Furthermore, these linearized models are solved with a non-negative least squares algorithm and together they provide other advantages including: 1) only one possible solution and they do not require a choice of starting parameter values, 2) parameter estimates are comparable in accuracy to those from nonlinear models, 3) significantly reduced computational time. Our simulated data show that when blood volume and permeability are estimated with DCE-CT, the bias of k{sub 3} estimation with our linearized model is 1.97 ± 38.5% for 1,000 runs with a signal-to-noise ratio of 10. In summary, we have developed a computationally efficient technique for accurate estimation of k{sub 3} from noisy dynamic PET data.« less

Comparative evaluation of sorption kinetics and isotherms of pyrene onto microplastics.

PubMed

Wang, Wenfeng; Wang, Jun

2018-02-01

Concerns regarding microplastics pollution and their potential to concentrate and transport organic contaminants in aquatic environments are growing in recent years. Sorption of organic chemicals by microplastics may affect the distribution and bioavailability of the chemicals. Here sorption process of pyrene (Pyr), a frequently encountered polycyclic aromatic hydrocarbon in aquatic environments, on three types of mass-produced plastic particles (high-density polyethylene (PE), polystyrene (PS) and polyvinylchloride (PVC)), was investigated by comparative analysis of different sorption kinetic and isotherm models. Optimum kinetic and isotherm models were predicted by the linear least-squares regression method. The pseudo-second-order kinetic model was more appropriate in describing the entire sorption process (R 2  > 0.99). Sorption rates of Pyr onto microplastics were mainly controlled by intraparticle diffusion. PE exhibited the highest affinity for Pyr, followed by PS and PVC. The sorption equilibrium data were best fitted to the Langmuir isotherm (R 2  > 0.99), indicating monolayer coverage of Pyr onto the microplastics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kinetic analysis of an anion exchange absorbent for CO2 capture from ambient air.

PubMed

Shi, Xiaoyang; Li, Qibin; Wang, Tao; Lackner, Klaus S

2017-01-01

This study reports a preparation method of a new moisture swing sorbent for CO2 capture from air. The new sorbent components include ion exchange resin (IER) and polyvinyl chloride (PVC) as a binder. The IER can absorb CO2 when surrounding is dry and release CO2 when surrounding is wet. The manuscript presents the studies of membrane structure, kinetic model of absorption process, performance of desorption process and the diffusivity of water molecules in the CO2 absorbent. It has been proved that the kinetic performance of CO2 absorption/desorption can be improved by using thin binder and hot water treatment. The fast kinetics of P-100-90C absorbent is due to the thin PVC binder, and high diffusion rate of H2O molecules in the sample. The impressive is this new CO2 absorbent has the fastest CO2 absorption rate among all absorbents which have been reported by other up-to-date literatures.

Kinetic analysis of an anion exchange absorbent for CO2 capture from ambient air

PubMed Central

Shi, Xiaoyang; Li, Qibin; Lackner, Klaus S.

2017-01-01

This study reports a preparation method of a new moisture swing sorbent for CO2 capture from air. The new sorbent components include ion exchange resin (IER) and polyvinyl chloride (PVC) as a binder. The IER can absorb CO2 when surrounding is dry and release CO2 when surrounding is wet. The manuscript presents the studies of membrane structure, kinetic model of absorption process, performance of desorption process and the diffusivity of water molecules in the CO2 absorbent. It has been proved that the kinetic performance of CO2 absorption/desorption can be improved by using thin binder and hot water treatment. The fast kinetics of P-100-90C absorbent is due to the thin PVC binder, and high diffusion rate of H2O molecules in the sample. The impressive is this new CO2 absorbent has the fastest CO2 absorption rate among all absorbents which have been reported by other up-to-date literatures. PMID:28640914

Real Time Computation of Kinetic Constraints to Support Equilibrium Reconstruction

NASA Astrophysics Data System (ADS)

Eggert, W. J.; Kolemen, E.; Eldon, D.

2016-10-01

A new method for quickly and automatically applying kinetic constraints to EFIT equilibrium reconstructions using readily available data is presented. The ultimate goal is to produce kinetic equilibrium reconstructions in real time and use them to constrain the DCON stability code as part of a disruption avoidance scheme. A first effort presented here replaces CPU-time expensive modules, such as the fast ion pressure profile calculation, with a simplified model. We show with a DIII-D database analysis that we can achieve reasonable predictions for selected applications by modeling the fast ion pressure profile and determining the fit parameters as functions of easily measured quantities including neutron rate and electron temperature on axis. Secondly, we present a strategy for treating Thomson scattering and Charge Exchange Recombination data to automatically form constraints for a kinetic equilibrium reconstruction, a process that historically was performed by hand. Work supported by US DOE DE-AC02-09CH11466 and DE-FC02-04ER54698.

Gait Analysis Methods for Rodent Models of Arthritic Disorders: Reviews and Recommendations

PubMed Central

Lakes, Emily H.; Allen, Kyle D.

2016-01-01

Gait analysis is a useful tool to understand behavioral changes in preclinical arthritis models. While observational scoring and spatiotemporal gait parameters are the most widely performed gait analyses in rodents, commercially available systems can now provide quantitative assessments of spatiotemporal patterns. However, inconsistencies remain between testing platforms, and laboratories often select different gait pattern descriptors to report in the literature. Rodent gait can also be described through kinetic and kinematic analyses, but systems to analyze rodent kinetics and kinematics are typically custom made and often require sensitive, custom equipment. While the use of rodent gait analysis rapidly expands, it is important to remember that, while rodent gait analysis is a relatively modern behavioral assay, the study of quadrupedal gait is not new. Nearly all gait parameters are correlated, and a collection of gait parameters is needed to understand a compensatory gait pattern used by the animal. As such, a change in a single gait parameter is unlikely to tell the full biomechanical story; and to effectively use gait analysis, one must consider how multiple different parameters contribute to an altered gait pattern. The goal of this article is to review rodent gait analysis techniques and provide recommendations on how to use these technologies in rodent arthritis models, including discussions on the strengths and limitations of observational scoring, spatiotemporal, kinetic, and kinematic measures. Recognizing rodent gait analysis is an evolving tool, we also provide technical recommendations we hope will improve the utility of these analyses in the future. PMID:26995111

Thermal decomposition and kinetic evaluation of decanted 2,4,6-trinitrotoluene (TNT) for reutilization as composite material

NASA Astrophysics Data System (ADS)

Ahmed, M. F.; Hussain, A.; Malik, A. Q.

2016-08-01

Use of energetic materials has long been considered for only military purposes. However, it is very recent that their practical applications in wide range of commercial fields such as mining, road building, under water blasting and rocket propulsion system have been considered. About 5mg of 2,4,6-trinitrotoluene (TNT) in serviceable (Svc) as well as unserviceable (Unsvc) form were used for their thermal decomposition and kinetic parameters investigation. Thermogravimetric/ differential thermal analysis (TG/DTA), X-ray diffraction (XRD) and Scanning electron microscope (SEM) were used to characterize two types of TNT. Arrhenius kinetic parameters like activation energy (E) and enthalpy (AH) of both TNT samples were determined using TG curves with the help of Horowitz and Metzger method. Simultaneously, thermal decomposition range was evaluated from DTA curves. Distinct diffraction peaks showing crystalline nature were obtained from XRD analysis. SEM results indicated that Unsvc TNT contained a variety of defects like cracks and porosity. Similarly, it is observed that thermal as well as kinetic behavior of both TNT samples vary to a great extent. Likewise, a prominent change in the activation energies (E) of both samples is observed. This in-depth study provides a way forward in finding solutions for the safe reutilization of decanted TNT.

Pyrolysis kinetics and thermal behavior of waste sawdust biomass using thermogravimetric analysis.

PubMed

Mishra, Ranjeet Kumar; Mohanty, Kaustubha

2018-03-01

The present study reports pyrolysis behavior of three waste biomass using thermogravimetric analysis to determine kinetic parameters at five different heating rates. Physiochemical characterization confirmed that these biomass have the potential for fuel and energy production. Pyrolysis experiments were carried out at five different heating rates (5-25 °C min -1 ). Five model-free methods such as Kissinger-Akahira-Sunose (KAS), Ozawa-Flynn-Wall (OFW), Friedman, Coats-Redfern, and distributed activation energy (DAEM) were used to calculate the kinetic parameters. The activation energy was found to be 171.66 kJ mol -1 , 148.44 kJ mol -1 , and 171.24 kJ mol -1 from KAS model; 179.29 kJ mol -1 , 156.58 kJ mol -1 , and 179.47 kJ mol -1 from OFW model; 168.58 kJ mol -1 , 181.53 kJ mol -1 , and 184.61 kJ mol -1 from Friedman model; and 206.62 kJ mol -1 , 171.63 kJ mol -1 , and 160.45 kJ mol -1 from DAEM model for PW, SW, AN biomass respectively. The calculated kinetic parameters are in good agreement with other reported biomass. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pyrolysis characteristics and kinetics of acid tar waste from crude benzol refining: A thermogravimetry-mass spectrometry analysis.

PubMed

Chihobo, Chido H; Chowdhury, Arindrajit; Kuipa, Pardon K; Simbi, David J

2016-12-01

Pyrolysis is an attractive thermochemical conversion technology that may be utilised as a safe disposal option for acid tar waste. The kinetics of acid tar pyrolysis were investigated using thermogravimetry coupled with mass spectrometry under a nitrogen atmosphere at different heating rates of 10, 15 and 20 K min -1 The thermogravimetric analysis shows three major reaction peaks centred around 178 °C, 258 °C, and 336 °C corresponding to the successive degradation of water soluble lower molecular mass sulphonic acids, sulphonated high molecular mass hydrocarbons, and high molecular mass hydrocarbons. The kinetic parameters were evaluated using the iso-conversional Kissinger-Akahira-Sunose method. A variation in the activation energy with conversion revealed that the pyrolysis of the acid tar waste progresses through complex multi-step kinetics. Mass spectrometry results revealed a predominance of gases such as hydrogen, methane and carbon monoxide, implying that the pyrolysis of acid tar waste is potentially an energy source. Thus the pyrolysis of acid tar waste may present a viable option for its environmental treatment. There are however, some limitations imposed by the co-evolution of corrosive gaseous components for which appropriate considerations must be provided in both pyrolysis reactor design and selection of construction materials. © The Author(s) 2016.

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.

Looking towards label-free biomolecular interaction analysis in a high-throughput format: a review of new surface plasmon resonance technologies.

PubMed

Boozer, Christina; Kim, Gibum; Cong, Shuxin; Guan, Hannwen; Londergan, Timothy

2006-08-01

Surface plasmon resonance (SPR) biosensors have enabled a wide range of applications in which researchers can monitor biomolecular interactions in real time. Owing to the fact that SPR can provide affinity and kinetic data, unique features in applications ranging from protein-peptide interaction analysis to cellular ligation experiments have been demonstrated. Although SPR has historically been limited by its throughput, new methods are emerging that allow for the simultaneous analysis of many thousands of interactions. When coupled with new protein array technologies, high-throughput SPR methods give users new and improved methods to analyze pathways, screen drug candidates and monitor protein-protein interactions.

Efficient use of single molecule time traces to resolve kinetic rates, models and uncertainties

NASA Astrophysics Data System (ADS)

Schmid, Sonja; Hugel, Thorsten

2018-03-01

Single molecule time traces reveal the time evolution of unsynchronized kinetic systems. Especially single molecule Förster resonance energy transfer (smFRET) provides access to enzymatically important time scales, combined with molecular distance resolution and minimal interference with the sample. Yet the kinetic analysis of smFRET time traces is complicated by experimental shortcomings—such as photo-bleaching and noise. Here we recapitulate the fundamental limits of single molecule fluorescence that render the classic, dwell-time based kinetic analysis unsuitable. In contrast, our Single Molecule Analysis of Complex Kinetic Sequences (SMACKS) considers every data point and combines the information of many short traces in one global kinetic rate model. We demonstrate the potential of SMACKS by resolving the small kinetic effects caused by different ionic strengths in the chaperone protein Hsp90. These results show an unexpected interrelation between conformational dynamics and ATPase activity in Hsp90.

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.

Growth of non-toxigenic Clostridium botulinum mutant LNT01 in cooked beef: One-step kinetic analysis and comparison with C. sporogenes and C. perfringens.

PubMed

Huang, Lihan

2018-05-01

The objective of this study was to investigate the growth kinetics of Clostridium botulinum LNT01, a non-toxigenic mutant of C. botulinum 62A, in cooked ground beef. The spores of C. botulinum LNT01 were inoculated to ground beef and incubated anaerobically under different temperature conditions to observe growth and develop growth curves. A one-step kinetic analysis method was used to analyze the growth curves simultaneously to minimize the global residual error. The data analysis was performed using the USDA IPMP-Global Fit, with the Huang model as the primary model and the cardinal parameters model as the secondary model. The results of data analysis showed that the minimum, optimum, and maximum growth temperatures of this mutant are 11.5, 36.4, and 44.3 °C, and the estimated optimum specific growth rate is 0.633 ln CFU/g per h, or 0.275 log CFU/g per h. The maximum cell density is 7.84 log CFU/g. The models and kinetic parameters were validated using additional isothermal and dynamic growth curves. The resulting residual errors of validation followed a Laplace distribution, with about 60% of the residual errors within ±0.5 log CFU/g of experimental observations, suggesting that the models could predict the growth of C. botulinum LNT01 in ground beef with reasonable accuracy. Comparing with C. perfringens, C. botulinum LNT01 grows at much slower rates and with much longer lag times. Its growth kinetics is also very similar to C. sporogenes in ground beef. The results of computer simulation using kinetic models showed that, while prolific growth of C. perfringens may occur in ground beef during cooling, no growth of C. botulinum LNT01 or C. sporogenes would occur under the same cooling conditions. The models developed in this study may be used for prediction of the growth and risk assessments of proteolytic C. botulinum in cooked meats. Published by Elsevier Ltd.

Intrinsic noise analyzer: a software package for the exploration of stochastic biochemical kinetics using the system size expansion.

PubMed

Thomas, Philipp; Matuschek, Hannes; Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen's system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA's performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license.

Intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion

PubMed Central

Grima, Ramon

2012-01-01

The accepted stochastic descriptions of biochemical dynamics under well-mixed conditions are given by the Chemical Master Equation and the Stochastic Simulation Algorithm, which are equivalent. The latter is a Monte-Carlo method, which, despite enjoying broad availability in a large number of existing software packages, is computationally expensive due to the huge amounts of ensemble averaging required for obtaining accurate statistical information. The former is a set of coupled differential-difference equations for the probability of the system being in any one of the possible mesoscopic states; these equations are typically computationally intractable because of the inherently large state space. Here we introduce the software package intrinsic Noise Analyzer (iNA), which allows for systematic analysis of stochastic biochemical kinetics by means of van Kampen’s system size expansion of the Chemical Master Equation. iNA is platform independent and supports the popular SBML format natively. The present implementation is the first to adopt a complementary approach that combines state-of-the-art analysis tools using the computer algebra system Ginac with traditional methods of stochastic simulation. iNA integrates two approximation methods based on the system size expansion, the Linear Noise Approximation and effective mesoscopic rate equations, which to-date have not been available to non-expert users, into an easy-to-use graphical user interface. In particular, the present methods allow for quick approximate analysis of time-dependent mean concentrations, variances, covariances and correlations coefficients, which typically outperforms stochastic simulations. These analytical tools are complemented by automated multi-core stochastic simulations with direct statistical evaluation and visualization. We showcase iNA’s performance by using it to explore the stochastic properties of cooperative and non-cooperative enzyme kinetics and a gene network associated with circadian rhythms. The software iNA is freely available as executable binaries for Linux, MacOSX and Microsoft Windows, as well as the full source code under an open source license. PMID:22723865

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.

Recovery of nickel and cobalt as MHP from limonitic ore leaching solution: Kinetics analysis and precipitate characterization

NASA Astrophysics Data System (ADS)

Safitri, Nina; Mubarok, M. Zaki; Winarko, Ronny; Tanlega, Zela

2018-05-01

In the present study, precipitation of nickel and cobalt as mixed hydroxide precipitate (MHP) from pregnant leach solution of nickel limonite ore from Soroako after iron removal stage was carried out. A series of MHP precipitation experiments was conducted by using MgO slurry as neutralizing agent and the effects of pH, temperature, duration of precipitation and the addition of MHP seed on the precipitation behavior of nickel, cobalt, as well as iron and manganese was studied. Characterization of MHP product was performed by particle size analyzer (PSA) as well as X-Ray Fluorescence (XRF), X-Ray Diffractometer (XRD) and Scanning Electron Microscope (SEM) analyses. Kinetics analysis was made by using differential-integral method for the rate of homogenous reaction. Precipitation at pH 7, temperature 50°C for 30 minute, without seed addition resulted in nickel and cobalt recoveries of 82.8% and 92%, respectively with co-precipitated iron and manganese of 70% and 24.2%, respectively. The seed addition increases nickel and cobalt precipitations significantly to 99.9% and 99.1%, respectively. However, the addition of seed into led to a significant increase of manganese co-precipitation from 24.2% without seed addition to 39.5% at the addition of 1 g seed per 200 mL of PLS. Kinetics analysis revealed that Ni precipitation to form MHP follows the second-order reaction kinetics with activation energy of 94.6 kJ/mol.

Near-wall turbulence model and its application to fully developed turbulent channel and pipe flows

NASA Technical Reports Server (NTRS)

Kim, S.-W.

1990-01-01

A near-wall turbulence model and its incorporation into a multiple-timescale turbulence model are presented. The near-wall turbulence model is obtained from a k-equation turbulence model and a near-wall analysis. In the method, the equations for the conservation of mass, momentum, and turbulent kinetic energy are integrated up to the wall, and the energy transfer and the dissipation rates inside the near-wall layer are obtained from algebraic equations. Fully developed turbulent channel and pipe flows are solved using a finite element method. The computational results compare favorably with experimental data. It is also shown that the turbulence model can resolve the overshoot phenomena of the turbulent kinetic energy and the dissipation rate in the region very close to the wall.

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Prediction of free turbulent mixing using a turbulent kinetic energy method

NASA Technical Reports Server (NTRS)

Harsha, P. T.

1973-01-01

Free turbulent mixing of two-dimensional and axisymmetric one- and two-stream flows is analyzed by a relatively simple turbulent kinetic energy method. This method incorporates a linear relationship between the turbulent shear and the turbulent kinetic energy and an algebraic relationship for the length scale appearing in the turbulent kinetic energy equation. Good results are obtained for a wide variety of flows. The technique is shown to be especially applicable to flows with heat and mass transfer, for which nonunity Prandtl and Schmidt numbers may be assumed.

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.

Multiensemble Markov models of molecular thermodynamics and kinetics.

PubMed

Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank

2016-06-07

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models-clustering of high-dimensional spaces and modeling of complex many-state systems-with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein-ligand binding model.

Multiensemble Markov models of molecular thermodynamics and kinetics

PubMed Central

Wu, Hao; Paul, Fabian; Noé, Frank

2016-01-01

We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model. PMID:27226302

Discrete kinetic models from funneled energy landscape simulations.

PubMed

Schafer, Nicholas P; Hoffman, Ryan M B; Burger, Anat; Craig, Patricio O; Komives, Elizabeth A; Wolynes, Peter G

2012-01-01

A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.

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.

An Analysis Method for Superconducting Resonator Parameter Extraction with Complex Baseline Removal

NASA Technical Reports Server (NTRS)

Cataldo, Giuseppe

2014-01-01

A new semi-empirical model is proposed for extracting the quality (Q) factors of arrays of superconducting microwave kinetic inductance detectors (MKIDs). The determination of the total internal and coupling Q factors enables the computation of the loss in the superconducting transmission lines. The method used allows the simultaneous analysis of multiple interacting discrete resonators with the presence of a complex spectral baseline arising from reflections in the system. The baseline removal allows an unbiased estimate of the device response as measured in a cryogenic instrumentation setting.

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.

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.

Evolving cell models for systems and synthetic biology.

PubMed

Cao, Hongqing; Romero-Campero, Francisco J; Heeb, Stephan; Cámara, Miguel; Krasnogor, Natalio

2010-03-01

This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm's results as well as of the resulting evolved cell models.

Synthesis and characterization of sulfur functionalized graphene oxide nanosheets as efficient sorbent for removal of Pb2+, Cd2+, Ni2+ and Zn2+ ions from aqueous solution: A combined thermodynamic and kinetic studies

NASA Astrophysics Data System (ADS)

Pirveysian, Mahtab; Ghiaci, Mehran

2018-01-01

A very simple, one pot method was used for preparation of sulfur functionalized graphene oxide (GO-SOxR) with sodium sulfide and water in reflux condition. The elemental analysis data showed high sulfur content up to 15%. EDS and XPS analysis also proved introduction of sulfur element. To make the sorbent more efficient operationally, the GO-SOxR was coated with a mesoporous shell of TiO2 or SiO2. The prepared sorbents were characterized by SEM, TEM, TGA, XPS, XRD, IR and EDS. GO-SOxR@TiO2 and GO-SOxR@SiO2 composites were tested for removal of Pb(II), Cd(II), Ni(II) and Zn(II) as heavy metal ions from aqueous solution in batch method. Adsorption of the heavy metal ions was studied kinetically, and the adsorption capacities of GO-SOxR, GO-SOxR@TiO2, and GO-SOxR@SiO2 were evaluated using equilibrium adsorption isotherms, and compared to other adsorbents used for removal of these heavy metals. Kinetic studies showed that the experimental data was fitted with pseudo second order model. The adsorption capacity of GO was significantly improved by sulfur functionalization and TiO2 coating.

Kinetics and mechanism of hydroxyapatite crystal dissolution in weak acid buffers using the rotating disk method.

PubMed

Wu, M S; Higuchi, W I; Fox, J L; Friedman, M

1976-01-01

The model given in this report and the rotating disk method provide a useful combination in the study of dental enamel and hydroxyapatite dissolution kinetics. The present approach is a significant improvement over earlier studies, and both the ionic activity product that governs the dissolution reaction and the apparent surface dissolution reaction rate constant may be simultaneously obtained. Thus, these investigations have established the baseline for the dissolution rate studies under sink conditions. Concurrent studies, under conditions where the acidic buffer mediums are partially saturated with respect to hydroxyapatite have shown another dissolution site for hydroxyapatite that operates at a higher ionic activity product but has a much smaller apparent surface reaction rate constant. This has raised the question of whether the presence of this second site may interfere with the proper theoretical analysis of the experimental results obtained under sink conditions. A preliminary analysis of the two-site model has shown that the dissolution kinetics of hydroxyapatite under sink conditions is almost completely governed by the sink condition site (KHAP = 10(-124.5), k' = 174) established in this report. The difference between the predicted dissolution rate for the one-site model and the two-site model are generally of the order of 4 to 5% where the experiments are conducted under sink conditions and over the range of variables covered in the present study.

Constrained Analysis of Fluorescence Anisotropy Decay:Application to Experimental Protein Dynamics

PubMed Central

Feinstein, Efraim; Deikus, Gintaras; Rusinova, Elena; Rachofsky, Edward L.; Ross, J. B. Alexander; Laws, William R.

2003-01-01

Hydrodynamic properties as well as structural dynamics of proteins can be investigated by the well-established experimental method of fluorescence anisotropy decay. Successful use of this method depends on determination of the correct kinetic model, the extent of cross-correlation between parameters in the fitting function, and differences between the timescales of the depolarizing motions and the fluorophore's fluorescence lifetime. We have tested the utility of an independently measured steady-state anisotropy value as a constraint during data analysis to reduce parameter cross correlation and to increase the timescales over which anisotropy decay parameters can be recovered accurately for two calcium-binding proteins. Mutant rat F102W parvalbumin was used as a model system because its single tryptophan residue exhibits monoexponential fluorescence intensity and anisotropy decay kinetics. Cod parvalbumin, a protein with a single tryptophan residue that exhibits multiexponential fluorescence decay kinetics, was also examined as a more complex model. Anisotropy decays were measured for both proteins as a function of solution viscosity to vary hydrodynamic parameters. The use of the steady-state anisotropy as a constraint significantly improved the precision and accuracy of recovered parameters for both proteins, particularly for viscosities at which the protein's rotational correlation time was much longer than the fluorescence lifetime. Thus, basic hydrodynamic properties of larger biomolecules can now be determined with more precision and accuracy by fluorescence anisotropy decay. PMID:12524313

Thermochemistry and kinetics for 2-butanone-1-yl radical (CH2·C(═O)CH2CH3) reactions with O2.

PubMed

Sebbar, N; Bozzelli, J W; Bockhorn, H

2014-01-09

Thermochemistry of reactants, intermediates, transition state structures, and products along with kinetics on the association of CH2·C(═O)CH2CH3 (2-butanone-1-yl) with O2 and dissociation of the peroxy adduct isomers are studied. Thermochemical properties are determined using ab initio (G3MP2B3 and G3) composite methods along with density functional theory (B3LYP/6-311g(d,p)). Entropy and heat capacity contributions versus temperature are determined from structures, vibration frequencies, and internal rotor potentials. The CH2·C(═O)CH2CH3 radical + O2 association results in a chemically activated peroxy radical with 27 kcal mol(-1) excess of energy. The chemically activated adduct can react to stabilized peroxy or hydroperoxide alkyl radical adducts, further react to lactones plus hydroxyl radical, or form olefinic ketones and a hydroperoxy radical. Kinetic parameters are determined from the G3 composite methods derived thermochemical parameters, and quantum Rice-Ramsperger-Kassel (QRRK) analysis to calculate k(E) with master equation analysis to evaluate falloff in the chemically activated and dissociation reactions. One new, not previously reported, peroxy chemistry reaction is presented. It has a low barrier path and involves a concerted reaction resulting in olefin formation, H2O elimination, and an alkoxy radical.

Quantification of metabotropic glutamate subtype 5 receptors in the brain by an equilibrium method using 18F-SP203.

PubMed

Kimura, Yasuyuki; Siméon, Fabrice G; Zoghbi, Sami S; Zhang, Yi; Hatazawa, Jun; Pike, Victor W; Innis, Robert B; Fujita, Masahiro

2012-02-01

A new PET ligand, 3-fluoro-5-(2-(2-(18)F-(fluoromethyl)-thiazol-4-yl)ethynyl)benzonitrile (18F-SP203) can quantify metabotropic glutamate subtype 5 receptors (mGluR5) in human brain by a bolus injection and kinetic modeling. As an alternative approach to a bolus injection, binding can simply be measured as a ratio of tissue to metabolite-corrected plasma at a single time point under equilibrium conditions achieved by administering the radioligand with a bolus injection followed by a constant infusion. The purpose of this study was to validate the equilibrium method as an alternative to the standard kinetic method for measuring 18F-SP203 binding in the brain. Nine healthy subjects were injected with 18F-SP203 using a bolus plus constant infusion for 300 min. A single ratio of bolus-to-constant infusion (the activity of bolus equaled to that of infusion over 219 min) was applied to all subjects to achieve equilibrium in approximately 120 min. As a measure of ligand binding, we compared total distribution volume (VT) calculated by the equilibrium and kinetic methods in each scan. The equilibrium method calculated VT by the ratio of radioactivity in the brain to the concentration of 18F-SP203 in arterial plasma at 120 min, and the kinetic method calculated VT by a two-tissue compartment model using brain and plasma dynamic data from 0 to 120 min. VT obtained via the equilibrium method was highly correlated with VT obtained via kinetic modeling. Inter-subject variability of VT obtained via the equilibrium method was slightly smaller than VT obtained via the kinetic method. VT obtained via the equilibrium method was ~10% higher than VT obtained via the kinetic method, indicating a small difference between the measurements. Taken together, the results of this study show that using the equilibrium method is an acceptable alternative to the standard kinetic method when using 18F-SP203 to measure mGluR5. Although small differences in the measurements obtained via the equilibrium and kinetic methods exist, both methods consistently measured mGluR5 as indicated by the highly correlated VT values; the equilibrium method was slightly more precise, as indirectly measured by the smaller coefficient of variability across subjects. In addition, when using 18F-SP203, the equilibrium method is more efficient because it requires much less data. Copyright © 2011. Published by Elsevier Inc.

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.

[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.

Effects of low molecular sugars on the retrogradation of tapioca starch gels during storage

PubMed Central

Li, Rongfang; Kang, Huaibin; Luo, Denglin; Fan, Jinling; Zhu, Wenxue; Liu, Xinfang; Tong, Qunyi

2017-01-01

The effects of low molecular sugars (sucrose, glucose and trehalose) on the retrogradation of tapioca starch (TS) gels stored at 4°C for different periods were examined with different methods. Decrease in melting enthalpy (ΔHmelt) were obtained through differential scanning calorimetry analysis. Analysis of decrease in crystallization rate constant (k) and increase in semi-crystallization time (τ1/2) results obtained from retrogradation kinetics indicated that low molecular sugars could retard the retrogradation of TS gels and further revealed trehalose as the best inhibitor among the sugars used in this study. Fourier transform infrared (FTIR) analysis indicated that the intensity ratio of 1047 to 1022 cm−1 was increased with the addition of sugars in the order of trehalose > sucrose > glucose. Decrease in hardness parameters and increase in springiness parameters obtained from texture profile analysis (TPA) analysis also indicated that low molecular sugars could retard the retrogradation of TS gels. The results of FTIR and TPA showed a consistent sugar effect on starch retrogradation with those of DSC and retrogradation kinetics analysis. PMID:29284007

Effects of low molecular sugars on the retrogradation of tapioca starch gels during storage.

PubMed

Zhang, Xiaoyu; Li, Rongfang; Kang, Huaibin; Luo, Denglin; Fan, Jinling; Zhu, Wenxue; Liu, Xinfang; Tong, Qunyi

2017-01-01

The effects of low molecular sugars (sucrose, glucose and trehalose) on the retrogradation of tapioca starch (TS) gels stored at 4°C for different periods were examined with different methods. Decrease in melting enthalpy (ΔHmelt) were obtained through differential scanning calorimetry analysis. Analysis of decrease in crystallization rate constant (k) and increase in semi-crystallization time (τ1/2) results obtained from retrogradation kinetics indicated that low molecular sugars could retard the retrogradation of TS gels and further revealed trehalose as the best inhibitor among the sugars used in this study. Fourier transform infrared (FTIR) analysis indicated that the intensity ratio of 1047 to 1022 cm-1 was increased with the addition of sugars in the order of trehalose > sucrose > glucose. Decrease in hardness parameters and increase in springiness parameters obtained from texture profile analysis (TPA) analysis also indicated that low molecular sugars could retard the retrogradation of TS gels. The results of FTIR and TPA showed a consistent sugar effect on starch retrogradation with those of DSC and retrogradation kinetics analysis.

Kinetic analysis of superparamagnetic iron oxide nanoparticles in the liver of body-temperature-controlled mice using dynamic susceptibility contrast magnetic resonance imaging and an empirical mathematical model.

PubMed

Murase, Kenya; Assanai, Purapan; Takata, Hiroshige; Matsumoto, Nozomi; Saito, Shigeyoshi; Nishiura, Motoko

2015-06-01

The purpose of this study was to develop a method for analyzing the kinetic behavior of superparamagnetic iron oxide nanoparticles (SPIONs) in the murine liver under control of body temperature using dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) and an empirical mathematical model (EMM). First, we investigated the influence of body temperature on the kinetic behavior of SPIONs in the liver by controlling body temperature using our temperature-control system. Second, we investigated the kinetic behavior of SPIONs in the liver when mice were injected with various doses of GdCl3, while keeping the body temperature at 36°C. Finally, we investigated it when mice were injected with various doses of zymosan, while keeping the body temperature at 36°C. We also investigated the effect of these substances on the number of Kupffer cells by immunohistochemical analysis using the specific surface antigen of Kupffer cells (CD68). To quantify the kinetic behavior of SPIONs in the liver, we calculated the upper limit of the relative enhancement (A), the rates of early contrast uptake (α) and washout or late contrast uptake (β), the parameter related to the slope of early uptake (q), the area under the curve (AUC), the maximum change of transverse relaxation rate (ΔR2) (ΔR2(max)), the time to ΔR2(max) (Tmax), and ΔR2 at the last time point (ΔR2(last)) from the time courses of ΔR2 using the EMM. The β and Tmax values significantly decreased and increased, respectively, with decreasing body temperature, suggesting that the phagocytic activity of Kupffer cells is significantly affected by body temperature. The AUC, ΔR2(max), and ΔR2(last) values decreased significantly with increasing dose of GdCl3, which was consistent with the change in the number of CD68-positive cells. They increased with increasing dose of zymosan, which was also consistent with the change in the number of CD68-positive cells. These results suggest that AUC, ΔR2(max), and ΔR2(last) reflect the number of Kupffer cells. In conclusion, we presented a method for analyzing the kinetic behavior of SPIONs in the liver using DSC-MRI and EMM, and investigated the influence of body temperature, GdCl3, and zymosan using body-temperature-controlled mice. The present study suggests that control of body temperature is essential for investigating the kinetic behavior of SPIONs in the liver and that our method will be applicable and useful for quantifying the responses of Kupffer cells to various drugs under control of body temperature. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

Engaging Students in Analyzing and Interpreting Data to Construct Mathematical Models: An Analysis of Students' Reasoning in a Method of Initial Rates Task

ERIC Educational Resources Information Center

Becker, Nicole M.; Rupp, Charlie A.; Brandriet, Alexandra

2017-01-01

Models related to the topic of chemical kinetics are critical for predicting and explaining chemical reactivity. Here we present a qualitative study of 15 general chemistry students' reasoning about a method of initial rates task. We asked students to discuss their understanding of the terms rate law and initial rate, and then analyze rate and…

Comparison of three-way and four-way calibration for the real-time quantitative analysis of drug hydrolysis in complex dynamic samples by excitation-emission matrix fluorescence.

PubMed

Yin, Xiao-Li; Gu, Hui-Wen; Liu, Xiao-Lu; Zhang, Shan-Hui; Wu, Hai-Long

2018-03-05

Multiway calibration in combination with spectroscopic technique is an attractive tool for online or real-time monitoring of target analyte(s) in complex samples. However, how to choose a suitable multiway calibration method for the resolution of spectroscopic-kinetic data is a troubling problem in practical application. In this work, for the first time, three-way and four-way fluorescence-kinetic data arrays were generated during the real-time monitoring of the hydrolysis of irinotecan (CPT-11) in human plasma by excitation-emission matrix fluorescence. Alternating normalization-weighted error (ANWE) and alternating penalty trilinear decomposition (APTLD) were used as three-way calibration for the decomposition of the three-way kinetic data array, whereas alternating weighted residual constraint quadrilinear decomposition (AWRCQLD) and alternating penalty quadrilinear decomposition (APQLD) were applied as four-way calibration to the four-way kinetic data array. The quantitative results of the two kinds of calibration models were fully compared from the perspective of predicted real-time concentrations, spiked recoveries of initial concentration, and analytical figures of merit. The comparison study demonstrated that both three-way and four-way calibration models could achieve real-time quantitative analysis of the hydrolysis of CPT-11 in human plasma under certain conditions. However, it was also found that both of them possess some critical advantages and shortcomings during the process of dynamic analysis. The conclusions obtained in this paper can provide some helpful guidance for the reasonable selection of multiway calibration models to achieve the real-time quantitative analysis of target analyte(s) in complex dynamic systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Estimation of Free Radical Ionization Energies by the Kinetic Method and the Relationship between the Kinetic Method and the Hammett Equation.

PubMed

Chen, G; Wong, P; Cooks, R G

1997-09-01

Substituted 1,2-diphenylethanes undergo competitive dissociations upon electron ionization (EI) to generate substituted benzyl cation and benzyl radical pairs. Application of the kinetic method to the previous reported EI mass spectra of these covalently bound precursor ions (data are taken from McLafferty et al. J. Am. Chem. Soc. 1970, 92, 6867)) is used to estimate the ionization energies of substituted benzyl free radicals. A correlation is observed between the Hammett σ constant of the substituents and the kinetic method parameter, ln(k(x)/k(H)), where k(x) is the rate of fragmentation to give the substituted product ion and k(H) is the rate to give the benzyl ion itself. Systems involving weakly bound cluster ions, including proton-bound dimers of meta- and para-substituted pyridines and meta- and para-substituted anilines, and electron-bound dimers of meta- and para-substituted nitrobenzenes, also show good correlations between the kinetic method parameter and the Hammett σ constant.

Nuclear reactor transient analysis via a quasi-static kinetics Monte Carlo method

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

Jo, YuGwon; Cho, Bumhee; Cho, Nam Zin, E-mail: nzcho@kaist.ac.kr

2015-12-31

The predictor-corrector quasi-static (PCQS) method is applied to the Monte Carlo (MC) calculation for reactor transient analysis. To solve the transient fixed-source problem of the PCQS method, fission source iteration is used and a linear approximation of fission source distributions during a macro-time step is introduced to provide delayed neutron source. The conventional particle-tracking procedure is modified to solve the transient fixed-source problem via MC calculation. The PCQS method with MC calculation is compared with the direct time-dependent method of characteristics (MOC) on a TWIGL two-group problem for verification of the computer code. Then, the results on a continuous-energy problemmore » are presented.« less

Photoplasma of optically excited metal vapors

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

Bezuglov, N.N.; Llyucharev, A.N.; Stacewicz, T.

1994-09-01

A wide range of questions associated with various aspects of photoplasma physics is considered. A comprehensive analysis of processes of optical excitation and de-excitation depending on optical characteristics of an absorbing gas medium is given. Analytical methods used for determining the excitation degree of photoresonance plasma in conditions of resonance radiation transfer are described. The accuracy of the Biberman approximation for effective lifetimes in population kinetics of resonance plasma states is analyzed for many experimental conditions. A detailed discussion of primary ionization mechanisms in photoplasma is given; the kinetics of ionization processes is discussed; and systematization of various types ofmore » photoresonance plasma is presented. Basis aspects of the LIBORS model, which is widely used for studying ionization kinetics of laser photoresonance plasma, and its limitations are considered. An ingenious method used to analytically solve a class of decay-type nonlinear problems, which arise for the capture equation in the case of noticeable saturation of a resonance transition by a short laser pulse, is described. A reliable quantitative description of fluorescence decay curve peculiarities that are associated with the bleaching of gases at resonance line frequencies can be obtained by this method. Some possible applications of photoplasma in problems of optics and spectroscopy are considered. 75 refs., 24 figs., 1 tab.« less

Preparation of Monodisperse Biodegradable Polymer Microparticles Using a Microfluidic Flow-focusing Device for Controlled Drug Delivery

PubMed Central

Xu, Qiaobing; Hashimoto, Michinao; Dang, Tram T.; Hoare, Todd; Kohane, Daniel S.; Whitesides, George M.; Langer, Robert; Anderson, Daniel G.

2009-01-01

Degradable microparticles have broad utility as vehicles for drug delivery and form the basis of several FDA-approved therapies. Conventional emulsion-based methods of manufacturing produce particles with a wide range of diameters (and thus kinetics of release) in each batch. This paper describes the fabrication of monodisperse, drug-loaded microparticles from biodegradable polymers using the microfluidic flow-focusing (FF) devices and the drug delivery properties of those particles. Particles were engineered with defined sizes, ranging from 10 μm to 50 μm. These particles were nearly monodisperse (polydispersity index = 3.9 %). We incorporated a model amphiphilic drug (bupivacaine) within the biodegradable matrix of the particles. Kinetic analysis showed that the release of drug from these monodisperse particles was slower than that from conventional methods of the same average size but a broader distribution of sizes and, most importantly, exhibited a significantly lower initial burst than that observed with conventional particles. The difference in the initial kinetics of drug release was attributed to the uniform distribution of drug inside the particles generated using the microfluidic methods. These results demonstrated the utility of microfluidic FF for the generation of homogenous systems of particles for the delivery of drugs. PMID:19296563

Spectral method for a kinetic swarming model

DOE PAGES

Gamba, Irene M.; Haack, Jeffrey R.; Motsch, Sebastien

2015-04-28

Here we present the first numerical method for a kinetic description of the Vicsek swarming model. The kinetic model poses a unique challenge, as there is a distribution dependent collision invariant to satisfy when computing the interaction term. We use a spectral representation linked with a discrete constrained optimization to compute these interactions. To test the numerical scheme we investigate the kinetic model at different scales and compare the solution with the microscopic and macroscopic descriptions of the Vicsek model. Lastly, we observe that the kinetic model captures key features such as vortex formation and traveling waves.

Empirical evaluation of a virtual laboratory approach to teach lactate dehydrogenase enzyme kinetics.

PubMed

Booth, Christine; Cheluvappa, Rajkumar; Bellinson, Zack; Maguire, Danni; Zimitat, Craig; Abraham, Joyce; Eri, Rajaraman

2016-06-01

Personalised instruction is increasingly recognised as crucial for efficacious learning today. Our seminal work delineates and elaborates on the principles, development and implementation of a specially-designed adaptive, virtual laboratory. We strived to teach laboratory skills associated with lactate dehydrogenase (LDH) enzyme kinetics to 2nd-year biochemistry students using our adaptive learning platform. Pertinent specific aims were to:(1)design/implement a web-based lesson to teach lactate dehydrogenase(LDH) enzyme kinetics to 2nd-year biochemistry students(2)determine its efficacious in improving students' comprehension of enzyme kinetics(3)assess their perception of its usefulness/manageability(vLab versus Conventional Tutorial). Our tools were designed using HTML5 technology. We hosted the program on an adaptive e-learning platform (AeLP). Provisions were made to interactively impart informed laboratory skills associated with measuring LDH enzyme kinetics. A series of e-learning methods were created. Tutorials were generated for interactive teaching and assessment. The learning outcomes herein were on par with that from a conventional classroom tutorial. Student feedback showed that the majority of students found the vLab learning experience "valuable"; and the vLab format/interface "well-designed". However, there were a few technical issues with the 1st roll-out of the platform. Our pioneering effort resulted in productive learning with the vLab, with parity with that from a conventional tutorial. Our contingent discussion emphasises not only the cornerstone advantages, but also the shortcomings of the AeLP method utilised. We conclude with an astute analysis of possible extensions and applications of our methodology.

Steady-state kinetic modeling constrains cellular resting states and dynamic behavior.

PubMed

Purvis, Jeremy E; Radhakrishnan, Ravi; Diamond, Scott L

2009-03-01

A defining characteristic of living cells is the ability to respond dynamically to external stimuli while maintaining homeostasis under resting conditions. Capturing both of these features in a single kinetic model is difficult because the model must be able to reproduce both behaviors using the same set of molecular components. Here, we show how combining small, well-defined steady-state networks provides an efficient means of constructing large-scale kinetic models that exhibit realistic resting and dynamic behaviors. By requiring each kinetic module to be homeostatic (at steady state under resting conditions), the method proceeds by (i) computing steady-state solutions to a system of ordinary differential equations for each module, (ii) applying principal component analysis to each set of solutions to capture the steady-state solution space of each module network, and (iii) combining optimal search directions from all modules to form a global steady-state space that is searched for accurate simulation of the time-dependent behavior of the whole system upon perturbation. Importantly, this stepwise approach retains the nonlinear rate expressions that govern each reaction in the system and enforces constraints on the range of allowable concentration states for the full-scale model. These constraints not only reduce the computational cost of fitting experimental time-series data but can also provide insight into limitations on system concentrations and architecture. To demonstrate application of the method, we show how small kinetic perturbations in a modular model of platelet P2Y(1) signaling can cause widespread compensatory effects on cellular resting states.

Determination of thermodynamics and kinetics of RNA reactions by force

PubMed Central

Tinoco, Ignacio; Li, Pan T. X.; Bustamante, Carlos

2008-01-01

Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force. PMID:17040613

Identification and quantification of human microcirculatory leukocytes using handheld video microscopes at the bedside.

PubMed

Uz, Zühre; van Gulik, Thomas M; Aydemirli, Mehtap Derya; Guerci, Philippe; Ince, Yasin; Cuppen, Diede V; Ergin, Bulent; Aksu, Ugur; de Mol, Bas A; Ince, Can

2018-03-08

Leukocyte recruitment and adhesion to the endothelium are hallmarks of systemic inflammation that manifest in a wide range of diseases. At present, no method is available to directly measure leukocyte kinetics at the bedside. In this study, we validate a new method to identify and quantify microcirculatory leukocytes observed by handheld vital microscopy (HVM) using space-time diagram (STD) analysis. Video clips (N=59) containing one capillary-post capillary venule (C-PCV) unit where leukocytes could be observed emanating from a capillary into a venule in cardiac surgery patients (N=20) were included. STD analysis and manual counting were used to quantify the number of leukocytes (total, rolling and non-rolling). Pearson's correlation and Bland-Altman analysis were used to determine agreement between the STDs and manual counting. For reproducibility, intra- and inter-observer coefficients of variation (CVs) were assessed. Leukocyte (rolling and non-rolling) and red blood cell velocities were assessed. The STDs and manual counting procedures for the quantification of rolling leukocytes showed good agreement (r=0.8197, P<0.0001), with a Bland-Altman analysis mean difference of -0.0 (-6.56; 6.56). The overall intra-observer CV for the STD method was 1.5%. The overall inter-observer CVs for the STD and the manual method were 5.6% and 9.4%, respectively. The non-rolling velocity was significantly higher than the rolling velocity (812{plus minus}519 µm/s vs 201{plus minus}149 µm/s, P=0.001). The STD results agreed with the manual counting procedure results, had a better reproducibility and could assess the leukocyte velocity. STD analysis using bedside HVM imaging presented a new methodology for quantifying leukocyte kinetics and functions in the microcirculation.

LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 1: Theory and numerical solution procedures

NASA Technical Reports Server (NTRS)

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 1 of a series of three reference publications that describe LENS, provide a detailed guide to its usage, and present many example problems. Part 1 derives the governing equations and describes the numerical solution procedures for the types of problems that can be solved. The accuracy and efficiency of LSENS are examined by means of various test problems, and comparisons with other methods and codes are presented. 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.

Effect of preliminary thermal treatment on decomposition kinetics of austenite in low-alloyed pipe steel in intercritical temperature interval

NASA Astrophysics Data System (ADS)

Makovetskii, A. N.; Tabatchikova, T. I.; Yakovleva, I. L.; Tereshchenko, N. A.; Mirzaev, D. A.

2013-06-01

The decomposition kinetics of austenite that appears in the 13KhFA low-alloyed pipe steel upon heating the samples in an intercritical temperature interval (ICI) and exposure for 5 or 30 min has been studied by the method of high-speed dilatometry. The results of dilatometry are supplemented by the microstructure analysis. Thermokinetic diagrams of the decomposition of the γ phase are represented. The conclusion has been drawn that an increase in the duration of exposure in the intercritical interval leads to a significant increase in the stability of the γ phase.

Multiplexed evaluation of capture agent binding kinetics using arrays of silicon photonic microring resonators.

PubMed

Byeon, Ji-Yeon; Bailey, Ryan C

2011-09-07

High affinity capture agents recognizing biomolecular targets are essential in the performance of many proteomic detection methods. Herein, we report the application of a label-free silicon photonic biomolecular analysis platform for simultaneously determining kinetic association and dissociation constants for two representative protein capture agents: a thrombin-binding DNA aptamer and an anti-thrombin monoclonal antibody. The scalability and inherent multiplexing capability of the technology make it an attractive platform for simultaneously evaluating the binding characteristics of multiple capture agents recognizing the same target antigen, and thus a tool complementary to emerging high-throughput capture agent generation strategies.

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.

[Enzyme kinetic glucose determination by the glucose dehydrogenase method. Enzyme kinetic substrate determination using competitive inhibitors, II (author's transl)].

PubMed

Müller-Matthesius, R

1975-05-01

The sensitivity of enzyme kinetic substrate determinations can be improved with the aid of competitive inhibitors. As an example, the determination of glucose dehydrogenase in the presence of potassium thiocyanate is described. The method has the advantage of rapid operation with satisfactory precision.

Study of free radicals in gamma irradiated cellulose of cultural heritage materials using Electron Paramagnetic Resonance

NASA Astrophysics Data System (ADS)

Kodama, Yasko; Rodrigues, Orlando, Jr.; Garcia, Rafael Henrique Lazzari; Santos, Paulo de Souza; Vasquez, Pablo A. S.

2016-07-01

Main subject of this article was to study room temperature stable radicals in Co-60 gamma irradiated contemporary paper using Electron Paramagnetic Resonance spectrometer (EPR). XRD was used to study the effect of ionizing radiation on the morphology of book paper. SEM images presented regions with cellulose fibers and regions with particles agglomeration on the cellulose fibers. Those agglomerations were rich in calcium, observed by EDS. XRD analysis confirmed presence of calcium carbonate diffraction peaks. The main objective of this study was to propose a method using conventional kinetics chemical reactions for the observed radical formed by ionizing radiation. Therefore, further analyses were made to study the half-life and the kinetics of the free radical created. This method can be suitably applied to study radicals on cultural heritage objects.

Nonequilibrium Statistical Operator Method and Generalized Kinetic Equations

NASA Astrophysics Data System (ADS)

Kuzemsky, A. L.

2018-01-01

We consider some principal problems of nonequilibrium statistical thermodynamics in the framework of the Zubarev nonequilibrium statistical operator approach. We present a brief comparative analysis of some approaches to describing irreversible processes based on the concept of nonequilibrium Gibbs ensembles and their applicability to describing nonequilibrium processes. We discuss the derivation of generalized kinetic equations for a system in a heat bath. We obtain and analyze a damped Schrödinger-type equation for a dynamical system in a heat bath. We study the dynamical behavior of a particle in a medium taking the dissipation effects into account. We consider the scattering problem for neutrons in a nonequilibrium medium and derive a generalized Van Hove formula. We show that the nonequilibrium statistical operator method is an effective, convenient tool for describing irreversible processes in condensed matter.

A Numerical Analysis of the Transient Response of an Ablation System Including Effects of Thermal Nonequilibrium, Mass Transfer and Chemical Kinetics. Ph.D Thesis - Virginia Polytechnic Inst. and State Univ.

NASA Technical Reports Server (NTRS)

Clark, R. K.

1972-01-01

The differential equations governing the transient response of a one-dimensional ablative thermal protection system undergoing stagnation ablation are derived. These equations are for thermal nonequilibrium effects between the pyrolysis gases and the char layer and kinetically controlled chemical reactions and mass transfer between the pyrolysis gases and the char layer. The boundary conditions are written for the particular case of stagnation heating with surface removal by oxidation or sublimation and pyrolysis of the uncharred layer occurring in a plane. The governing equations and boundary conditions are solved numerically using the modified implicit method (Crank-Nicolson method). Numerical results are compared with exact solutions for a number of simplified cases. The comparison is favorable in each instance.

Elementary solutions of coupled model equations in the kinetic theory of gases

NASA Technical Reports Server (NTRS)

Kriese, J. T.; Siewert, C. E.; Chang, T. S.

1974-01-01

The method of elementary solutions is employed to solve two coupled integrodifferential equations sufficient for determining temperature-density effects in a linearized BGK model in the kinetic theory of gases. Full-range completeness and orthogonality theorems are proved for the developed normal modes and the infinite-medium Green's function is constructed as an illustration of the full-range formalism. The appropriate homogeneous matrix Riemann problem is discussed, and half-range completeness and orthogonality theorems are proved for a certain subset of the normal modes. The required existence and uniqueness theorems relevant to the H matrix, basic to the half-range analysis, are proved, and an accurate and efficient computational method is discussed. The half-space temperature-slip problem is solved analytically, and a highly accurate value of the temperature-slip coefficient is reported.

Thermoluminescence kinetic features of Lithium Iodide (LiI) single crystal grown by vertical Bridgman technique

NASA Astrophysics Data System (ADS)

Daniel, D. Joseph; Kim, H. J.; Kim, Sunghwan; Khan, Sajid

2017-08-01

Single crystal of pure Lithium Iodide (LiI) has been grown from melt by using the vertical Bridgman technique. Thermoluminescence (TL) Measurements were carried out at 1 K/s following X-ray irradiation. The TL glow curve consists of a dominant peak at (peak-maximum Tm) 393 K and one low temperature peak of weaker intensity at 343 K. The order of kinetics (b), activation energy (E), and the frequency factor (S) for a prominent TL glow peak observed around 393 K for LiI crystals are reported for the first time. The peak shape analysis of the glow peak indicates the kinetics to be of the first order. The value of E is calculated using various standard methods such as initial rise (IR), whole glow peak (WGP), peak shape (PS), computerized glow curve deconvolution (CGCD) and Variable Heating rate (VHR) methods. An average value of 1.06 eV is obtained in this case. In order to validate the obtained parameters, numerically integrated TL glow curve has been generated using experimentally determined kinetic parameters. The effective atomic number (Zeff) for this material was determined and found to be 52. X-ray induced emission spectra of pure LiI single crystal are studied at room temperature and it is found that the sample exhibit sharp emission at 457 nm and broad emission at 650 nm.

Fourier transform infrared spectroscopic analysis of cell differentiation

NASA Astrophysics Data System (ADS)

Ishii, Katsunori; Kimura, Akinori; Kushibiki, Toshihiro; Awazu, Kunio

2007-02-01

Stem cells and its differentiations have got a lot of attentions in regenerative medicine. The process of differentiations, the formation of tissues, has become better understood by the study using a lot of cell types progressively. These studies of cells and tissue dynamics at molecular levels are carried out through various approaches like histochemical methods, application of molecular biology and immunology. However, in case of using regenerative sources (cells, tissues and biomaterials etc.) clinically, they are measured and quality-controlled by non-invasive methods from the view point of safety. Recently, the use of Fourier Transform Infrared spectroscopy (FT-IR) has been used to monitor biochemical changes in cells, and has gained considerable importance. The objective of this study is to establish the infrared spectroscopy of cell differentiation as a quality control of cell sources for regenerative medicine. In the present study, as a basic study, we examined the adipose differentiation kinetics of preadipocyte (3T3-L1) and the osteoblast differentiation kinetics of bone marrow mesenchymal stem cells (Kusa-A1) to analyze the infrared absorption spectra. As a result, we achieved to analyze the adipose differentiation kinetics using the infrared absorption peak at 1739 cm-1 derived from ester bonds of triglyceride and osteoblast differentiation kinetics using the infrared absorption peak at 1030 cm-1 derived from phosphate groups of calcium phosphate.

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

Zinc pharmacokinetic parameters in the determination of body zinc status in children.

PubMed

Vale, S H L; Leite, L D; Alves, C X; Dantas, M M G; Costa, J B S; Marchini, J S; França, M C; Brandão-Neto, J

2014-02-01

Serum or tissue zinc concentrations are often used to assess body zinc status. However, all of these methods are relatively inaccurate. Thus, we investigated three different kinetic methods for the determination of zinc clearance to establish which of these could detect small changes in the body zinc status of children. Forty apparently healthy children were studied. Renal handling of zinc was investigated during intravenous zinc administration (0.06537 mg Zn/kg of body weight), both before and after oral zinc supplementation (5 mg Zn/day for 3 months). Three kinetic methods were used to determine zinc clearance: CZn-Formula A and CZn-Formula B were both used to calculate systemic clearance; the first is a general formula and the second is used for the specific analysis of a single-compartment model; CZn-Formula C is widely used in medical practices to analyze kinetic routine. Basal serum zinc values, which were within the reference range for healthy children, increased significantly after oral zinc supplementation. The three formulas used gave different results for zinc clearance both before and after oral zinc supplementation. CZn-Formula B showed a positive correlation with basal serum zinc concentration after oral supplementation (R2=0.1172, P=0.0306). In addition, CZn-Formula B (P=0.0002) was more effective than CZn-Formula A (P=0.6028) and CZn-Formula C (P=0.0732) in detecting small variations in body zinc status. All three of the formulas used are suitable for studying zinc kinetics; however, CZn-Formula B is particularly effective at detecting small changes in body zinc status in healthy children.

Whole body creatine and protein kinetics in healthy men and women: effects of creatine and amino acid supplementation.

PubMed

Kalhan, Satish C; Gruca, Lourdes; Marczewski, Susan; Bennett, Carole; Kummitha, China

2016-03-01

Creatine kinetics were measured in young healthy subjects, eight males and seven females, age 20-30 years, after an overnight fast on creatine-free diet. Whole body turnover of glycine and its appearance in creatine was quantified using [1-(13)C] glycine and the rate of protein turnover was quantified using L-ring [(2)H5] phenylalanine. The creatine pool size was estimated by the dilution of a bolus [C(2)H3] creatine. Studies were repeated following a five days supplement creatine 21 g.day(-1) and following supplement amino acids 14.3 g day(-1). Creatine caused a ten-fold increase in the plasma concentration of creatine and a 50 % decrease in the concentration of guanidinoacetic acid. Plasma amino acids profile showed a significant decrease in glycine, glutamine, and taurine and a significant increase in citrulline, valine, lysine, and cysteine. There was a significant decrease in the rate of appearance of glycine, suggesting a decrease in de-novo synthesis (p = 0.006). The fractional and absolute rate of synthesis of creatine was significantly decreased by supplemental creatine. Amino acid supplement had no impact on any of the parameters. This is the first detailed analysis of creatine kinetics and the effects of creatine supplement in healthy young men and women. These methods can be applied for the analysis of creatine kinetics in different physiological states.

Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation.

PubMed

Fang, Jiansong; Wu, Ping; Yang, Ranyao; Gao, Li; Li, Chao; Wang, Dongmei; Wu, Song; Liu, Ai-Lin; Du, Guan-Hua

2014-12-01

In this study two genistein derivatives (G1 and G2) are reported as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and differences in the inhibition of AChE are described. Although they differ in structure by a single methyl group, the inhibitory effect of G1 (IC50=264 nmol/L) on AChE was 80 times stronger than that of G2 (IC50=21,210 nmol/L). Enzyme-kinetic analysis, molecular docking and molecular dynamics (MD) simulations were conducted to better understand the molecular basis for this difference. The results obtained by kinetic analysis demonstrated that G1 can interact with both the catalytic active site and peripheral anionic site of AChE. The predicted binding free energies of two complexes calculated by the molecular mechanics/generalized born surface area (MM/GBSA) method were consistent with the experimental data. The analysis of the individual energy terms suggested that a difference between the net electrostatic contributions (ΔE ele+ΔG GB) was responsible for the binding affinities of these two inhibitors. Additionally, analysis of the molecular mechanics and MM/GBSA free energy decomposition revealed that the difference between G1 and G2 originated from interactions with Tyr124, Glu292, Val294 and Phe338 of AChE. In conclusion, the results reveal significant differences at the molecular level in the mechanism of inhibition of AChE by these structurally related compounds.

Extraction of Antioxidant Phenolic Compounds from Brewer’s Spent Grain: Optimization and Kinetics Modeling

PubMed Central

Sologubik, Carlos A.; Fernández, María B.; Manrique, Guillermo D.

2018-01-01

The kinetics of polyphenol extraction from brewer’s spent grain (BSG), using a batch system, ultrasound assistance, and microwave assistance and the evolution of antioxidant capacity of these extracts over time, were studied. The main parameters of extraction employed in the batch system were evaluated, and, by applying response surface analysis, the following optimal conditions were obtained: Liquid/solid ratio of 30:1 mL/g at 80 °C, using 72% (v/v) ethanol:water as the solvent system. Under these optimized conditions, ultrasound assistance demonstrated the highest extraction rate and equilibrium yield, as well as shortest extraction times, followed by microwave assistance. Among the mathematical models used, Patricelli’s model proved the most suitable for describing the extraction kinetics for each method tested, and is therefore able to predict the response values and estimate the extraction rates and potential maximum yields in each case. PMID:29570683

Analytical solutions for coagulation and condensation kinetics of composite particles

NASA Astrophysics Data System (ADS)

Piskunov, Vladimir N.

2013-04-01

The processes of composite particles formation consisting of a mixture of different materials are essential for many practical problems: for analysis of the consequences of accidental releases in atmosphere; for simulation of precipitation formation in clouds; for description of multi-phase processes in chemical reactors and industrial facilities. Computer codes developed for numerical simulation of these processes require optimization of computational methods and verification of numerical programs. Kinetic equations of composite particle formation are given in this work in a concise form (impurity integrated). Coagulation, condensation and external sources associated with nucleation are taken into account. Analytical solutions were obtained in a number of model cases. The general laws for fraction redistribution of impurities were defined. The results can be applied to develop numerical algorithms considerably reducing the simulation effort, as well as to verify the numerical programs for calculation of the formation kinetics of composite particles in the problems of practical importance.

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.

Equilibrium, kinetics and process design of acid yellow 132 adsorption onto red pine sawdust.

PubMed

Can, Mustafa

2015-01-01

Linear and non-linear regression procedures have been applied to the Langmuir, Freundlich, Tempkin, Dubinin-Radushkevich, and Redlich-Peterson isotherms for adsorption of acid yellow 132 (AY132) dye onto red pine (Pinus resinosa) sawdust. The effects of parameters such as particle size, stirring rate, contact time, dye concentration, adsorption dose, pH, and temperature were investigated, and interaction was characterized by Fourier transform infrared spectroscopy and field emission scanning electron microscope. The non-linear method of the Langmuir isotherm equation was found to be the best fitting model to the equilibrium data. The maximum monolayer adsorption capacity was found as 79.5 mg/g. The calculated thermodynamic results suggested that AY132 adsorption onto red pine sawdust was an exothermic, physisorption, and spontaneous process. Kinetics was analyzed by four different kinetic equations using non-linear regression analysis. The pseudo-second-order equation provides the best fit with experimental data.

Statistical Ring Opening Metathesis Copolymerization of Norbornene and Cyclopentene by Grubbs' 1st-Generation Catalyst.

PubMed

Nikovia, Christiana; Maroudas, Andreas-Philippos; Goulis, Panagiotis; Tzimis, Dionysios; Paraskevopoulou, Patrina; Pitsikalis, Marinos

2015-08-27

Statistical copolymers of norbornene (NBE) with cyclopentene (CP) were prepared by ring-opening metathesis polymerization, employing the 1st-generation Grubbs' catalyst, in the presence or absence of triphenylphosphine, PPh₃. The reactivity ratios were estimated using the Finemann-Ross, inverted Finemann-Ross, and Kelen-Tüdos graphical methods, along with the computer program COPOINT, which evaluates the parameters of binary copolymerizations from comonomer/copolymer composition data by integrating a given copolymerization equation in its differential form. Structural parameters of the copolymers were obtained by calculating the dyad sequence fractions and the mean sequence length, which were derived using the monomer reactivity ratios. The kinetics of thermal decomposition of the copolymers along with the respective homopolymers was studied by thermogravimetric analysis within the framework of the Ozawa-Flynn-Wall and Kissinger methodologies. Finally, the effect of triphenylphosphine on the kinetics of copolymerization, the reactivity ratios, and the kinetics of thermal decomposition were examined.

Grain formation in astronomical systems: A critical review of condensation processes

NASA Technical Reports Server (NTRS)

Donn, B.

1978-01-01

An analysis is presented of the assumption and the applicability of the three theoretical methods for calculating condensations in cosmic clouds where no pre-existing nuclei exist. The three procedures are: thermodynamic equilibrium calculations, nucleation theory, and a kinetic treatment which would take into account the characteristics of each individual collision. Thermodynamics provide detailed results on the composition temperature and composition of the condensate provided the system attains equilibrium. Because of the cosmic abundance mixture of elements, large supersaturations in some cases and low pressures, equilibrium is not expected in astronomical clouds. Nucleation theory, a combination of thermodynamics and kinetics, has the limitations of each scheme. Kinetics, not requiring equilibrium, avoids nearly all the thermodynamics difficulties but requires detailed knowledge of many reactions which thermodynamics avoids. It appears to be the only valid way to treat grain formation in space. A review of experimental studies is given.

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.

The kinetic energy operator for distance-dependent effective nuclear masses: Derivation for a triatomic molecule.

PubMed

Khoma, Mykhaylo; Jaquet, Ralph

2017-09-21

The kinetic energy operator for triatomic molecules with coordinate or distance-dependent nuclear masses has been derived. By combination of the chain rule method and the analysis of infinitesimal variations of molecular coordinates, a simple and general technique for the construction of the kinetic energy operator has been proposed. The asymptotic properties of the Hamiltonian have been investigated with respect to the ratio of the electron and proton mass. We have demonstrated that an ad hoc introduction of distance (and direction) dependent nuclear masses in Cartesian coordinates preserves the total rotational invariance of the problem. With the help of Wigner rotation functions, an effective Hamiltonian for nuclear motion can be derived. In the derivation, we have focused on the effective trinuclear Hamiltonian. All necessary matrix elements are given in closed analytical form. Preliminary results for the influence of non-adiabaticity on vibrational band origins are presented for H 3 + .

Temperature Responses of C4 Photosynthesis: Biochemical Analysis of Rubisco, Phosphoenolpyruvate Carboxylase, and Carbonic Anhydrase in Setaria viridis.

PubMed

Boyd, Ryan A; Gandin, Anthony; Cousins, Asaph B

2015-11-01

The photosynthetic assimilation of CO2 in C4 plants is potentially limited by the enzymatic rates of Rubisco, phosphoenolpyruvate carboxylase (PEPc), and carbonic anhydrase (CA). Therefore, the activity and kinetic properties of these enzymes are needed to accurately parameterize C4 biochemical models of leaf CO2 exchange in response to changes in CO2 availability and temperature. There are currently no published temperature responses of both Rubisco carboxylation and oxygenation kinetics from a C4 plant, nor are there known measurements of the temperature dependency of the PEPc Michaelis-Menten constant for its substrate HCO3 (-), and there is little information on the temperature response of plant CA activity. Here, we used membrane inlet mass spectrometry to measure the temperature responses of Rubisco carboxylation and oxygenation kinetics, PEPc carboxylation kinetics, and the activity and first-order rate constant for the CA hydration reaction from 10°C to 40°C using crude leaf extracts from the C4 plant Setaria viridis. The temperature dependencies of Rubisco, PEPc, and CA kinetic parameters are provided. These findings describe a new method for the investigation of PEPc kinetics, suggest an HCO3 (-) limitation imposed by CA, and show similarities between the Rubisco temperature responses of previously measured C3 species and the C4 plant S. viridis. © 2015 American Society of Plant Biologists. All Rights Reserved.

Ionic liquid thermal stabilities: decomposition mechanisms and analysis tools.

PubMed

Maton, Cedric; De Vos, Nils; Stevens, Christian V

2013-07-07

The increasing amount of papers published on ionic liquids generates an extensive quantity of data. The thermal stability data of divergent ionic liquids are collected in this paper with attention to the experimental set-up. The influence and importance of the latter parameters are broadly addressed. Both ramped temperature and isothermal thermogravimetric analysis are discussed, along with state-of-the-art methods, such as TGA-MS and pyrolysis-GC. The strengths and weaknesses of the different methodologies known to date demonstrate that analysis methods should be in line with the application. The combination of data from advanced analysis methods allows us to obtain in-depth information on the degradation processes. Aided with computational methods, the kinetics and thermodynamics of thermal degradation are revealed piece by piece. The better understanding of the behaviour of ionic liquids at high temperature allows selective and application driven design, as well as mathematical prediction for engineering purposes.

Fundamental electrode kinetics

NASA Technical Reports Server (NTRS)

Elder, J. P.

1968-01-01

Report presents the fundamentals of electrode kinetics and the methods used in evaluating the characteristic parameters of rapid-charge transfer processes at electrode-electrolyte interfaces. The concept of electrode kinetics is outlined, followed by the principles underlying the experimental techniques for the investigation of electrode kinetics.

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 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.

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.

Turbulent Chemically Reacting Flows According to a Kinetic Theory. Ph.D. Thesis; [statistical analysis/gas flow

NASA Technical Reports Server (NTRS)

Hong, Z. C.

1975-01-01

A review of various methods of calculating turbulent chemically reacting flow such as the Green Function, Navier-Stokes equation, and others is presented. Nonequilibrium degrees of freedom were employed to study the mixing behavior of a multiscale turbulence field. Classical and modern theories are discussed.

An Experiment with Manifold Purposes: The Chemical Reactivity of Crystal Defects upon Crystal Dissolution.

ERIC Educational Resources Information Center

Lazzarini, Annaluisa Fantola; Lazzarini, Ennio

1983-01-01

Background information and procedures are provided for an experiment designed to introduce (1) crystal defects and their reactivity upon crystal dissolution; (2) hydrates electron and its reactivity; (3) application of radiochemical method of analysis; and (4) the technique of competitive kinetics. Suggested readings and additional experiments are…

Projective Drawings of Mothers and Children Exposed to Intimate Partner Violence: A Mixed Methods Analysis

ERIC Educational Resources Information Center

Backos, Amy; Samuelson, Kristin W.

2017-01-01

The Kinetic Family Drawing (KFD) and the Draw-A-Person: Screening Procedure for Emotional Disturbance (DAP:SPED) are intended to facilitate therapeutic discussion and assess emotional disturbance; however, little research exists on their use with victims of trauma or for identifying posttraumatic stress disorder (PTSD). This study examined…

The CRDS method application for study of the gas-phase processes in the hot CVD diamond thin film.

NASA Astrophysics Data System (ADS)

Buzaianumakarov, Vladimir; Hidalgo, Arturo; Morell, Gerardo; Weiner, Brad; Buzaianu, Madalina

2006-03-01

For detailed analysis of problem related to the hot CVD carbon-containing nano-material growing, we have to detect different intermediate species forming during the growing process as well as investigate dependences of concentrations of these species on different experimental parameters (concentrations of the CJH4, H2S stable chemical compounds and distance from the filament system to the substrate surface). In the present study, the HS and CS radicals were detected using the Cavity Ring Down Spectroscopic (CRDS) method in the hot CVD diamond thin film for the CH4(0.4 %) + H2 mixture doped by H2S (400 ppm). The absolute absorption density spectra of the HS and CS radicals were obtained as a function of different experimental parameters. This study proofs that the HS and CS radicals are an intermediate, which forms during the hot filament CVD process. The kinetics approach was developed for detailed analysis of the experimental data obtained. The kinetics scheme includes homogenous and heterogenous processes as well as processes of the chemical species transport in the CVD chamber.

Study of the Low Temperature Oxidation of Propane

PubMed Central

Cord, Maximilien; Husson, Benoit; Huerta, Juan Carlos Lizardo; Herbinet, Olivier; Glaude, Pierre-Alexandre; Fournet, René; Sirjean, Baptiste; Battin-Leclerc, Frédérique; Ruiz-Lopez, Manuel; Wang, Zhandong; Xie, Mingfeng; Cheng, Zhanjun; Qi, Fei

2013-01-01

The low-temperature oxidation of propane was investigated using a jet-stirred reactor at atmospheric pressure and two methods of analysis: gas chromatography and synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS) with direct sampling through a molecular jet. The second method allowed the identification of products, such as molecules with hydroperoxy functions, which are not stable enough to be detected by gas chromatography. Mole fractions of the reactants and reaction products were measured as a function of the temperature (530-730 K), with a particular attention to reaction products involved in the low temperature oxidation, such as cyclic ethers, aldehydes, alcohols, ketones, and hydroperoxides. A new model has been obtained from an automatically generated one, which was used as a starting point, with a large number of re-estimated thermochemical and kinetic data. The kinetic data of the most sensitive reactions, i.e., isomerizations of alkylperoxy radicals and the subsequent decompositions, have been calculated at the CBS-QB3 level of theory. The model allows a satisfactory prediction of the experimental data. A flow rate analysis has allowed highlighting the important reaction channels. PMID:23181456

A novel method to measure regional muscle blood flow continuously using NIRS kinetics information

PubMed Central

Nioka, Shoko; Kime, Ryotaro; Sunar, Ulas; Im, Joohee; Izzetoglu, Meltem; Zhang, Jun; Alacam, Burak; Chance, Britton

2006-01-01

Background This article introduces a novel method to continuously monitor regional muscle blood flow by using Near Infrared Spectroscopy (NIRS). We demonstrate the feasibility of the new method in two ways: (1) by applying this new method of determining blood flow to experimental NIRS data during exercise and ischemia; and, (2) by simulating muscle oxygenation and blood flow values using these newly developed equations during recovery from exercise and ischemia. Methods Deoxy (Hb) and oxyhemoglobin (HbO2), located in the blood ofthe skeletal muscle, carry two internal relationships between blood flow and oxygen consumption. One is a mass transfer principle and the other describes a relationship between oxygen consumption and Hb kinetics in a two-compartment model. To monitor blood flow continuously, we transfer these two relationships into two equations and calculate the blood flow with the differential information of HbO2 and Hb. In addition, these equations are used to simulate the relationship between blood flow and reoxygenation kinetics after cuff ischemia and a light exercise. Nine healthy subjects volunteered for the cuff ischemia, light arm exercise and arm exercise with cuff ischemia for the experimental study. Results Analysis of experimental data of both cuff ischemia and light exercise using the new equations show greater blood flow (four to six times more than resting values) during recovery, agreeing with previous findings. Further, the simulation and experimental studies of cuff ischemia and light exercise agree with each other. Conclusion We demonstrate the accuracy of this new method by showing that the blood flow obtained from the method agrees with previous data as well as with simulated data. We conclude that this novel continuous blood flow monitoring method can provide blood flow information non-invasively with NIRS. PMID:16704736

A comparison of quantitative methods for clinical imaging with hyperpolarized (13)C-pyruvate.

PubMed

Daniels, Charlie J; McLean, Mary A; Schulte, Rolf F; Robb, Fraser J; Gill, Andrew B; McGlashan, Nicholas; Graves, Martin J; Schwaiger, Markus; Lomas, David J; Brindle, Kevin M; Gallagher, Ferdia A

2016-04-01

Dissolution dynamic nuclear polarization (DNP) enables the metabolism of hyperpolarized (13)C-labelled molecules, such as the conversion of [1-(13)C]pyruvate to [1-(13)C]lactate, to be dynamically and non-invasively imaged in tissue. Imaging of this exchange reaction in animal models has been shown to detect early treatment response and correlate with tumour grade. The first human DNP study has recently been completed, and, for widespread clinical translation, simple and reliable methods are necessary to accurately probe the reaction in patients. However, there is currently no consensus on the most appropriate method to quantify this exchange reaction. In this study, an in vitro system was used to compare several kinetic models, as well as simple model-free methods. Experiments were performed using a clinical hyperpolarizer, a human 3 T MR system, and spectroscopic imaging sequences. The quantitative methods were compared in vivo by using subcutaneous breast tumours in rats to examine the effect of pyruvate inflow. The two-way kinetic model was the most accurate method for characterizing the exchange reaction in vitro, and the incorporation of a Heaviside step inflow profile was best able to describe the in vivo data. The lactate time-to-peak and the lactate-to-pyruvate area under the curve ratio were simple model-free approaches that accurately represented the full reaction, with the time-to-peak method performing indistinguishably from the best kinetic model. Finally, extracting data from a single pixel was a robust and reliable surrogate of the whole region of interest. This work has identified appropriate quantitative methods for future work in the analysis of human hyperpolarized (13)C data. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

Dynamic Modeling of the Human Coagulation Cascade Using Reduced Order Effective Kinetic Models (Open Access)

DTIC Science & Technology

2015-03-16

shaded region around each total sensitivity value was the maximum uncertainty in that value estimated by the Sobol method. 2.4. Global Sensitivity...Performance We conducted a global sensitivity analysis, using the variance-based method of Sobol , to estimate which parameters controlled the...Hunter, J.D. Matplotlib: A 2D Graphics Environment. Comput. Sci. Eng. 2007, 9, 90–95. 69. Sobol , I. Global sensitivity indices for nonlinear

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

A BAYESIAN METHOD OF ESTIMATING KINETIC PARAMETERS FOR THE INACTIVATION OF CRYPTOSPORIDIUM PARVUM OOCYSTS WITH CHLORINE DIOXIDE AND OZONE

EPA Science Inventory

The main objective of this paper is to use Bayesian methods to estimate the kinetic parameters for the inactivation kinetics of Cryptosporidium parvum oocysts with chlorine dioxide or ozone which are characterized by the delayed Chick-Watson model, i.e., a lag phase or shoulder f...

Measurement of Enzyme Kinetics by Use of a Blood Glucometer: Hydrolysis of Sucrose and Lactose

ERIC Educational Resources Information Center

Heinzerling, Peter; Schrader, Frank; Schanze, Sascha

2012-01-01

An alternative analytical method for measuring the kinetic parameters of the enzymes invertase and lactase is described. Invertase hydrolyzes sucrose to glucose and fructose and lactase hydrolyzes lactose to glucose and galactose. In most enzyme kinetics studies, photometric methods or test strips are used to quantify the derivates of the…

Laser-induced volatilization and ionization of microparticles

NASA Technical Reports Server (NTRS)

Sinha, M. P.

1984-01-01

A method for the laser vaporization and ionization of individual micron-size particles is presented whereby a particle is ionized by a laser pulse while in flight in the beam. Ionization in the beam offers a real-time analytical capability and eliminates any possible substrate-sample interferences during an analysis. An experimental arrangement using a high-energy Nd-YAG laser is described, and results are presented for ions generated from potassium biphthalate particles (1.96 micron in diameter). The method proposed here is useful for the chemical analysis of aerosol particles by mass spectrometry and for other spectroscopic and chemical kinetic studies.

An approximate analysis of the diffusing flow in a self-controlled heat pipe.

NASA Technical Reports Server (NTRS)

Somogyi, D.; Yen, H. H.

1973-01-01

Constant-density two-dimensional axisymmetric equations are presented for the diffusing flow of a class of self-controlled heat pipes. The analysis is restricted to the vapor space. Condensation of the vapor is related to its mass fraction at the wall by the gas kinetic formula. The Karman-Pohlhausen integral method is applied to obtain approximate solutions. Solutions are presented for a water heat pipe with neon control gas.

A study of the kinetics of isothermal nicotine desorption from silicon dioxide

NASA Astrophysics Data System (ADS)

Adnadjevic, Borivoj; Lazarevic, Natasa; Jovanovic, Jelena

2010-12-01

The isothermal kinetics of nicotine desorption from silicon dioxide (SiO 2) was investigated. The isothermal thermogravimetric curves of nicotine at temperatures of 115 °C, 130 °C and 152 °C were recorded. The kinetic parameters ( Ea, ln A) of desorption of nicotine were calculated using various methods (stationary point, model constants and differential isoconversion method). By applying the "model-fitting" method, it was found that the kinetic model of nicotine desorption from silicon dioxide was a phase boundary controlled reaction (contracting volume). The values of the kinetic parameters, Ea,α and ln Aα, complexly change with changing degree of desorption and a compensation effect exists. A new mechanism of activation for the desorption of the absorbed molecules of nicotine was suggested in agreement with model of selective energy transfer.

Simulation Research on Vehicle Active Suspension Controller Based on G1 Method

NASA Astrophysics Data System (ADS)

Li, Gen; Li, Hang; Zhang, Shuaiyang; Luo, Qiuhui

2017-09-01

Based on the order relation analysis method (G1 method), the optimal linear controller of vehicle active suspension is designed. The system of the main and passive suspension of the single wheel vehicle is modeled and the system input signal model is determined. Secondly, the system motion state space equation is established by the kinetic knowledge and the optimal linear controller design is completed with the optimal control theory. The weighting coefficient of the performance index coefficients of the main passive suspension is determined by the relational analysis method. Finally, the model is simulated in Simulink. The simulation results show that: the optimal weight value is determined by using the sequence relation analysis method under the condition of given road conditions, and the vehicle acceleration, suspension stroke and tire motion displacement are optimized to improve the comprehensive performance of the vehicle, and the active control is controlled within the requirements.

Kinetic Description of the Impedance Probe

NASA Astrophysics Data System (ADS)

Oberrath, Jens; Lapke, Martin; Mussenbrock, Thomas; Brinkmann, Ralf

2011-10-01

Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. The authors acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG) via the Ruhr University Research School and the Federal Ministry of Education and Research in frame of the PluTO project.

Optimization of a direct spectrophotometric method to investigate the kinetics and inhibition of sialidases

PubMed Central

2012-01-01

Backgrounds Streptococcus pneumoniae expresses three distinct sialidases, NanA, NanB, and NanC, that are believed to be key virulence factors and thus, potential important drug targets. We previously reported that the three enzymes release different products from sialosides, but could share a common catalytic mechanism before the final step of product formation. However, the kinetic investigations of the three sialidases have not been systematically done thus far, due to the lack of an easy and steady measurement of sialidase reaction rate. Results In this work, we present further kinetic characterization of pneumococcal sialidases by using a direct spectrophotometric method with the chromogenic substrate p-nitrophenyl-N-acetylneuraminic acid (p-NP-Neu5Ac). Using our assay, the measured kinetic parameters of the three purified pneumococcal sialidase, NanA, NanB and NanC, were obtained and were in perfect agreement with the previously published data. The major advantage of this alternative method resides in the direct measurement of the released product, allowing to readily determine of initial reaction rates and record complete hydrolysis time courses. Conclusion We developed an accurate, fast and sensitive spectrophotometric method to investigate the kinetics of sialidase-catalyzed reactions. This fast, sensitive, inexpensive and accurate method could benefit the study of the kinetics and inhibition of sialidases in general. PMID:23031230

From Lattice Boltzmann to hydrodynamics in dissipative relativistic fluids

NASA Astrophysics Data System (ADS)

Gabbana, Alessandro; Mendoza, Miller; Succi, Sauro; Tripiccione, Raffaele

2017-11-01

Relativistic fluid dynamics is currently applied to several fields of modern physics, covering many physical scales, from astrophysics, to atomic scales (e.g. in the study of effective 2D systems such as graphene) and further down to subnuclear scales (e.g. quark-gluon plasmas). This talk focuses on recent progress in the largely debated connection between kinetic transport coefficients and macroscopic hydrodynamic parameters in dissipative relativistic fluid dynamics. We use a new relativistic Lattice Boltzmann method (RLBM), able to handle from ultra-relativistic to almost non-relativistic flows, and obtain strong evidence that the Chapman-Enskog expansion provides the correct pathway from kinetic theory to hydrodynamics. This analysis confirms recently obtained theoretical results, which can be used to obtain accurate calibrations for RLBM methods applied to realistic physics systems in the relativistic regime. Using this calibration methodology, RLBM methods are able to deliver improved physical accuracy in the simulation of the physical systems described above. European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 642069.

Development and evaluation of kinetic spectrophotometric assays for horseradish peroxidase by catalytic coupling of paraphenylenediamine and mequinol.

PubMed

Nagaraja, Padmarajaiah; Shivakumar, Anantharaman; Kumar Shrestha, Ashwinee

2009-10-01

This paper presents a novel spectrophotometric method to measure peroxidase activity using paraphenylenediamine dihydrochloride (PPDD) and Mequinol (MQ). The PPDD traps the free radical, and gets oxidized to electrophilic 1,4-diimine; this couples with MQ to an give intense violet-colored chromogenic species with the maximum absorbance at 560 nm. This assay was adopted for the quantification of hydrogen peroxide between 10 x 10(-6) to 80 x 10(-6) M. From the kinetic data, a two-substrate ping-pong mechanism of peroxidase was established. Catalytic efficiency and catalytic power of commercial peroxidase were 0.204 x 10(6) M(-1) min(-1) and 2.86 x 10(-4) min(-1), respectively. The catalytic constant (k(cat)) of the proposed method was 0.2080 x 10(3) min(-1). As a simple, rapid, precise and sensitive technique, PPDD-MQ stands as a potential replacement for the traditional guaiacol method. Applications to the plant extracts increase its relevance in the field of biochemical analysis.

Comparison of enzyme kinetics of warfarin analyzed by LC-MS/MS QTrap and differential mobility spectrometry.

PubMed

Shaik, Abdul Naveed; Grater, Richard; Lulla, Mukesh; Williams, David A; Gan, Lawrence L; Bohnert, Tonika; LeDuc, Barbara W

2016-01-01

Warfarin is an anticoagulant used in the treatment of thrombosis and thromboembolism. It is given as a racemic mixture of R and S enantiomers. These two enantiomers show differences in metabolism by CYPs: S-warfarin undergoes 7 hydroxylation by CYP2C9 and R-warfarin by CYP3A4 to form 10 hydroxy warfarin. In addition, warfarin is acted upon by different CYPs to form the minor metabolites 3'-hydroxy, 4'-hydroxy, 6-hydroxy, and 8-hydroxy warfarin. For analysis, separation of these metabolites is necessary since all have the same m/z ratio and similar fragmentation pattern. Enzyme kinetics for the formation of all of the six hydroxylated metabolites of warfarin from human liver microsomes were determined using an LC-MS/MS QTrap and LC-MS/MS with a differential mobility spectrometry (DMS) (SelexION™) interface to compare the kinetic parameters. These two methods were chosen to compare their selectivity and sensitivity. Substrate curves for 3'-OH, 4'-OH, 6-OH, 7-OH, 8-OH and 10-OH warfarin formation were generated to determine the kinetic parameters (Km and Vmax) in human liver microsomal preparations. The limit of quantitation (LOQ) for all the six hydroxylated metabolites of warfarin were in the range of 1-3nM using an LC-MS/MS QTrap method which had a run time of 22min. In contrast, the LOQ for all the six hydroxylated metabolites using DMS interface technology was 100nM with a run time of 2.8min. We compare these two MS methods and discuss the kinetics of metabolite formation for the metabolites generated from racemic warfarin. In addition, we show inhibition of major metabolic pathways of warfarin by sulfaphenazole and ketoconazole which are known specific inhibitors of CYP2C9 and CYP3A4 respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

Cardiovascular Magnetic Resonance and prognosis in cardiac amyloidosis

PubMed Central

Maceira, Alicia M; Prasad, Sanjay K; Hawkins, Philip N; Roughton, Michael; Pennell, Dudley J

2008-01-01

Background Cardiac involvement is common in amyloidosis and associated with a variably adverse outcome. We have previously shown that cardiovascular magnetic resonance (CMR) can assess deposition of amyloid protein in the myocardial interstitium. In this study we assessed the prognostic value of late gadolinium enhancement (LGE) and gadolinium kinetics in cardiac amyloidosis in a prospective longitudinal study. Materials and methods The pre-defined study end point was all-cause mortality. We prospectively followed a cohort of 29 patients with proven cardiac amyloidosis. All patients underwent biopsy, 2D-echocardiography and Doppler studies, 123I-SAP scintigraphy, serum NT pro BNP assay, and CMR with a T1 mapping method and late gadolinium enhancement (LGE). Results Patients with were followed for a median of 623 days (IQ range 221, 1436), during which 17 (58%) patients died. The presence of myocardial LGE by itself was not a significant predictor of mortality. However, death was predicted by gadolinium kinetics, with the 2 minute post-gadolinium intramyocardial T1 difference between subepicardium and subendocardium predicting mortality with 85% accuracy at a threshold value of 23 ms (the lower the difference the worse the prognosis). Intramyocardial T1 gradient was a better predictor of survival than FLC response to chemotherapy (Kaplan Meier analysis P = 0.049) or diastolic function (Kaplan-Meier analysis P = 0.205). Conclusion In cardiac amyloidosis, CMR provides unique information relating to risk of mortality based on gadolinium kinetics which reflects the severity of the cardiac amyloid burden. PMID:19032744

Kinetic analysis of manure pyrolysis and combustion processes.

PubMed

Fernandez-Lopez, M; Pedrosa-Castro, G J; Valverde, J L; Sanchez-Silva, L

2016-12-01

Due to the depletion of fossil fuel reserves and the environmental issues derived from their use, biomass seems to be an excellent source of renewable energy. In this work, the kinetics of the pyrolysis and combustion of three different biomass waste samples (two dairy manure samples before (Pre) and after (Dig R) anaerobic digestion and one swine manure sample (SW)) was studied by means of thermogravimetric analysis. In this work, three iso-conversional methods (Friedman, Flynn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS)) were compared with the Coats-Redfern method. The E a values of devolatilization stages were in the range of 152-170kJ/mol, 148-178kJ/mol and 156-209kJ/mol for samples Pre, Dig R and SW, respectively. Concerning combustion process, char oxidation stages showed lower E a values than that obtained for the combustion devolatilization stage, being in the range of 140-175kJ/mol, 178-199kJ/mol and 122-144kJ/mol for samples Pre, Dig R and SW, respectively. These results were practically the same for samples Pre and Dig R, which means that the kinetics of the thermochemical processes were not affected by anaerobic digestion. Finally, the distributed activation energy model (DAEM) and the pseudo-multi component stage model (PMSM) were applied to predict the weight loss curves of pyrolysis and combustion. DAEM was the best model that fitted the experimental data. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Role of Metal Electronegativity in the Dehydrogenation Thermodynamics and Kinetics of Composite Metal Borohydride-LiNH2 Hydrogen Storage Materials.

PubMed

Bai, Ying; Pei, Ziwei; Wu, Feng; Wu, Chuan

2018-03-21

The composites of M(BH 4 ) n -LiNH 2 (1/2 n molar ratio, n = 1 or 2, M = Ca, Mg, Li) were synthesized by liquid ball milling. Samples were characterized by X-ray diffraction, thermogravimetry-differential thermal analysis-mass spectroscopy (TG-DTA-MS), and kinetic models (Achar differential/Coats-Redfern integral method). The higher-electronegativity metal M in M(BH 4 ) n -4LiNH 2 (M = Ca, Mg) samples not only enables [BH 4 ] - group to release easily, so as to facilitate the interaction of [BH 4 ] - and [NH 2 ] - groups, but also restrains the NH 3 release and slightly decreases the onset dehydrogenation temperature concluded by TG-MS. Moreover, in stage 1 (200-350 °C), the kinetics performances of M(BH 4 ) n -4LiNH 2 (M = Ca, Mg) samples are distinctly improved, that is, the activation energies of them are reduced by ca. 30% compared to those of sample LiBH 4 -2LiNH 2 . The outstanding contribution of the replacement of M(BH 4 ) n with high-electronegativity metal ion is to both improve the kinetics performance by changing the kinetics mechanism and decrease the temperature range of the initial dehydrogenation region.

Coformer screening using thermal analysis based on binary phase diagrams.

PubMed

Yamashita, Hiroyuki; Hirakura, Yutaka; Yuda, Masamichi; Terada, Katsuhide

2014-08-01

The advent of cocrystals has demonstrated a growing need for efficient and comprehensive coformer screening in search of better development forms, including salt forms. Here, we investigated a coformer screening system for salts and cocrystals based on binary phase diagrams using thermal analysis and examined the effectiveness of the method. Indomethacin and tenoxicam were used as models of active pharmaceutical ingredients (APIs). Physical mixtures of an API and 42 kinds of coformers were analyzed using Differential Scanning Calorimetry (DSC) and X-ray DSC. We also conducted coformer screening using a conventional slurry method and compared these results with those from the thermal analysis method and previous studies. Compared with the slurry method, the thermal analysis method was a high-performance screening system, particularly for APIs with low solubility and/or propensity to form solvates. However, this method faced hurdles for screening coformers combined with an API in the presence of kinetic hindrance for salt or cocrystal formation during heating or if there is degradation near the metastable eutectic temperature. The thermal analysis and slurry methods are considered complementary to each other for coformer screening. Feasibility of the thermal analysis method in drug discovery practice is ensured given its small scale and high throughput.

Thermal analysis and kinetics of coal during oxy-fuel combustion

NASA Astrophysics Data System (ADS)

Kosowska-Golachowska, Monika

2017-08-01

The pyrolysis and oxy-fuel combustion characteristics of Polish bituminous coal were studied using non-isothermal thermogravimetric analysis. Pyrolysis tests showed that the mass loss profiles were almost similar up to 870°C in both N2 and CO2 atmospheres, while further mass loss occurred in CO2 atmosphere at higher temperatures due to char-CO2 gasification. Replacement of N2 in the combustion environment by CO2 delayed the combustion of bituminous coal. At elevated oxygen levels, TG/DTG profiles shifted through lower temperature zone, ignition and burnout temperatures decreased and mass loss rate significantly increased and complete combustion was achieved at lower temperatures and shorter times. Kinetic analysis for the tested coal was performed using Kissinger-Akahira-Sunose (KAS) method. The activation energies of bituminous coal combustion at the similar oxygen content in oxy-fuel with that of air were higher than that in air atmosphere. The results indicated that, with O2 concentration increasing, the activation energies decreased.

Use of spectral analysis with iterative filter for voxelwise determination of regional rates of cerebral protein synthesis with L-[1-11C]leucine PET.

PubMed

Veronese, Mattia; Schmidt, Kathleen C; Smith, Carolyn Beebe; Bertoldo, Alessandra

2012-06-01

A spectral analysis approach was used to estimate kinetic parameters of the L-[1-(11)C]leucine positron emission tomography (PET) method and regional rates of cerebral protein synthesis (rCPS) on a voxel-by-voxel basis. Spectral analysis applies to both heterogeneous and homogeneous tissues; it does not require prior assumptions concerning number of tissue compartments. Parameters estimated with spectral analysis can be strongly affected by noise, but numerical filters improve estimation performance. Spectral analysis with iterative filter (SAIF) was originally developed to improve estimation of leucine kinetic parameters and rCPS in region-of-interest (ROI) data analyses. In the present study, we optimized SAIF for application at the voxel level. In measured L-[1-(11)C]leucine PET data, voxel-level SAIF parameter estimates averaged over all voxels within a ROI (mean voxel-SAIF) generally agreed well with corresponding estimates derived by applying the originally developed SAIF to ROI time-activity curves (ROI-SAIF). Region-of-interest-SAIF and mean voxel-SAIF estimates of rCPS were highly correlated. Simulations showed that mean voxel-SAIF rCPS estimates were less biased and less variable than ROI-SAIF estimates in the whole brain and cortex; biases were similar in white matter. We conclude that estimation of rCPS with SAIF is improved when the method is applied at voxel level than in ROI analysis.

Experiments on Nucleation in Different Flow Regimes

NASA Technical Reports Server (NTRS)

Bayuzick, R. J.; Hofmeister, W. H.; Morton, C. M.; Robinson, M. B.

1999-01-01

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. Dilatometry 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.

Starting Block Performance in Sprinters: A Statistical Method for Identifying Discriminative Parameters of the Performance and an Analysis of the Effect of Providing Feedback over a 6-Week Period

PubMed Central

Fortier, Sylvie; Basset, Fabien A.; Mbourou, Ginette A.; Favérial, Jérôme; Teasdale, Normand

2005-01-01

The purpose of this study was twofold: (a) to examine if kinetic and kinematic parameters of the sprint start could differentiate elite from sub-elite sprinters and, (b) to investigate whether providing feedback (FB) about selected parameters could improve starting block performance of intermediate sprinters over a 6-week training period. Twelve male sprinters, assigned to an elite or a sub-elite group, participated in Experiment 1. Eight intermediate sprinters participated in Experiment 2. All athletes were required to perform three sprint starts at maximum intensity followed by a 10-m run. To detect differences between elite and sub-elite groups, comparisons were made using t-tests for independent samples. Parameters reaching a significant group difference were retained for the linear discriminant analysis (LDA). The LDA yielded four discriminative kinetic parameters. Feedback about these selected parameters was given to sprinters in Experiment 2. For this experiment, data acquisition was divided into three periods. The first six sessions were without specific FB, whereas the following six sessions were enriched by kinetic FB. Finally, athletes underwent a retention session (without FB) 4 weeks after the twelfth session. Even though differences were found in the time to front peak force, the time to rear peak force, and the front peak force in the retention session, the results of the present study showed that providing FB about selected kinetic parameters differentiating elite from sub-elite sprinters did not improve the starting block performance of intermediate sprinters. Key Points The linear discriminative analysis allows the identification of starting block parameters differentiating elite from sub-elite athletes. 6-week of feedback does not alter starting block performance in training context. The present results failed to confirm previous studies since feedback did not improve targeted kinetic parameters of the complex motor task in real-world context. PMID:24431969

Starting Block Performance in Sprinters: A Statistical Method for Identifying Discriminative Parameters of the Performance and an Analysis of the Effect of Providing Feedback over a 6-Week Period.

PubMed

Fortier, Sylvie; Basset, Fabien A; Mbourou, Ginette A; Favérial, Jérôme; Teasdale, Normand

2005-06-01

(a) to examine if kinetic and kinematic parameters of the sprint start could differentiate elite from sub-elite sprinters and, (b) to investigate whether providing feedback (FB) about selected parameters could improve starting block performance of intermediate sprinters over a 6-week training period. Twelve male sprinters, assigned to an elite or a sub-elite group, participated in Experiment 1. Eight intermediate sprinters participated in Experiment 2. All athletes were required to perform three sprint starts at maximum intensity followed by a 10-m run. To detect differences between elite and sub-elite groups, comparisons were made using t-tests for independent samples. Parameters reaching a significant group difference were retained for the linear discriminant analysis (LDA). The LDA yielded four discriminative kinetic parameters. Feedback about these selected parameters was given to sprinters in Experiment 2. For this experiment, data acquisition was divided into three periods. The first six sessions were without specific FB, whereas the following six sessions were enriched by kinetic FB. Finally, athletes underwent a retention session (without FB) 4 weeks after the twelfth session. Even though differences were found in the time to front peak force, the time to rear peak force, and the front peak force in the retention session, the results of the present study showed that providing FB about selected kinetic parameters differentiating elite from sub-elite sprinters did not improve the starting block performance of intermediate sprinters. Key PointsThe linear discriminative analysis allows the identification of starting block parameters differentiating elite from sub-elite athletes.6-week of feedback does not alter starting block performance in training context.The present results failed to confirm previous studies since feedback did not improve targeted kinetic parameters of the complex motor task in real-world context.

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.

Faster heart rate and muscular oxygen uptake kinetics in type 2 diabetes patients following endurance training.

PubMed

Koschate, Jessica; Drescher, Uwe; Brinkmann, Christian; Baum, Klaus; Schiffer, Thorsten; Latsch, Joachim; Brixius, Klara; Hoffmann, Uwe

2016-11-01

Cardiorespiratory kinetics were analyzed in type 2 diabetes patients before and after a 12-week endurance exercise-training intervention. It was hypothesized that muscular oxygen uptake and heart rate (HR) kinetics would be faster after the training intervention and that this would be detectable using a standardized work rate protocol with pseudo-random binary sequences. The cardiorespiratory kinetics of 13 male sedentary, middle-aged, overweight type 2 diabetes patients (age, 60 ± 8 years; body mass index, 33 ± 4 kg·m -2 ) were tested before and after the 12-week exercise intervention. Subjects performed endurance training 3 times a week on nonconsecutive days. Pseudo-random binary sequences exercise protocols in combination with time series analysis were used to estimate kinetics. Greater maxima in cross-correlation functions (CCF max ) represent faster kinetics of the respective parameter. CCF max of muscular oxygen uptake (pre-training: 0.31 ± 0.03; post-training: 0.37 ± 0.1, P = 0.024) and CCF max of HR (pre-training: 0.25 ± 0.04; post-training: 0.29 ± 0.06, P = 0.007) as well as peak oxygen uptake (pre-training: 24.4 ± 4.7 mL·kg -1 ·min -1 ; post-training: 29.3 ± 6.5 mL·kg -1 ·min -1 , P = 0.004) increased significantly over the course of the exercise intervention. In conclusion, kinetic responses to changing work rates in the moderate-intensity range are similar to metabolic demands occurring in everyday habitual activities. Moderate endurance training accelerated the kinetic responses of HR and muscular oxygen uptake. Furthermore, the applicability of the used method to detect these accelerations was demonstrated.

Kinetics of thermal decomposition of hydrated minerals associated with hematite ore in a fluidized bed reactor

NASA Astrophysics Data System (ADS)

Beuria, P. C.; Biswal, S. K.; Mishra, B. K.; Roy, G. G.

2017-03-01

The kinetics of removal of loss on ignition (LOI) by thermal decomposition of hydrated minerals present in natural iron ores (i.e., kaolinite, gibbsite, and goethite) was investigated in a laboratory-scale vertical fluidized bed reactor (FBR) using isothermal methods of kinetic analysis. Experiments in the FBR in batch processes were carried out at different temperatures (300 to 1200°C) and residence time (1 to 30 min) for four different iron ore samples with various LOIs (2.34wt% to 9.83wt%). The operating velocity was maintained in the range from 1.2 to 1.4 times the minimum fluidization velocity ( U mf). We observed that, below a certain critical temperature, the FBR did not effectively reduce the LOI to a desired level even with increased residence time. The results of this study indicate that the LOI level could be reduced by 90% within 1 min of residence time at 1100°C. The kinetics for low-LOI samples (<6wt%) indicates two different reaction mechanisms in two temperature regimes. At lower temperatures (300 to 700°C), the kinetics is characterized by a lower activation energy (diffusion-controlled physical moisture removal), followed by a higher activation energy (chemically controlled removal of LOI). In the case of high-LOI samples, three different kinetics mechanisms prevail at different temperature regimes. At temperature up to 450°C, diffusion kinetics prevails (removal of physical moisture); at temperature from 450 to 650°C, chemical kinetics dominates during removal of matrix moisture. At temperatures greater than 650°C, nucleation and growth begins to influence the rate of removal of LOI.

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.

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.

Kinetic Modeling of Accelerated Stability Testing Enabled by Second Harmonic Generation Microscopy.

PubMed

Song, Zhengtian; Sarkar, Sreya; Vogt, Andrew D; Danzer, Gerald D; Smith, Casey J; Gualtieri, Ellen J; Simpson, Garth J

2018-04-03

The low limits of detection afforded by second harmonic generation (SHG) microscopy coupled with image analysis algorithms enabled quantitative modeling of the temperature-dependent crystallization of active pharmaceutical ingredients (APIs) within amorphous solid dispersions (ASDs). ASDs, in which an API is maintained in an amorphous state within a polymer matrix, are finding increasing use to address solubility limitations of small-molecule APIs. Extensive stability testing is typically performed for ASD characterization, the time frame for which is often dictated by the earliest detectable onset of crystal formation. Here a study of accelerated stability testing on ritonavir, a human immunodeficiency virus (HIV) protease inhibitor, has been conducted. Under the condition for accelerated stability testing at 50 °C/75%RH and 40 °C/75%RH, ritonavir crystallization kinetics from amorphous solid dispersions were monitored by SHG microscopy. SHG microscopy coupled by image analysis yielded limits of detection for ritonavir crystals as low as 10 ppm, which is about 2 orders of magnitude lower than other methods currently available for crystallinity detection in ASDs. The four decade dynamic range of SHG microscopy enabled quantitative modeling with an established (JMAK) kinetic model. From the SHG images, nucleation and crystal growth rates were independently determined.

Flammability and oxidation kinetics of hydrophobic silica aerogels.

PubMed

Li, Zhi; Cheng, Xudong; Shi, Long; He, Song; Gong, Lunlun; Li, Congcong; Zhang, Heping

2016-12-15

Silica aerogels (SAs) present great application prospects especially on thermal insulation, but their flammability is usually ignored. A combined study on the combustion behaviors and oxidation kinetics of hydrophobic silica aerogels prepared by ambient pressure drying (SA-apd) and supercritical drying (SA-sd) was performed by employing cone calorimeter and thermal analysis. The whole combustion process for SAs could be divided into three stages in which a fire propagation phenomenon was observed with the radial propagation velocity of 6.6-8.3cms -1 . Current investigations forcefully demonstrated that hydrophobic SAs were combustible and easy to flashover when exposed to a heat flux higher than 25kWm -2 . Compared between the two SAs, the SA-sd owned a less fire risk with presenting a less fire hazard and a lower smoke toxicity than those of SA-apd. The oxidation kinetics by Ozawa-Flynn-Wall method revealed that SA-sd had larger apparent activation energies than those of SA-apd which conformed to the thermal stability analysis by TG-DSC. Furthermore, a two-step combustion mechanism was proposed to explain the combustion behaviors of SAs. Copyright © 2016 Elsevier B.V. All rights reserved.

Validated selective spectrophotometric methods for the kinetic determination of desloratidine in tablets and in the presence of its parent drug.

PubMed

Derayea, S M Sayed

2014-11-01

Two novel selective validated methods have been developed for analysis of desloratidine (DSL) in its tablets formulation. Both were kinetic spectrophotometric methods, depend on the interaction of the secondary amino group in DSL with acetaldehyde to give N-vinylpiperidyl product. The formed N-vinylpiperidyl compound was reacted with 2,3,5,6-tetrachloro-1,4-benzoquinone (chloranil) to form colored N-vinylpiperidyl-substituted benzoquinone derivatives. The formed blue-colored derivative was measured at 672 nm. The reaction conditions were carefully studied and all factors were optimized. The molar ratio between the reactants was estimated and a suggested reaction mechanism was presented. The analysis was carried out using initial rate and fixed time (at 6 min) methods. The linear concentration ranges were 3-50 and 10 - 60 μg mL-1 with limits of detection of 3.2 and 2.2 μg mL-1 for the initial rate and fixed time methods, respectively. ICH guidelines were applied for analytical performance validation of the proposed methods. The presence of common excipients in the pharmaceutical formulation did not produce any significant interference, as well as from loratadine, which is the parent compound of DSL. Different commercially available tablets formulations containing were successfully analyzed, with, the percentage recovery ranging from 97.28-100.90 ± 0.7 2-1.41%. The obtained results were compared statistically with the reported method results. The proposed methods have similar accuracy and precision as the reported as indicated from the F- and t-test data.

Thermoluminescence glow curve analysis and CGCD method for erbium doped CaZrO{sub 3} phosphor

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

Tiwari, Ratnesh, E-mail: 31rati@gmail.com; Chopra, Seema

2016-05-06

The manuscript report the synthesis, thermoluminescence study at fixed concentration of Er{sup 3+} (1 mol%) doped CaZrO{sub 3} phosphor. The phosphors were prepared by modified solid state reaction method. The powder sample was characterized by thermoluminescence (TL) glow curve analysis. In TL glow curve the optimized concentration in 1mol% for UV irradiated sample. The kinetic parameters were calculated by computerized glow curve deconvolution (CGCD) techniaue. Trapping parameters gives the information of dosimetry loss in prepared phosphor and its usability in environmental monitoring and for personal monitoring. CGCD is the advance tool for analysis of complicated TL glow curves.

Methods for the Measurement of a Bacterial Enzyme Activity in Cell Lysates and Extracts

PubMed Central

Mendz, George; Hazell, Stuart

1998-01-01

The kinetic characteristics and regulation of aspartate carbamoyltransferase activity were studied in lysates and cell extracts of Helicobacter pylori by three diffirent methods. Nuclear magnetic resonance spectroscopy, radioactive tracer analysis, and spectrophotometry were employed in conjunction to identify the properties of the enzyme activity and to validate the results obtained with each assay. NMR spectroscopy was the most direct method to provide proof of ACTase activity; radioactive tracer analysis was the most sensitive technique and a microtitre-based colorimetric assay was the most cost-and time-efficient for large scale analyses. Freeze-thawing was adopted as the preferred method for cell lysis in studying enzyme activity in situ. This study showed the benefits of employing several different complementary methods to investigate bacterial enzyme activity. PMID:12734591

Semi-Lagrangian particle methods for high-dimensional Vlasov-Poisson systems

NASA Astrophysics Data System (ADS)

Cottet, Georges-Henri

2018-07-01

This paper deals with the implementation of high order semi-Lagrangian particle methods to handle high dimensional Vlasov-Poisson systems. It is based on recent developments in the numerical analysis of particle methods and the paper focuses on specific algorithmic features to handle large dimensions. The methods are tested with uniform particle distributions in particular against a recent multi-resolution wavelet based method on a 4D plasma instability case and a 6D gravitational case. Conservation properties, accuracy and computational costs are monitored. The excellent accuracy/cost trade-off shown by the method opens new perspective for accurate simulations of high dimensional kinetic equations by particle methods.

Slowest kinetic modes revealed by metabasin renormalization

NASA Astrophysics Data System (ADS)

Okushima, Teruaki; Niiyama, Tomoaki; Ikeda, Kensuke S.; Shimizu, Yasushi

2018-02-01

Understanding the slowest relaxations of complex systems, such as relaxation of glass-forming materials, diffusion in nanoclusters, and folding of biomolecules, is important for physics, chemistry, and biology. For a kinetic system, the relaxation modes are determined by diagonalizing its transition rate matrix. However, for realistic systems of interest, numerical diagonalization, as well as extracting physical understanding from the diagonalization results, is difficult due to the high dimensionality. Here, we develop an alternative and generally applicable method of extracting the long-time scale relaxation dynamics by combining the metabasin analysis of Okushima et al. [Phys. Rev. E 80, 036112 (2009), 10.1103/PhysRevE.80.036112] and a Jacobi method. We test the method on an illustrative model of a four-funnel model, for which we obtain a renormalized kinematic equation of much lower dimension sufficient for determining slow relaxation modes precisely. The method is successfully applied to the vacancy transport problem in ionic nanoparticles [Niiyama et al., Chem. Phys. Lett. 654, 52 (2016), 10.1016/j.cplett.2016.04.088], allowing a clear physical interpretation that the final relaxation consists of two successive, characteristic processes.

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.

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

Calculation of kinetic rate constants from thermodynamic data

NASA Technical Reports Server (NTRS)

Marek, C. John

1995-01-01

A new scheme for relating the absolute value for the kinetic rate constant k to the thermodynamic constant Kp is developed for gases. In this report the forward and reverse rate constants are individually related to the thermodynamic data. The kinetic rate constants computed from thermodynamics compare well with the current kinetic rate constants. This method is self consistent and does not have extensive rules. It is first demonstrated and calibrated by computing the HBr reaction from H2 and Br2. This method then is used on other reactions.

High-order continuum kinetic method for modeling plasma dynamics in phase space

DOE PAGES

Vogman, G. V.; Colella, P.; Shumlak, U.

2014-12-15

Continuum methods offer a high-fidelity means of simulating plasma kinetics. While computationally intensive, these methods are advantageous because they can be cast in conservation-law form, are not susceptible to noise, and can be implemented using high-order numerical methods. Advances in continuum method capabilities for modeling kinetic phenomena in plasmas require the development of validation tools in higher dimensional phase space and an ability to handle non-cartesian geometries. To that end, a new benchmark for validating Vlasov-Poisson simulations in 3D (x,v x,v y) is presented. The benchmark is based on the Dory-Guest-Harris instability and is successfully used to validate a continuummore » finite volume algorithm. To address challenges associated with non-cartesian geometries, unique features of cylindrical phase space coordinates are described. Preliminary results of continuum kinetic simulations in 4D (r,z,v r,v z) phase space are presented.« less

Simulating Chemical Kinetics Without Differential Equations: A Quantitative Theory Based on Chemical Pathways.

PubMed

Bai, Shirong; Skodje, Rex T

2017-08-17

A new approach is presented for simulating the time-evolution of chemically reactive systems. This method provides an alternative to conventional modeling of mass-action kinetics that involves solving differential equations for the species concentrations. The method presented here avoids the need to solve the rate equations by switching to a representation based on chemical pathways. In the Sum Over Histories Representation (or SOHR) method, any time-dependent kinetic observable, such as concentration, is written as a linear combination of probabilities for chemical pathways leading to a desired outcome. In this work, an iterative method is introduced that allows the time-dependent pathway probabilities to be generated from a knowledge of the elementary rate coefficients, thus avoiding the pitfalls involved in solving the differential equations of kinetics. The method is successfully applied to the model Lotka-Volterra system and to a realistic H 2 combustion model.

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.

Kinetics of thermolysis of lanthanum nitrate with hexamethylenetetramine: Crystal structure, TG-DSC, impact and friction sensitivity studies, Part-96

NASA Astrophysics Data System (ADS)

Nibha; Baranwal, B. P.; Singh, Gurdip; Singh, C. P.; Daniliuc, Constantin G.; Soni, P. K.; Nath, Yogeshwar

2014-11-01

The development of high energetic materials includes process ability and the ability to attain insensitive munitions (IM). This paper investigates the preparation of lanthanum metal nitrate complex of hexamethylenetetramine in water at room temperature. This complex of molecular formulae [La (NO3)2(H2O)6] (2HMTA) (NO3-) (H2O) was characterized by X-ray crystallography. Thermal decomposition was investigated using TG, TG-DSC and ignition delay measurements. Kinetic analysis of isothermal TG data has been investigated using model fitting methods as well as model free isoconversional methods. The sensitivity measurements towards mechanical destructive stimuli such as impact and friction were carried out and the complex was found to be insensitive. In order to identify the end product of thermolysis, X-ray diffraction patterns of end product was carried out which proves the formation of La2O3.

Kinetics of scrap tyre pyrolysis under vacuum conditions

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

Lopez, Gartzen; Aguado, Roberto; Olazar, Martin

2009-10-15

Scrap tyre pyrolysis under vacuum is attractive because it allows easier product condensation and control of composition (gas, liquid and solid). With the aim of determining the effect of vacuum on the pyrolysis kinetics, a study has been carried out in thermobalance. Two data analysis methods have been used in the kinetic study: (i) the treatment of experimental data of weight loss and (ii) the deconvolution of DTG (differential thermogravimetry) curve. The former allows for distinguishing the pyrolysis of the three main components (volatile components, natural rubber and styrene-butadiene rubber) according to three successive steps. The latter method identifies themore » kinetics for the pyrolysis of individual components by means of DTG curve deconvolution. The effect of vacuum in the process is significant. The values of activation energy for the pyrolysis of individual components of easier devolatilization (volatiles and NR) are lower for pyrolysis under vacuum with a reduction of 12 K in the reaction starting temperature. The kinetic constant at 503 K for devolatilization of volatile additives at 0.25 atm is 1.7 times higher than that at 1 atm, and that corresponding to styrene-butadiene rubber at 723 K is 2.8 times higher. Vacuum enhances the volatilization and internal diffusion of products in the pyrolysis process, which contributes to attenuating the secondary reactions of the repolymerization and carbonization of these products on the surface of the char (carbon black). The higher quality of carbon black is interesting for process viability. The large-scale implementation of this process in continuous mode requires a comparison to be made between the economic advantages of using a vacuum and the energy costs, which will be lower when the technologies used for pyrolysis require a lower ratio between reactor volume and scrap tyre flow rate.« less

Kinetics of scrap tyre pyrolysis under vacuum conditions.

PubMed

Lopez, Gartzen; Aguado, Roberto; Olazar, Martín; Arabiourrutia, Miriam; Bilbao, Javier

2009-10-01

Scrap tyre pyrolysis under vacuum is attractive because it allows easier product condensation and control of composition (gas, liquid and solid). With the aim of determining the effect of vacuum on the pyrolysis kinetics, a study has been carried out in thermobalance. Two data analysis methods have been used in the kinetic study: (i) the treatment of experimental data of weight loss and (ii) the deconvolution of DTG (differential thermogravimetry) curve. The former allows for distinguishing the pyrolysis of the three main components (volatile components, natural rubber and styrene-butadiene rubber) according to three successive steps. The latter method identifies the kinetics for the pyrolysis of individual components by means of DTG curve deconvolution. The effect of vacuum in the process is significant. The values of activation energy for the pyrolysis of individual components of easier devolatilization (volatiles and NR) are lower for pyrolysis under vacuum with a reduction of 12K in the reaction starting temperature. The kinetic constant at 503K for devolatilization of volatile additives at 0.25atm is 1.7 times higher than that at 1atm, and that corresponding to styrene-butadiene rubber at 723K is 2.8 times higher. Vacuum enhances the volatilization and internal diffusion of products in the pyrolysis process, which contributes to attenuating the secondary reactions of the repolymerization and carbonization of these products on the surface of the char (carbon black). The higher quality of carbon black is interesting for process viability. The large-scale implementation of this process in continuous mode requires a comparison to be made between the economic advantages of using a vacuum and the energy costs, which will be lower when the technologies used for pyrolysis require a lower ratio between reactor volume and scrap tyre flow rate.

Synthesis, characterization, shrinkage and curing kinetics of a new low-shrinkage urethane dimethacrylate monomer for dental applications.

PubMed

Atai, Mohammad; Ahmadi, Mehdi; Babanzadeh, Samal; Watts, David C

2007-08-01

The aim of the study was to synthesize and characterize an isophorone-based urethane dimethacrylate (IP-UDMA) resin-monomer and to investigate its shrinkage and curing kinetics. The IP-UDMA monomer was synthesized through the reaction of polyethylene glycol 400 and isophorone diisocyanate followed by reacting with HEMA to terminate it with methacrylate end groups. The reaction was followed using a standard back titration method and FTIR spectroscopy. The final product was purified and characterized using FTIR, (1)H NMR, elemental analysis and refractive index measurement. The shrinkage-strain of the specimens photopolymerized at circa 700mW/cm(2) was measured using the bonded-disk technique at 23, 35, and 45 degrees C. Initial shrinkage-strain-rates were obtained by numerical differentiation of shrinkage-strain data with respect to time. Degree-of-conversion of the specimens was measured using FTIR spectroscopy. The thermal curing kinetics of the monomer were also studied by differential scanning calorimetry (DSC). The characterization methods confirmed the suggested reaction route and the synthesized monomer. A low shrinkage-strain of about 4% was obtained for the new monomer. The results showed that the shrinkage-strain-rate of the monomer followed the autocatalytic model of Kamal and Sourour [Kamal MR, Sourour S. Kinetic and thermal characterization of thermoset cure. Polym Eng Sci 1973;13(1):59-64], which is used to describe the reaction kinetics of thermoset resins. The model parameters were calculated by linearization of the equation. The model prediction was in a good agreement with the experimental data. The properties of the new monomer compare favorably with properties of the commercially available resins.

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.

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.

Kinetics and evolved gas analysis for pyrolysis of food processing wastes using TGA/MS/FT-IR.

PubMed

Özsin, Gamzenur; Pütün, Ayşe Eren

2017-06-01

The objective of this study was to identify the pyrolysis of different bio-waste produced by food processing industry in a comprehensible manner. For this purpose, pyrolysis behaviors of chestnut shells (CNS), cherry stones (CS) and grape seeds (GS) were investigated by thermogravimetric analysis (TGA) combined with a Fourier-transform infrared (FT-IR) spectrometer and a mass spectrometer (MS). In order to make available theoretical groundwork for biomass pyrolysis, activation energies were calculated with the help of four different model-free kinetic methods. The results are attributed to the complex reaction schemes which imply parallel, competitive and complex reactions during pyrolysis. During pyrolysis, the evolution of volatiles was also characterized by FT-IR and MS. The main evolved gases were determined as H 2 O, CO 2 and hydrocarbons such as CH 4 and temperature dependent profiles of the species were obtained. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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.

Contact Kinetics in Fractal Macromolecules.

PubMed

Dolgushev, Maxim; Guérin, Thomas; Blumen, Alexander; Bénichou, Olivier; Voituriez, Raphaël

2015-11-13

We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the mean first contact time for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the nonequilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the mean first contact time between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations.

Ion induced electron emission statistics under Agm- cluster bombardment of Ag

NASA Astrophysics Data System (ADS)

Breuers, A.; Penning, R.; Wucher, A.

2018-05-01

The electron emission from a polycrystalline silver surface under bombardment with Agm- cluster ions (m = 1, 2, 3) is investigated in terms of ion induced kinetic excitation. The electron yield γ is determined directly by a current measurement method on the one hand and implicitly by the analysis of the electron emission statistics on the other hand. Successful measurements of the electron emission spectra ensure a deeper understanding of the ion induced kinetic electron emission process, with particular emphasis on the effect of the projectile cluster size to the yield as well as to emission statistics. The results allow a quantitative comparison to computer simulations performed for silver atoms and clusters impinging onto a silver surface.

Elucidation of molecular kinetic schemes from macroscopic traces using system identification

PubMed Central

González-Maeso, Javier; Sealfon, Stuart C.; Galocha-Iragüen, Belén; Brezina, Vladimir

2017-01-01

Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE). SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology can be successfully applied to accurately derive molecular kinetic schemes from experimental macroscopic traces, and we anticipate that it may be useful in the study of a wide variety of biological systems. PMID:28192423

Pursuing reliable thermal analysis techniques for energetic materials: decomposition kinetics and thermal stability of dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50).

PubMed

Muravyev, Nikita V; Monogarov, Konstantin A; Asachenko, Andrey F; Nechaev, Mikhail S; Ananyev, Ivan V; Fomenkov, Igor V; Kiselev, Vitaly G; Pivkina, Alla N

2016-12-21

Thermal decomposition of a novel promising high-performance explosive dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) was studied using a number of thermal analysis techniques (thermogravimetry, differential scanning calorimetry, and accelerating rate calorimetry, ARC). To obtain more comprehensive insight into the kinetics and mechanism of TKX-50 decomposition, a variety of complementary thermoanalytical experiments were performed under various conditions. Non-isothermal and isothermal kinetics were obtained at both atmospheric and low (up to 0.3 Torr) pressures. The gas products of thermolysis were detected in situ using IR spectroscopy, and the structure of solid-state decomposition products was determined by X-ray diffraction and scanning electron microscopy. Diammonium 5,5'-bistetrazole-1,1'-diolate (ABTOX) was directly identified to be the most important intermediate of the decomposition process. The important role of bistetrazole diol (BTO) in the mechanism of TKX-50 decomposition was also rationalized by thermolysis experiments with mixtures of TKX-50 and BTO. Several widely used thermoanalytical data processing techniques (Kissinger, isoconversional, formal kinetic approaches, etc.) were independently benchmarked against the ARC data, which are more germane to the real storage and application conditions of energetic materials. Our study revealed that none of the Arrhenius parameters reported before can properly describe the complex two-stage decomposition process of TKX-50. In contrast, we showed the superior performance of the isoconversional methods combined with isothermal measurements, which yielded the most reliable kinetic parameters of TKX-50 thermolysis. In contrast with the existing reports, the thermal stability of TKX-50 was determined in the ARC experiments to be lower than that of hexogen, but close to that of hexanitrohexaazaisowurtzitane (CL-20).

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.

New approach for determination of sulfadiazine in pharmaceutical preparations using 4(4-sulphophenylazo)pyrogallol: Kinetic spectrophotometric method.

PubMed

Naser, Naser A; Alasedi, Kasim M; Khan, Zainab A

2018-05-04

A new trend describes the development and validation of a simple, sensitive and selective kinetic spectrophotometric methods for the determination of sulfadiazine in pharmaceutical formulations has been conducted. In this paper, sulfadiazine was derivatized as a new organic compound 4(4-sulphophenylazo) pyrogallol, 4-SPAP, by coupling pyrogallol with diazotized sulfadiazine in medium of controlled pH. 4-SPAP was characterized by techniques of FT-IR, H-NMR, GC-Mass, TG and DSC thermal analysis methods. Solvatochromic behavior in solvents of various polarities was also investigated. The determination of sulfadiazine was accomplished by initial rate and fixed time methods. These methods were based on the reaction of the compound containing sulfadiazine, 4-SPAP, with Ca(II) to form colored product with a maximum absorbance at 520 nm. The two methods were adopted for constructing the calibration curves and examined for their suitability for the quantitation of sulfadiazine in pharmaceuticals. The limit of detection (LOD) and limit of quantification (LOQ) were found to be, by initial rate method, 0.35 and 1.05 μg·mL -1 and that by fixed time method were found to be 0.69 and 2.07 μg·mL -1 , respectively. The percent relative standard deviations (%RSD) for the results ranged from 1.04% to 1.76% and 0.85% to 1.42% for the initial rate and fixed time methods of the proposed kinetic spectrophotometric method, respectively. The existence of common excipients in the pharmaceutical formulation did not produce any significant interference. Statistical comparison was reported as indicated from the F- and t-test data of the proposed methods with that of reference method showing excellent agreement and indicating no significant difference in their accuracy and precision. Copyright © 2018 Elsevier B.V. All rights reserved.

From atomistic interfaces to dendritic patterns

NASA Astrophysics Data System (ADS)

Galenko, P. K.; Alexandrov, D. V.

2018-01-01

Transport processes around phase interfaces, together with thermodynamic properties and kinetic phenomena, control the formation of dendritic patterns. Using the thermodynamic and kinetic data of phase interfaces obtained on the atomic scale, one can analyse the formation of a single dendrite and the growth of a dendritic ensemble. This is the result of recent progress in theoretical methods and computational algorithms calculated using powerful computer clusters. Great benefits can be attained from the development of micro-, meso- and macro-levels of analysis when investigating the dynamics of interfaces, interpreting experimental data and designing the macrostructure of samples. The review and research articles in this theme issue cover the spectrum of scales (from nano- to macro-length scales) in order to exhibit recently developing trends in the theoretical analysis and computational modelling of dendrite pattern formation. Atomistic modelling, the flow effect on interface dynamics, the transition from diffusion-limited to thermally controlled growth existing at a considerable driving force, two-phase (mushy) layer formation, the growth of eutectic dendrites, the formation of a secondary dendritic network due to coalescence, computational methods, including boundary integral and phase-field methods, and experimental tests for theoretical models-all these themes are highlighted in the present issue. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

Experimental study of crack initiation and propagation in high- and gigacycle fatigue in titanium alloys

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

Bannikov, Mikhail, E-mail: mbannikov@icmm.ru, E-mail: oborin@icmm.ru, E-mail: naimark@icmm.ru; Oborin, Vladimir, E-mail: mbannikov@icmm.ru, E-mail: oborin@icmm.ru, E-mail: naimark@icmm.ru; Naimark, Oleg, E-mail: mbannikov@icmm.ru, E-mail: oborin@icmm.ru, E-mail: naimark@icmm.ru

Fatigue (high- and gigacycle) crack initiation and its propagation in titanium alloys with coarse and fine grain structure are studied by fractography analysis of fracture surface. Fractured specimens were analyzed by interferometer microscope and SEM to improve methods of monitoring of damage accumulation during fatigue test and to verify the models for fatigue crack kinetics. Fatigue strength was estimated for high cycle fatigue regime using the Luong method [1] by “in-situ” infrared scanning of the sample surface for the step-wise loading history for different grain size metals. Fine grain alloys demonstrated higher fatigue resistance for both high cycle fatigue andmore » gigacycle fatigue regimes. Fracture surface analysis for plane and cylindrical samples was carried out using optical and electronic microscopy method. High resolution profilometry (interferometer-profiler New View 5010) data of fracture surface roughness allowed us to estimate scale invariance (the Hurst exponent) and to establish the existence of two characteristic areas of damage localization (different values of the Hurst exponent). Area 1 with diameter ∼300 μm has the pronounced roughness and is associated with damage localization hotspot. Area 2 shows less amplitude roughness, occupies the rest fracture surface and considered as the trace of the fatigue crack path corresponding to the Paris kinetics.« less

High temperature polymer degradation: Rapid IR flow-through method for volatile quantification

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

Giron, Nicholas H.; Celina, Mathew C.

Accelerated aging of polymers at elevated temperatures often involves the generation of volatiles. These can be formed as the products of oxidative degradation reactions or intrinsic pyrolytic decomposition as part of polymer scission reactions. A simple analytical method for the quantification of water, CO 2, and CO as fundamental signatures of degradation kinetics is required. Here, we describe an analytical framework and develops a rapid mid-IR based gas analysis methodology to quantify volatiles that are contained in small ampoules after aging exposures. The approach requires identification of unique spectral signatures, systematic calibration with known concentrations of volatiles, and a rapidmore » acquisition FTIR spectrometer for time resolved successive spectra. Furthermore, the volatiles are flushed out from the ampoule with dry N2 carrier gas and are then quantified through spectral and time integration. This method is sufficiently sensitive to determine absolute yields of ~50 μg water or CO 2, which relates to probing mass losses of less than 0.01% for a 1 g sample, i.e. the early stages in the degradation process. Such quantitative gas analysis is not easily achieved with other approaches. Our approach opens up the possibility of quantitative monitoring of volatile evolution as an avenue to explore polymer degradation kinetics and its dependence on time and temperature.« less

High temperature polymer degradation: Rapid IR flow-through method for volatile quantification

DOE PAGES

Giron, Nicholas H.; Celina, Mathew C.

2017-05-19

Accelerated aging of polymers at elevated temperatures often involves the generation of volatiles. These can be formed as the products of oxidative degradation reactions or intrinsic pyrolytic decomposition as part of polymer scission reactions. A simple analytical method for the quantification of water, CO 2, and CO as fundamental signatures of degradation kinetics is required. Here, we describe an analytical framework and develops a rapid mid-IR based gas analysis methodology to quantify volatiles that are contained in small ampoules after aging exposures. The approach requires identification of unique spectral signatures, systematic calibration with known concentrations of volatiles, and a rapidmore » acquisition FTIR spectrometer for time resolved successive spectra. Furthermore, the volatiles are flushed out from the ampoule with dry N2 carrier gas and are then quantified through spectral and time integration. This method is sufficiently sensitive to determine absolute yields of ~50 μg water or CO 2, which relates to probing mass losses of less than 0.01% for a 1 g sample, i.e. the early stages in the degradation process. Such quantitative gas analysis is not easily achieved with other approaches. Our approach opens up the possibility of quantitative monitoring of volatile evolution as an avenue to explore polymer degradation kinetics and its dependence on time and temperature.« less

A resource facility for kinetic analysis: modeling using the SAAM computer programs.

PubMed

Foster, D M; Boston, R C; Jacquez, J A; Zech, L

1989-01-01

Kinetic analysis and integrated system modeling have contributed significantly to understanding the physiology and pathophysiology of metabolic systems in humans and animals. Many experimental biologists are aware of the usefulness of these techniques and recognize that kinetic modeling requires special expertise. The Resource Facility for Kinetic Analysis (RFKA) provides this expertise through: (1) development and application of modeling technology for biomedical problems, and (2) development of computer-based kinetic modeling methodologies concentrating on the computer program Simulation, Analysis, and Modeling (SAAM) and its conversational version, CONversational SAAM (CONSAM). The RFKA offers consultation to the biomedical community in the use of modeling to analyze kinetic data and trains individuals in using this technology for biomedical research. Early versions of SAAM were widely applied in solving dosimetry problems; many users, however, are not familiar with recent improvements to the software. The purpose of this paper is to acquaint biomedical researchers in the dosimetry field with RFKA, which, together with the joint National Cancer Institute-National Heart, Lung and Blood Institute project, is overseeing SAAM development and applications. In addition, RFKA provides many service activities to the SAAM user community that are relevant to solving dosimetry problems.

A second-order accurate kinetic-theory-based method for inviscid compressible flows

NASA Technical Reports Server (NTRS)

Deshpande, Suresh M.

1986-01-01

An upwind method for the numerical solution of the Euler equations is presented. This method, called the kinetic numerical method (KNM), is based on the fact that the Euler equations are moments of the Boltzmann equation of the kinetic theory of gases when the distribution function is Maxwellian. The KNM consists of two phases, the convection phase and the collision phase. The method is unconditionally stable and explicit. It is highly vectorizable and can be easily made total variation diminishing for the distribution function by a suitable choice of the interpolation strategy. The method is applied to a one-dimensional shock-propagation problem and to a two-dimensional shock-reflection problem.

Mathematical methods to analysis of topology, functional variability and evolution of metabolic systems based on different decomposition concepts.

PubMed

Mrabet, Yassine; Semmar, Nabil

2010-05-01

Complexity of metabolic systems can be undertaken at different scales (metabolites, metabolic pathways, metabolic network map, biological population) and under different aspects (structural, functional, evolutive). To analyse such a complexity, metabolic systems need to be decomposed into different components according to different concepts. Four concepts are presented here consisting in considering metabolic systems as sets of metabolites, chemical reactions, metabolic pathways or successive processes. From a metabolomic dataset, such decompositions are performed using different mathematical methods including correlation, stiochiometric, ordination, classification, combinatorial and kinetic analyses. Correlation analysis detects and quantifies affinities/oppositions between metabolites. Stoichiometric analysis aims to identify the organisation of a metabolic network into different metabolic pathways on the hand, and to quantify/optimize the metabolic flux distribution through the different chemical reactions of the system. Ordination and classification analyses help to identify different metabolic trends and their associated metabolites in order to highlight chemical polymorphism representing different variability poles of the metabolic system. Then, metabolic processes/correlations responsible for such a polymorphism can be extracted in silico by combining metabolic profiles representative of different metabolic trends according to a weighting bootstrap approach. Finally evolution of metabolic processes in time can be analysed by different kinetic/dynamic modelling approaches.

Measuring two-dimensional receptor-ligand binding kinetics by micropipette.

PubMed Central

Chesla, S E; Selvaraj, P; Zhu, C

1998-01-01

We report a novel method for measuring forward and reverse kinetic rate constants, kf0 and kr0, for the binding of individual receptors and ligands anchored to apposing surfaces in cell adhesion. Not only does the method examine adhesion between a single pair of cells; it also probes predominantly a single receptor-ligand bond. The idea is to quantify the dependence of adhesion probability on contact duration and densities of the receptors and ligands. The experiment was an extension of existing micropipette protocols. The analysis was based on analytical solutions to the probabilistic formulation of kinetics for small systems. This method was applied to examine the interaction between Fc gamma receptor IIIA (CD16A) expressed on Chinese hamster ovary cell transfectants and immunoglobulin G (IgG) of either human or rabbit origin coated on human erythrocytes, which were found to follow a monovalent biomolecular binding mechanism. The measured rate constants are Ackf0 = (2.6 +/- 0.32) x 10(-7) micron 4 s-1 and kr0 = (0.37 +/- 0.055) s-1 for the CD16A-hIgG interaction and Ackf0 = (5.7 +/- 0.31) X 10(-7) micron 4 s-1 and kr0 = (0.20 +/- 0.042) s-1 for the CD16A-rIgG interaction, respectively, where Ac is the contact area, estimated to be a few percent of 3 micron 2. PMID:9726957

Non-animal approaches for toxicokinetics in risk evaluations of food chemicals.

PubMed

Punt, Ans; Peijnenburg, Ad A C M; Hoogenboom, Ron L A P; Bouwmeester, Hans

2017-01-01

The objective of the present work was to review the availability and predictive value of non-animal toxicokinetic approaches and to evaluate their current use in European risk evaluations of food contaminants, additives and food contact materials, as well as pesticides and medicines. Results revealed little use of quantitative animal or human kinetic data in risk evaluations of food chemicals, compared with pesticides and medicines. Risk evaluations of medicines provided sufficient in vivo kinetic data from different species to evaluate the predictive value of animal kinetic data for humans. These data showed a relatively poor correlation between the in vivo bioavailability in rats and dogs versus that in humans. In contrast, in vitro (human) kinetic data have been demonstrated to provide adequate predictions of the fate of compounds in humans, using appropriate in vitro-in vivo scalers and by integration of in vitro kinetic data with in silico kinetic modelling. Even though in vitro kinetic data were found to be occasionally included within risk evaluations of food chemicals, particularly results from Caco-2 absorption experiments and in vitro data on gut-microbial conversions, only minor use of in vitro methods for metabolism and quantitative in vitro-in vivo extrapolation methods was identified. Yet, such quantitative predictions are essential in the development of alternatives to animal testing as well as to increase human relevance of toxicological risk evaluations. Future research should aim at further improving and validating quantitative alternative methods for kinetics, thereby increasing regulatory acceptance of non-animal kinetic data.

Hypothesis testing for the validation of the kinetic spectrophotometric methods for the determination of lansoprazole in bulk and drug formulations via Fe(III) and Zn(II) chelates.

PubMed

Rahman, Nafisur; Kashif, Mohammad

2010-03-01

Point and interval hypothesis tests performed to validate two simple and economical, kinetic spectrophotometric methods for the assay of lansoprazole are described. The methods are based on the formation of chelate complex of the drug with Fe(III) and Zn(II). The reaction is followed spectrophotometrically by measuring the rate of change of absorbance of coloured chelates of the drug with Fe(III) and Zn(II) at 445 and 510 nm, respectively. The stoichiometric ratio of lansoprazole to Fe(III) and Zn(II) complexes were found to be 1:1 and 2:1, respectively. The initial-rate and fixed-time methods are adopted for determination of drug concentrations. The calibration graphs are linear in the range 50-200 µg ml⁻¹ (initial-rate method), 20-180 µg ml⁻¹ (fixed-time method) for lansoprazole-Fe(III) complex and 120-300 (initial-rate method), and 90-210 µg ml⁻¹ (fixed-time method) for lansoprazole-Zn(II) complex. The inter-day and intra-day precision data showed good accuracy and precision of the proposed procedure for analysis of lansoprazole. The point and interval hypothesis tests indicate that the proposed procedures are not biased. Copyright © 2010 John Wiley & Sons, Ltd.

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.

Kinetics of waterborne fluoropolymers prepared by one-step semi-continuous emulsion polymerization of chlorotrifluoroethylene, vinyl acetate, butyl acrylate and Veova 10

NASA Astrophysics Data System (ADS)

Liu, H. Z.; Wang, M. H.; Wang, Z. F.; Bian, J. M.

2018-01-01

Due to using gaseous fluorine monomer with toxicity, waterborne fluoropolymers are synthesized by semi-continuous high-pressure emulsion polymerization method which differs from free-pressure emulsion polymerization. To dates, the research on preparing process and kinetics for high-pressure emulsion polymerization is reported relatively less, which hinders researchers from understanding of mechanisms for monomer-fluorinated emulsion polymerization. The paper also provides a new method by element auxiliary analysis to calculate kinetics parameters of high-pressure emulsion polymerization. Based on aforementioned consideration, waterborne fluoropolymers were prepared by copolymerization of chlorotrifluoroethylene (CTFE), vinyl acetate (VAc), butyl acrylate (BA) and vinyl ester of versatic acid (Veova 10) using potassium persulfate as initiator and mixed surfactants. The kinetics of emulsion polymerization of waterborne fluoropolymers was then investigated. Effects of emulsifier concentration, initiator concentration, and polymerization temperature on polymerization rate (Rp) were evaluated, and relationship was described as Rp∝[I]0.10 and Rp∝[E]0.12. The apparent activation energy was determined to be 33.61 kJ·mol-1. Moreover, the relative conversion rate of CTFE with the other monomers was observed, and results indicated that CTFE monomer more uniformly copolymerized with the other monomers. The resulting emulsion properties and pressure change in an autoclave were evaluated at different stirring rates. The initial reaction time, defined as the beginning time of dropwise addition, was determined by the change in solid content and particle size of emulsion.

Effect of biochar particle size on hydrophobic organic compound sorption kinetics: Applicability of using representative size.

PubMed

Kang, Seju; Jung, Jihyeun; Choe, Jong Kwon; Ok, Yong Sik; Choi, Yongju

2018-04-01

Particle size of biochar may strongly affect the kinetics of hydrophobic organic compound (HOC) sorption. However, challenges exist in characterizing the effect of biochar particle size on the sorption kinetics because of the wide size range of biochar. The present study suggests a novel method to determine a representative value that can be used to show the dependence of HOC sorption kinetics to biochar particle size on the basis of an intra-particle diffusion model. Biochars derived from three different feedstocks are ground and sieved to obtain three daughter products each having different size distributions. Phenanthrene sorption kinetics to the biochars are well described by the intra-particle diffusion model with significantly greater sorption rates observed for finer grained biochars. The time to reach 95% of equilibrium for phenanthrene sorption to biochar is reduced from 4.6-17.9days for the original biochars to <1-4.6days for the powdered biochars with <125μm in size. A moderate linear correlation is found between the inverse square of the representative biochar particle radius obtained using particle size distribution analysis and the apparent phenanthrene sorption rates determined by the sorption kinetics experiments and normalized to account for the variation of the sorption rate-determining factors other than the biochar particle radius. The results suggest that the representative biochar particle radius reasonably describes the dependence of HOC sorption rates on biochar particle size. Copyright © 2017 Elsevier B.V. All rights reserved.

Kinetic models in industrial biotechnology - Improving cell factory performance.

PubMed

Almquist, Joachim; Cvijovic, Marija; Hatzimanikatis, Vassily; Nielsen, Jens; Jirstrand, Mats

2014-07-01

An increasing number of industrial bioprocesses capitalize on living cells by using them as cell factories that convert sugars into chemicals. These processes range from the production of bulk chemicals in yeasts and bacteria to the synthesis of therapeutic proteins in mammalian cell lines. One of the tools in the continuous search for improved performance of such production systems is the development and application of mathematical models. To be of value for industrial biotechnology, mathematical models should be able to assist in the rational design of cell factory properties or in the production processes in which they are utilized. Kinetic models are particularly suitable towards this end because they are capable of representing the complex biochemistry of cells in a more complete way compared to most other types of models. They can, at least in principle, be used to in detail understand, predict, and evaluate the effects of adding, removing, or modifying molecular components of a cell factory and for supporting the design of the bioreactor or fermentation process. However, several challenges still remain before kinetic modeling will reach the degree of maturity required for routine application in industry. Here we review the current status of kinetic cell factory modeling. Emphasis is on modeling methodology concepts, including model network structure, kinetic rate expressions, parameter estimation, optimization methods, identifiability analysis, model reduction, and model validation, but several applications of kinetic models for the improvement of cell factories are also discussed. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

An inlet analysis for the NASA hypersonic research engine aerothermodynamic integration model

NASA Technical Reports Server (NTRS)

Andrews, E. H., Jr.; Russell, J. W.; Mackley, E. A.; Simmonds, A. L.

1974-01-01

A theoretical analysis for the inlet of the NASA Hypersonic Research Engine (HRE) Aerothermodynamic Integration Model (AIM) has been undertaken by use of a method-of-characteristics computer program. The purpose of the analysis was to obtain pretest information on the full-scale HRE inlet in support of the experimental AIM program (completed May 1974). Mass-flow-ratio and additive-drag-coefficient schedules were obtained that well defined the range effected in the AIM tests. Mass-weighted average inlet total-pressure recovery, kinetic energy efficiency, and throat Mach numbers were obtained.

Whole Body Creatine and Protein Kinetics in Healthy Men and Women: Effects of creatine and amino acid supplementation

PubMed Central

Kalhan, Satish C; Gruca, Lourdes; Marczewski, Susan; Bennett, Carole; Kummitha, China

2015-01-01

Creatine kinetics were measured in young healthy subjects, eight males and seven females, age 20–30 years, after an overnight fast on creatine free diet. Whole body turnover of glycine and its appearance in creatine was quantified using [1-13C] glycine and the rate of protein turnover was quantified using L-ring [2H5] phenylalanine. The creatine pool size was estimated by the dilution of a bolus [C2H3] creatine. Studies were repeated following a five days supplement creatine 21g.day−1 and following supplement amino acids 14.3 g.day−1. Creatine caused a ten folds increase in the plasma concentration of creatine and a 50% decrease in the concentration of guanidinoacetic acid. Plasma amino acids profile showed a significant decrease in glycine, glutamine and taurine and a significant increase in citrulline, valine, lysine and cysteine. There was a significant decrease in the rate of appearance of glycine, suggesting a decrease in de-novo synthesis (p=0.006). The fractional and absolute rate of synthesis of creatine was significantly decreased by supplemental creatine. Amino acid supplement had no impact on any of the parameters. Creatine supplement caused a significant decrease in the rate of synthesis of creatine. This is the first detailed analysis of creatine kinetics and the effects of creatine supplement in healthy young men and women. These methods can be applied for the analysis of creatine kinetics in different physiological states. PMID:26480831

Kinetics of enzymatic high-solid hydrolysis of lignocellulosic biomass studied by calorimetry.

PubMed

Olsen, Søren N; Lumby, Erik; McFarland, Kc; Borch, Kim; Westh, Peter

2011-03-01

Enzymatic hydrolysis of high-solid biomass (>10% w/w dry mass) has become increasingly important as a key step in the production of second-generation bioethanol. To this end, development of quantitative real-time assays is desirable both for empirical optimization and for detailed kinetic analysis. In the current work, we have investigated the application of isothermal calorimetry to study the kinetics of enzymatic hydrolysis of two substrates (pretreated corn stover and Avicel) at high-solid contents (up to 29% w/w). It was found that the calorimetric heat flow provided a true measure of the hydrolysis rate with a detection limit of about 500 pmol glucose s(-1). Hence, calorimetry is shown to be a highly sensitive real-time method, applicable for high solids, and independent on the complexity of the substrate. Dose-response experiments with a typical cellulase cocktail enabled a multidimensional analysis of the interrelationships of enzyme load and the rate, time, and extent of the reaction. The results suggest that the hydrolysis rate of pretreated corn stover is limited initially by available attack points on the substrate surface (<10% conversion) but becomes proportional to enzyme dosage (excess of attack points) at later stages (>10% conversion). This kinetic profile is interpreted as an increase in polymer end concentration (substrate for CBH) as the hydrolysis progresses, probably due to EG activity in the enzyme cocktail. Finally, irreversible enzyme inactivation did not appear to be the source of reduced hydrolysis rate over time.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data.

PubMed

Kotasidis, F A; Mehranian, A; Zaidi, H

2016-05-07

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data

NASA Astrophysics Data System (ADS)

Kotasidis, F. A.; Mehranian, A.; Zaidi, H.

2016-05-01

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Optimization of PET-MR Registrations for Nonhuman Primates Using Mutual Information Measures: A Multi-Transform Method (MTM)

PubMed Central

Sandiego, Christine M.; Weinzimmer, David; Carson, Richard E.

2012-01-01

An important step in PET brain kinetic analysis is the registration of functional data to an anatomical MR image. Typically, PET-MR registrations in nonhuman primate neuroreceptor studies used PET images acquired early post-injection, (e.g., 0–10 min) to closely resemble the subject’s MR image. However, a substantial fraction of these registrations (~25%) fail due to the differences in kinetics and distribution for various radiotracer studies and conditions (e.g., blocking studies). The Multi-Transform Method (MTM) was developed to improve the success of registrations between PET and MR images. Two algorithms were evaluated, MTM-I and MTM-II. The approach involves creating multiple transformations by registering PET images of different time intervals, from a dynamic study, to a single reference (i.e., MR image) (MTM-I) or to multiple reference images (i.e., MR and PET images pre-registered to the MR) (MTM-II). Normalized mutual information was used to compute similarity between the transformed PET images and the reference image(s) to choose the optimal transformation. This final transformation is used to map the dynamic dataset into the animal’s anatomical MR space, required for kinetic analysis. The chosen transformed from MTM-I and MTM-II were evaluated using visual rating scores to assess the quality of spatial alignment between the resliced PET and reference. One hundred twenty PET datasets involving eleven different tracers from 3 different scanners were used to evaluate the MTM algorithms. Studies were performed with baboons and rhesus monkeys on the HR+, HRRT, and Focus-220. Successful transformations increased from 77.5%, 85.8%, to 96.7% using the 0–10 min method, MTM-I, and MTM-II, respectively, based on visual rating scores. The Multi-Transform Methods proved to be a robust technique for PET-MR registrations for a wide range of PET studies. PMID:22926293

Modeling of ultrasonic degradation of non-volatile organic compounds by Langmuir-type kinetics.

PubMed

Chiha, Mahdi; Merouani, Slimane; Hamdaoui, Oualid; Baup, Stéphane; Gondrexon, Nicolas; Pétrier, Christian

2010-06-01

Sonochemical degradation of phenol (Ph), 4-isopropylphenol (4-IPP) and Rhodamine B (RhB) in aqueous solutions was investigated for a large range of initial concentrations in order to analyze the reaction kinetics. The initial rates of substrate degradation and H(2)O(2) formation as a function of initial concentrations were determined. The obtained results show that the degradation rate increases with increasing initial substrate concentration up to a plateau and that the sonolytic destruction occurs mainly through reactions with hydroxyl radicals in the interfacial region of cavitation bubbles. The rate of H(2)O(2) formation decreases with increasing substrate concentration and reaches a minimum, followed by almost constant production rate for higher substrate concentrations. Sonolytic degradation data were analyzed by the models of Okitsu et al. [K. Okitsu, K. Iwasaki, Y. Yobiko, H. Bandow, R. Nishimura, Y. Maeda, Sonochemical degradation of azo dyes in aqueous solution: a new heterogeneous kinetics model taking into account the local concentration OH radicals and azo dyes, Ultrason. Sonochem. 12 (2005) 255-262.] and Seprone et al. [N. Serpone, R. Terzian, H. Hidaka, E. Pelizzetti, Ultrasonic induced dehalogenation and oxidation of 2-, 3-, and 4-chlorophenol in air-equilibrated aqueous media. Similarities with irradiated semiconductor particulates, J. Phys. Chem. 98 (1994) 2634-2640.] developed on the basis of a Langmuir-type mechanism. The five linearized forms of the Okitsu et al.'s equation as well as the non-linear curve fitting analysis method were discussed. Results show that it is not appropriate to use the coefficient of determination of the linear regression method for comparing the best-fitting. Among the five linear expressions of the Okitsu et al.'s kinetic model, form-2 expression very well represent the degradation data for Ph and 4-IPP. Non-linear curve fitting analysis method was found to be the more appropriate method to determine the model parameters. An excellent representation of the experimental results of sonolytic destruction of RhB was obtained using the Serpone et al.'s model. The Serpone et al.'s model gives a worse fit for the sonolytic degradation data of Ph and 4-IPP. These results indicate that Ph and 4-IPP undergo degradation predominantly at the bubble/solution interface, whereas RhB undergoes degradation at both bubble/solution interface and in the bulk solution. (c) 2010 Elsevier B.V. All rights reserved.

Optimal back-extrapolation method for estimating plasma volume in humans using the indocyanine green dilution method.

PubMed

Polidori, David; Rowley, Clarence

2014-07-22

The indocyanine green dilution method is one of the methods available to estimate plasma volume, although some researchers have questioned the accuracy of this method. We developed a new, physiologically based mathematical model of indocyanine green kinetics that more accurately represents indocyanine green kinetics during the first few minutes postinjection than what is assumed when using the traditional mono-exponential back-extrapolation method. The mathematical model is used to develop an optimal back-extrapolation method for estimating plasma volume based on simulated indocyanine green kinetics obtained from the physiological model. Results from a clinical study using the indocyanine green dilution method in 36 subjects with type 2 diabetes indicate that the estimated plasma volumes are considerably lower when using the traditional back-extrapolation method than when using the proposed back-extrapolation method (mean (standard deviation) plasma volume = 26.8 (5.4) mL/kg for the traditional method vs 35.1 (7.0) mL/kg for the proposed method). The results obtained using the proposed method are more consistent with previously reported plasma volume values. Based on the more physiological representation of indocyanine green kinetics and greater consistency with previously reported plasma volume values, the new back-extrapolation method is proposed for use when estimating plasma volume using the indocyanine green dilution method.

Chiral pathways in DNA dinucleotides using gradient optimized refinement along metastable borders

NASA Astrophysics Data System (ADS)

Romano, Pablo; Guenza, Marina

We present a study of DNA breathing fluctuations using Markov state models (MSM) with our novel refinement procedure. MSM have become a favored method of building kinetic models, however their accuracy has always depended on using a significant number of microstates, making the method costly. We present a method which optimizes macrostates by refining borders with respect to the gradient along the free energy surface. As the separation between macrostates contains highest discretization errors, this method corrects for any errors produced by limited microstate sampling. Using our refined MSM methods, we investigate DNA breathing fluctuations, thermally induced conformational changes in native B-form DNA. Running several microsecond MD simulations of DNA dinucleotides of varying sequences, to include sequence and polarity effects, we've analyzed using our refined MSM to investigate conformational pathways inherent in the unstacking of DNA bases. Our kinetic analysis has shown preferential chirality in unstacking pathways that may be critical in how proteins interact with single stranded regions of DNA. These breathing dynamics can help elucidate the connection between conformational changes and key mechanisms within protein-DNA recognition. NSF Chemistry Division (Theoretical Chemistry), the Division of Physics (Condensed Matter: Material Theory), XSEDE.

Comment on: "Split kinetic energy method for quantum systems with competing potentials", Ann. Phys. 327 (2012) 2061

NASA Astrophysics Data System (ADS)

Fernández, Francisco M.

2018-06-01

We show that the kinetic-energy partition method (KEP) is a particular example of the well known Rayleigh-Ritz variational method. We discuss some of the KEP results and compare them with those coming from other approaches.

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.

Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations.

PubMed

Varga, Matthew J; Schwartz, Steven D

2016-04-12

In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems.

Kinetics and mechanism of catalytic hydroprocessing of components of coal-derived liquids. Sixteenth quarterly report, February 16, 1983-May 15, 1983.

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

Gates, B. C.; Olson, H. H.; Schuit, G. C.A.

1983-08-22

A new method of structural analysis is applied to a group of hydroliquefied coal samples. The method uses elemental analysis and NMR data to estimate the concentrations of functional groups in the samples. The samples include oil and asphaltene fractions obtained in a series of hydroliquefaction experiments, and a set of 9 fractions separated from a coal-derived oil. The structural characterization of these samples demonstrates that estimates of functional group concentrations can be used to provide detailed structural profiles of complex mixtures and to obtain limited information about reaction pathways. 11 references, 1 figure, 7 tables.

Label-free integrative pharmacology on-target of drugs at the β2-adrenergic receptor

NASA Astrophysics Data System (ADS)

Ferrie, Ann M.; Sun, Haiyan; Fang, Ye

2011-07-01

We describe a label-free integrative pharmacology on-target (iPOT) method to assess the pharmacology of drugs at the β2-adrenergic receptor. This method combines dynamic mass redistribution (DMR) assays using an array of probe molecule-hijacked cells with similarity analysis. The whole cell DMR assays track cell system-based, ligand-directed, and kinetics-dependent biased activities of the drugs, and translates their on-target pharmacology into numerical descriptors which are subject to similarity analysis. We demonstrate that the approach establishes an effective link between the label-free pharmacology and in vivo therapeutic indications of drugs.

Iterative Addition of Kinetic Effects to Cold Plasma RF Wave Solvers

NASA Astrophysics Data System (ADS)

Green, David; Berry, Lee; RF-SciDAC Collaboration

2017-10-01

The hot nature of fusion plasmas requires a wave vector dependent conductivity tensor for accurate calculation of wave heating and current drive. Traditional methods for calculating the linear, kinetic full-wave plasma response rely on a spectral method such that the wave vector dependent conductivity fits naturally within the numerical method. These methods have seen much success for application to the well-confined core plasma of tokamaks. However, quantitative prediction of high power RF antenna designs for fusion applications has meant a requirement of resolving the geometric details of the antenna and other plasma facing surfaces for which the Fourier spectral method is ill-suited. An approach to enabling the addition of kinetic effects to the more versatile finite-difference and finite-element cold-plasma full-wave solvers was presented by where an operator-split iterative method was outlined. Here we expand on this approach, examine convergence and present a simplified kinetic current estimator for rapidly updating the right-hand side of the wave equation with kinetic corrections. This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

Simulated maximum likelihood method for estimating kinetic rates in gene expression.

PubMed

Tian, Tianhai; Xu, Songlin; Gao, Junbin; Burrage, Kevin

2007-01-01

Kinetic rate in gene expression is a key measurement of the stability of gene products and gives important information for the reconstruction of genetic regulatory networks. Recent developments in experimental technologies have made it possible to measure the numbers of transcripts and protein molecules in single cells. Although estimation methods based on deterministic models have been proposed aimed at evaluating kinetic rates from experimental observations, these methods cannot tackle noise in gene expression that may arise from discrete processes of gene expression, small numbers of mRNA transcript, fluctuations in the activity of transcriptional factors and variability in the experimental environment. In this paper, we develop effective methods for estimating kinetic rates in genetic regulatory networks. The simulated maximum likelihood method is used to evaluate parameters in stochastic models described by either stochastic differential equations or discrete biochemical reactions. Different types of non-parametric density functions are used to measure the transitional probability of experimental observations. For stochastic models described by biochemical reactions, we propose to use the simulated frequency distribution to evaluate the transitional density based on the discrete nature of stochastic simulations. The genetic optimization algorithm is used as an efficient tool to search for optimal reaction rates. Numerical results indicate that the proposed methods can give robust estimations of kinetic rates with good accuracy.

Effects of process variables and kinetics on the degradation of 2,4-dichlorophenol using advanced reduction processes (ARP).

PubMed

Yu, Xingyue; Cabooter, Deirdre; Dewil, Raf

2018-05-24

This study aims at investigating the efficiency and kinetics of 2,4-DCP degradation via advanced reduction processes (ARP). Using UV light as activation method, the highest degradation efficiency of 2,4-DCP was obtained when using sulphite as a reducing agent. The highest degradation efficiency was observed under alkaline conditions (pH = 10.0), for high sulphite dosage and UV intensity, and low 2,4-DCP concentration. For all process conditions, first-order reaction rate kinetics were applicable. A quadratic polynomial equation fitted by a Box-Behnken Design was used as a statistical model and proved to be precise and reliable in describing the significance of the different process variables. The analysis of variance demonstrated that the experimental results were in good agreement with the predicted model (R 2  = 0.9343), and solution pH, sulphite dose and UV intensity were found to be key process variables in the sulphite/UV ARP. Consequently, the present study provides a promising approach for the efficient degradation of 2,4-DCP with fast degradation kinetics. Copyright © 2018 Elsevier B.V. All rights reserved.

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

Solving Kinetic Equations for the Laser Flash Photolysis Experiment on Nitric Oxide Synthases: Effect of Conformational Dynamics on the Interdomain Electron Transfer.

PubMed

Astashkin, Andrei V; Feng, Changjian

2015-11-12

The production of nitric oxide by the nitric oxide synthase (NOS) enzyme depends on the interdomain electron transfer (IET) between the flavin mononucleotide (FMN) and heme domains. Although the rate of this IET has been measured by laser flash photolysis (LFP) for various NOS proteins, no rigorous analysis of the relevant kinetic equations was performed so far. In this work, we provide an analytical solution of the kinetic equations underlying the LFP approach. The derived expressions reveal that the bulk IET rate is significantly affected by the conformational dynamics that determines the formation and dissociation rates of the docking complex between the FMN and heme domains. We show that in order to informatively study the electron transfer across the NOS enzyme, LFP should be used in combination with other spectroscopic methods that could directly probe the docking equilibrium and the conformational change rate constants. The implications of the obtained analytical expressions for the interpretation of the LFP results from various native and modified NOS proteins are discussed. The mathematical formulas derived in this work should also be applicable for interpreting the IET kinetics in other modular redox enzymes.

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.

[CoCuMnOx Photocatalyzed Oxidation of Multi-component VOCs and Kinetic Analysis].

PubMed

Meng, Hai-long; Bo, Long-li; Liu, Jia-dong; Gao, Bo; Feng, Qi-qi; Tan, Na; Xie, Shuai

2016-05-15

Solar energy absorption coating CoCuMnOx was prepared by co-precipitation method and applied to photodegrade multi- component VOCs including toluene, ethyl acetate and acetone under visible light irradiation. The photocatalytic oxidation performance of toluene, ethyl acetate and acetone was analyzed and reaction kinetics of VOCs were investigated synchronously. The research indicated that removal rates of single-component toluene, ethyl acetate and acetone were 57%, 62% and 58% respectively under conditions of 400 mg · m⁻³ initial concentration, 120 mm illumination distance, 1 g/350 cm² dosage of CoCuMnOx and 6 h of irradiation time by 100 W tungsten halogen lamp. Due to the competition among different VOCs, removal efficiencies in three-component mixture were reduced by 5%-26% as compared with single VOC. Degradation processes of single-component VOC and three-component VOCs both fitted pseudo first order reaction kinetics, and kinetic constants of toluene, ethyl acetate and acetone were 0.002, 0.002 8 and 0.002 33 min⁻¹ respectively under single-component condition. Reaction rates of VOCs in three-component mixture were 0.49-0.88 times of single components.

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.

Monochloramine disinfection kinetics of Nitrosomonas europaea by propidium monoazide quantitative PCR and Live/Dead BacLight Methods

EPA Science Inventory

Monochloramine disinfection kinetics were determined for the pure culture ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) by two culture independent methods: (1) LIVE/DEAD® BacLight™ (LD) and (2) propidium monoazide quantitative PCR (PMA-qPCR). Both methods were f...

Simulation of Nuclear Reactor Kinetics by the Monte Carlo Method

NASA Astrophysics Data System (ADS)

Gomin, E. A.; Davidenko, V. D.; Zinchenko, A. S.; Kharchenko, I. K.

2017-12-01

The KIR computer code intended for calculations of nuclear reactor kinetics using the Monte Carlo method is described. The algorithm implemented in the code is described in detail. Some results of test calculations are given.

Structure and Dynamics of Replication-Mutation Systems

NASA Astrophysics Data System (ADS)

Schuster, Peter

1987-03-01

The kinetic equations of polynucleotide replication can be brought into fairly simple form provided certain environmental conditions are fulfilled. Two flow reactors, the continuously stirred tank reactor (CSTR) and a special dialysis reactor are particularly suitable for the analysis of replication kinetics. An experimental setup to study the chemical reaction network of RNA synthesis was derived from the bacteriophage Qβ. It consists of a virus specific RNA polymerase, Qβ replicase, the activated ribonucleosides GTP, ATP, CTP and UTP as well as a template suitable for replication. The ordinary differential equations for replication and mutation under the conditions of the flow reactors were analysed by the qualitative methods of bifurcation theory as well as by numerical integration. The various kinetic equations are classified according to their dynamical properties: we distinguish "quasilinear systems" which have uniquely stable point attractors and "nonlinear systems" with inherent nonlinearities which lead to multiple steady states, Hopf bifuractions, Feigenbaum-like sequences and chaotic dynamics for certain parameter ranges. Some examples which are relevant in molecular evolution and population genetics are discussed in detail.

Quantifying cancer cell receptors with paired-agent fluorescent imaging: a novel method to account for tissue optical property effects

NASA Astrophysics Data System (ADS)

Sadeghipour, Negar; Davis, Scott C.; Tichauer, Kenneth M.

2018-02-01

Dynamic fluorescence imaging approaches can be used to estimate the concentration of cell surface receptors in vivo. Kinetic models are used to generate the final estimation by taking the targeted imaging agent concentration as a function of time. However, tissue absorption and scattering properties cause the final readout signal to be on a different scale than the real fluorescent agent concentration. In paired-agent imaging approaches, simultaneous injection of a suitable control imaging agent with a targeted one can account for non-specific uptake and retention of the targeted agent. Additionally, the signal from the control agent can be a normalizing factor to correct for tissue optical property differences. In this study, the kinetic model used for paired-agent imaging analysis (i.e., simplified reference tissue model) is modified and tested in simulation and experimental data in a way that accounts for the scaling correction within the kinetic model fit to the data to ultimately extract an estimate of the targeted biomarker concentration.

Computational modelling of mesoscale dislocation patterning and plastic deformation of single crystals

NASA Astrophysics Data System (ADS)

Xia, Shengxu; El-Azab, Anter

2015-07-01

We present a continuum dislocation dynamics model that predicts the formation of dislocation cell structure in single crystals at low strains. The model features a set of kinetic equations of the curl type that govern the space and time evolution of the dislocation density in the crystal. These kinetic equations are coupled to stress equilibrium and deformation kinematics using the eigenstrain approach. A custom finite element method has been developed to solve the coupled system of equations of dislocation kinetics and crystal mechanics. The results show that, in general, dislocations self-organize in patterns under their mutual interactions. However, the famous dislocation cell structure has been found to form only when cross slip is implemented in the model. Cross slip is also found to lower the yield point, increase the hardening rate, and sustain an increase in the dislocation density over the hardening regime. Analysis of the cell structure evolution reveals that the average cell size decreases with the applied stress, which is consistent with the similitude principle.

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.

Focus: Nucleation kinetics of shear bands in metallic glass.

PubMed

Wang, J Q; Perepezko, J H

2016-12-07

The development of shear bands is recognized as the primary mechanism in controlling the plastic deformability of metallic glasses. However, the kinetics of the nucleation of shear bands has received limited attention. The nucleation of shear bands in metallic glasses (MG) can be investigated using a nanoindentation method to monitor the development of the first pop-in event that is a signature of shear band nucleation. The analysis of a statistically significant number of first pop-in events demonstrates the stochastic behavior that is characteristic of nucleation and reveals a multimodal behavior associated with local spatial heterogeneities. The shear band nucleation rate of the two nucleation modes and the associated activation energy, activation volume, and site density were determined by loading rate experiments. The nucleation activation energy is very close to the value that is characteristic of the β relaxation in metallic glass. The identification of the rate controlling kinetics for shear band nucleation offers guidance for promoting plastic flow in metallic glass.

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].

Discernment of synergism in pyrolysis of biomass blends using thermogravimetric analysis.

PubMed

Mallick, Debarshi; Poddar, Maneesh Kumar; Mahanta, Pinakeswar; Moholkar, Vijayanand S

2018-08-01

This study reports pyrolysis kinetics of biomass blends using isoconversional methods, viz. Friedman, FWO and KAS. Blends of three biomasses, viz. saw dust, bamboo dust and rice husk, were used. Extractives and volatiles in biomass and minerals in ash had marked influence on enhancement of reaction kinetics during co-pyrolysis, as indicated by reduction in activation energy and increase in decomposition intensity. Pyrolysis kinetics of saw dust and rice husk accelerated (positive synergy), while that of bamboo dust decelerated after blending (negative synergy). Predominant reaction mechanism of all biomass blends was 3-D diffusion in lower conversion range (α ≤ 0.5), while for α ≥ 0.5 pyrolysis followed random nucleation (or nucleation and growth mechanism). Higher reaction order for pyrolysis of blends of rice husk with saw dust and bamboo dust was attributed to catalytic effect of minerals in ash. Positive ΔH and ΔG was obtained for pyrolysis of all biomass blends. Copyright © 2018 Elsevier Ltd. All rights reserved.

Solid-State Kinetic Investigations of Nonisothermal Reduction of Iron Species Supported on SBA-15

PubMed Central

2017-01-01

Iron oxide catalysts supported on nanostructured silica SBA-15 were synthesized with various iron loadings using two different precursors. Structural characterization of the as-prepared FexOy/SBA-15 samples was performed by nitrogen physisorption, X-ray diffraction, DR-UV-Vis spectroscopy, and Mössbauer spectroscopy. An increasing size of the resulting iron species correlated with an increasing iron loading. Significantly smaller iron species were obtained from (Fe(III), NH4)-citrate precursors compared to Fe(III)-nitrate precursors. Moreover, smaller iron species resulted in a smoother surface of the support material. Temperature-programmed reduction (TPR) of the FexOy/SBA-15 samples with H2 revealed better reducibility of the samples originating from Fe(III)-nitrate precursors. Varying the iron loading led to a change in reduction mechanism. TPR traces were analyzed by model-independent Kissinger method, Ozawa, Flynn, and Wall (OFW) method, and model-dependent Coats-Redfern method. JMAK kinetic analysis afforded a one-dimensional reduction process for the FexOy/SBA-15 samples. The Kissinger method yielded the lowest apparent activation energy for the lowest loaded citrate sample (Ea ≈ 39 kJ/mol). Conversely, the lowest loaded nitrate sample possessed the highest apparent activation energy (Ea ≈ 88 kJ/mol). For samples obtained from Fe(III)-nitrate precursors, Ea decreased with increasing iron loading. Apparent activation energies from model-independent analysis methods agreed well with those from model-dependent methods. Nucleation as rate-determining step in the reduction of the iron oxide species was consistent with the Mampel solid-state reaction model. PMID:29230346

Thermal Analysis Study of Antihypertensive Drugs Telmisartan and Cilazapril

PubMed Central

Saber, Refaat Ahmed; Attia, Ali Kamal; Salem, Waheed Mohamed

2014-01-01

Purpose: The aim of the present work is to study the thermal analysis of telmisartan and cilazapril. Methods: Thermogravimetry (TGA), derivative thermogravimetry (DTG) and differential thermal analysis (DTA) were used through the work to achieve the thermal analysis study of some antihypertensive drugs, telmisartan and cilazapril. Results: The results led to thermal stability data and also to the interpretation concerning the thermal decomposition. Thermogravimetry data allowed determination of the kinetic parameters such as, activation energy and frequency factor. Conclusion: The simplicity, speed and low operational costs of thermal analysis justify its application in the quality control of pharmaceutical compounds for medications. PMID:24754013

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.

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.

Analysis of Protein Adduction Kinetics by Quantitative Mass Spectrometry. Competing Adduction Reactions of Glutathione-S-Transferase P1-1 with Electrophiles

PubMed Central

Orton, Christopher R.; Liebler, Daniel C.

2007-01-01

Defining the mechanisms and consequences of protein adduction is crucial to understanding the toxicity of reactive electrophiles. Application of tandem mass spectrometry and data analysis algorithms enables detection and mapping of chemical adducts at the level of amino acid sequence. Nevertheless, detection of adducts does not indicate relative reactivity of different sites. Here we describe a method to measure the kinetics of competing adduction reactions at different sites on the same protein. Adducts are formed by electrophiles at Cys14 and Cys47 on the metabolic enzyme glutathione-S-transferase P1-1 and modification is accompanied by a loss of enzymatic activity. Relative quantitation of protein adducts was done by tagging N-termini of peptide digests with isotopically labeled phenyl isocyanate and tracking the ratio of light-tagged peptide adducts to heavy-tagged reference samples in liquid chromatography-tandem mass spectrometry analyses using a multiple reaction monitoring method. This approach was used to measure rate constants for adduction at both positions with two different model electrophiles, N-iodoacetyl-N-biotinylhexylenediamine and 1-biotinamido-4-(4′-[maleimidoethyl-cyclohexane]-carboxamido)butane. The results indicate that Cys47 was approximately 2–3-fold more reactive toward both electrophiles than was Cys14. This result was consistent with the relative reactivity of these electrophiles in a complex proteome system and with previously reported trends in reactivity of these sites. Kinetic analyses of protein modification reactions provide a means of evaluating the selectivity of reactive mediators of chemical toxicity. PMID:17433278

Factor analysis for delineation of organ structures, creation of in- and output functions, and standardization of multicenter kinetic modeling

NASA Astrophysics Data System (ADS)

Schiepers, Christiaan; Hoh, Carl K.; Dahlbom, Magnus; Wu, Hsiao-Ming; Phelps, Michael E.

1999-05-01

PET imaging can quantify metabolic processes in-vivo; this requires the measurement of an input function which is invasive and labor intensive. A non-invasive, semi-automated, image based method of input function generation would be efficient, patient friendly, and allow quantitative PET to be applied routinely. A fully automated procedure would be ideal for studies across institutions. Factor analysis (FA) was applied as processing tool for definition of temporally changing structures in the field of view. FA has been proposed earlier, but the perceived mathematical difficulty has prevented widespread use. FA was utilized to delineate structures and extract blood and tissue time-activity-curves (TACs). These TACs were used as input and output functions for tracer kinetic modeling, the results of which were compared with those from an input function obtained with serial blood sampling. Dynamic image data of myocardial perfusion studies with N-13 ammonia, O-15 water, or Rb-82, cancer studies with F-18 FDG, and skeletal studies with F-18 fluoride were evaluated. Correlation coefficients of kinetic parameters obtained with factor and plasma input functions were high. Linear regression usually furnished a slope near unity. Processing time was 7 min/patient on an UltraSPARC. Conclusion: FA can non-invasively generate input functions from image data eliminating the need for blood sampling. Output (tissue) functions can be simultaneously generated. The method is simple, requires no sophisticated operator interaction and has little inter-operator variability. FA is well suited for studies across institutions and standardized evaluations.

Multicomponent kinetic spectrophotometric determination of pefloxacin and norfloxacin in pharmaceutical preparations and human plasma samples with the aid of chemometrics

NASA Astrophysics Data System (ADS)

Ni, Yongnian; Wang, Yong; Kokot, Serge

2008-10-01

A spectrophotometric method for the simultaneous determination of the important pharmaceuticals, pefloxacin and its structurally similar metabolite, norfloxacin, is described for the first time. The analysis is based on the monitoring of a kinetic spectrophotometric reaction of the two analytes with potassium permanganate as the oxidant. The measurement of the reaction process followed the absorbance decrease of potassium permanganate at 526 nm, and the accompanying increase of the product, potassium manganate, at 608 nm. It was essential to use multivariate calibrations to overcome severe spectral overlaps and similarities in reaction kinetics. Calibration curves for the individual analytes showed linear relationships over the concentration ranges of 1.0-11.5 mg L -1 at 526 and 608 nm for pefloxacin, and 0.15-1.8 mg L -1 at 526 and 608 nm for norfloxacin. Various multivariate calibration models were applied, at the two analytical wavelengths, for the simultaneous prediction of the two analytes including classical least squares (CLS), principal component regression (PCR), partial least squares (PLS), radial basis function-artificial neural network (RBF-ANN) and principal component-radial basis function-artificial neural network (PC-RBF-ANN). PLS and PC-RBF-ANN calibrations with the data collected at 526 nm, were the preferred methods—%RPE T ˜ 5, and LODs for pefloxacin and norfloxacin of 0.36 and 0.06 mg L -1, respectively. Then, the proposed method was applied successfully for the simultaneous determination of pefloxacin and norfloxacin present in pharmaceutical and human plasma samples. The results compared well with those from the alternative analysis by HPLC.

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.

Probing the oxidation kinetics of small permalloy particles

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

Dong, Xiaolei; Song, Xiao; Yin, Shiliu

2017-02-15

The oxidation of permalloys is important to apply in a wide range. The oxidation and diffusion mechanisms of small permalloy particles with different Fe content are studied by using thermal gravimetric analysis (TGA) and microstructure characterizations. Fe{sub 2}O{sub 3}/(Ni, Fe){sub 3}O{sub 4} plays a key role in the morphology evolution and diffusion mechanisms of small NiFe particles upon oxidation. The activation energies of grain boundary diffusion for the NiFe alloys increase from 141 kJ/mol to 208 kJ/mol as the Fe content increases from 0 to ~50 wt%. We have developed a diffusion process resolved temperature programed oxidation (PR-TPO) analysis method.more » Three diffusion mechanisms have been recognized by using this method: In addition to the grain boundary diffusion and lattice diffusion, our TGA analysis suggests that the phase conversion from Fe{sub 2}O{sub 3} to (Ni, Fe){sub 3}O{sub 4} induces diffusion change and affects the diffusion process at the intermediate temperature. Relevant oxidation kinetics and diffusion mechanisms are discussed. - Graphical abstract: The oxidation mechanisms of small Permalloy particles with different Fe content is studied by using thermal gravimetric analysis (TGA) and microstructure characterizations. The activation energies of grain boundary diffusion for the NiFe alloys increases from 140 kJ/mol to 208 kJ/mol as the Fe content increases from 0 to 50 wt% as determined by TGA. We have developed a diffusion process resolved temperature programed oxidation (DPR-TPO) analysis method, and three diffusion mechanisms have been recognized by using this method: In addition to the well-known grain boundary diffusion and lattice diffusion, we found that the phase conversion from Fe{sub 2}O{sub 3} to (Ni, Fe){sub 3}O{sub 4} will induce diffusion changes and affect the diffusion process at the intermediate temperature. The diffusion processes can be characterized by the corresponding characteristic peak temperatures in temperature programmed oxidation (TPO) analysis. This work not only give insight knowledge about the oxidation and diffusion processes of small permalloy particles, but also, provides a useful tool for analyzing solid-gas reactions of other materials. - Highlights: • The oxidation kinetics of small NiFe particles were studied by using thermoanalysis. • Grain boundary, lattice, and phase conversion induced diffusions were recognized. • The activation energy of oxidation increases with the Fe content in the alloy. • Each diffusion process corresponds to a characteristic temperature in TPO analysis. • NiFe alloys with ~5–10 wt% Fe content have the lowest oxidation rates.« less

Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.

PubMed

Cobbs, Gary

2012-08-16

Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give better estimates of initial target concentration. Model 1 was found to be slightly more robust than model 2 giving better estimates of initial target concentration when estimation of parameters was done for qPCR curves with very different initial target concentration. Both models may be used to estimate the initial absolute concentration of target sequence when a standard curve is not available. It is argued that the kinetic approach to modeling and interpreting quantitative PCR data has the potential to give more precise estimates of the true initial target concentrations than other methods currently used for analysis of qPCR data. The two models presented here give a unified model of the qPCR process in that they explain the shape of the qPCR curve for a wide variety of initial target concentrations.

Optimal back-extrapolation method for estimating plasma volume in humans using the indocyanine green dilution method

PubMed Central

2014-01-01

Background The indocyanine green dilution method is one of the methods available to estimate plasma volume, although some researchers have questioned the accuracy of this method. Methods We developed a new, physiologically based mathematical model of indocyanine green kinetics that more accurately represents indocyanine green kinetics during the first few minutes postinjection than what is assumed when using the traditional mono-exponential back-extrapolation method. The mathematical model is used to develop an optimal back-extrapolation method for estimating plasma volume based on simulated indocyanine green kinetics obtained from the physiological model. Results Results from a clinical study using the indocyanine green dilution method in 36 subjects with type 2 diabetes indicate that the estimated plasma volumes are considerably lower when using the traditional back-extrapolation method than when using the proposed back-extrapolation method (mean (standard deviation) plasma volume = 26.8 (5.4) mL/kg for the traditional method vs 35.1 (7.0) mL/kg for the proposed method). The results obtained using the proposed method are more consistent with previously reported plasma volume values. Conclusions Based on the more physiological representation of indocyanine green kinetics and greater consistency with previously reported plasma volume values, the new back-extrapolation method is proposed for use when estimating plasma volume using the indocyanine green dilution method. PMID:25052018

Atomic-Scale Design of Iron Fischer-Tropsch Catalysts; A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

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

Manos Mavrikakis; James Dumesic; Rahul Nabar

2008-09-29

This work focuses on (1) searching/summarizing published Fischer-Tropsch synthesis (FTS) mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) preparation and characterization of unsupported iron catalysts with/without potassium/platinum promoters; (3) measurement of H{sub 2} and CO adsorption/dissociation kinetics on iron catalysts using transient methods; (3) analysis of the transient rate data to calculate kinetic parameters of early elementary steps in FTS; (4) construction of a microkinetic model of FTS on iron, and (5) validation of the model from collection of steady-state rate data for FTS on iron catalysts. Three unsupported iron catalysts and three alumina-supported iron catalysts weremore » prepared by non-aqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, temperature-programmed reduction (TPR), extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2} and thus ideal for kinetic and mechanistic studies. Kinetic parameters for CO adsorption, CO dissociation, and surface carbon hydrogenation on these catalysts were determined from temperature-programmed desorption (TPD) of CO and temperature programmed surface hydrogenation (TPSR), temperature-programmed hydrogenation (TPH), and isothermal, transient hydrogenation (ITH). A microkinetic model was constructed for the early steps in FTS on polycrystalline iron from the kinetic parameters of elementary steps determined experimentally in this work and from literature values. Steady-state rate data were collected in a Berty reactor and used for validation of the microkinetic model. These rate data were fitted to 'smart' Langmuir-Hinshelwood rate expressions derived from a sequence of elementary steps and using a combination of fitted steady-state parameters and parameters specified from the transient measurements. The results provide a platform for further development of microkinetic models of FTS on Fe and a basis for more precise modeling of FTS activity of Fe catalysts. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on various realistic models of industrial, Fe-based FTS catalysts. Close-packed, most stable Fe(110) facet was analyzed and subsequently carbide formation was found to be facile leading to the choice of the FeC(110) model representing a Fe facet with a sub-surface C atom. The Pt adatom (Fe{sup Pt}(110)) was found to be the most stable model for our studies into Pt promotion and finally the role of steps was elucidated by recourse to the defected Fe(211) facet. Binding Energies(BEs), preferred adsorption sites and geometries for all FTS relevant stable species and intermediates were evaluated on each model catalyst facet. A mechanistic model (comprising of 32 elementary steps involving 19 species) was constructed and each elementary step therein was fully characterized with respect to its thermochemistry and kinetics. Kinetic calculations involved evaluation of the Minimum Energy Pathways (MEPs) and activation energies (barriers) for each step. Vibrational frequencies were evaluated for the preferred adsorption configuration of each species with the aim of evaluating entropy-changes, pre exponential factors and serving as a useful connection with experimental surface science techniques. Comparative analysis among these four facets revealed important trends in their relative behavior and roles in FTS catalysis. Overall the First Principles Calculations afforded us a new insight into FTS catalysis on Fe and modified-Fe catalysts.« less

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

Majewski, Pawel W.; Yager, Kevin G.

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. Here, wemore » also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.« less

Consistent Chemical Mechanism from Collaborative Data Processing

DOE PAGES

Slavinskaya, Nadezda; Starcke, Jan-Hendrik; Abbasi, Mehdi; ...

2016-04-01

Numerical tool of Process Informatics Model (PrIMe) is mathematically rigorous and numerically efficient approach for analysis and optimization of chemical systems. It handles heterogeneous data and is scalable to a large number of parameters. The Boundto-Bound Data Collaboration module of the automated data-centric infrastructure of PrIMe was used for the systematic uncertainty and data consistency analyses of the H 2/CO reaction model (73/17) and 94 experimental targets (ignition delay times). The empirical rule for evaluation of the shock tube experimental data is proposed. The initial results demonstrate clear benefits of the PrIMe methods for an evaluation of the kinetic datamore » quality and data consistency and for developing predictive kinetic models.« less

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.

Torque and power outputs on different subjects during manual wheelchair propulsion under different conditions

NASA Astrophysics Data System (ADS)

Hwang, Seonhong; Kim, Seunghyeon; Son, Jongsang; Kim, Youngho

2012-02-01

Manual wheelchair users are at a high risk of pain and injuries to the upper extremities due to mechanical inefficiency of wheelchair propulsion motion. The kinetic analysis of the upper extremities during manual wheelchair propulsion in various conditions needed to be investigated. We developed and calibrated a wheelchair dynamometer for measuring kinetic parameters during propulsion. We utilized the dynamometer to investigate and compare the propulsion torque and power values of experienced and novice users under four different conditions. Experienced wheelchair users generated lower torques with more power than novice users and reacted alertly and sensitively to changing conditions. We expect that these basic methods and results may help to quantitatively evaluate the mechanical efficiency of manual wheelchair propulsion.

Rapid ordering of block copolymer thin films

NASA Astrophysics Data System (ADS)

Majewski, Pawel W.; Yager, Kevin G.

2016-10-01

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. We also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.

Heterogeneous reaction of particulate chlorpyrifos with NO3 radicals: Products, pathways, and kinetics

NASA Astrophysics Data System (ADS)

Li, Nana; Zhang, Peng; Yang, Bo; Shu, Jinian; Wang, Youfeng; Sun, Wanqi

2014-08-01

Chlorpyrifos is a typical chlorinated organophosphorus pesticide. The heterogeneous reaction of chlorpyrifos particles with NO3 radicals was investigated using a vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer (VUV-ATOFMS) and a real-time atmospheric gas analysis mass spectrometer. Chlorpyrifos oxon, 3,5,6-trichloro-2-pyridinol, O,O-diethyl O-hydrogen phosphorothioate, O,O-diethyl ester thiophosphoric acid, diethyl hydrogen phosphate and a phosphinyl disulfide compound were identified as the main degradation products. The heterogeneous reaction pathways were proposed and their kinetic processes were investigated via a mixed-phase relative rate method. The observed effective rate constant is 3.4 ± 0.2 × 10-12 cm3 molecule-1 s-1.

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.

Discrete stochastic simulation methods for chemically reacting systems.

PubMed

Cao, Yang; Samuels, David C

2009-01-01

Discrete stochastic chemical kinetics describe the time evolution of a chemically reacting system by taking into account the fact that, in reality, chemical species are present with integer populations and exhibit some degree of randomness in their dynamical behavior. In recent years, with the development of new techniques to study biochemistry dynamics in a single cell, there are increasing studies using this approach to chemical kinetics in cellular systems, where the small copy number of some reactant species in the cell may lead to deviations from the predictions of the deterministic differential equations of classical chemical kinetics. This chapter reviews the fundamental theory related to stochastic chemical kinetics and several simulation methods based on that theory. We focus on nonstiff biochemical systems and the two most important discrete stochastic simulation methods: Gillespie's stochastic simulation algorithm (SSA) and the tau-leaping method. Different implementation strategies of these two methods are discussed. Then we recommend a relatively simple and efficient strategy that combines the strengths of the two methods: the hybrid SSA/tau-leaping method. The implementation details of the hybrid strategy are given here and a related software package is introduced. Finally, the hybrid method is applied to simple biochemical systems as a demonstration of its application.

Influence of film structure on the dewetting kinetics of thin polymer films in the solvent annealing process.

PubMed

Zhang, Huanhuan; Xu, Lin; Lai, Yuqing; Shi, Tongfei

2016-06-28

On a non-wetting solid substrate, the solvent annealing process of a thin polymer film includes the swelling process and the dewetting process. Owing to difficulties in the in situ analysis of the two processes simultaneously, a quantitative study on the solvent annealing process of thin polymer films on the non-wetting solid substrate is extremely rare. In this paper, we design an experimental method by combining spectroscopic ellipsometry with optical microscopy to achieve the simultaneous in situ study. Using this method, we investigate the influence of the structure of swollen film on its dewetting kinetics during the solvent annealing process. The results show that for a thin PS film with low Mw (Mw = 4.1 kg mol(-1)), acetone molecules can form an ultrathin enriched layer between the PS film and the solid substrate during the swelling process. The presence of the acetone enriched layer accounts for the exponential kinetic behavior in the case of a thin PS film with low Mw. However, the acetone enriched layer is not observed in the case of a thin PS film with high Mw (Mw = 400 kg mol(-1)) and the slippage effect of polymer chains is valid during the dewetting process.

“Towards building better linkages between aqueous phase ...

EPA Pesticide Factsheets

Currently, CMAQ’s aqueous phase chemistry routine (AQCHEM-base) assumes Henry’s Law equilibrium and employs a forward Euler method to solve a small set of oxidation equations, considering the additional processes of aitken scavenging and wet deposition in series and employing a bisection method to calculate H+ concentrations. With potentially hundreds of reactions that may be important in cloud water and only seven reactions in the current model, expansion of the existing mechanism is an important area of investigation. However, with the current mechanism hardwired into the solver code, the module is difficult to expand with additional chemistry. It also ignores the impacts of mass transfer limitations on cloud chemistry which may be significant. Here, the Kinetic PreProcessor has been applied to generate a Rosenbrock solver for the CMAQ v5.0.1 aqueous phase chemistry mechanism. The module has been updated to simultaneously solve kinetic mass transfer between the phases, dissociation/association, chemical kinetics, Aitken scavenging, and wet deposition. This will allow for easier expansion of the chemical mechanism in the future and a better link between aqueous phase chemistry and droplet microphysics. The National Exposure Research Laboratory (NERL) Atmospheric Modeling and Analysis Division (AMAD) conducts research in support of EPA mission to protect human health and the environment. AMAD research program is engaged in developing and evaluating pre

Thermal stability of synthetic thyroid hormone l-thyroxine and l-thyroxine sodium salt hydrate both pure and in pharmaceutical formulations.

PubMed

Ledeţi, Ionuţ; Ledeţi, Adriana; Vlase, Gabriela; Vlase, Titus; Matusz, Petru; Bercean, Vasile; Şuta, Lenuţa-Maria; Piciu, Doina

2016-06-05

In this paper, the thermal stability of pure l-thyroxine (THY) and l-thyroxine sodium salt hydrate (THYSS) vs. two pharmaceutical solid formulations commercialized on both Romanian and European market (with a content of 100μg, respectively 200μg THYSS per tablet) were investigated. In order to determine whether the presence of excipients affects the thermal stability of the active pharmaceutical ingredient (API), the preliminary study of thermal stability in air atmosphere was completed with an in-depth solid-state kinetic study. By kinetic analysis, the non-isothermal degradation of the selected active pharmaceutical ingredients vs. the solid formulation with strength of 200μg THYSS per tablet was investigated. Isoconversional methods (Kissinger-Akahira-Sunose, Flynn-Wall-Ozawa and Friedman) were employed for the estimation of activation energies values, at five different heating rates, β=5, 7, 10, 12 and 15°Cmin(-1). Also, a fourth method was applied in the processing of data, namely NPK, allowing an objective separation in the physical and chemical processes that contribute to the thermal degradation of the selected compounds. A discussion of thermal stability from the kinetic point of view is also presented. Copyright © 2016 Elsevier B.V. All rights reserved.

Effective scheme of photolysis of GFP in live cell as revealed with confocal fluorescence microscopy

NASA Astrophysics Data System (ADS)

Glazachev, Yu I.; Orlova, D. Y.; Řezníčková, P.; Bártová, E.

2018-05-01

We proposed an effective kinetics scheme of photolysis of green fluorescent protein (GFP) observed in live cells with a commercial confocal fluorescence microscope. We investigated the photolysis of GFP-tagged heterochromatin protein, HP1β-GFP, in live nucleus with the pulse position modulation approach, which has several advantages over the classical pump-and-probe method. At the basis of the proposed scheme lies a process of photoswitching from the native fluorescence state to the intermediate fluorescence state, which has a lower fluorescence yield and recovers back to native state in the dark. This kinetics scheme includes four effective parameters (photoswitching, reverse switching, photodegradation rate constants, and relative brightness of the intermediate state) and covers the time scale from dozens of milliseconds to minutes of the experimental fluorescence kinetics. Additionally, the applicability of the scheme was demonstrated in the cases of continuous irradiation and the classical pump-and-probe approach using numerical calculations and analytical solutions. An interesting finding of experimental data analysis was that the overall photodegradation of GFP proceeds dominantly from the intermediate state, and demonstrated approximately the second-order reaction versus irradiation power. As a practical example, the proposed scheme elucidates the artifacts of fluorescence recovery after the photobleaching method, and allows us to propose some suggestions on how to diminish them.

Effective scheme of photolysis of GFP in live cell as revealed with confocal fluorescence microscopy.

PubMed

Glazachev, Yu I; Orlova, D Y; Řezníčková, P; Bártová, E

2018-03-23

We proposed an effective kinetics scheme of photolysis of green fluorescent protein (GFP) observed in live cells with a commercial confocal fluorescence microscope. We investigated the photolysis of GFP-tagged heterochromatin protein, HP1β-GFP, in live nucleus with the pulse position modulation approach, which has several advantages over the classical pump-and-probe method. At the basis of the proposed scheme lies a process of photoswitching from the native fluorescence state to the intermediate fluorescence state, which has a lower fluorescence yield and recovers back to native state in the dark. This kinetics scheme includes four effective parameters (photoswitching, reverse switching, photodegradation rate constants, and relative brightness of the intermediate state) and covers the time scale from dozens of milliseconds to minutes of the experimental fluorescence kinetics. Additionally, the applicability of the scheme was demonstrated in the cases of continuous irradiation and the classical pump-and-probe approach using numerical calculations and analytical solutions. An interesting finding of experimental data analysis was that the overall photodegradation of GFP proceeds dominantly from the intermediate state, and demonstrated approximately the second-order reaction versus irradiation power. As a practical example, the proposed scheme elucidates the artifacts of fluorescence recovery after the photobleaching method, and allows us to propose some suggestions on how to diminish them.

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.

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.

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.

Thermogravimetric characteristics and kinetics of scrap tyre and Juglans regia shell co-pyrolysis.

PubMed

Uzun, B B; Yaman, E

2014-10-01

The degradation kinetics of Juglans regia shell, scrap tyre and their blends were investigated using a thermogravimetric analysis method. Experiments were performed under dynamic conditions and a nitrogen atmosphere in the range 293 to 973 K at different heating rates. During pyrolysis of J. regia shell three mass loss zones were specified as removal of water, decomposition of hemicelluloses and cellulose, and decomposition of lignin. The degradation curves of scrap tyre showed merely one stage which was due to decomposition of styrene butadiene rubber. The kinetic parameters were calculated using both Arrhenius and Coats-Redfern methods. By adopting the Arrhenius method, the average value of activation energies of J. regia shell, scrap tyre and their 1 : 1 blends were found to be 69.22, 71.48 and 47.03 kJ mol(-1), respectively. Additionally, by using the Coats-Redfern method, the average value of activation energies of J. regia shell, scrap tyre and their 1 : 1 blend were determined as 99.85, 78.72 and 63.81 kJ mol(-1), respectively. The addition of J. regia shell to scrap tyre caused a reduction in the activation energies. The difference of weight loss was measured to examine interactions between raw materials. The maximum difference between experimental and theoretical mass loss was 5% at about 648 K with a heating rate of 20 K min(-1). These results indicated a significant synergistic effect was available during co-pyrolysis of J. regia shell and scrap tyre in the high temperature region. © The Author(s) 2014.

How Four Scientists Integrate Thermodynamic and Kinetic Theory, Context, Analogies, and Methods in Protein-Folding and Dynamics Research: Implications for Biochemistry Instruction.

PubMed

Jeffery, Kathleen A; Pelaez, Nancy; Anderson, Trevor R

2018-01-01

To keep biochemistry instruction current and relevant, it is crucial to expose students to cutting-edge scientific research and how experts reason about processes governed by thermodynamics and kinetics such as protein folding and dynamics. This study focuses on how experts explain their research into this topic with the intention of informing instruction. Previous research has modeled how expert biologists incorporate research methods, social or biological context, and analogies when they talk about their research on mechanisms. We used this model as a guiding framework to collect and analyze interview data from four experts. The similarities and differences that emerged from analysis indicate that all experts integrated theoretical knowledge with their research context, methods, and analogies when they explained how phenomena operate, in particular by mapping phenomena to mathematical models; they explored different processes depending on their explanatory aims, but readily transitioned between different perspectives and explanatory models; and they explained thermodynamic and kinetic concepts of relevance to protein folding in different ways that aligned with their particular research methods. We discuss how these findings have important implications for teaching and future educational research. © 2018 K. A. Jeffery et al. CBE—Life Sciences Education © 2018 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). 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).

Adsorption dynamics of methyl violet onto granulated mesoporous carbon: Facile synthesis and adsorption kinetics.

PubMed

Kim, Yohan; Bae, Jiyeol; Park, Hosik; Suh, Jeong-Kwon; You, Young-Woo; Choi, Heechul

2016-09-15

A new and facile one-step synthesis method for preparing granulated mesoporous carbon (GMC) with three-dimensional spherical mesoporous symmetry is prepared to remove large molecular weight organic compounds in aqueous phase. GMC is synthesized in a single step using as-synthesized mesoporous carbon particles and organic binders through a simple and economical synthesis approach involving a simultaneous calcination and carbonization process. Characterization results obtained from SEM, XRD, as well as surface and porosity analysis indicate that the synthesized GMC has similar physical properties to those of the powdered mesoporous carbon and maintains the Brunauer-Emmett-Teller (BET) surface area and pore volume because the new synthesis method prevents the collapse of the pores during the granulation process. Batch adsorption experiments revealed GMC showed a substantial adsorption capacity (202.8 mg/g) for the removal of methyl violet as a target large molecular contaminant in aqueous phase. The mechanisms and dynamics modeling of GMC adsorption were also fully examined, which revealed that surface diffusion was rate limiting step on adsorption process of GMC. Adsorption kinetics of GMC enables 3 times faster than that of granular activated carbon in terms of surface diffusion coefficient. This is the first study, to the best of our knowledge, to synthesize GMC as an adsorbent for water purification by using facile granulation method and to investigate the adsorption kinetics and characteristics of GMC. This study introduces a new and simple method for the synthesis of GMC and reveals its adsorption characteristics for large molecular compounds in a water treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Arterial input function of an optical tracer for dynamic contrast enhanced imaging can be determined from pulse oximetry oxygen saturation measurements

NASA Astrophysics Data System (ADS)

Elliott, Jonathan T.; Wright, Eric A.; Tichauer, Kenneth M.; Diop, Mamadou; Morrison, Laura B.; Pogue, Brian W.; Lee, Ting-Yim; St. Lawrence, Keith

2012-12-01

In many cases, kinetic modeling requires that the arterial input function (AIF)—the time-dependent arterial concentration of a tracer—be characterized. A straightforward method to measure the AIF of red and near-infrared optical dyes (e.g., indocyanine green) using a pulse oximeter is presented. The method is motivated by the ubiquity of pulse oximeters used in both preclinical and clinical applications, as well as the gap in currently available technologies to measure AIFs in small animals. The method is based on quantifying the interference that is observed in the derived arterial oxygen saturation (SaO2) following a bolus injection of a light-absorbing dye. In other words, the change in SaO2 can be converted into dye concentration knowing the chromophore-specific extinction coefficients, the true arterial oxygen saturation, and total hemoglobin concentration. A simple error analysis was performed to highlight potential limitations of the approach, and a validation of the method was conducted in rabbits by comparing the pulse oximetry method with the AIF acquired using a pulse dye densitometer. Considering that determining the AIF is required for performing quantitative tracer kinetics, this method provides a flexible tool for measuring the arterial dye concentration that could be used in a variety of applications.

Arterial input function of an optical tracer for dynamic contrast enhanced imaging can be determined from pulse oximetry oxygen saturation measurements.

PubMed

Elliott, Jonathan T; Wright, Eric A; Tichauer, Kenneth M; Diop, Mamadou; Morrison, Laura B; Pogue, Brian W; Lee, Ting-Yim; St Lawrence, Keith

2012-12-21

In many cases, kinetic modeling requires that the arterial input function (AIF)--the time-dependent arterial concentration of a tracer--be characterized. A straightforward method to measure the AIF of red and near-infrared optical dyes (e.g., indocyanine green) using a pulse oximeter is presented. The method is motivated by the ubiquity of pulse oximeters used in both preclinical and clinical applications, as well as the gap in currently available technologies to measure AIFs in small animals. The method is based on quantifying the interference that is observed in the derived arterial oxygen saturation (SaO₂) following a bolus injection of a light-absorbing dye. In other words, the change in SaO₂ can be converted into dye concentration knowing the chromophore-specific extinction coefficients, the true arterial oxygen saturation, and total hemoglobin concentration. A simple error analysis was performed to highlight potential limitations of the approach, and a validation of the method was conducted in rabbits by comparing the pulse oximetry method with the AIF acquired using a pulse dye densitometer. Considering that determining the AIF is required for performing quantitative tracer kinetics, this method provides a flexible tool for measuring the arterial dye concentration that could be used in a variety of applications.

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.

Analysis of kinematic, kinetic and electromyographic patterns during root canal preparation with rotary and manual instruments.

PubMed

Pasternak, Braulio; Sousa Neto, Manoel Damião de; Dionísio, Valdeci Carlos; Pécora, Jesus Djalma; Silva, Ricardo Gariba

2012-02-01

This study assessed the muscular activity during root canal preparation through kinematics, kinetics, and electromyography (EMG). The operators prepared one canal with RaCe rotary instruments and another with Flexo-files. The kinematics of the major joints was reconstructed using an optoelectronic system and electromyographic responses of the flexor carpi radialis, extensor carpi radialis, brachioradialis, biceps brachii, triceps brachii, middle deltoid, and upper trapezius were recorded. The joint torques of the shoulder, elbow and wrist were calculated using inverse dynamics. In the kinematic analysis, angular movements of the wrist and elbow were classified as low risk factors for work-related musculoskeletal disorders. With respect to the shoulder, the classification was medium-risk. There was no significant difference revealed by the kinetic reports. The EMG results showed that for the middle deltoid and upper trapezius the rotary instrumentation elicited higher values. The flexor carpi radialis and extensor carpi radialis, as well as the brachioradialis showed a higher value with the manual method. The muscular recruitment for accomplishment of articular movements for root canal preparation with either the rotary or manual techniques is distinct. Nevertheless, the rotary instrument presented less difficulty in the generation of the joint torque in each articulation, thus, presenting a greater uniformity of joint torques.

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.

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.

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.

Heavy Metal Adsorption onto Kappaphycus sp. from Aqueous Solutions: The Use of Error Functions for Validation of Isotherm and Kinetics Models

PubMed Central

Rahman, Md. Sayedur; Sathasivam, Kathiresan V.

2015-01-01

Biosorption process is a promising technology for the removal of heavy metals from industrial wastes and effluents using low-cost and effective biosorbents. In the present study, adsorption of Pb2+, Cu2+, Fe2+, and Zn2+ onto dried biomass of red seaweed Kappaphycus sp. was investigated as a function of pH, contact time, initial metal ion concentration, and temperature. The experimental data were evaluated by four isotherm models (Langmuir, Freundlich, Temkin, and Dubinin-Radushkevich) and four kinetic models (pseudo-first-order, pseudo-second-order, Elovich, and intraparticle diffusion models). The adsorption process was feasible, spontaneous, and endothermic in nature. Functional groups in the biomass involved in metal adsorption process were revealed as carboxylic and sulfonic acids and sulfonate by Fourier transform infrared analysis. A total of nine error functions were applied to validate the models. We strongly suggest the analysis of error functions for validating adsorption isotherm and kinetic models using linear methods. The present work shows that the red seaweed Kappaphycus sp. can be used as a potentially low-cost biosorbent for the removal of heavy metal ions from aqueous solutions. Further study is warranted to evaluate its feasibility for the removal of heavy metals from the real environment. PMID:26295032

Heavy Metal Adsorption onto Kappaphycus sp. from Aqueous Solutions: The Use of Error Functions for Validation of Isotherm and Kinetics Models.

PubMed

Rahman, Md Sayedur; Sathasivam, Kathiresan V

2015-01-01

Biosorption process is a promising technology for the removal of heavy metals from industrial wastes and effluents using low-cost and effective biosorbents. In the present study, adsorption of Pb(2+), Cu(2+), Fe(2+), and Zn(2+) onto dried biomass of red seaweed Kappaphycus sp. was investigated as a function of pH, contact time, initial metal ion concentration, and temperature. The experimental data were evaluated by four isotherm models (Langmuir, Freundlich, Temkin, and Dubinin-Radushkevich) and four kinetic models (pseudo-first-order, pseudo-second-order, Elovich, and intraparticle diffusion models). The adsorption process was feasible, spontaneous, and endothermic in nature. Functional groups in the biomass involved in metal adsorption process were revealed as carboxylic and sulfonic acids and sulfonate by Fourier transform infrared analysis. A total of nine error functions were applied to validate the models. We strongly suggest the analysis of error functions for validating adsorption isotherm and kinetic models using linear methods. The present work shows that the red seaweed Kappaphycus sp. can be used as a potentially low-cost biosorbent for the removal of heavy metal ions from aqueous solutions. Further study is warranted to evaluate its feasibility for the removal of heavy metals from the real environment.

Flutriciclamide (18F-GE180) PET: First-in-Human PET Study of Novel Third-Generation In Vivo Marker of Human Translocator Protein.

PubMed

Fan, Zhen; Calsolaro, Valeria; Atkinson, Rebecca A; Femminella, Grazia D; Waldman, Adam; Buckley, Christopher; Trigg, William; Brooks, David J; Hinz, Rainer; Edison, Paul

2016-11-01

Neuroinflammation is associated with neurodegenerative disease. PET radioligands targeting the 18-kDa translocator protein (TSPO) have been used as in vivo markers of neuroinflammation, but there is an urgent need for novel probes with improved signal-to-noise ratio. Flutriciclamide ( 18 F-GE180) is a recently developed third-generation TSPO ligand. In this first study, we evaluated the optimum scan duration and kinetic modeling strategies for 18 F-GE180 PET in (older) healthy controls. Ten healthy controls, 6 TSPO high-affinity binders, and 4 mixed-affinity binders were recruited. All subjects underwent detailed neuropsychologic tests, MRI, and a 210-min 18 F-GE180 dynamic PET/CT scan using metabolite-corrected arterial plasma input function. We evaluated 5 different kinetic models: irreversible and reversible 2-tissue-compartment models, a reversible 1-tissue model, and 2 models with an extra irreversible vascular compartment. The minimal scan duration was established using 210-min scan data. The feasibility of generating parametric maps was also investigated using graphical analysis. 18 F-GE180 concentration was higher in plasma than in whole blood during the entire scan duration. The volume of distribution (V T ) was 0.17 in high-affinity binders and 0.12 in mixed-affinity binders using the kinetic model. The model that best represented brain 18 F-GE180 kinetics across regions was the reversible 2-tissue-compartment model (2TCM4k), and 90 min resulted as the optimum scan length required to obtain stable estimates. Logan graphical analysis with arterial input function gave a V T highly consistent with V T in the kinetic model, which could be used for voxelwise analysis. We report for the first time, to our knowledge, the kinetic properties of the novel third-generation TSPO PET ligand 18 F-GE180 in humans: 2TCM4k is the optimal method to quantify the brain uptake, 90 min is the optimal scan length, and the Logan approach could be used to generate parametric maps. Although these control subjects have shown relatively low V T , the methodology presented here forms the basis for quantification for future PET studies using 18 F-GE180 in different pathologies. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Kinetics of pulse photothermal surface deformation as a method of studying the phase interface movement in a first-order phase transition

NASA Astrophysics Data System (ADS)

Vintzentz, S. V.; Kiselev, V. F.; Levshin, N. L.; Sandomirskii, V. B.

1991-01-01

The photothermal surface deformation (PTSD) method is used for characterization of the first-order phase transition (PT) for the first time. The advantages of the method are demonstrated experimentally for the well known metal-to-semiconductor PT in VO 2. It is found that near the PT temperature the PTSD pulse in a VO 2 film has a sign opposite to that of the thermoelastic response. The conclusion is drawn that this phenomenon is determined primarily by the contribution of the decrease in the specific volume (Δ V/ V) of the substance involved in the semiconductor-to-metal PT. The sign of Δ V/ V for a submicron polycrystalline VO 2 film is determined. Besides, analysis shows that in the PTSD kinetics measured as a whole we can "separate" a law for the metal-semicon- ductor interface movement (i.e. the interface moves towards the interior of the film when the latter is heated and back towards the surface when it is cooling down). The relative density change due to the PT is estimated based on this law.

Kinetic Monte Carlo Method for Rule-based Modeling of Biochemical Networks

PubMed Central

Yang, Jin; Monine, Michael I.; Faeder, James R.; Hlavacek, William S.

2009-01-01

We present a kinetic Monte Carlo method for simulating chemical transformations specified by reaction rules, which can be viewed as generators of chemical reactions, or equivalently, definitions of reaction classes. A rule identifies the molecular components involved in a transformation, how these components change, conditions that affect whether a transformation occurs, and a rate law. The computational cost of the method, unlike conventional simulation approaches, is independent of the number of possible reactions, which need not be specified in advance or explicitly generated in a simulation. To demonstrate the method, we apply it to study the kinetics of multivalent ligand-receptor interactions. We expect the method will be useful for studying cellular signaling systems and other physical systems involving aggregation phenomena. PMID:18851068

A kinetic study of hydrolysis of polyester elastomer in magnetic tape

NASA Technical Reports Server (NTRS)

Yamamoto, K.; Watanabe, H.

1994-01-01

A useful method for kinetic study of the hydrolysis of polyester elastomer is established which uses the number-average molecular weight. The reasonableness of this method is confirmed and the effect of magnetic particles on hydrolysis is considered.

PET Imaging of D2/3 agonist binding in healthy human subjects with the radiotracer [11C]-N-propyl-nor-apomorphine (NPA): preliminary evaluation and reproducibility studies

PubMed Central

Narendran, Rajesh; Frankle, W. Gordon; Mason, N. Scott; Laymon, Charles M.; Lopresti, Brian J; Price, Julie C.; Kendro, Steve; Vora, Shivangi; Litschge, Maralee; Mountz, James M.; Mathis, Chester A.

2009-01-01

Objective (-)-N-[11C]-Propyl-norapomorphine (NPA) is a full dopamine D2/3 receptor agonist radiotracer suitable for imaging D2/3 receptors configured in a state of high affinity for agonists using Positron Emission Tomography (PET). The aim of the present study was to define the optimal analytic method to derive accurate and reliable D2/3 receptor parameters with [11C]NPA. Methods Six healthy subjects (4 females/2 males) underwent two [11C]NPA scans in the same day. D2/3 receptor binding parameters were estimated using kinetic analysis (using 1- and 2- tissue compartment models) as well as simplified reference tissue method in the three functional subdivisions of the striatum (associative striatum, AST; limbic striatum LST and sensorimotor striatum SMST). The test-retest variability and intraclass correlation coefficient were assessed for distribution volume (VT), binding potential relative to plasma concentration (BPP), and binding potential relative to nondisplaceable uptake (BPND) Results A two-tissue compartment kinetic model adequately described the functional subdivisions of the striatum as well as cerebellum time-activity data. The reproducibility of VT was excellent (≤ 10%) in all regions, for this approach. The reproducibility of both BPP (≤ 12%) and BPND (≤ 10%) was also excellent. The intraclass correlation coefficient of BPP and BPND were acceptable as well (> 0.75) in the three functional subdivisions of the striatum. Although SRTM led to an underestimation of BPND values relative to that estimated by kinetic analysis by 8 to 13%, the values derived using both the methods were reasonably well correlated (r2 = 0.89, n = 84). Both methods were similarly effective at detecting the differences in [11C]NPA BPND between subjects. Conclusion The results of this study indicate that [11C]NPA can be used to measure D2/3 receptors configured in a state of high affinity for the agonists with high reliability and reproducibility in the functional subdivisions of the human striatum. PMID:19301416

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

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2005-01-01

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

Is automated kinetic measurement superior to end-point for advanced oxidation protein product?

PubMed

Oguz, Osman; Inal, Berrin Bercik; Emre, Turker; Ozcan, Oguzhan; Altunoglu, Esma; Oguz, Gokce; Topkaya, Cigdem; Guvenen, Guvenc

2014-01-01

Advanced oxidation protein product (AOPP) was first described as an oxidative protein marker in chronic uremic patients and measured with a semi-automatic end-point method. Subsequently, the kinetic method was introduced for AOPP assay. We aimed to compare these two methods by adapting them to a chemistry analyzer and to investigate the correlation between AOPP and fibrinogen, the key molecule responsible for human plasma AOPP reactivity, microalbumin, and HbA1c in patients with type II diabetes mellitus (DM II). The effects of EDTA and citrate-anticogulated tubes on these two methods were incorporated into the study. This study included 93 DM II patients (36 women, 57 men) with HbA1c levels > or = 7%, who were admitted to the diabetes and nephrology clinics. The samples were collected in EDTA and in citrate-anticoagulated tubes. Both methods were adapted to a chemistry analyzer and the samples were studied in parallel. In both types of samples, we found a moderate correlation between the kinetic and the endpoint methods (r = 0.611 for citrate-anticoagulated, r = 0.636 for EDTA-anticoagulated, p = 0.0001 for both). We found a moderate correlation between fibrinogen-AOPP and microalbumin-AOPP levels only in the kinetic method (r = 0.644 and 0.520 for citrate-anticoagulated; r = 0.581 and 0.490 for EDTA-anticoagulated, p = 0.0001). We conclude that adaptation of the end-point method to automation is more difficult and it has higher between-run CV% while application of the kinetic method is easier and it may be used in oxidative stress studies.

Solid State Kinetic Parameters and Chemical Mechanism of the Dehydration of CoCl2.6H2O.

ERIC Educational Resources Information Center

Ribas, Joan; And Others

1988-01-01

Presents an experimental example illustrating the most common methods for the determination of kinetic parameters. Discusses the different theories and equations to be applied and the mechanism derived from the kinetic results. (CW)

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

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.

Evaluation of joint findings with gait analysis in children with hemophilia.

PubMed

Cayir, Atilla; Yavuzer, Gunes; Sayli, Revide Tülin; Gurcay, Eda; Culha, Vildan; Bozkurt, Murat

2014-01-01

Hemophilic arthropathy due to recurrent joint bleeding leads to physical, psychological and socioeconomic problems in children with hemophilia and reduces their quality of life. The purpose of this study was to evaluate joint damage through various parameters and to determine functional deterioration in the musculoskeletal system during walking using kinetic and kinematic gait analysis. Physical examination and kinetic and kinematic gait analysis findings of 19 hemophilic patients aged 7-20 years were compared with those of age, sex and leg length matched controls. Stride time was longer in the hemophilia group (p=0.001) compared to the age matched healthy control group, while hip, knee and ankle joint rotation angles were more limited (p=0.001, p=0.035 and p=0.001, respectively). In the hemophilia group, the extensor moment of the knee joint in the stance phase was less than that in the control group (p=0.001). Stride time was longer in the severe hemophilia group compared to the mild-moderate hemophilia and control groups (p=0.011 and p=0.001, respectively). Rotation angle of the ankle was wider in the control group compared to the other two groups (p=0.001 for both). Rotation angle of the ankle joint was narrower in the severe hemophilia group compared to the others (p=0.001 for each). Extensor moment of the knee joint was greater in the control group compared to the other two groups (p=0.003 and p=0.001, respectively). Walking velocity was higher in the control group compared to the severe hemophilia group. Kinetic and kinematic gait analysis has the sensitivity to detect minimal changes in biomechanical parameters. Gait analysis can be used as a reliable method to detect early joint damage.