Numerical methods for solving moment equations in kinetic theory of neuronal network dynamics

NASA Astrophysics Data System (ADS)

Rangan, Aaditya V.; Cai, David; Tao, Louis

2007-02-01

Recently developed kinetic theory and related closures for neuronal network dynamics have been demonstrated to be a powerful theoretical framework for investigating coarse-grained dynamical properties of neuronal networks. The moment equations arising from the kinetic theory are a system of (1 + 1)-dimensional nonlinear partial differential equations (PDE) on a bounded domain with nonlinear boundary conditions. The PDEs themselves are self-consistently specified by parameters which are functions of the boundary values of the solution. The moment equations can be stiff in space and time. Numerical methods are presented here for efficiently and accurately solving these moment equations. The essential ingredients in our numerical methods include: (i) the system is discretized in time with an implicit Euler method within a spectral deferred correction framework, therefore, the PDEs of the kinetic theory are reduced to a sequence, in time, of boundary value problems (BVPs) with nonlinear boundary conditions; (ii) a set of auxiliary parameters is introduced to recast the original BVP with nonlinear boundary conditions as BVPs with linear boundary conditions - with additional algebraic constraints on the auxiliary parameters; (iii) a careful combination of two Newton's iterates for the nonlinear BVP with linear boundary condition, interlaced with a Newton's iterate for solving the associated algebraic constraints is constructed to achieve quadratic convergence for obtaining the solutions with self-consistent parameters. It is shown that a simple fixed-point iteration can only achieve a linear convergence for the self-consistent parameters. The practicability and efficiency of our numerical methods for solving the moment equations of the kinetic theory are illustrated with numerical examples. It is further demonstrated that the moment equations derived from the kinetic theory of neuronal network dynamics can very well capture the coarse-grained dynamical properties of integrate-and-fire neuronal networks.

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

PubMed Central

Erickson, David W; Schink, Severin J.; Patsalo, Vadim; Williamson, James R.; Gerland, Ulrich; Hwa, Terence

2018-01-01

A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms1–3 and they remain a topic of active investigation4–11. Although much is known about the molecular interactions that govern the regulation of key metabolic processes in response to applied perturbations12–17, they are insufficiently quantified for predictive bottom-up modelling. Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models15,18–20 from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux balance, we derive a quantitative model of bacterial growth transitions that is independent of inaccessible kinetic parameters. The resulting flux-controlled regulation model accurately predicts the time course of gene expression and biomass accumulation in response to carbon upshifts and downshifts (for example, diauxic shifts) without adjustable parameters. As predicted by the model and validated by quantitative proteomics, cells exhibit suboptimal recovery kinetics in response to nutrient shifts owing to a rigid strategy of protein synthesis allocation, which is not directed towards alleviating specific metabolic bottlenecks. Our approach does not rely on kinetic parameters, and therefore points to a theoretical framework for describing a broad range of such kinetic processes without detailed knowledge of the underlying biochemical reactions. PMID:29072300

Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis

PubMed Central

Zhao, Linjie; Sun, Tanlin; Pei, Jianfeng; Ouyang, Qi

2015-01-01

It has been a consensus in cancer research that cancer is a disease caused primarily by genomic alterations, especially somatic mutations. However, the mechanism of mutation-induced oncogenesis is not fully understood. Here, we used the mitochondrial apoptotic pathway as a case study and performed a systematic analysis of integrating pathway dynamics with protein interaction kinetics to quantitatively investigate the causal molecular mechanism of mutation-induced oncogenesis. A mathematical model of the regulatory network was constructed to establish the functional role of dynamic bifurcation in the apoptotic process. The oncogenic mutation enrichment of each of the protein functional domains involved was found strongly correlated with the parameter sensitivity of the bifurcation point. We further dissected the causal mechanism underlying this correlation by evaluating the mutational influence on protein interaction kinetics using molecular dynamics simulation. We analyzed 29 matched mutant–wild-type and 16 matched SNP—wild-type protein systems. We found that the binding kinetics changes reflected by the changes of free energy changes induced by protein interaction mutations, which induce variations in the sensitive parameters of the bifurcation point, were a major cause of apoptosis pathway dysfunction, and mutations involved in sensitive interaction domains show high oncogenic potential. Our analysis provided a molecular basis for connecting protein mutations, protein interaction kinetics, network dynamics properties, and physiological function of a regulatory network. These insights provide a framework for coupling mutation genotype to tumorigenesis phenotype and help elucidate the logic of cancer initiation. PMID:26170328

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.

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.

Dry-thermophilic anaerobic digestion of organic fraction of municipal solid waste: Methane production modeling

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

Fdez-Gueelfo, L.A., E-mail: alberto.fdezguelfo@uca.es; Alvarez-Gallego, C.; Sales, D.

2012-03-15

Highlights: Black-Right-Pointing-Pointer Methane generation may be modeled by means of modified product generation model of Romero Garcia (1991). Black-Right-Pointing-Pointer Organic matter content and particle size influence the kinetic parameters. Black-Right-Pointing-Pointer Higher organic matter content and lower particle size enhance the biomethanization. - Abstract: The influence of particle size and organic matter content of organic fraction of municipal solid waste (OFMSW) in the overall kinetics of dry (30% total solids) thermophilic (55 Degree-Sign C) anaerobic digestion have been studied in a semi-continuous stirred tank reactor (SSTR). Two types of wastes were used: synthetic OFMSW (average particle size of 1 mm; 0.71more » g Volatile Solids/g waste), and OFMSW coming from a composting full scale plant (average particle size of 30 mm; 0.16 g Volatile Solids/g waste). A modification of a widely-validated product-generation kinetic model has been proposed. Results obtained from the modified-model parameterization at steady-state (that include new kinetic parameters as K, Y{sub pMAX} and {theta}{sub MIN}) indicate that the features of the feedstock strongly influence the kinetics of the process. The overall specific growth rate of microorganisms ({mu}{sub max}) with synthetic OFMSW is 43% higher compared to OFMSW coming from a composting full scale plant: 0.238 d{sup -1} (K = 1.391 d{sup -1}; Y{sub pMAX} = 1.167 L CH{sub 4}/gDOC{sub c}; {theta}{sub MIN} = 7.924 days) vs. 0.135 d{sup -1} (K = 1.282 d{sup -1}; Y{sub pMAX} = 1.150 L CH{sub 4}/gDOC{sub c}; {theta}{sub MIN} = 9.997 days) respectively. Finally, it could be emphasized that the validation of proposed modified-model has been performed successfully by means of the simulation of non-steady state data for the different SRTs tested with each waste.« less

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.

Impact of Harness Attachment Point on Kinetics and Kinematics During Sled Towing.

PubMed

Bentley, Ian; Atkins, Steve J; Edmundson, Christopher J; Metcalfe, John; Sinclair, Jonathan K

2016-03-01

Resisted sprint training is performed in a horizontal direction and involves similar muscles, velocities, and ranges of motion (ROM) to those of normal sprinting. Generally, sleds are attached to the athletes through a lead (3 m) and harness; the most common attachment points are the shoulder or waist. At present, it is not known how the different harness point's impact on the kinematics and kinetics associated with sled towing (ST). The aim of the current investigation was to examine the kinetics and kinematics of shoulder and waist harness attachment points in relation to the acceleration phase of ST. Fourteen trained men completed normal and ST trials, loaded at 10% reduction of sprint velocity. Sagittal plane kinematics from the trunk, hip, knee, and ankle were measured, together with stance phase kinetics (third footstrike). Kinetic and kinematic parameters were compared between harness attachments using one-way repeated-measures analysis of variance. The results indicated that various kinetic differences were present between the normal and ST conditions. Significantly greater net horizontal mean force, net horizontal impulses, propulsive mean force, and propulsive impulses were measured (p < 0.05). Interestingly, the waist harness also led to greater net horizontal impulse when compared with the shoulder attachment (p < 0.001). In kinematic terms, ST conditions significantly increased peak flexion in hip, knee, and ankle joints compared with the normal trials (p < 0.05). Results highlighted that the shoulder harness had a greater impact on trunk and knee joint kinematics when compared with the waist harness (p < 0.05). In summary, waist harnesses seem to be the most suitable attachment point for the acceleration phase of sprinting. Sled towing with these attachments resulted in fewer kinematic alterations and greater net horizontal impulse when compared with the shoulder harness. Future research is necessary in order to explore the long-term adaptations of these acute changes.

Therapeutic effects of an anti-gravity treadmill (AlterG) training on gait and lower limbs kinematics and kinetics in children with cerebral palsy.

PubMed

Lotfian, M; Kharazi, M R; Mirbagheri, A; Dadashi, F; Nourian, R; Mirbagheri, M M

2017-07-01

We aimed to investigate the effects of the lower body weight support treadmill (AlterG) training on kinetics and kinematics of the lower extremities in children with cerebral palsy (CP). We provided a 45-minute training program, 3 times a week for 8 weeks. AlterG can support the subject's weight up to 70% so that the subject will be able to walk more comfortably to reach a more correct walking pattern. The kinematics and kinetics were evaluated using an isokinetic dynamometer. The locomotion parameters were assessed in the gait laboratory. Subjects performance was evaluated at four time points: baseline (prior to training), 1 and 2 months after the beginning of training, and one month after the end of the training (as a follow-up evaluation). The results showed that the major gait, kinematic, and kinetic parameters improved after the AlterG training and were persistent. These findings suggest that the AlterG training can be considered as a therapeutic tool for improving the lower limb performance and locomotion in children with CP.

Global investigation of potential energy surfaces for the pyrolysis of C(1)-C(3) hydrocarbons: toward the development of detailed kinetic models from first principles.

PubMed

Ryazantsev, Mikhail N; Jamal, Adeel; Maeda, Satoshi; Morokuma, Keiji

2015-11-07

Detailed kinetic models (DKMs) are the most fundamental "bottom-up" approaches to computational investigation of the pyrolysis and oxidation of fuels. The weakest points of existing DKMs are incomplete information about the reaction types that can be involved in the potential energy surfaces (PESs) in pyrolysis and oxidation processes. Also, the computational thermodynamic parameters available in the literature vary widely with the level of theory employed. More sophisticated models require improvement both in our knowledge of the type of the reactions involved and the consistency of thermodynamic and kinetic parameters. In this paper, we aim to address these issues by developing ab initio models that can be used to describe early stages of pyrolysis of C1-C3 hydrocarbons. We applied a recently developed global reaction route mapping (GRRM) strategy to systematically investigate the PES of the pyrolysis of C1-C3 hydrocarbons at a consistent level of theory. The reactions are classified into 14 reaction types. The critical points on the PES for all reactions in the network are calculated at the highly accurate UCCSD(T)-F12b/cc-pVTZ//UM06-2X/cc-pVTZ level of theory. The data reported in this paper can be used for first principle calculations of kinetic constants and for a subsequent study on modeling the evolution of the species from the reaction network of the pyrolysis and oxidation of C1-C3 hydrocarbons.

Differential scanning calorimetry study and computer modeling of β ⇒ α phase transformation in a Ti-6Al-4V alloy

NASA Astrophysics Data System (ADS)

Malinov, S.; Guo, Z.; Sha, W.; Wilson, A.

2001-04-01

The relationship between heat-treatment parameters and microstructure in titanium alloys has so far been mainly studied empirically, using characterization techniques such as microscopy. Calculation and modeling of the kinetics of phase transformation have not yet been widely used for these alloys. Differential scanning calorimetry (DSC) has been widely used for the study of a variety of phase transformations. There has been much work done on the calculation and modeling of the kinetics of phase transformations for different systems based on the results from DSC study. In the present work, the kinetics of the β ⇒ α transformation in a Ti-6Al-4V titanium alloy were studied using DSC, at continuous cooling conditions with constant cooling rates of 5 °C, 10 °C, 20 °C, 30 °C, 40 °C, and 50 °C/min. The results from calorimetry were then used to trace and model the transformation kinetics in continuous cooling conditions. Based on suitably interpreted DSC results, continuous cooling-transformation (CCT) diagrams were calculated with lines of isotransformed fraction. The kinetics of transformation were modeled using the Johnson-Mehl-Avrami (JMA) theory and by applying the “concept of additivity.” The JMA kinetic parameters were derived. Good agreement between the calculated and experimental transformed fractions is demonstrated. Using the derived kinetic parameters, the β ⇒ α transformation in a Ti-6Al-4V alloy can be described for any cooling path and condition. An interpretation of the results from the point of view of activation energy for nucleation is also presented.

Predicting protein folding rate change upon point mutation using residue-level coevolutionary information.

PubMed

Mallik, Saurav; Das, Smita; Kundu, Sudip

2016-01-01

Change in folding kinetics of globular proteins upon point mutation is crucial to a wide spectrum of biological research, such as protein misfolding, toxicity, and aggregations. Here we seek to address whether residue-level coevolutionary information of globular proteins can be informative to folding rate changes upon point mutations. Generating residue-level coevolutionary networks of globular proteins, we analyze three parameters: relative coevolution order (rCEO), network density (ND), and characteristic path length (CPL). A point mutation is considered to be equivalent to a node deletion of this network and respective percentage changes in rCEO, ND, CPL are found linearly correlated (0.84, 0.73, and -0.61, respectively) with experimental folding rate changes. The three parameters predict the folding rate change upon a point mutation with 0.031, 0.045, and 0.059 standard errors, respectively. © 2015 Wiley Periodicals, Inc.

Review of chemical-kinetic problems of future NASA missions, II: Mars entries

NASA Technical Reports Server (NTRS)

Park, Chul; Howe, John T.; Jaffe, Richard L.; Candler, Graham V.

1994-01-01

The present work aims to derive a set of thermomechanical relaxation rate parameters and chemical reaction rate coefficients relevant to future interplanetary missions. It also attempts to assess the impact of thermochemical nonequilibrium phenomena on radiative heating rates for the stagnation point of the Martian entry vehicle.

Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation

PubMed Central

2011-01-01

Background Higher plants and algae are able to fix atmospheric carbon dioxide through photosynthesis and store this fixed carbon in large quantities as starch, which can be hydrolyzed into sugars serving as feedstock for fermentation to biofuels and precursors. Rational engineering of carbon flow in plant cells requires a greater understanding of how starch breakdown fluxes respond to variations in enzyme concentrations, kinetic parameters, and metabolite concentrations. We have therefore developed and simulated a detailed kinetic ordinary differential equation model of the degradation pathways for starch synthesized in plants and green algae, which to our knowledge is the most complete such model reported to date. Results Simulation with 9 internal metabolites and 8 external metabolites, the concentrations of the latter fixed at reasonable biochemical values, leads to a single reference solution showing β-amylase activity to be the rate-limiting step in carbon flow from starch degradation. Additionally, the response coefficients for stromal glucose to the glucose transporter kcat and KM are substantial, whereas those for cytosolic glucose are not, consistent with a kinetic bottleneck due to transport. Response coefficient norms show stromal maltopentaose and cytosolic glucosylated arabinogalactan to be the most and least globally sensitive metabolites, respectively, and β-amylase kcat and KM for starch to be the kinetic parameters with the largest aggregate effect on metabolite concentrations as a whole. The latter kinetic parameters, together with those for glucose transport, have the greatest effect on stromal glucose, which is a precursor for biofuel synthetic pathways. Exploration of the steady-state solution space with respect to concentrations of 6 external metabolites and 8 dynamic metabolite concentrations show that stromal metabolism is strongly coupled to starch levels, and that transport between compartments serves to lower coupling between metabolic subsystems in different compartments. Conclusions We find that in the reference steady state, starch cleavage is the most significant determinant of carbon flux, with turnover of oligosaccharides playing a secondary role. Independence of stationary point with respect to initial dynamic variable values confirms a unique stationary point in the phase space of dynamically varying concentrations of the model network. Stromal maltooligosaccharide metabolism was highly coupled to the available starch concentration. From the most highly converged trajectories, distances between unique fixed points of phase spaces show that cytosolic maltose levels depend on the total concentrations of arabinogalactan and glucose present in the cytosol. In addition, cellular compartmentalization serves to dampen much, but not all, of the effects of one subnetwork on another, such that kinetic modeling of single compartments would likely capture most dynamics that are fast on the timescale of the transport reactions. PMID:21682905

Systems approach to excitation-energy and electron transfer reaction networks in photosystem II complex: model studies for chlorophyll a fluorescence induction kinetics.

PubMed

Matsuoka, Takeshi; Tanaka, Shigenori; Ebina, Kuniyoshi

2015-09-07

Photosystem II (PS II) is a protein complex which evolves oxygen and drives charge separation for photosynthesis employing electron and excitation-energy transfer processes over a wide timescale range from picoseconds to milliseconds. While the fluorescence emitted by the antenna pigments of this complex is known as an important indicator of the activity of photosynthesis, its interpretation was difficult because of the complexity of PS II. In this study, an extensive kinetic model which describes the complex and multi-timescale characteristics of PS II is analyzed through the use of the hierarchical coarse-graining method proposed in the authors׳ earlier work. In this coarse-grained analysis, the reaction center (RC) is described by two states, open and closed RCs, both of which consist of oxidized and neutral special pairs being in quasi-equilibrium states. Besides, the PS II model at millisecond scale with three-state RC, which was studied previously, could be derived by suitably adjusting the kinetic parameters of electron transfer between tyrosine and RC. Our novel coarse-grained model of PS II can appropriately explain the light-intensity dependent change of the characteristic patterns of fluorescence induction kinetics from O-J-I-P, which shows two inflection points, J and I, between initial point O and peak point P, to O-J-D-I-P, which shows a dip D between J and I inflection points. Copyright © 2015 Elsevier Ltd. All rights reserved.

Determination of char combustion kinetics parameters: Comparison of point detector and imaging-based particle-sizing pyrometry

NASA Astrophysics Data System (ADS)

Schiemann, Martin; Geier, Manfred; Shaddix, Christopher R.; Vorobiev, Nikita; Scherer, Viktor

2014-07-01

In this study, the char burnout characteristics of two German coals (a lignite and a high-volatile bituminous coal) were investigated using two different experimental configurations and optical techniques in two distinct laboratories for measurement of temperature and size of burning particles. The optical diagnostic hardware is quite different in the two systems, but both perform two-color pyrometry and optical sizing measurements on individual particles burning in isolation from each other in high-temperature laminar flows to characterize the char consumption kinetics. The performance of the specialized systems is compared for two different combustion atmospheres (with 6.6 and 12 vol.% O2) and gas temperatures between 1700 and 1800 K. The measured particle temperatures and diameters are converted to char burning rate parameters for several residence times during the course of the particles' burnout. The results confirm that comparable results are obtained with the two configurations, although higher levels of variability in the measured data were observed in the imaging-based pyrometer setup. Corresponding uncertainties in kinetics parameters were larger, and appear to be more sensitive to systematic measurement errors when lower oxygen contents are used in the experiments. Consequently, burnout experiments in environments with sufficiently high O2 contents may be used to measure reliable char burning kinetics rates. Based on simulation results for the two coals, O2 concentrations in the range 10%-30% are recommended for kinetic rate measurements on 100 μm particles.

Tracking of cell nuclei for assessment of in vitro uptake kinetics in ultrasound-mediated drug delivery using fibered confocal fluorescence microscopy.

PubMed

Derieppe, Marc; de Senneville, Baudouin Denis; Kuijf, Hugo; Moonen, Chrit; Bos, Clemens

2014-10-01

Previously, we demonstrated the feasibility to monitor ultrasound-mediated uptake of a cell-impermeable model drug in real time with fibered confocal fluorescence microscopy. Here, we present a complete post-processing methodology, which corrects for cell displacements, to improve the accuracy of pharmacokinetic parameter estimation. Nucleus detection was performed based on the radial symmetry transform algorithm. Cell tracking used an iterative closest point approach. Pharmacokinetic parameters were calculated by fitting a two-compartment model to the time-intensity curves of individual cells. Cells were tracked successfully, improving time-intensity curve accuracy and pharmacokinetic parameter estimation. With tracking, 93 % of the 370 nuclei showed a fluorescence signal variation that was well-described by a two-compartment model. In addition, parameter distributions were narrower, thus increasing precision. Dedicated image analysis was implemented and enabled studying ultrasound-mediated model drug uptake kinetics in hundreds of cells per experiment, using fiber-based confocal fluorescence microscopy.

Nuclear-coupled thermal-hydraulic stability analysis of boiling water reactors

NASA Astrophysics Data System (ADS)

Karve, Atul A.

We have studied the nuclear-coupled thermal-hydraulic stability of boiling water reactors (BWRs) using a model we developed from: the space-time modal neutron kinetics equations based on spatial omega-modes, the equations for two-phase flow in parallel boiling channels, the fuel rod heat conduction equations, and a simple model for the recirculation loop. The model is represented as a dynamical system comprised of time-dependent nonlinear ordinary differential equations, and it is studied using stability analysis, modern bifurcation theory, and numerical simulations. We first determine the stability boundary (SB) in the most relevant parameter plane, the inlet-subcooling-number/external-pressure-drop plane, for a fixed control rod induced external reactivity equal to the 100% rod line value and then transform the SB to the practical power-flow map. Using this SB, we show that the normal operating point at 100% power is very stable, stability of points on the 100% rod line decreases as the flow rate is reduced, and that points are least stable in the low-flow/high-power region. We also determine the SB when the modal kinetics is replaced by simple point reactor kinetics and show that the first harmonic mode has no significant effect on the SB. Later we carry out the relevant numerical simulations where we first show that the Hopf bifurcation, that occurs as a parameter is varied across the SB is subcritical, and that, in the important low-flow/high-power region, growing oscillations can result following small finite perturbations of stable steady-states on the 100% rod line. Hence, a point on the 100% rod line in the low-flow/high-power region, although stable, may nevertheless be a point at which a BWR should not be operated. Numerical simulations are then done to calculate the decay ratios (DRs) and frequencies of oscillations for various points on the 100% rod line. It is determined that the NRC requirement of DR < 0.75-0.8 is not rigorously satisfied in the low-flow/high-power region and hence these points should be avoided during normal startup and shutdown operations. The frequency of oscillation is shown to decrease as the flow rate is reduced and the frequency of 0.5Hz observed in the low-flow/high-power region is consistent with those observed during actual instability incidents. Additional numerical simulations show that in the low-flow/high-power region, for the same initial conditions, the use of point kinetics leads to damped oscillations, whereas the model that includes the modal kinetics equations results in growing nonlinear oscillations. Thus, we show that side-by-side out-of-phase growing power oscillations result due to the very important first harmonic mode effect and that the use of point kinetics, which fails to predict these growing oscillations, leads to dramatically nonconservative results. Finally, the effect of a simple recirculation loop model that we develop is studied by carrying out additional stability analyses and additional numerical simulations. It is shown that the loop has a stabilizing effect on certain points on the 100% rod line for time delays equal to integer multiples of the natural period of oscillation, whereas it has a destabilizing effect for half-integer multiples. However, for more practical time delays, it is determined that the overall effect generally is destabilizing.

Effect of Thermocycling on the Structure of Martensite and Kinetics of Martensitic Transformation in Alloy Fe - 30% Ni - 3% Pd

NASA Astrophysics Data System (ADS)

Yildiz, Yasin Gokturk; Yildiz, Gokcen Dikici

2017-11-01

The methods of scanning electron microscopy, differential scanning calorimetry and x-ray diffraction are used to study the morphological and thermal characteristics of cooling-induced martensite in alloy Fe - 30% Ni - 3% Pd. It is shown that the kinetics of the martensitic transformation is athermal and the morphology is lamellar. The mean values of the parameters of the austenite and martensite lattices are 0.35704 and 0.28614 nm respectively. The thermocycling leaves the points A s and A f invariable.

Differential effects on enzyme stability and kinetic parameters of mutants related to human triosephosphate isomerase deficiency.

PubMed

Cabrera, Nallely; Torres-Larios, Alfredo; García-Torres, Itzhel; Enríquez-Flores, Sergio; Perez-Montfort, Ruy

2018-06-01

Human triosephosphate isomerase (TIM) deficiency is a very rare disease, but there are several mutations reported to be causing the illness. In this work, we produced nine recombinant human triosephosphate isomerases which have the mutations reported to produce TIM deficiency. These enzymes were characterized biophysically and biochemically to determine their kinetic and stability parameters, and also to substitute TIM activity in supporting the growth of an Escherichia coli strain lacking the tim gene. Our results allowed us to rate the deleteriousness of the human TIM mutants based on the type and severity of the alterations observed, to classify four "unknown severity mutants" with altered residues in positions 62, 72, 122 and 154 and to explain in structural terms the mutation V231M, the most affected mutant from the kinetic point of view and the only homozygous mutation reported besides E104D. Copyright © 2018 Elsevier B.V. All rights reserved.

Extracting survival parameters from isothermal, isobaric, and "iso-concentration" inactivation experiments by the "3 end points method".

PubMed

Corradini, M G; Normand, M D; Newcomer, C; Schaffner, D W; Peleg, M

2009-01-01

Theoretically, if an organism's resistance can be characterized by 3 survival parameters, they can be found by solving 3 simultaneous equations that relate the final survival ratio to the lethal agent's intensity. (For 2 resistance parameters, 2 equations will suffice.) In practice, the inevitable experimental scatter would distort the results of such a calculation or render the method unworkable. Averaging the results obtained with more than 3 final survival ratio triplet combinations, determined in four or more treatments, can remove this impediment. This can be confirmed by the ability of a kinetic inactivation model derived from the averaged parameters to predict survival patterns under conditions not employed in their determination, as demonstrated with published isothermal survival data of Clostridium botulinum spores, isobaric data of Escherichia coli under HPP, and Pseudomonas exposed to hydrogen peroxide. Both the method and the underlying assumption that the inactivation followed a Weibull-Log logistic (WeLL) kinetics were confirmed in this way, indicating that when an appropriate survival model is available, it is possible to predict the entire inactivation curves from several experimental final survival ratios alone. Where applicable, the method could simplify the experimental procedure and lower the cost of microbial resistance determinations. In principle, the methodology can be extended to deteriorative chemical reactions if they too can be characterized by 2 or 3 kinetic parameters.

The influence of non-ionisable excipients on precipitation parameters measured using the CheqSol method.

PubMed

Etherson, Kelly; Halbert, Gavin; Elliott, Moira

2016-09-01

The aim of this study was to determine the influence of non-ionisable excipients hydroxypropyl-β-cyclodextrin (HPβCD) and poloxamers 407 and 188 on the supersaturation and precipitation kinetics of ibuprofen, gliclazide, propranolol and atenolol induced through solution pH shifts using the CheqSol method. The drug's kinetic and intrinsic aqueous solubilities were measured in the presence of increasing excipient concentrations using the CheqSol method. Experimental data rate of change of pH with time was also examined to determine excipient-induced parachute effects and influence on precipitation rates. The measured kinetic and intrinsic solubilities provide a determination of the influence of each excipient on supersaturation index, and the area under the CheqSol curve can measure the parachute capability of excipients. The excipients influence on precipitation kinetics can be measured with novel parameters; for example, the precipitation pH or percentage ionised drug at the precipitation point, which provide further information on the excipient-induced changes in precipitation performance. This method can therefore be employed to measure the influence of non-ionisable excipients on the kinetic solubility behaviour of supersaturated solutions of ionisable drugs and to provide data, which discriminates between excipient systems during precipitation. © 2016 Royal Pharmaceutical Society.

Malonic acid concentration as a control parameter in the kinetic analysis of the Belousov-Zhabotinsky reaction under batch conditions.

PubMed

Blagojević, Slavica M; Anić, Slobodan R; Cupić, Zeljko D; Pejić, Natasa D; Kolar-Anić, Ljiljana Z

2008-11-28

The influence of the initial malonic acid concentration [MA]0 (8.00 x 10(-3) < or = [MA]0 < or = 4.30 x 10(-2) mol dm(-3)) in the presence of bromate (6.20 x 10(-2) mol dm(-3)), bromide (1.50 x 10(-5) mol dm(-3)), sulfuric acid (1.00 mol dm(-3)) and cerium sulfate (2.50 x 10(-3) mol dm(-3)) on the dynamics and the kinetics of the Belousov-Zhabotinsky (BZ) reactions was examined under batch conditions at 30.0 degrees C. The kinetics of the BZ reaction was analyzed by the earlier proposed method convenient for the examinations of the oscillatory reactions. In the defined region of parameters where oscillograms with only large-amplitude relaxation oscillations appeared, the pseudo-first order of the overall malonic acid decomposition with a corresponding rate constant of 2.14 x 10(-2) min(-1) was established. The numerical results on the dynamics and kinetics of the BZ reaction, carried out by the known skeleton model including the Br2O species, were in good agreement with the experimental ones. The already found saddle node infinite period (SNIPER) bifurcation point in transition from a stable quasi-steady state to periodic orbits and vice versa is confirmed by both experimental and numerical investigations of the system under consideration. Namely, the large-amplitude relaxation oscillations with increasing periods between oscillations in approaching the bifurcation points at the beginning and the end of the oscillatory domain, together with excitability of the stable quasi-steady states in their vicinity are obtained.

On the modeling of breath-by-breath oxygen uptake kinetics at the onset of high-intensity exercises: simulated annealing vs. GRG2 method.

PubMed

Bernard, Olivier; Alata, Olivier; Francaux, Marc

2006-03-01

Modeling in the time domain, the non-steady-state O2 uptake on-kinetics of high-intensity exercises with empirical models is commonly performed with gradient-descent-based methods. However, these procedures may impair the confidence of the parameter estimation when the modeling functions are not continuously differentiable and when the estimation corresponds to an ill-posed problem. To cope with these problems, an implementation of simulated annealing (SA) methods was compared with the GRG2 algorithm (a gradient-descent method known for its robustness). Forty simulated Vo2 on-responses were generated to mimic the real time course for transitions from light- to high-intensity exercises, with a signal-to-noise ratio equal to 20 dB. They were modeled twice with a discontinuous double-exponential function using both estimation methods. GRG2 significantly biased two estimated kinetic parameters of the first exponential (the time delay td1 and the time constant tau1) and impaired the precision (i.e., standard deviation) of the baseline A0, td1, and tau1 compared with SA. SA significantly improved the precision of the three parameters of the second exponential (the asymptotic increment A2, the time delay td2, and the time constant tau2). Nevertheless, td2 was significantly biased by both procedures, and the large confidence intervals of the whole second component parameters limit their interpretation. To compare both algorithms on experimental data, 26 subjects each performed two transitions from 80 W to 80% maximal O2 uptake on a cycle ergometer and O2 uptake was measured breath by breath. More than 88% of the kinetic parameter estimations done with the SA algorithm produced the lowest residual sum of squares between the experimental data points and the model. Repeatability coefficients were better with GRG2 for A1 although better with SA for A2 and tau2. Our results demonstrate that the implementation of SA improves significantly the estimation of most of these kinetic parameters, but a large inaccuracy remains in estimating the parameter values of the second exponential.

Understanding the oriented-attachment growth of nanocrystals from an energy point of view: a review

NASA Astrophysics Data System (ADS)

Lv, Weiqiang; He, Weidong; Wang, Xiaoning; Niu, Yinghua; Cao, Huanqi; Dickerson, James H.; Wang, Zhiguo

2014-02-01

Since Penn et al. first discovered the oriented attachment growth of crystals, the oriented attachment mechanism has now become a major research focus in the crystal field, and extensive efforts have been carried out over the past decade to systematically investigate the growth mechanism and the statistical kinetic models. However, most of the work mainly focuses on the experimental results on the oriented attachment growth. In contrast to the previous reviews, our review provides an overview of the recent theoretical advances in oriented attachment kinetics combined with experimental evidences. After a brief introduction to the van der Waals interaction and Coulombic interaction in a colloidal system, the correlation between the kinetic models of oriented attachment growth and the interactions is then our focus. The impact of in situ experimental observation techniques on the study of oriented attachment growth is examined with insightful examples. In addition, the advances in theoretical simulations mainly investigating the thermodynamic origin of these interactions at the atomic level are reviewed. This review seeks to understand the oriented attachment crystal growth from a kinetic point of view and provide a quantitative methodology to rationally design an oriented attachment system with pre-evaluated crystal growth parameters.

Influence of the partial volume correction method on 18F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM

PubMed Central

Bowen, Spencer L.; Byars, Larry G.; Michel, Christian J.; Chonde, Daniel B.; Catana, Ciprian

2014-01-01

Kinetic parameters estimated from dynamic 18F-fluorodeoxyglucose PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For OSEM, image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting 18F-fluorodeoxyglucose dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation GTM PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in CMRGlc estimates, although by less than 5% in most cases compared to the other PVC methods. The results indicate that the PVC implementation and choice of PSF modelling in the reconstruction can significantly impact model parameters. PMID:24052021

Gravity at a Quantum Condensate

NASA Astrophysics Data System (ADS)

Atanasov, Victor

2017-07-01

Provided a quantum superconducting condensate is allowed to occupy a curved hyper-plane of space-time, a geometric potential from the kinetic term arises. An energy conservation relation involving the geometric field at every material point in the superconductor can be demonstrated. The induced three-dimensional scalar curvature is directly related to the wavefunction/order parameter of the quantum condensate thus pointing the way to a possible experimental procedure to artificially induce curvature of space-time via change in the electric/probability current density.

"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.

Rubisco Catalytic Properties and Temperature Response in Crops1

PubMed Central

2016-01-01

Rubisco catalytic traits and their thermal dependence are two major factors limiting the CO2 assimilation potential of plants. In this study, we present the profile of Rubisco kinetics for 20 crop species at three different temperatures. The results largely confirmed the existence of significant variation in the Rubisco kinetics among species. Although some of the species tended to present Rubisco with higher thermal sensitivity (e.g. Oryza sativa) than others (e.g. Lactuca sativa), interspecific differences depended on the kinetic parameter. Comparing the temperature response of the different kinetic parameters, the Rubisco Km for CO2 presented higher energy of activation than the maximum carboxylation rate and the CO2 compensation point in the absence of mitochondrial respiration. The analysis of the Rubisco large subunit sequence revealed the existence of some sites under adaptive evolution in branches with specific kinetic traits. Because Rubisco kinetics and their temperature dependency were species specific, they largely affected the assimilation potential of Rubisco from the different crops, especially under those conditions (i.e. low CO2 availability at the site of carboxylation and high temperature) inducing Rubisco-limited photosynthesis. As an example, at 25°C, Rubisco from Hordeum vulgare and Glycine max presented, respectively, the highest and lowest potential for CO2 assimilation at both high and low chloroplastic CO2 concentrations. In our opinion, this information is relevant to improve photosynthesis models and should be considered in future attempts to design more efficient Rubiscos. PMID:27329223

Rubisco Catalytic Properties and Temperature Response in Crops.

PubMed

Hermida-Carrera, Carmen; Kapralov, Maxim V; Galmés, Jeroni

2016-08-01

Rubisco catalytic traits and their thermal dependence are two major factors limiting the CO2 assimilation potential of plants. In this study, we present the profile of Rubisco kinetics for 20 crop species at three different temperatures. The results largely confirmed the existence of significant variation in the Rubisco kinetics among species. Although some of the species tended to present Rubisco with higher thermal sensitivity (e.g. Oryza sativa) than others (e.g. Lactuca sativa), interspecific differences depended on the kinetic parameter. Comparing the temperature response of the different kinetic parameters, the Rubisco Km for CO2 presented higher energy of activation than the maximum carboxylation rate and the CO2 compensation point in the absence of mitochondrial respiration. The analysis of the Rubisco large subunit sequence revealed the existence of some sites under adaptive evolution in branches with specific kinetic traits. Because Rubisco kinetics and their temperature dependency were species specific, they largely affected the assimilation potential of Rubisco from the different crops, especially under those conditions (i.e. low CO2 availability at the site of carboxylation and high temperature) inducing Rubisco-limited photosynthesis. As an example, at 25°C, Rubisco from Hordeum vulgare and Glycine max presented, respectively, the highest and lowest potential for CO2 assimilation at both high and low chloroplastic CO2 concentrations. In our opinion, this information is relevant to improve photosynthesis models and should be considered in future attempts to design more efficient Rubiscos. © 2016 American Society of Plant Biologists. All Rights Reserved.

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

Phase-plane analysis of the totally asymmetric simple exclusion process with binding kinetics and switching between antiparallel lanes

PubMed Central

Kuan, Hui-Shun; Betterton, Meredith D.

2016-01-01

Motor protein motion on biopolymers can be described by models related to the totally asymmetric simple exclusion process (TASEP). Inspired by experiments on the motion of kinesin-4 motors on antiparallel microtubule overlaps, we analyze a model incorporating the TASEP on two antiparallel lanes with binding kinetics and lane switching. We determine the steady-state motor density profiles using phase-plane analysis of the steady-state mean field equations and kinetic Monte Carlo simulations. We focus on the density-density phase plane, where we find an analytic solution to the mean field model. By studying the phase-space flows, we determine the model’s fixed points and their changes with parameters. Phases previously identified for the single-lane model occur for low switching rate between lanes. We predict a multiple coexistence phase due to additional fixed points that appear as the switching rate increases: switching moves motors from the higher-density to the lower-density lane, causing local jamming and creating multiple domain walls. We determine the phase diagram of the model for both symmetric and general boundary conditions. PMID:27627345

Comparison of petroleum generation kinetics by isothermal hydrous and nonisothermal open-system pyrolysis

USGS Publications Warehouse

Lewan, M.D.; Ruble, T.E.

2002-01-01

This study compares kinetic parameters determined by open-system pyrolysis and hydrous pyrolysis using aliquots of source rocks containing different kerogen types. Kinetic parameters derived from these two pyrolysis methods not only differ in the conditions employed and products generated, but also in the derivation of the kinetic parameters (i.e., isothermal linear regression and non-isothermal nonlinear regression). Results of this comparative study show that there is no correlation between kinetic parameters derived from hydrous pyrolysis and open-system pyrolysis. Hydrous-pyrolysis kinetic parameters determine narrow oil windows that occur over a wide range of temperatures and depths depending in part on the organic-sulfur content of the original kerogen. Conversely, open-system kinetic parameters determine broad oil windows that show no significant differences with kerogen types or their organic-sulfur contents. Comparisons of the kinetic parameters in a hypothetical thermal-burial history (2.5 ??C/my) show open-system kinetic parameters significantly underestimate the extent and timing of oil generation for Type-US kerogen and significantly overestimate the extent and timing of petroleum formation for Type-I kerogen compared to hydrous pyrolysis kinetic parameters. These hypothetical differences determined by the kinetic parameters are supported by natural thermal-burial histories for the Naokelekan source rock (Type-IIS kerogen) in the Zagros basin of Iraq and for the Green River Formation (Type-I kerogen) in the Uinta basin of Utah. Differences in extent and timing of oil generation determined by open-system pyrolysis and hydrous pyrolysis can be attributed to the former not adequately simulating natural oil generation conditions, products, and mechanisms.

Influence of temperature on the hydrolysis, acidogenesis and methanogenesis in mesophilic anaerobic digestion: parameter identification and modeling application.

PubMed

Donoso-Bravo, A; Retamal, C; Carballa, M; Ruiz-Filippi, G; Chamy, R

2009-01-01

The effect of temperature on the kinetic parameters involved in the main reactions of the anaerobic digestion process was studied. Batch tests with starch, glucose and acetic acid as substrates for hydrolysis, acidogenesis and methanogenesis, respectively, were performed in a temperature range between 15 and 45 degrees C. First order kinetics was assumed to determine the hydrolysis rate constant, while Monod and Haldane kinetics were considered for acidogenesis and methanogenesis, respectively. The results obtained showed that the anaerobic process is strongly influenced by temperature, with acidogenesis exerting the highest effect. The Cardinal Temperature Model 1 with an inflection point (CTM1) fitted properly the experimental data in the whole temperature range, except for the maximum degradation rate of acidogenesis. A simple case-study assessing the effect of temperature on an anaerobic CSTR performance indicated that with relatively simple substrates, like starch, the limiting reaction would change depending on temperature. However, when more complex substrates are used (e.g. sewage sludge), the hydrolysis might become more quickly into the limiting step.

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

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.

Pharmacokinetic modeling: Prediction and evaluation of route dependent dosimetry of bisphenol A in monkeys with extrapolation to humans

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

Fisher, Jeffrey W., E-mail: jeffrey.fisher@fda.hhs.gov; Twaddle, Nathan C.; Vanlandingham, Michelle

A physiologically based pharmacokinetic (PBPK) model was developed for bisphenol A (BPA) in adult rhesus monkeys using intravenous (iv) and oral bolus doses of 100 {mu}g d6-BPA/kg (). This calibrated PBPK adult monkey model for BPA was then evaluated against published monkey kinetic studies with BPA. Using two versions of the adult monkey model based on monkey BPA kinetic data from and , the aglycone BPA pharmacokinetics were simulated for human oral ingestion of 5 mg d16-BPA per person (Voelkel et al., 2002). Voelkel et al. were unable to detect the aglycone BPA in plasma, but were able to detectmore » BPA metabolites. These human model predictions of the aglycone BPA in plasma were then compared to previously published PBPK model predictions obtained by simulating the Voelkel et al. kinetic study. Our BPA human model, using two parameter sets reflecting two adult monkey studies, both predicted lower aglycone levels in human serum than the previous human BPA PBPK model predictions. BPA was metabolized at all ages of monkey (PND 5 to adult) by the gut wall and liver. However, the hepatic metabolism of BPA and systemic clearance of its phase II metabolites appear to be slower in younger monkeys than adults. The use of the current non-human primate BPA model parameters provides more confidence in predicting the aglycone BPA in serum levels in humans after oral ingestion of BPA. -- Highlights: Black-Right-Pointing-Pointer A bisphenol A (BPA) PBPK model for the infant and adult monkey was constructed. Black-Right-Pointing-Pointer The hepatic metabolic rate of BPA increased with age of the monkey. Black-Right-Pointing-Pointer The systemic clearance rate of metabolites increased with age of the monkey. Black-Right-Pointing-Pointer Gut wall metabolism of orally administered BPA was substantial across all ages of monkeys. Black-Right-Pointing-Pointer Aglycone BPA plasma concentrations were predicted in humans orally given oral doses of deuterated BPA.« less

Influence of the partial volume correction method on 18F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM

NASA Astrophysics Data System (ADS)

Bowen, Spencer L.; Byars, Larry G.; Michel, Christian J.; Chonde, Daniel B.; Catana, Ciprian

2013-10-01

Kinetic parameters estimated from dynamic 18F-fluorodeoxyglucose (18F-FDG) PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For ordered subsets expectation maximization (OSEM), image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting 18F-FDG dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation geometric transfer matrix PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in cerebral metabolic rate of glucose estimates, although by less than 5% in most cases compared to the other PVC methods. The results indicate that the PVC implementation and choice of PSF modelling in the reconstruction can significantly impact model parameters.

Influence of the partial volume correction method on (18)F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM.

PubMed

Bowen, Spencer L; Byars, Larry G; Michel, Christian J; Chonde, Daniel B; Catana, Ciprian

2013-10-21

Kinetic parameters estimated from dynamic (18)F-fluorodeoxyglucose ((18)F-FDG) PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For ordered subsets expectation maximization (OSEM), image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting (18)F-FDG dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation geometric transfer matrix PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in cerebral metabolic rate of glucose estimates, although by less than 5% in most cases compared to the other PVC methods. The results indicate that the PVC implementation and choice of PSF modelling in the reconstruction can significantly impact model parameters.

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

PubMed

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

2017-05-01

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

Kinetic Analysis of Benign and Malignant Breast Lesions With Ultrafast Dynamic Contrast-Enhanced MRI: Comparison With Standard Kinetic Assessment.

PubMed

Abe, Hiroyuki; Mori, Naoko; Tsuchiya, Keiko; Schacht, David V; Pineda, Federico D; Jiang, Yulei; Karczmar, Gregory S

2016-11-01

The purposes of this study were to evaluate diagnostic parameters measured with ultrafast MRI acquisition and with standard acquisition and to compare diagnostic utility for differentiating benign from malignant lesions. Ultrafast acquisition is a high-temporal-resolution (7 seconds) imaging technique for obtaining 3D whole-breast images. The dynamic contrast-enhanced 3-T MRI protocol consists of an unenhanced standard and an ultrafast acquisition that includes eight contrast-enhanced ultrafast images and four standard images. Retrospective assessment was performed for 60 patients with 33 malignant and 29 benign lesions. A computer-aided detection system was used to obtain initial enhancement rate and signal enhancement ratio (SER) by means of identification of a voxel showing the highest signal intensity in the first phase of standard imaging. From the same voxel, the enhancement rate at each time point of the ultrafast acquisition and the AUC of the kinetic curve from zero to each time point of ultrafast imaging were obtained. There was a statistically significant difference between benign and malignant lesions in enhancement rate and kinetic AUC for ultrafast imaging and also in initial enhancement rate and SER for standard imaging. ROC analysis showed no significant differences between enhancement rate in ultrafast imaging and SER or initial enhancement rate in standard imaging. Ultrafast imaging is useful for discriminating benign from malignant lesions. The differential utility of ultrafast imaging is comparable to that of standard kinetic assessment in a shorter study time.

Serial sectioning of grain microstructures under junction control: An old problem in a new guise

NASA Astrophysics Data System (ADS)

Zöllner, D.; Streitenberger, P.

2015-04-01

In the present work the importance of 3D and 4D microstructure analyses are shown. To that aim, we study polycrystalline grain microstructures obtained by grain growth under grain boundary, triple line and quadruple point control. The microstructures themselves are obtained by mesoscopic computer simulations, which enjoy a far greater control over the kinetic and thermodynamic parameters affecting grain growth than can be realized experimentally. In extensive simulation studies we find by 3D respectively 4D microstructure analyses that metrical and topological properties of the microstructures depend strongly on the microstructural feature controlling the growth kinetics. However, the differences between the growth kinetics vanish when we look at classical 2D sections of the 3D ensembles making a differentiation of the controlling grain feature near impossible.

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

Fluctuating bottleneck model studies on kinetics of DNA escape from α-hemolysin nanopores

NASA Astrophysics Data System (ADS)

Bian, Yukun; Wang, Zilin; Chen, Anpu; Zhao, Nanrong

2015-11-01

We have proposed a fluctuation bottleneck (FB) model to investigate the non-exponential kinetics of DNA escape from nanometer-scale pores. The basic idea is that the escape rate is proportional to the fluctuating cross-sectional area of DNA escape channel, the radius r of which undergoes a subdiffusion dynamics subjected to fractional Gaussian noise with power-law memory kernel. Such a FB model facilitates us to obtain the analytical result of the averaged survival probability as a function of time, which can be directly compared to experimental results. Particularly, we have applied our theory to address the escape kinetics of DNA through α-hemolysin nanopores. We find that our theoretical framework can reproduce the experimental results very well in the whole time range with quite reasonable estimation for the intrinsic parameters of the kinetics processes. We believe that FB model has caught some key features regarding the long time kinetics of DNA escape through a nanopore and it might provide a sound starting point to study much wider problems involving anomalous dynamics in confined fluctuating channels.

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

Seapan, M.; Crynes, B.L.; Dale, S.

The objectives of this study were to analyze alternate crudes kinetic hydrotreatment data in the literature, develop a mathematical model for interpretation of these data, develop an experimental procedure and apparatus to collect accurate kinetic data, and finally, to combine the model and experimental data to develop a general model which, with a few experimental parameters, could be used in design of future hydrotreatment processes. These objectives were to cover a four year program (1980 to 1984) and were subjective to sufficient funding. Only partial funding has been available thus far to cover activities for two years. A hydrotreatment datamore » base is developed which contains over 2000 citations, stored in a microcomputer. About 50% of these are reviewed, classified and can be identified by feedstock, catalyst, reactor type and other process characteristics. Tests of published hydrodesulfurization data indicate the problems with simple n-th order, global kinetic models, and point to the value of developing intrinsic reaction kinetic models to describe the reaction processes. A Langmuir-Hinshelwood kinetic model coupled with a plug flow reactor design equation has been developed and used for published data evaluation. An experimental system and procedure have been designed and constructed, which can be used for kinetic studies. 30 references, 4 tables.« less

Kinetic parameter estimation model for anaerobic co-digestion of waste activated sludge and microalgae.

PubMed

Lee, Eunyoung; Cumberbatch, Jewel; Wang, Meng; Zhang, Qiong

2017-03-01

Anaerobic co-digestion has a potential to improve biogas production, but limited kinetic information is available for co-digestion. This study introduced regression-based models to estimate the kinetic parameters for the co-digestion of microalgae and Waste Activated Sludge (WAS). The models were developed using the ratios of co-substrates and the kinetic parameters for the single substrate as indicators. The models were applied to the modified first-order kinetics and Monod model to determine the rate of hydrolysis and methanogenesis for the co-digestion. The results showed that the model using a hyperbola function was better for the estimation of the first-order kinetic coefficients, while the model using inverse tangent function closely estimated the Monod kinetic parameters. The models can be used for estimating kinetic parameters for not only microalgae-WAS co-digestion but also other substrates' co-digestion such as microalgae-swine manure and WAS-aquatic plants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nonequilibrium magnetic properties in a two-dimensional kinetic mixed Ising system within the effective-field theory and Glauber-type stochastic dynamics approach.

PubMed

Ertaş, Mehmet; Deviren, Bayram; Keskin, Mustafa

2012-11-01

Nonequilibrium magnetic properties in a two-dimensional kinetic mixed spin-2 and spin-5/2 Ising system in the presence of a time-varying (sinusoidal) magnetic field are studied within the effective-field theory (EFT) with correlations. The time evolution of the system is described by using Glauber-type stochastic dynamics. The dynamic EFT equations are derived by employing the Glauber transition rates for two interpenetrating square lattices. We investigate the time dependence of the magnetizations for different interaction parameter values in order to find the phases in the system. We also study the thermal behavior of the dynamic magnetizations, the hysteresis loop area, and dynamic correlation. The dynamic phase diagrams are presented in the reduced magnetic field amplitude and reduced temperature plane and we observe that the system exhibits dynamic tricritical and reentrant behaviors. Moreover, the system also displays a double critical end point (B), a zero-temperature critical point (Z), a critical end point (E), and a triple point (TP). We also performed a comparison with the mean-field prediction in order to point out the effects of correlations and found that some of the dynamic first-order phase lines, which are artifacts of the mean-field approach, disappeared.

Bubble contraction in free-boundary Hele-Shaw flow with surface tension and kinetic undercooling regularisation

NASA Astrophysics Data System (ADS)

Dallaston, Michael; McCue, Scott

2012-11-01

When an inviscid bubble expands into a viscous fluid in a Hele-Shaw cell, the bubble boundary is unstable, in general forming long fingers (the Saffman-Taylor instability). In order to make the problem well-posed, a regularising boundary effect must be included. The most widely studied of these are surface tension, which penalises high curvatures, and kinetic undercooling, which penalises high velocities. Both these effects act as a stabilising influence on the free boundary. Less attention has been paid to the case of contracting bubbles, which shrink to a single point (or points) in finite time. In this case, the two effects are in competition, as surface tension stabilises the boundary, while kinetic undercooling destabilises it. This leads to bifurcation behaviour in the asymptotic (near-extinction) shape of the bubble as the relative strengths of the two effects are varied. In particular, there is a critical range of parameter values for which both circular and slit-type bubbles are stable, with a third (unstable) oval-type shape also present. We discuss some numerical and analytic techniques for solving the full free boundary problem and for exploring this interesting extinction behaviour.

Jet Aeroacoustics: Noise Generation Mechanism and Prediction

NASA Technical Reports Server (NTRS)

Tam, Christopher

1998-01-01

This report covers the third year research effort of the project. The research work focussed on the fine scale mixing noise of both subsonic and supersonic jets and the effects of nozzle geometry and tabs on subsonic jet noise. In publication 1, a new semi-empirical theory of jet mixing noise from fine scale turbulence is developed. By an analogy to gas kinetic theory, it is shown that the source of noise is related to the time fluctuations of the turbulence kinetic theory. On starting with the Reynolds Averaged Navier-Stokes equations, a formula for the radiated noise is derived. An empirical model of the space-time correlation function of the turbulence kinetic energy is adopted. The form of the model is in good agreement with the space-time two-point velocity correlation function measured by Davies and coworkers. The parameters of the correlation are related to the parameters of the k-epsilon turbulence model. Thus the theory is self-contained. Extensive comparisons between the computed noise spectrum of the theory and experimental measured have been carried out. The parameters include jet Mach number from 0.3 to 2.0 and temperature ratio from 1.0 to 4.8. Excellent agreements are found in the spectrum shape, noise intensity and directivity. It is envisaged that the theory would supercede all semi-empirical and totally empirical jet noise prediction methods in current use.

Kinetic Monte Carlo simulations of thermally activated magnetization reversal in dual-layer Exchange Coupled Composite recording media

NASA Astrophysics Data System (ADS)

Plumer, M. L.; Almudallal, A. M.; Mercer, J. I.; Whitehead, J. P.; Fal, T. J.

The kinetic Monte Carlo (KMC) method developed for thermally activated magnetic reversal processes in single-layer recording media has been extended to study dual-layer Exchange Coupled Composition (ECC) media used in current and next generations of disc drives. The attempt frequency is derived from the Langer formalism with the saddle point determined using a variant of Bellman Ford algorithm. Complication (such as stagnation) arising from coupled grains having metastable states are addressed. MH-hysteresis loops are calculated over a wide range of anisotropy ratios, sweep rates and inter-layer coupling parameter. Results are compared with standard micromagnetics at fast sweep rates and experimental results at slow sweep rates.

A generalized electron energy probability function for inductively coupled plasmas under conditions of nonlocal electron kinetics

NASA Astrophysics Data System (ADS)

Mouchtouris, S.; Kokkoris, G.

2018-01-01

A generalized equation for the electron energy probability function (EEPF) of inductively coupled Ar plasmas is proposed under conditions of nonlocal electron kinetics and diffusive cooling. The proposed equation describes the local EEPF in a discharge and the independent variable is the kinetic energy of electrons. The EEPF consists of a bulk and a depleted tail part and incorporates the effect of the plasma potential, Vp, and pressure. Due to diffusive cooling, the break point of the EEPF is eVp. The pressure alters the shape of the bulk and the slope of the tail part. The parameters of the proposed EEPF are extracted by fitting to measure EEPFs (at one point in the reactor) at different pressures. By coupling the proposed EEPF with a hybrid plasma model, measurements in the gaseous electronics conference reference reactor concerning (a) the electron density and temperature and the plasma potential, either spatially resolved or at different pressure (10-50 mTorr) and power, and (b) the ion current density of the electrode, are well reproduced. The effect of the choice of the EEPF on the results is investigated by a comparison to an EEPF coming from the Boltzmann equation (local electron kinetics approach) and to a Maxwellian EEPF. The accuracy of the results and the fact that the proposed EEPF is predefined renders its use a reliable alternative with a low computational cost compared to stochastic electron kinetic models at low pressure conditions, which can be extended to other gases and/or different electron heating mechanisms.

The research of the coupled orbital-attitude controlled motion of celestial body in the neighborhood of the collinear libration point L1

NASA Astrophysics Data System (ADS)

Shmyrov, A.; Shmyrov, V.; Shymanchuk, D.

2017-10-01

This article considers the motion of a celestial body within the restricted three-body problem of the Sun-Earth system. The equations of controlled coupled attitude-orbit motion in the neighborhood of collinear libration point L1 are investigated. The translational orbital motion of a celestial body is described using Hill's equations of circular restricted three-body problem of the Sun-Earth system. Rotational orbital motion is described using Euler's dynamic equations and quaternion kinematic equation. We investigate the problem of stability of celestial body rotational orbital motion in relative equilibrium positions and stabilization of celestial body rotational orbital motion with proposed control laws in the neighborhood of collinear libration point L1. To study stabilization problem, Lyapunov function is constructed in the form of the sum of the kinetic energy and special "kinematic function" of the Rodriguez-Hamiltonian parameters. Numerical modeling of the controlled rotational motion of a celestial body at libration point L1 is carried out. The numerical characteristics of the control parameters and rotational motion are given.

Cell shape characterization and classification with discrete Fourier transforms and self-organizing maps.

PubMed

Kriegel, Fabian L; Köhler, Ralf; Bayat-Sarmadi, Jannike; Bayerl, Simon; Hauser, Anja E; Niesner, Raluca; Luch, Andreas; Cseresnyes, Zoltan

2018-03-01

Cells in their natural environment often exhibit complex kinetic behavior and radical adjustments of their shapes. This enables them to accommodate to short- and long-term changes in their surroundings under physiological and pathological conditions. Intravital multi-photon microscopy is a powerful tool to record this complex behavior. Traditionally, cell behavior is characterized by tracking the cells' movements, which yields numerous parameters describing the spatiotemporal characteristics of cells. Cells can be classified according to their tracking behavior using all or a subset of these kinetic parameters. This categorization can be supported by the a priori knowledge of experts. While such an approach provides an excellent starting point for analyzing complex intravital imaging data, faster methods are required for automated and unbiased characterization. In addition to their kinetic behavior, the 3D shape of these cells also provide essential clues about the cells' status and functionality. New approaches that include the study of cell shapes as well may also allow the discovery of correlations amongst the track- and shape-describing parameters. In the current study, we examine the applicability of a set of Fourier components produced by Discrete Fourier Transform (DFT) as a tool for more efficient and less biased classification of complex cell shapes. By carrying out a number of 3D-to-2D projections of surface-rendered cells, the applied method reduces the more complex 3D shape characterization to a series of 2D DFTs. The resulting shape factors are used to train a Self-Organizing Map (SOM), which provides an unbiased estimate for the best clustering of the data, thereby characterizing groups of cells according to their shape. We propose and demonstrate that such shape characterization is a powerful addition to, or a replacement for kinetic analysis. This would make it especially useful in situations where live kinetic imaging is less practical or not possible at all. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

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.

Continuous Dynamic Simulation of Nonlinear Aerodynamics/Nonlinear Structure Interaction (NANSI) for Morphing Vehicles

DTIC Science & Technology

2010-03-31

presented in the AFRL organized Aeroelastic Workshop in Sedona October 2008, and at the AVT-168 Symposium on Morphing Vehicles, Lisbon, Portugal April 2009...surface geometry. - Conventional deforming grid methods will fail at a point when the geometry change becomes large, no matter how good the method...Numb’ Martian Entry* Knudson number: Kn _ M.a GasKinetic parameter ASU . flttA TKHNOLOGY Overview • Ballute aeroelastic problem requires

Scrape-off layer modeling with kinetic or diffusion description of charge-exchange atoms

NASA Astrophysics Data System (ADS)

Tokar, M. Z.

2016-12-01

Hydrogen isotope atoms, generated by charge-exchange (c-x) of neutral particles recycling from the first wall of a fusion reactor, are described either kinetically or in a diffusion approximation. In a one-dimensional (1-D) geometry, kinetic calculations are accelerated enormously by applying an approximate pass method for the assessment of integrals in the velocity space. This permits to perform an exhaustive comparison of calculations done with both approaches. The diffusion approximation is deduced directly from the velocity distribution function of c-x atoms in the limit of charge-exchanges with ions occurring much more frequently than ionization by electrons. The profiles across the flux surfaces of the plasma parameters averaged along the main part of the scrape-off layer (SOL), beyond the X-point and divertor regions, are calculated from the one-dimensional equations where parallel flows of charged particles and energy towards the divertor are taken into account as additional loss terms. It is demonstrated that the heat losses can be firmly estimated from the SOL averaged parameters only; for the particle loss the conditions in the divertor are of importance and the sensitivity of the results to the so-called "divertor impact factor" is investigated. The coupled 1-D models for neutral and charged species, with c-x atoms described either kinetically or in the diffusion approximation, are applied to assess the SOL conditions in a fusion reactor, with the input parameters from the European DEMO project. It is shown that the diffusion approximation provides practically the same profiles across the flux surfaces for the plasma density, electron, and ion temperatures, as those obtained with the kinetic description for c-x atoms. The main difference between the two approaches is observed in the characteristics of these species themselves. In particular, their energy flux onto the wall is underestimated in calculations with the diffusion approximation by 20 % - 30 % . This discrepancy can be significantly reduced if after the convergence of coupled plasma-neutral calculations, the final computation for c-x atoms is done kinetically.

Study on Synthesis of Thoreau-modified 3, 5-Dimethyl-Thioltoluenediamine Used as Epoxy Resin Curing Agent and Its Performance

NASA Astrophysics Data System (ADS)

Peng, Yongli; Xiao, Wenzheng

2017-06-01

A novel curing agent Thoreau modified 3, 5-Dimethyl-thioltoluenediamine was synthesized and its molecular structure was characterized by FTIR and DSC. The curing kinetics of a high toughness and low volume shrinkage ratio epoxy system (modified DMTDA/DGEBA) was studied by differential scanning calorimetry (DSC) under noni so thermal conditions. The data were fitted to an order model and autocatalytic model respectively. The results indicate that in order model deviates significantly from experimental data. Malik’s method was used to prove that the curing kinetics of the system concerned follow single-step autocatalytic model, and a “single-point model-free” approach was employed to calculate meaningful kinetic parameters. The DSC curves derived from autocatalytic model gave satisfactory agreement with that of experiment in the range 5K/min∼25K/min. As the heating rate increased, the predicted DSC curves deviated from experimental curves, and the total exothermic enthalpy declined owing to the transition of competition relationship between kinetics control and diffusion control.

Enhanced von Weizsäcker Wang-Govind-Carter kinetic energy density functional for semiconductors

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

Shin, Ilgyou; Carter, Emily A., E-mail: eac@princeton.edu

2014-05-14

We propose a new form of orbital-free (OF) kinetic energy density functional (KEDF) for semiconductors that is based on the Wang-Govind-Carter (WGC99) nonlocal KEDF. We enhance within the latter the semi-local von Weizsäcker KEDF term, which is exact for a single orbital. The enhancement factor we introduce is related to the extent to which the electron density is localized. The accuracy of the new KEDF is benchmarked against Kohn-Sham density functional theory (KSDFT) by comparing predicted energy differences between phases, equilibrium volumes, and bulk moduli for various semiconductors, along with metal-insulator phase transition pressures. We also compare point defect andmore » (100) surface energies in silicon for a broad test of its applicability. This new KEDF accurately reproduces the exact non-interacting kinetic energy of KSDFT with only one additional adjustable parameter beyond the three parameters in the WGC99 KEDF; it exhibits good transferability between semiconducting to metallic silicon phases and between various III-V semiconductors without parameter adjustment. Overall, this KEDF is more accurate than previously proposed OF KEDFs (e.g., the Huang-Carter (HC) KEDF) for semiconductors, while the computational efficiency remains at the level of the WGC99 KEDF (several hundred times faster than the HC KEDF). This accurate, fast, and transferable new KEDF holds considerable promise for large-scale OFDFT simulations of metallic through semiconducting materials.« less

Thermodynamical transcription of density functional theory with minimum Fisher information

NASA Astrophysics Data System (ADS)

Nagy, Á.

2018-03-01

Ghosh, Berkowitz and Parr designed a thermodynamical transcription of the ground-state density functional theory and introduced a local temperature that varies from point to point. The theory, however, is not unique because the kinetic energy density is not uniquely defined. Here we derive the expression of the phase-space Fisher information in the GBP theory taking the inverse temperature as the Fisher parameter. It is proved that this Fisher information takes its minimum for the case of constant temperature. This result is consistent with the recently proven theorem that the phase-space Shannon information entropy attains its maximum at constant temperature.

The alpha dynamo parameter and measurability of helicities in magnetohydrodynamic turbulence

NASA Technical Reports Server (NTRS)

Matthaeus, W. H.; Goldstein, M. L.; Lantz, S. R.

1986-01-01

Alpha, an important parameter in dynamo theory, is shown to be proportional to either the kinetic, current, magnetic, or velocity helicities of the fluctuating magnetic field and fluctuating velocity field. The particular helicity to which alpha is proportional depends on the assumptions used in deriving the first-order smoothed equations that describe the alpha effect. In two cases, viz., when alpha is proportional to either the magnetic helicity or velocity helicity, alpha can be determined experimentally from two-point measurements of the fluctuating fields in incompressible, homogeneous turbulence with arbitrary rotational symmetry. For the other two possibilities, alpha can be determined if the turbulence is isotropic.

Parameter Balancing in Kinetic Models of Cell Metabolism†

PubMed Central

2010-01-01

Kinetic modeling of metabolic pathways has become a major field of systems biology. It combines structural information about metabolic pathways with quantitative enzymatic rate laws. Some of the kinetic constants needed for a model could be collected from ever-growing literature and public web resources, but they are often incomplete, incompatible, or simply not available. We address this lack of information by parameter balancing, a method to complete given sets of kinetic constants. Based on Bayesian parameter estimation, it exploits the thermodynamic dependencies among different biochemical quantities to guess realistic model parameters from available kinetic data. Our algorithm accounts for varying measurement conditions in the input data (pH value and temperature). It can process kinetic constants and state-dependent quantities such as metabolite concentrations or chemical potentials, and uses prior distributions and data augmentation to keep the estimated quantities within plausible ranges. An online service and free software for parameter balancing with models provided in SBML format (Systems Biology Markup Language) is accessible at www.semanticsbml.org. We demonstrate its practical use with a small model of the phosphofructokinase reaction and discuss its possible applications and limitations. In the future, parameter balancing could become an important routine step in the kinetic modeling of large metabolic networks. PMID:21038890

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.

Application of Hill's equation for estimating area under the concentration-time curve (AUC) and use of time to AUC 90% for expressing kinetics of drug disposition.

PubMed

Cheng, Hsien C

2009-01-01

Half life and its derived pharmacokinetic parameters are calculated on an assumption that the terminal phase of drug disposition follows a constant rate of disposition. In reality, this assumption may not necessarily be the case. A new method is needed for analyzing PK parameters if the disposition does not follow a first order PK kinetic. Cumulative area under the concentration-time curve (AUC) is plotted against time to yield a hyperbolic (or sigmoidal) AUC-time relationship curve which is then analyzed by Hill's equation to yield AUC(inf), time to achieving AUC50% (T(AUC50%)) or AUC90% (T(AUC90%)), and the Hill's slope. From these parameters, an AUC-time relationship curve can be reconstructed. Projected plasma concentration can be calculated for any time point. Time at which cumulative AUC reaches 90% (T(AUC90%)) can be used as an indicator for expressing how fast a drug is cleared. Clearance is calculated in a traditional manner (i.v. dose/AUC(inf)), and the volume of distribution is proposed to be calculated at T(AUC50%) (0.5 i.v. dose/plasma concentration at T(AUC50%)). This method of estimating AUC is applicable for both i.v. and oral data. It is concluded that the Hill's equation can be used as an alternative method for estimating AUC and analysis of PK parameters if the disposition does not follow a first order kinetic. T(AUC90%) is proposed to be used as an indicator for expressing how fast a drug is cleared from the system.

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.

Utilization of integrated Michaelis-Menten equations for enzyme inhibition diagnosis and determination of kinetic constants using Solver supplement of Microsoft Office Excel.

PubMed

Bezerra, Rui M F; Fraga, Irene; Dias, Albino A

2013-01-01

Enzyme kinetic parameters are usually determined from initial rates nevertheless, laboratory instruments only measure substrate or product concentration versus reaction time (progress curves). To overcome this problem we present a methodology which uses integrated models based on Michaelis-Menten equation. The most severe practical limitation of progress curve analysis occurs when the enzyme shows a loss of activity under the chosen assay conditions. To avoid this problem it is possible to work with the same experimental points utilized for initial rates determination. This methodology is illustrated by the use of integrated kinetic equations with the well-known reaction catalyzed by alkaline phosphatase enzyme. In this work nonlinear regression was performed with the Solver supplement (Microsoft Office Excel). It is easy to work with and track graphically the convergence of SSE (sum of square errors). The diagnosis of enzyme inhibition was performed according to Akaike information criterion. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Study of the kinetic parameters for synthesis and hydrolysis of pharmacologically active salicin isomer catalyzed by baker's yeast maltase

NASA Astrophysics Data System (ADS)

Veličković, D. V.; Dimitrijević, A. S.; Bihelović, F. J.; Jankov, R. M.; Milosavić, N.

2011-12-01

One of the key elements for understanding enzyme reactions is determination of its kinetic parameters. Since transglucosylation is kinetically controlled reaction, besides the reaction of synthesis, very important is the reaction of enzymatic hydrolysis of created product. Therefore, in this study, kinetic parameters for synthesis and secondary hydrolysis of pharmacologically active α isosalicin by baker's yeast maltase were calculated, and it was shown that specifity of maltase for hydrolysis is approximately 150 times higher then for synthesis.

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)

Size effects in tin-based lead-free solder joints: Kinetics of bond formation and mechanical characteristics

NASA Astrophysics Data System (ADS)

Abdelhadi, Ousama Mohamed Omer

Continuous miniaturization of microelectronic interconnects demands smaller joints with comparable microstructural and structural sizes. As the size of joints become smaller, the volume of intermetallics (IMCs) becomes comparable with the joint size. As a result, the kinetics of bond formation changes and the types and thicknesses of IMC phases that form within the constrained region of the bond varies. This dissertation focuses on investigating combination effects of process parameters and size on kinetics of bond formation, resulting microstructure and the mechanical properties of joints that are formed under structurally constrained conditions. An experiment is designed where several process parameters such as time of bonding, temperature, and pressure, and bond thickness as structural chracteristic, are varied at multiple levels. The experiment is then implemented on the process. Scanning electron microscope (SEM) is then utilized to determine the bond thickness, IMC phases and their thicknesses, and morphology of the bonds. Electron backscatter diffraction (EBSD) is used to determine the grain size in different regions, including the bulk solder, and different IMC phases. Physics-based analytical models have been developed for growth kinetics of IMC compounds and are verified using the experimental results. Nanoindentation is used to determine the mechanical behavior of IMC phases in joints in different scales. Four-point bending notched multilayer specimen and four-point bending technique were used to determine fracture toughness of the bonds containing IMCs. Analytical modeling of peeling and shear stresses and fracture toughness in tri-layer four-point bend specimen containing intermetallic layer was developed and was verified and validated using finite element simulation and experimental results. The experiment is used in conjunction with the model to calculate and verify the fracture toughness of Cu6Sn5 IMC materials. As expected two different IMC phases, η-phase (Cu6Sn 5) and epsilon-phase (Cu3Sn), were found in almost all the cases regardless of the process parameters and size levels. The physics-based analytical model was successfully able to capture the governing mechanisms of IMC growth: chemical reaction controlled and diffusion-controlled. Examination of microstructures of solder joints of different sizes revealed the size of the solder joint has no effect on the type of IMCs formed during the process. Joint size, however, affected the thickness of IMC layers significantly. IMC layers formed in the solder joints of smaller sizes were found to be thicker than those in the solder joints of larger sizes. The growth rate constants and activation energies of Cu3Sn IMC layer were also reported and related to joint thickness. In an effort to optimize the EBSD imaging in the multi-layer configuration, an improved specimen preparation technique and optimum software parameters were determined. Nanoindentation results show that size effects play a major role on the mechanical properties of micro-scale solder joints. Smaller joints show higher Young's modulus, hardness, and yield strength and lower work hardening exponents comparing to thicker joints. To obtain the stress concentration factors in a multilayer specimen with IMC layer as bonding material, a four-point bending notched configuration was used. The analytical solutions developed for peeling and shear stresses in notched structure were used to evaluate the stresses at IMC interface layers. Results were in good agreement with the finite-element simulation. The values of interfacial stresses were utilized in obtaining fracture toughness of the IMC material. (Abstract shortened by UMI.)

Adsorption Properties of Low-Cost Biomaterial Derived from Prunus amygdalus L. for Dye Removal from Water

PubMed Central

Deniz, Fatih

2013-01-01

The capability of Prunus amygdalus L. (almond) shell for dye removal from aqueous solutions was investigated and methyl orange was used as a model compound. The effects of operational parameters including pH, ionic strength, adsorbent concentration and mesh size, dye concentration, contact time, and temperature on the removal of dye were evaluated. The adsorption kinetics conformed to the pseudo-second-order kinetic model. The equilibrium data pointed out excellent fit to the Langmuir isotherm model with maximum monolayer adsorption capacity of 41.34 mg g−1 at 293 K. Thermodynamic analysis proved a spontaneous, favorable, and exothermic process. It can be concluded that almond shell might be a potential low-cost adsorbent for methyl orange removal from aqueous media. PMID:23935442

Organic and nitrogen removal from landfill leachate in aerobic granular sludge sequencing batch reactors

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

Wei Yanjie; Key Laboratory of Environmental Protection in Water Transport Engineering Ministry of Communications, Tianjin Research Institute of Water Transport Engineering, Tianjin 300456; Ji Min, E-mail: jmtju@yahoo.cn

2012-03-15

Highlights: Black-Right-Pointing-Pointer Aerobic granular sludge SBR was used to treat real landfill leachate. Black-Right-Pointing-Pointer COD removal was analyzed kinetically using a modified model. Black-Right-Pointing-Pointer Characteristics of nitrogen removal at different ammonium inputs were explored. Black-Right-Pointing-Pointer DO variations were consistent with the GSBR performances at low ammonium inputs. - Abstract: Granule sequencing batch reactors (GSBR) were established for landfill leachate treatment, and the COD removal was analyzed kinetically using a modified model. Results showed that COD removal rate decreased as influent ammonium concentration increasing. Characteristics of nitrogen removal at different influent ammonium levels were also studied. When the ammonium concentration inmore » the landfill leachate was 366 mg L{sup -1}, the dominant nitrogen removal process in the GSBR was simultaneous nitrification and denitrification (SND). Under the ammonium concentration of 788 mg L{sup -1}, nitrite accumulation occurred and the accumulated nitrite was reduced to nitrogen gas by the shortcut denitrification process. When the influent ammonium increased to a higher level of 1105 mg L{sup -1}, accumulation of nitrite and nitrate lasted in the whole cycle, and the removal efficiencies of total nitrogen and ammonium decreased to only 35.0% and 39.3%, respectively. Results also showed that DO was a useful process controlling parameter for the organics and nitrogen removal at low ammonium input.« less

Determining Kinetic Parameters for Isothermal Crystallization of Glasses

NASA Technical Reports Server (NTRS)

Ray, C. S.; Zhang, T.; Reis, S. T.; Brow, R. K.

2006-01-01

Non-isothermal crystallization techniques are frequently used to determine the kinetic parameters for crystallization in glasses. These techniques are experimentally simple and quick compared to the isothermal techniques. However, the analytical models used for non-isothermal data analysis, originally developed for describing isothermal transformation kinetics, are fundamentally flawed. The present paper describes a technique for determining the kinetic parameters for isothermal crystallization in glasses, which eliminates most of the common problems that generally make the studies of isothermal crystallization laborious and time consuming. In this technique, the volume fraction of glass that is crystallized as a function of time during an isothermal hold was determined using differential thermal analysis (DTA). The crystallization parameters for the lithium-disilicate (Li2O.2SiO2) model glass were first determined and compared to the same parameters determined by other techniques to establish the accuracy and usefulness of the present technique. This technique was then used to describe the crystallization kinetics of a complex Ca-Sr-Zn-silicate glass developed for sealing solid oxide fuel cells.

Stability analysis of BWR nuclear-coupled thermal-hyraulics using a simple model

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

Karve, A.A.; Rizwan-uddin; Dorning, J.J.

1995-09-01

A simple mathematical model is developed to describe the dynamics of the nuclear-coupled thermal-hydraulics in a boiling water reactor (BWR) core. The model, which incorporates the essential features of neutron kinetics, and single-phase and two-phase thermal-hydraulics, leads to simple dynamical system comprised of a set of nonlinear ordinary differential equations (ODEs). The stability boundary is determined and plotted in the inlet-subcooling-number (enthalpy)/external-reactivity operating parameter plane. The eigenvalues of the Jacobian matrix of the dynamical system also are calculated at various steady-states (fixed points); the results are consistent with those of the direct stability analysis and indicate that a Hopf bifurcationmore » occurs as the stability boundary in the operating parameter plane is crossed. Numerical simulations of the time-dependent, nonlinear ODEs are carried out for selected points in the operating parameter plane to obtain the actual damped and growing oscillations in the neutron number density, the channel inlet flow velocity, and the other phase variables. These indicate that the Hopf bifurcation is subcritical, hence, density wave oscillations with growing amplitude could result from a finite perturbation of the system even where the steady-state is stable. The power-flow map, frequently used by reactor operators during start-up and shut-down operation of a BWR, is mapped to the inlet-subcooling-number/neutron-density (operating-parameter/phase-variable) plane, and then related to the stability boundaries for different fixed inlet velocities corresponding to selected points on the flow-control line. The stability boundaries for different fixed inlet subcooling numbers corresponding to those selected points, are plotted in the neutron-density/inlet-velocity phase variable plane and then the points on the flow-control line are related to their respective stability boundaries in this plane.« less

Metronidazole removal in powder-activated carbon and concrete-containing graphene adsorption systems: Estimation of kinetic, equilibrium and thermodynamic parameters and optimization of adsorption by a central composite design.

PubMed

Manjunath, S V; Kumar, S Mathava; Ngo, Huu Hao; Guo, Wenshan

2017-12-06

Metronidazole (MNZ) removal by two adsorbents, i.e., concrete-containing graphene (CG) and powder-activated carbon (PAC), was investigated via batch-mode experiments and the outcomes were used to analyze the kinetics, equilibrium and thermodynamics of MNZ adsorption. MNZ sorption on CG and PAC has followed the pseudo-second-order kinetic model, and the thermodynamic parameters revealed that MNZ adsorption was spontaneous on PAC and non-spontaneous on CG. Subsequently, two-parameter isotherm models, i.e., Langmuir, Freundlich, Temkin, Dubinin-Radushkevich and Elovich models, were applied to evaluate the MNZ adsorption capacity. The maximum MNZ adsorption capacities ([Formula: see text]) of PAC and CG were found to be between 25.5-32.8 mg/g and 0.41-0.002 mg/g, respectively. Subsequently, the effects of pH, temperature and adsorbent dosage on MNZ adsorption were evaluated by a central composite design (CCD) approach. The CCD experiments have pointed out the complete removal of MNZ at a much lower PAC dosage by increasing the system temperature (i.e., from 20°C to 40°C). On the other hand, a desorption experiment has shown 3.5% and 1.7% MNZ removal from the surface of PAC and CG, respectively, which was insignificant compared to the sorbed MNZ on the surface by adsorption. The overall findings indicate that PAC and CG with higher graphene content could be useful in MNZ removal from aqueous systems.

Estimations of ABL fluxes and other turbulence parameters from Doppler lidar data

NASA Technical Reports Server (NTRS)

Tzvi, Gal-Chen; Mei, XU; Eberhard, Wynn

1990-01-01

Techniques for extracting boundary layer parameters from measurements of a short pulse CO2 Doppler Lidar are described. The radial velocity measurements have a range resolution of 150 m. With a pulse repetition rate of 20 Hz, it is possible to perform scannings in two perpendicular vertical planes in approx. 72 s. By continuously operating the Lidar for about an hour, one can extract stable statistics of the radial velocities. Assuming that the turbulence is horizontally homogeneous, the mean wind, its standard deviations, and the momentum fluxes were estimated. From the vertically pointing beam, the first, second, and third moments of the vertical velocity were also estimated. Spectral analysis of the radial velocities is also performed from which, by examining the amplitude of the power spectrum at the inertial range, the kinetic energy dissipation was deduced. Finally, using the statistical form of the Navier-Stokes equations, the surface heat flux is derived as the residual balance between the vertical gradient of the third moment of the vertical velocity and the kinetic energy dissipation.

Surface kinetics for catalytic combustion of hydrogen-air mixtures on platinum at atmospheric pressure in stagnation flows

NASA Astrophysics Data System (ADS)

Ikeda, H.; Sato, J.; Williams, F. A.

1995-03-01

Experimental studies of the combustion of premixed hydrogen-air mixtures impinging on the surface of a heated platinum plate at normal atmospheric pressure were performed and employed to draw inferences concerning surface reaction mechanisms and rate parameters applicable under practical conditions of catalytic combustion. Plate and gas temperatures were measured by thermocouples, and concentration profiles of major stable species in the gas were measured by gas-chromatographic analyses of samples withdrawn by quartz probes. In addition, ignition and extinction phenomena were recorded and interpreted with the aid of a heat balance at the surface and a previous flow-field analysis of the stagnation-point boundary layer. From the experimental and theoretical results, conclusions were drawn concerning the surface chemical-kinetic mechanisms and values of the elementary rate parameters that are consistent with the observations. In particular, the activation energy for the surface oxidation step H + OH → H 2O is found to be appreciably less at these high surface coverages than in the low-coverage limit.

Estimation of kinetic parameters from list-mode data using an indirect apporach

NASA Astrophysics Data System (ADS)

Ortiz, Joseph Christian

This dissertation explores the possibility of using an imaging approach to model classical pharmacokinetic (PK) problems. The kinetic parameters which describe the uptake rates of a drug within a biological system, are parameters of interest. Knowledge of the drug uptake in a system is useful in expediting the drug development process, as well as providing a dosage regimen for patients. Traditionally, the uptake rate of a drug in a system is obtained via sampling the concentration of the drug in a central compartment, usually the blood, and fitting the data to a curve. In a system consisting of multiple compartments, the number of kinetic parameters is proportional to the number of compartments, and in classical PK experiments, the number of identifiable parameters is less than the total number of parameters. Using an imaging approach to model classical PK problems, the support region of each compartment within the system will be exactly known, and all the kinetic parameters are uniquely identifiable. To solve for the kinetic parameters, an indirect approach, which is a two part process, was used. First the compartmental activity was obtained from data, and next the kinetic parameters were estimated. The novel aspect of the research is using listmode data to obtain the activity curves from a system as opposed to a traditional binned approach. Using techniques from information theoretic learning, particularly kernel density estimation, a non-parametric probability density function for the voltage outputs on each photo-multiplier tube, for each event, was generated on the fly, which was used in a least squares optimization routine to estimate the compartmental activity. The estimability of the activity curves for varying noise levels as well as time sample densities were explored. Once an estimate for the activity was obtained, the kinetic parameters were obtained using multiple cost functions, and the compared to each other using the mean squared error as the figure of merit.

Numerical Simulation of Measurements during the Reactor Physical Startup at Unit 3 of Rostov NPP

NASA Astrophysics Data System (ADS)

Tereshonok, V. A.; Kryakvin, L. V.; Pitilimov, V. A.; Karpov, S. A.; Kulikov, V. I.; Zhylmaganbetov, N. M.; Kavun, O. Yu.; Popykin, A. I.; Shevchenko, R. A.; Shevchenko, S. A.; Semenova, T. V.

2017-12-01

The results of numerical calculations and measurements of some reactor parameters during the physical startup tests at unit 3 of Rostov NPP are presented. The following parameters are considered: the critical boron acid concentration and the currents from ionization chambers (IC) during the scram system efficiency evaluation. The scram system efficiency was determined using the inverse point kinetics equation with the measured and simulated IC currents. The results of steady-state calculations of relative power distribution and efficiency of the scram system and separate groups of control rods of the control and protection system are also presented. The calculations are performed using several codes, including precision ones.

Modification of the kinetic parameters of aldolase on binding to the actin-containing filaments of skeletal muscle.

PubMed Central

Walsh, T P; Clarke, F M; Masters, C J

1977-01-01

The kinetic parameters of fructose bisphosphate aldolase (EC 4.1.2.13) were shown to be modified on binding of the enzyme to the actin-containing filaments of skeletal muscle. Although binding to F-actin or F-actin-tropomyosin filaments results in relative minor changes in kinetic properties, binding to F-actin-tropomyosin-troponin filaments produces major alterations in the kinetic parameters, and, in addition, renders them Ca2+-sensitive. These observations may be relevant to an understanding of the function of this enzyme within the muscle fibre. PMID:889571

Asymptotic orderings and approximations of the Master kinetic equation for large hard spheres systems

NASA Astrophysics Data System (ADS)

Tessarotto, Massimo; Asci, Claudio

2017-05-01

In this paper the problem is posed of determining the physically-meaningful asymptotic orderings holding for the statistical description of a large N-body system of hard spheres, i.e., formed by N ≡1/ε ≫ 1 particles, which are allowed to undergo instantaneous and purely elastic unary, binary or multiple collisions. Starting point is the axiomatic treatment recently developed [Tessarotto et al., 2013-2016] and the related discovery of an exact kinetic equation realized by Master equation which advances in time the 1-body probability density function (PDF) for such a system. As shown in the paper the task involves introducing appropriate asymptotic orderings in terms of ε for all the physically-relevant parameters. The goal is that of identifying the relevant physically-meaningful asymptotic approximations applicable for the Master kinetic equation, together with their possible relationships with the Boltzmann and Enskog kinetic equations, and holding in appropriate asymptotic regimes. These correspond either to dilute or dense systems and are formed either by small-size or finite-size identical hard spheres, the distinction between the various cases depending on suitable asymptotic orderings in terms of ε.

Experimental and modeling study on decomposition kinetics of methane hydrates in different media.

PubMed

Liang, Minyan; Chen, Guangjin; Sun, Changyu; Yan, Lijun; Liu, Jiang; Ma, Qinglan

2005-10-13

The decomposition kinetic behaviors of methane hydrates formed in 5 cm3 porous wet activated carbon were studied experimentally in a closed system in the temperature range of 275.8-264.4 K. The decomposition rates of methane hydrates formed from 5 cm3 of pure free water and an aqueous solution of 650 g x m(-3) sodium dodecyl sulfate (SDS) were also measured for comparison. The decomposition rates of methane hydrates in seven different cases were compared. The results showed that the methane hydrates dissociate more rapidly in porous activated carbon than in free systems. A mathematical model was developed for describing the decomposition kinetic behavior of methane hydrates below ice point based on an ice-shielding mechanism in which a porous ice layer was assumed to be formed during the decomposition of hydrate, and the diffusion of methane molecules through it was assumed to be one of the control steps. The parameters of the model were determined by correlating the decomposition rate data, and the activation energies were further determined with respect to three different media. The model was found to well describe the decomposition kinetic behavior of methane hydrate in different media.

NMR structural and kinetic assignment of fluoro-3H-naphthopyran photomerocyanines.

PubMed

Delbaere, S; Micheau, J C; Teral, Y; Bochu, C; Campredon, M; Vermeersch, G

2001-11-01

The kinetic and structural behavior of a photochromic compound, 3-(2-fluorophenyl)-3-phenyl-3H-naphtho[2,1-b]pyran (F-Py), was investigated using 1H and 19F nuclear magnetic resonance (NMR) spectroscopy. Upon irradiation, the four theoretically predicted photomerocyanines appear along with a fifth form X, whose final structure has not been elucidated. This last form and two of the photomerocyanines are thermally labile, whereas the other two do not show any signs of decay. The system has been analyzed by NMR spectroscopy. This led to the structural assignment of each photomerocyanine. The kinetics of the thermal bleaching were monitored by directly and separately measuring the concentrations of each species at regular time intervals using 19F NMR spectroscopy. We therefore propose a plausible reaction mechanism. On the basis of this mechanism, the mathematical treatment and the study of the effects of temperature led to the determination of the kinetic and thermodynamic parameters (rate coefficients, enthalpy and entropy of activation) of this photochromic system. The leading role of the labile intermediate X on the formation of trans-transoid-cis (TTC) and cis-transoid-cis (CTC) photomerocyanines is pointed out.

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

Kinetic freeze-out conditions for the production of resonances, hadronic molecules, and light nuclei

NASA Astrophysics Data System (ADS)

Cho, Sungtae; Song, Taesoo; Lee, Su Houng

2018-02-01

We investigate the freeze-out conditions of a particle in an expanding system of interacting particles in order to understand the productions of resonances, hadronic molecules, and light nuclei in heavy-ion collisions. Applying the kinetic freeze-out condition with explicit hydrodynamic calculations for the expanding hadronic phase to the daughter particles of K* mesons, we find that the larger suppression of the yield ratio of K*/K at the Large Hadron Collider (LHC) than at the Relativisitic Heavy Ion Collider (RHIC) compared to the expectations from the statistical hadronization model based on chemical freeze-out parameters reflects the lower kinetic freeze-out temperature at LHC than at RHIC. Furthermore, we point out that for the light nuclei or hadronic molecules that are bound, the freeze-out condition should be applied to the respective particle in the hadronic matter. It is then shown through the rate equation that when the nucleon and pion numbers are kept constant at the chemical freeze-out value during the hadronic phase, the deuteron number quickly approaches an asymptotic value that is close to the statistical model prediction at the chemical freeze-out point. We argue that the reduction seen in K* numbers is a typical result for a particle that has a large natural decay width decaying into daughter particles, while that for deuteron is typical for a stable hadronic bound state.

Toward laboratory torsional spine magnetic reconnection

NASA Astrophysics Data System (ADS)

Chesny, David L.; Orange, N. Brice; Oluseyi, Hakeem M.; Valletta, David R.

2017-12-01

Magnetic reconnection is a fundamental energy conversion mechanism in nature. Major attempts to study this process in controlled settings on Earth have largely been limited to reproducing approximately two-dimensional (2-D) reconnection dynamics. Other experiments describing reconnection near three-dimensional null points are non-driven, and do not induce any of the 3-D modes of spine fan, torsional fan or torsional spine reconnection. In order to study these important 3-D modes observed in astrophysical plasmas (e.g. the solar atmosphere), laboratory set-ups must be designed to induce driven reconnection about an isolated magnetic null point. As such, we consider the limited range of fundamental resistive magnetohydrodynamic (MHD) and kinetic parameters of dynamic laboratory plasmas that are necessary to induce the torsional spine reconnection (TSR) mode characterized by a driven rotational slippage of field lines - a feature that has yet to be achieved in operational laboratory magnetic reconnection experiments. Leveraging existing reconnection models, we show that within a 3$ apparatus, TSR can be achieved in dense plasma regimes ( 24~\\text{m}-3$ ) in magnetic fields of -1~\\text{T}$ . We find that MHD and kinetic parameters predict reconnection in thin current sheets on time scales of . While these plasma regimes may not explicitly replicate the plasma parameters of observed astrophysical phenomena, studying the dynamics of the TSR mode within achievable set-ups signifies an important step in understanding the fundamentals of driven 3-D magnetic reconnection and the self-organization of current sheets. Explicit control of this reconnection mode may have implications for understanding particle acceleration in astrophysical environments, and may even have practical applications to fields such as spacecraft propulsion.

A chlorhexidine-loaded biodegradable cellulosic device for periodontal pockets treatment.

PubMed

Tabary, Nicolas; Chai, Feng; Blanchemain, Nicolas; Neut, Christel; Pauchet, Lucile; Bertini, Sabrina; Delcourt-Debruyne, Elisabeth; Hildebrand, Hartmut Frederic; Martel, Bernard

2014-01-01

Absorbent points widely used in endodontic therapy were transformed into bioresorbable chlorhexidine delivery systems for the treatment of the periodontal pocket by preventing its recolonization by the subgingival microflora. These paper points (PPs) were first oxidized to promote their resorption, then grafted with β-cyclodextrin (CD) or maltodextrin (MD) in order to achieve sustained delivery of chlorhexidine. We investigated the oxidation step parameters through the time of reaction and the nitric and phosphoric acid ratios in the oxidizing mixture, and then the dextrin grafting step parameters through the time and temperature of reaction. A first selection of the appropriate functionalization parameters was undertaken in relation to the degradation profile kinetics of the oxidized (PPO) and oxidized-grafted samples (PPO-CD and PPO-MD). Samples were then loaded with chlorhexidine digluconate (digCHX), a widely used antiseptic agent in periodontal therapy. The release kinetics of digCHX from PPO-CD and PPO-MD samples were compared to PP, PPO and to PerioChip(®) (a commercial digCHX containing gelatine chip) in phosphate buffered saline (pH 7.4) by ultraviolet spectrophotometry. The cytocompatibility of the oxidized-grafted PP was demonstrated by cell proliferation assays. Finally, the disc diffusion test from digCHX loaded PPO-MD samples immersed in human plasma was developed on pre-inoculated agar plates with four common periodontal pathogenic strains: Fusobacterium nucleatum, Prevotella melaninogenica, Aggregatibacter actinomycetem comitans and Porphyromonas gingivalis. To conclude, the optimized oxidized-dextrin-grafted PPs responded to our initial specifications in terms of resorption and digCHX release rates and therefore could be adopted as a reliable complementary periodontal therapy. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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.

Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

PubMed

Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

2008-12-25

Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

Characterization of breast lesion using T1-perfusion magnetic resonance imaging: Qualitative vs. quantitative analysis.

PubMed

Thakran, S; Gupta, P K; Kabra, V; Saha, I; Jain, P; Gupta, R K; Singh, A

2018-06-14

The objective of this study was to quantify the hemodynamic parameters using first pass analysis of T 1 -perfusion magnetic resonance imaging (MRI) data of human breast and to compare these parameters with the existing tracer kinetic parameters, semi-quantitative and qualitative T 1 -perfusion analysis in terms of lesion characterization. MRI of the breast was performed in 50 women (mean age, 44±11 [SD] years; range: 26-75) years with a total of 15 benign and 35 malignant breast lesions. After pre-processing, T 1 -perfusion MRI data was analyzed using qualitative approach by two radiologists (visual inspection of the kinetic curve into types I, II or III), semi-quantitative (characterization of kinetic curve types using empirical parameters), generalized-tracer-kinetic-model (tracer kinetic parameters) and first pass analysis (hemodynamic-parameters). Chi-squared test, t-test, one-way analysis-of-variance (ANOVA) using Bonferroni post-hoc test and receiver-operating-characteristic (ROC) curve were used for statistical analysis. All quantitative parameters except leakage volume (Ve), qualitative (type-I and III) and semi-quantitative curves (type-I and III) provided significant differences (P<0.05) between benign and malignant lesions. Kinetic parameters, particularly volume transfer coefficient (K trans ) provided a significant difference (P<0.05) between all grades except grade-II vs III. The hemodynamic parameter (relative-leakage-corrected-breast-blood-volume [rBBVcorr) provided a statistically significant difference (P<0.05) between all grades. It also provided highest sensitivity and specificity among all parameters in differentiation between different grades of malignant breast lesions. Quantitative parameters, particularly rBBVcorr and K trans provided similar sensitivity and specificity in differentiating benign from malignant breast lesions for this cohort. Moreover, rBBVcorr provided better differentiation between different grades of malignant breast lesions among all the parameters. Copyright © 2018. Published by Elsevier Masson SAS.

Exergy parametric study of carbon monoxide oxidation in moist air

NASA Astrophysics Data System (ADS)

Souidi, Ferhat; Benmalek, Toufik; Yesaad, Billel; Baik, Mouloud

2015-12-01

This study aims to analyze the oxidation of carbon monoxide in moist air from the second thermodynamic law aspect. A mathematical model of laminar premixed flame in a stagnation point flow has been achieved by numerical solution of the boundary layer equation using a self-made code. The chemical kinetic mechanism for flameless combustion of fuel, which is a mixture of carbon monoxide, oxygen, and water vapor, is modeled by 34 elementary reactions that incorporate (09) nine chemical species: CO, O, CO2, O2, H2O, H, H2, HO2, and OH. The salient point is that for all the parameters we considered, the exergy of the process is completely destroyed by irreversibilities. From the chemical viewpoint, the OH radical plays an essential role in CO oxidation. This latter point has already been mentioned by previous investigators.

Kinetic operational models of agonism for G-protein-coupled receptors.

PubMed

Hoare, Samuel R J; Pierre, Nicolas; Moya, Arturo Gonzalez; Larson, Brad

2018-06-07

The application of kinetics to research and therapeutic development of G-protein-coupled receptors has become increasingly valuable. Pharmacological models provide the foundation of pharmacology, providing concepts and measurable parameters such as efficacy and potency that have underlain decades of successful drug discovery. Currently there are few pharmacological models that incorporate kinetic activity in such a way as to yield experimentally-accessible drug parameters. In this study, a kinetic model of pharmacological response was developed that provides a kinetic descriptor of efficacy (the transduction rate constant, k τ ) and allows measurement of receptor-ligand binding kinetics from functional data. The model assumes: (1) receptor interacts with a precursor of the response ("Transduction potential") and converts it to the response. (2) The response can decay. Familiar response vs time plots emerge, depending on whether transduction potential is depleted and/or response decays. These are the straight line, the "association" exponential curve, and the rise-and-fall curve. Convenient, familiar methods are described for measuring the model parameters and files are provided for the curve-fitting program Prism (GraphPad Software) that can be used as a guide. The efficacy parameter k τ is straightforward to measure and accounts for receptor reserve; all that is required is measurement of response over time at a maximally-stimulating concentration of agonist. The modular nature of the model framework allows it to be extended. Here this is done to incorporate antagonist-receptor binding kinetics and slow agonist-receptor equilibration. In principle, the modular framework can incorporate other cellular processes, such as receptor desensitization. The kinetic response model described here can be applied to measure kinetic pharmacological parameters than can be used to advance the understanding of GPCR pharmacology and optimize new and improved therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Inverse modeling approach for evaluation of kinetic parameters of a biofilm reactor using tabu search.

PubMed

Kumar, B Shiva; Venkateswarlu, Ch

2014-08-01

The complex nature of biological reactions in biofilm reactors often poses difficulties in analyzing such reactors experimentally. Mathematical models could be very useful for their design and analysis. However, application of biofilm reactor models to practical problems proves somewhat ineffective due to the lack of knowledge of accurate kinetic models and uncertainty in model parameters. In this work, we propose an inverse modeling approach based on tabu search (TS) to estimate the parameters of kinetic and film thickness models. TS is used to estimate these parameters as a consequence of the validation of the mathematical models of the process with the aid of measured data obtained from an experimental fixed-bed anaerobic biofilm reactor involving the treatment of pharmaceutical industry wastewater. The results evaluated for different modeling configurations of varying degrees of complexity illustrate the effectiveness of TS for accurate estimation of kinetic and film thickness model parameters of the biofilm process. The results show that the two-dimensional mathematical model with Edward kinetics (with its optimum parameters as mu(max)rho(s)/Y = 24.57, Ks = 1.352 and Ki = 102.36) and three-parameter film thickness expression (with its estimated parameters as a = 0.289 x 10(-5), b = 1.55 x 10(-4) and c = 15.2 x 10(-6)) better describes the biofilm reactor treating the industry wastewater.

Synthesis and Characterization of Liquid Crystalline Epoxy Resins

DTIC Science & Technology

2014-01-01

Temperature dependence of the four parameters in the Burgers model. ......... 81 Figure 4.7 Dependence of creep compliance on creep time at different...Kinetic parameters for LCERs. ......................................................................... 65 Table 3.4 Kinetic parameters for non-LCERs...curing in a high strength magnetic field. The orientation was quantified by an orientation parameter determined with two-dimensional X-ray diffraction

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.

Kinetic parameters and structural variations in Cu-Al-Mn and Cu-Al-Mn-Mg shape memory alloys

NASA Astrophysics Data System (ADS)

Canbay, Canan Aksu

2017-02-01

In this work polycrystalline Cu-Al-Mn and Cu-Al-Mn-Mg SMAs were fabricated by arc melting. The thermal analysis was made to determine the characteristic transformation temperatures of the samples and kinetic parameters. Also the effect of Mg on transformation temperatures and kinetic parameters detected. The structural analysis was made to designate the diffraction planes of martensite phase at room temperature and this was supported by optical measurement observations.

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...

Kinetic study of olive oil degradation monitored by fourier transform infrared spectrometry. Application to oil characterization.

PubMed

Román Falcó, Iván P; Grané Teruel, Nuria; Prats Moya, Soledad; Martín Carratalá, M Luisa

2012-11-28

A new approach for the determination of kinetic parameters of the cis/trans isomerization during the oxidation process of 24 virgin olive oils belonging to 8 different varieties is presented. The accelerated process of degradation at 100 °C was monitored by recording the Fourier transform infrared spectra. The parameters obtained confirm pseudo-first-order kinetics for the degradation of cis and the appearance of trans double bonds. The kinetic approach affords the induction time and the rate coefficient; these parameters are related to the fatty acid profile of the fresh olive oils. The data obtained were used to compare the oil stability of the samples with the help of multivariate statistical techniques. Fatty acid allowed a classification of the samples in five groups, one of them constituted by the cultivars with higher stability. Meanwhile, the kinetic parameters showed greater ability for the characterization of olive oils, allowing the classification in seven groups.

High resolution approach to the native state ensemble kinetics and thermodynamics.

PubMed

Wu, Sangwook; Zhuravlev, Pavel I; Papoian, Garegin A

2008-12-15

Many biologically interesting functions such as allosteric switching or protein-ligand binding are determined by the kinetics and mechanisms of transitions between various conformational substates of the native basin of globular proteins. To advance our understanding of these processes, we constructed a two-dimensional free energy surface (FES) of the native basin of a small globular protein, Trp-cage. The corresponding order parameters were defined using two native substructures of Trp-cage. These calculations were based on extensive explicit water all-atom molecular dynamics simulations. Using the obtained two-dimensional FES, we studied the transition kinetics between two Trp-cage conformations, finding that switching process shows a borderline behavior between diffusive and weakly-activated dynamics. The transition is well-characterized kinetically as a biexponential process. We also introduced a new one-dimensional reaction coordinate for the conformational transition, finding reasonable qualitative agreement with the two-dimensional kinetics results. We investigated the distribution of all the 38 native nuclear magnetic resonance structures on the obtained FES, analyzing interactions that stabilize specific low-energy conformations. Finally, we constructed a FES for the same system but with simple dielectric model of water instead of explicit water, finding that the results were surprisingly similar in a small region centered on the native conformations. The dissimilarities between the explicit and implicit model on the larger-scale point to the important role of water in mediating interactions between amino acid residues.

LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 3: Illustrative test problems

NASA Technical Reports Server (NTRS)

Bittker, David A.; Radhakrishnan, Krishnan

1994-01-01

LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 3 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 3 explains the kinetics and kinetics-plus-sensitivity analysis problems supplied with LSENS and presents sample results. These problems illustrate the various capabilities of, and reaction models that can be solved by, the code and may provide a convenient starting point for the user to construct the problem data file required to execute LSENS. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

Oil-generation kinetics for organic facies with Type-II and -IIS kerogen in the Menilite Shales of the Polish Carpathians

USGS Publications Warehouse

Lewan, M.D.; Kotarba, M.J.; Curtis, John B.; Wieclaw, D.; Kosakowski, P.

2006-01-01

The Menilite Shales (Oligocene) of the Polish Carpathians are the source of low-sulfur oils in the thrust belt and some high-sulfur oils in the Carpathian Foredeep. These oil occurrences indicate that the high-sulfur oils in the Foredeep were generated and expelled before major thrusting and the low-sulfur oils in the thrust belt were generated and expelled during or after major thrusting. Two distinct organic facies have been observed in the Menilite Shales. One organic facies has a high clastic sediment input and contains Type-II kerogen. The other organic facies has a lower clastic sediment input and contains Type-IIS kerogen. Representative samples of both organic facies were used to determine kinetic parameters for immiscible oil generation by isothermal hydrous pyrolysis and S2 generation by non-isothermal open-system pyrolysis. The derived kinetic parameters showed that timing of S2 generation was not as different between the Type-IIS and -II kerogen based on open-system pyrolysis as compared with immiscible oil generation based on hydrous pyrolysis. Applying these kinetic parameters to a burial history in the Skole unit showed that some expelled oil would have been generated from the organic facies with Type-IIS kerogen before major thrusting with the hydrous-pyrolysis kinetic parameters but not with the open-system pyrolysis kinetic parameters. The inability of open-system pyrolysis to determine earlier petroleum generation from Type-IIS kerogen is attributed to the large polar-rich bitumen component in S2 generation, rapid loss of sulfur free-radical initiators in the open system, and diminished radical selectivity and rate constant differences at higher temperatures. Hydrous-pyrolysis kinetic parameters are determined in the presence of water at lower temperatures in a closed system, which allows differentiation of bitumen and oil generation, interaction of free-radical initiators, greater radical selectivity, and more distinguishable rate constants as would occur during natural maturation. Kinetic parameters derived from hydrous pyrolysis show good correlations with one another (compensation effect) and kerogen organic-sulfur contents. These correlations allow for indirect determination of hydrous-pyrolysis kinetic parameters on the basis of the organic-sulfur mole fraction of an immature Type-II or -IIS kerogen. ?? 2006 Elsevier Inc. All rights reserved.

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

PubMed

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

2009-06-01

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

Albumin's Influence on Carprofen Enantiomers-Hymecromone Interaction.

PubMed

Tang, Mingjie; Guo, Yanjie; Gao, Youshui; Tang, Chao; Dang, Xiaoqian; Zhou, Zubin; Sun, Yuqiang; Wang, Kunzheng

2016-03-01

Hymecromone is an important coumarin drug, and carprofen is one of the most important nonsteroidal antiinflammatory drugs (NSAIDs). The present study aims to determine the influence of bovine serum albumin (BSA) on the carprofen-hymecromone interaction. The inhibition of carprofen enantiomers on the UDP-glucuronosyltransferase (UGT) 2B7-catalyzed glucuronidation of hymecromone was investigated in the UGTs incubation system with and without BSA. The inhibition capability of increased by 20% (P < 0.001) of (R)-carprofen after the addition of 0.5% BSA in the incubation mixture. In contrast, no significant difference was observed for the inhibition of (S)-carprofen on UGT2B7 activity in the absence or presence of 0.5% BSA in the incubation system. The Lineweaver-Burk plot showed that the intersection point was located in the vertical axis, indicating the competitive inhibition of (R)-carprofen on UGT2B7 in the incubation system with BSA, which is consistent with the inhibition kinetic type of (R)-carprofen on UGT2B7 in the incubation system without BSA. Furthermore, the second plot using the slopes from the Lineweaver-Burk versus the concentrations of (R)-carprofen showed that the fitting equation was y=39.997x+50. Using this equation, the inhibition kinetic parameter was calculated to be 1.3 μM. For (S)-carprofen, the intersection point was located in the horizontal axis in the Lineweaver-Burk plot for the incubation system with BSA, indicating the noncompetitive inhibition of (S)-carprofen on the activity of UGT2B7. The fitting plot of the second plot was y=24.6x+180, and the inhibition kinetic parameter was 7.3 μM. In conclusion, the present study gives a short summary of BSA's influence on the carprofen enantiomers-hymecromone interaction, which will guide the clinical application of carprofen and hymecromone. © 2015 Wiley Periodicals, Inc.

Thermodynamics and kinetics of protein folding on the ribosome: Alteration in energy landscapes, denatured state, and transition state ensembles

NASA Astrophysics Data System (ADS)

O'Brien, Edward; Vendruscolo, Michele; Dobson, Christopher

2010-03-01

In vitro experiments examining cotranslational folding utilize ribosome-nascent chain complexes (RNCs) in which the nascent chain is stalled at different points of its biosynthesis on the ribosome. We investigate the thermodynamics, kinetics, and structural properties of RNCs containing five different globular and repeat proteins stalled at ten different nascent chain lengths using coarse grained replica exchange simulations. We find that when the proteins are stalled near the ribosome exit tunnel opening they exhibit altered folding coopserativity, quantified by the van't Hoff enthalpy criterion; a significantly altered denatured state ensemble, in terms of Rg and shape parameters (Rg tensor); and the appearance of partially folded intermediates during cotranslation, evidenced by the appearance of a third basin in the free energy profile. These trends are due in part to excluded volume (crowding) interactions between the ribosome and nascent chain. We perform in silico temperature-jump experiments on the RNCs and examine nascent chain folding kinetics and structural changes in the transition state ensemble at various stall lengths.

Impact of processing conditions on the kinetic of vitamin C degradation and 2-furoylmethyl amino acid formation in dried strawberries.

PubMed

Gamboa-Santos, Juliana; Megías-Pérez, Roberto; Soria, A Cristina; Olano, Agustín; Montilla, Antonia; Villamiel, Mar

2014-06-15

In this paper, a study on the usefulness of the determination of vitamin C together with indicators of the initial steps of Maillard reaction (2-furoylmethyl amino acids, 2-FM-AA) during the convective drying of strawberries has been carried out for the first time, paying special attention to the kinetics of degradation and formation, respectively, of both parameters. Formation of 2-FM-AA of Lys, Arg and GABA and vitamin C loss increased with time and temperature following, respectively, a zero and first-order kinetics. As supported by its lower activation energy, 2-FM-GABA (55.9 kJ/mol) and 2-FM-Lys+2-FM-Arg (58.2 kJ/mol) were shown to be slightly more sensitive indicators than vitamin C (82.1 kJ/mol). The obtained results, together with a complementary study on the rehydration ability and sensorial attributes of samples, pointed out the suitability of the convective drying system to obtain dried strawberries of high nutritive quality and bioactivity and good consumer acceptance. Copyright © 2013 Elsevier Ltd. All rights reserved.

Drug Resistance and the Kinetics of Metastatic Cancer

NASA Astrophysics Data System (ADS)

Blagoev, Krastan B.

2012-02-01

Most metastatic cancers after initial response to current drug therapies develop resistance to the treatment. We present cancer data and a theory that explains the observed kinetics of tumor growth in cancer patients and using a stochastic model based on this theory we relate the kinetics of tumor growth to Kaplan-Meyer survival curves. The theory points to the tumor growth rate as the most important parameter determining the outcome of a drug treatment. The overall tumor growth or decay rate is a reflection of the balance between cell division, senescence and apoptosis and we propose that the deviation of the decay rate from exponential is a measure of the emergence of drug resistance. In clinical trials the progression free survival, the overall survival, and the shape of the Kaplan-Meyer plots are determined by the tumor growth rate probability distribution among the patients in the trial. How drug treatments modify this distribution will also be described. At the end of the talk we will discuss the connection between the theory described here and the age related cancer mortality rates in the United States.

One-step global parameter estimation of kinetic inactivation parameters for Bacillus sporothermodurans spores under static and dynamic thermal processes.

PubMed

Cattani, F; Dolan, K D; Oliveira, S D; Mishra, D K; Ferreira, C A S; Periago, P M; Aznar, A; Fernandez, P S; Valdramidis, V P

2016-11-01

Bacillus sporothermodurans produces highly heat-resistant endospores, that can survive under ultra-high temperature. High heat-resistant sporeforming bacteria are one of the main causes for spoilage and safety of low-acid foods. They can be used as indicators or surrogates to establish the minimum requirements for heat processes, but it is necessary to understand their thermal inactivation kinetics. The aim of the present work was to study the inactivation kinetics under both static and dynamic conditions in a vegetable soup. Ordinary least squares one-step regression and sequential procedures were applied for estimating these parameters. Results showed that multiple dynamic heating profiles, when analyzed simultaneously, can be used to accurately estimate the kinetic parameters while significantly reducing estimation errors and data collection. Copyright © 2016 Elsevier Ltd. All rights reserved.

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.

Relationship of biomechanical factors to baseball pitching velocity: within pitcher variation.

PubMed

Stodden, David F; Fleisig, Glenn S; McLean, Scott P; Andrews, James R

2005-02-01

To reach the level of elite, most baseball pitchers need to consistently produce high ball velocity but avoid high joint loads at the shoulder and elbow that may lead to injury. This study examined the relationship between fastball velocity and variations in throwing mechanics within 19 baseball pitchers who were analyzed via 3-D high-speed motion analysis. Inclusion in the study required each one to demonstrate a variation in velocity of at least 1.8 m/s (range 1.8-3.5 m/s) during 6 to 10 fastball pitch trials. Three mixed model analyses were performed to assess the independent effects of 7 kinetic, 11 temporal, and 12 kinematic parameters on pitched ball velocity. Results indicated that elbow flexion torque, shoulder proximal force, and elbow proximal force were the only three kinetic parameters significantly associated with increased ball velocity. Two temporal parameters (increased time to max shoulder horizontal adduction and decreased time to max shoulder internal rotation) and three kinematic parameters (decreased shoulder horizontal adduction at foot contact, decreased shoulder abduction during acceleration, and increased trunk tilt forward at release) were significantly related to increased ball velocity. These results point to variations in an individual's throwing mechanics that relate to pitched ball velocity, and also suggest that pitchers should focus on consistent mechanics to produce consistently high fastball velocities. In addition, pitchers should strengthen shoulder and elbow musculature that resist distraction as well as improve trunk strength and flexibility to maximize pitching velocity and help prevent injury.

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

Transport equations for partially ionized reactive plasma in magnetic field

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

Zhdanov, V. M.; Stepanenko, A. A.

2016-06-08

Transport equations for partially ionized reactive plasma in magnetic field taking into account the internal degrees of freedom and electronic excitation of plasma particles are derived. As a starting point of analysis the kinetic equation with a binary collision operator written in the Wang-Chang and Uhlenbeck form and with a reactive collision integral allowing for arbitrary chemical reactions is used. The linearized variant of Grad’s moment method is applied to deduce the systems of moment equations for plasma and also full and reduced transport equations for plasma species nonequilibrium parameters.

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

PubMed

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

2015-07-29

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

Comparison Of A Neutron Kinetics Parameter For A Polyethylene Moderated Highly Enriched Uranium System

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

McKenzie, IV, George Espy; Goda, Joetta Marie; Grove, Travis Justin

This paper examines the comparison of MCNP® code’s capability to calculate kinetics parameters effectively for a thermal system containing highly enriched uranium (HEU). The Rossi-α parameter was chosen for this examination because it is relatively easy to measure as well as easy to calculate using MCNP®’s kopts card. The Rossi-α also incorporates many other parameters of interest in nuclear kinetics most of which are more difficult to precisely measure. The comparison looks at two different nuclear data libraries for comparison to the experimental data. These libraries are ENDF/BVI (.66c) and ENDF/BVII (.80c).

Curcumin and kaempferol prevent lysozyme fibril formation by modulating aggregation kinetic parameters.

PubMed

Borana, Mohanish S; Mishra, Pushpa; Pissurlenkar, Raghuvir R S; Hosur, Ramakrishna V; Ahmad, Basir

2014-03-01

Interaction of small molecule inhibitors with protein aggregates has been studied extensively, but how these inhibitors modulate aggregation kinetic parameters is little understood. In this work, we investigated the ability of two potential aggregation inhibiting drugs, curcumin and kaempferol, to control the kinetic parameters of aggregation reaction. Using thioflavin T fluorescence and static light scattering, the kinetic parameters such as amplitude, elongation rate constant and lag time of guanidine hydrochloride-induced aggregation reactions of hen egg white lysozyme were studied. We observed a contrasting effect of inhibitors on the kinetic parameters when aggregation reactions were measured by these two probes. The interactions of these inhibitors with hen egg white lysozyme were investigated using fluorescence quench titration method and molecular dynamics simulations coupled with binding free energy calculations. We conclude that both the inhibitors prolong nucleation of amyloid aggregation through binding to region of the protein which is known to form the core of the protein fibril, but once the nucleus is formed the rate of elongation is not affected by the inhibitors. This work would provide insight into the mechanism of aggregation inhibition by these potential drug molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

Estimation of beech pyrolysis kinetic parameters by Shuffled Complex Evolution.

PubMed

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

2016-01-01

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

Kinetics modelling of color deterioration during thermal processing of tomato paste with the use of response surface methodology

NASA Astrophysics Data System (ADS)

Ganje, Mohammad; Jafari, Seid Mahdi; Farzaneh, Vahid; Malekjani, Narges

2018-06-01

To study the kinetics of color degradation, the tomato paste was designed to be processed at three different temperatures including 60, 70 and 80 °C for 25, 50, 75 and 100 min. a/b ratio, total color difference, saturation index and hue angle were calculated with the use of three main color parameters including L (lightness), a (redness-greenness) and b (yellowness-blueness) values. Kinetics of color degradation was developed by Arrhenius equation and the alterations were modelled with the use of response surface methodology (RSM). It was detected that all of the studied responses followed a first order reaction kinetics with an exception in TCD parameter (zeroth order). TCD and a/b respectively with the highest and lowest activation energy presented the highest sensitivity to the temperature alterations. The maximum and minimum rates of alterations were observed by TCD and b parameters, respectively. It was obviously determined that all of the studied parameters (responses) were affected by the selected independent parameters.

Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation cycle in extremely thermoacidophilic archaea

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

Loder, Andrew J.; Han, Yejun; Hawkins, Aaron B.

Here, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO 2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35%–65% split of carbon flux throughmore » the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO 2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxyproprionate.« less

Effects of catalysts on combustion characteristics and kinetics of coal-char blends

NASA Astrophysics Data System (ADS)

Hu, Yingjie; Wang, Zhiqiang; Cheng, Xingxing; Liu, Ming; Ma, Chunyuan

2018-04-01

The effects of Fe2O3, CaO, and MnO2 on the combustion characteristics and kinetics of coal-char blends were investigated using thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The results indicated that catalysts exhibited positive effects on the combustion characteristics of coal-char blends, especially in the initial period of coal-char blends combustion. With catalysts addition (mass 1.5%), it could improves volatile matter release, and reduces ignition point, promotes char to begin burning under lower temperature. The ignition index (C) was increased, respectively, by 27% for Fe2O3, 6% for CaO, 11.3% for MnO2, and the combustion characteristic index ( S ) was increased respectively, by 29% for Fe2O3, 5% for CaO, 8.3% for MnO2. In addition, two kinetic models (R2 and F1) were adopted to calculate the kinetic parameters in different stage of combustion processes. The results showed that with Fe2O3 or CaO addition, the activation energy at second stage decreases from 86.0 KJ/mol to 76.92 KJ/mol and 75.12 KJ/mol, respectively. There are no obvious decreases at the third stage of samples combustion process.

Reaction kinetic analysis of the 3-hydroxypropionate/4-hydroxybutyrate CO 2 fixation cycle in extremely thermoacidophilic archaea

DOE PAGES

Loder, Andrew J.; Han, Yejun; Hawkins, Aaron B.; ...

2016-10-19

Here, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle fixes CO 2 in extremely thermoacidophilic archaea and holds promise for metabolic engineering because of its thermostability and potentially rapid pathway kinetics. A reaction kinetics model was developed to examine the biological and biotechnological attributes of the 3HP/4HB cycle as it operates in Metallosphaera sedula, based on previous information as well as on kinetic parameters determined here for recombinant versions of five of the cycle enzymes (malonyl-CoA/succinyl-CoA reductase, 3-hydroxypropionyl-CoA synthetase, 3-hydroxypropionyl-CoA dehydratase, acryloyl-CoA reductase, and succinic semialdehyde reductase). The model correctly predicted previously observed features of the cycle: the 35%–65% split of carbon flux throughmore » the acetyl-CoA and succinate branches, the high abundance and relative ratio of acetyl-CoA/propionyl-CoA carboxylase (ACC) and MCR, and the significance of ACC and hydroxybutyryl-CoA synthetase (HBCS) as regulated control points for the cycle. The model was then used to assess metabolic engineering strategies for incorporating CO 2 into chemical intermediates and products of biotechnological importance: acetyl-CoA, succinate, and 3-hydroxyproprionate.« less

Finite size effects in phase transformation kinetics in thin films and surface layers

NASA Astrophysics Data System (ADS)

Trofimov, Vladimir I.; Trofimov, Ilya V.; Kim, Jong-Il

2004-02-01

In studies of phase transformation kinetics in thin films, e.g. crystallization of amorphous films, until recent time is widely used familiar Kolmogorov-Johnson-Mehl-Avrami (KJMA) statistical model of crystallization despite it is applicable only to an infinite medium. In this paper a model of transformation kinetics in thin films based on a concept of the survival probability for randomly chosen point during transformation process is presented. Two model versions: volume induced transformation (VIT) when the second-phase grains nucleate over a whole film volume and surface induced transformation (SIT) when they form on an interface with two nucleation mode: instantaneous nucleation at transformation onset and continuous one during all the process are studied. At VIT-process due to the finite film thickness effects the transformation profile has a maximum in a film middle, whereas that of the grains population reaches a minimum inhere, the grains density is always higher than in a volume material, and the thinner film the slower it transforms. The transformation kinetics in a thin film obeys a generalized KJMA equation with parameters depending on a film thickness and in limiting cases of extremely thin and thick film it reduces to classical KJMA equation for 2D- and 3D-system, respectively.

Application of point kinetics equations to the design of a reactivity meter

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

Binney, S.E.; Bakir, A.J.M.

1988-01-01

The time-dependent reactivity of a nuclear reactor is obviously one of the most important reactor parameters that describes the state of the reactor. Although several different types of techniques exist to measure reactivity, only the kinetic method is described here. The paper illustrates the measured reactor power and calculated reactivity for a 70 cents step change in reactivity. These data were taken at 1-s time intervals. It is seen that the reactivity, initially at zero, rises rapidly to a predetermined value (determined by the reactivity change induced in the system) and then returns to zero as the reactor is reestablishedmore » in a critical situation by insertion of another control rod. It is concluded that the method of Tuttle has been adapted to produce a reliable, on-line calculation of reactivity from a time-dependent reactor power signal.« less

Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

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

Parker, Stephen S.; White, Josh; Hosemann, Peter

High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. We measured the oxidation kinetic constant (k) as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3–5 orders of magnitude lower across the experimental temperature range. Our results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

DOE PAGES

Parker, Stephen S.; White, Josh; Hosemann, Peter; ...

2017-11-03

High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. We measured the oxidation kinetic constant (k) as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3–5 orders of magnitude lower across the experimental temperature range. Our results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

NASA Astrophysics Data System (ADS)

Parker, Stephen S.; White, Josh; Hosemann, Peter; Nelson, Andrew

2018-02-01

High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. The oxidation kinetic constant ( k) was measured as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3-5 orders of magnitude lower across the experimental temperature range. The results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

Assessment of methane biodegradation kinetics in two-phase partitioning bioreactors by pulse respirometry.

PubMed

Ordaz, Alberto; López, Juan C; Figueroa-González, Ivonne; Muñoz, Raúl; Quijano, Guillermo

2014-12-15

Biological methane biodegradation is a promising treatment alternative when the methane produced in waste management facilities cannot be used for energy generation. Two-phase partitioning bioreactors (TPPBs), provided with a non-aqueous phase (NAP) with high affinity for the target pollutant, are particularly suitable for the treatment of poorly water-soluble compounds such as methane. Nevertheless, little is known about the influence of the presence of the NAP on the resulting biodegradation kinetics in TPPBs. In this study, an experimental framework based on the in situ pulse respirometry technique was developed to assess the impact of NAP addition on the methane biodegradation kinetics using Methylosinus sporium as a model methane-degrading microorganism. A comprehensive mass transfer characterization was performed in order to avoid mass transfer limiting scenarios and ensure a correct kinetic parameter characterization. The presence of the NAP mediated significant changes in the apparent kinetic parameters of M. sporium during methane biodegradation, with variations of 60, 120, and 150% in the maximum oxygen uptake rate, half-saturation constant and maximum specific growth rate, respectively, compared with the intrinsic kinetic parameters retrieved from a control without NAP. These significant changes in the kinetic parameters mediated by the NAP must be considered for the design, operation and modeling of TPPBs devoted to air pollution control. Copyright © 2014 Elsevier Ltd. All rights reserved.

Combining experimental techniques with non-linear numerical models to assess the sorption of pesticides on soils

NASA Astrophysics Data System (ADS)

Magga, Zoi; Tzovolou, Dimitra N.; Theodoropoulou, Maria A.; Tsakiroglou, Christos D.

2012-03-01

The risk assessment of groundwater pollution by pesticides may be based on pesticide sorption and biodegradation kinetic parameters estimated with inverse modeling of datasets from either batch or continuous flow soil column experiments. In the present work, a chemical non-equilibrium and non-linear 2-site sorption model is incorporated into solute transport models to invert the datasets of batch and soil column experiments, and estimate the kinetic sorption parameters for two pesticides: N-phosphonomethyl glycine (glyphosate) and 2,4-dichlorophenoxy-acetic acid (2,4-D). When coupling the 2-site sorption model with the 2-region transport model, except of the kinetic sorption parameters, the soil column datasets enable us to estimate the mass-transfer coefficients associated with solute diffusion between mobile and immobile regions. In order to improve the reliability of models and kinetic parameter values, a stepwise strategy that combines batch and continuous flow tests with adequate true-to-the mechanism analytical of numerical models, and decouples the kinetics of purely reactive steps of sorption from physical mass-transfer processes is required.

Development of a Kinetic Assay for Late Endosome Movement.

PubMed

Esner, Milan; Meyenhofer, Felix; Kuhn, Michael; Thomas, Melissa; Kalaidzidis, Yannis; Bickle, Marc

2014-08-01

Automated imaging screens are performed mostly on fixed and stained samples to simplify the workflow and increase throughput. Some processes, such as the movement of cells and organelles or measuring membrane integrity and potential, can be measured only in living cells. Developing such assays to screen large compound or RNAi collections is challenging in many respects. Here, we develop a live-cell high-content assay for tracking endocytic organelles in medium throughput. We evaluate the added value of measuring kinetic parameters compared with measuring static parameters solely. We screened 2000 compounds in U-2 OS cells expressing Lamp1-GFP to label late endosomes. All hits have phenotypes in both static and kinetic parameters. However, we show that the kinetic parameters enable better discrimination of the mechanisms of action. Most of the compounds cause a decrease of motility of endosomes, but we identify several compounds that increase endosomal motility. In summary, we show that kinetic data help to better discriminate phenotypes and thereby obtain more subtle phenotypic clustering. © 2014 Society for Laboratory Automation and Screening.

Influence of the power supply parameters on the projectile energy in the permanent magnet electrodynamic accelerator

NASA Astrophysics Data System (ADS)

Waindok, Andrzej; Piekielny, Paweł

2017-10-01

The main objective of the research is to investigate, how the power supply parameters influence the kinetic energy of the movable element, called commonly a projectile or bullet. A calculation and measurement results of transient characteristics for an electrodynamic accelerator with permanent magnet support were presented in the paper. The calculations were made with using field-circuit model, which includes the parameters of the power supply, mass of the bullet and friction phenomenon. Characteristics of energy and muzzle velocity verso supply voltage (50 V to 350 V) and capacitance value (60 mF to 340.5 mF) were determined, as well. A measurement verification of selected points of calculation characteristics were carried out for investigated values of muzzle velocity. A good conformity between calculation and measurement results was obtained. Concluding, presented characteristics of the muzzle velocity and energy of the projectile vs. power supply parameters indicate, that accelerators could be used for fatigue testing of materials.

Ammonium Removal from Aqueous Solutions by Clinoptilolite: Determination of Isotherm and Thermodynamic Parameters and Comparison of Kinetics by the Double Exponential Model and Conventional Kinetic Models

PubMed Central

Tosun, İsmail

2012-01-01

The adsorption isotherm, the adsorption kinetics, and the thermodynamic parameters of ammonium removal from aqueous solution by using clinoptilolite in aqueous solution was investigated in this study. Experimental data obtained from batch equilibrium tests have been analyzed by four two-parameter (Freundlich, Langmuir, Tempkin and Dubinin-Radushkevich (D-R)) and four three-parameter (Redlich-Peterson (R-P), Sips, Toth and Khan) isotherm models. D-R and R-P isotherms were the models that best fitted to experimental data over the other two- and three-parameter models applied. The adsorption energy (E) from the D-R isotherm was found to be approximately 7 kJ/mol for the ammonium-clinoptilolite system, thereby indicating that ammonium is adsorbed on clinoptilolite by physisorption. Kinetic parameters were determined by analyzing the nth-order kinetic model, the modified second-order model and the double exponential model, and each model resulted in a coefficient of determination (R2) of above 0.989 with an average relative error lower than 5%. A Double Exponential Model (DEM) showed that the adsorption process develops in two stages as rapid and slow phase. Changes in standard free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) of ammonium-clinoptilolite system were estimated by using the thermodynamic equilibrium coefficients. PMID:22690177

Ammonium removal from aqueous solutions by clinoptilolite: determination of isotherm and thermodynamic parameters and comparison of kinetics by the double exponential model and conventional kinetic models.

PubMed

Tosun, Ismail

2012-03-01

The adsorption isotherm, the adsorption kinetics, and the thermodynamic parameters of ammonium removal from aqueous solution by using clinoptilolite in aqueous solution was investigated in this study. Experimental data obtained from batch equilibrium tests have been analyzed by four two-parameter (Freundlich, Langmuir, Tempkin and Dubinin-Radushkevich (D-R)) and four three-parameter (Redlich-Peterson (R-P), Sips, Toth and Khan) isotherm models. D-R and R-P isotherms were the models that best fitted to experimental data over the other two- and three-parameter models applied. The adsorption energy (E) from the D-R isotherm was found to be approximately 7 kJ/mol for the ammonium-clinoptilolite system, thereby indicating that ammonium is adsorbed on clinoptilolite by physisorption. Kinetic parameters were determined by analyzing the nth-order kinetic model, the modified second-order model and the double exponential model, and each model resulted in a coefficient of determination (R(2)) of above 0.989 with an average relative error lower than 5%. A Double Exponential Model (DEM) showed that the adsorption process develops in two stages as rapid and slow phase. Changes in standard free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) of ammonium-clinoptilolite system were estimated by using the thermodynamic equilibrium coefficients.

Non-Isothermal Kinetics.

ERIC Educational Resources Information Center

Brown, M. E.; Phillpotts, C. A. R.

1978-01-01

Discusses the principle of nonisothermal kinetics and some of the factors involved in such reactions, especially when considering the reliability of the kinetic parameters, compared to those of isothermal conditions. (GA)

Individual differences in the forced swimming test and neurochemical kinetics in the rat brain.

PubMed

Sequeira-Cordero, Andrey; Mora-Gallegos, Andrea; Cuenca-Berger, Patricia; Fornaguera-Trías, Jaime

2014-04-10

Individual differences in the forced swimming test (FST) could be associated with differential temporal dynamics of gene expression and neurotransmitter activity. We tested juvenile male rats in the FST and classified the animals into those with low and high immobility according to the amount of immobility time recorded in FST. These groups and a control group which did not undergo the FST were sacrificed either 1, 6 or 24 h after the test. We analyzed the expression of the CRF, CRFR1, BDNF and TrkB in the prefrontal cortex, hippocampus and nucleus accumbens as well as norepinephrine, dopamine, serotonin, glutamate, GABA and glutamine in the hippocampus and nucleus accumbens. Animals with low immobility showed significant reductions of BDNF expression across time points in both the prefrontal cortex and the nucleus accumbens when compared with non-swim control. Moreover, rats with high immobility only showed a significant decrease of BDNF expression in the prefrontal cortex 6h after the FST. Regarding neurotransmitters, only accumbal dopamine turnover and hippocampal glutamate content showed an effect of individual differences (i.e. animals with low and high immobility), whereas nearly all parameters showed significant differences across time points. Correlational analyses suggest that immobility in the FST, probably reflecting despair, is related to prefrontal cortical BDNF and to the kinetics observed in several other neurochemical parameters. Taken together, our results suggest that individual differences observed in depression-like behavior can be associated not only with changes in the concentrations of key neurochemical factors but also with differential time courses of such factors. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

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.

Theoretical and experimental study on the effects of particle size and temperature on the reaction kinetics of cubic nano-Cu2O

NASA Astrophysics Data System (ADS)

Tang, Huanfeng; Huang, Zaiyin; Xiao, Ming; Liang, Min; Chen, Liying; Tan, XueCai

2017-09-01

The activities, selectivities, and stabilities of nanoparticles in heterogeneous reactions are size-dependent. In order to investigate the influencing laws of particle size and temperature on kinetic parameters in heterogeneous reactions, cubic nano-Cu2O particles of four different sizes in the range of 40-120 nm have been controllably synthesized. In situ microcalorimetry has been used to attain thermodynamic data on the reaction of Cu2O with aqueous HNO3 and, combined with thermodynamic principles and kinetic transition-state theory, the relevant reaction kinetic parameters have been evaluated. The size dependences of the kinetic parameters are discussed in terms of the established kinetic model and the experimental results. It was found that the reaction rate constants increased with decreasing particle size. Accordingly, the apparent activation energy, pre-exponential factor, activation enthalpy, activation entropy, and activation Gibbs energy decreased with decreasing particle size. The reaction rate constants and activation Gibbs energies increased with increasing temperature. Moreover, the logarithms of the apparent activation energies, pre-exponential factors, and rate constants were found to be linearly related to the reciprocal of particle size, consistent with the kinetic models. The influence of particle size on these reaction kinetic parameters may be explained as follows: the apparent activation energy is affected by the partial molar enthalpy, the pre-exponential factor is affected by the partial molar entropy, and the reaction rate constant is affected by the partial molar Gibbs energy. [Figure not available: see fulltext.

Kinetics of hydrophobic organic contaminant extraction from sediment by granular activated carbon.

PubMed

Rakowska, M I; Kupryianchyk, D; Smit, M P J; Koelmans, A A; Grotenhuis, J T C; Rijnaarts, H H M

2014-03-15

Ex situ solid phase extraction with granular activated carbon (GAC) is a promising technique to remediate contaminated sediments. The methods' efficiency depends on the rate by which contaminants are transferred from the sediment to the surface of GAC. Here, we derive kinetic parameters for extraction of polycyclic aromatic hydrocarbons (PAH) from sediment by GAC, using a first-order multi-compartment kinetic model. The parameters were obtained by modeling sediment-GAC exchange kinetic data following a tiered model calibration approach. First, parameters for PAH desorption from sediment were calibrated using data from systems with 50% (by weight) GAC acting as an infinite sink. Second, the estimated parameters were used as fixed input to obtain GAC uptake kinetic parameters in sediment slurries with 4% GAC, representing the ex situ remediation scenario. PAH uptake rate constants (kGAC) by GAC ranged from 0.44 to 0.0005 d(-1), whereas GAC sorption coefficients (KGAC) ranged from 10(5.57) to 10(8.57) L kg(-1). These values are the first provided for GAC in the presence of sediment and show that ex situ extraction with GAC is sufficiently fast and effective to reduce the risks of the most available PAHs among those studied, such as fluorene, phenanthrene and anthracene. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modeling of the interfacial separation work in relation to impurity concentration in adjoining materials

NASA Astrophysics Data System (ADS)

Alekseev, Ilia M.; Makhviladze, Tariel M.; Minushev, Airat Kh.; Sarychev, Mikhail E.

2009-10-01

On the basis of the general thermodynamic approach developed in a model describing the influence of point defects on the separation work at an interface of solid materials is developed. The kinetic equations describing the defect exchange between the interface and the material bulks are formulated. The model have been applied to the case when joined materials contain such point defects as impurity atoms (interstitial and substitutional), concretized the main characteristic parameters required for a numerical modeling as well as clarified their domains of variability. The results of the numerical modeling concerning the dependences on impurity concentrations and the temperature dependences are obtained and analyzed. Particularly, the effects of interfacial strengthening and adhesion incompatibility predicted analytically for the case of impurity atoms are verified and analyzed.

Modeling of the interfacial separation work in relation to impurity concentration in adjoining materials

NASA Astrophysics Data System (ADS)

Alekseev, Ilia M.; Makhviladze, Tariel M.; Minushev, Airat Kh.; Sarychev, Mikhail E.

2010-02-01

On the basis of the general thermodynamic approach developed in a model describing the influence of point defects on the separation work at an interface of solid materials is developed. The kinetic equations describing the defect exchange between the interface and the material bulks are formulated. The model have been applied to the case when joined materials contain such point defects as impurity atoms (interstitial and substitutional), concretized the main characteristic parameters required for a numerical modeling as well as clarified their domains of variability. The results of the numerical modeling concerning the dependences on impurity concentrations and the temperature dependences are obtained and analyzed. Particularly, the effects of interfacial strengthening and adhesion incompatibility predicted analytically for the case of impurity atoms are verified and analyzed.

Parameter identification of thermophilic anaerobic degradation of valerate.

PubMed

Flotats, Xavier; Ahring, Birgitte K; Angelidaki, Irini

2003-01-01

The considered mathematical model of the decomposition of valerate presents three unknown kinetic parameters, two unknown stoichiometric coefficients, and three unknown initial concentrations for biomass. Applying a structural identifiability study, we concluded that it is necessary to perform simultaneous batch experiments with different initial conditions for estimating these parameters. Four simultaneous batch experiments were conducted at 55 degrees C, characterized by four different initial acetate concentrations. Product inhibition of valerate degradation by acetate was considered. Practical identification was done optimizing the sum of the multiple determination coefficients for all measured state variables and for all experiments simultaneously. The estimated values of kinetic parameters and stoichiometric coefficients were characterized by the parameter correlation matrix, the confidence interval, and the student's t-test at 5% significance level with positive results except for the saturation constant, for which more experiments for improving its identifiability should be conducted. In this article, we discuss kinetic parameter estimation methods.

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.

Kinetics of cross-slope running.

PubMed

Willwacher, Steffen; Fischer, Katina Mira; Benker, Rita; Dill, Stephan; Brüggemann, Gert-Peter

2013-11-15

The purpose of the present study was to identify kinetic responses to running on mediolaterally elevated (cross-sloped) running surfaces. Ground reaction forces (GRFs), GRF lever arms and joint moment characteristics of 19 male runners were analyzed when running at 3.5m/s on a custom-made, tiltable runway. Tilt angles of 3° and 6° for medial and lateral elevation were analyzed using a 10 camera Vicon Nexus system and a force platform. The point of force application of the GRF showed a systematic shift in the order of 1-1.5cm to either the lateral or medial aspect of the foot for lateral or medial inclinations, respectively. Consequently, the strongest significant effects of tilt orientation and level on joint kinetics and ground reaction force lever arms were identified at the ankle, knee and hip joint in the frontal plane of movement. External eversion moments at the ankle were significantly increased by 35% for 6° of lateral elevation and decreased by 16% for 6° of medial elevation. Altering the cross-slope of the running surface changed the pattern of ankle joint moments in the transversal plane. Effect sizes were on average larger for laterally elevated conditions, indicating a higher sensitivity of kinetic parameters to this kind of surface tilt. These alterations in joint kinetics should be considered in the choice of the running environment, especially for specific risk groups, like runners in rehabilitation processes. © 2013 Elsevier Ltd. All rights reserved.

Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

DOE PAGES

Trochet, Mickaël; Béland, Laurent Karim; Joly, Jean -François; ...

2015-06-16

We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion pathsmore » and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. In conclusion, this study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.« less

Accuracy and precision of loadsol® insole force-sensors for the quantification of ground reaction force-based biomechanical running parameters.

PubMed

Seiberl, Wolfgang; Jensen, Elisabeth; Merker, Josephine; Leitel, Marco; Schwirtz, Ansgar

2018-05-29

Force plates represent the "gold standard" in measuring running kinetics to predict performance or to identify the sources of running-related injuries. As these measurements are generally limited to laboratory analyses, wireless high-quality sensors for measuring in the field are needed. This work analysed the accuracy and precision of a new wireless insole forcesensor for quantifying running-related kinetic parameters. Vertical ground reaction force (GRF) was simultaneously measured with pit-mounted force plates (1 kHz) and loadsol ® sensors (100 Hz) under unshod forefoot and rearfoot running-step conditions. GRF data collections were repeated four times, each separated by 30 min treadmill running, to test influence of extended use. A repeated-measures ANOVA was used to identify differences between measurement devices. Additionally, mean bias and Bland-Altman limits of agreement (LoA) were calculated. We found a significant difference (p < .05) in ground contact time, peak force, and force rate, while there was no difference in parameters impulse, time to peak, and negative force rate. There was no influence of time point of measurement. The mean bias of ground contact time, impulse, peak force, and time to peak ranged between 0.6% and 3.4%, demonstrating high accuracy of loadsol ® devices for these parameters. For these same parameters, the LoA analysis showed that 95% of all measurement differences between insole and force plate measurements were less than 12%, demonstrating high precision of the sensors. However, highly dynamic behaviour of GRF, such as force rate, is not yet sufficiently resolved by the insole devices, which is likely explained by the low sampling rate.

Study of Metal-NH[subscript 3] Interfaces (Metal= Cu, Ni, Ag) Using Potentiostatic Curves

ERIC Educational Resources Information Center

Nunes, Nelson; Martins, Angela; Leitao, Ruben Elvas

2007-01-01

Experiment is conducted to determine the kinetic parameters of metal-solution interfaces. During the experiment the kinetic parameters for the interfaces Cu-NH[subscript 3], Ag-NH[subscript 3] and Ni-NH[subscript 3] is easily determined.

Associations between timing in the baseball pitch and shoulder kinetics, elbow kinetics, and ball speed.

PubMed

Urbin, M A; Fleisig, Glenn S; Abebe, Asheber; Andrews, James R

2013-02-01

A baseball pitcher's ability to maximize ball speed while avoiding shoulder and elbow injuries is an important determinant of a successful career. Pitching injuries are attributed to microtrauma brought about by the repetitive stress of high-magnitude shoulder and elbow kinetics. Over a number of pitches, variations in timing peak angular velocities of trunk segment rotations will be significantly associated with ball speed and upper extremity kinetic parameters. Descriptive laboratory study. Kinematic and kinetic data were derived from 9 to 15 fastball pitches performed by 16 active, healthy collegiate (n = 8) and professional (n = 8) pitchers via 3-dimensional motion capture (240 Hz). Each pitch was decomposed into 4 phases corresponding to the time between peak angular velocities of sequential body segment rotations. Four mixed models were used to evaluate which phases varied significantly in relation to ball speed, peak shoulder proximal force, peak shoulder internal rotation torque, and peak elbow varus torque. Mixed-model parameter coefficient estimates were used to quantify the influence of these variations in timing on ball speed and upper extremity kinetics. All 4 mixed models were significant (P < .05). The time from stride-foot contact to peak pelvis angular velocity varied significantly in relation to all upper extremity kinetic parameters and ball speed. Increased time in this phase correlated with decreases in all parameters. Decreased ball speed also correlated with increased time between peak upper torso and elbow extension angular velocities. Decreased shoulder proximal force also correlated with increased time between peak pelvis and upper torso angular velocities. There are specific phases that vary in relation to ball speed and upper extremity kinetic parameters, reinforcing the importance of effectively and consistently timing segmental interactions. For the specific interactions that varied significantly, increased phase times were associated with decreased kinetics and ball speed. Although increased time within specific phases correlates with decreases in the magnitude of upper extremity kinetics linked to overuse injuries, it also correlates with decreased ball speed. Based on these findings, it may appear that minimizing the risk of injury (ie, decreased kinetics) and maximizing performance quality (ie, increased ball speed) are incompatible with one another. However, there may be an optimal balance in timing that is effective for satisfying both outcomes.

Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth

NASA Astrophysics Data System (ADS)

Zhang, Hong; Zuo, Ran; Zhang, Guoyi

2017-11-01

In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.

78 FR 40511 - RG Steel Sparrows Point LLC, Formerly Known as Severstal Sparrows Point LLC, a Subsidiary of RG...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-05

..., Alliance Engineering, Inc., Washington Group International, Javan & Walter, Inc., Kinetic Technical... Consulting, Crown Security, Eastern Automation, Eds(Hp), Teksystems, URS Corporation, B More Industrial..., Alliance Engineering, Inc., Washington Group International, Javan & Walter, Inc., Kinetic Technical...

A Proposal for a Subcritical Reactivity Meter based on Gandini and Salvatores' point kinetics equations for Multiplying Subcritical Systems

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

Pinto, Leticia N.; Dos Santos, Adimir

2015-07-01

Multiplying Subcritical Systems were for a long time poorly studied and its theoretical description remains with plenty open questions. Great interest on such systems arose partly due to the improvement of hybrid concepts, such as the Accelerator-Driven Systems (ADS). Along with the need for new technologies to be developed, further study and understanding of subcritical systems are essential also in more practical situations, such as in the case of a PWR criticalization in their physical startup tests. Point kinetics equations are fundamental to continuously monitor the reactivity behavior to a possible variation of external sources intensity. In this case, quicklymore » and accurately predicting power transients and reactivity becomes crucial. It is known that conventional Reactivity Meters cannot operate in subcritical levels nor describe the dynamics of multiplying systems in these conditions, by the very structure of the classical kinetic equations. Several theoretical models have been proposed to characterize the kinetics of such systems with special regard to the reactivity, as the one developed by Gandini and Salvatores among others. This work presents a discussion about the derivation of point kinetics equations for subcritical systems and the importance of considering the external source. From the point of view of the Gandini and Salvatores' point kinetics model and based on the experimental results provided by Lee and dos Santos, it was possible to develop an innovative approach. This article proposes an algorithm that describes the subcritical reactivity with external source, contributing to the advancement of studies in the field. (authors)« less

The influence of pH adjustment on kinetics parameters in tapioca wastewater treatment using aerobic sequencing batch reactor system

NASA Astrophysics Data System (ADS)

Mulyani, Happy; Budianto, Gregorius Prima Indra; Margono, Kaavessina, Mujtahid

2018-02-01

The present investigation deals with the aerobic sequencing batch reactor system of tapioca wastewater treatment with varying pH influent conditions. This project was carried out to evaluate the effect of pH on kinetics parameters of system. It was done by operating aerobic sequencing batch reactor system during 8 hours in many tapioca wastewater conditions (pH 4.91, pH 7, pH 8). The Chemical Oxygen Demand (COD) and Mixed Liquor Volatile Suspended Solids (MLVSS) of the aerobic sequencing batch reactor system effluent at steady state condition were determined at interval time of two hours to generate data for substrate inhibition kinetics parameters. Values of the kinetics constants were determined using Monod and Andrews models. There was no inhibition constant (Ki) detected in all process variation of aerobic sequencing batch reactor system for tapioca wastewater treatment in this study. Furthermore, pH 8 was selected as the preferred aerobic sequencing batch reactor system condition in those ranging pH investigated due to its achievement of values of kinetics parameters such µmax = 0.010457/hour and Ks = 255.0664 mg/L COD.

Kinetic sensitivity of a receptor-binding radiopharmaceutical: Technetium-99m galactosyl-neoglycoalbumin

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

Vera, D.R.; Woodle, E.S.; Stadalnik, R.C.

1989-09-01

Kinetic sensitivity is the ability of a physiochemical parameter to alter the time-activity curve of a radiotracer. The kinetic sensitivity of liver and blood time-activity data resulting from a single bolus injection of ({sup 99m}Tc)galactosyl-neoglycoalbumin (( Tc)NGA) into healthy pigs was examined. Three parameters, hepatic plasma flow scaled as flow per plasma volume, ligand-receptor affinity, and total receptor concentration, were tested using (Tc)NGA injections of various molar doses and affinities. Simultaneous measurements of plasma volume (iodine-125 human serum albumin dilution), and hepatic plasma flow (indocyanine green extraction) were performed during 12 (Tc)NGA studies. Paired data sets demonstrated differences (P(chi v2)more » less than 0.01) in liver and blood time-activity curves in response to changes in each of the tested parameters. We conclude that the (Tc)NGA radiopharmacokinetic system is therefore sensitive to hepatic plasma flow, ligand-receptor affinity, and receptor concentration. In vivo demonstration of kinetic sensitivity permits delineation of the physiologic parameters that determine the biodistribution of a radiopharmaceutical. This delineation is a prerequisite to a valid analytic assessment of receptor biochemistry via kinetic modeling.« less

Nonlinear mechanics of thermoreversibly associating dendrimer glasses

NASA Astrophysics Data System (ADS)

Srikanth, Arvind; Hoy, Robert S.; Rinderspacher, Berend C.; Andzelm, Jan W.

2013-10-01

We model the mechanics of associating trivalent dendrimer network glasses with a focus on their energy dissipation properties. Various combinations of sticky bond (SB) strength and kinetics are employed. The toughness (work to fracture) of these systems displays a surprising deformation-protocol dependence; different association parameters optimize different properties. In particular, “strong, slow” SBs optimize strength, while “weak, fast” SBs optimize ductility via self-healing during deformation. We relate these observations to breaking, reformation, and partner switching of SBs during deformation. These studies point the way to creating associating-polymer network glasses with tailorable mechanical properties.

Improved accuracy and precision of tracer kinetic parameters by joint fitting to variable flip angle and dynamic contrast enhanced MRI data.

PubMed

Dickie, Ben R; Banerji, Anita; Kershaw, Lucy E; McPartlin, Andrew; Choudhury, Ananya; West, Catharine M; Rose, Chris J

2016-10-01

To improve the accuracy and precision of tracer kinetic model parameter estimates for use in dynamic contrast enhanced (DCE) MRI studies of solid tumors. Quantitative DCE-MRI requires an estimate of precontrast T1 , which is obtained prior to fitting a tracer kinetic model. As T1 mapping and tracer kinetic signal models are both a function of precontrast T1 it was hypothesized that its joint estimation would improve the accuracy and precision of both precontrast T1 and tracer kinetic model parameters. Accuracy and/or precision of two-compartment exchange model (2CXM) parameters were evaluated for standard and joint fitting methods in well-controlled synthetic data and for 36 bladder cancer patients. Methods were compared under a number of experimental conditions. In synthetic data, joint estimation led to statistically significant improvements in the accuracy of estimated parameters in 30 of 42 conditions (improvements between 1.8% and 49%). Reduced accuracy was observed in 7 of the remaining 12 conditions. Significant improvements in precision were observed in 35 of 42 conditions (between 4.7% and 50%). In clinical data, significant improvements in precision were observed in 18 of 21 conditions (between 4.6% and 38%). Accuracy and precision of DCE-MRI parameter estimates are improved when signal models are fit jointly rather than sequentially. Magn Reson Med 76:1270-1281, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Kinetics of laser irradiated nanoparticles cloud

NASA Astrophysics Data System (ADS)

Mishra, S. K.; Upadhyay Kahaly, M.; Misra, Shikha

2018-02-01

A comprehensive kinetic model describing the complex kinetics of a laser irradiated nanoparticle ensemble has been developed. The absorbed laser radiation here serves dual purpose, viz., photoenhanced thermionic emission via rise in its temperature and direct photoemission of electrons. On the basis of mean charge theory along with the equations for particle (electron) and energy flux balance over the nanoparticles, the transient processes of charge/temperature evolution over its surface and mass diminution on account of the sublimation (phase change) process have been elucidated. Using this formulation phenomenon of nanoparticle charging, its temperature rise to the sublimation point, mass ablation, and cloud disintegration have been investigated; afterwards, typical timescales of disintegration, sublimation and complete evaporation in reference to a graphite nanoparticle cloud (as an illustrative case) have been parametrically investigated. Based on a numerical analysis, an adequate parameter space describing the nanoparticle operation below the sublimation temperature, in terms of laser intensity, wavelength and nanoparticle material work function, has been identified. The cloud disintegration is found to be sensitive to the nanoparticle charging through photoemission; as a consequence, it illustrates that radiation operating below the photoemission threshold causes disintegration in the phase change state, while above the threshold, it occurs with the onset of surface heating.

Comparison of test particle acceleration in torsional spine and fan reconnection regimes

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

Hosseinpour, M., E-mail: hosseinpour@tabrizu.ac.ir; Mehdizade, M.; Mohammadi, M. A.

2014-10-15

Magnetic reconnection is a common phenomenon taking place in astrophysical and space plasmas, especially in solar flares which are rich sources of highly energetic particles. Torsional spine and fan reconnections are important mechanisms proposed for steady-state three-dimensional null-point reconnection. By using the magnetic and electric fields for these regimes, we numerically investigate the features of test particle acceleration in both regimes with input parameters for the solar corona. By comparison, torsional spine reconnection is found to be more efficient than torsional fan reconnection in an acceleration of a proton to a high kinetic energy. A proton can gain as highmore » as 100 MeV of relativistic kinetic energy within only a few milliseconds. Moreover, in torsional spine reconnection, an accelerated particle can escape either along the spine axis or on the fan plane depending on its injection position. However, in torsional fan reconnection, the particle is only allowed to accelerate along the spine axis. In addition, in both regimes, the particle's trajectory and final kinetic energy depend on the injection position but adopting either spatially uniform or non-uniform localized plasma resistivity does not much influence the features of trajectory.« less

Quantitative Kinetics Evaluation of Blocks Versus Granules of Biphasic Calcium Phosphate Scaffolds (HA/β-TCP 30/70) by Synchrotron Radiation X-ray Microtomography: A Human Study.

PubMed

Giuliani, Alessandra; Manescu, Adrian; Mohammadi, Sara; Mazzoni, Serena; Piattelli, Adriano; Mangano, Francesco; Iezzi, Giovanna; Mangano, Carlo

2016-02-01

Successful bone regeneration using both granules and blocks of biphasic calcium phosphate materials has been reported in the recent literature, in some clinical applications for maxillary sinus elevation, but the long-term kinetics of bone regeneration has still not been fully investigated. Twenty-four bilateral sinus augmentation procedures were performed and grafted with hydroxyapatite/β-tricalcium phosphate 30/70, 12 with granules and 12 with blocks. The samples were retrieved at different time points and were evaluated for bone regeneration, graft resorption, neovascularization, and morphometric parameters by computed microtomography and histology. A large amount of newly formed bone was detected in the retrieved specimens, together with a good rate of biomaterial resorption and the formation of a homogeneous and rich net of new vessels. The morphometric values were comparable at 5/6 months from grafting but, 9 months after grafting, revealed that the block-based specimens mimicked slightly better than granule-based samples the healthy native bone of the maxillary site. The scaffold morphology was confirmed to influence the long-term kinetics of bone regeneration.

Adsorption characteristics of (-)-epigallocatechin gallate and caffeine in the extract of waste tea on macroporous adsorption resins functionalized with chloromethyl, amino, and phenylamino groups.

PubMed

Liu, Yongfeng; Bai, Qingqing; Lou, Song; Di, Duolong; Li, Jintian; Guo, Mei

2012-02-15

According to the Friedel-Crafts and amination reaction, a series of macroporous adsorption resins (MARs) with novel structures were synthesized and identified by the Brunauer-Emmett-Teller (BET) method and Fourier transform infrared (FTIR) spectra, and corresponding adsorption behaviors for (-)-epigallocatechin gallate (EGCG) and caffeine (CAF) extracted from waste tea were systemically investigated. Based on evaluation of adsorption kinetics, the kinetic data were well fitted by pseudo-second-order kinetics. Langmuir, Freundlich, Temkin-Pyzhev, and Dubinin-Radushkevich isotherms were selected to illustrate the adsorption process of EGCG and CAF on the MARs. Thermodynamic parameters were adopted to explain in-depth information of inherent energetic changes associated with the adsorption process. The effect of temperature on EGCG and CAF adsorption by D101-3 was further expounded. Van der Waals force, hydrogen bonding, and electrostatic interaction were the main driving forces for the adsorption of EGCG and CAF on the MARs. This study might provide a scientific reference point to aid the industrial large-scale separation and enrichment of EGCG from the extracts of waste tea using modified MARs.

Estimation of kinetics parameters for the adsorption of human serum albumin onto hydroxyapatite-modified silver electrodes by piezoelectric quartz crystal impedance analysis.

PubMed

Tian, Lu; Wei, Wan-Zhi; Mao, You-An

2004-04-01

The adsorption of human serum albumin onto hydroxyapatite-modified silver electrodes has been in situ investigated by utilizing the piezoelectric quartz crystal impedance technique. The changes of equivalent circuit parameters were used to interpret the adsorption process. A kinetic model of two consecutive steps was derived to describe the process and compared with a first-order kinetic model by using residual analysis. The experimental data of frequency shift fitted to the model and kinetics parameters, k1, k2, psi1, psi2 and qr, were obtained. All fitted results were in reasonable agreement with the corresponding experimental results. Two adsorption constants (7.19 kJ mol(-1) and 22.89 kJ mol(-1)) were calculated according to the Arrhenius formula.

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.

Design requirements for ERD in diffusion-dominated media: how do injection interval, bioactive zones and reaction kinetics affect remediation performance?

NASA Astrophysics Data System (ADS)

Chambon, J.; Lemming, G.; Manoli, G.; Broholm, M. M.; Bjerg, P.; Binning, P. J.

2011-12-01

Enhanced Reductive Dechlorination (ERD) has been successfully used in high permeability media, such as sand aquifers, and is considered to be a promising technology for low permeability settings. Pilot and full-scale applications of ERD at several sites in Denmark have shown that the main challenge is to get contact between the injected bacteria and electron donor and the contaminants trapped in the low-permeability matrix. Sampling of intact cores from the low-permeability matrix has shown that the bioactive zones (where degradation occurs) are limited in the matrix, due to the slow diffusion transport processes, and this affects the timeframes for the remediation. Due to the limited ERD applications and the complex transport and reactive processes occurring in low-permeability media, design guidelines are currently not available for ERD in such settings, and remediation performance assessments are limited. The objective of this study is to combine existing knowledge from several sites with numerical modeling to assess the effect of the injection interval, development of bioactive zones and reaction kinetics on the remediation efficiency for ERD in diffusion-dominated media. A numerical model is developed to simulate ERD at a contaminated site, where the source area (mainly TCE) is located in a clayey till with fractures and interbedded sand lenses. Such contaminated sites are common in North America and Europe. Hydro-geological characterization provided information on geological heterogeneities and hydraulic parameters, which are relevant for clay till sites in general. The numerical model couples flow and transport in the fracture network and low-permeability matrix. Sequential degradation of TCE to ethene is modeled using Monod kinetics, and the kinetic parameters are obtained from laboratory experiments. The influence of the reaction kinetics on remediation efficiency is assessed by varying the biomass concentration of the specific degraders. The injected reactants (donor and bacteria) are assumed to spread in horizontal injection zones of various widths, depending on the development of bioactive zones. These injection zones are spaced at various intervals over depth, corresponding to the injection interval chosen. The results from the numerical model show that remediation timeframes can be reduced significantly by using closely spaced injection intervals and by ensuring the efficient spreading of the reactants into the clay till matrix. In contrast the reaction kinetics affect mass removal only up to a point where diffusive transport becomes limiting. Based on these results, guidelines on when ERD can be an effective remediation strategy in practice are provided. These take the form of dimensionless groupings (such as the Damkohler number), which combine site specific (physical and biogeochemical) and design parameters, and graphs showing how the main parameters affect remediation timeframes. Finally it is shown how model results can be used as input to other decision making tools such as life cycle assessment to guide remedial choices.

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...

Multisubstrate biodegradation kinetics of naphthalene, phenanthrene, and pyrene mixtures

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

Guha, S.; Peters, C.A.; Jaffe, P.R.

Biodegradation kinetics of naphthalene, phenanthrene and pyrene were studied in sole-substrate systems, and in binary and ternary mixtures to examine substrate interactions. The experiments were conducted in aerobic batch aqueous systems inoculated with a mixed culture that had been isolated from soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Monod kinetic parameters and yield coefficients for the individual parameters and yield coefficients for the individual compounds were estimated from substrate depletion and CO{sub 2} evolution rate data in sole-substrate experiments. In all three binary mixture experiments, biodegradation kinetics were comparable to the sole-substrate kinetics. In the ternary mixture, biodegradation of naphthalenemore » was inhibited and the biodegradation rates of phenanthrene and pyrene were enhanced. A multisubstrate form of the Monod kinetic model was found to adequately predict substrate interactions in the binary and ternary mixtures using only the parameters derived from sole-substrate experiments. Numerical simulations of biomass growth kinetics explain the observed range of behaviors in PAH mixtures. In general, the biodegradation rates of the more degradable and abundant compounds are reduced due to competitive inhibition, but enhanced biodegradation of the more recalcitrant PAHs occurs due to simultaneous biomass growth on multiple substrates. In PAH-contaminated environments, substrate interactions may be very large due to additive effects from the large number of compounds present.« less

Study of temperature, air dew point temperature and reactant flow effects on proton exchange membrane fuel cell performances using electrochemical spectroscopy and voltammetry techniques

NASA Astrophysics Data System (ADS)

Wasterlain, S.; Candusso, D.; Hissel, D.; Harel, F.; Bergman, P.; Menard, P.; Anwar, M.

A single PEMFC has been operated by varying the assembly temperature, the air dew point temperature and the anode/cathode stoichiometry rates with the aim to identify the parameters and combinations of factors affecting the cell performance. Some of the experiments were conducted with low humidified reactants (relative humidity of 12%). The FC characterizations tests have been conducted using in situ electrochemical methods based on load current and cell voltage signal analysis, namely: polarization curves, EIS measurements, cyclic and linear sweep voltammetries (CV and LSV). The impacts of the parameters on the global FC performances were observed using the polarization curves whereas EIS, CV and LSV test results were used to discriminate the different voltage loss sources. The test results suggest that some parameter sets allow maximal output voltages but can also induce material degradation. For instance, higher FC temperature and air flow values can induce significant electrical efficiency benefits, notably by increasing the reversible potential and the reaction kinetics. However, raising the cell temperature can also gradually dry the FC and increase the risk of membrane failure. LSV has also shown that elevated FC temperature and relative humidity can also accelerate the electrolyte degradation (i.e. slightly higher fuel crossover rate) and reduce the lifetime consequently.

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

NASA Astrophysics Data System (ADS)

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

2017-03-01

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

Kinetic studies of chemical shrinkage and residual stress formation in thermoset epoxy adhesives under confined curing conditions

NASA Astrophysics Data System (ADS)

Schumann, M.; Geiß, P. L.

2015-05-01

Faultless processing of thermoset polymers in demanding applications requires a profound mastering of the curing kinetics considering both the physico-chemical changes in the transition from the liquid to the solid state and the consolidation of the polymers network in the diffusion controlled curing regime past the gel point. Especially in adhesive joints shrinkage stress occurring at an early state of the curing process under confined conditions is likely to cause defects due to local debonding and thus reduce their strength and durability1. Rheometry is considered the method of choice to investigate the change of elastic and viscous properties in the progress of curing. Drawbacks however relate to experimental challenges in accessing the full range of kinetic parameters of thermoset resins with low initial viscosity from the very beginning of the curing reaction to the post-cure consolidation of the polymer due to the formation of secondary chemical bonds. Therefore the scope of this study was to interrelate rheological data with results from in-situ measurements of the shrinkage stress formation in adhesive joints and with the change of refractive index in the progress of curing. This combination of different methods has shown to be valuable in gaining advanced insight into the kinetics of the curing reaction. The experimental results are based on a multi component thermoset epoxy-amine adhesive.

Sorption of albendazole in sediments and soils: Isotherms and kinetics.

PubMed

Mutavdžić Pavlović, Dragana; Glavač, Antonija; Gluhak, Mihaela; Runje, Mislav

2018-02-01

Albendazole is a broad-spectrum anthelmintic drug effective against gastrointestinal parasites in humans and animals. Despite the fact that it has been detected in environment (water, sediment and soil), there is no information on its fate in the environment. So, in order to understand the sorption process of albendazole in environment, the sorption mechanism and kinetic properties were investigated through sorption equilibrium and sorption rate experiments. For that purpose, batch sorption of albendazole on five sediment samples and five soil samples from Croatia's region with different physico-chemical properties was investigated. Except physico-chemical properties of used environmental solid samples, the effects of various parameters such as contact time, initial concentration, ionic strength and pH on the albendazole sorption were studied. The K d parameter from linear sorption model was determined by linear regression analysis, while the Freundlich and Langmuir sorption models were applied to describe the equilibrium isotherms. The estimated K d values varied from 29.438 to 104.43 mLg -1 at 0.01 M CaCl 2 and for natural pH value of albendazole solution (pH 6.6). Experimental data showed that the best agreement was obtained with the linear model (R 2  > 0.99), while the rate of albendazole sorption is the best described with the kinetic model of pseudo-second-order. Obtained results point to a medium or even strong sorption of albendazole for soil or sediment particles, which is particularly dependent on the proportion of organic matter, pH, copper and zinc in them. Copyright © 2017 Elsevier Ltd. All rights reserved.

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.

PubMed

Schillings, Claudia; Sunnåker, Mikael; Stelling, Jörg; Schwab, Christoph

2015-08-01

Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is "non-intrusive" and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design.

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks

PubMed Central

Schillings, Claudia; Sunnåker, Mikael; Stelling, Jörg; Schwab, Christoph

2015-01-01

Parametric uncertainty is a particularly challenging and relevant aspect of systems analysis in domains such as systems biology where, both for inference and for assessing prediction uncertainties, it is essential to characterize the system behavior globally in the parameter space. However, current methods based on local approximations or on Monte-Carlo sampling cope only insufficiently with high-dimensional parameter spaces associated with complex network models. Here, we propose an alternative deterministic methodology that relies on sparse polynomial approximations. We propose a deterministic computational interpolation scheme which identifies most significant expansion coefficients adaptively. We present its performance in kinetic model equations from computational systems biology with several hundred parameters and state variables, leading to numerical approximations of the parametric solution on the entire parameter space. The scheme is based on adaptive Smolyak interpolation of the parametric solution at judiciously and adaptively chosen points in parameter space. As Monte-Carlo sampling, it is “non-intrusive” and well-suited for massively parallel implementation, but affords higher convergence rates. This opens up new avenues for large-scale dynamic network analysis by enabling scaling for many applications, including parameter estimation, uncertainty quantification, and systems design. PMID:26317784

Kinetics of Mixed Microbial Assemblages Enhance Removal of Highly Dilute Organic Substrates

PubMed Central

Lewis, David L.; Hodson, Robert E.; Hwang, Huey-Min

1988-01-01

Our experiments with selected organic substrates reveal that the rate-limiting process governing microbial degradation rates changes with substrate concentration, S, in such a manner that substrate removal is enhanced at lower values of S. This enhancement is the result of the dominance of very efficient systems for substrate removal at low substrate concentrations. The variability of dominant kinetic parameters over a range of S causes the kinetics of complex assemblages to be profoundly dissimilar to those of systems possessing a single set of kinetic parameters; these findings necessitate taking a new approach to predicting substrate removal rates over wide ranges of S. PMID:16347715

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

PubMed Central

Liebermeister, Wolfram; Klipp, Edda

2006-01-01

Background Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. Results We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. Conclusion Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases. PMID:17173669

OFF-DESIGN PERFORMANCE OF RADIAL INFLOW TURBINES

NASA Technical Reports Server (NTRS)

Wasserbauer, C. A.

1994-01-01

This program calculates off design performance of radial inflow turbines. The program uses a one dimensional solution of flow conditions through the turbine along the main streamline. The loss model accounts for stator, rotor, incidence, and exit losses. Program features include consideration of stator and rotor trailing edge blockage and computation of performance to limiting load. Stator loss (loss in kinetic energy across the stator) is proportional to the average kinetic energy in the blade row and is represented in the program by an equation which includes a stator loss coefficient determined from design point performance and then assumed to be constant for the off design calculations. Minimum incidence loss does not occur at zero incidence angle with respect to the rotor blade, but at some optimum flow angle. At high pressure ratios the level of rotor inlet velocity seemed to have an excessive influence on the loss. Using the component of velocity in the direction of the optimum flow angle gave better correlations with experimental results. Overall turbine geometry and design point values of efficiency, pressure ratio, and mass flow are needed as input information. The output includes performance and velocity diagram parameters for any number of given speeds over a range of turbine pressure ratio. The program has been implemented on the IBM 7094 and operates in batch mode.

Kinetics of nickel electrodeposition from low electrolyte concentration and at a narrow interelectrode gap

NASA Astrophysics Data System (ADS)

Widayatno, Tri

2015-12-01

Electrodeposition of nickel onto copper in a system of low Ni2+ concentration and at a narrow interelectrode gap has been carried out. This electrochemical system was required for maskless pattern transfer through electroplating (Enface technique). Kinetics of Electrochemical reaction of Nickel is relatively slow, where such electrochemical system has never been used in this technology. Study on the kinetics of the electrochemical reaction of nickel in such system is essential due to the fact that the quality of an electrodeposited nickel is affected by kinetics. Analytical and graphical methods were utilised to determine kinetic parameters. The kinetic model was approximated by Butler-Volmer and j-η equation. Kinetic parameters such as exchange current density (j0) and charge transfer coefficient (α) were also graphically determined using the plot of η vs. log|j| known as Tafel plot. The polarisation data for an unstirred 0.19 M nickel sulfamate solution at 0.5 mV/s scan rate and RDE system was used. The results indicate that both methods are fairly accurate. For the analytical, the Tafel slope, the exchange current density, and charge transfer coefficient were found to be 149 mV/dec, 1.60 × 10-4 mA/cm2, and 0.39 respectively, whilst for the graphical method were 159 mV/dec, 3.16 × 10-4 mA/cm2, and 0.37. The kinetics parameters in this current study were also compared to those in literature. Significant differences were observed which might be due to the effect of composition and concentration of the electrolytes, operating temperature, and pH leading to the different reaction mechanism. However, the results obtained in this work are in the range of acceptable values. These kinetic parameters will then be used in further study of nickel deposition by modelling and simulation

Simultaneous versus sequential optimal experiment design for the identification of multi-parameter microbial growth kinetics as a function of temperature.

PubMed

Van Derlinden, E; Bernaerts, K; Van Impe, J F

2010-05-21

Optimal experiment design for parameter estimation (OED/PE) has become a popular tool for efficient and accurate estimation of kinetic model parameters. When the kinetic model under study encloses multiple parameters, different optimization strategies can be constructed. The most straightforward approach is to estimate all parameters simultaneously from one optimal experiment (single OED/PE strategy). However, due to the complexity of the optimization problem or the stringent limitations on the system's dynamics, the experimental information can be limited and parameter estimation convergence problems can arise. As an alternative, we propose to reduce the optimization problem to a series of two-parameter estimation problems, i.e., an optimal experiment is designed for a combination of two parameters while presuming the other parameters known. Two different approaches can be followed: (i) all two-parameter optimal experiments are designed based on identical initial parameter estimates and parameters are estimated simultaneously from all resulting experimental data (global OED/PE strategy), and (ii) optimal experiments are calculated and implemented sequentially whereby the parameter values are updated intermediately (sequential OED/PE strategy). This work exploits OED/PE for the identification of the Cardinal Temperature Model with Inflection (CTMI) (Rosso et al., 1993). This kinetic model describes the effect of temperature on the microbial growth rate and encloses four parameters. The three OED/PE strategies are considered and the impact of the OED/PE design strategy on the accuracy of the CTMI parameter estimation is evaluated. Based on a simulation study, it is observed that the parameter values derived from the sequential approach deviate more from the true parameters than the single and global strategy estimates. The single and global OED/PE strategies are further compared based on experimental data obtained from design implementation in a bioreactor. Comparable estimates are obtained, but global OED/PE estimates are, in general, more accurate and reliable. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

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

A Study of the Optimal Model of the Flotation Kinetics of Copper Slag from Copper Mine BOR

NASA Astrophysics Data System (ADS)

Stanojlović, Rodoljub D.; Sokolović, Jovica M.

2014-10-01

In this study the effect of mixtures of copper slag and flotation tailings from copper mine Bor, Serbia on the flotation results of copper recovery and flotation kinetics parameters in a batch flotation cell has been investigated. By simultaneous adding old flotation tailings in the ball mill at the rate of 9%, it is possible to increase copper recovery for about 20%. These results are compared with obtained copper recovery of pure copper slag. The results of batch flotation test were fitted by MatLab software for modeling the first-order flotation kinetics in order to determine kinetics parameters and define an optimal model of the flotation kinetics. Six kinetic models are tested on the batch flotation copper recovery against flotation time. All models showed good correlation, however the modified Kelsall model provided the best fit.

Virus Neutralisation: New Insights from Kinetic Neutralisation Curves

PubMed Central

Magnus, Carsten

2013-01-01

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

Effects of time-temperature profiles on glow curves of germanium-doped optical fibre

NASA Astrophysics Data System (ADS)

Lam, S. E.; Alawiah, A.; Bradley, D. A.; Mohd Noor, N.

2017-08-01

The Germanium (Ge) doped silica optical fibres have demonstrated the great potential to be developed as a thermoluminescent (TL) dosimeter that can be used in various applications in radiotherapy, diagnostic radiology, UV dosimetry system and food irradiation industry. Different time-temperature profile (TTP) parameters of the TL reader have been employed by many researchers in various of TL studies. Nevertheless, none of those studies adequately addressed the effects of the reader's preheat temperature and heating rate on the kinetic parameters of the TL glow curve specifically, the Ge-doped silica optical fibres. This research addresses the issue of TTP parameters with special attention to the determination of the kinetic parameters of the glow curve. The glow curve responses were explored and the kinetic parameters were analyzed by the WinGCF software, to show the effect of the preheat temperature and heating rate of the reader on Ge-doped fibre irradiated with 18 Gy of 6 MV photons radiation. The effect of TTP parameters was discussed and compared against the commercial fibre and tailored made fibre of 6 mol% Ge-doped of flat and cylindrical shape. The deconvolution of glow peaks and the kinetic parameters were obtained by the WinGCF software. This enables to fit accurately (1.5%

Flux estimation of the FIFE planetary boundary layer (PBL) with 10.6 micron Doppler lidar

NASA Technical Reports Server (NTRS)

Gal-Chen, Tzvi; Xu, Mei; Eberhard, Wynn

1990-01-01

A method is devised for calculating wind, momentum, and other flux parameters that characterize the planetary boundary layer (PBL) and thereby facilitate the calibration of spaceborne vs. in situ flux estimates. Single Doppler lidar data are used to estimate the variance of the mean wind and the covariance related to the vertically pointing fluxes of horizontal momentum. The skewness of the vertical velocity and the range of kinetic energy dissipation are also estimated, and the surface heat flux is determined by means of a statistical Navier-Stokes equation. The conclusion shows that the PBL structure combines both 'bottom-up' and 'top-down' processes suggesting that the relevant parameters for the atmospheric boundary layer be revised. The conclusions are of significant interest to the modeling techniques used in General Circulation Models as well as to flux estimation.

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.

Nonlinear Acoustical Assessment of Precipitate Nucleation

NASA Technical Reports Server (NTRS)

Cantrell, John H.; Yost, William T.

2004-01-01

The purpose of the present work is to show that measurements of the acoustic nonlinearity parameter in heat treatable alloys as a function of heat treatment time can provide quantitative information about the kinetics of precipitate nucleation and growth in such alloys. Generally, information on the kinetics of phase transformations is obtained from time-sequenced electron microscopical examination and differential scanning microcalorimetry. The present nonlinear acoustical assessment of precipitation kinetics is based on the development of a multiparameter analytical model of the effects on the nonlinearity parameter of precipitate nucleation and growth in the alloy system. A nonlinear curve fit of the model equation to the experimental data is then used to extract the kinetic parameters related to the nucleation and growth of the targeted precipitate. The analytical model and curve fit is applied to the assessment of S' precipitation in aluminum alloy 2024 during artificial aging from the T4 to the T6 temper.

The usefulness of cytogenetic parameters, level of p53 protein and endogenous glutathione as intermediate end-points in raw betel-nut genotoxicity.

PubMed

Kumpawat, K; Chatterjee, A

2003-07-01

Betel-nut (BN) chewing related oral mucosal lesions are potential hazards to a large population worldwide. Genotoxicity of betel alkaloids, polyphenol and tannin fractions have been reported. It has been shown earlier that BN ingredients altered the level of endogenous glutathione (GSH) which could modulate the host susceptibility to the action of other chemical carcinogens. The north-east Indian variety of BN, locally known as 'kwai', is raw, wet and consumed unprocessed with betel-leaf and slaked lime and contains higher alkaloids, polyphenol and tannins as compared to the dried one. Therefore, the purpose of this study was to investigate the extent of DNA damage, pattern of cell kinetics, the level of p53-protein and endogenous GSH in kwai chewers in the tribal population of Meghalaya state in the northeastern region of India with an aim to see whether these end-points could serve as biomarkers of genetic damage of relevance for genotoxic/carcinogenic process. The present data show higher DNA damage, delay in cell kinetics, p53 expression and lower GSH-level in heavy chewers (HC) than nonchewers (NC). The influence of bleomycin (BLM) on chromatid break induction in G2-phase of peripheral blood lymphocytes in NC and HC has been analysed to determine individual susceptibility to carcinogenic assaults. HC showed higher induction of chromatid breaks than NC. Risk assessment in this study suggests an interaction between carcinogen exposure and mutagen sensitivity measures, risk estimates being higher in those individuals who both consume kwai and express sensitivity to free radical oxygen damage in vitro. From this study it seems that besides cytogenetical parameters, the level of endogenous GSH and the level of p53 protein could act as effective biomarkers for kwai chewers.

Performance of U3Si2 Fuel in a Reactivity Insertion Accident

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

Cheng, Lap Y.; Cuadra, Arantxa; Todosow, Michael

In this study we examined the performance of the U3Si2 fuel cladded with Zircaloy (Zr) in a reactivity insertion accident (RIA) in a PWR core. The power excursion as a result of a $1 reactivity insertion was calculated by a TRACE PWR plant model using point-kinetics, for alternative cores with UO2 and U3Si2 fuel assemblies. The point-kinetics parameters (feedback coefficients, prompt-neutron lifetime and group constants for six delayed-neutron groups) were obtained from beginning-of-cycle equilibrium full core calculations with PARCS. In the PARCS core calculations, the few-group parameters were developed utilizing the TRITON/NEWT tools in the SCALE package. In order tomore » assess the fuel response in finer detail (e.g. the maximum fuel temperature) the power shape and thermal boundary conditions from the TRACE/PARCS calculations were used to drive a BISON model of a fuel pin with U3Si2 and UO2 respectively. For a $1 reactivity transient both TRACE and BISON predicted a higher maximum fuel temperature for the UO2 fuel than the U3Si2 fuel. Furthermore, BISON is noted to calculate a narrower gap and a higher gap heat transfer coefficient than TRACE. This resulted in BISON predicting consistently lower fuel temperatures than TRACE. This study also provides a systematic comparison between TRACE and BISON using consistent transient boundary conditions. The TRACE analysis of the RIA only reflects the core-wide response in power. A refinement to the analysis would be to predict the local peaking in a three-dimensional core as a result of control rod ejection.« less

Usefulness of CA125 and their kinetic parameters and positron emission tomography/computed tomography (PET/CT) with fluorodeoxyglucose ([18F] FDG) in the detection of recurrent ovarian cancer levels.

PubMed

Palomar Muñoz, Azahara; Cordero García, José Manuel; Talavera Rubio, Prado; García Vicente, Ana M; González García, Beatriz; Bellón Guardia, María Emiliana; Soriano Castrejón, Ángel; Aranda Aguilar, Enrique

2017-12-21

To assess the usefulness of cancer antigen 125 (CA125) serum levels and kinetic values, velocity (CA125vel) and doubling time (CA125dt), as well as fluorodeoxyglucose ([ 18 F]FDG) positron emission tomography/computed tomography (PET/CT), in the detection of ovarian cancer recurrence. To assess the optimal cut-off for CA125, CA125vel and CA125dt to detect relapse with [ 18 F]FDG-PET/CT. A retrospective analysis was performed of 59 [ 18 F]FDG-PET/CT (48 patients) for suspected recurrence of ovarian cancer. Receiver operating characteristic (ROC) curves were plotted and area-under-the curve (AUC) statistics were computed for CA125, CA125vel and CA125dt. The results obtained in the group with normal and high (>35U/ml) CA125 levels were compared. Forty-four cases of recurrence were diagnosed (7 had CA125 ≤35U/ml), whereas 15 showed no disease. All of them were correctly catalogued by PET/CT. In ROC analysis, the discriminatory power of CA125 was relatively high (AUC 0.835) and the optimal cut-off point to reflect active disease was 23.9U/ml. The ROC analyses for the CA125vel and CA125dt showed an AUC of 0.849 and 0.728, respectively, with an optimal cut-off point of 1.96U/ml/month and 0.76 months, respectively. In patients with normal CA125 and recurrence of ovarian cancer, the CA125vel was significantly higher than in patients without recurrence (p=0.029). [ 18 F]FDG-PET/CT is more accurate than CA125 parameters in the detection of ovarian cancer recurrence. CA125 serum levels are essential; nevertheless, CA125 kinetic values must be considered to detect relapse. Particularly in patients with CA125 within normal values, in which a higher CA125vel is indicative of recurrence. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

Compartmental analysis of [11C]flumazenil kinetics for the estimation of ligand transport rate and receptor distribution using positron emission tomography.

PubMed

Koeppe, R A; Holthoff, V A; Frey, K A; Kilbourn, M R; Kuhl, D E

1991-09-01

The in vivo kinetic behavior of [11C]flumazenil ([11C]FMZ), a non-subtype-specific central benzodiazepine antagonist, is characterized using compartmental analysis with the aim of producing an optimized data acquisition protocol and tracer kinetic model configuration for the assessment of [11C]FMZ binding to benzodiazepine receptors (BZRs) in human brain. The approach presented is simple, requiring only a single radioligand injection. Dynamic positron emission tomography data were acquired on 18 normal volunteers using a 60- to 90-min sequence of scans and were analyzed with model configurations that included a three-compartment, four-parameter model, a three-compartment, three-parameter model, with a fixed value for free plus nonspecific binding; and a two-compartment, two-parameter model. Statistical analysis indicated that a four-parameter model did not yield significantly better fits than a three-parameter model. Goodness of fit was improved for three- versus two-parameter configurations in regions with low receptor density, but not in regions with moderate to high receptor density. Thus, a two-compartment, two-parameter configuration was found to adequately describe the kinetic behavior of [11C]FMZ in human brain, with stable estimates of the model parameters obtainable from as little as 20-30 min of data. Pixel-by-pixel analysis yields functional images of transport rate (K1) and ligand distribution volume (DV"), and thus provides independent estimates of ligand delivery and BZR binding.

Kinetics of hydrogen peroxide decomposition by catalase: hydroxylic solvent effects.

PubMed

Raducan, Adina; Cantemir, Anca Ruxandra; Puiu, Mihaela; Oancea, Dumitru

2012-11-01

The effect of water-alcohol (methanol, ethanol, propan-1-ol, propan-2-ol, ethane-1,2-diol and propane-1,2,3-triol) binary mixtures on the kinetics of hydrogen peroxide decomposition in the presence of bovine liver catalase is investigated. In all solvents, the activity of catalase is smaller than in water. The results are discussed on the basis of a simple kinetic model. The kinetic constants for product formation through enzyme-substrate complex decomposition and for inactivation of catalase are estimated. The organic solvents are characterized by several physical properties: dielectric constant (D), hydrophobicity (log P), concentration of hydroxyl groups ([OH]), polarizability (α), Kamlet-Taft parameter (β) and Kosower parameter (Z). The relationships between the initial rate, kinetic constants and medium properties are analyzed by linear and multiple linear regression.

Linear and non-linear regression analysis for the sorption kinetics of methylene blue onto activated carbon.

PubMed

Kumar, K Vasanth

2006-10-11

Batch kinetic experiments were carried out for the sorption of methylene blue onto activated carbon. The experimental kinetics were fitted to the pseudo first-order and pseudo second-order kinetics by linear and a non-linear method. The five different types of Ho pseudo second-order expression have been discussed. A comparison of linear least-squares method and a trial and error non-linear method of estimating the pseudo second-order rate kinetic parameters were examined. The sorption process was found to follow a both pseudo first-order kinetic and pseudo second-order kinetic model. Present investigation showed that it is inappropriate to use a type 1 and type pseudo second-order expressions as proposed by Ho and Blanachard et al. respectively for predicting the kinetic rate constants and the initial sorption rate for the studied system. Three correct possible alternate linear expressions (type 2 to type 4) to better predict the initial sorption rate and kinetic rate constants for the studied system (methylene blue/activated carbon) was proposed. Linear method was found to check only the hypothesis instead of verifying the kinetic model. Non-linear regression method was found to be the more appropriate method to determine the rate kinetic parameters.

Evanescent field microscopy techniques for studying dynamics at the surface of living cells

NASA Astrophysics Data System (ADS)

Sund, Susan E.

This thesis presents two distinct optical microscopy techniques for applications in cell biophysics: (a)the extension to living cells of an established technique, total internal reflection/fluorescence recovery after photobleaching (TIR/FRAP) for the first time in imaging mode; and (b)the novel development of polarized total internal reflection fluorescence (p- TIRF) to study membrane orientation in living cells. Although reversible chemistry is crucial to dynamical processes in living cells, relatively little is known about the relevant chemical kinetic rates in vivo. TIR/FRAP, an established technique which can measure reversible biomolecular kinetic rates at surfaces, is extended here to measure kinetic parameters of microinjected rhodamine actin at the cytofacial surface of the plasma membrane of living cultured smooth muscle cells. For the first time, spatial imaging (with a CCD camera) is used in conjunction with TIR/FRAP. TIR/FRAP imaging allows production of spatially resolved images of kinetic data, and calculation of correlation distances, cell-wide gradients, and kinetic parameter dependence on initial fluorescence intensity. In living cells, membrane curvature occurs both in easily imaged large scale morphological features, and also in less visualizable submicroscopic regions of activity such as endocytosis, exocytosis, and cell surface ruffling. A fluorescence microscopic method, p-TIRF, is introduced here to visualize such regions. The method is based on fluorescence of the oriented membrane probe diI- C18-(3) (diI) excited by evanescent field light polarized either perpendicular or parallel to the plane of the substrate coverslip. The excitation efficiency from each polarization depends on the membrane orientation, and thus the ratio of the observed fluorescence excited by these two polarizations vividly shows regions of microscopic and submicroscopic curvature of the membrane. A theoretical background of the technique and experimental verifications are presented in samples of protein solutions, model lipid bilayers, and living cells. Sequential digital images of the polarized TIR fluorescence ratios show spatially-resolved time- course maps of membrane orientations on diI labeled macrophages from which low visibility membrane structures can be identified and quantified. The TIR images are sharpened and contrast-enhanced by deconvoluting them with an experimentally-measured point spread function.

VO2 Off Transient Kinetics in Extreme Intensity Swimming.

PubMed

Sousa, Ana; Figueiredo, Pedro; Keskinen, Kari L; Rodríguez, Ferran A; Machado, Leandro; Vilas-Boas, João P; Fernandes, Ricardo J

2011-01-01

Inconsistencies about dynamic asymmetry between the on- and off- transient responses in oxygen uptake are found in the literature. Therefore, the purpose of this study was to characterize the oxygen uptake off-transient kinetics during a maximal 200-m front crawl effort, as examining the degree to which the on/off regularity of the oxygen uptake kinetics response was preserved. Eight high level male swimmers performed a 200-m front crawl at maximal speed during which oxygen uptake was directly measured through breath-by-breath oxymetry (averaged every 5 s). This apparatus was connected to the swimmer by a low hydrodynamic resistance respiratory snorkel and valve system. The on- and off-transient phases were symmetrical in shape (mirror image) once they were adequately fitted by a single-exponential regression models, and no slow component for the oxygen uptake response was developed. Mean (± SD) peak oxygen uptake was 69.0 (± 6.3) mL·kg(-1)·min(-1), significantly correlated with time constant of the off- transient period (r = 0.76, p < 0.05) but not with any of the other oxygen off-transient kinetic parameters studied. A direct relationship between time constant of the off-transient period and mean swimming speed of the 200-m (r = 0.77, p < 0.05), and with the amplitude of the fast component of the effort period (r = 0.72, p < 0.05) were observed. The mean amplitude and time constant of the off-transient period values were significantly greater than the respective on- transient. In conclusion, although an asymmetry between the on- and off kinetic parameters was verified, both the 200-m effort and the respectively recovery period were better characterized by a single exponential regression model. Key pointsThe VO2 slow component was not observed in the recovery period of swimming extreme efforts;The on and off transient periods were better fitted by a single exponential function, and so, these effort and recovery periods of swimming extreme efforts are symmetrical;The rate of VO2 decline during the recovery period may be due to not only the magnitude of oxygen debt but also the VO2peak obtained during the effort period.

Actin dynamics at the living cell submembrane imaged by total internal reflection fluorescence photobleaching.

PubMed Central

Sund, S E; Axelrod, D

2000-01-01

Although reversible chemistry is crucial to dynamical processes in living cells, relatively little is known about relevant chemical kinetic rates in vivo. Total internal reflection/fluorescence recovery after photobleaching (TIR/FRAP), an established technique previously demonstrated to measure reversible biomolecular kinetic rates at surfaces in vitro, is extended here to measure reversible biomolecular kinetic rates of actin at the cytofacial (subplasma membrane) surface of living cells. For the first time, spatial imaging (with a charge-coupled device camera) is used in conjunction with TIR/FRAP. TIR/FRAP imaging produces both spatial maps of kinetic parameters (off-rates and mobile fractions) and estimates of kinetic correlation distances, cell-wide kinetic gradients, and dependences of kinetic parameters on initial fluorescence intensity. For microinjected rhodamine actin in living cultured smooth muscle (BC3H1) cells, the unbinding rate at or near the cytofacial surface of the plasma membrane (averaged over the entire cell) is measured at 0.032 +/- 0.007 s(-1). The corresponding rate for actin marked by microinjected rhodamine phalloidin is very similar, 0.033 +/- 0.013 s(-1), suggesting that TIR/FRAP is reporting the dynamics of entire filaments or protofilaments. For submembrane fluorescence-marked actin, the intensity, off-rate, and mobile fraction show a positive correlation over a characteristic distance of 1-3 microm and a negative correlation over larger distances greater than approximately 7-14 microm. Furthermore, the kinetic parameters display a statistically significant cell-wide gradient, with the cell having a "fast" and "slow" end with respect to actin kinetics. PMID:10969025

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.

Estimation of fundamental kinetic parameters of polyhydroxybutyrate fermentation process of Azohydromonas australica using statistical approach of media optimization.

PubMed

Gahlawat, Geeta; Srivastava, Ashok K

2012-11-01

Polyhydroxybutyrate or PHB is a biodegradable and biocompatible thermoplastic with many interesting applications in medicine, food packaging, and tissue engineering materials. The present study deals with the enhanced production of PHB by Azohydromonas australica using sucrose and the estimation of fundamental kinetic parameters of PHB fermentation process. The preliminary culture growth inhibition studies were followed by statistical optimization of medium recipe using response surface methodology to increase the PHB production. Later on batch cultivation in a 7-L bioreactor was attempted using optimum concentration of medium components (process variables) obtained from statistical design to identify the batch growth and product kinetics parameters of PHB fermentation. A. australica exhibited a maximum biomass and PHB concentration of 8.71 and 6.24 g/L, respectively in bioreactor with an overall PHB production rate of 0.75 g/h. Bioreactor cultivation studies demonstrated that the specific biomass and PHB yield on sucrose was 0.37 and 0.29 g/g, respectively. The kinetic parameters obtained in the present investigation would be used in the development of a batch kinetic mathematical model for PHB production which will serve as launching pad for further process optimization studies, e.g., design of several bioreactor cultivation strategies to further enhance the biopolymer production.

Kinetics and mechanisms of thiol-disulfide exchange covering direct substitution and thiol oxidation-mediated pathways.

PubMed

Nagy, Péter

2013-05-01

Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol-disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. This review is focused on the kinetics and mechanisms of thiol-disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery.

Identification of the most sensitive parameters in the activated sludge model implemented in BioWin software.

PubMed

Liwarska-Bizukojc, Ewa; Biernacki, Rafal

2010-10-01

In order to simulate biological wastewater treatment processes, data concerning wastewater and sludge composition, process kinetics and stoichiometry are required. Selection of the most sensitive parameters is an important step of model calibration. The aim of this work is to verify the predictability of the activated sludge model, which is implemented in BioWin software, and select its most influential kinetic and stoichiometric parameters with the help of sensitivity analysis approach. Two different measures of sensitivity are applied: the normalised sensitivity coefficient (S(i,j)) and the mean square sensitivity measure (delta(j)(msqr)). It occurs that 17 kinetic and stoichiometric parameters of the BioWin activated sludge (AS) model can be regarded as influential on the basis of S(i,j) calculations. Half of the influential parameters are associated with growth and decay of phosphorus accumulating organisms (PAOs). The identification of the set of the most sensitive parameters should support the users of this model and initiate the elaboration of determination procedures for the parameters, for which it has not been done yet. Copyright 2010 Elsevier Ltd. All rights reserved.

Antioxidant pool in beer and kinetics of EPR spin-trapping.

PubMed

Kocherginsky, Nikolai M; Kostetski, Yuri Yu; Smirnov, Alex I

2005-08-24

The kinetics of spin-trap adduct formation in beer oxidation exhibits an induction period if the reaction is carried out at elevated temperatures and in the presence of air. This lag period lasts until the endogenous antioxidants are almost completely depleted, and its duration is used as an indicator of the flavor stability and shelf life of beer. This paper demonstrates that the total kinetics of the process can be characterized by three parameters-the lag period, the rate of spin-trap adduct formation, and, finally, the steady-state spin-adduct concentration. A steady-state chain reaction mechanism is described, and quantitative estimates of the main kinetic parameters such as the initiation rate, antioxidant pool, effective content of organic molecules participating in the chain reactions, and the rate constant of the 1-hydroxyethyl radical EtOH(*) spin-adduct disappearance are given. An additional new dimensionless parameter is suggested to characterize the antioxidant pool-the product of the lag time and the rate of spin-trap radical formation immediately after the lag time, normalized by the steady-state concentration of the adducts. The results of spin-tapping EPR experiments are compared with the nitroxide reduction kinetics measured in the same beer samples. It is shown that although the kinetics of nitroxide reduction in beer can be used to evaluate the reducing power of beer, the latter parameter does not correlate with the antioxidant pool. The relationship of free radical processes, antioxidant pool, reducing power, and beer staling is discussed.

Thermodynamic, Kinetic, and Equilibrium Parameters for the Removal of Lead and Cadmium from Aqueous Solutions with Calcium Alginate Beads

PubMed Central

Alfaro-Cuevas-Villanueva, Ruth; Hidalgo-Vázquez, Aura Roxana; Cortés Penagos, Consuelo de Jesús; Cortés-Martínez, Raúl

2014-01-01

The sorption of cadmium (Cd) and lead (Pb) by calcium alginate beads (CAB) from aqueous solutions in batch systems was investigated. The kinetic and thermodynamic parameters, as well as the sorption capacities of CAB in each system at different temperatures, were evaluated. The rate of sorption for both metals was rapid in the first 10 minutes and reached a maximum in 50 minutes. Sorption kinetic data were fitted to Lagergren, pseudo-second-order and Elovich models and it was found that the second-order kinetic model describes these data for the two metals; comparing kinetic parameters for Cd and Pb sorption a higher kinetic rate (K 2) for Pb was observed, indicating that the interaction between lead cations and alginate beads was faster than for cadmium. Similarly, isotherm data were fitted to different models reported in literature and it was found that the Langmuir-Freundlich (L-F) and Dubinin-Radushkevich (D-R) models describe the isotherms in all cases. CAB sorption capacity for cadmium was 27.4 mg/g and 150.4 mg/g for lead, at 25°C. Sorption capacities of Cd and Pb increase as temperature rises. According to the thermodynamic parameters, the cadmium and lead adsorption process was spontaneous and endothermic. It was also found that pH has an important effect on the adsorption of these metals by CAB, as more were removed at pH values between 6 and 7. PMID:24587740

Thermodynamic, electronic and magnetic properties of intermetallic compounds through statistical models

NASA Astrophysics Data System (ADS)

Cadeville, M. C.; Pierron-Bohnes, V.; Bouzidi, L.; Sanchez, J. M.

1993-01-01

Local and average electronic and magnetic properties of transition metal alloys are strongly correlated to the distribution of atoms on the lattice sites. The ability of some systems to form long range ordered structures at low temperature allows to discuss their properties in term of well identified occupation operators as those related to long range order (LRO) parameters. We show that using theoretical determinations of these LRO parameters through statistical models like the cluster variation method (CVM) developed to simulate the experimental phase diagrams, we are able to reproduce a lot of physical properties. In this paper we focus on two points: (i) a comparison between CVM results and an experimental determination of the LRO parameter by NMR at 59Co in a CoPt3 compound, and (ii) the modelling of the resistivity of ferromagnetic and paramagnetic intermetallic compounds belonging to Co-Pt, Ni-Pt and Fe-Al systems. All experiments were performed on samples in identified thermodynamic states, implying that kinetic effects are thoroughly taken into account.

Effect of experimental and sample factors on dehydration kinetics of mildronate dihydrate: mechanism of dehydration and determination of kinetic parameters.

PubMed

Bērziņš, Agris; Actiņš, Andris

2014-06-01

The dehydration kinetics of mildronate dihydrate [3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propionate dihydrate] was analyzed in isothermal and nonisothermal modes. The particle size, sample preparation and storage, sample weight, nitrogen flow rate, relative humidity, and sample history were varied in order to evaluate the effect of these factors and to more accurately interpret the data obtained from such analysis. It was determined that comparable kinetic parameters can be obtained in both isothermal and nonisothermal mode. However, dehydration activation energy values obtained in nonisothermal mode showed variation with conversion degree because of different rate-limiting step energy at higher temperature. Moreover, carrying out experiments in this mode required consideration of additional experimental complications. Our study of the different sample and experimental factor effect revealed information about changes of the dehydration rate-limiting step energy, variable contribution from different rate limiting steps, as well as clarified the dehydration mechanism. Procedures for convenient and fast determination of dehydration kinetic parameters were offered. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Inter-trial and test–retest reliability of kinematic and kinetic gait parameters among subjects with adolescent idiopathic scoliosis

PubMed Central

Nadeau, Sylvie; Labelle, Hubert

2007-01-01

Gait analysis is actually used in subjects with scoliosis to determine the change in lower limb parameters after surgery, but the reliability of these parameters still remained unknown. The purpose of this study was to assess the repeatability of traditional gait parameters in subjects with adolescent idiopathic scoliosis (AIS) and to estimate the associated standard error of measurement (SEM). A test–retest design was used to assess the reliability of gait parameters at self-selected and fast speeds. A convenience sample of 20 girls aged from 12 to 17 years, with an idiopathic scoliosis (King classification: types I, II or III; Cobb angle 17–50°) participated in the study. Five good trials were recorded on two occasions. The time-distance, kinematic, and kinetic gait parameters were recorded using foot-switches in combination with a three-dimensional motion analysis system (Optotrak) and Advanced Mechanical Technologies Inc., (AMTI) Watertown, MA, USA; force plates. The coefficients of dependability and SEM derived from the generalizability theory were used to assess the reliability. Inter-trial reliability was good for time-distance, kinematic, and kinetic (absolute and normalized) gait parameters except for the medio-lateral ground reaction force (GRF) component and the ankle dorsiflexor moment (ϕ = 0.60–0.77). Test–retest reliability was higher for the kinetic than for the kinematic parameters. These coefficients ranged from 0.42 to 0.58 for the time-distance parameters; from 0.55 to 0.88 for the angular displacements and from 0.25 to 0.99 for the kinetic parameters. The SEMs were lower than 3.3° for the angular displacements and lower than 8 Nm (0.15 Nm/kg) and 36 W (0.54 W/Kg) for the joint moments and powers regardless of the speed. Several gait parameters are reliable among subjects with AIS and can be used to assess the evolution of the spinal modifications and the impact of treatment on their lower limb gait pattern. PMID:17891424

Effect of heating rate on kinetic parameters of β-irradiated Li2B4O7:Cu,Ag,P in TSL measurements

NASA Astrophysics Data System (ADS)

Türkler Ege, A.; Ekdal, E.; Karali, T.; Can, N.; Prokic, M.

2007-03-01

The effect of heating rate on the thermally stimulated luminescence (TSL) emission due to the temperature lag (TLA) between the TSL material and the heating element has been investigated using Li2B4O7:Cu,Ag,P dosimetric materials. The TLA becomes significant when the material is heated at high heating rates. TSL glow curves of Li2B4O7:Cu,Ag,P material showed two main peaks after β-irradiation. The kinetic parameters, namely activation energy (E) and frequency factor (s) associated with the high temperature main peak of Li2B4O7:Cu,Ag,P were determined using the method of various heating rates (VHR), in which heating rates from 1 to 40 K s-1 were used. It is assumed that non-ideal heat transfer between the heater and the material may cause significant inconsistency of kinetic parameter values obtained with different methods. The effect of TLA on kinetic parameters of the dosimeter was examined.

Formation kinetics of furfuryl alcohol in a coffee model system.

PubMed

Albouchi, Abdullatif; Murkovic, Michael

2018-03-15

The production of furfuryl alcohol from green coffee during roasting and the effect of multiple parameters on its formation were studied employing HPLC-DAD. Results show that coffee produces furfuryl alcohol in larger quantities (418µg/g) compared to other beans or seeds (up to 132µg/g) roasted under the same conditions. The kinetics of furfuryl alcohol production resemble those of other process contaminants (e.g., HMF, acrylamide) produced in coffee roasting, with temperature and time of roasting playing significant roles in quantities formed. Different coffee species yielded different amounts of furfuryl alcohol. The data point out that the amounts of furfuryl alcohol found in roasted coffee do not reflect the total amounts produced during roasting because great amounts of furfuryl alcohol (up to 57%) are evaporating and released to the atmosphere during roasting. Finally the effect of the moisture content on furfuryl alcohol formation was found to be of little impact. Copyright © 2017 Elsevier Ltd. All rights reserved.

Theoretical Investigation of Kinetic Processes in Small Radicals of Importance in Combustion

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

Alexander, Millard; Dagdigian, Paul J.

Our group studies inelastic and reactive collisions of small molecules, focusing on radicals important in combustion environments. The goal is the better understanding of kinetic processes that may be difficult to access experimentally. An essential component is the accurate determination and fitting of potential energy surfaces (PESs). After fitting the ab initio points to obtain global PESs, we treat the dynamics using time-independent (close-coupling) methods. Cross sections and rate constants for collisions of are determined with our Hibridon program suite . We have studied energy transfer (rotationally, vibrationally, and/or electronically inelastic) in small hydrocarbon radicals (CH 2 and CH 3)more » and the CN radical. We have made a comparison with experimental measurements of relevant rate constants for collisions of these radicals. Also, we have calculated accurate transport properties using state-of-the-art PESs and to investigate the sensitivity to these parameters in 1-dimensional flame simulations. Of particular interest are collision pairs involving the light H atom.« less

Adiabatic and nonadiabatic perturbation theory for coherence vector description of neutrino oscillations

NASA Astrophysics Data System (ADS)

Hollenberg, Sebastian; Päs, Heinrich

2012-01-01

The standard wave function approach for the treatment of neutrino oscillations fails in situations where quantum ensembles at a finite temperature with or without an interacting background plasma are encountered. As a first step to treat such phenomena in a novel way, we propose a unified approach to both adiabatic and nonadiabatic two-flavor oscillations in neutrino ensembles with finite temperature and generic (e.g., matter) potentials. Neglecting effects of ensemble decoherence for now, we study the evolution of a neutrino ensemble governed by the associated quantum kinetic equations, which apply to systems with finite temperature. The quantum kinetic equations are solved formally using the Magnus expansion and it is shown that a convenient choice of the quantum mechanical picture (e.g., the interaction picture) reveals suitable parameters to characterize the physics of the underlying system (e.g., an effective oscillation length). It is understood that this method also provides a promising starting point for the treatment of the more general case in which decoherence is taken into account.

Removal of Direct Red 12B by garlic peel as a cheap adsorbent: Kinetics, thermodynamic and equilibrium isotherms study of removal

NASA Astrophysics Data System (ADS)

Asfaram, A.; Fathi, M. R.; Khodadoust, S.; Naraki, M.

2014-06-01

The removal of dyes from industrial waste is very important from health and hygiene point of view and for environmental protection. In this work, efficiency and performance of garlic peel (GP) adsorbent for the removal of Direct Red 12B (DR12B) from wastewater was investigated. The influence of variables including pH, concentration of the dye and amount of adsorbent, particle size, contact time and temperature on the dye removal has been investigated. It was observed that the pseudo-second-order kinetic model fits better with good correlation coefficient and the equilibrium data fitted well with the Langmuir model. More than 99% removal efficiency was obtained within 25 min at adsorbent dose of 0.2 g per 50 ml for initial dye concentration of 50 mg L-1. Calculation of various thermodynamic parameters such as, Gibb's free energy, entropy and enthalpy of the on-going adsorption process indicate feasibility and endothermic nature of DR12B adsorption.

Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points

PubMed Central

Barenholz, Uri; Davidi, Dan; Reznik, Ed; Bar-On, Yinon; Antonovsky, Niv; Noor, Elad; Milo, Ron

2017-01-01

A set of chemical reactions that require a metabolite to synthesize more of that metabolite is an autocatalytic cycle. Here, we show that most of the reactions in the core of central carbon metabolism are part of compact autocatalytic cycles. Such metabolic designs must meet specific conditions to support stable fluxes, hence avoiding depletion of intermediate metabolites. As such, they are subjected to constraints that may seem counter-intuitive: the enzymes of branch reactions out of the cycle must be overexpressed and the affinity of these enzymes to their substrates must be relatively weak. We use recent quantitative proteomics and fluxomics measurements to show that the above conditions hold for functioning cycles in central carbon metabolism of E. coli. This work demonstrates that the topology of a metabolic network can shape kinetic parameters of enzymes and lead to seemingly wasteful enzyme usage. DOI: http://dx.doi.org/10.7554/eLife.20667.001 PMID:28169831

Kinetics of Thermal Decomposition of Ammonium Perchlorate by TG/DSC-MS-FTIR

NASA Astrophysics Data System (ADS)

Zhu, Yan-Li; Huang, Hao; Ren, Hui; Jiao, Qing-Jie

2014-01-01

The method of thermogravimetry/differential scanning calorimetry-mass spectrometry-Fourier transform infrared (TG/DSC-MS-FTIR) simultaneous analysis has been used to study thermal decomposition of ammonium perchlorate (AP). The processing of nonisothermal data at various heating rates was performed using NETZSCH Thermokinetics. The MS-FTIR spectra showed that N2O and NO2 were the main gaseous products of the thermal decomposition of AP, and there was a competition between the formation reaction of N2O and that of NO2 during the process with an iso-concentration point of N2O and NO2. The dependence of the activation energy calculated by Friedman's iso-conversional method on the degree of conversion indicated that the AP decomposition process can be divided into three stages, which are autocatalytic, low-temperature diffusion and high-temperature, stable-phase reaction. The corresponding kinetic parameters were determined by multivariate nonlinear regression and the mechanism of the AP decomposition process was proposed.

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.

On-rate based optimization of structure-kinetic relationship--surfing the kinetic map.

PubMed

Schoop, Andreas; Dey, Fabian

2015-10-01

In the lead discovery process residence time has become an important parameter for the identification and characterization of the most efficacious compounds in vivo. To enable the success of compound optimization by medicinal chemistry toward a desired residence time the understanding of structure-kinetic relationship (SKR) is essential. This article reviews various approaches to monitor SKR and suggests using the on-rate as the key monitoring parameter. The literature is reviewed and examples of compound series with low variability as well as with significant changes in on-rates are highlighted. Furthermore, findings of kinetic on-rate changes are presented and potential underlying rationales are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Removal of ibuprofen, naproxen and carbamazepine in aqueous solution onto natural clay: equilibrium, kinetics, and thermodynamic study

NASA Astrophysics Data System (ADS)

Khazri, Hassen; Ghorbel-Abid, Ibtissem; Kalfat, Rafik; Trabelsi-Ayadi, Malika

2017-10-01

This study aimed to describe the adsorption of three pharmaceuticals compounds (ibuprofen, naproxen and carbamazepine) onto natural clay on the basis of equilibrium parameters such as a function of time, effect of pH, varying of the concentration and the temperature. Adsorption kinetic data were modeled using the Lagergren's first-order and the pseudo-second-order kinetic equations. The kinetic results of adsorption are described better using the pseudo-second order model. The isotherm results were tested in the Langmuir, Freundlich and Dubinin-Radushkevich models. The thermodynamic parameters obtained indicate that the adsorption of pharmaceuticals on the clay is a spontaneous and endothermic process.

Oxidizing of ferulic acid with the use of polyoxometalates as catalysts

NASA Astrophysics Data System (ADS)

Povarnitsyna, T. V.; Popova, N. R.; Bogolitsyn, K. G.; Beloglazova, A. L.; Pryakhin, A. N.; Lunin, V. V.

2010-12-01

The kinetics of catalytic oxidation for ferulic acid with polyoxometalates used as catalysts was studied. The effect of pH and concentrations of the principal reacting components on the process kinetics was studied. A kinetic scheme of oxidation is proposed, and the values of a number of kinetic parameters of the process are determined.

The Interface Influence in TiN/SiN x Multilayer Nanocomposite Under Irradiation

NASA Astrophysics Data System (ADS)

Uglov, V. V.; Safronov, I. V.; Kvasov, N. T.; Remnev, G. E.; Shimanski, V. I.

2018-01-01

The paper focuses on studying the kinetics of radiation-induced point defects formed in TiN/SiN x multilayer nanocomposites with account of their generation, diffusion recombination, and the influence of sinks functioning as interfaces. In order to describe the kinetics in nanocrystalline TiN and amorphous SiN x phases, a finite-difference method is used to solve the system of balance kinetic equations for absolute defect concentrations depending on the spatiotemporal variables. A model of the disclination-dislocation interface structure is used to study the absorption of radiation-induced point defects on the boundaries in created stress fields. It is shown that the interface effectively absorbs point defects in these phases of TiN/SiN x multilayer nanocomposite, thereby reducing their amount within the space between phases. This behavior of point defects partially explains a mechanism of the radiation resistance in this type of nanocomposites.

Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes

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

García-Gen, Santiago; Sousbie, Philippe; Rangaraj, Ganesh

2015-01-15

Highlights: • Fractionation of solid wastes into readily and slowly biodegradable fractions. • Kinetic coefficients estimation from mono-digestion batch assays. • Validation of kinetic coefficients with a co-digestion continuous experiment. • Simulation of batch and continuous experiments with an ADM1-based model. - Abstract: A methodology to estimate disintegration and hydrolysis kinetic parameters of solid wastes and validate an ADM1-based anaerobic co-digestion model is presented. Kinetic parameters of the model were calibrated from batch reactor experiments treating individually fruit and vegetable wastes (among other residues) following a new protocol for batch tests. In addition, decoupled disintegration kinetics for readily and slowlymore » biodegradable fractions of solid wastes was considered. Calibrated parameters from batch assays of individual substrates were used to validate the model for a semi-continuous co-digestion operation treating simultaneously 5 fruit and vegetable wastes. The semi-continuous experiment was carried out in a lab-scale CSTR reactor for 15 weeks at organic loading rate ranging between 2.0 and 4.7 g VS/L d. The model (built in Matlab/Simulink) fit to a large extent the experimental results in both batch and semi-continuous mode and served as a powerful tool to simulate the digestion or co-digestion of solid wastes.« less

Passive neutralization of acid mine drainage using basic oxygen furnace slag as neutralization material: experimental and modelling.

PubMed

Zvimba, John N; Siyakatshana, Njabulo; Mathye, Matlhodi

2017-03-01

This study investigated passive neutralization of acid mine drainage using basic oxygen furnace slag as neutralization material over 90 days, with monitoring of the parameters' quality and assessment of their removal kinetics. The quality was observed to significantly improve over time with most parameters removed from the influent during the first 10 days. In this regard, removal of acidity, Fe(II), Mn, Co, Ni and Zn was characterized by fast kinetics while removal kinetics for Mg and SO 4 2- were observed to proceed slowly. The fast removal kinetics of acidity was attributed to fast release of alkalinity from slag minerals under mildly acidic conditions of the influent water. The removal of acidity through generation of alkalinity from the passive treatment system was also observed to generally govern the removal of metallic parameters through hydroxide formation, with overall percentage removals of 88-100% achieved. The removal kinetics for SO 4 2- was modelled using two approaches, yielding rate constant values of 1.56 and 1.53 L/(day mol) respectively, thereby confirming authenticity of SO 4 2- removal kinetics experimental data. The study findings provide insights into better understanding of the potential use of slags and their limitations, particularly in mine closure, as part of addressing this challenge in South Africa.

Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin in Populus trichocarpa[W

PubMed Central

Wang, Jack P.; Naik, Punith P.; Chen, Hsi-Chuan; Shi, Rui; Lin, Chien-Yuan; Liu, Jie; Shuford, Christopher M.; Li, Quanzi; Sun, Ying-Hsuan; Tunlaya-Anukit, Sermsawat; Williams, Cranos M.; Muddiman, David C.; Ducoste, Joel J.; Sederoff, Ronald R.; Chiang, Vincent L.

2014-01-01

We established a predictive kinetic metabolic-flux model for the 21 enzymes and 24 metabolites of the monolignol biosynthetic pathway using Populus trichocarpa secondary differentiating xylem. To establish this model, a comprehensive study was performed to obtain the reaction and inhibition kinetic parameters of all 21 enzymes based on functional recombinant proteins. A total of 104 Michaelis-Menten kinetic parameters and 85 inhibition kinetic parameters were derived from these enzymes. Through mass spectrometry, we obtained the absolute quantities of all 21 pathway enzymes in the secondary differentiating xylem. This extensive experimental data set, generated from a single tissue specialized in wood formation, was used to construct the predictive kinetic metabolic-flux model to provide a comprehensive mathematical description of the monolignol biosynthetic pathway. The model was validated using experimental data from transgenic P. trichocarpa plants. The model predicts how pathway enzymes affect lignin content and composition, explains a long-standing paradox regarding the regulation of monolignol subunit ratios in lignin, and reveals novel mechanisms involved in the regulation of lignin biosynthesis. This model provides an explanation of the effects of genetic and transgenic perturbations of the monolignol biosynthetic pathway in flowering plants. PMID:24619611

Kinetic study on ferulic acid production from banana stem waste via mechanical extraction

NASA Astrophysics Data System (ADS)

Zainol, Norazwina; Masngut, Nasratun; Khairi Jusup, Muhamad

2018-04-01

Banana is the tropical plants associated with lots of medicinal properties. It has been reported to be a potential source of phenolic compounds such as ferulic acid (FA). FA has excellent antioxidant properties higher than vitamin C and E. FA also have a wide range of biological activities, such as antioxidant activities and anti-microbial activities. This paper presents an experimental and kinetic study on ferulic acid (FA) production from banana stem waste (BSW) via mechanical extraction. The objective of this research is to determine the kinetic parameters in the ferulic acid production. The banana stem waste was randomly collected from the local banana plantation in Felda Lepar Hilir, Pahang. The banana stem juice was mechanically extracted by using sugarcane press machine (KR3176) and further analyzed in high performance liquid chromatography. The differential and integral method was applied to determine the kinetic parameter of the extraction process and the data obtained were fitted into the 0th, 1st and 2nd order of extraction process. Based on the results, the kinetic parameter and R2 value from were 0.05 and 0.93, respectively. It was determined that the 0th kinetic order fitted the reaction processes to best represent the mechanical extraction.

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

Estimating kinetic mechanisms with prior knowledge I: Linear parameter constraints.

PubMed

Salari, Autoosa; Navarro, Marco A; Milescu, Mirela; Milescu, Lorin S

2018-02-05

To understand how ion channels and other proteins function at the molecular and cellular levels, one must decrypt their kinetic mechanisms. Sophisticated algorithms have been developed that can be used to extract kinetic parameters from a variety of experimental data types. However, formulating models that not only explain new data, but are also consistent with existing knowledge, remains a challenge. Here, we present a two-part study describing a mathematical and computational formalism that can be used to enforce prior knowledge into the model using constraints. In this first part, we focus on constraints that enforce explicit linear relationships involving rate constants or other model parameters. We develop a simple, linear algebra-based transformation that can be applied to enforce many types of model properties and assumptions, such as microscopic reversibility, allosteric gating, and equality and inequality parameter relationships. This transformation converts the set of linearly interdependent model parameters into a reduced set of independent parameters, which can be passed to an automated search engine for model optimization. In the companion article, we introduce a complementary method that can be used to enforce arbitrary parameter relationships and any constraints that quantify the behavior of the model under certain conditions. The procedures described in this study can, in principle, be coupled to any of the existing methods for solving molecular kinetics for ion channels or other proteins. These concepts can be used not only to enforce existing knowledge but also to formulate and test new hypotheses. © 2018 Salari et al.

The analysis of thermoluminescent glow peaks of natural calcite after beta irradiation.

PubMed

Yildirim, R Güler; Kafadar, V Emir; Yazici, A Necmeddin; Gün, Esen

2012-09-01

In this study, the thermoluminescence properties of natural calcite samples were examined in detail. The glow curve of the sample irradiated with beta radiation shows two main peaks, P1 (at 115 °C) and P4 (at 254 °C). The additive dose, variable heating rate, computer glow curve deconvolution, peak shape and three point methods have been used to evaluate the trapping parameters, namely the order of kinetics (b), activation energy (E) and the frequency factor (s) associated with the dosimetric thermoluminescent glow peaks (P1 and P4) of natural calcite after different dose levels with beta irradiation.

Kinetic Parameters for the Noncatalyzed and Enzyme-Catalyzed Mutarotation of Glucose Using a Blood Glucometer

ERIC Educational Resources Information Center

Hardee, John R.; Delgado, Bryan; Jones, Wray

2011-01-01

The kinetic parameters for the conversion of alpha-D-glucose to beta-D-glucose were measured using a blood glucometer. The reaction order, rate constant, and Arrhenius activation energy are reported for the noncatalyzed reaction and turnover number and Michaelis constant are reported for the reaction catalyzed by porcine kidney mutarotase. The…

Non-Isothermic Chemical Kinetics in the Undergraduate Laboratory: Arrhenius Parameters from Experiments with Hyperbolic Temperature Variation.

ERIC Educational Resources Information Center

Salvador, F.; And Others

1984-01-01

Describes a method which adapts itself to the characteristics of the kinetics of a chemical reaction in solution, enabling students to determine the Arrhenius parameters with satisfactory accuracy by means of a single non-isothermic experiment. Both activation energy and the preexponential factor values can be obtained by the method. (JN)

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Kinetics and Mechanisms of Thiol–Disulfide Exchange Covering Direct Substitution and Thiol Oxidation-Mediated Pathways

PubMed Central

2013-01-01

Abstract Significance: Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol–disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. Critical Issues: This review is focused on the kinetics and mechanisms of thiol–disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Recent Advances and Future Directions: Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery. Antioxid. Redox Signal. 18, 1623–1641. PMID:23075118

Extracting surface diffusion coefficients from batch adsorption measurement data: application of the classic Langmuir kinetics model.

PubMed

Chu, Khim Hoong

2017-11-09

Surface diffusion coefficients may be estimated by fitting solutions of a diffusion model to batch kinetic data. For non-linear systems, a numerical solution of the diffusion model's governing equations is generally required. We report here the application of the classic Langmuir kinetics model to extract surface diffusion coefficients from batch kinetic data. The use of the Langmuir kinetics model in lieu of the conventional surface diffusion model allows derivation of an analytical expression. The parameter estimation procedure requires determining the Langmuir rate coefficient from which the pertinent surface diffusion coefficient is calculated. Surface diffusion coefficients within the 10 -9 to 10 -6  cm 2 /s range obtained by fitting the Langmuir kinetics model to experimental kinetic data taken from the literature are found to be consistent with the corresponding values obtained from the traditional surface diffusion model. The virtue of this simplified parameter estimation method is that it reduces the computational complexity as the analytical expression involves only an algebraic equation in closed form which is easily evaluated by spreadsheet computation.

Comparison of kinetic and extended magnetohydrodynamics computational models for the linear ion temperature gradient instability in slab geometry

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

Schnack, D. D.; Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706; Cheng, J.

We perform linear stability studies of the ion temperature gradient (ITG) instability in unsheared slab geometry using kinetic and extended magnetohydrodynamics (MHD) models, in the regime k{sub ∥}/k{sub ⊥}≪1. The ITG is a parallel (to B) sound wave that may be destabilized by finite ion Larmor radius (FLR) effects in the presence of a gradient in the equilibrium ion temperature. The ITG is stable in both ideal and resistive MHD; for a given temperature scale length L{sub Ti0}, instability requires that either k{sub ⊥}ρ{sub i} or ρ{sub i}/L{sub Ti0} be sufficiently large. Kinetic models capture FLR effects to all ordersmore » in either parameter. In the extended MHD model, these effects are captured only to lowest order by means of the Braginskii ion gyro-viscous stress tensor and the ion diamagnetic heat flux. We present the linear electrostatic dispersion relations for the ITG for both kinetic Vlasov and extended MHD (two-fluid) models in the local approximation. In the low frequency fluid regime, these reduce to the same cubic equation for the complex eigenvalue ω=ω{sub r}+iγ. An explicit solution is derived for the growth rate and real frequency in this regime. These are found to depend on a single non-dimensional parameter. We also compute the eigenvalues and the eigenfunctions with the extended MHD code NIMROD, and a hybrid kinetic δf code that assumes six-dimensional Vlasov ions and isothermal fluid electrons, as functions of k{sub ⊥}ρ{sub i} and ρ{sub i}/L{sub Ti0} using a spatially dependent equilibrium. These solutions are compared with each other, and with the predictions of the local kinetic and fluid dispersion relations. Kinetic and fluid calculations agree well at and near the marginal stability point, but diverge as k{sub ⊥}ρ{sub i} or ρ{sub i}/L{sub Ti0} increases. There is good qualitative agreement between the models for the shape of the unstable global eigenfunction for L{sub Ti0}/ρ{sub i}=30 and 20. The results quantify how far fluid calculations can be extended accurately into the kinetic regime. We conclude that for the linear ITG problem in slab geometry with unsheared magnetic field when k{sub ∥}/k{sub ⊥}≪1, the extended MHD model may be a reliable physical model for this problem when ρ{sub i}/L{sub Ti0}<10{sup −2} and k{sub ⊥}ρ{sub i}<0.2.« less

Evaluation of the cure kinetics of the wood/pMDI bondline

Treesearch

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

2001-01-01

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

Biosorptive uptake of arsenic(V) by steam activated carbon from mung bean husk: equilibrium, kinetics, thermodynamics and modeling

NASA Astrophysics Data System (ADS)

Mondal, Sandip; Aikat, Kaustav; Halder, Gopinath

2017-12-01

The present investigation emphasizes on the biosorptive removal of toxic pentavalent arsenic from water using steam activated carbon prepared from mung bean husk (SAC-MBH). Characterization of the synthesized sorbent was done using different instrumental techniques, i.e., SEM, BET and point of zero charge. Sorptive uptake of As(V) over steam activated MBH as a function of pH (3-9), agitation speed (40-200 rpm), dosage (50-1000 mg) and temperature (298-313 K) was studied by batch process at arsenic concentration of 2 mg L-1. Lower pH increases the arsenic removal over the pH range of 3-9. Among three adsorption isotherm models examined, Langmuir model was observed to show superior results over Freundlich model. The mean sorption energy (E) estimated by Dubinin-Radushkevich model suggested that the process of adsorption was chemisorption. Thermodynamic parameters confer that the sorption process was spontaneous, exothermic and feasible in nature. The pseudo-second-order rate kinetics of arsenic gave better correlation coefficients as compared to pseudo-first-order kinetics equation. Three process parameters, viz. adsorbent dosage, agitation speed and pH were opted for optimizing As(V) elimination using central composite design matrix of response surface methodology (RSM). The identical design setup was used for artificial neural network (ANN) for comparing its prediction capability with RSM towards As(V) removal. Maximum arsenic removal was observed to be 98.75% at sorbent dosage 0.75 gm L-1, pH 3.0, agitation speed 160 rpm and temperature 308 K. The study concluded that SAC-MBH could be a competent adsorbent for As(V) removal and ANN model was better in arsenic removal predictability results than RSM model.

A theoretical and numerical study of the flow of granular materials down an inclined plane. Final report

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

Rajagopal, K.R.

The mechanics of the flowing granular materials such as coal, agricultural products, at deal of attention as it has fertilizers, dry chemicals, metal ores, etc. have received a great deal of attention as it has relevance to several important technological problems. Despite wide interest and more than five decades of experimental and theoretical investigations, most aspects of the behavior of flowing granular materials are still not well understood. So Experiments have to be devised which quantify and describe the non-linear behavior of the modular materials, and theories developed which can explain the experimentally observed facts. As many models have beenmore » suggested for describing the behavior of granular materials, from both continuum and kinetic theory viewpoints, we proposed to investigate the validity and usefulness of representative models from both the continuum and kinetic theory points of view, by determining the prediction of such a theory, in a representative flow, with respect to existence, non-existence, multiplicity and stability of solutions. The continuum model to be investigated is an outgrowth of a model due to Goodman and Cowin (1971, 1972) and the kinetic theory models being those due to Jenkins and Richman (1985) and Boyle and Massoudi (1989). In this report we present detailed results regarding the same. Interestingly, we find that the predictions of all the theories, in certain parameter space associated with these models, are qualitatively similar. This ofcourse depends on the values assumed for various material parameters in the models, which as yet are unknown, as reliable experiments have not been carried out as yet for their determination.« less

Identifying and Characterizing Kinetic Instabilities using Solar Wind Observations of Non-Maxwellian Plasmas

NASA Astrophysics Data System (ADS)

Klein, K. G.

2016-12-01

Weakly collisional plasmas, of the type typically observed in the solar wind, are commonly in a state other than local thermodynamic equilibrium. This deviation from a Maxwellian velocity distribution can be characterized by pressure anisotropies, disjoint beams streaming at differing speeds, leptokurtic distributions at large energies, and other non-thermal features. As these features may be artifacts of dynamic processes, including the the acceleration and expansion of the solar wind, and as the free energy contained in these features can drive kinetic micro-instabilities, accurate measurement and modeling of these features is essential for characterizing the solar wind. After a review of these features, a technique is presented for the efficient calculation of kinetic instabilities associated with a general, non-Maxwellian plasma. As a proof of principle, this technique is applied to bi-Maxwellian systems for which kinetic instability thresholds are known, focusing on parameter scans including beams and drifting heavy minor ions. The application of this technique to fits of velocity distribution functions from current, forthcoming, and proposed missions including WIND, DSCOVR, Solar Probe Plus, and THOR, as well as the underlying measured distribution functions, is discussed. Particular attention is paid to the effects of instrument pointing and integration time, as well as potential deviation between instabilities associated with the Maxwellian fits and those associated with the observed, potentially non-Maxwellian, velocity distribution. Such application may further illuminate the role instabilities play in the evolution of the solar wind.

Passive films on magnesium anodes in primary batteries

NASA Technical Reports Server (NTRS)

Ratnakumar, B. V.

1988-01-01

The characteristics of the passive films over Mg anodes, which essentially govern the voltage delay of the latter, have been determined nondestructively from an analysis of the transient and steady-state response of the electrode potential to low amplitude galvanostatic polarization under various experimental conditions viz., with different corrosion inhibitor coatings on Mg, after various periods of ageing of anode in solutions containing corrosion inhibitors, at various low temperatures etc. Using these parameters, the kinetics of film build-up or dissolution under these conditions have been monitored. The morphology of the anode film has been verified with scanning electron microscopy. Similar transients at low temperatures point out a steep rise in the film resistivity which is essentially responsible for the severe voltage delay. Finally, possible application of this technique in secondary Li batteries to improve cycling characteristics of the Li anode has been pointed out.

Weak phase stiffness and nature of the quantum critical point in underdoped cuprates

DOE PAGES

Yildirim, Yucel; Ku, Wei

2015-11-02

We demonstrate that the zero-temperature superconducting phase diagram of underdoped cuprates can be quantitatively understood in the strong binding limit, using only the experimental spectral function of the “normal” pseudogap phase without any free parameter. In the prototypical (La 1–xSr x) 2CuO 4, a kinetics-driven d-wave superconductivity is obtained above the critical doping δ c ~ 5.2%, below which complete loss of superfluidity results from local quantum fluctuation involving local p-wave pairs. Near the critical doping, an enormous mass enhancement of the local pairs is found responsible for the observed rapid decrease of phase stiffness. Lastly, a striking mass divergencemore » is predicted at δ c that dictates the occurrence of the observed quantum critical point and the abrupt suppression of the Nernst effects in the nearby region.« less

G0-G1 Transition and the Restriction Point in Pancreatic β-Cells In Vivo

PubMed Central

Hija, Ayat; Salpeter, Seth; Klochendler, Agnes; Grimsby, Joseph; Brandeis, Michael; Glaser, Benjamin; Dor, Yuval

2014-01-01

Most of our knowledge on cell kinetics stems from in vitro studies of continuously dividing cells. In this study, we determine in vivo cell-cycle parameters of pancreatic β-cells, a largely quiescent population, using drugs that mimic or prevent glucose-induced replication of β-cells in mice. Quiescent β-cells exposed to a mitogenic glucose stimulation require 8 h to enter the G1 phase of the cell cycle, and this time is prolonged in older age. The duration of G1, S, and G2/M is ∼5, 8, and 6 h, respectively. We further provide the first in vivo demonstration of the restriction point at the G0-G1 transition, discovered by Arthur Pardee 40 years ago. The findings may have pharmacodynamic implications in the design of regenerative therapies aimed at increasing β-cell replication and mass in patients with diabetes. PMID:24130333

Fast pyrolysis kinetics of alkali lignin: Evaluation of apparent rate parameters and product time evolution.

PubMed

Ojha, Deepak Kumar; Viju, Daniel; Vinu, R

2017-10-01

In this study, the apparent kinetics of fast pyrolysis of alkali lignin was evaluated by obtaining isothermal mass loss data in the timescale of 2-30s at 400-700°C in an analytical pyrolyzer. The data were analyzed using different reaction models to determine the rate constants and apparent rate parameters. First order and one dimensional diffusion models resulted in good fits with experimental data with apparent activation energy of 23kJmol -1 . Kinetic compensation effect was established using a large number of kinetic parameters reported in the literature for pyrolysis of different lignins. The time evolution of the major functional groups in the pyrolysate was analyzed using in situ Fourier transform infrared spectroscopy. Maximum production of the volatiles occurred around 10-12s. A clear transformation of guaiacols to phenol, catechol and their derivatives, and aromatic hydrocarbons was observed with increasing temperature. The plausible reaction steps involved in various transformations are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of NBG-18, NBG-17, IG-110 and IG-11 oxidation kinetics in air

NASA Astrophysics Data System (ADS)

Lee, Jo Jo; Ghosh, Tushar K.; Loyalka, Sudarshan K.

2018-03-01

The oxidation rates of several nuclear-grade graphites, NBG-18, NBG-17, IG-110 and IG-11, were measured in air using thermogravimetry. Kinetic parameters and oxidation behavior for each grade were compared by coke type, filler grain size and microstructure. The thickness of the oxidized layer for each grade was determined by layer peeling and direct density measurements. The results for NBG-17 and IG-11 were compared with those available in the literature and our recently reported results for NBG-18 and IG-110 oxidation in air. The finer-grained graphites IG-110 and IG-11 were more oxidized than medium-grained NBG-18 and NBG-17 because of deeper oxidant penetration, higher porosity and higher probability of available active sites. Variation in experimental conditions also had a marked effect on the reported kinetic parameters by several studies. Kinetic parameters such as activation energy and transition temperature were sensitive to air flow rates as well as sample size and geometry.

Use of reduction rate as a quantitative knob for controlling the twin structure and shape of palladium nanocrystals.

PubMed

Wang, Yi; Peng, Hsin-Chieh; Liu, Jingyue; Huang, Cheng Zhi; Xia, Younan

2015-02-11

Kinetic control is a powerful means for maneuvering the twin structure and shape of metal nanocrystals and thus optimizing their performance in a variety of applications. However, there is only a vague understanding of the explicit roles played by reaction kinetics due to the lack of quantitative information about the kinetic parameters. With Pd as an example, here we demonstrate that kinetic parameters, including rate constant and activation energy, can be derived from spectroscopic measurements and then used to calculate the initial reduction rate and further have this parameter quantitatively correlated with the twin structure of a seed and nanocrystal. On a quantitative basis, we were able to determine the ranges of initial reduction rates required for the formation of nanocrystals with a specific twin structure, including single-crystal, multiply twinned, and stacking fault-lined. This work represents a major step forward toward the deterministic syntheses of colloidal noble-metal nanocrystals with specific twin structures and shapes.

Determination of kinetic parameters for 123-I thyroid uptake in healthy Japanese

NASA Astrophysics Data System (ADS)

Kusuhara, Hiroyuki; Maeda, Kazuya

2017-09-01

The purpose of this study was to compare the kinetic parameters for iodide thyroid accumulation in Japanese today with previously reported values. We determined the thyroid uptake of 123-I at 24 hours after the oral administration in healthy male Japanese without any diet restriction. The mean value was 16.1±5.4%, which was similar or rather lower than those previously reported in Japan (1958-1972). Kinetic model analysis was conducted to obtain the clearance for thyroid uptake from the blood circulation. The thyroid uptake clearance of 123-I was 0.540±0.073 ml/min, which was almost similar to those reported previously. There is no obvious difference in the thyroid uptake for 24 hours, and kinetic parameters in healthy Japanese for these 50 years. The fraction of distributed to the thyroid gland is lower than the ICRP reference man, and such difference must be taken into consideration to estimate the radiation exposure upon Fukushima accident in Japan.

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.

Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes.

PubMed

García-Gen, Santiago; Sousbie, Philippe; Rangaraj, Ganesh; Lema, Juan M; Rodríguez, Jorge; Steyer, Jean-Philippe; Torrijos, Michel

2015-01-01

A methodology to estimate disintegration and hydrolysis kinetic parameters of solid wastes and validate an ADM1-based anaerobic co-digestion model is presented. Kinetic parameters of the model were calibrated from batch reactor experiments treating individually fruit and vegetable wastes (among other residues) following a new protocol for batch tests. In addition, decoupled disintegration kinetics for readily and slowly biodegradable fractions of solid wastes was considered. Calibrated parameters from batch assays of individual substrates were used to validate the model for a semi-continuous co-digestion operation treating simultaneously 5 fruit and vegetable wastes. The semi-continuous experiment was carried out in a lab-scale CSTR reactor for 15 weeks at organic loading rate ranging between 2.0 and 4.7 gVS/Ld. The model (built in Matlab/Simulink) fit to a large extent the experimental results in both batch and semi-continuous mode and served as a powerful tool to simulate the digestion or co-digestion of solid wastes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Thermodynamic and kinetic characterization of polycyclic aromatic hydrocarbons in reversed-phase liquid chromatography.

PubMed

Howerton, Samuel B; McGuffin, Victoria L

2003-07-15

The retention of six polycyclic aromatic hydrocarbons (PAHs) was characterized by reversed-phase liquid chromatography. The PAHs were detected by laser-induced fluorescence at four points along an optically transparent capillary column. The profiles were characterized in space and time using an exponentially modified Gaussian equation. The resulting parameters were used to calculate the retention factors, as well as the concomitant changes in molar enthalpy and molar volume, for each PAH on monomeric (2.7 micromol/m2) and polymeric (5.4 micromol/m2) octadecylsilica. The changes in molar enthalpy become more exothermic as ring number increases and as annelation structure becomes less condensed. The changes in molar volume become more negative as ring number increases for the planar PAHs, but are positive for the nonplanar solutes. In addition, the rate constants, as well as the concomitant activation enthalpy and activation volume, are calculated for the first time. The kinetic data demonstrate that many of the PAHs exhibit very fast transitions between the mobile and stationary phases. The transition state is very high in energy, and the activation enthalpies and volumes become greater as ring number increases and as annelation structure becomes less condensed. The changes in thermodynamic and kinetic behavior are much more pronounced for the polymeric phase than for the monomeric phase.

Crystallization kinetics and molecular mobility of an amorphous active pharmaceutical ingredient: A case study with Biclotymol.

PubMed

Schammé, Benjamin; Couvrat, Nicolas; Malpeli, Pascal; Delbreilh, Laurent; Dupray, Valérie; Dargent, Éric; Coquerel, Gérard

2015-07-25

The present case study focuses on the crystallization kinetics and molecular mobility of an amorphous mouth and throat drug namely Biclotymol, through differential scanning calorimetry (DSC), temperature resolved X-ray powder diffraction (TR-XRPD) and hot stage microscopy (HSM). Kinetics of crystallization above the glass transition through isothermal and non-isothermal cold crystallization were considered. Avrami model was used for isothermal crystallization process. Non-isothermal cold crystallization was investigated through Augis and Bennett model. Differences between crystallization processes have been ascribed to a site-saturated nucleation mechanism of the metastable form, confirmed by optical microscopy images. Regarding molecular mobility, a feature of molecular dynamics in glass-forming liquids as thermodynamic fragility index m was determined through calorimetric measurements. It turned out to be around m=100, describing Biclotymol as a fragile glass-former for Angell's classification. Relatively long-term stability of amorphous Biclotymol above Tg was analyzed indirectly by calorimetric monitoring to evaluate thermodynamic parameters and crystallization behavior of glassy Biclotymol. Within eight months of storage above Tg (T=Tg+2°C), amorphous Biclotymol does not show a strong inclination to crystallize and forms a relatively stable glass. This case study, involving a multidisciplinary approach, points out the importance of continuing looking for stability predictors. Copyright © 2015 Elsevier B.V. All rights reserved.

Dynamical patterns and regime shifts in the nonlinear model of soil microorganisms growth

NASA Astrophysics Data System (ADS)

Zaitseva, Maria; Vladimirov, Artem; Winter, Anna-Marie; Vasilyeva, Nadezda

2017-04-01

Dynamical model of soil microorganisms growth and turnover is formulated as a system of nonlinear partial differential equations of reaction-diffusion type. We consider spatial distributions of concentrations of several substrates and microorganisms. Biochemical reactions are modelled by chemical kinetic equations. Transport is modelled by simple linear diffusion for all chemical substances, while for microorganisms we use different transport functions, e.g. some of them can actively move along gradient of substrate concentration, while others cannot move. We solve our model in two dimensions, starting from uniform state with small initial perturbations for various parameters and find parameter range, where small initial perturbations grow and evolve. We search for bifurcation points and critical regime shifts in our model and analyze time-space profile and phase portraits of these solutions approaching critical regime shifts in the system, exploring possibility to detect such shifts in advance. This work is supported by NordForsk, project #81513.

Two-dimensional strain gradient damage modeling: a variational approach

NASA Astrophysics Data System (ADS)

Placidi, Luca; Misra, Anil; Barchiesi, Emilio

2018-06-01

In this paper, we formulate a linear elastic second gradient isotropic two-dimensional continuum model accounting for irreversible damage. The failure is defined as the condition in which the damage parameter reaches 1, at least in one point of the domain. The quasi-static approximation is done, i.e., the kinetic energy is assumed to be negligible. In order to deal with dissipation, a damage dissipation term is considered in the deformation energy functional. The key goal of this paper is to apply a non-standard variational procedure to exploit the damage irreversibility argument. As a result, we derive not only the equilibrium equations but, notably, also the Karush-Kuhn-Tucker conditions. Finally, numerical simulations for exemplary problems are discussed as some constitutive parameters are varying, with the inclusion of a mesh-independence evidence. Element-free Galerkin method and moving least square shape functions have been employed.

Parametrizing the Reionization History with the Redshift Midpoint, Duration, and Asymmetry

NASA Astrophysics Data System (ADS)

Trac, Hy

2018-05-01

A new parametrization of the reionization history is presented to facilitate robust comparisons between different observations and with theory. The evolution of the ionization fraction with redshift can be effectively captured by specifying the midpoint, duration, and asymmetry parameters. Lagrange interpolating functions are then used to construct analytical curves that exactly fit corresponding ionization points. The shape parametrizations are excellent matches to theoretical results from radiation-hydrodynamic simulations. The comparative differences for reionization observables are: ionization fraction | {{Δ }}{x}{{i}}| ≲ 0.03, 21 cm brightness temperature | {{Δ }}{T}{{b}}| ≲ 0.7 {mK}, Thomson optical depth | {{Δ }}τ | ≲ 0.001, and patchy kinetic Sunyaev–Zel’dovich angular power | {{Δ }}{D}{\\ell }| ≲ 0.1 μ {{{K}}}2. This accurate and flexible approach will allow parameter-space studies and self-consistent constraints on the reionization history from 21 cm, cosmic microwave background (CMB), and high-redshift galaxies and quasars.

Effects of Borax on the Reduction of Pre-oxidized Panzhihua Ilmenite

NASA Astrophysics Data System (ADS)

Guo, Yufeng; Zheng, Fuqiang; Jiang, Tao; Chen, Feng; Wang, Shuai; Qiu, Guanzhou

2018-01-01

The effects of borax (sodium borate) on the enhancement reduction of pre-oxidized Panzhihua ilmenite were investigated. The effects of borax on the mineral phase transformation, microstructures, crystal cell parameter, melting point and Mg distribution were studied to reveal the mechanism of enhancement reduction. Under the constant reduction conditions, the borax could reduce the reduction activation energy of pre-oxidized ilmenite. The reduction kinetics analysis indicated that the reduction rate was controlled by interfacial chemical reaction. The reduction activation energy of the pre-oxidized ilmenite with 4% borax was 80.263 kJ/mol, which was 28.585 kJ/mol less than that of the pre-oxidized ilmenite without borax. Borax could eliminate the migration of Mg into the reduced particle center. The crystal cell parameter of the reduced product was increased by adding borax. Borax could improve the growth of dendritic crystals in the pre-oxidized ilmenite.

Relationships between PEMFC Cathode Kinetic Losses and Contaminants’ Dipole Moment and Adsorption Energy on Pt

DOE PAGES

St-Pierre, Jean; Zhai, Yunfeng; Ge, Junjie

2016-01-05

A database summarizing the effects of 21 contaminants on the performance of proton exchange membrane fuel cells (PEMFCs) was used to examine relationships between cathode kinetic losses and contaminant physicochemical parameters. Impedance spectroscopy data were employed to obtain oxygen reduction kinetic resistances by fitting data in the 10-158 Hz range to a simplified equivalent circuit. The contaminant dipole moment and the adsorption energy of the contaminant on a Pt surface were chosen as parameters. Dipole moments did not correlate with dimensionless cathode kinetic resistances. In contrast, adsorption energies were quantitatively and linearly correlated with minimum dimensionless cathode kinetic resistances. Contaminantsmore » influence the oxygen reduction for contaminant adsorption energies smaller than -24.5 kJ mol -1, a value near the high limit of the adsorption energy of O 2 on Pt. Dimensionless cathode kinetic resistances linearly increase with decreasing O 2 adsorption energies below -24.5 kJ mol -1. Measured total cell voltage losses are mostly larger than the cathode kinetic losses calculated from kinetic resistance changes, which indicates the existence of other sources of performance degradation. Modifications to the experimental procedure are proposed to ensure that data are comparable on a similar basis and improve the correlation between contaminant adsorption energy and kinetic cell voltage losses.« less

Relationships between PEMFC Cathode Kinetic Losses and Contaminants’ Dipole Moment and Adsorption Energy on Pt

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

St-Pierre, Jean; Zhai, Yunfeng; Ge, Junjie

A database summarizing the effects of 21 contaminants on the performance of proton exchange membrane fuel cells (PEMFCs) was used to examine relationships between cathode kinetic losses and contaminant physicochemical parameters. Impedance spectroscopy data were employed to obtain oxygen reduction kinetic resistances by fitting data in the 10-158 Hz range to a simplified equivalent circuit. The contaminant dipole moment and the adsorption energy of the contaminant on a Pt surface were chosen as parameters. Dipole moments did not correlate with dimensionless cathode kinetic resistances. In contrast, adsorption energies were quantitatively and linearly correlated with minimum dimensionless cathode kinetic resistances. Contaminantsmore » influence the oxygen reduction for contaminant adsorption energies smaller than -24.5 kJ mol -1, a value near the high limit of the adsorption energy of O 2 on Pt. Dimensionless cathode kinetic resistances linearly increase with decreasing O 2 adsorption energies below -24.5 kJ mol -1. Measured total cell voltage losses are mostly larger than the cathode kinetic losses calculated from kinetic resistance changes, which indicates the existence of other sources of performance degradation. Modifications to the experimental procedure are proposed to ensure that data are comparable on a similar basis and improve the correlation between contaminant adsorption energy and kinetic cell voltage losses.« less

Elucidation of Iron Gettering Mechanisms in Boron-Implanted Silicon Solar Cells

DOE PAGES

Laine, Hannu S.; Vahanissi, Ville; Liu, Zhengjun; ...

2017-12-15

To facilitate cost-effective manufacturing of boron-implanted silicon solar cells as an alternative to BBr 3 diffusion, we performed a quantitative test of the gettering induced by solar-typical boron-implants with the potential for low saturation current density emitters (< 50 fA/cm 2). We show that depending on the contamination level and the gettering anneal chosen, such boron-implanted emitters can induce more than a 99.9% reduction in bulk iron point defect concentration. The iron point defect results as well as synchrotron-based Nano-X-ray-fluorescence investigations of iron precipitates formed in the implanted layer imply that, with the chosen experimental parameters, iron precipitation is themore » dominant gettering mechanism, with segregation-based gettering playing a smaller role. We reproduce the measured iron point defect and precipitate distributions via kinetics modeling. First, we simulate the structural defect distribution created by the implantation process, and then we model these structural defects as heterogeneous precipitation sites for iron. Unlike previous theoretical work on gettering via boron- or phosphorus-implantation, our model is free of adjustable simulation parameters. The close agreement between the model and experimental results indicates that the model successfully captures the necessary physics to describe the iron gettering mechanisms operating in boron-implanted silicon. Furthermore, this modeling capability allows high-performance, cost-effective implanted silicon solar cells to be designed.« less

Elucidation of Iron Gettering Mechanisms in Boron-Implanted Silicon Solar Cells

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

Laine, Hannu S.; Vahanissi, Ville; Liu, Zhengjun

To facilitate cost-effective manufacturing of boron-implanted silicon solar cells as an alternative to BBr 3 diffusion, we performed a quantitative test of the gettering induced by solar-typical boron-implants with the potential for low saturation current density emitters (< 50 fA/cm 2). We show that depending on the contamination level and the gettering anneal chosen, such boron-implanted emitters can induce more than a 99.9% reduction in bulk iron point defect concentration. The iron point defect results as well as synchrotron-based Nano-X-ray-fluorescence investigations of iron precipitates formed in the implanted layer imply that, with the chosen experimental parameters, iron precipitation is themore » dominant gettering mechanism, with segregation-based gettering playing a smaller role. We reproduce the measured iron point defect and precipitate distributions via kinetics modeling. First, we simulate the structural defect distribution created by the implantation process, and then we model these structural defects as heterogeneous precipitation sites for iron. Unlike previous theoretical work on gettering via boron- or phosphorus-implantation, our model is free of adjustable simulation parameters. The close agreement between the model and experimental results indicates that the model successfully captures the necessary physics to describe the iron gettering mechanisms operating in boron-implanted silicon. Furthermore, this modeling capability allows high-performance, cost-effective implanted silicon solar cells to be designed.« less

Approach to the origin of turbulence on the basis of two-point kinetic theory

NASA Technical Reports Server (NTRS)

Tsuge, S.

1974-01-01

Equations for the fluctuation correlation in an incompressible shear flow are derived on the basis of kinetic theory, utilizing the two-point distribution function which obeys the BBGKY hierarchy equation truncated with the hypothesis of 'ternary' molecular chaos. The step from the molecular to the hydrodynamic description is accomplished by a moment expansion which is a two-point version of the thirteen-moment method, and which leads to a series of correlation equations, viz., the two-point counterparts of the continuity equation, the Navier-Stokes equation, etc. For almost parallel shearing flows the two-point equation is separable and reduces to two Orr-Sommerfeld equations with different physical implications.

Kinetics of heterotrophic biomass and storage mechanism in wetland cores measured by respirometry.

PubMed

Ortigara, A R C; Foladori, P; Andreottola, G

2011-01-01

Although oxygen uptake rate has been widely used in activated sludge for measuring kinetic and stoichiometric parameters or for wastewater characterization, its application in constructed wetlands (CWs) cores has been recently proposed. The aim of this research is to estimate the kinetic and stoichiometric parameters of the heterotrophic biomass in CW cores. Respirometric tests were carried out with pure carbonaceous substrate and real wastewater. Endogenous respiration was about 2 gO2 m(-3) h(-1) (per unit of bed volume), while the kinetic parameters obtained for COD oxidation were very high (maximum rate per unit of bed volume of 10.7-26.8 gCOD m(-3) h(-1)) which indicates high biodegradation potential in fully aerobic environment. Regarding to stoichiometric parameter, the maximum growth yield, Y(H), was 0.56-0.59 mgCOD/mgCOD, while the storage yield, Y(STO), was 0.75-0.77 mgCOD/mgCOD. The storage mechanism was observed in CW cores during COD oxidation, which leads to the transformation of the external soluble substrate in internal storage products, probably as response to intermittent loads applied in CW systems, transient concentrations of readily biodegradable substrate and alternance of feast/famine periods.

Determination of kinetic parameters of 1,3-propanediol fermentation by Clostridium diolis using statistically optimized medium.

PubMed

Kaur, Guneet; Srivastava, Ashok K; Chand, Subhash

2012-09-01

1,3-propanediol (1,3-PD) is a chemical compound of immense importance primarily used as a raw material for fiber and textile industry. It can be produced by the fermentation of glycerol available abundantly as a by-product from the biodiesel plant. The present study was aimed at determination of key kinetic parameters of 1,3-PD fermentation by Clostridium diolis. Initial experiments on microbial growth inhibition were followed by optimization of nutrient medium recipe by statistical means. Batch kinetic data from studies in bioreactor using optimum concentration of variables obtained from statistical medium design was used for estimation of kinetic parameters of 1,3-PD production. Direct use of raw glycerol from biodiesel plant without any pre-treatment for 1,3-PD production using this strain investigated for the first time in this work gave results comparable to commercial glycerol. The parameter values obtained in this study would be used to develop a mathematical model for 1,3-PD to be used as a guide for designing various reactor operating strategies for further improving 1,3-PD production. An outline of protocol for model development has been discussed in the present work.

PH-dependence of detergent-induced hemolysis and vesiculation of erythrocytes.

PubMed

Chernitsky, E A; Rozin, V V; Senkovich, O A

2001-01-01

The influence of pH of the medium on the parameters of detergent-induced fast hemolysis and vesiculation of human erythrocytes was studied. In the range of pH 6.3-7.2 neither the extent nor the rate of the vesiculation induced by 25 microM sodium dodecyl sulfate (SDS) changed. However, a decrease of pH from 8.0 to 5.8 strongly modified both the extent and the rate of the hemolysis induced by SDS. Within the range of pH 8.0-6.4, the effect can be ascribed to the increase of the positive charge of the membrane. This could lead to the accumulation of the membrane-bound anion detergent and, hence, to the change of the hemolysis parameters. Non-charged detergent Triton X-100 did not display any pH-dependence. At pH between 6.4 and 5.8 the extent and rate of hemolysis changed in a complicated manner. The kinetic curves of hemolysis could be approximated by a single exponential within the pH range between 8.0 and 7.2. Upon further reduction of pH, a second exponential component, with a larger time constant, appeared in the kinetic curves. At 5.8 < pH < 7.2, the contribution of the "fast" hemolysis dropped virtually to zero, with pK about 6.0. This points to a structural transition of the membrane, possibly involving histidine. We suggest that the parameters of the detergent-induced hemolysis are sensitive to the changes of the charge and structural state of erythrocyte membrane.

Cyanide binding to human plasma heme-hemopexin: A comparative study

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

Ascenzi, Paolo, E-mail: ascenzi@uniroma3.it; Istituto Nazionale di Biostrutture e Biosistemi, Roma; Leboffe, Loris

Highlights: Black-Right-Pointing-Pointer Cyanide binding to ferric HHPX-heme-Fe. Black-Right-Pointing-Pointer Cyanide binding to ferrous HHPX-heme-Fe. Black-Right-Pointing-Pointer Dithionite-mediated reduction of ferric HHPX-heme-Fe-cyanide. Black-Right-Pointing-Pointer Cyanide binding to HHPX-heme-Fe is limited by ligand deprotonation. Black-Right-Pointing-Pointer Cyanide dissociation from HHPX-heme-Fe-cyanide is limited by ligand protonation. -- Abstract: Hemopexin (HPX) displays a pivotal role in heme scavenging and delivery to the liver. In turn, heme-Fe-hemopexin (HPX-heme-Fe) displays heme-based spectroscopic and reactivity properties. Here, kinetics and thermodynamics of cyanide binding to ferric and ferrous hexa-coordinate human plasma HPX-heme-Fe (HHPX-heme-Fe(III) and HHPX-heme-Fe(II), respectively), and for the dithionite-mediated reduction of the HHPX-heme-Fe(III)-cyanide complex, at pH 7.4 and 20.0 Degree-Sign C,more » are reported. Values of thermodynamic and kinetic parameters for cyanide binding to HHPX-heme-Fe(III) and HHPX-heme-Fe(II) are K = (4.1 {+-} 0.4) Multiplication-Sign 10{sup -6} M, k{sub on} = (6.9 {+-} 0.5) Multiplication-Sign 10{sup 1} M{sup -1} s{sup -1}, and k{sub off} = 2.8 Multiplication-Sign 10{sup -4} s{sup -1}; and H = (6 {+-} 1) Multiplication-Sign 10{sup -1} M, h{sub on} = 1.2 Multiplication-Sign 10{sup -1} M{sup -1} s{sup -1}, and h{sub off} = (7.1 {+-} 0.8) Multiplication-Sign 10{sup -2} s{sup -1}, respectively. The value of the rate constant for the dithionite-mediated reduction of the HHPX-heme-Fe(III)-cyanide complex is l = 8.9 {+-} 0.8 M{sup -1/2} s{sup -1}. HHPX-heme-Fe reactivity is modulated by proton acceptor/donor amino acid residue(s) (e.g., His236) assisting the deprotonation and protonation of the incoming and outgoing ligand, respectively.« less

Ocean Turbulence. Paper 3; Two-Point Closure Model Momentum, Heat and Salt Vertical Diffusivities in the Presence of Shear

NASA Technical Reports Server (NTRS)

Canuto, V. M.; Dubovikov, M. S.; Howard, A.; Cheng, Y.

1999-01-01

In papers 1 and 2 we have presented the results of the most updated 1-point closure model for the turbulent vertical diffusivities of momentum, heat and salt, K(sub m,h,s). In this paper, we derive the analytic expressions for K(sub m,h,s) using a new 2-point closure model that has recently been developed and successfully tested against some approx. 80 turbulence statistics for different flows. The new model has no free parameters. The expressions for K(sub m, h. s) are analytical functions of two stability parameters: the Turner number R(sub rho) (salinity gradient/temperature gradient) and the Richardson number R(sub i) (temperature gradient/shear). The turbulent kinetic energy K and its rate of dissipation may be taken local or non-local (K-epsilon model). Contrary to all previous models that to describe turbulent mixing below the mixed layer (ML) have adopted three adjustable "background diffusivities" for momentum. heat and salt, we propose a model that avoids such adjustable diffusivities. We assume that below the ML, K(sub m,h,s) have the same functional dependence on R(sub i) and R(sub rho) derived from the turbulence model. However, in order to compute R(sub i) below the ML, we use data of vertical shear due to wave-breaking measured by Gargett et al. (1981). The procedure frees the model from adjustable background diffusivities and indeed we use the same model throughout the entire vertical extent of the ocean. Using the new K(sub m,h, s), we run an O-GCM and present a variety of results that we compare with Levitus and the KPP model. Since the traditional 1-point (used in papers 1 and 2) and the new 2-point closure models used here represent different modeling philosophies and procedures, testing them in an O-GCM is indispensable. The basic motivation is to show that the new 2-point closure model gives results that are overall superior to the 1-point closure in spite of the fact that the latter rely on several adjustable parameters while the new 2-point closure has none. After the extensive comparisons presented in papers 1 and 2, we conclude that the new model presented here is overall superior for it not only is parameter free but also 2 because is part of a more general turbulence model that has been previously successfully tested on a wide variety of other types of turbulent flows.

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

PubMed Central

2013-01-01

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

A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions

PubMed Central

Saa, Pedro; Nielsen, Lars K.

2015-01-01

Kinetic models provide the means to understand and predict the dynamic behaviour of enzymes upon different perturbations. Despite their obvious advantages, classical parameterizations require large amounts of data to fit their parameters. Particularly, enzymes displaying complex reaction and regulatory (allosteric) mechanisms require a great number of parameters and are therefore often represented by approximate formulae, thereby facilitating the fitting but ignoring many real kinetic behaviours. Here, we show that full exploration of the plausible kinetic space for any enzyme can be achieved using sampling strategies provided a thermodynamically feasible parameterization is used. To this end, we developed a General Reaction Assembly and Sampling Platform (GRASP) capable of consistently parameterizing and sampling accurate kinetic models using minimal reference data. The former integrates the generalized MWC model and the elementary reaction formalism. By formulating the appropriate thermodynamic constraints, our framework enables parameterization of any oligomeric enzyme kinetics without sacrificing complexity or using simplifying assumptions. This thermodynamically safe parameterization relies on the definition of a reference state upon which feasible parameter sets can be efficiently sampled. Uniform sampling of the kinetics space enabled dissecting enzyme catalysis and revealing the impact of thermodynamics on reaction kinetics. Our analysis distinguished three reaction elasticity regions for common biochemical reactions: a steep linear region (0> ΔGr >-2 kJ/mol), a transition region (-2> ΔGr >-20 kJ/mol) and a constant elasticity region (ΔGr <-20 kJ/mol). We also applied this framework to model more complex kinetic behaviours such as the monomeric cooperativity of the mammalian glucokinase and the ultrasensitive response of the phosphoenolpyruvate carboxylase of Escherichia coli. In both cases, our approach described appropriately not only the kinetic behaviour of these enzymes, but it also provided insights about the particular features underpinning the observed kinetics. Overall, this framework will enable systematic parameterization and sampling of enzymatic reactions. PMID:25874556

Note: Proton microbeam formation with continuously variable kinetic energy using a compact system for three-dimensional proton beam writing

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

Ohkubo, T., E-mail: ohkubo.takeru@jaea.go.jp; Ishii, Y.

A compact focused gaseous ion beam system has been developed to form proton microbeams of a few hundreds of keV with a penetration depth of micrometer range in 3-dimensional proton beam writing. Proton microbeams with kinetic energies of 100-140 keV were experimentally formed on the same point at a constant ratio of the kinetic energy of the object side to that of the image side. The experimental results indicate that the beam diameters were measured to be almost constant at approximately 6 μm at the same point with the kinetic energy range. These characteristics of the system were experimentally andmore » numerically demonstrated to be maintained as long as the ratio was constant.« 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.

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations

NASA Astrophysics Data System (ADS)

Wu, Hao; Nüske, Feliks; Paul, Fabian; Klus, Stefan; Koltai, Péter; Noé, Frank

2017-04-01

Markov state models (MSMs) and master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variational approach conformation dynamics/molecular kinetics (VAC) and its special case the time-lagged independent component analysis (TICA), which allow us to approximate slow collective variables and molecular kinetics by linear combinations of smooth basis functions or order parameters. While it is known how to estimate MSMs from trajectories whose starting points are not sampled from an equilibrium ensemble, this has not yet been the case for TICA and the VAC. Previous estimates from short trajectories have been strongly biased and thus not variationally optimal. Here, we employ the Koopman operator theory and the ideas from dynamic mode decomposition to extend the VAC and TICA to non-equilibrium data. The main insight is that the VAC and TICA provide a coefficient matrix that we call Koopman model, as it approximates the underlying dynamical (Koopman) operator in conjunction with the basis set used. This Koopman model can be used to compute a stationary vector to reweight the data to equilibrium. From such a Koopman-reweighted sample, equilibrium expectation values and variationally optimal reversible Koopman models can be constructed even with short simulations. The Koopman model can be used to propagate densities, and its eigenvalue decomposition provides estimates of relaxation time scales and slow collective variables for dimension reduction. Koopman models are generalizations of Markov state models, TICA, and the linear VAC and allow molecular kinetics to be described without a cluster discretization.

A Comprehensive Enzyme Kinetic Exercise for Biochemistry

ERIC Educational Resources Information Center

Barton, Janice S.

2011-01-01

This article describes a comprehensive treatment of experimental enzyme kinetics strongly coupled to electronic data acquisition and use of spreadsheets to organize data and perform linear and nonlinear least-squares analyses, all in a manner that promotes development of important reasoning skills. Kinetic parameters are obtained for the stable…

Simulation and fitting of complex reaction network TPR: The key is the objective function

DOE PAGES

Savara, Aditya Ashi

2016-07-07

In this research, a method has been developed for finding improved fits during simulation and fitting of data from complex reaction network temperature programmed reactions (CRN-TPR). It was found that simulation and fitting of CRN-TPR presents additional challenges relative to simulation and fitting of simpler TPR systems. The method used here can enable checking the plausibility of proposed chemical mechanisms and kinetic models. The most important finding was that when choosing an objective function, use of an objective function that is based on integrated production provides more utility in finding improved fits when compared to an objective function based onmore » the rate of production. The response surface produced by using the integrated production is monotonic, suppresses effects from experimental noise, requires fewer points to capture the response behavior, and can be simulated numerically with smaller errors. For CRN-TPR, there is increased importance (relative to simple reaction network TPR) in resolving of peaks prior to fitting, as well as from weighting of experimental data points. Using an implicit ordinary differential equation solver was found to be inadequate for simulating CRN-TPR. Lastly, the method employed here was capable of attaining improved fits in simulation and fitting of CRN-TPR when starting with a postulated mechanism and physically realistic initial guesses for the kinetic parameters.« less

Energy-dependent expansion of .177 caliber hollow-point air gun projectiles.

PubMed

Werner, Ronald; Schultz, Benno; Bockholdt, Britta; Ekkernkamp, Axel; Frank, Matthias

2017-05-01

Amongst hundreds of different projectiles for air guns available on the market, hollow-point air gun pellets are of special interest. These pellets are characterized by a tip or a hollowed-out shape in their tip which, when fired, makes the projectiles expand to an increased diameter upon entering the target medium. This results in an increase in release of energy which, in turn, has the potential to cause more serious injuries than non-hollow-point projectiles. To the best of the authors' knowledge, reliable data on the terminal ballistic features of hollow-point air gun projectiles compared to standard diabolo pellets have not yet been published in the forensic literature. The terminal ballistic performance (energy-dependent expansion and penetration) of four different types of .177 caliber hollow-point pellets discharged at kinetic energy levels from approximately 3 J up to 30 J into water, ordnance gelatin, and ordnance gelatin covered with natural chamois as a skin simulant was the subject of this investigation. Energy-dependent expansion of the tested hollow-point pellets was observed after being shot into all investigated target media. While some hollow-point pellets require a minimum kinetic energy of approximately 10 J for sufficient expansion, there are also hollow-point pellets which expand at kinetic energy levels of less than 5 J. The ratio of expansion (RE, calculated by the cross-sectional area (A) after impact divided by the cross-sectional area (A 0 ) of the undeformed pellet) of hollow-point air gun pellets reached values up of to 2.2. The extent of expansion relates to the kinetic energy of the projectile with a peak for pellet expansion at the 15 to 20 J range. To conclude, this work demonstrates that the hollow-point principle, i.e., the design-related enlargement of the projectiles' frontal area upon impact into a medium, does work in air guns as claimed by the manufacturers.

Comparison of dynamic contrast-enhanced MRI parameters of breast lesions at 1.5 and 3.0 T: a pilot study

PubMed Central

Pineda, F D; Medved, M; Fan, X; Ivancevic, M K; Abe, H; Shimauchi, A; Newstead, G M

2015-01-01

Objective: To compare dynamic contrast-enhanced (DCE) MRI parameters from scans of breast lesions at 1.5 and 3.0 T. Methods: 11 patients underwent paired MRI examinations in both Philips 1.5 and 3.0 T systems (Best, Netherlands) using a standard clinical fat-suppressed, T1 weighted DCE-MRI protocol, with 70–76 s temporal resolution. Signal intensity vs time curves were fit with an empirical mathematical model to obtain semi-quantitative measures of uptake and washout rates as well as time-to-peak enhancement (TTP). Maximum percent enhancement and signal enhancement ratio (SER) were also measured for each lesion. Percent differences between parameters measured at the two field strengths were compared. Results: TTP and SER parameters measured at 1.5 and 3.0 T were similar; with mean absolute differences of 19% and 22%, respectively. Maximum percent signal enhancement was significantly higher at 3 T than at 1.5 T (p = 0.006). Qualitative assessment showed that image quality was significantly higher at 3 T (p = 0.005). Conclusion: Our results suggest that TTP and SER are more robust to field strength change than other measured kinetic parameters, and therefore measurements of these parameters can be more easily standardized than measurements of other parameters derived from DCE-MRI. Semi-quantitative measures of overall kinetic curve shape showed higher reproducibility than do discrete classification of kinetic curve early and delayed phases in a majority of the cases studied. Advances in knowledge: Qualitative measures of curve shape are not consistent across field strength even when acquisition parameters are standardized. Quantitative measures of overall kinetic curve shape, by contrast, have higher reproducibility. PMID:25785918

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

PubMed

Du, Bin; Zielinski, Daniel C; Kavvas, Erol S; Dräger, Andreas; Tan, Justin; Zhang, Zhen; Ruggiero, Kayla E; Arzumanyan, Garri A; Palsson, Bernhard O

2016-06-06

The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question. In this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations. Overall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches.

Compressible Heating in the Condense Phase due to Pore Collapse in HMX

NASA Astrophysics Data System (ADS)

Zhang, Ju; Jackson, Thomas

Axisymmetric pore collapse in HMX is studied numerically by solving multi-phase reactive Euler equations. The generation of hot spots in the condense phase due to compressible heating is examined. The motivation is to improve the understanding of the role of embedded cavities in the initiation of reaction in explosives, and to investigate the effect of hot spots in the condense phase due to compressible heating alone, complementing previous study on hot spots due to the reaction in the gas phase and at the interface. It is found that the shock-cavity interaction results in pressures and thus temperatures that are substantially higher than the post-shock values in the condense phase. However, these hot spots in the condense phase due to compressible heating alone do not seem to be sufficiently hot to lead to ignition at shock pressures of 1-3 GPa. Thus, compressible heating in the condense phase may be excluded as a mechanism for initiation of explosives. It should be pointed out that the ignition threshold for the temperature, the so-called ``switch-on'' temperature, of hot spots depend on chemistry kinetics parameters. Switch-on temperature is lower for faster reaction rate. The current chemistry kinetics parameters are based on previous experimental work. This work was supported in part by the Defense Threat Reduction Agency and by the U.S. Department of Energy.

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.

Effects of Different PER Translational Kinetics on the Dynamics of a Core Circadian Clock Model

PubMed Central

Nieto, Paula S.; Revelli, Jorge A.; Garbarino-Pico, Eduardo; Condat, Carlos A.; Guido, Mario E.; Tamarit, Francisco A.

2015-01-01

Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis. PMID:25607544

Effects of different per translational kinetics on the dynamics of a core circadian clock model.

PubMed

Nieto, Paula S; Revelli, Jorge A; Garbarino-Pico, Eduardo; Condat, Carlos A; Guido, Mario E; Tamarit, Francisco A

2015-01-01

Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.

Parameter estimation and order selection for an empirical model of VO2 on-kinetics.

PubMed

Alata, O; Bernard, O

2007-04-27

In humans, VO2 on-kinetics are noisy numerical signals that reflect the pulmonary oxygen exchange kinetics at the onset of exercise. They are empirically modelled as a sum of an offset and delayed exponentials. The number of delayed exponentials; i.e. the order of the model, is commonly supposed to be 1 for low-intensity exercises and 2 for high-intensity exercises. As no ground truth has ever been provided to validate these postulates, physiologists still need statistical methods to verify their hypothesis about the number of exponentials of the VO2 on-kinetics especially in the case of high-intensity exercises. Our objectives are first to develop accurate methods for estimating the parameters of the model at a fixed order, and then, to propose statistical tests for selecting the appropriate order. In this paper, we provide, on simulated Data, performances of Simulated Annealing for estimating model parameters and performances of Information Criteria for selecting the order. These simulated Data are generated with both single-exponential and double-exponential models, and noised by white and Gaussian noise. The performances are given at various Signal to Noise Ratio (SNR). Considering parameter estimation, results show that the confidences of estimated parameters are improved by increasing the SNR of the response to be fitted. Considering model selection, results show that Information Criteria are adapted statistical criteria to select the number of exponentials.

Maximum Entropy Approach in Dynamic Contrast-Enhanced Magnetic Resonance Imaging.

PubMed

Farsani, Zahra Amini; Schmid, Volker J

2017-01-01

In the estimation of physiological kinetic parameters from Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) data, the determination of the arterial input function (AIF) plays a key role. This paper proposes a Bayesian method to estimate the physiological parameters of DCE-MRI along with the AIF in situations, where no measurement of the AIF is available. In the proposed algorithm, the maximum entropy method (MEM) is combined with the maximum a posterior approach (MAP). To this end, MEM is used to specify a prior probability distribution of the unknown AIF. The ability of this method to estimate the AIF is validated using the Kullback-Leibler divergence. Subsequently, the kinetic parameters can be estimated with MAP. The proposed algorithm is evaluated with a data set from a breast cancer MRI study. The application shows that the AIF can reliably be determined from the DCE-MRI data using MEM. Kinetic parameters can be estimated subsequently. The maximum entropy method is a powerful tool to reconstructing images from many types of data. This method is useful for generating the probability distribution based on given information. The proposed method gives an alternative way to assess the input function from the existing data. The proposed method allows a good fit of the data and therefore a better estimation of the kinetic parameters. In the end, this allows for a more reliable use of DCE-MRI. Schattauer GmbH.

IPMP Global Fit - A one-step direct data analysis tool for predictive microbiology.

PubMed

Huang, Lihan

2017-12-04

The objective of this work is to develop and validate a unified optimization algorithm for performing one-step global regression analysis of isothermal growth and survival curves for determination of kinetic parameters in predictive microbiology. The algorithm is incorporated with user-friendly graphical interfaces (GUIs) to develop a data analysis tool, the USDA IPMP-Global Fit. The GUIs are designed to guide the users to easily navigate through the data analysis process and properly select the initial parameters for different combinations of mathematical models. The software is developed for one-step kinetic analysis to directly construct tertiary models by minimizing the global error between the experimental observations and mathematical models. The current version of the software is specifically designed for constructing tertiary models with time and temperature as the independent model parameters in the package. The software is tested with a total of 9 different combinations of primary and secondary models for growth and survival of various microorganisms. The results of data analysis show that this software provides accurate estimates of kinetic parameters. In addition, it can be used to improve the experimental design and data collection for more accurate estimation of kinetic parameters. IPMP-Global Fit can be used in combination with the regular USDA-IPMP for solving the inverse problems and developing tertiary models in predictive microbiology. Published by Elsevier B.V.

Lamtoro charcoal (l. leucocephala) as bioreductor in nickel laterite reduction: performance and kinetics study

NASA Astrophysics Data System (ADS)

Petrus, H. T. B. M.; Diga, A.; Rhamdani, A. R.; Warmada, I. W.; Yuliansyah, A. T.; Perdana, I.

2017-04-01

The performance and kinetic of nickel laterite reduction were studied. In this work, the reduction of nickel laterite ores by anthracite coal, representing the high-grade carbon content matter, and lamtoro charcoal, representing the bioreductor, were conducted in air and CO2 atmosphere, within the temperature ranged from 800°C and 1000°C. XRD analysis was applied to observe the performance of anthracite and lamtoro as a reductor. Two models were applied, sphere particle geometry model and Ginstling-Brounhstein diffusion model, to study the kinetic parameters. The results indicated that the type of reductant and the reduction atmosphere used greatly influence the kinetic parameters. The obtained values of activation energy vary in the range of 13.42-18.12 kcal/mol.

Blind identification of the kinetic parameters in three-compartment models

NASA Astrophysics Data System (ADS)

Riabkov, Dmitri Y.; Di Bella, Edward V. R.

2004-03-01

Quantified knowledge of tissue kinetic parameters in the regions of the brain and other organs can offer information useful in clinical and research applications. Dynamic medical imaging with injection of radioactive or paramagnetic tracer can be used for this measurement. The kinetics of some widely used tracers such as [18F]2-fluoro-2-deoxy-D-glucose can be described by a three-compartment physiological model. The kinetic parameters of the tissue can be estimated from dynamically acquired images. Feasibility of estimation by blind identification, which does not require knowledge of the blood input, is considered analytically and numerically in this work for the three-compartment type of tissue response. The non-uniqueness of the two-region case for blind identification of kinetic parameters in three-compartment model is shown; at least three regions are needed for the blind identification to be unique. Numerical results for the accuracy of these blind identification methods in different conditions were considered. Both a separable variables least-squares (SLS) approach and an eigenvector-based algorithm for multichannel blind deconvolution approach were used. The latter showed poor accuracy. Modifications for non-uniform time sampling were also developed. Also, another method which uses a model for the blood input was compared. Results for the macroparameter K, which reflects the metabolic rate of glucose usage, using three regions with noise showed comparable accuracy for the separable variables least squares method and for the input model-based method, and slightly worse accuracy for SLS with the non-uniform sampling modification.

Two-order parameters theory of the metal-insulator phase transition kinetics in the magnetic field

NASA Astrophysics Data System (ADS)

Dubovskii, L. B.

2018-05-01

The metal-insulator phase transition is considered within the framework of the Ginzburg-Landau approach for the phase transition described with two coupled order parameters. One of the order parameters is the mass density which variation is responsible for the origin of nonzero overlapping of the two different electron bands and the appearance of free electron carriers. This transition is assumed to be a first-order phase one. The free electron carriers are described with the vector-function representing the second-order parameter responsible for the continuous phase transition. This order parameter determines mostly the physical properties of the metal-insulator transition and leads to a singularity of the surface tension at the metal-insulator interface. The magnetic field is involved into the consideration of the system. The magnetic field leads to new singularities of the surface tension at the metal-insulator interface and results in a drastic variation of the phase transition kinetics. A strong singularity in the surface tension results from the Landau diamagnetism and determines anomalous features of the metal-insulator transition kinetics.

The effect of heart motion on parameter bias in dynamic cardiac SPECT

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

Ross, S.G.; Gullberg, G.T.; Huesman, R.H.

1996-12-31

Dynamic cardiac SPECT can be used to estimate kinetic rate parameters which describe the wash-in and wash-out of tracer activity between the blood and the myocardial tissue. These kinetic parameters can in turn be correlated to myocardial perfusion. There are, however, many physical aspects associated with dynamic SPECT which can introduce errors into the estimates. This paper describes a study which investigates the effect of heart motion on kinetic parameter estimates. Dynamic SPECT simulations are performed using a beating version of the MCAT phantom. The results demonstrate that cardiac motion has a significant effect on the blood, tissue, and backgroundmore » content of regions of interest. This in turn affects estimates of wash-in, while it has very little effect on estimates of wash-out. The effect of cardiac motion on parameter estimates appears not to be as great as effects introduced by photon noise and geometric collimator response. It is also shown that cardiac motion results in little extravascular contamination of the left ventricle blood region of interest.« less

Comparison in waterborne Cu, Ni and Pb bioaccumulation kinetics between different gammarid species and populations: Natural variability and influence of metal exposure history.

PubMed

Urien, N; Farfarana, A; Uher, E; Fechner, L C; Chaumot, A; Geffard, O; Lebrun, J D

2017-12-01

Kinetic parameters (uptake from solution and elimination rate constants) of Cu, Ni and Pb bioaccumulation were determined from two Gammarus pulex and three Gammarus fossrum wild populations collected from reference sites throughout France in order to assess the inter-species and the natural inter-population variability of metal bioaccumulation kinetics in that sentinel organism. For that, each population was independently exposed for seven days to either 2.5μgL -1 Cu (39.3nM), 40μgL -1 Ni (681nM) or 10μgL -1 Pb (48.3nM) in laboratory controlled conditions, and then placed in unexposed microcosms for a 7-day depuration period. In the same way, the possible influence of metal exposure history on subsequent metal bioaccumulation kinetics was addressed by collecting wild gammarids from three populations inhabiting stations contaminated either by Cd, Pb or both Pb and Ni (named pre-exposed thereafter). In these pre-exposed organisms, assessment of any changes in metal bioaccumulation kinetics was achieved by comparison with the natural variability of kinetic parameters defined from reference populations. Results showed that in all studied populations (reference and pre-exposed) no significant Cu bioaccumulation was observed at the exposure concentration of 2.5μgL -1 . Concerning the reference populations, no significant differences in Ni and Pb bioaccumulation kinetics between the two species (G. pulex and G. fossarum) was observed allowing us to consider all the five reference populations to determine the inter-population natural variability, which was found to be relatively low (kinetic parameters determined for each population remained within a factor of 2 of the minimum and maximum values). Organisms from the population exhibiting a Pb exposure history presented reduced Ni uptake and elimination rate constants, whereas no influence on Ni kinetic parameters was observed in organisms from the population exhibiting an exposure history to both Ni and Pb. Furthermore Pb bioaccumulation kinetics were unaffected whatever the condition of pre-exposure in natural environment. Finally, these results highlight the complexity of confounding factors, such as metal exposure history, that influence metal bioaccumulation processes and showed that pre-exposure to one metal can cause changes in the bioaccumulation kinetics of other metals. These results also address the question of the underlying mechanisms developed by organisms to cope with metal contamination. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2011-01-01

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

Rational Design of Glucose-Responsive Insulin Using Pharmacokinetic Modeling.

PubMed

Bakh, Naveed A; Bisker, Gili; Lee, Michael A; Gong, Xun; Strano, Michael S

2017-11-01

A glucose responsive insulin (GRI) is a therapeutic that modulates its potency, concentration, or dosing of insulin in relation to a patient's dynamic glucose concentration, thereby approximating aspects of a normally functioning pancreas. Current GRI design lacks a theoretical basis on which to base fundamental design parameters such as glucose reactivity, dissociation constant or potency, and in vivo efficacy. In this work, an approach to mathematically model the relevant parameter space for effective GRIs is induced, and design rules for linking GRI performance to therapeutic benefit are developed. Well-developed pharmacokinetic models of human glucose and insulin metabolism coupled to a kinetic model representation of a freely circulating GRI are used to determine the desired kinetic parameters and dosing for optimal glycemic control. The model examines a subcutaneous dose of GRI with kinetic parameters in an optimal range that results in successful glycemic control within prescribed constraints over a 24 h period. Additionally, it is demonstrated that the modeling approach can find GRI parameters that enable stable glucose levels that persist through a skipped meal. The results provide a framework for exploring the parameter space of GRIs, potentially without extensive, iterative in vivo animal testing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method.

PubMed

Jia, Gengjie; Stephanopoulos, Gregory N; Gunawan, Rudiyanto

2011-07-15

Time-series measurements of metabolite concentration have become increasingly more common, providing data for building kinetic models of metabolic networks using ordinary differential equations (ODEs). In practice, however, such time-course data are usually incomplete and noisy, and the estimation of kinetic parameters from these data is challenging. Practical limitations due to data and computational aspects, such as solving stiff ODEs and finding global optimal solution to the estimation problem, give motivations to develop a new estimation procedure that can circumvent some of these constraints. In this work, an incremental and iterative parameter estimation method is proposed that combines and iterates between two estimation phases. One phase involves a decoupling method, in which a subset of model parameters that are associated with measured metabolites, are estimated using the minimization of slope errors. Another phase follows, in which the ODE model is solved one equation at a time and the remaining model parameters are obtained by minimizing concentration errors. The performance of this two-phase method was tested on a generic branched metabolic pathway and the glycolytic pathway of Lactococcus lactis. The results showed that the method is efficient in getting accurate parameter estimates, even when some information is missing.

Distributed activation energy model parameters of some Turkish coals

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

Gunes, M.; Gunes, S.K.

2008-07-01

A multi-reaction model based on distributed activation energy has been applied to some Turkish coals. The kinetic parameters of distributed activation energy model were calculated via computer program developed for this purpose. It was observed that the values of mean of activation energy distribution vary between 218 and 248 kJ/mol, and the values of standard deviation of activation energy distribution vary between 32 and 70 kJ/mol. The correlations between kinetic parameters of the distributed activation energy model and certain properties of coal have been investigated.

Cluster kinetics model for mixtures of glassformers

NASA Astrophysics Data System (ADS)

Brenskelle, Lisa A.; McCoy, Benjamin J.

2007-10-01

For glassformers we propose a binary mixture relation for parameters in a cluster kinetics model previously shown to represent pure compound data for viscosity and dielectric relaxation as functions of either temperature or pressure. The model parameters are based on activation energies and activation volumes for cluster association-dissociation processes. With the mixture parameters, we calculated dielectric relaxation times and compared the results to experimental values for binary mixtures. Mixtures of sorbitol and glycerol (seven compositions), sorbitol and xylitol (three compositions), and polychloroepihydrin and polyvinylmethylether (three compositions) were studied.

Development of a point-kinetic verification scheme for nuclear reactor applications

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

Demazière, C., E-mail: demaz@chalmers.se; Dykin, V.; Jareteg, K.

In this paper, a new method that can be used for checking the proper implementation of time- or frequency-dependent neutron transport models and for verifying their ability to recover some basic reactor physics properties is proposed. This method makes use of the application of a stationary perturbation to the system at a given frequency and extraction of the point-kinetic component of the system response. Even for strongly heterogeneous systems for which an analytical solution does not exist, the point-kinetic component follows, as a function of frequency, a simple analytical form. The comparison between the extracted point-kinetic component and its expectedmore » analytical form provides an opportunity to verify and validate neutron transport solvers. The proposed method is tested on two diffusion-based codes, one working in the time domain and the other working in the frequency domain. As long as the applied perturbation has a non-zero reactivity effect, it is demonstrated that the method can be successfully applied to verify and validate time- or frequency-dependent neutron transport solvers. Although the method is demonstrated in the present paper in a diffusion theory framework, higher order neutron transport methods could be verified based on the same principles.« less

SigrafW: An easy-to-use program for fitting enzyme kinetic data.

PubMed

Leone, Francisco Assis; Baranauskas, José Augusto; Furriel, Rosa Prazeres Melo; Borin, Ivana Aparecida

2005-11-01

SigrafW is Windows-compatible software developed using the Microsoft® Visual Basic Studio program that uses the simplified Hill equation for fitting kinetic data from allosteric and Michaelian enzymes. SigrafW uses a modified Fibonacci search to calculate maximal velocity (V), the Hill coefficient (n), and the enzyme-substrate apparent dissociation constant (K). The estimation of V, K, and the sum of the squares of residuals is performed using a Wilkinson nonlinear regression at any Hill coefficient (n). In contrast to many currently available kinetic analysis programs, SigrafW shows several advantages for the determination of kinetic parameters of both hyperbolic and nonhyperbolic saturation curves. No initial estimates of the kinetic parameters are required, a measure of the goodness-of-the-fit for each calculation performed is provided, the nonlinear regression used for calculations eliminates the statistical bias inherent in linear transformations, and the software can be used for enzyme kinetic simulations either for educational or research purposes. Persons interested in receiving a free copy of the software should contact Dr. F. A. Leone. Copyright © 2005 International Union of Biochemistry and Molecular Biology, Inc.

New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.

PubMed

Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda

2014-01-01

Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms. © 2013 FEBS.

Monochloramine Cometabolism by Mixed-Culture Nitrifiers ...

EPA Pesticide Factsheets

The current research investigated monochloramine cometabolism by nitrifying mixed cultures grown under drinking water relevant conditions and harvested from sand-packed reactors before conducting suspended growth batch kinetic experiments. Three batch reactors were used in each experiment: (1) a positive control to estimate ammonia kinetic parameters, (2) a negative control to account for abiotic reactions, and (3) a cometabolism reactor to estimate cometabolism kinetic constants. Kinetic parameters were estimated in AQUASIM with a simultaneous fit to all experimental data. Cometabolism kinetics were best described by a first order model. Monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism was a significant loss mechanism (30% of the observed monochloramine loss). These results demonstrated that monochloramine cometabolism occurred in mixed cultures similar to those found in drinking water distribution systems; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in drinking water distribution systems. The results demonstrated that monochloramine cometabolism occurred in mixed cultures similar to those found in drinking water distribution systems; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in drinking water distribution systems.

Degradation kinetics of cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside during hot air and vacuum drying in mulberry (Morus alba L.) fruit: A comparative study based on solid food system.

PubMed

Zhou, Mo; Chen, Qinqin; Bi, Jinfeng; Wang, Yixiu; Wu, Xinye

2017-08-15

The aim of this study is to ascertain the degradation kinetic of anthocyanin in dehydration process of solid food system. Mulberry fruit was treated by hot air and vacuum drying at 60 and 75°C. The contents of cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside were determined by using high performance liquid chromatography. Kinetic and thermodynamic parameters were calculated for analysing the degradation characteristics. Model fitting results showed monomeric anthocyanin degradations were followed the second-order kinetic. Vacuum drying presented high kinetic rate constants and low t 1/2 values. Thermodynamic parameters including the activation energy, enthalpy change and entropy change appeared significant differences between hot air and vacuum drying. Both heating techniques showed similar effects on polyphenol oxidase activities. These results indicate the anthocyanin degradation kinetic in solid food system is different from that in liquid and the oxygen can be regarded as a catalyst to accelerate the degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thermal oxidative degradation kinetics of agricultural residues using distributed activation energy model and global kinetic model.

PubMed

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

2018-08-01

The study concerned the thermal oxidative degradation kinetics of agricultural residues, peanut shell (PS) and sunflower shell (SS). The thermal behaviors were evaluated via thermogravimetric analysis and the kinetic parameters were determined by using distributed activation energy model (DAEM) and global kinetic model (GKM). Results showed that thermal oxidative decomposition of two samples processed in three zones; the ignition, burnout, and comprehensive combustibility between two agricultural residues were of great difference; and the combustion performance could be improved by boosting heating rate. The activation energy ranges calculated by the DAEM for the thermal oxidative degradation of PS and SS were 88.94-145.30 kJ mol -1 and 94.86-169.18 kJ mol -1 , respectively. The activation energy obtained by the GKM for the oxidative decomposition of hemicellulose and cellulose was obviously lower than that for the lignin oxidation at identical heating rate. To some degree, the determined kinetic parameters could acceptably simulate experimental data. Copyright © 2018 Elsevier Ltd. All rights reserved.

Modeling of the dispersion of depleted uranium aerosol.

PubMed

Mitsakou, C; Eleftheriadis, K; Housiadas, C; Lazaridis, M

2003-04-01

Depleted uranium is a low-cost radioactive material that, in addition to other applications, is used by the military in kinetic energy weapons against armored vehicles. During the Gulf and Balkan conflicts concern has been raised about the potential health hazards arising from the toxic and radioactive material released. The aerosol produced during impact and combustion of depleted uranium munitions can potentially contaminate wide areas around the impact sites or can be inhaled by civilians and military personnel. Attempts to estimate the extent and magnitude of the dispersion were until now performed by complex modeling tools employing unclear assumptions and input parameters of high uncertainty. An analytical puff model accommodating diffusion with simultaneous deposition is developed, which can provide a reasonable estimation of the dispersion of the released depleted uranium aerosol. Furthermore, the period of the exposure for a given point downwind from the release can be estimated (as opposed to when using a plume model). The main result is that the depleted uranium mass is deposited very close to the release point. The deposition flux at a couple of kilometers from the release point is more than one order of magnitude lower than the one a few meters near the release point. The effects due to uncertainties in the key input variables are addressed. The most influential parameters are found to be atmospheric stability, height of release, and wind speed, whereas aerosol size distribution is less significant. The output from the analytical model developed was tested against the numerical model RPM-AERO. Results display satisfactory agreement between the two models.

Nonlinear Dynamics and Nucleation Kinetics in Near-Critical Liquids

NASA Technical Reports Server (NTRS)

Patashinski, Alexander Z.; Ratner, Mark A.; Pines, Vladimir

1996-01-01

The objective of our study is to model the nonlinear behavior of a near-critical liquid following a rapid change of the temperature and/or other thermodynamic parameters (pressure, external electric or gravitational field). The thermodynamic critical point is manifested by large, strongly correlated fluctuations of the order parameter (particle density in liquid-gas systems, concentration in binary solutions) in the critical range of scales. The largest critical length scale is the correlation radius r(sub c). According to the scaling theory, r(sub c) increases as r(sub c) = r(sub 0)epsilon(exp -alpha) when the nondimensional distance epsilon = (T - T(sub c))/T(sub c) to the critical point decreases. The normal gravity alters the nature of correlated long-range fluctuations when one reaches epsilon approximately equal to 10(exp -5), and correspondingly the relaxation time, tau(r(sub c)), is approximately equal to 10(exp -3) seconds; this time is short when compared to the typical experimental time. Close to the critical point, a rapid, relatively small temperature change may perturb the thermodynamic equilibrium on many scales. The critical fluctuations have a hierarchical structure, and the relaxation involves many length and time scales. Above the critical point, in the one-phase region, we consider the relaxation of the liquid following a sudden temperature change that simultaneously violates the equilibrium on many scales. Below T(sub c), a non-equilibrium state may include a distribution of small scale phase droplets; we consider the relaxation of such a droplet following a temperature change that has made the phase of the matrix stable.

Kinetic Simulations of Type II Radio Burst Emission Processes

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro

PubMed Central

Rudorf, Sophia; Thommen, Michael; Rodnina, Marina V.; Lipowsky, Reinhard

2014-01-01

The molecular machinery of life relies on complex multistep processes that involve numerous individual transitions, such as molecular association and dissociation steps, chemical reactions, and mechanical movements. The corresponding transition rates can be typically measured in vitro but not in vivo. Here, we develop a general method to deduce the in-vivo rates from their in-vitro values. The method has two basic components. First, we introduce the kinetic distance, a new concept by which we can quantitatively compare the kinetics of a multistep process in different environments. The kinetic distance depends logarithmically on the transition rates and can be interpreted in terms of the underlying free energy barriers. Second, we minimize the kinetic distance between the in-vitro and the in-vivo process, imposing the constraint that the deduced rates reproduce a known global property such as the overall in-vivo speed. In order to demonstrate the predictive power of our method, we apply it to protein synthesis by ribosomes, a key process of gene expression. We describe the latter process by a codon-specific Markov model with three reaction pathways, corresponding to the initial binding of cognate, near-cognate, and non-cognate tRNA, for which we determine all individual transition rates in vitro. We then predict the in-vivo rates by the constrained minimization procedure and validate these rates by three independent sets of in-vivo data, obtained for codon-dependent translation speeds, codon-specific translation dynamics, and missense error frequencies. In all cases, we find good agreement between theory and experiment without adjusting any fit parameter. The deduced in-vivo rates lead to smaller error frequencies than the known in-vitro rates, primarily by an improved initial selection of tRNA. The method introduced here is relatively simple from a computational point of view and can be applied to any biomolecular process, for which we have detailed information about the in-vitro kinetics. PMID:25358034

Sulfide binding properties of truncated hemoglobins.

PubMed

Nicoletti, Francesco P; Comandini, Alessandra; Bonamore, Alessandra; Boechi, Leonardo; Boubeta, Fernando Martin; Feis, Alessandro; Smulevich, Giulietta; Boffi, Alberto

2010-03-16

The truncated hemoglobins from Bacillus subtilis (Bs-trHb) and Thermobifida fusca (Tf-trHb) have been shown to form high-affinity complexes with hydrogen sulfide in their ferric state. The recombinant proteins, as extracted from Escherichia coli cells after overexpression, are indeed partially saturated with sulfide, and even highly purified samples still contain a small but significant amount of iron-bound sulfide. Thus, a complete thermodynamic and kinetic study has been undertaken by means of equilibrium and kinetic displacement experiments to assess the relevant sulfide binding parameters. The body of experimental data indicates that both proteins possess a high affinity for hydrogen sulfide (K = 5.0 x 10(6) and 2.8 x 10(6) M(-1) for Bs-trHb and Tf-trHb, respectively, at pH 7.0), though lower with respect to that reported previously for the sulfide avid Lucina pectinata I hemoglobins (2.9 x 10(8) M(-1)). From the kinetic point of view, the overall high affinity resides in the slow rate of sulfide release, attributed to hydrogen bonding stabilization of the bound ligand by distal residue WG8. A set of point mutants in which these residues have been replaced with Phe indicates that the WG8 residue represents the major kinetic barrier to the escape of the bound sulfide species. Accordingly, classical molecular dynamics simulations of SH(-)-bound ferric Tf-trHb show that WG8 plays a key role in the stabilization of coordinated SH(-) whereas the YCD1 and YB10 contributions are negligible. Interestingly, the triple Tf-trHb mutant bearing only Phe residues in the relevant B10, G8, and CD1 positions is endowed with a higher overall affinity for sulfide characterized by a very fast second-order rate constant and 2 order of magnitude faster kinetics of sulfide release with respect to the wild-type protein. Resonance Raman spectroscopy data indicate that the sulfide adducts are typical of a ferric iron low-spin derivative. In analogy with other low-spin ferric sulfide adducts, the strong band at 375 cm(-1) is tentatively assigned to a Fe-S stretching band. The high affinity for hydrogen sulfide is thought to have a possible physiological significance as H(2)S is produced in bacteria at metabolic steps involved in cysteine biosynthesis and hence in thiol redox homeostasis.

Electrostatic stability of electron-positron plasmas in dipole geometry

NASA Astrophysics Data System (ADS)

Mishchenko, Alexey; Plunk, Gabriel G.; Helander, Per

2018-04-01

The electrostatic stability of electron-positron plasmas is investigated in the point-dipole and Z-pinch limits of dipole geometry. The kinetic dispersion relation for sub-bounce-frequency instabilities is derived and solved. For the zero-Debye-length case, the stability diagram is found to exhibit singular behaviour. However, when the Debye length is non-zero, a fluid mode appears, which resolves the observed singularity, and also demonstrates that both the temperature and density gradients can drive instability. It is concluded that a finite Debye length is necessary to determine the stability boundaries in parameter space. Landau damping is investigated at scales sufficiently smaller than the Debye length, where instability is absent.

Synchronization behaviors of coupled systems composed of hidden attractors

NASA Astrophysics Data System (ADS)

Zhang, Ge; Wu, Fuqiang; Wang, Chunni; Ma, Jun

2017-10-01

Based on a class of chaotic system composed of hidden attractors, in which the equilibrium points are described by a circular function, complete synchronization between two identical systems, pattern formation and synchronization of network is investigated, respectively. A statistical factor of synchronization is defined and calculated by using the mean field theory, the dependence of synchronization on bifurcation parameters discussed in numerical way. By setting a chain network, which local kinetic is described by hidden attractors, synchronization approach is investigated. It is found that the synchronization and pattern formation are dependent on the coupling intensity and also the selection of coupling variables. In the end, open problems are proposed for readers’ extensive guidance and investigation.

Integral Design Methodology of Photocatalytic Reactors for Air Pollution Remediation.

PubMed

Passalía, Claudio; Alfano, Orlando M; Brandi, Rodolfo J

2017-06-07

An integral reactor design methodology was developed to address the optimal design of photocatalytic wall reactors to be used in air pollution control. For a target pollutant to be eliminated from an air stream, the proposed methodology is initiated with a mechanistic derived reaction rate. The determination of intrinsic kinetic parameters is associated with the use of a simple geometry laboratory scale reactor, operation under kinetic control and a uniform incident radiation flux, which allows computing the local superficial rate of photon absorption. Thus, a simple model can describe the mass balance and a solution may be obtained. The kinetic parameters may be estimated by the combination of the mathematical model and the experimental results. The validated intrinsic kinetics obtained may be directly used in the scaling-up of any reactor configuration and size. The bench scale reactor may require the use of complex computational software to obtain the fields of velocity, radiation absorption and species concentration. The complete methodology was successfully applied to the elimination of airborne formaldehyde. The kinetic parameters were determined in a flat plate reactor, whilst a bench scale corrugated wall reactor was used to illustrate the scaling-up methodology. In addition, an optimal folding angle of the corrugated reactor was found using computational fluid dynamics tools.

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.

Identification of temporal pathomechanical factors during the tennis serve.

PubMed

Martin, Caroline; Kulpa, Richard; Ropars, Mickaël; Delamarche, Paul; Bideau, Benoit

2013-11-01

The purpose of this study was twofold: (a) to measure the effects of temporal parameters on both ball velocity and upper limb joint kinetics to identify pathomechanical factors during the tennis serve and (b) to validate these pathomechanical factors by comparing injured and noninjured players. The serves of expert tennis players were recorded with an optoelectronic motion capture system. These experts were then followed during two seasons to identify overuse injuries of the upper limb. Correlation coefficients assessed the relationships between temporal parameters, ball velocity, and peaks of upper limb joint kinetics to identify pathomechanical factors. Temporal parameters and ball velocity were compared between injured and noninjured groups. Temporal pathomechanical factors were identified. The timings of peak angular velocities of pelvis longitudinal rotation, upper torso longitudinal rotation, trunk sagittal rotation, and trunk transverse rotation and the duration between instants of shoulder horizontal adduction and external rotation were significantly related to upper limb joint kinetics and ball velocity. Injured players demonstrated later timings of trunk rotations, improper differences in time between instants of shoulder horizontal adduction and external rotation, lower ball velocities, and higher joint kinetics. The findings of this study imply that improper temporal mechanics during the tennis serve can decrease ball velocity, increase upper limb joint kinetics, and thus possibly increase overuse injuries of the upper limb.

Charged boson stars and black holes with nonminimal coupling to gravity

NASA Astrophysics Data System (ADS)

Verbin, Y.; Brihaye, Y.

2018-02-01

We find new spherically symmetric charged boson star solutions of a complex scalar field coupled nonminimally to gravity by a "John-type" term of Horndeski theory, that is a coupling between the kinetic scalar term and Einstein tensor. We study the parameter space of the solutions and find two distinct families according to their position in parameter space. More widespread is the family of solutions (which we call branch 1) existing for a finite interval of the central value of the scalar field starting from zero and ending at some finite maximal value. This branch contains as a special case the charged boson stars of the minimally coupled theory. In some regions of parameter space we find a new second branch ("branch 2") of solutions which are more massive and more stable than those of branch 1. This second branch exists also in a finite interval of the central value of the scalar field, but its end points (either both or in some cases only one) are extremal Reissner-Nordström black hole solutions.

Comparative evaluation of thermal oxidative decomposition for oil-plant residues via thermogravimetric analysis: Thermal conversion characteristics, kinetics, and thermodynamics.

PubMed

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

2017-11-01

Thermal oxidative decomposition characteristics, kinetics, and thermodynamics of rape straw (RS), rapeseed meal (RM), camellia seed shell (CS), and camellia seed meal (CM) were evaluated via thermogravimetric analysis (TGA). TG-DTG-DSC curves demonstrated that the combustion of oil-plant residues proceeded in three stages, including dehydration, release and combustion of organic volatiles, and chars oxidation. As revealed by combustion characteristic parameters, the ignition, burnout, and comprehensive combustion performance of residues were quite distinct from each other, and were improved by increasing heating rate. The kinetic parameters were determined by Coats-Redfern approach. The results showed that the most possible combustion mechanisms were order reaction models. The existence of kinetic compensation effect was clearly observed. The thermodynamic parameters (ΔH, ΔG, ΔS) at peak temperatures were calculated through the activated complex theory. With the combustion proceeding, the variation trends of ΔH, ΔG, and ΔS for RS (RM) similar to those for CS (CM). Copyright © 2017 Elsevier Ltd. All rights reserved.

Rock Cutting Depth Model Based on Kinetic Energy of Abrasive Waterjet

NASA Astrophysics Data System (ADS)

Oh, Tae-Min; Cho, Gye-Chun

2016-03-01

Abrasive waterjets are widely used in the fields of civil and mechanical engineering for cutting a great variety of hard materials including rocks, metals, and other materials. Cutting depth is an important index to estimate operating time and cost, but it is very difficult to predict because there are a number of influential variables (e.g., energy, geometry, material, and nozzle system parameters). In this study, the cutting depth is correlated to the maximum kinetic energy expressed in terms of energy (i.e., water pressure, water flow rate, abrasive feed rate, and traverse speed), geometry (i.e., standoff distance), material (i.e., α and β), and nozzle system parameters (i.e., nozzle size, shape, and jet diffusion level). The maximum kinetic energy cutting depth model is verified with experimental test data that are obtained using one type of hard granite specimen for various parameters. The results show a unique curve for a specific rock type in a power function between cutting depth and maximum kinetic energy. The cutting depth model developed here can be very useful for estimating the process time when cutting rock using an abrasive waterjet.

Comparison of NBG-18, NBG-17, IG-110 and IG-11 oxidation kinetics in air

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

Lee, Jo Jo; Ghosh, Tushar K.; Loyalka, Sudarshan K.

In this paper, the oxidation rates of several nuclear-grade graphites, NBG-18, NBG-17, IG-110 and IG-11, were measured in air using thermogravimetry. Kinetic parameters and oxidation behavior for each grade were compared by coke type, filler grain size and microstructure. The thickness of the oxidized layer for each grade was determined by layer peeling and direct density measurements. The results for NBG-17 and IG-11 were compared with those available in the literature and our recently reported results for NBG-18 and IG-110 oxidation in air. The finer-grained graphites IG-110 and IG-11 were more oxidized than medium-grained NBG-18 and NBG-17 because of deepermore » oxidant penetration, higher porosity and higher probability of available active sites. Variation in experimental conditions also had a marked effect on the reported kinetic parameters by several studies. Finally, kinetic parameters such as activation energy and transition temperature were sensitive to air flow rates as well as sample size and geometry.« less

Comparison of NBG-18, NBG-17, IG-110 and IG-11 oxidation kinetics in air

DOE PAGES

Lee, Jo Jo; Ghosh, Tushar K.; Loyalka, Sudarshan K.

2017-12-14

In this paper, the oxidation rates of several nuclear-grade graphites, NBG-18, NBG-17, IG-110 and IG-11, were measured in air using thermogravimetry. Kinetic parameters and oxidation behavior for each grade were compared by coke type, filler grain size and microstructure. The thickness of the oxidized layer for each grade was determined by layer peeling and direct density measurements. The results for NBG-17 and IG-11 were compared with those available in the literature and our recently reported results for NBG-18 and IG-110 oxidation in air. The finer-grained graphites IG-110 and IG-11 were more oxidized than medium-grained NBG-18 and NBG-17 because of deepermore » oxidant penetration, higher porosity and higher probability of available active sites. Variation in experimental conditions also had a marked effect on the reported kinetic parameters by several studies. Finally, kinetic parameters such as activation energy and transition temperature were sensitive to air flow rates as well as sample size and geometry.« less

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.

Direct Parametric Image Reconstruction in Reduced Parameter Space for Rapid Multi-Tracer PET Imaging.

PubMed

Cheng, Xiaoyin; Li, Zhoulei; Liu, Zhen; Navab, Nassir; Huang, Sung-Cheng; Keller, Ulrich; Ziegler, Sibylle; Shi, Kuangyu

2015-02-12

The separation of multiple PET tracers within an overlapping scan based on intrinsic differences of tracer pharmacokinetics is challenging, due to limited signal-to-noise ratio (SNR) of PET measurements and high complexity of fitting models. In this study, we developed a direct parametric image reconstruction (DPIR) method for estimating kinetic parameters and recovering single tracer information from rapid multi-tracer PET measurements. This is achieved by integrating a multi-tracer model in a reduced parameter space (RPS) into dynamic image reconstruction. This new RPS model is reformulated from an existing multi-tracer model and contains fewer parameters for kinetic fitting. Ordered-subsets expectation-maximization (OSEM) was employed to approximate log-likelihood function with respect to kinetic parameters. To incorporate the multi-tracer model, an iterative weighted nonlinear least square (WNLS) method was employed. The proposed multi-tracer DPIR (MTDPIR) algorithm was evaluated on dual-tracer PET simulations ([18F]FDG and [11C]MET) as well as on preclinical PET measurements ([18F]FLT and [18F]FDG). The performance of the proposed algorithm was compared to the indirect parameter estimation method with the original dual-tracer model. The respective contributions of the RPS technique and the DPIR method to the performance of the new algorithm were analyzed in detail. For the preclinical evaluation, the tracer separation results were compared with single [18F]FDG scans of the same subjects measured 2 days before the dual-tracer scan. The results of the simulation and preclinical studies demonstrate that the proposed MT-DPIR method can improve the separation of multiple tracers for PET image quantification and kinetic parameter estimations.

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.

On kinetic modelling for solar redox thermochemical H2O and CO2 splitting over NiFe2O4 for H2, CO and syngas production.

PubMed

Dimitrakis, Dimitrios A; Syrigou, Maria; Lorentzou, Souzana; Kostoglou, Margaritis; Konstandopoulos, Athanasios G

2017-10-11

This study aims at developing a kinetic model that can adequately describe solar thermochemical water and carbon dioxide splitting with nickel ferrite powder as the active redox material. The kinetic parameters of water splitting of a previous study are revised to include transition times and new kinetic parameters for carbon dioxide splitting are developed. The computational results show a satisfactory agreement with experimental data and continuous multicycle operation under varying operating conditions is simulated. Different test cases are explored in order to improve the product yield. At first a parametric analysis is conducted, investigating the appropriate duration of the oxidation and the thermal reduction step that maximizes the hydrogen yield. Subsequently, a non-isothermal oxidation step is simulated and proven as an interesting option for increasing the hydrogen production. The kinetic model is adapted to simulate the production yields in structured solar reactor components, i.e. extruded monolithic structures, as well.

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.

Co-pyrolysis kinetics of sewage sludge and bagasse using multiple normal distributed activation energy model (M-DAEM).

PubMed

Lin, Yan; Chen, Zhihao; Dai, Minquan; Fang, Shiwen; Liao, Yanfen; Yu, Zhaosheng; Ma, Xiaoqian

2018-07-01

In this study, the kinetic models of bagasse, sewage sludge and their mixture were established by the multiple normal distributed activation energy model. Blending with sewage sludge, the initial temperature declined from 437 K to 418 K. The pyrolytic species could be divided into five categories, including analogous hemicelluloses I, hemicelluloses II, cellulose, lignin and bio-char. In these species, the average activation energies and the deviations situated at reasonable ranges of 166.4673-323.7261 kJ/mol and 0.1063-35.2973 kJ/mol, respectively, which were conformed to the references. The kinetic models were well matched to experimental data, and the R 2 were greater than 99.999%y. In the local sensitivity analysis, the distributed average activation energy had stronger effect on the robustness than other kinetic parameters. And the content of pyrolytic species determined which series of kinetic parameters were more important. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effect of CNT addition on cure kinetics of glass fiber/epoxy composite

NASA Astrophysics Data System (ADS)

Fulmali, A. O.; Kattaguri, R.; Mahato, K. K.; Prusty, R. K.; Ray, B. C.

2018-03-01

In present time, developments in reinforced polymer composites have acquired preferential attention for high performance and high precision applications like aerospace, marine and transportation. Fibre reinforced polymer (FRP) composites are being substituted because of their low density, higher strength, stiffness, impact resistance, and improved corrosion resistance. Further laminated composites exhibit superior in-plane mechanical properties that are mostly governed by the fibers. However, laminated FRP composites suffer from poor out of plane properties in some applications. These properties can further be improved by the addition of Nano fillers like carbon nanotube (CNT), graphene and so on. Curing cycle plays a very important role in drawing out the optimum property of glass fiber/epoxy (GE) composite. It is expected that the cure kinetics can further be altered by addition of CNT due to its higher aspect ratio. The main objective of this work is to study the effect of CNT addition on cure kinetics of GE composite as multi-segment adsorption of polymer takes place on the CNT surface. In this study effects of curing parameters on mechanical properties and glass transition temperature of CNT embedded glass fiber/epoxy composite (CNT-GE) has been evaluated. For this study control GE and CNT-GE (with 0.1 wt. %) laminates were fabricated using hand lay-up technique followed by hot compression. The curing parameters that were considered in the present investigation were temperature (80°C, 110°C, and 140°C) and time (0.5 hr, 3 hr and 6 hr). For different combination of above mentioned temperature and time, samples of GE and CNT-GE composites were post cured. Mechanical properties were determined by flexural testing using 3 point bending fixture on INSTRON-5967 and thermal properties i.e. glass transition temperature (Tg) determined by Differential Scanning Calorimeter (DSC) to evaluate the effects of curing parameters. For CNT-GE samples, No much variation observed in flexural modulus with increase in post curing temperature and time, but swift increment was observed in flexural strength at 140°C with increase in post cure time. Elevation in Tg observed with increase in temperature and time duration of post curing; highest Tg noted at 140°C-6hr. Optimum post curing parameters for CNT-GE composite observed to be 140°C-6hr.

Kinetic and isotherm analyses for thorium (IV) adsorptive removal from aqueous solutions by modified magnetite nanoparticle using response surface methodology (RSM)

NASA Astrophysics Data System (ADS)

Karimi, Mohammad; Milani, Saeid Alamdar; Abolgashemi, Hossein

2016-10-01

In this study, the ability and the adsorption capacity of magnetite/aminopropyltriethoxysilane/glutaraldehyde (Fe3O4/APTES/GA) adsorbent were evaluated for the adsorption of thorium (IV) ions from aqueous solutions. The influence of the several variables such as pH (1-5), Th (IV) initial concentration (50-300 mg L-1) and adsorbent concentration (1-5 g L-1) on the Th (IV) adsorption were investigated by response surface methodology (RSM). The results showed that the highest absorption capacity (q) was 107.23 mg g-1 with respect to pH = 4.5, initial concentration of 250 mg L-1 and adsorbent concentration of 1 g L-1 for 90 min. Modeling equilibrium sorption data with the Langmuir, Freundlich and Dubinin-Radushkevich models pointed out that the results were in good agreement with Langmuir model. The experimental kinetic data were well fitted to pseudo-second-order equation with R2 = 0.9739. Also thermodynamic parameters (ΔGo, ΔHo, ΔSo) declared that the Th (IV) adsorption was endothermic and spontaneous.

Preparation and characterization of corn cob activated carbon coated with nano-sized magnetite particles for the removal of Cr(VI).

PubMed

Nethaji, S; Sivasamy, A; Mandal, A B

2013-04-01

Activated carbon prepared from corn cob biomass, magnetized by magnetite nanoparticles (MCCAC) was used for the adsorption of hexavalent chromium from aqueous solution. The adsorbent was characterized by SEM, TEM, XRD, VSM, surface functionality and zero-point charge. The iron oxide nanoparticles were of 50 nm sizes and the saturation magnetization value for the adsorbent is 48.43 emu/g. Adsorption was maximum at pH 2. Isotherm data were modeled using Langmuir, Freundlich and Temkin isotherm. The prepared MCCAC had a heterogeneous surface. The maximum monolayer adsorption capacity was 57.37 mg/g. Kinetic studies were carried out and the data fitted the pseudo second-order equation. The mechanism of the adsorption process was studied by incorporating the kinetic data with intraparticle diffusion model, Bangham equation and Boyd plot. The adsorption was by chemisorption and the external mass transfer was the rate-determining step. A micro column was designed and the basic column parameters were estimated. Copyright © 2013 Elsevier Ltd. All rights reserved.

Production, purification, and characterization of metalloprotease from Candida kefyr 41 PSB.

PubMed

Yavuz, Sevgi; Kocabay, Samet; Çetinkaya, Serap; Akkaya, Birnur; Akkaya, Recep; Yenidunya, Ali Fazil; Bakıcı, Mustafa Zahir

2017-01-01

A thermostable metalloprotease, produced from an environmental strain of Candida kefyr 41 PSB, was purified 16 fold with a 60% yield by cold ethanol precipitation and affinity chromatography (bentonite-acrylamide-cysteine microcomposite). The purified enzyme appeared as a single protein band at 43kDa. Its optimum pH and temperature points were found to be 7.0 and 105°C, respectively. K m and V max values of the enzyme were determined to be 3.5mg/mL and 4.4μmolmL -1 min -1 , 1.65mg/mL and 6.1μmolmL -1 min -1 , using casein and gelatine as the substrates, respectively. The activity was inhibited by using ethylenediamine tetraacetic acid (EDTA), indicating that the enzyme was a metalloprotease. Stability of the enzyme was investigated by using thermodynamic and kinetic parameters. The thermal inactivation profile of the enzyme conformed to the first order kinetics. The half life of the enzyme at 95, 105, 115, 125 and 135°C was 1310, 610, 220, 150, and 86min, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

"First-principles" kinetic Monte Carlo simulations revisited: CO oxidation over RuO2 (110).

PubMed

Hess, Franziska; Farkas, Attila; Seitsonen, Ari P; Over, Herbert

2012-03-15

First principles-based kinetic Monte Carlo (kMC) simulations are performed for the CO oxidation on RuO(2) (110) under steady-state reaction conditions. The simulations include a set of elementary reaction steps with activation energies taken from three different ab initio density functional theory studies. Critical comparison of the simulation results reveals that already small variations in the activation energies lead to distinctly different reaction scenarios on the surface, even to the point where the dominating elementary reaction step is substituted by another one. For a critical assessment of the chosen energy parameters, it is not sufficient to compare kMC simulations only to experimental turnover frequency (TOF) as a function of the reactant feed ratio. More appropriate benchmarks for kMC simulations are the actual distribution of reactants on the catalyst's surface during steady-state reaction, as determined by in situ infrared spectroscopy and in situ scanning tunneling microscopy, and the temperature dependence of TOF in the from of Arrhenius plots. Copyright © 2012 Wiley Periodicals, Inc.

Kinetic modelling of passive transport and active efflux of a fluoroquinolone across Caco-2 cells using a compartmental approach in NONMEM.

PubMed

González-Alvarez, I; Fernández-Teruel, C; Garrigues, T M; Casabo, V G; Ruiz-García, A; Bermejo, M

2005-12-01

The purpose was to develop a general mathematical model for estimating passive permeability and efflux transport parameters from in vitro cell culture experiments. The procedure is applicable for linear and non-linear transport of drug with time, <10 or >10% of drug transport, negligible or relevant back flow, and would allow the adequate correction in the case of relevant mass balance problems. A compartmental kinetic approach was used and the transport barriers were described quantitatively in terms of apical and basolateral clearances. The method can be applied when sink conditions are not achieved and it allows the evaluation of the location of the transporter and its binding site. In this work it was possible to demonstrate, from a functional point of view, the higher efflux capacity of the TC7 clone and to identify the apical membrane as the main resistance for the xenobiotic transport. This methodology can be extremely useful as a complementary tool for molecular biology approaches in order to establish meaningful hypotheses about transport mechanisms.

The processive kinetics of gene conversion in bacteria

PubMed Central

Paulsson, Johan; El Karoui, Meriem; Lindell, Monica

2017-01-01

Summary Gene conversion, non‐reciprocal transfer from one homologous sequence to another, is a major force in evolutionary dynamics, promoting co‐evolution in gene families and maintaining similarities between repeated genes. However, the properties of the transfer – where it initiates, how far it proceeds and how the resulting conversion tracts are affected by mismatch repair – are not well understood. Here, we use the duplicate tuf genes in Salmonella as a quantitatively tractable model system for gene conversion. We selected for conversion in multiple different positions of tuf, and examined the resulting distributions of conversion tracts in mismatch repair‐deficient and mismatch repair‐proficient strains. A simple stochastic model accounting for the essential steps of conversion showed excellent agreement with the data for all selection points using the same value of the conversion processivity, which is the only kinetic parameter of the model. The analysis suggests that gene conversion effectively initiates uniformly at any position within a tuf gene, and proceeds with an effectively uniform conversion processivity in either direction limited by the bounds of the gene. PMID:28256783

Kinetic theory of situated agents applied to pedestrian flow in a corridor

NASA Astrophysics Data System (ADS)

Rangel-Huerta, A.; Muñoz-Meléndez, A.

2010-03-01

A situated agent-based model for simulation of pedestrian flow in a corridor is presented. In this model, pedestrians choose their paths freely and make decisions based on local criteria for solving collision conflicts. The crowd consists of multiple walking agents equipped with a function of perception as well as a competitive rule-based strategy that enables pedestrians to reach free access areas. Pedestrians in our model are autonomous entities capable of perceiving and making decisions. They apply socially accepted conventions, such as avoidance rules, as well as individual preferences such as the use of specific exit points, or the execution of eventual comfort turns resulting in spontaneous changes of walking speed. Periodic boundary conditions were considered in order to determine the density-average walking speed, and the density-average activity with respect to specific parameters: comfort angle turn and frequency of angle turn of walking agents. The main contribution of this work is an agent-based model where each pedestrian is represented as an autonomous agent. At the same time the pedestrian crowd dynamics is framed by the kinetic theory of biological systems.

Nonlinear saturation of the slab ITG instability and zonal flow generation with fully kinetic ions

NASA Astrophysics Data System (ADS)

Miecnikowski, Matthew T.; Sturdevant, Benjamin J.; Chen, Yang; Parker, Scott E.

2018-05-01

Fully kinetic turbulence models are of interest for their potential to validate or replace gyrokinetic models in plasma regimes where the gyrokinetic expansion parameters are marginal. Here, we demonstrate fully kinetic ion capability by simulating the growth and nonlinear saturation of the ion-temperature-gradient instability in shearless slab geometry assuming adiabatic electrons and including zonal flow dynamics. The ion trajectories are integrated using the Lorentz force, and the cyclotron motion is fully resolved. Linear growth and nonlinear saturation characteristics show excellent agreement with analogous gyrokinetic simulations across a wide range of parameters. The fully kinetic simulation accurately reproduces the nonlinearly generated zonal flow. This work demonstrates nonlinear capability, resolution of weak gradient drive, and zonal flow physics, which are critical aspects of modeling plasma turbulence with full ion dynamics.

Inflection point in running kinetic term inflation

NASA Astrophysics Data System (ADS)

Gao, Tie-Jun; Xiu, Wu-Tao; Yang, Xiu-Yi

2017-04-01

In this work, we calculate the general form of the scalar potential with polynomial superpotential in the framework of running kinetic term inflation, then focus on a polynomial superpotential with two terms and obtain the inflection point inflationary model. We study the inflationary dynamics and show that the predicted value of the scalar spectral index and tensor-to-scalar ratio can lie within the 1σ confidence region allowed by the result of Planck 2015.

Characterization of 12 GnRH peptide agonists - a kinetic perspective.

PubMed

Nederpelt, Indira; Georgi, Victoria; Schiele, Felix; Nowak-Reppel, Katrin; Fernández-Montalván, Amaury E; IJzerman, Adriaan P; Heitman, Laura H

2016-01-01

Drug-target residence time is an important, yet often overlooked, parameter in drug discovery. Multiple studies have proposed an increased residence time to be beneficial for improved drug efficacy and/or longer duration of action. Currently, there are many drugs on the market targeting the gonadotropin-releasing hormone (GnRH) receptor for the treatment of hormone-dependent diseases. Surprisingly, the kinetic receptor-binding parameters of these analogues have not yet been reported. Therefore, this project focused on determining the receptor-binding kinetics of 12 GnRH peptide agonists, including many marketed drugs. A novel radioligand-binding competition association assay was developed and optimized for the human GnRH receptor with the use of a radiolabelled peptide agonist, [(125) I]-triptorelin. In addition to radioligand-binding studies, a homogeneous time-resolved FRET Tag-lite™ method was developed as an alternative assay for the same purpose. Two novel competition association assays were successfully developed and applied to determine the kinetic receptor-binding characteristics of 12 high-affinity GnRH peptide agonists. Results obtained from both methods were highly correlated. Interestingly, the binding kinetics of the peptide agonists were more divergent than their affinities with residence times ranging from 5.6 min (goserelin) to 125 min (deslorelin). Our research provides new insights by incorporating kinetic, next to equilibrium, binding parameters in current research and development that can potentially improve future drug discovery targeting the GnRH receptor. © 2015 The British Pharmacological Society.

Characterization of 12 GnRH peptide agonists – a kinetic perspective

PubMed Central

Nederpelt, Indira; Georgi, Victoria; Schiele, Felix; Nowak‐Reppel, Katrin; Fernández‐Montalván, Amaury E.; IJzerman, Adriaan P.

2015-01-01

Background and Purpose Drug‐target residence time is an important, yet often overlooked, parameter in drug discovery. Multiple studies have proposed an increased residence time to be beneficial for improved drug efficacy and/or longer duration of action. Currently, there are many drugs on the market targeting the gonadotropin‐releasing hormone (GnRH) receptor for the treatment of hormone‐dependent diseases. Surprisingly, the kinetic receptor‐binding parameters of these analogues have not yet been reported. Therefore, this project focused on determining the receptor‐binding kinetics of 12 GnRH peptide agonists, including many marketed drugs. Experimental Approach A novel radioligand‐binding competition association assay was developed and optimized for the human GnRH receptor with the use of a radiolabelled peptide agonist, [125I]‐triptorelin. In addition to radioligand‐binding studies, a homogeneous time‐resolved FRET Tag‐lite™ method was developed as an alternative assay for the same purpose. Key Results Two novel competition association assays were successfully developed and applied to determine the kinetic receptor‐binding characteristics of 12 high‐affinity GnRH peptide agonists. Results obtained from both methods were highly correlated. Interestingly, the binding kinetics of the peptide agonists were more divergent than their affinities with residence times ranging from 5.6 min (goserelin) to 125 min (deslorelin). Conclusions and Implications Our research provides new insights by incorporating kinetic, next to equilibrium, binding parameters in current research and development that can potentially improve future drug discovery targeting the GnRH receptor. PMID:26398856

Elucidation of the naproxen sodium adsorption onto activated carbon prepared from waste apricot: kinetic, equilibrium and thermodynamic characterization.

PubMed

Onal, Y; Akmil-Başar, C; Sarici-Ozdemir, C

2007-09-30

In this study, activated carbon (WA11Zn5) was prepared from waste apricot, which is waste in apricot plants in Malatya, by chemical activation with ZnCl(2). BET surface area of activated carbon is determined as 1060 m(2)/g. The ability of WA11Zn5, to remove naproxen sodium from effluent solutions by adsorption has been studied. Equilibrium isotherms for the adsorption of naproxen sodium on activated carbon were measured experimentally. Results were analyzed by the Langmiur, Freundlich equation using linearized correlation coefficient at 298 K. The characteristic parameters for each isotherm have been determined. Langmiur equation is found to best represent the equilibrium data for naproxen sodium-WA11Zn5 systems. The monolayer adsorption capacity of WA11Zn5 for naproxen sodium was found to be 106.38 mg/g at 298 K. The process was favorable and spontaneous. The kinetics of adsorption of naproxen sodium have been discussed using three kinetic models, i.e., the pseudo first-order model, the pseudo second-order model, the intraparticle diffusion model. Kinetic parameters and correlation coefficients were determined. It was shown that the pseudo second-order kinetic equation could describe the adsorption kinetics for naproxen sodium onto WA11Zn5. The thermodynamic parameters, such as DeltaG degrees , DeltaS degrees and DeltaH degrees, were calculated. The thermodynamics of naproxen sodium-WA11Zn5 system indicates endothermic process.

Nonequilibrium phase coexistence and criticality near the second explosion limit of hydrogen combustion

NASA Astrophysics Data System (ADS)

Newcomb, Lucas B.; Alaghemandi, Mohammad; Green, Jason R.

2017-07-01

While hydrogen is a promising source of clean energy, the safety and optimization of hydrogen technologies rely on controlling ignition through explosion limits: pressure-temperature boundaries separating explosive behavior from comparatively slow burning. Here, we show that the emergent nonequilibrium chemistry of combustible mixtures can exhibit the quantitative features of a phase transition. With stochastic simulations of the chemical kinetics for a model mechanism of hydrogen combustion, we show that the boundaries marking explosive domains of kinetic behavior are nonequilibrium critical points. Near the pressure of the second explosion limit, these critical points terminate the transient coexistence of dynamical phases—one that autoignites and another that progresses slowly. Below the critical point temperature, the chemistry of these phases is indistinguishable. In the large system limit, the pseudo-critical temperature converges to the temperature of the second explosion limit derived from mass-action kinetics.

Effects of point defect concentrations of the reactive element oxides on the oxidation kinetics of pure Ni and Ni-Cr alloys

NASA Astrophysics Data System (ADS)

Yan, Ruey-Fong

The addition of some reactive element oxides, e.g. Ysb2Osb3 or ZrOsb2, has significant effects, e.g. improvement in scale adhesion and reduction in oxidation rate, on the oxidation behavior of chromia and alumina scale forming alloys at high temperatures. However, there is little agreement about how a small addition of an oxygen-active element can cause such profound effects. It was the goal of this project to study the growth kinetics of an oxide scale when different reactive-element oxides were added to pure Ni and Ni-Cr alloys and, consequently, to aid in clarifying the mechanism of reactive element effects. The oxidation kinetics were measured using a thermogravimetric analysis (TGA) method and the material characterization of oxide scale was conducted. The relationship between point defect structures and oxidation kinetics was discussed. The results in this research showed that Ysb2Osb3 and ZrOsb2 exhibited the reactive element effects on the oxidation behaviors of Ni and Ni-Cr alloys. In addition, the point defect concentrations of the reactive element oxide, Ysb2Osb3, were changed by doping of different valent oxides. The modification of point defect concentrations of the reactive element oxide dispersed phases did change the oxidation kinetics of the pure Ni and Ni-Cr alloys containing Ysb2Osb3. These results indicate that the transport properties of the reactive element oxide dispersed phases are one of the important factors in determining the growth rate of an oxide scale.

Impact of physicochemical parameters on in vitro assembly and disassembly kinetics of recombinant triple-layered rotavirus-like particles.

PubMed

Mellado, Maria Candida M; Mena, Jimmy A; Lopes, António; Ramírez, Octavio T; Carrondo, Manuel J T; Palomares, Laura A; Alves, Paula M

2009-11-01

Virus-like particles constitute potentially relevant vaccine candidates. Nevertheless, their behavior in vitro and assembly process needs to be understood in order to improve their yield and quality. In this study we aimed at addressing these issues and for that purpose triple- and double-layered rotavirus-like particles (TLP 2/6/7 and DLP 2/6, respectively) size and zeta potential were measured using dynamic light scattering at different physicochemical conditions, namely pH, ionic strength, and temperature. Both TLP and DLP were stable within a pH range of 3-7 and at 5-25 degrees C. Aggregation occurred at 35-45 degrees C and their disassembly became evident at 65 degrees C. The isoelectric points of TLP and DLP were 3.0 and 3.8, respectively. In vitro kinetics of TLP disassembly was monitored. Ionic strength, temperature, and the chelating agent employed determined disassembly kinetics. Glycerol (10%) stabilized TLP by preventing its disassembly. Disassembled TLP was able to reassemble by dialysis at high calcium conditions. VP7 monomers were added to DLP in the presence of calcium to follow in vitro TLP assembly kinetics; its assembly rate being mostly affected by pH. Finally, DLP and TLP were found to coexist under certain conditions as determined from all reaction products analyzed by capillary electrophoresis. Overall, these results contribute to the design of new strategies for the improvement of TLP yield and quality by reducing the VP7 detachment from TLP. Copyright 2009 Wiley Periodicals, Inc.

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…

The regrowth kinetic of the surviving population is independent of acute and chronic responses to temozolomide in glioblastoma cell lines

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

Silva, Andrew Oliveira, E-mail: andrewbiomed@gmail.com; Dalsin, Eloisa, E-mail: dalsineloisa@gmail.com; Onzi, Giovana Ravizzoni, E-mail: gioonzi@gmail.com

Chemotherapy acts on cancer cells by producing multiple effects on a cell population including cell cycle arrest, necrosis, apoptosis and senescence. However, often a subpopulation of cells survives and the behavior of this subpopulation, which is responsible for cancer recurrence, remains obscure. Here we investigated the in vitro short- and long-term responses of six glioblastoma cell lines to clinically relevant doses of temozolomide for 5 days followed by 23 days of recovery, mimicking the standard schedule used in glioblastoma patient for this drug. These cells presented different profiles of sensitivity to temozolomide with varying levels of cell cycle arrest, autophagymore » and senescence, followed by a regrowth of the surviving cells. The initial reduction in cell number and the subsequent regrowth was analyzed with four new parameters applied to Cumulative Population Doubling (CPD) curves that describe the overall sensitivity of the population and the characteristic of the regrowth: the relative end point CPD (RendCPD); the relative Area Under Curve (rAUC); the Relative Time to Cross a Threshold (RTCT); and the Relative Proliferation Rate (RPR). Surprisingly, the kinetics of regrowth were not predicted by the mechanisms activated after treatment nor by the acute or overall sensitivity. With this study we added new parameters that describe key responses of glioblastoma cell populations to temozolomide treatment. These parameters can also be applied to other cell types and treatments and will help to understand the behavior of the surviving cancer cells after treatment and shed light on studies of cancer resistance and recurrence. - Highlights: • Little is known about the behavior of the glioma cells surviving to TMZ. • The short- and long-term response of six glioma cells lines to TMZ varies considerably. • These glioma cells lines recovered proliferation after therapeutic levels of TMZ. • The growth velocity of the surviving cells was different from the untreated cells. • The kinetic of regrowth was not predicted by any TMZ-triggered mechanism.« less

Toroidal Alfvén eigenmode triggered by trapped anisotropic energetic particles in a toroidal resistive plasma with free boundary

NASA Astrophysics Data System (ADS)

Yang, S. X.; Hao, G. Z.; Liu, Y. Q.; Wang, Z. X.; Hu, Y. J.; Zhu, J. X.; He, H. D.; Wang, A. K.

2018-04-01

The toroidal Alfvén eigenmode (TAE), excited by trapped energetic particles (EPs), is numerically investigated in a tokamak plasma, using the non-perturbative magnetohydrodynamic-kinetic hybrid formulation based MARS-K code (Liu et al 2008 Phys. Plasmas 15 112503). Compared with the fixed boundary condition at the plasma edge, a free boundary enhances the critical value of the EPs kinetic contribution for driving the TAE. Free boundary also induces finite perturbations at the plasma edge as expected. An anisotropic distribution of EPs, in the particle pitch angle space, strongly enhances the instability and results in a more global mode structure, compared with the isotropic case. The plasma resistivity is also found to play a role in the EPs-destabilized TAE. In particular, the mode stability domain is mapped out, in the 2D parameter space of the plasma resistivity and a quantity defining the width of the particle distribution in pitch angle (for anisotropic distribution). A resonance layer in the poloidal mode structure, with the layer width increasing with the plasma resistivity, appears at the large width of the particle distribution in pitch angle space. A mode conversion, from the modified ideal kink by the EPs kinetic effect to the TAE, is also observed while increasing the birth energy of EPs. Computational results suggest that the TAE mode structure can be modified by certain key plasma parameters, such as the EPs kinetic contribution, the equilibrium pressure, the plasma resistivity, the distribution of EPs, as well as the birth energy of EPs. Such modification of the eigenmode structure can only be obtained following the non-perturbative hybrid approach (Wang et al 2013 Phys. Rev. Lett. 111 145003, Wang et al 2015 Phys. Plasmas 22 022509), as adopted in this study. More importantly, numerical results show that near the marginal stability point, the dominant poloidal harmonics of the TAE overlap with each other, and are localized at the tip positions of the Alfvén continua. This kind of TAE structure in high beta plasma with unstable ideal kink is substantially different from that of the conventional TAE.

Exact solutions for kinetic models of macromolecular dynamics.

PubMed

Chemla, Yann R; Moffitt, Jeffrey R; Bustamante, Carlos

2008-05-15

Dynamic biological processes such as enzyme catalysis, molecular motor translocation, and protein and nucleic acid conformational dynamics are inherently stochastic processes. However, when such processes are studied on a nonsynchronized ensemble, the inherent fluctuations are lost, and only the average rate of the process can be measured. With the recent development of methods of single-molecule manipulation and detection, it is now possible to follow the progress of an individual molecule, measuring not just the average rate but the fluctuations in this rate as well. These fluctuations can provide a great deal of detail about the underlying kinetic cycle that governs the dynamical behavior of the system. However, extracting this information from experiments requires the ability to calculate the general properties of arbitrarily complex theoretical kinetic schemes. We present here a general technique that determines the exact analytical solution for the mean velocity and for measures of the fluctuations. We adopt a formalism based on the master equation and show how the probability density for the position of a molecular motor at a given time can be solved exactly in Fourier-Laplace space. With this analytic solution, we can then calculate the mean velocity and fluctuation-related parameters, such as the randomness parameter (a dimensionless ratio of the diffusion constant and the velocity) and the dwell time distributions, which fully characterize the fluctuations of the system, both commonly used kinetic parameters in single-molecule measurements. Furthermore, we show that this formalism allows calculation of these parameters for a much wider class of general kinetic models than demonstrated with previous methods.

The Kinetics of Heterogeneous Electron Transfer Reactions in Polar Solvents

DTIC Science & Technology

1994-04-20

focussed on systems for which rate constants and activation parameters are available as a function of the solvent, and as a function of temperature . The... temperature . The role of reactant structure in determining the kinetic parameters is also considered. Double layer effects both at unmodified and...that the Gibbs activation energy to form a monovalent cation from a neutral molecule via electrooxidation is different from that to form a monovalent

Chemiomics: network reconstruction and kinetics of port wine aging.

PubMed

Monforte, Ana Rita; Jacobson, Dan; Silva Ferreira, A C

2015-03-11

Network reconstruction (NR) has proven to be useful in the detection and visualization of relationships among the compounds present in a Port wine aging data set. This view of the data provides a considerable amount of information with which to understand the kinetic contexts of the molecules represented by peaks in each chromatogram. The aim of this study was to use NR together with the determination of kinetic parameters to extract more information about the mechanisms involved in Port wine aging. The volatile compounds present in samples of Port wines spanning 128 years in age were measured with the use of GC-MS. After chromatogram alignment, a peak matrix was created, and all peak vectors were compared to one another to determine their Pearson correlations over time. A correlation network was created and filtered on the basis of the resulting correlation values. Some nodes in the network were further studied in experiments on Port wines stored under different conditions of oxygen and temperature in order to determine their kinetic parameters. The resulting network can be divided into three main branches. The first branch is related to compounds that do not directly correlate to age, the second branch contains compounds affected by temperature, and the third branch contains compounds associated with oxygen. Compounds clustered in the same branch of the network have similar expression patterns over time as well as the same kinetic order, thus are likely to be dependent on the same technological parameters. Network construction and visualization provides more information with which to understand the probable kinetic contexts of the molecules represented by peaks in each chromatogram. The approach described here is a powerful tool for the study of mechanisms and kinetics in complex systems and should aid in the understanding and monitoring of wine quality.

[Evaluation of the influence of humidity and temperature on the drug stability by initial average rate experiment].

PubMed

He, Ning; Sun, Hechun; Dai, Miaomiao

2014-05-01

To evaluate the influence of temperature and humidity on the drug stability by initial average rate experiment, and to obtained the kinetic parameters. The effect of concentration error, drug degradation extent, humidity and temperature numbers, humidity and temperature range, and average humidity and temperature on the accuracy and precision of kinetic parameters in the initial average rate experiment was explored. The stability of vitamin C, as a solid state model, was investigated by an initial average rate experiment. Under the same experimental conditions, the kinetic parameters obtained from this proposed method were comparable to those from classical isothermal experiment at constant humidity. The estimates were more accurate and precise by controlling the extent of drug degradation, changing humidity and temperature range, or by setting the average temperature closer to room temperature. Compared with isothermal experiments at constant humidity, our proposed method saves time, labor, and materials.

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.

Fuzzy C-mean clustering on kinetic parameter estimation with generalized linear least square algorithm in SPECT

NASA Astrophysics Data System (ADS)

Choi, Hon-Chit; Wen, Lingfeng; Eberl, Stefan; Feng, Dagan

2006-03-01

Dynamic Single Photon Emission Computed Tomography (SPECT) has the potential to quantitatively estimate physiological parameters by fitting compartment models to the tracer kinetics. The generalized linear least square method (GLLS) is an efficient method to estimate unbiased kinetic parameters and parametric images. However, due to the low sensitivity of SPECT, noisy data can cause voxel-wise parameter estimation by GLLS to fail. Fuzzy C-Mean (FCM) clustering and modified FCM, which also utilizes information from the immediate neighboring voxels, are proposed to improve the voxel-wise parameter estimation of GLLS. Monte Carlo simulations were performed to generate dynamic SPECT data with different noise levels and processed by general and modified FCM clustering. Parametric images were estimated by Logan and Yokoi graphical analysis and GLLS. The influx rate (K I), volume of distribution (V d) were estimated for the cerebellum, thalamus and frontal cortex. Our results show that (1) FCM reduces the bias and improves the reliability of parameter estimates for noisy data, (2) GLLS provides estimates of micro parameters (K I-k 4) as well as macro parameters, such as volume of distribution (Vd) and binding potential (BP I & BP II) and (3) FCM clustering incorporating neighboring voxel information does not improve the parameter estimates, but improves noise in the parametric images. These findings indicated that it is desirable for pre-segmentation with traditional FCM clustering to generate voxel-wise parametric images with GLLS from dynamic SPECT data.

Computational analysis of liquid chromatography-tandem mass spectrometric steroid profiling in NCI H295R cells following angiotensin II, forskolin and abiraterone treatment.

PubMed

Mangelis, Anastasios; Dieterich, Peter; Peitzsch, Mirko; Richter, Susan; Jühlen, Ramona; Hübner, Angela; Willenberg, Holger S; Deussen, Andreas; Lenders, Jacques W M; Eisenhofer, Graeme

2016-01-01

Adrenal steroid hormones, which regulate a plethora of physiological functions, are produced via tightly controlled pathways. Investigations of these pathways, based on experimental data, can be facilitated by computational modeling for calculations of metabolic rate alterations. We therefore used a model system, based on mass balance and mass reaction equations, to kinetically evaluate adrenal steroidogenesis in human adrenal cortex-derived NCI H295R cells. For this purpose a panel of 10 steroids was measured by liquid chromatographic-tandem mass spectrometry. Time-dependent changes in cell incubate concentrations of steroids - including cortisol, aldosterone, dehydroepiandrosterone and their precursors - were measured after incubation with angiotensin II, forskolin and abiraterone. Model parameters were estimated based on experimental data using weighted least square fitting. Time-dependent angiotensin II- and forskolin-induced changes were observed for incubate concentrations of precursor steroids with peaks that preceded maximal increases in aldosterone and cortisol. Inhibition of 17-alpha-hydroxylase/17,20-lyase with abiraterone resulted in increases in upstream precursor steroids and decreases in downstream products. Derived model parameters, including rate constants of enzymatic processes, appropriately quantified observed and expected changes in metabolic pathways at multiple conversion steps. Our data demonstrate limitations of single time point measurements and the importance of assessing pathway dynamics in studies of adrenal cortical cell line steroidogenesis. Our analysis provides a framework for evaluation of steroidogenesis in adrenal cortical cell culture systems and demonstrates that computational modeling-derived estimates of kinetic parameters are an effective tool for describing perturbations in associated metabolic pathways. Copyright © 2015 Elsevier Ltd. All rights reserved.

Kinetics of swelling of polyelectrolyte gels: Fixed degree of ionization

NASA Astrophysics Data System (ADS)

Sen, Swati; Kundagrami, Arindam

2015-12-01

The swelling kinetics of uncharged and charged polymer (polyelectrolyte) gels in salt-free conditions is studied in one dimension by solving the constitutive equation of motion (Newton's law for the elementary gel volume) of the displacement variable by two theoretical methods: one in which the classical definition of stress is used with the bulk modulus taken as a parameter, and the other in which a phenomenological expression of the osmotic stress as a function of polymer density and degree of ionization is taken as an input to the dynamics. The time-evolution profiles for spatially varying polymer density and stress, along with the location of the gel-solvent interface, are obtained from the two methods. We show that both the polymer density (volume fraction) and stress inside the gel follow expected behaviours of being maximum for the uniformly shrunken gel, and relaxing slowly to the lowest values as the gel approaches equilibrium. We further show that, by comparing the temporal profiles of the gel-solvent interface and other variables between the two methods, one may attempt to assign an effective bulk modulus to the polyelectrolyte gel as a function of the degree of ionization and other parameters of the gel such as hydrophobicity, cross-link density, and the temperature. The major result we get is that the effective bulk modulus of a polyelectrolyte gel increases monotonically with its degree of ionization. In the process of identifying the parameters for a monotonic swelling, we calculated using a well-known expression of the free energy the equilibrium results of two-phase co-existence and the critical point of a polyelectrolyte gel with a fixed degree of ionization.

Kinetics of swelling of polyelectrolyte gels: Fixed degree of ionization.

PubMed

Sen, Swati; Kundagrami, Arindam

2015-12-14

The swelling kinetics of uncharged and charged polymer (polyelectrolyte) gels in salt-free conditions is studied in one dimension by solving the constitutive equation of motion (Newton's law for the elementary gel volume) of the displacement variable by two theoretical methods: one in which the classical definition of stress is used with the bulk modulus taken as a parameter, and the other in which a phenomenological expression of the osmotic stress as a function of polymer density and degree of ionization is taken as an input to the dynamics. The time-evolution profiles for spatially varying polymer density and stress, along with the location of the gel-solvent interface, are obtained from the two methods. We show that both the polymer density (volume fraction) and stress inside the gel follow expected behaviours of being maximum for the uniformly shrunken gel, and relaxing slowly to the lowest values as the gel approaches equilibrium. We further show that, by comparing the temporal profiles of the gel-solvent interface and other variables between the two methods, one may attempt to assign an effective bulk modulus to the polyelectrolyte gel as a function of the degree of ionization and other parameters of the gel such as hydrophobicity, cross-link density, and the temperature. The major result we get is that the effective bulk modulus of a polyelectrolyte gel increases monotonically with its degree of ionization. In the process of identifying the parameters for a monotonic swelling, we calculated using a well-known expression of the free energy the equilibrium results of two-phase co-existence and the critical point of a polyelectrolyte gel with a fixed degree of ionization.

Cosmology with nonminimal kinetic coupling and a Higgs-like potential

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

Matsumoto, Jiro; Sushkov, Sergey V., E-mail: jmatsumoto@kpfu.ru, E-mail: sergey_sushkov@mail.ru

2015-11-01

We consider cosmological dynamics in the theory of gravity with the scalar field possessing the nonminimal kinetic coupling to curvature given as κG{sup μν}φ{sub ,μ}φ{sub ,ν}, and the Higgs-like potential . Using the dynamical system method, we analyze stationary points, their stability, and all possible asymptotical regimes of the model under consideration. We show that the Higgs field with the kinetic coupling provides an existence of accelerated regimes of the Universe evolution. There are three possible cosmological scenarios with acceleration: (i) The late-time de Sitter epoch when the Hubble parameter tends to the constant value, as t → ∞, while the scalarmore » field tends to zero, 0φ(t)→ , so that the Higgs potential reaches its local maximum . (ii) The Big Rip when H(t)∼(t{sub *}−t){sup −1} → ∞ and φ(t)∼(t{sub *}−t){sup −2} → ∞ as t →  t{sub *}. (iii) The Little Rip when H(t)∼ t{sup 1/2} → ∞ and φ(t)∼ t{sup 1/4} → ∞ as t → ∞. Also, we derive modified slow-roll conditions for the Higgs field and demonstrate that they lead to the Little Rip scenario.« less

Misconceptions regarding basic thermodynamics and enzyme kinetics have led to erroneous conclusions regarding the metabolic importance of lactate dehydrogenase isoenzyme expression.

PubMed

Bak, Lasse K; Schousboe, Arne

2017-11-01

Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate involving the coenzyme NAD + . Part of the foundation for the proposed shuttling of lactate from astrocytes to neurons during brain activation is the differential distribution of LDH isoenzymes between the two cell types. In this short review, we outline the basic kinetic properties of the LDH isoenzymes expressed in neurons and astrocytes, and argue that the distribution of LDH isoenzymes does not in any way govern directional flow of lactate between the two cellular compartments. The two main points are as follows. First, in line with the general concept of chemical catalysis, enzymes do not influence the thermodynamic equilibrium of a chemical reaction but merely the speed at which equilibrium is obtained. Thus, differential distribution of LDH isoenzymes with different kinetic parameters does not predict which cells are producing and which are consuming lactate. Second, the thermodynamic equilibrium of the reaction is toward the reduced substrate (i.e., lactate), which is reflected in the concentrations measured in brain tissue, suggesting that the reaction is at near-equilibrium at steady state. To conclude, the cellular distribution of LDH isoenzymes is of little if any consequence in determining any directional flow of lactate between neurons and astrocytes. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Lipo-Protein Emulsion Structure in the Diet Affects Protein Digestion Kinetics, Intestinal Mucosa Parameters and Microbiota Composition.

PubMed

Oberli, Marion; Douard, Véronique; Beaumont, Martin; Jaoui, Daphné; Devime, Fabienne; Laurent, Sandy; Chaumontet, Catherine; Mat, Damien; Le Feunteun, Steven; Michon, Camille; Davila, Anne-Marie; Fromentin, Gilles; Tomé, Daniel; Souchon, Isabelle; Leclerc, Marion; Gaudichon, Claire; Blachier, François

2018-01-01

Food structure is a key factor controlling digestion and nutrient absorption. We test the hypothesis that protein emulsion structure in the diet may affect digestive and absorptive processes. Rats (n = 40) are fed for 3 weeks with two diets chemically identical but based on lipid-protein liquid-fine (LFE) or gelled-coarse (GCE) emulsions that differ at the macro- and microstructure levels. After an overnight fasting, they ingest a 15 N-labeled LFE or GCE test meal and are euthanized 0, 15 min, 1 h, and 5 h later. 15 N enrichment in intestinal contents and blood are measured. Gastric emptying, protein digestion kinetics, 15 N absorption, and incorporation in blood protein and urea are faster with LFE than GCE. At 15 min time point, LFE group shows higher increase in GIP portal levels than GCE. Three weeks of dietary adaptation leads to higher expression of cationic amino acid transporters in ileum of LFE compared to GCE. LFE diet raises cecal butyrate and isovalerate proportion relative to GCE, suggesting increased protein fermentation. LFE diet increases fecal Parabacteroides relative abundance but decreases Bifidobacterium, Sutterella, Parasutterella genera, and Clostridium cluster XIV abundance. Protein emulsion structure regulates digestion kinetics and gastrointestinal physiology, and could be targeted to improve food health value. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Testing the nonlocal kinetic energy functional of an inhomogeneous, two-dimensional degenerate Fermi gas within the average density approximation

NASA Astrophysics Data System (ADS)

Towers, J.; van Zyl, B. P.; Kirkby, W.

2015-08-01

In a recent paper [B. P. van Zyl et al., Phys. Rev. A 89, 022503 (2014), 10.1103/PhysRevA.89.022503], the average density approximation (ADA) was implemented to develop a parameter-free, nonlocal kinetic energy functional to be used in the orbital-free density functional theory of an inhomogeneous, two-dimensional (2D) Fermi gas. In this work, we provide a detailed comparison of self-consistent calculations within the ADA with the exact results of the Kohn-Sham density functional theory and the elementary Thomas-Fermi (TF) approximation. We demonstrate that the ADA for the 2D kinetic energy functional works very well under a wide variety of confinement potentials, even for relatively small particle numbers. Remarkably, the TF approximation for the kinetic energy functional, without any gradient corrections, also yields good agreement with the exact kinetic energy for all confining potentials considered, although at the expense of the spatial and kinetic energy densities exhibiting poor pointwise agreement, particularly near the TF radius. Our findings illustrate that the ADA kinetic energy functional yields accurate results for both the local and global equilibrium properties of an inhomogeneous 2D Fermi gas, without the need for any fitting parameters.

WE-FG-206-06: Dual-Input Tracer Kinetic Modeling and Its Analog Implementation for Dynamic Contrast-Enhanced (DCE-) MRI of Malignant Mesothelioma (MPM)

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

Lee, S; Rimner, A; Hayes, S

Purpose: To use dual-input tracer kinetic modeling of the lung for mapping spatial heterogeneity of various kinetic parameters in malignant MPM Methods: Six MPM patients received DCE-MRI as part of their radiation therapy simulation scan. 5 patients had the epitheloid subtype of MPM, while one was biphasic. A 3D fast-field echo sequence with TR/TE/Flip angle of 3.62ms/1.69ms/15° was used for DCE-MRI acquisition. The scan was collected for 5 minutes with a temporal resolution of 5-9 seconds depending on the spatial extent of the tumor. A principal component analysis-based groupwise deformable registration was used to co-register all the DCE-MRI series formore » motion compensation. All the images were analyzed using five different dual-input tracer kinetic models implemented in analog continuous-time formalism: the Tofts-Kety (TK), extended TK (ETK), two compartment exchange (2CX), adiabatic approximation to the tissue homogeneity (AATH), and distributed parameter (DP) models. The following parameters were computed for each model: total blood flow (BF), pulmonary flow fraction (γ), pulmonary blood flow (BF-pa), systemic blood flow (BF-a), blood volume (BV), mean transit time (MTT), permeability-surface area product (PS), fractional interstitial volume (vi), extraction fraction (E), volume transfer constant (Ktrans) and efflux rate constant (kep). Results: Although the majority of patients had epitheloid histologies, kinetic parameter values varied across different models. One patient showed a higher total BF value in all models among the epitheloid histologies, although the γ value was varying among these different models. In one tumor with a large area of necrosis, the TK and ETK models showed higher E, Ktrans, and kep values and lower interstitial volume as compared to AATH and DP and 2CX models. Kinetic parameters such as BF-pa, BF-a, PS, Ktrans values were higher in surviving group compared to non-surviving group across most models. Conclusion: Dual-input tracer kinetic modeling is feasible in determining micro-vascular characteristics of MPM. This project was supported from Cycle for Survival and MSK Imaging and radiation science (IMRAS) grants.« less

Predicting heavy metals' adsorption edges and adsorption isotherms on MnO2 with the parameters determined from Langmuir kinetics.

PubMed

Hu, Qinghai; Xiao, Zhongjin; Xiong, Xinmei; Zhou, Gongming; Guan, Xiaohong

2015-01-01

Although surface complexation models have been widely used to describe the adsorption of heavy metals, few studies have verified the feasibility of modeling the adsorption kinetics, edge, and isotherm data with one pH-independent parameter. A close inspection of the derivation process of Langmuir isotherm revealed that the equilibrium constant derived from the Langmuir kinetic model, KS-kinetic, is theoretically equivalent to the adsorption constant in Langmuir isotherm, KS-Langmuir. The modified Langmuir kinetic model (MLK model) and modified Langmuir isotherm model (MLI model) incorporating pH factor were developed. The MLK model was employed to simulate the adsorption kinetics of Cu(II), Co(II), Cd(II), Zn(II) and Ni(II) on MnO2 at pH3.2 or 3.3 to get the values of KS-kinetic. The adsorption edges of heavy metals could be modeled with the modified metal partitioning model (MMP model), and the values of KS-Langmuir were obtained. The values of KS-kinetic and KS-Langmuir are very close to each other, validating that the constants obtained by these two methods are basically the same. The MMP model with KS-kinetic constants could predict the adsorption edges of heavy metals on MnO2 very well at different adsorbent/adsorbate concentrations. Moreover, the adsorption isotherms of heavy metals on MnO2 at various pH levels could be predicted reasonably well by the MLI model with the KS-kinetic constants. Copyright © 2014. Published by Elsevier B.V.

Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters.

PubMed

Chiang, Austin W T; Liu, Wei-Chung; Charusanti, Pep; Hwang, Ming-Jing

2014-01-15

A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system's dynamics. We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli. Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

Optimization of the lithium/thionyl chloride battery

NASA Technical Reports Server (NTRS)

White, Ralph E.

1989-01-01

A 1-D math model for the lithium/thionyl chloride primary cell is used in conjunction with a parameter estimation technique in order to estimate the electro-kinetic parameters of this electrochemical system. The electro-kinetic parameters include the anodic transfer coefficient and exchange current density of the lithium oxidation, alpha sub a,1 and i sub o,i,ref, the cathodic transfer coefficient and the effective exchange current density of the thionyl chloride reduction, alpha sub c,2 and a sup o i sub o,2,ref, and a morphology parameter, Xi. The parameter estimation is performed on simulated data first in order to gain confidence in the method. Data, reported in the literature, for a high rate discharge of an experimental lithium/thionyl chloride cell is used for an analysis.

Kinetic characterisation of primer mismatches in allele-specific PCR: a quantitative assessment.

PubMed

Waterfall, Christy M; Eisenthal, Robert; Cobb, Benjamin D

2002-12-20

A novel method of estimating the kinetic parameters of Taq DNA polymerase during rapid cycle PCR is presented. A model was constructed using a simplified sigmoid function to represent substrate accumulation during PCR in combination with the general equation describing high substrate inhibition for Michaelis-Menten enzymes. The PCR progress curve was viewed as a series of independent reactions where initial rates were accurately measured for each cycle. Kinetic parameters were obtained for allele-specific PCR (AS-PCR) amplification to examine the effect of mismatches on amplification. A high degree of correlation was obtained providing evidence of substrate inhibition as a major cause of the plateau phase that occurs in the later cycles of PCR.

Kinetics of acid hydrolysis and reactivity of some antibacterial hydrophilic iron(II) imino-complexes

NASA Astrophysics Data System (ADS)

Shaker, Ali Mohamed; Nassr, Lobna Abdel-Mohsen Ebaid; Adam, Mohamed Shaker Saied; Mohamed, Ibrahim Mohamed Abdelhalim

2015-05-01

Kinetic study of acid hydrolysis of some hydrophilic Fe(II) Schiff base amino acid complexes with antibacterial properties was performed using spectrophotometry. The Schiff base ligands were derived from sodium 2-hydroxybenzaldehyde-5-sulfonate and glycine, L-alanine, L-leucine, L-isoleucine, DL-methionine, DL-serine, or L-phenylalanine. The reaction was studied in aqueous media under conditions of pseudo-first order kinetics. Moreover, the acid hydrolysis was studied at different temperatures and the activation parameters were calculated. The general rate equation was suggested as follows: rate = k obs [Complex], where k obs = k 2 [H+]. The evaluated rate constants and activation parameters are consistent with the hydrophilicity of the investigated complexes.

Enzyme Kinetics Experiment with the Multienzyme Complex Viscozyme L and Two Substrates for the Accurate Determination of Michaelian Parameters

ERIC Educational Resources Information Center

Guerra, Nelson Pérez

2017-01-01

A laboratory experiment in which students study the kinetics of the Viscozyme-L-catalyzed hydrolysis of cellulose and starch comparatively was designed for an upper-division biochemistry laboratory. The main objective of this experiment was to provide an opportunity to perform enhanced enzyme kinetics data analysis using appropriate informatics…

General solutions for the oxidation kinetics of polymers

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

Gillen, K.T.; Clough, R.L.; Wise, J.

1996-08-01

The simplest general kinetic schemes applicable to the oxidation of polymers are presented, discussed and analyzed in terms of the underlying kinetic assumptions. For the classic basic autoxidation scheme (BAS), which involves three bimolecular termination steps and is applicable mainly to unstabilized polymers, typical assumptions used singly or in groups include (1) long kinetic chain length, (2) a specific ratio of the termination rate constants and (3) insensitivity to the oxygen concentration (e.g., domination by a single termination step). Steady-state solutions for the rate of oxidation are given in terms of one, two, three, or four parameters, corresponding respectively tomore » three, two, one, or zero kinetic assumptions. The recently derived four-parameter solution predicts conditions yielding unusual dependencies of the oxidation rate on oxygen concentration and on initiation rate, as well as conditions leading to some unusual diffusion-limited oxidation profile shapes. For stabilized polymers, unimolecular termination schemes are typically more appropriate than bimolecular. Kinetics incorporating unimolecular termination reactions are shown to result in very simple oxidation expressions which have been experimentally verified for both radiation-initiated oxidation of an EPDM and thermoxidative degradation of nitrile and chloroprene elastomers.« less

Characterization, kinetic, and thermodynamic studies of marine pectinase from Bacillus subtilis.

PubMed

Joshi, Manasi; Nerurkar, Madhura; Adivarekar, Ravindra

2015-01-01

Characterization, kinetic and thermodynamic parameters of purified pectinase from Bacillus subtilis, isolated from a marine sediment sample collected from Chinchani beach at Tarapore, India, were studied. Marine pectinase produced under submerged growth conditions was purified by ammonium sulfate precipitation followed by gel filtration chromatography using DEAE cellulose. Partial characterization of the marine pectinase was carried out in terms of effect of pH, temperature, substrate concentration, and metal ions. It was found that pectinase from marine B. subtilis showed maximal activity in alkaline buffer at pH 9.0 and at 40°C. It was also found that metal ions, namely, Mn(2+) and Fe(2+), stimulate pectinase activity. Marine pectinase followed Michaelis-Menten kinetics. The kinetics and thermodynamic parameters of the purified marine pectinase from B. subtilis were studied as the characterization of the enzyme is vital for its use in industrial processes.

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.

EasyDelta: A spreadsheet for kinetic modeling of the stable carbon isotope composition of natural gases

NASA Astrophysics Data System (ADS)

Zou, Yan-Rong; Wang, Lianyuan; Shuai, Yanhua; Peng, Ping'an

2005-08-01

A new kinetic model and an Excel © spreadsheet program for modeling the stable carbon isotope composition of natural gases is provided in this paper. The model and spreadsheet could be used to describe and predict the variances in stable carbon isotope of natural gases under both experimental and geological conditions with heating temperature or geological time. It is a user-friendly convenient tool for the modeling of isotope variation with time under experimental and geological conditions. The spreadsheet, based on experimental data, requires the input of the kinetic parameters of gaseous hydrocarbons generation. Some assumptions are made in this model: the conventional (non-isotope species) kinetic parameters represent the light isotope species; the initial isotopic value is the same for all parallel chemical reaction of gaseous hydrocarbons generation for simplicity, the re-exponential factor ratio, 13A/ 12A, is a constant, and both heavy and light isotope species have similar activation energy distribution. These assumptions are common in modeling of isotope ratios. The spreadsheet is used for searching the best kinetic parameters of the heavy isotope species to reach the minimum errors compared with experimental data, and then extrapolating isotopic changes to the thermal history of sedimentary basins. A short calculation example on the variation in δ13C values of methane is provided in this paper to show application to geological conditions.

Impact of process parameters on the breakage kinetics of poorly water-soluble drugs during wet stirred media milling: a microhydrodynamic view.

PubMed

Afolabi, Afolawemi; Akinlabi, Olakemi; Bilgili, Ecevit

2014-01-23

Wet stirred media milling has proven to be a robust process for producing nanoparticle suspensions of poorly water-soluble drugs. As the process is expensive and energy-intensive, it is important to study the breakage kinetics, which determines the cycle time and production rate for a desired fineness. Although the impact of process parameters on the properties of final product suspensions has been investigated, scant information is available regarding their impact on the breakage kinetics. Here, we elucidate the impact of stirrer speed, bead concentration, and drug loading on the breakage kinetics via a microhydrodynamic model for the bead-bead collisions. Suspensions of griseofulvin, a model poorly water-soluble drug, were prepared in the presence of two stabilizers: hydroxypropyl cellulose and sodium dodecyl sulfate. Laser diffraction, scanning electron microscopy, and rheometry were used to characterize them. Various microhydrodynamic parameters including a newly defined milling intensity factor was calculated. An increase in either the stirrer speed or the bead concentration led to an increase in the specific energy and the milling intensity factor, consequently faster breakage. On the other hand, an increase in the drug loading led to a decrease in these parameters and consequently slower breakage. While all microhydrodynamic parameters provided significant physical insight, only the milling intensity factor was capable of explaining the influence of all parameters directly through its strong correlation with the process time constant. Besides guiding process optimization, the analysis rationalizes the preparation of a single high drug-loaded batch (20% or higher) instead of multiple dilute batches. Copyright © 2013 Elsevier B.V. All rights reserved.

Process model comparison and transferability across bioreactor scales and modes of operation for a mammalian cell bioprocess.

PubMed

Craven, Stephen; Shirsat, Nishikant; Whelan, Jessica; Glennon, Brian

2013-01-01

A Monod kinetic model, logistic equation model, and statistical regression model were developed for a Chinese hamster ovary cell bioprocess operated under three different modes of operation (batch, bolus fed-batch, and continuous fed-batch) and grown on two different bioreactor scales (3 L bench-top and 15 L pilot-scale). The Monod kinetic model was developed for all modes of operation under study and predicted cell density, glucose glutamine, lactate, and ammonia concentrations well for the bioprocess. However, it was computationally demanding due to the large number of parameters necessary to produce a good model fit. The transferability of the Monod kinetic model structure and parameter set across bioreactor scales and modes of operation was investigated and a parameter sensitivity analysis performed. The experimentally determined parameters had the greatest influence on model performance. They changed with scale and mode of operation, but were easily calculated. The remaining parameters, which were fitted using a differential evolutionary algorithm, were not as crucial. Logistic equation and statistical regression models were investigated as alternatives to the Monod kinetic model. They were less computationally intensive to develop due to the absence of a large parameter set. However, modeling of the nutrient and metabolite concentrations proved to be troublesome due to the logistic equation model structure and the inability of both models to incorporate a feed. The complexity, computational load, and effort required for model development has to be balanced with the necessary level of model sophistication when choosing which model type to develop for a particular application. Copyright © 2012 American Institute of Chemical Engineers (AIChE).

Application of lab derived kinetic biodegradation parameters at the field scale

NASA Astrophysics Data System (ADS)

Schirmer, M.; Barker, J. F.; Butler, B. J.; Frind, E. O.

2003-04-01

Estimating the intrinsic remediation potential of an aquifer typically requires the accurate assessment of the biodegradation kinetics, the level of available electron acceptors and the flow field. Zero- and first-order degradation rates derived at the laboratory scale generally overpredict the rate of biodegradation when applied to the field scale, because limited electron acceptor availability and microbial growth are typically not considered. On the other hand, field estimated zero- and first-order rates are often not suitable to forecast plume development because they may be an oversimplification of the processes at the field scale and ignore several key processes, phenomena and characteristics of the aquifer. This study uses the numerical model BIO3D to link the laboratory and field scale by applying laboratory derived Monod kinetic degradation parameters to simulate a dissolved gasoline field experiment at Canadian Forces Base (CFB) Borden. All additional input parameters were derived from laboratory and field measurements or taken from the literature. The simulated results match the experimental results reasonably well without having to calibrate the model. An extensive sensitivity analysis was performed to estimate the influence of the most uncertain input parameters and to define the key controlling factors at the field scale. It is shown that the most uncertain input parameters have only a minor influence on the simulation results. Furthermore it is shown that the flow field, the amount of electron acceptor (oxygen) available and the Monod kinetic parameters have a significant influence on the simulated results. Under the field conditions modelled and the assumptions made for the simulations, it can be concluded that laboratory derived Monod kinetic parameters can adequately describe field scale degradation processes, if all controlling factors are incorporated in the field scale modelling that are not necessarily observed at the lab scale. In this way, there are no scale relationships to be found that link the laboratory and the field scale, accurately incorporating the additional processes, phenomena and characteristics, such as a) advective and dispersive transport of one or more contaminants, b) advective and dispersive transport and availability of electron acceptors, c) mass transfer limitations and d) spatial heterogeneities, at the larger scale and applying well defined lab scale parameters should accurately describe field scale processes.

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

PubMed

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

2011-01-01

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

A study of biochemical route on construction of waste battery ferrite applying for nickel removal.

PubMed

Niu, Zhirui; Zhang, Shaokang; Zhu, Lin

2018-05-21

Mn-Zn ferrite (Mn 1 - x Zn x Fe 2 O 4 , x = 0.2, 0.4, 0.6, and 0.8) nanomaterials were prepared by bioleaching and hydrothermal synthesis from waste Zn-Mn batteries. The materials were characterized by XRD, SEM, BET, VSM, CEC, and isoelectric point. It turned out when x = 0.4, synthesized Mn-Zn ferrite had best performance which was nanoferrite crystal structure with a specific surface area that reached 37.77 m 2 /g, the saturation magnetization was 62.85 emu/g, and isoelectric point and the CEC value were 7.33 and 43.51 mmol/100 g, respectively. In addition, the adsorption characteristics on Ni 2+ were explored. The results of experiment suggested that data was more in line with the Freundlich model compared with Langmuir and Dubinin-Radushkevich isotherm models. Kinetics studies showed that pseudo-second-order kinetics was more suitable for describing the Ni 2+ adsorption process where the maximum theoretical adsorption quantity was 52.99 mg/g. Thermodynamic parameters indicated the adsorption process can be spontaneous as an endothermic reaction, and warming was advantageous to adsorption. Besides, the adsorbent could be reused for six cycles with high removal efficiency. The magnetic and adsorptive properties of the adsorbent were promising, which had a high application value. Graphical abstract Fabrication process of nanometer ferrite by biological technology and hydrothermal synthesis for removal of Ni2.

Estimating Reaction Rate Coefficients Within a Travel-Time Modeling Framework

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

Gong, R; Lu, C; Luo, Jian

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

Modelling of the physico-chemical behaviour of clay minerals with a thermo-kinetic model taking into account particles morphology in compacted material.

NASA Astrophysics Data System (ADS)

Sali, D.; Fritz, B.; Clément, C.; Michau, N.

2003-04-01

Modelling of fluid-mineral interactions is largely used in Earth Sciences studies to better understand the involved physicochemical processes and their long-term effect on the materials behaviour. Numerical models simplify the processes but try to preserve their main characteristics. Therefore the modelling results strongly depend on the data quality describing initial physicochemical conditions for rock materials, fluids and gases, and on the realistic way of processes representations. The current geo-chemical models do not well take into account rock porosity and permeability and the particle morphology of clay minerals. In compacted materials like those considered as barriers in waste repositories, low permeability rocks like mudstones or compacted powders will be used : they contain mainly fine particles and the geochemical models used for predicting their interactions with fluids tend to misjudge their surface areas, which are fundamental parameters in kinetic modelling. The purpose of this study was to improve how to take into account the particles morphology in the thermo-kinetic code KINDIS and the reactive transport code KIRMAT. A new function was integrated in these codes, considering the reaction surface area as a volume depending parameter and the calculated evolution of the mass balance in the system was coupled with the evolution of reactive surface areas. We made application exercises for numerical validation of these new versions of the codes and the results were compared with those of the pre-existing thermo-kinetic code KINDIS. Several points are highlighted. Taking into account reactive surface area evolution during simulation modifies the predicted mass transfers related to fluid-minerals interactions. Different secondary mineral phases are also observed during modelling. The evolution of the reactive surface parameter helps to solve the competition effects between different phases present in the system which are all able to fix the chemical elements mobilised by the water-minerals interaction processes. To validate our model we simulated the compacted bentonite (MX80) studied for engineered barriers for radioactive waste confinement and mainly composed of Na-Ca-montmorillonite. The study of particles morphology and reactive surfaces evolutions reveals that aqueous ions have a complex behaviour, especially when competitions between various mineral phases occur. In that case, our model predicts a preferential precipitation of finest particles, favouring smectites instead of zeolites. This work is a part of a PhD Thesis supported by Andra, the French Radioactive Waste Management Agency.

SUMO-fusion, purification, and characterization of a (+)-zizaene synthase from Chrysopogon zizanioides

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

Hartwig, S.; Frister, T.; Alemdar, S.

2015-03-20

An uncharacterized plant cDNA coding for a polypeptide presumably having sesquiterpene synthase activity, was expressed in soluble and active form. Two expression strategies were evaluated in Escherichia coli. The enzyme was fused to a highly soluble SUMO domain, in addition to being produced in an unfused form by a cold-shock expression system. Yields up to ∼325 mg/L{sup −1} were achieved in batch cultivations. The 6x-His-tagged enzyme was purified employing an Ni{sup 2+}-IMAC-based procedure. Identity of the protein was established by Western Blot analysis as well as peptide mass fingerprinting. A molecular mass of 64 kDa and an isoelectric point of pImore » 4.95 were determined by 2D gel electrophoresis. Cleavage of the fusion domain was possible by digestion with specific SUMO protease. The synthase was active in Mg{sup 2+} containing buffer and catalyzed the production of (+)-zizaene (syn. khusimene), a precursor of khusimol, from farnesyl diphosphate. Product identity was confirmed by GC–MS and comparison of retention indices. Enzyme kinetics were determined by measuring initial reaction rates for the product, using varying substrate concentrations. By assuming a Michaelis–Menten model, kinetic parameters of K{sub M} = 1.111 μM (±0.113), v{sub max} = 0.3245 μM min{sup −1} (±0.0035), k{sub cat} = 2.95 min{sup −1}, as well as a catalytic efficiency k{sub cat}/K{sub M} = 4.43 × 10{sup 4} M{sup −1} s{sup −1} were calculated. Fusion to a SUMO moiety can substantially increase soluble expression levels of certain hard to express terpene synthases in E. coli. The kinetic data determined for the recombinant synthase are comparable to other described plant sesquiterpene synthases and in the typical range of enzymes belonging to the secondary metabolism. This leaves potential for optimizing catalytic parameters through methods like directed evolution. - Highlights: • Uncharacterized (+)-zizaene synthase from C. zizanoides was cloned and expressed. • Fusion to SUMO and cold-shock induction enhanced soluble yields in E. coli. • Ni{sup 2+}-IMAC purification of the SUMO-fused and unfused enzyme. • (+)-Zizaene identified as main cyclization product by GC–MS. • Enzyme kinetic parameters comparable to related sesquiterpene synthases.« less

Kinetics and its accompanying thermodynamics studies on simultaneous complexation of heterobimetallic neodymium (III) with zinc (II) and L-tryptophan in aquated DMF using 4f-4f absorption spectra.

PubMed

Huidrom, Bimola; Singh, N Rajmuhon

2014-01-24

The 4f-4f absorption spectra of the simultaneous heterobimetallic complexation of trivalent neodymium ion with l-tryptophan and divalent zinc ion in aquated DMF (50%, v/v) at pH 6.0 was recorded at the time interval of 1h. From the observed absorption spectra, the values of intensity parameters such as oscillator strength (P) and Judd-Ofelt intensity (Tλ) parameters, kinetics and thermodynamics parameters were evaluated. The rate constant increases with an increase in the temperature along with the oscillator strengths and Judd-Ofelt intensity parameters. The positive values of the change in the standard enthalpy (ΔH°) and entropy (ΔS°) indicate that the complexation is endothermic. The negative values of the change in the standard free energy (ΔG°) in the range from 293.15 K to 308.15 K, indicate that the reaction occurs spontaneously and hence the formation of heterobimetallic complex in the solution is favored kinetically and thermodynamically. Copyright © 2013 Elsevier B.V. All rights reserved.

Kinetics and its accompanying thermodynamics studies on simultaneous complexation of heterobimetallic neodymium (III) with zinc (II) and L-tryptophan in aquated DMF using 4f-4f absorption spectra

NASA Astrophysics Data System (ADS)

Huidrom, Bimola; Rajmuhon Singh, N.

2014-01-01

The 4f-4f absorption spectra of the simultaneous heterobimetallic complexation of trivalent neodymium ion with L-tryptophan and divalent zinc ion in aquated DMF (50%, v/v) at pH 6.0 was recorded at the time interval of 1 h. From the observed absorption spectra, the values of intensity parameters such as oscillator strength (P) and Judd-Ofelt intensity (Tλ) parameters, kinetics and thermodynamics parameters were evaluated. The rate constant increases with an increase in the temperature along with the oscillator strengths and Judd-Ofelt intensity parameters. The positive values of the change in the standard enthalpy (ΔH°) and entropy (ΔS°) indicate that the complexation is endothermic. The negative values of the change in the standard free energy (ΔG°) in the range from 293.15 K to 308.15 K, indicate that the reaction occurs spontaneously and hence the formation of heterobimetallic complex in the solution is favored kinetically and thermodynamically.

Biophysical Neural Spiking, Bursting, and Excitability Dynamics in Reconfigurable Analog VLSI.

PubMed

Yu, T; Sejnowski, T J; Cauwenberghs, G

2011-10-01

We study a range of neural dynamics under variations in biophysical parameters underlying extended Morris-Lecar and Hodgkin-Huxley models in three gating variables. The extended models are implemented in NeuroDyn, a four neuron, twelve synapse continuous-time analog VLSI programmable neural emulation platform with generalized channel kinetics and biophysical membrane dynamics. The dynamics exhibit a wide range of time scales extending beyond 100 ms neglected in typical silicon models of tonic spiking neurons. Circuit simulations and measurements show transition from tonic spiking to tonic bursting dynamics through variation of a single conductance parameter governing calcium recovery. We similarly demonstrate transition from graded to all-or-none neural excitability in the onset of spiking dynamics through the variation of channel kinetic parameters governing the speed of potassium activation. Other combinations of variations in conductance and channel kinetic parameters give rise to phasic spiking and spike frequency adaptation dynamics. The NeuroDyn chip consumes 1.29 mW and occupies 3 mm × 3 mm in 0.5 μm CMOS, supporting emerging developments in neuromorphic silicon-neuron interfaces.

Thermodynamic criteria for estimating the kinetic parameters of catalytic reactions

NASA Astrophysics Data System (ADS)

Mitrichev, I. I.; Zhensa, A. V.; Kol'tsova, E. M.

2017-01-01

Kinetic parameters are estimated using two criteria in addition to the traditional criterion that considers the consistency between experimental and modeled conversion data: thermodynamic consistency and the consistency with entropy production (i.e., the absolute rate of the change in entropy due to exchange with the environment is consistent with the rate of entropy production in the steady state). A special procedure is developed and executed on a computer to achieve the thermodynamic consistency of a set of kinetic parameters with respect to both the standard entropy of a reaction and the standard enthalpy of a reaction. A problem of multi-criterion optimization, reduced to a single-criterion problem by summing weighted values of the three criteria listed above, is solved. Using the reaction of NO reduction with CO on a platinum catalyst as an example, it is shown that the set of parameters proposed by D.B. Mantri and P. Aghalayam gives much worse agreement with experimental values than the set obtained on the basis of three criteria: the sum of the squares of deviations for conversion, the thermodynamic consistency, and the consistency with entropy production.

Simulation of 2D rarefied gas flows based on the numerical solution of the Boltzmann equation

NASA Astrophysics Data System (ADS)

Poleshkin, Sergey O.; Malkov, Ewgenij A.; Kudryavtsev, Alexey N.; Shershnev, Anton A.; Bondar, Yevgeniy A.; Kohanchik, A. A.

2017-10-01

There are various methods for calculating rarefied gas flows, in particular, statistical methods and deterministic methods based on the finite-difference solutions of the Boltzmann nonlinear kinetic equation and on the solutions of model kinetic equations. There is no universal method; each has its disadvantages in terms of efficiency or accuracy. The choice of the method depends on the problem to be solved and on parameters of calculated flows. Qualitative theoretical arguments help to determine the range of parameters of effectively solved problems for each method; however, it is advisable to perform comparative tests of calculations of the classical problems performed by different methods and with different parameters to have quantitative confirmation of this reasoning. The paper provides the results of the calculations performed by the authors with the help of the Direct Simulation Monte Carlo method and finite-difference methods of solving the Boltzmann equation and model kinetic equations. Based on this comparison, conclusions are made on selecting a particular method for flow simulations in various ranges of flow parameters.

Phase space analysis for a scalar-tensor model with kinetic and Gauss-Bonnet couplings

NASA Astrophysics Data System (ADS)

Granda, L. N.; Loaiza, E.

2016-09-01

We study the phase space for a scalar-tensor string inspired model of dark energy with nonminimal kinetic and Gauss-Bonnet couplings. The form of the scalar potential and of the coupling terms is of the exponential type, which gives rise to appealing cosmological solutions. The critical points describe a variety of cosmological scenarios that go from a matter or radiation dominated universe to a dark energy dominated universe. Trajectories were found in the phase space departing from unstable or saddle fixed points and arriving at the stable scalar field dominated point corresponding to late-time accelerated expansion.

Quantifying stream nutrient uptake from ambient to saturation with instantaneous tracer additions

NASA Astrophysics Data System (ADS)

Covino, T. P.; McGlynn, B. L.; McNamara, R.

2009-12-01

Stream nutrient tracer additions and spiraling metrics are frequently used to quantify stream ecosystem behavior. However, standard approaches limit our understanding of aquatic biogeochemistry. Specifically, the relationship between in-stream nutrient concentration and stream nutrient spiraling has not been characterized. The standard constant rate (steady-state) approach to stream spiraling parameter estimation, either through elevating nutrient concentration or adding isotopically labeled tracers (e.g. 15N), provides little information regarding the stream kinetic curve that represents the uptake-concentration relationship analogous to the Michaelis-Menten curve. These standard approaches provide single or a few data points and often focus on estimating ambient uptake under the conditions at the time of the experiment. Here we outline and demonstrate a new method using instantaneous nutrient additions and dynamic analyses of breakthrough curve (BTC) data to characterize the full relationship between spiraling metrics and nutrient concentration. We compare the results from these dynamic analyses to BTC-integrated, and standard steady-state approaches. Our results indicate good agreement between these three approaches but we highlight the advantages of our dynamic method. Specifically, our new dynamic method provides a cost-effective and efficient approach to: 1) characterize full concentration-spiraling metric curves; 2) estimate ambient spiraling metrics; 3) estimate Michaelis-Menten parameters maximum uptake (Umax) and the half-saturation constant (Km) from developed uptake-concentration kinetic curves, and; 4) measure dynamic nutrient spiraling in larger rivers where steady-state approaches are impractical.

Importance of the structure and nanoporosity of organic matter on the desorption kinetics of benzo[a]pyrene in sediments.

PubMed

Huang, Youda; Zhang, Dainan; Duan, Dandan; Yang, Yu; Xiong, Yongqiang; Ran, Yong

2017-06-01

The desorption kinetics and mechanism were investigated using a Tenax extraction technique on different sediments spiked with radiocarbon-labeled benzo[a]pyrene (BaP). Five sedimentary fractions were sequentially fractionated, and the only nonhydrolyzable organic carbon fractions (NHC) were characterized using advanced solid-state 13 C nuclear magnetic resonance spectroscopy (NMR), improved six end-member model, and a CO 2 gas adsorption technique. The sediments contained high percentages of algaenan and/or sporopollenin but low percentages of black carbon and lignin. A first-order, two-compartment kinetics model described the desorption process very well (R 2  > 0.990). Although some of the organic carbon fractions were significantly related to the desorption kinetics parameters, the NHC fractions showed the highly significant correlation. Moreover, the nanoporosity or specific surface area (SSA) of the NHC fractions was highly related to their OC contents and aliphatic C (R 2  = 0.960, p < 0.01). The multiple regression equations among the desorption kinetics parameters, structural parameters, and nanoporosity were well established (R 2 =>0.999). Nanoporosity and aromatic C were the dominant contributors. Furthermore, the enhanced percentages of desorbed BaP at elevated temperatures significantly showed a linear regression with the structure and nanoporosity. To our knowledge, the above evidence demonstrates for the first time that the transfer (or diffusion) of BaP in the nanopores of condensed aromatic components is the dominant mechanism of the desorption kinetics of BaP at organic matter particle scale. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hafnium-Based Bulk Metallic Glasses for Kinetic Energy Penetrators

DTIC Science & Technology

2004-12-01

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

An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways.

PubMed

Ismail, Ahmad Muhaimin; Mohamad, Mohd Saberi; Abdul Majid, Hairudin; Abas, Khairul Hamimah; Deris, Safaai; Zaki, Nazar; Mohd Hashim, Siti Zaiton; Ibrahim, Zuwairie; Remli, Muhammad Akmal

2017-12-01

Mathematical modelling is fundamental to understand the dynamic behavior and regulation of the biochemical metabolisms and pathways that are found in biological systems. Pathways are used to describe complex processes that involve many parameters. It is important to have an accurate and complete set of parameters that describe the characteristics of a given model. However, measuring these parameters is typically difficult and even impossible in some cases. Furthermore, the experimental data are often incomplete and also suffer from experimental noise. These shortcomings make it challenging to identify the best-fit parameters that can represent the actual biological processes involved in biological systems. Computational approaches are required to estimate these parameters. The estimation is converted into multimodal optimization problems that require a global optimization algorithm that can avoid local solutions. These local solutions can lead to a bad fit when calibrating with a model. Although the model itself can potentially match a set of experimental data, a high-performance estimation algorithm is required to improve the quality of the solutions. This paper describes an improved hybrid of particle swarm optimization and the gravitational search algorithm (IPSOGSA) to improve the efficiency of a global optimum (the best set of kinetic parameter values) search. The findings suggest that the proposed algorithm is capable of narrowing down the search space by exploiting the feasible solution areas. Hence, the proposed algorithm is able to achieve a near-optimal set of parameters at a fast convergence speed. The proposed algorithm was tested and evaluated based on two aspartate pathways that were obtained from the BioModels Database. The results show that the proposed algorithm outperformed other standard optimization algorithms in terms of accuracy and near-optimal kinetic parameter estimation. Nevertheless, the proposed algorithm is only expected to work well in small scale systems. In addition, the results of this study can be used to estimate kinetic parameter values in the stage of model selection for different experimental conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Slow relaxation of cascade-induced defects in Fe

DOE PAGES

Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.; ...

2015-02-17

On-the-fly kinetic Monte Carlo (KMC) simulations are performed to investigate slow relaxation of non-equilibrium systems. Point defects induced by 25 keV cascades in α -Fe are shown to lead to a characteristic time-evolution, described by the replenish and relax mechanism. Then, we produce an atomistically-based assessment of models proposed to explain the slow structural relaxation by focusing on the aggregation of 50 vacancies and 25 self-interstital atoms (SIA) in 10-lattice-parameter α-Fe boxes, two processes that are closely related to cascade annealing and exhibit similar time signature. Four atomistic effects explain the timescales involved in the evolution: defect concentration heterogeneities, concentration-enhancedmore » mobility, cluster-size dependent bond energies and defect-induced pressure. In conclusion, these findings suggest that the two main classes of models to explain slow structural relaxation, the Eyring model and the Gibbs model, both play a role to limit the rate of relaxation of these simple point-defect systems.« less

Anhydrous Weight Loss Prediction of Meranti Sawdust during Torrefaction using Rousset Model

NASA Astrophysics Data System (ADS)

Harun, Nur Hazirah Huda Mohd; Samad, Noor Asma Fazli Abdul; Saleh, Suriyati

2018-03-01

In torrefaction, the mass loss distribution is evaluated in terms of anhydrous weight loss (AWL). Since temperature gives significant effects on AWL and the behaviour of biomass is highly associated with the AWL, therefore a suitable model for estimating the reaction kinetics is necessary for describing the thermal degradation and predicting the AWL in order to improve its process. In this study, the kinetic parameters of Meranti sawdust are estimated by applying three-parallel reaction models namely the Rousset Model for torrefaction of Meranti sawdust at temperatures of 240°C, 270°C and 300°C. All kinetic parameters are estimated according to the degradation of biomass constituents which are lignin, cellulose and hemicellulose by following the Arrhenius Law. The result shows that AWL estimation using the kinetic parameters predicted from the Rousset model is in good agreement with the experimental result as the R2 value obtained is 0.99. It shows that the Rousset Model successfully described the degradation of lignin, cellulose and hemicellulose as well as the formation of char, volatile, tar and intermediate compound. Therefore it can be concluded that the Rousset Model is applicable to represent the torrefaction behaviour.

Kinetic Analysis of Rhodamines Efflux Mediated by the Multidrug Resistance Protein (MRP1)

PubMed Central

Saengkhae, Chantarawan; Loetchutinat, Chatchanok; Garnier-Suillerot, Arlette

2003-01-01

Characterization of rhodamine 123 as functional assay for MDR has been primarily focused on P-glycoprotein-mediated MDR. Several studies have suggested that Rh123 is also a substrate for MRP1. However, no quantitative studies of the MRP1-mediated efflux of rhodamines have, up to now, been performed. Measurement of the kinetic characteristics of substrate transport is a powerful approach to enhancing our understanding of their function and mechanism. In the present study, we have used a continuous fluorescence assay with four rhodamine dyes (rhodamine 6G, tetramethylrosamine, tetramethylrhodamine ethyl ester, and tetramethylrhodamine methyl ester) to quantify drug transport by MRP1 in living GLC4/ADR cells. The formation of a substrate concentration gradient was observed. MRP1-mediated transport of rhodamine was glutathione-dependent. The kinetics parameter, ka = VM/km, was very similar for the four rhodamine analogs but ∼10-fold less than the values of the same parameter determined previously for the MRP1-mediated efflux of anthracycline. The findings presented here are the first to show quantitative information about the kinetics parameters for MRP1-mediated efflux of rhodamine dyes. PMID:12944313

Intrinsic kinetic parameters of Thermococcus onnurineus NA1 strains and prediction of optimum carbon monoxide level for ideal bioreactor operation.

PubMed

Jeong, Yeseul; Jang, Nulee; Yasin, Muhammad; Park, Shinyoung; Chang, In Seop

2016-02-01

This study determines and compares the intrinsic kinetic parameters (Ks and Ki) of selected Thermococcus onnurineus NA1 strains (wild-type (WT), and mutants MC01, MC02, and WTC156T) using the substrate inhibition model. Ks and Ki values were used to find the optimum dissolved CO (CL) conditions inside the reactor. The results showed that in terms of the maximum specific CO consumption rates (qCO(max)) of WT, MC01, MC02, and WTC156T the optimum activities can be achieved by maintaining the CL levels at 0.56mM, 0.52mM, 0.58mM, and 0.75mM, respectively. The qCO(max) value of WTC156T at 0.75mM was found to be 1.5-fold higher than for the WT strain, confirming its superiority. Kinetic modeling was then used to predict the conditions required to maintain the optimum CL levels and high cell concentrations in the reactor, based on the kinetic parameters of the WTC156T strain. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimization of kinetic parameters for the degradation of plasmid DNA in rat plasma

NASA Astrophysics Data System (ADS)

Chaudhry, Q. A.

2014-12-01

Biotechnology is a rapidly growing area of research work in the field of pharmaceutical sciences. The study of pharmacokinetics of plasmid DNA (pDNA) is an important area of research work. It has been observed that the process of gene delivery faces many troubles on the transport of pDNA towards their target sites. The topoforms of pDNA has been termed as super coiled (S-C), open circular (O-C) and linear (L), the kinetic model of which will be presented in this paper. The kinetic model gives rise to system of ordinary differential equations (ODEs), the exact solution of which has been found. The kinetic parameters, which are responsible for the degradation of super coiled, and the formation of open circular and linear topoforms have a great significance not only in vitro but for modeling of further processes as well, therefore need to be addressed in great detail. For this purpose, global optimization techniques have been adopted, thus finding the optimal results for the said model. The results of the model, while using the optimal parameters, were compared against the measured data, which gives a nice agreement.

NEMA NU 4-Optimized Reconstructions for Therapy Assessment in Cancer Research with the Inveon Small Animal PET/CT System.

PubMed

Lasnon, Charline; Dugue, Audrey Emmanuelle; Briand, Mélanie; Blanc-Fournier, Cécile; Dutoit, Soizic; Louis, Marie-Hélène; Aide, Nicolas

2015-06-01

We compared conventional filtered back-projection (FBP), two-dimensional-ordered subsets expectation maximization (OSEM) and maximum a posteriori (MAP) NEMA NU 4-optimized reconstructions for therapy assessment. Varying reconstruction settings were used to determine the parameters for optimal image quality with two NEMA NU 4 phantom acquisitions. Subsequently, data from two experiments in which nude rats bearing subcutaneous tumors had received a dual PI3K/mTOR inhibitor were reconstructed with the NEMA NU 4-optimized parameters. Mann-Whitney tests were used to compare mean standardized uptake value (SUV(mean)) variations among groups. All NEMA NU 4-optimized reconstructions showed the same 2-deoxy-2-[(18)F]fluoro-D-glucose ([(18)F]FDG) kinetic patterns and detected a significant difference in SUV(mean) relative to day 0 between controls and treated groups for all time points with comparable p values. In the framework of therapy assessment in rats bearing subcutaneous tumors, all algorithms available on the Inveon system performed equally.

Stoichiometric network analysis and associated dimensionless kinetic equations. Application to a model of the Bray-Liebhafsky reaction.

PubMed

Schmitz, Guy; Kolar-Anić, Ljiljana Z; Anić, Slobodan R; Cupić, Zeljko D

2008-12-25

The stoichiometric network analysis (SNA) introduced by B. L. Clarke is applied to a simplified model of the complex oscillating Bray-Liebhafsky reaction under batch conditions, which was not examined by this method earlier. This powerful method for the analysis of steady-states stability is also used to transform the classical differential equations into dimensionless equations. This transformation is easy and leads to a form of the equations combining the advantages of classical dimensionless equations with the advantages of the SNA. The used dimensionless parameters have orders of magnitude given by the experimental information about concentrations and currents. This simplifies greatly the study of the slow manifold and shows which parameters are essential for controlling its shape and consequently have an important influence on the trajectories. The effectiveness of these equations is illustrated on two examples: the study of the bifurcations points and a simple sensitivity analysis, different from the classical one, more based on the chemistry of the studied system.

Common amino acid domain among endopolygalacturonases of ascomycete fungi.

PubMed Central

Keon, J P; Waksman, G

1990-01-01

The endopolygalacturonase (EC 3.2.1.15) enzymes produced in vitro by three ascomycete fungi, Aspergillus niger, Sclerotinia sclerotiorum, and Colletotrichum lindemuthianum were studied by using thin-layer isoelectric focusing and activity stain overlay techniques. The polygalacturonases from A. niger and S. sclerotiorum consisted of numerous isoforms, whereas the endopolygalacturonase from C. lindemuthianum consisted of a single protein species. The most abundant endopolygalacturonase isoform produced by each of these organisms was purified and characterized. Biochemical parameters, including molecular weight, isoelectric point, kinetic parameters, temperature and pH optima, and thermal stability, were determined. Considerable differences in physical and chemical properties were demonstrated among these fungal polygalacturonases. Antibodies raised against individual proteins exhibited little cross-reaction, suggesting that these enzymes differ structurally as well as biochemically. In contrast, the analysis of the N-terminal amino acid sequences of the three proteins showed extensive homology, particularly in a region labeled domain 1 in which 84% of the amino acids were conserved. Images PMID:2403258

A strategy to determine operating parameters in tissue engineering hollow fiber bioreactors

PubMed Central

Shipley, RJ; Davidson, AJ; Chan, K; Chaudhuri, JB; Waters, SL; Ellis, MJ

2011-01-01

The development of tissue engineering hollow fiber bioreactors (HFB) requires the optimal design of the geometry and operation parameters of the system. This article provides a strategy for specifying operating conditions for the system based on mathematical models of oxygen delivery to the cell population. Analytical and numerical solutions of these models are developed based on Michaelis–Menten kinetics. Depending on the minimum oxygen concentration required to culture a functional cell population, together with the oxygen uptake kinetics, the strategy dictates the model needed to describe mass transport so that the operating conditions can be defined. If cmin ≫ Km we capture oxygen uptake using zero-order kinetics and proceed analytically. This enables operating equations to be developed that allow the user to choose the medium flow rate, lumen length, and ECS depth to provide a prescribed value of cmin. When , we use numerical techniques to solve full Michaelis–Menten kinetics and present operating data for the bioreactor. The strategy presented utilizes both analytical and numerical approaches and can be applied to any cell type with known oxygen transport properties and uptake kinetics. PMID:21370228

[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.

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

GELATIN CARRIERS FOR DRUG AND CELL DELIVERY IN TISSUE ENGINEERING

PubMed Central

Santoro, Marco; Tatara, Alexander M.; Mikos, Antonios G.

2014-01-01

The ability of gelatin to form complexes with different drugs has been investigated for controlled release applications. Gelatin parameters, such as crosslinking density and isoelectric point, have been tuned in order to optimize gelatin degradation and drug delivery kinetics. In recent years, focus has shifted away from the use of gelatin in isolation towards the modification of gelatin with functional groups and the fabrication of material composites with embedded gelatin carriers. In this review, we highlight some of the latest work being performed in these areas and comment on trends in the field. Specifically, we discuss gelatin modifications for immune system evasion, drug stabilization, and targeted delivery, as well as gelatin composite systems based on ceramics, naturally-occurring polymers, and synthetic polymers. PMID:24746627

Deactivation of Zeolite Catalyst H-ZSM-5 during Conversion of Methanol to Gasoline: Operando Time- and Space-Resolved X-ray Diffraction.

PubMed

Rojo-Gama, Daniel; Mentel, Lukasz; Kalantzopoulos, Georgios N; Pappas, Dimitrios K; Dovgaliuk, Iurii; Olsbye, Unni; Lillerud, Karl Petter; Beato, Pablo; Lundegaard, Lars F; Wragg, David S; Svelle, Stian

2018-03-15

The deactivation of zeolite catalyst H-ZSM-5 by coking during the conversion of methanol to hydrocarbons was monitored by high-energy space- and time-resolved operando X-ray diffraction (XRD) . Space resolution was achieved by continuous scanning along the axial length of a capillary fixed bed reactor with a time resolution of 10 s per scan. Using real structural parameters obtained from XRD, we can track the development of coke at different points in the reactor and link this to a kinetic model to correlate catalyst deactivation with structural changes occurring in the material. The "burning cigar" model of catalyst bed deactivation is directly observed in real time.

Port wine oxidation management: a multiparametric kinetic approach.

PubMed

Martins, Rui Costa; Monforte, Ana Rita; Silva Ferreira, António

2013-06-05

Port wine is a flagship fortified wine of Portugal, which undergoes a particularly long aging period, developing a dynamic sensory profile over time, responsible for several wine categories, which is dependent upon the type of aging (bottle or barrel). Therefore, the quality of the product is dependent upon the chemical mechanisms occurring during the aging process, such as oxidation or Maillard reactions. To attain the desired quality management, it is necessary to understand how technological parameters, such as temperature or oxygen exposure, affect the kinetics of the formation of key odorants, such as sotolon. There is a lack of information about the impact of the storage conditions (oxygen and temperature) on Port wine quality. In this study, the effect of these two parameters were investigated to increase the knowledge database concerning aging management of Port wines. It was found that sotolon formation is highly dependent upon oxygen and temperature. There is however a synergistic effect between these two parameters that could significantly increase the concentration. The kinetic parameters of oxygen, sotolon, and other compounds related to Port aging (cis- and trans-5-hydroxy-2-methyl-1,3-dioxan, 2-furfural, 5-hydroxy-methyl-furfural, and 5-methyl-furfural) are also reported. Kinetic models with Monte Carlo simulations, where the oxygen permeability dispersion and temperature are the parameters under evaluation, were applied. On the basis of the modeling predictions, it would seem that the temperature of a cellar would have a more significant impact on the Port wines stored in containers where the oxygen intake is higher (barrels) when compared to containers with low oxygen permeability (bottles using cork stoppers).

Dry mechanochemical synthesis of hydroxyapatites from DCPD and CaO: influence of instrumental parameters on the reaction kinetics.

PubMed

Mochales, Carolina; El Briak-BenAbdeslam, Hassane; Ginebra, Maria Pau; Terol, Alain; Planell, Josep A; Boudeville, Philippe

2004-01-01

Mechanochemistry is a possible route to synthesize calcium deficient hydroxyapatite (CDHA) with an expected molar calcium-to-phosphate (Ca/P) ratio +/-0.01. To optimize the experimental conditions of CDHA preparation from dicalcium phosphate dihydrate (DCPD) and calcium oxide by dry mechanosynthesis reaction, we performed the kinetic study varying some experimental parameters. This kinetic study was carried out with two different planetary ball mills (Retsch or Fritsch Instuments). Results obtained with the two mills led to the same conclusions although the values of the rate constants of DCPD disappearance and times for complete reaction were very different. Certainly, the origin of these differences was from the mills used, thus we investigated the influence of instrumental parameters such as the mass and the surface area of the balls or the rotation velocity on the mechanochemical reaction kinetics of DCPD with CaO. Results show that the DCPD reaction rate constant and the inverse of the time for complete disappearance of CaO both vary linearly with (i) the square of the rotation velocity, (ii) the square of eccentricity of the vial on the rotating disc and (iii) the product of the mass by the surface area of the balls. These observations comply with theoretical models developed for mechanical alloying. The consideration of these four parameters allows the transposition of experimental conditions from one mill to another or the comparison between results obtained with different planetary ball mills. These instrumental parameters have to be well described in papers concerning mechanochemistry or when grinding is an important stage in a process.

Kinetics of reactions of aquacobalamin with aspartic and glutamic acids and their amides in water solutions

NASA Astrophysics Data System (ADS)

Bui, T. T. T.; Sal'nikov, D. S.; Dereven'kov, I. A.; Makarov, S. V.

2017-04-01

The kinetics of aquacobalamin reaction with aspartic and glutamic acids, and with their amides in water solutions, is studied via spectrophotometry. The kinetic and activation parameters of the process are determined. It is shown that the reaction product is cobalamin-amino acid complex. The data are compared to results on the reaction between aquacobalamin and primary amines.

Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach

PubMed Central

Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M.; El Fakhri, Georges

2013-01-01

Purpose: Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Methods: Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. Results: At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%–29% and 32%–70% for 50 × 106 and 10 × 106 detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40–50 iterations), while more than 500 iterations were needed for CG. Conclusions: The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method. PMID:24089922

Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach.

PubMed

Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M; El Fakhri, Georges

2013-10-01

Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%-29% and 32%-70% for 50 × 10(6) and 10 × 10(6) detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40-50 iterations), while more than 500 iterations were needed for CG. The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method.

A pharmacokinetic study of two modified-release methylphenidate formulations under different food conditions in healthy volunteers.

PubMed

Haessler, F; Tracik, F; Dietrich, H; Stammer, H; Klatt, J

2008-09-01

Primary objective was to investigate bioequivalence of Ritalin LA(R); 40 mg compared to Medikinet retard 40 mg in healthy male volunteers under fasted and fed conditions. Secondary objectives included assessment of tolerability and determination of further pharmacokinetic parameters. The difference between the kinetic profiles of Ritalin LA(R) and Medikinet retard with respect to breakfast intake was additionally explored. 28 subjects were randomized in this open-label, four-treatment, cross-over-design study. Pharmacokinetic evaluations included AUC(0-inf), Cmax, tmax, elimination half life (t1/2) and mean residence time MRT(0-inf)). The relative bioavailability of Ritalin LA(R) and Medikinet retard and the food effect were assessed using a 90% confidence interval (CI) based on the lower and upper endpoints of the CI for the ratios of the geometric means being within the 80 - 125% equivalence criterion. 25 volunteers completed all treatment arms. Frequency of adverse events were comparable for all treatments. Under fasted condition Ritalin LA(R) showed a consistent bimodal concentration time profile with two tmax peaks. Medikinet retard showed a steady absorption with a single tmax peak. The point estimators for AUC(0-inf) and Cmax were found to be 99.7% and 85.9%, respectively. Under fed condition both Ritalin LA(R) and Medikinet retard showed a bimodal concentration time profile with two tmax peaks. The point estimators for AUC(0-inf) and Cmax were estimated as 89.8% and 68.6%, respectively. Both methylphenidate formulations were safe and well tolerated. Ritalin LA and Medikinet retard were bioequivalent in fasted state but not in fed state. Only Ritalin LA had a biphasic kinetic profile under both fasted and fed conditions. This difference in the kinetic profiles might be of clinical relevance and might offer a potential advantage of Ritalin LA.

Advanced model for the prediction of the neutron-rich fission product yields

NASA Astrophysics Data System (ADS)

Rubchenya, V. A.; Gorelov, D.; Jokinen, A.; Penttilä, H.; Äystö, J.

2013-12-01

The consistent models for the description of the independent fission product formation cross sections in the spontaneous fission and in the neutron and proton induced fission at the energies up to 100 MeV is developed. This model is a combination of new version of the two-component exciton model and a time-dependent statistical model for fusion-fission process with inclusion of dynamical effects for accurate calculations of nucleon composition and excitation energy of the fissioning nucleus at the scission point. For each member of the compound nucleus ensemble at the scission point, the primary fission fragment characteristics: kinetic and excitation energies and their yields are calculated using the scission-point fission model with inclusion of the nuclear shell and pairing effects, and multimodal approach. The charge distribution of the primary fragment isobaric chains was considered as a result of the frozen quantal fluctuations of the isovector nuclear matter density at the scission point with the finite neck radius. Model parameters were obtained from the comparison of the predicted independent product fission yields with the experimental results and with the neutron-rich fission product data measured with a Penning trap at the Accelerator Laboratory of the University of Jyväskylä (JYFLTRAP).

Thermal contact through a two-temperature kinetic Ising chain

NASA Astrophysics Data System (ADS)

Bauer, M.; Cornu, F.

2018-05-01

We consider a model for thermal contact through a diathermal interface between two macroscopic bodies at different temperatures: an Ising spin chain with nearest neighbor interactions is endowed with a Glauber dynamics with different temperatures and kinetic parameters on alternating sites. The inhomogeneity of the kinetic parameter is a novelty with respect to the model of Racz and Zia (1994 Phys. Rev. E 49 139), and we exhibit its influence upon the stationary non equilibrium values of the two-spin correlations at any distance. By mapping to the dynamics of spin domain walls and using free fermion techniques, we determine the scaled generating function for the cumulants of the exchanged heat amounts per unit of time in the long time limit.

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.

Evaluation of limited blood sampling population input approaches for kinetic quantification of [18F]fluorothymidine PET data.

PubMed

Contractor, Kaiyumars B; Kenny, Laura M; Coombes, Charles R; Turkheimer, Federico E; Aboagye, Eric O; Rosso, Lula

2012-03-24

Quantification of kinetic parameters of positron emission tomography (PET) imaging agents normally requires collecting arterial blood samples which is inconvenient for patients and difficult to implement in routine clinical practice. The aim of this study was to investigate whether a population-based input function (POP-IF) reliant on only a few individual discrete samples allows accurate estimates of tumour proliferation using [18F]fluorothymidine (FLT). Thirty-six historical FLT-PET data with concurrent arterial sampling were available for this study. A population average of baseline scans blood data was constructed using leave-one-out cross-validation for each scan and used in conjunction with individual blood samples. Three limited sampling protocols were investigated including, respectively, only seven (POP-IF7), five (POP-IF5) and three (POP-IF3) discrete samples of the historical dataset. Additionally, using the three-point protocol, we derived a POP-IF3M, the only input function which was not corrected for the fraction of radiolabelled metabolites present in blood. The kinetic parameter for net FLT retention at steady state, Ki, was derived using the modified Patlak plot and compared with the original full arterial set for validation. Small percentage differences in the area under the curve between all the POP-IFs and full arterial sampling IF was found over 60 min (4.2%-5.7%), while there were, as expected, larger differences in the peak position and peak height.A high correlation between Ki values calculated using the original arterial input function and all the population-derived IFs was observed (R2 = 0.85-0.98). The population-based input showed good intra-subject reproducibility of Ki values (R2 = 0.81-0.94) and good correlation (R2 = 0.60-0.85) with Ki-67. Input functions generated using these simplified protocols over scan duration of 60 min estimate net PET-FLT retention with reasonable accuracy.

Some fundamental questions concerning the kinetic theory of electrons in molecular gases and the e H2 vibrational cross section controversy

NASA Astrophysics Data System (ADS)

Robson, R. E.; White, R. D.; Morrison, Michael A.

2003-10-01

We commence a fundamental re-examination of the kinetic theory of charged particle swarms in molecular gases, focusing on collisional excitation of molecular rotational and ro-vibrational states by electrons. Modern day analysis of electron swarms has been based upon the kinetic equation of Wang-Chang et al, which simply treats all processes as scalar energy excitations, and ignores angular momentum conservation and the vector dynamics associated with rotational excitation. It is pointed out that there is no alternative, more exact kinetic equation readily available for electrons which enables one to directly ascertain the degree of error introduced by this approximation. Thus in this preliminary study, we approach the problem indirectly, from the standpoint of the neutral molecules, using the Waldmann-Snider quantum kinetic equation, and insist that an electron-molecule collision must look the same from the perspective of both electron and molecule. We give a formula for quantitatively assessing the importance of scalar versus vectorial treatments of rotational excitation by looking at the post-collisional 'echo' produced by an electron swarm as it passes through the gas. It is then pointed out that in order to remedy any deficiency, it will be necessary to introduce a kinetic collisional operator non-local in space to properly account for angular momentum conservation, as has long been established in the literature. This is a major exercise and given the preliminary nature of this study, we consider the inclusion of such effects from a formal point of view only. In particular we show how non-local effects lead to a spatially dependent 'source' term in the equation of continuity, and hence to corrections for both drift velocity and diffusion coefficients. The magnitude of these corrections has yet to be established.

Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology.

PubMed

Kundu, Siddhartha

2015-01-01

Can the stimulus-driven synergistic association of 2-oxoglutarate dependent dioxygenases be influenced by the kinetic parameters of binding and catalysis?In this manuscript, I posit that these indices are necessary and specific for a particular stimulus, and are key determinants of a dynamic clustering that may function to mitigate the effects of this trigger. The protein(s)/sequence(s) that comprise this group are representative of all major kingdoms of life, and catalyze a generic hydroxylation, which is, in most cases accompanied by a specialized conversion of the substrate molecule. Iron is an essential co-factor for this transformation and the response to waning levels is systemic, and mandates the simultaneous participation of molecular sensors, transporters, and signal transducers. Here, I present a proof-of-concept model, that an evolving molecular network of 2OG-dependent enzymes can maintain iron homeostasis in the cytosol of root hair cells of members of the family Gramineae by actuating a non-reductive compensatory chelation by the phytosiderophores. Regression models of empirically available kinetic data (iron and alpha-ketoglutarate) were formulated, analyzed, and compared. The results, when viewed in context of the superfamily responding as a unit, suggest that members can indeed, work together to accomplish system-level function. This is achieved by the establishment of transient metabolic conduits, wherein the flux is dictated by kinetic compatibility of the participating enzymes. The approach adopted, i.e., predictive mathematical modeling, is integral to the hypothesis-driven acquisition of experimental data points and, in association with suitable visualization aids may be utilized for exploring complex plant biochemical systems.

Thermodynamics and kinetics of binary nucleation in ideal-gas mixtures.

PubMed

Alekseechkin, Nikolay V

2015-08-07

The nonisothermal single-component theory of droplet nucleation [N. V. Alekseechkin, Physica A 412, 186 (2014)] is extended to binary case; the droplet volume V, composition x, and temperature T are the variables of the theory. An approach based on macroscopic kinetics (in contrast to the standard microscopic model of nucleation operating with the probabilities of monomer attachment and detachment) is developed for the droplet evolution and results in the derived droplet motion equations in the space (V, x, T)—equations for V̇≡dV/dt, ẋ, and Ṫ. The work W(V, x, T) of the droplet formation is obtained in the vicinity of the saddle point as a quadratic form with diagonal matrix. Also, the problem of generalizing the single-component Kelvin equation for the equilibrium vapor pressure to binary case is solved; it is presented here as a problem of integrability of a Pfaffian equation. The equation for Ṫ is shown to be the first law of thermodynamics for the droplet, which is a consequence of Onsager's reciprocal relations and the linked-fluxes concept. As an example of ideal solution for demonstrative numerical calculations, the o-xylene-m-xylene system is employed. Both nonisothermal and enrichment effects are shown to exist; the mean steady-state overheat of droplets and their mean steady-state enrichment are calculated with the help of the 3D distribution function. Some qualitative peculiarities of the nucleation thermodynamics and kinetics in the water-sulfuric acid system are considered in the model of regular solution. It is shown that there is a small kinetic parameter in the theory due to the small amount of the acid in the vapor and, as a consequence, the nucleation process is isothermal.

Energy of the quasi-free electron in supercritical krypton near the critical point.

PubMed

Li, Luxi; Evans, C M; Findley, G L

2005-12-01

Field ionization measurements of high-n CH(3)I and C(2)H(5)I Rydberg states doped into krypton are presented as a function of krypton number density along the critical isotherm. These data exhibit a decrease in the krypton-induced shift of the dopant ionization energy near the critical point. This change in shift is modeled to within +/-0.2% of experiment using a theory that accounts for the polarization of krypton by the dopant ion, the polarization of krypton by the quasi-free electron that arises from field ionization of the dopant, and the zero point kinetic energy of the free electron. The overall decrease in the shift of the dopant ionization energy near the critical point of krypton, which is a factor of 2 larger than that observed in argon, is dominated by the increase in the zero point kinetic energy of the quasi-free electron.

Electro-kinetically driven peristaltic transport of viscoelastic physiological fluids through a finite length capillary: Mathematical modeling.

PubMed

Tripathi, Dharmendra; Yadav, Ashu; Bég, O Anwar

2017-01-01

Analytical solutions are developed for the electro-kinetic flow of a viscoelastic biological liquid in a finite length cylindrical capillary geometry under peristaltic waves. The Jefferys' non-Newtonian constitutive model is employed to characterize rheological properties of the fluid. The unsteady conservation equations for mass and momentum with electro-kinetic and Darcian porous medium drag force terms are reduced to a system of steady linearized conservation equations in an axisymmetric coordinate system. The long wavelength, creeping (low Reynolds number) and Debye-Hückel linearization approximations are utilized. The resulting boundary value problem is shown to be controlled by a number of parameters including the electro-osmotic parameter, Helmholtz-Smoluchowski velocity (maximum electro-osmotic velocity), and Jefferys' first parameter (ratio of relaxation and retardation time), wave amplitude. The influence of these parameters and also time on axial velocity, pressure difference, maximum volumetric flow rate and streamline distributions (for elucidating trapping phenomena) is visualized graphically and interpreted in detail. Pressure difference magnitudes are enhanced consistently with both increasing electro-osmotic parameter and Helmholtz-Smoluchowski velocity, whereas they are only elevated with increasing Jefferys' first parameter for positive volumetric flow rates. Maximum time averaged flow rate is enhanced with increasing electro-osmotic parameter, Helmholtz-Smoluchowski velocity and Jefferys' first parameter. Axial flow is accelerated in the core (plug) region of the conduit with greater values of electro-osmotic parameter and Helmholtz-Smoluchowski velocity whereas it is significantly decelerated with increasing Jefferys' first parameter. The simulations find applications in electro-osmotic (EO) transport processes in capillary physiology and also bio-inspired EO pump devices in chemical and aerospace engineering. Copyright © 2016 Elsevier Inc. All rights reserved.

Toxicokinetics of perfluorooctane sulfonate in rabbits under environmentally realistic exposure conditions and comparative assessment between mammals and birds.

PubMed

Tarazona, J V; Rodríguez, C; Alonso, E; Sáez, M; González, F; San Andrés, M D; Jiménez, B; San Andrés, M I

2016-01-22

This article describes the toxicokinetics of perfluorooctane sulfonate (PFOS) in rabbits under low repeated dosing, equivalent to 0.085μg/kg per day, and the observed differences between rabbits and chickens. The best fitting for both species was provided by a simple pseudo monocompartmental first-order kinetics model, regulated by two rates, and accounting for real elimination as well as binding of PFOS to non-exchangeable structures. Elimination was more rapid in rabbits, with a pseudo first-order dissipation half-life of 88 days compared to the 230 days observed for chickens. By contrast, the calculated assimilation efficiency for rabbits was almost 1, very close to full absorption, significantly higher than the 0.66 with confidence intervals of 0.64 and 0.68 observed for chickens. The results confirm a very different kinetics than that observed in single-dose experiments confirming clear dose-related differences in apparent elimination rates in rabbits, as previously described for humans and other mammals; suggesting the role of a capacity-limited saturable process resulting in different kinetic behaviours for PFOS in high dose versus environmentally relevant low dose exposure conditions. The model calculations confirmed that the measured maximum concentrations were still far from the steady state situation, and that the different kinetics between birds and mammals should may play a significant role in the biomagnifications assessment and potential exposure for humans and predators. For the same dose regime, the steady state concentration was estimated at about 36μg PFOS/L serum for rabbits, slightly above one-half of the 65μg PFOS/L serum estimated for chickens. The toxicokinetic parameters presented here can be used for higher-tier bioaccumulation estimations of PFOS in rabbits and chickens as starting point for human health exposure assessments and as surrogate values for modeling PFOS kinetics in wild mammals and bird in exposure assessment of predatory species. Published by Elsevier Ireland Ltd.

Novel methods to estimate the enantiomeric ratio and the kinetic parameters of enantiospecific enzymatic reactions.

PubMed

Machado, G D.C.; Paiva, L M.C.; Pinto, G F.; Oestreicher, E G.

2001-03-08

1The Enantiomeric Ratio (E) of the enzyme, acting as specific catalysts in resolution of enantiomers, is an important parameter in the quantitative description of these chiral resolution processes. In the present work, two novel methods hereby called Method I and II, for estimating E and the kinetic parameters Km and Vm of enantiomers were developed. These methods are based upon initial rate (v) measurements using different concentrations of enantiomeric mixtures (C) with several molar fractions of the substrate (x). Both methods were tested using simulated "experimental data" and actual experimental data. Method I is easier to use than Method II but requires that one of the enantiomers is available in pure form. Method II, besides not requiring the enantiomers in pure form shown better results, as indicated by the magnitude of the standard errors of estimates. The theoretical predictions were experimentally confirmed by using the oxidation of 2-butanol and 2-pentanol catalyzed by Thermoanaerobium brockii alcohol dehydrogenase as reaction models. The parameters E, Km and Vm were estimated by Methods I and II with precision and were not significantly different from those obtained experimentally by direct estimation of E from the kinetic parameters of each enantiomer available in pure form.

Extraction kinetics and properties of proanthocyanidins from pomegranate peel

USDA-ARS?s Scientific Manuscript database

With an objective of developing a safe and efficient method to extract proanthocyanidins products from pomegranate peel for use in nutraceuticals or as food additives, the effects of extraction parameters on the production efficiency, product properties, and extraction kinetics were systematically s...

Budgets of divergent and rotational kinetic energy during two periods of intense convection

NASA Technical Reports Server (NTRS)

Buechler, D. E.; Fuelberg, H. E.

1986-01-01

The derivations of the energy budget equations for divergent and rotational components of kinetic energy are provided. The intense convection periods studied are: (1) synoptic scale data of 3 or 6 hour intervals and (2) mesoalphascale data every 3 hours. Composite energies and averaged budgets for the periods are presented; the effects of random data errors on derived energy parameters is investigated. The divergent kinetic energy and rotational kinetic energy budgets are compared; good correlation of the data is observed. The kinetic energies and budget terms increase with convective development; however, the conversion of the divergent and rotational energies are opposite.

A kinetic and thermochemical database for organic sulfur and oxygen compounds.

PubMed

Class, Caleb A; Aguilera-Iparraguirre, Jorge; Green, William H

2015-05-28

Potential energy surfaces and reaction kinetics were calculated for 40 reactions involving sulfur and oxygen. This includes 11 H2O addition, 8 H2S addition, 11 hydrogen abstraction, 7 beta scission, and 3 elementary tautomerization reactions, which are potentially relevant in the combustion and desulfurization of sulfur compounds found in various fuel sources. Geometry optimizations and frequencies were calculated for reactants and transition states using B3LYP/CBSB7, and potential energies were calculated using CBS-QB3 and CCSD(T)-F12a/VTZ-F12. Rate coefficients were calculated using conventional transition state theory, with corrections for internal rotations and tunneling. Additionally, thermochemical parameters were calculated for each of the compounds involved in these reactions. With few exceptions, rate parameters calculated using the two potential energy methods agreed reasonably, with calculated activation energies differing by less than 5 kJ mol(-1). The computed rate coefficients and thermochemical parameters are expected to be useful for kinetic modeling.

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

Kinetics of Static Strain Aging in Polycrystalline NiAl-based Alloys

NASA Technical Reports Server (NTRS)

Weaver, M. L.; Kaufman, M. J.; Noebe, R. D.

1996-01-01

The kinetics of yield point return have been studied in two NiAl-based alloys as a function of aging time at temperatures between 300 and 700 K. The results indicate that the upper yield stress increment, Delta sigma(sub u) (i.e., stress difference between the upper yield point and the final flow stress achieved during prestraining), in conventional purity (CP-NiAl) and in high purity carbon-doped (NiAl-C) material first increased with a t(exp 2/3) relationship before reaching a plateau. This behavior suggests that a Cottrell locking mechanism is the cause for yield points in NiAl. In addition, positive y-axis intercepts were observed in plots of Delta sigma(sub u) versus t(exp 2/3) suggesting the operation of a Snoek mechanism. Analysis according to the Cottrell Bilby model of atmosphere formation around dislocations yields an activation energy for yield point return in the range 70 to 76 kJ/mol which is comparable to the activation energy for diffusion of interstitial impurities in bcc metals. It is, thus, concluded that the kinetics of static strain aging in NiAl are controlled by the locking of dislocations by Cottrell atmospheres of carbon atoms around dislocations.

Nuclear Quantum Effects in Water at the Triple Point: Using Theory as a Link Between Experiments.

PubMed

Cheng, Bingqing; Behler, Jörg; Ceriotti, Michele

2016-06-16

One of the most prominent consequences of the quantum nature of light atomic nuclei is that their kinetic energy does not follow a Maxwell-Boltzmann distribution. Deep inelastic neutron scattering (DINS) experiments can measure this effect. Thus, the nuclear quantum kinetic energy can be probed directly in both ordered and disordered samples. However, the relation between the quantum kinetic energy and the atomic environment is a very indirect one, and cross-validation with theoretical modeling is therefore urgently needed. Here, we use state of the art path integral molecular dynamics techniques to compute the kinetic energy of hydrogen and oxygen nuclei in liquid, solid, and gas-phase water close to the triple point, comparing three different interatomic potentials and validating our results against equilibrium isotope fractionation measurements. We will then show how accurate simulations can draw a link between extremely precise fractionation experiments and DINS, therefore establishing a reliable benchmark for future measurements and providing key insights to increase further the accuracy of interatomic potentials for water.

On the Convenience of Using a Computer Simulation to Teach Enzyme Kinetics to Undergraduate Students with Biological Chemistry-Related Curricula

ERIC Educational Resources Information Center

Gonzalez-Cruz, Javier; Rodriguez-Sotres, Rogelio; Rodriguez-Penagos, Mireya

2003-01-01

Enzyme kinetics is a difficult subject for students to learn and for tutors to teach. During the practicals included in the biochemical courses at the Faculty of Chemistry of Universidad Nacional Autonoma de Mexico, we found that the students acquire good training in the calculations to obtain kinetic parameters such as K[subscript m], V[subscript…

Kinetics and mechanism of olefin catalytic hydroalumination by organoaluminum compounds

NASA Astrophysics Data System (ADS)

Koledina, K. F.; Gubaidullin, I. M.

2016-05-01

The complex reaction mechanism of α-olefin catalytic hydroalumination by alkylalanes is investigated via mathematical modeling that involves plotting the kinetic models for the individual reactions that make up a complex system and a separate study of their principles. Kinetic parameters of olefin catalytic hydroalumination are estimated. Activation energies of the possible steps of the schemes of complex reaction mechanisms are compared and possible reaction pathways are determined.

Detonation initiation in a model of explosive: Comparative atomistic and hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Murzov, S. A.; Sergeev, O. V.; Dyachkov, S. A.; Egorova, M. S.; Parshikov, A. N.; Zhakhovsky, V. V.

2016-11-01

Here we extend consistent simulations to reactive materials by the example of AB model explosive. The kinetic model of chemical reactions observed in a molecular dynamics (MD) simulation of self-sustained detonation wave can be used in hydrodynamic simulation of detonation initiation. Kinetic coefficients are obtained by minimization of difference between profiles of species calculated from the kinetic model and observed in MD simulations of isochoric thermal decomposition with a help of downhill simplex method combined with random walk in multidimensional space of fitting kinetic model parameters.

Kinetics of adsorption of dyes from aqueous solution using activated carbon prepared from waste apricot.

PubMed

Onal, Yunus

2006-10-11

Adsorbent (WA11Zn5) has been prepared from waste apricot by chemical activation with ZnCl(2). Pore properties of the activated carbon such as BET surface area, pore volume, pore size distribution, and pore diameter were characterized by N(2) adsorption and DFT plus software. Adsorption of three dyes, namely, Methylene Blue (MB), Malachite Green (MG), Crystal Violet (CV), onto activated carbon in aqueous solution was studied in a batch system with respect to contact time, temperature. The kinetics of adsorption of MB, MG and CV have been discussed using six kinetic models, i.e., the pseudo-first-order model, the pseudo-second-order model, the Elovich equation, the intraparticle diffusion model, the Bangham equation, the modified Freundlich equation. Kinetic parameters and correlation coefficients were determined. It was shown that the second-order kinetic equation could describe the adsorption kinetics for three dyes. The dyes uptake process was found to be controlled by external mass transfer at earlier stages (before 5 min) and by intraparticle diffusion at later stages (after 5 min). Thermodynamic parameters, such as DeltaG, DeltaH and DeltaS, have been calculated by using the thermodynamic equilibrium coefficient obtained at different temperatures and concentrations. The thermodynamics of dyes-WA11Zn5 system indicates endothermic process.

An investigation on the modelling of kinetics of thermal decomposition of hazardous mercury wastes.

PubMed

Busto, Yailen; M G Tack, Filip; Peralta, Luis M; Cabrera, Xiomara; Arteaga-Pérez, Luis E

2013-09-15

The kinetics of mercury removal from solid wastes generated by chlor-alkali plants were studied. The reaction order and model-free method with an isoconversional approach were used to estimate the kinetic parameters and reaction mechanism that apply to the thermal decomposition of hazardous mercury wastes. As a first approach to the understanding of thermal decomposition for this type of systems (poly-disperse and multi-component), a novel scheme of six reactions was proposed to represent the behaviour of mercury compounds in the solid matrix during the treatment. An integration-optimization algorithm was used in the screening of nine mechanistic models to develop kinetic expressions that best describe the process. The kinetic parameters were calculated by fitting each of these models to the experimental data. It was demonstrated that the D₁-diffusion mechanism appeared to govern the process at 250°C and high residence times, whereas at 450°C a combination of the diffusion mechanism (D₁) and the third order reaction mechanism (F3) fitted the kinetics of the conversions. The developed models can be applied in engineering calculations to dimension the installations and determine the optimal conditions to treat a mercury containing sludge. Copyright © 2013 Elsevier B.V. All rights reserved.

Adsorptive Removal of Cadmium (II) from Aqueous Solution by Multi-Carboxylic-Functionalized Silica Gel: Equilibrium, Kinetics and Thermodynamics

NASA Astrophysics Data System (ADS)

Li, Min; Meng, Xiaojing; Yuan, Jinhai; Deng, Wenwen; Liang, Xiuke

2018-01-01

In the present study, the adsorption behavior of cadmium (II) ion from aqueous solution onto multi-carboxylic-functionalized silica gel (SG-MCF) has been investigated in detail by means of batch and column experiments. Batch experiments were performed to evaluate the effects of various experimental parameters such as pH value, contact time and initial concentration on adsorption capacity of cadmium (II) ion. The kinetic data were analyzed on the basis of the pseudo-first-order kinetic and the pseudo-second-order kinetic models and consequently, the pseudo-second-order kinetic can better describe the adsorption process than the pseudo-first-order kinetic model. Equilibrium isotherms for the adsorption of cadmium (II) ion were analyzed by Freundlich and Langmuir isotherm models, the results indicate that Langmuir isotherm model was found to be credible to express the data for cadmium (II) ion from aqueous solution onto the SG-MCF. Various thermodynamics parameters of the adsorption process, including free energy of adsorption (ΔG0 ), the enthalpy of adsorption (ΔH0 ) and standard entropy changes (ΔS0 ), were calculated to predict the nature of adsorption. The positive value of the enthalpy change and the negative value of free energy change indicate that the process is endothermic and spontaneous process.

Ischemia reperfusion dysfunction changes model-estimated kinetics of myofilament interaction due to inotropic drugs in isolated hearts

PubMed Central

Rhodes, Samhita S; Camara, Amadou KS; Ropella, Kristina M; Audi, Said H; Riess, Matthias L; Pagel, Paul S; Stowe, David F

2006-01-01

Background The phase-space relationship between simultaneously measured myoplasmic [Ca2+] and isovolumetric left ventricular pressure (LVP) in guinea pig intact hearts is altered by ischemic and inotropic interventions. Our objective was to mathematically model this phase-space relationship between [Ca2+] and LVP with a focus on the changes in cross-bridge kinetics and myofilament Ca2+ sensitivity responsible for alterations in Ca2+-contraction coupling due to inotropic drugs in the presence and absence of ischemia reperfusion (IR) injury. Methods We used a four state computational model to predict LVP using experimentally measured, averaged myoplasmic [Ca2+] transients from unpaced, isolated guinea pig hearts as the model input. Values of model parameters were estimated by minimizing the error between experimentally measured LVP and model-predicted LVP. Results We found that IR injury resulted in reduced myofilament Ca2+ sensitivity, and decreased cross-bridge association and dissociation rates. Dopamine (8 μM) reduced myofilament Ca2+ sensitivity before, but enhanced it after ischemia while improving cross-bridge kinetics before and after IR injury. Dobutamine (4 μM) reduced myofilament Ca2+ sensitivity while improving cross-bridge kinetics before and after ischemia. Digoxin (1 μM) increased myofilament Ca2+ sensitivity and cross-bridge kinetics after but not before ischemia. Levosimendan (1 μM) enhanced myofilament Ca2+ affinity and cross-bridge kinetics only after ischemia. Conclusion Estimated model parameters reveal mechanistic changes in Ca2+-contraction coupling due to IR injury, specifically the inefficient utilization of Ca2+ for contractile function with diastolic contracture (increase in resting diastolic LVP). The model parameters also reveal drug-induced improvements in Ca2+-contraction coupling before and after IR injury. PMID:16512898

On the Nonequilibrium Interface Kinetics of Rapid Coupled Eutectic Growth

NASA Astrophysics Data System (ADS)

Dong, H.; Chen, Y. Z.; Shan, G. B.; Zhang, Z. R.; Liu, F.

2017-08-01

Nonequilibrium interface kinetics (NEIK) is expected to play an important role in coupled growth of eutectic alloys, when solidification velocity is high and intermetallic compound or topologically complex phases form in the crystallized product. In order to quantitatively evaluate the effect of NEIK on the rapid coupled eutectic growth, in this work, two nonequilibrium interface kinetic effects, i.e., atom attachment and solute trapping at the solid-liquid interface, were incorporated into the analyses of the coupled eutectic growth under the rapid solidification condition. First, a coupled growth model incorporating the preceding two nonequilibrium kinetic effects was derived. On this basis, an expression of kinetic undercooling (Δ T k), which is used to characterize the NEIK, was defined. The calculations based on the as-derived couple growth model show good agreement with the reported experimental results achieved in rapidly solidified eutectic Al-Sm alloys consisting of a solid solution phase ( α-Al) and an intermetallic compound phase (Al11Sm3). In terms of the definition of Δ T k defined in this work, the role of NEIK in the coupled growth of the Al-Sm eutectic system was analyzed. The results show that with increasing the coupled growth velocity, Δ T k increases continuously, and its ratio to the total undercooling reaches 0.32 at the maximum growth velocity for coupled eutectic growth. Parametric analyses on two key alloy parameters that influence Δ T k, i.e., interface kinetic parameter ( μ i ) and solute distribution coefficient ( k e ), indicate that both μ i and k e influence the NEIK significantly and the decrease of either these two parameters enhances the NEIK effect.

Parameter estimation in tree graph metabolic networks.

PubMed

Astola, Laura; Stigter, Hans; Gomez Roldan, Maria Victoria; van Eeuwijk, Fred; Hall, Robert D; Groenenboom, Marian; Molenaar, Jaap J

2016-01-01

We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis-Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree-like structure. Secondly, it is relatively fast compared to usually applied methods that estimate the model derivatives together with the network parameters. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

Displacement cascades and defect annealing in tungsten, Part III: The sensitivity of cascade annealing in tungsten to the values of kinetic parameters

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

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2015-07-01

Object kinetic Monte Carlo (OKMC) simulations have been performed to investigate various aspects of cascade aging in bulk tungsten and to determine the sensitivity of the results to the kinetic parameters. The primary focus is on how the kinetic parameters affect the initial recombination of defects in the first few ns of a simulation. The simulations were carried out using the object kinetic Monte Carlo (OKMC) code KSOME (kinetic simulations of microstructure evolution), using a database of cascades obtained from results of molecular dynamics (MD) simulations at various primary knock-on atom (PKA) energies and directions at temperatures of 300, 1025more » and 2050 K. The OKMC model was parameterized using defect migration barriers and binding energies from ab initio calculations. Results indicate that, due to the disparate mobilities of SIA and vacancy clusters in tungsten, annealing is dominated by SIA migration even at temperatures as high as 2050 K. For 100 keV cascades initiated at 300 K recombination is dominated by annihilation of large defect clusters. But for all other PKA energies and temperatures most of the recombination is due to the migration and rotation of small SIA clusters, while all the large SIA clusters escape the cubic simulation cell. The inverse U-shape behavior exhibited by the annealing efficiency as a function of temperature curve, especially for cascades of large PKA energies, is due to asymmetry in SIA and vacancy clustering assisted by the large difference in mobilities of SIAs and vacancies. This annealing behavior is unaffected by the dimensionality of SIA migration persists over a broad range of relative mobilities of SIAs and vacancies.« less

Prediction of Breakthrough Curves for Conservative and Reactive Transport from the Structural Parameters of Highly Heterogeneous Media

NASA Astrophysics Data System (ADS)

Hansen, S. K.; Haslauer, C. P.; Cirpka, O. A.; Vesselinov, V. V.

2016-12-01

It is desirable to predict the shape of breakthrough curves downgradient of a solute source from subsurface structural parameters (as in the small-perturbation macrodispersion theory) both for realistically heterogeneous fields, and at early time, before any sort of Fickian model is applicable. Using a combination of a priori knowledge, large-scale Monte Carlo simulation, and regression techniques, we have developed closed-form predictive expressions for pre- and post-Fickian flux-weighted solute breakthrough curves as a function of distance from the source (in integral scales) and variance of the log hydraulic conductivity field. Using the ensemble of Monte Carlo realizations, we have simultaneously computed error envelopes for the estimated flux-weighted breakthrough, and for the divergence of point breakthrough curves from the flux-weighted average, as functions of the predictive parameters. We have also obtained implied late-time macrodispersion coefficients for highly heterogeneous environments from the breakthrough statistics. This analysis is relevant for the modelling of reactive as well as conservative transport, since for many kinetic sorption and decay reactions, Laplace-domain modification of the breakthrough curve for conservative solute produces the correct curve for the reactive system.

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models

PubMed Central

Rosenblatt, Marcus; Timmer, Jens; Kaschek, Daniel

2016-01-01

Ordinary differential equation models have become a wide-spread approach to analyze dynamical systems and understand underlying mechanisms. Model parameters are often unknown and have to be estimated from experimental data, e.g., by maximum-likelihood estimation. In particular, models of biological systems contain a large number of parameters. To reduce the dimensionality of the parameter space, steady-state information is incorporated in the parameter estimation process. For non-linear models, analytical steady-state calculation typically leads to higher-order polynomial equations for which no closed-form solutions can be obtained. This can be circumvented by solving the steady-state equations for kinetic parameters, which results in a linear equation system with comparatively simple solutions. At the same time multiplicity of steady-state solutions is avoided, which otherwise is problematic for optimization. When solved for kinetic parameters, however, steady-state constraints tend to become negative for particular model specifications, thus, generating new types of optimization problems. Here, we present an algorithm based on graph theory that derives non-negative, analytical steady-state expressions by stepwise removal of cyclic dependencies between dynamical variables. The algorithm avoids multiple steady-state solutions by construction. We show that our method is applicable to most common classes of biochemical reaction networks containing inhibition terms, mass-action and Hill-type kinetic equations. Comparing the performance of parameter estimation for different analytical and numerical methods of incorporating steady-state information, we show that our approach is especially well-tailored to guarantee a high success rate of optimization. PMID:27243005

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models.

PubMed

Rosenblatt, Marcus; Timmer, Jens; Kaschek, Daniel

2016-01-01

Ordinary differential equation models have become a wide-spread approach to analyze dynamical systems and understand underlying mechanisms. Model parameters are often unknown and have to be estimated from experimental data, e.g., by maximum-likelihood estimation. In particular, models of biological systems contain a large number of parameters. To reduce the dimensionality of the parameter space, steady-state information is incorporated in the parameter estimation process. For non-linear models, analytical steady-state calculation typically leads to higher-order polynomial equations for which no closed-form solutions can be obtained. This can be circumvented by solving the steady-state equations for kinetic parameters, which results in a linear equation system with comparatively simple solutions. At the same time multiplicity of steady-state solutions is avoided, which otherwise is problematic for optimization. When solved for kinetic parameters, however, steady-state constraints tend to become negative for particular model specifications, thus, generating new types of optimization problems. Here, we present an algorithm based on graph theory that derives non-negative, analytical steady-state expressions by stepwise removal of cyclic dependencies between dynamical variables. The algorithm avoids multiple steady-state solutions by construction. We show that our method is applicable to most common classes of biochemical reaction networks containing inhibition terms, mass-action and Hill-type kinetic equations. Comparing the performance of parameter estimation for different analytical and numerical methods of incorporating steady-state information, we show that our approach is especially well-tailored to guarantee a high success rate of optimization.

Combined Yamamoto approach for simultaneous estimation of adsorption isotherm and kinetic parameters in ion-exchange chromatography.

PubMed

Rüdt, Matthias; Gillet, Florian; Heege, Stefanie; Hitzler, Julian; Kalbfuss, Bernd; Guélat, Bertrand

2015-09-25

Application of model-based design is appealing to support the development of protein chromatography in the biopharmaceutical industry. However, the required efforts for parameter estimation are frequently perceived as time-consuming and expensive. In order to speed-up this work, a new parameter estimation approach for modelling ion-exchange chromatography in linear conditions was developed. It aims at reducing the time and protein demand for the model calibration. The method combines the estimation of kinetic and thermodynamic parameters based on the simultaneous variation of the gradient slope and the residence time in a set of five linear gradient elutions. The parameters are estimated from a Yamamoto plot and a gradient-adjusted Van Deemter plot. The combined approach increases the information extracted per experiment compared to the individual methods. As a proof of concept, the combined approach was successfully applied for a monoclonal antibody on a cation-exchanger and for a Fc-fusion protein on an anion-exchange resin. The individual parameter estimations for the mAb confirmed that the new approach maintained the accuracy of the usual Yamamoto and Van Deemter plots. In the second case, offline size-exclusion chromatography was performed in order to estimate the thermodynamic parameters of an impurity (high molecular weight species) simultaneously with the main product. Finally, the parameters obtained from the combined approach were used in a lumped kinetic model to simulate the chromatography runs. The simulated chromatograms obtained for a wide range of gradient lengths and residence times showed only small deviations compared to the experimental data. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Chemiomics: Network Reconstruction and Kinetics of Port Wine Aging

DOE PAGES

Monforte, Ana Rita; Jacobson, Dan; Silva Ferreira, A. C.

2015-02-11

Network reconstruction (NR) has proven to be useful in the detection and visualization of relationships among the compounds present in a Port wine aging data set. This view of the data provides a considerable amount of information with which to understand the kinetic contexts of the molecules represented by peaks in each chromatogram. The aim of this paper was to use NR together with the determination of kinetic parameters to extract more information about the mechanisms involved in Port wine aging. The volatile compounds present in samples of Port wines spanning 128 years in age were measured with the usemore » of GC-MS. After chromatogram alignment, a peak matrix was created, and all peak vectors were compared to one another to determine their Pearson correlations over time. A correlation network was created and filtered on the basis of the resulting correlation values. Some nodes in the network were further studied in experiments on Port wines stored under different conditions of oxygen and temperature in order to determine their kinetic parameters. The resulting network can be divided into three main branches. The first branch is related to compounds that do not directly correlate to age, the second branch contains compounds affected by temperature, and the third branch contains compounds associated with oxygen. Compounds clustered in the same branch of the network have similar expression patterns over time as well as the same kinetic order, thus are likely to be dependent on the same technological parameters. Network construction and visualization provides more information with which to understand the probable kinetic contexts of the molecules represented by peaks in each chromatogram. Finally, the approach described here is a powerful tool for the study of mechanisms and kinetics in complex systems and should aid in the understanding and monitoring of wine quality.« less

Calcite Dissolution Kinetics

NASA Astrophysics Data System (ADS)

Berelson, W.; Subhas, A.; Dong, S.; Naviaux, J.; Adkins, J. F.

2016-12-01

A geological buffer for high atmospheric CO2 concentrations is neutralization via reaction with CaCO3. We have been studying the dissolution kinetics of carbonate minerals using labeled 13C calcite and Picarro-based measurements of 13C enrichments in solution DIC. This methodology has greatly facilitated our investigation of dissolution kinetics as a function of water carbonate chemistry, temperature and pressure. One can adjust the saturation state Omega by changing the ion activity product (e.g. adjusting carbonate ion concentration), or by changing the solubility product (e.g. adjusting temperature or pressure). The canonical formulation of dissolution rate vs. omega has been refined (Subhas et al. 2015) and shows distinct non-linear behavior near equilibrium and rates in sea water of 1-3 e-6 g/cm2day at omega = 0.8. Carbonic anhydrase (CA), an enzyme that catalyzes the hydration of dissolved CO2 to carbonic acid, was shown (in concentrations <=0.04 g/L) to enhance the dissolution rate at low degrees of undersaturation by >500x. This result points to the importance of carbonic acid in enhancing dissolution at low degrees of undersaturation. CA activity and abundance in nature must be considered regarding the role it plays in catalyzing dissolution. We also have been investigating the role of temperature on dissolution kinetics. An increase of 16C yields an order of magnitude increase in dissolution rate. Temperature (and P) also change Omega critical, the saturation state where dissolution rates change substantially. Increasing pressure (achieved in a pressure reaction chamber we built) also shifts Omega critical closer to equilibrium and small pressure increases have large impact on dissolution kinetics. Dissolution rates are enhanced by an order of magnitude for a change in pressure of 1500 psi relative to the dissolution rate achieved by water chemistry effects alone for an omega of 0.8. We've shown that the thermodynamic determination of saturation state does not adequately describe the kinetics of dissolution. The interplay of mineral composition and surface area, solution carbonate chemistry, temperature and pressure are factors the impact carbonate dissolution rates in natural settings. We suggest that these parameters be considered in CO2 mitigation strategies.

Theoretical studies of solar lasers and converters

NASA Technical Reports Server (NTRS)

Heinbockel, John

1988-01-01

The geometry and setup for the n-C3F7I iodine laser are illustrated. The mathematical modeling of this system is described. The chemical kinetics are summarized. A sensitivity analysis was performed on the parameters occurring in the differential equations describing the chemical kinetics.

Solidification kinetics of a near eutectic Al-Si alloy, unmodified and modified with Sr

NASA Astrophysics Data System (ADS)

Aparicio, R.; Barrera, G.; Trapaga, G.; Ramirez-Argaez, M.; Gonzalez-Rivera, C.

2013-07-01

The purpose of this work was to explore the differences in solidification kinetics between unmodified and Sr modified eutectic Al-Si alloy as revealed by Fourier Thermal Analysis (FTA) and grain-growth kinetics characterization. Thermal analysis were performed in cylindrical stainless steel cups coated with a thin layer of boron nitride, using two type-K thermocouples connected to a data acquisition system. Grain growth kinetics characterization was carried out using solid fraction evolution and grain density data. FTA results for the non modified and modified alloys suggest that there are changes in the solidification rate during eutectic nucleation followed, during growth, by similar solidification rate evolutions, suggesting that this parameter is governed principally by the heat extraction conditions. On the other hand the change of the grain growth parameters estimated for the experimental probes suggest that the presence of Sr may modify the relationship between grain growth rate and undercooling in eutectic Al-Si.

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.

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

Solvolysis kinetics of three components of biomass using polyhydric alcohols as solvents.

PubMed

Shi, Yan; Xia, Xueying; Li, Jingdan; Wang, Jing; Zhao, Tiantian; Yang, Hongmin; Jiang, Jianchun; Jiang, Xiaoxiang

2016-12-01

The solvolysis behavior and reaction kinetics of the three components of biomass (cellulose, hemicelluloses and lignin) liquefied in polyhydric alcohols (PEG 400 or glycerol) were investigated in this paper. Three stages were observed during the solvolysis process and the main degradation stage could be further divided into two zones. The influences of solvents on the liquefaction process of three main components were compared. Based on Starink and Malek methods, kinetic parameters and mechanism functions were obtained. The derived average activation energy of cellulose, hemicellulose and lignin were 108.73, 95.66 and 94.13kJmol -1 in PEG 400, while the values were 102.16, 77.43 and 89.10kJmol -1 in glycerol, respectively. Higher efficiency was observed when using glycerol as solvent, which could be ascribed to the higher polarity value of glycerol. The conversion curves calculated with obtained mechanism models and kinetic parameters were in good agreement with the experimental data. Copyright © 2016 Elsevier Ltd. All rights reserved.

Kinetics of enzymatic synthesis of liquid wax ester from oleic acid and oleyl alcohol.

PubMed

Radzi, Salina Mat; Mohamad, Rosfarizan; Basri, Mahiran; Salleh, Abu Bakar; Ariff, Arbakariya; Rahman, Mohammad Basyaruddin Abdul; Rahman, Raja Noor Zaliha Raja Abdul

2010-01-01

The kinetics of wax ester synthesis from oleic acid and oleyl alcohol using immobilized lipase from Candida antartica as catalyst was studied with different types of impeller (Rushton turbine and AL-hydrofoil) to create different mixing conditions in 2l stirred tank reactor. The effects of catalyst concentration, reaction temperature, and impeller tip speed on the synthesis were also evaluated. Rushton turbine impeller exhibited highest conversion rate at lower impeller tip speed as compared to AL-hydrofoil impeller. A second-order reversible kinetic model from single progress curve for the prediction of fractional conversion at given reaction time was proposed and the corresponding kinetic parameter values were calculated by non-linear regression method. The results from the simulation using the proposed model showed satisfactory agreement with the experimental data. Activation energy shows a value of 21.77 Kcal/mol. The thermodynamic parameters of the process, enthalpy and entropy, were 21.15 Kcal/mol and 52.07 cal/mol.K, respectively.

Kinklike structures in models of the Dirac-Born-Infeld type

NASA Astrophysics Data System (ADS)

Bazeia, D.; Lima, Elisama E. M.; Losano, L.

2018-01-01

The present work investigates several models of a single real scalar field, engendering kinetic term of the Dirac-Born- Infeld type. Such theories introduce nonlinearities to the kinetic part of the Lagrangian, which presents a square root restricting the field evolution and including additional powers in derivatives of the scalar field, controlled by a real parameter. In order to obtain topological solutions analytically, we propose a first-order framework that simplifies the equation of motion ensuring solutions that are linearly stable. This is implemented using the deformation method, and we introduce examples presenting two categories of potentials, one having polynomial interactions and the other with nonpolynomial interactions. We also explore how the Dirac-Born-Infeld kinetic term affects the properties of the solutions. In particular, we note that the kinklike solutions are similar to the ones obtained through models with standard kinetic term and canonical potential, but their energy densities and stability potentials vary according to the parameter introduced to control the new models.

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.

Cyclic voltammetry of fast conducting electrocatalytic films.

PubMed

Costentin, Cyrille; Savéant, Jean-Michel

2015-07-15

In the framework of contemporary energy challenges, cyclic voltammetry is a particularly useful tool for deciphering the kinetics of catalytic films. The case of fast conducting films is analyzed, whether conduction is of the ohmic type or proceeds through rapid electron hopping. The rate-limiting factors are then the diffusion of the substrate in solution and through the film as well as the catalytic reaction itself. The dimensionless combination of the characteristics of these factors allows reducing the number of actual parameters to a maximum of two. The kinetics of the system may then be fully analyzed with the help of a kinetic zone diagram. Observing the variations of the current-potential responses with operational parameters such as film thickness, the potential scan rate and substrate concentration allows a precise assessment of the interplay between these factors and of the values of the rate controlling factors. A series of thought experiments is described in order to render the kinetic analysis more palpable.

Characterizing the kinetics of suspended cylindrical particles by polarization measurements

NASA Astrophysics Data System (ADS)

Liao, Ran; Ou, Xueheng; Ma, Hui

2015-09-01

Polarization has promising potential to retrieve the information of the steady samples, such as tissues. However, for the fast changing sample such as the suspended algae in the water, the kinetics of the particles also influence the scattered polarization. The present paper will show our recent results to extract the information about the kinetics of the suspended cylindrical particles by polarization measurements. The sample is the aqueous suspension of the glass fibers stirred by a magnetic stirrer. We measure the scattered polarization of the fibers by use of a simultaneous polarization measurement system and obtain the time series of two orthogonal polarization components. By use of correlation analysis, we obtain the time parameters from the auto-correlation functions of the polarization components, and observe the changes with the stirring speeds. Results show that these time parameters indicate the immigration of the fibers. After discussion, we find that they may further characterize the kinetics, including the translation and rotation, of the glass fibers in the fluid field.

The effect of carbon-chain oxygenation in the carbon-carbon dissociation.

PubMed

Dos Santos, Lisandra Paulino; Baptista, Leonardo

2018-06-01

Currently, there is a trend of moving away from the use of fossil fuels to the use of biofuels. This modification changes the molecular structure of gasoline and diesel constituents, which should impact pollutant emissions and engine efficiency. An important property of automotive fuels is the resistance to autoignition. The goal of the present work is to evaluate thermochemical and kinetic parameters that govern the carbon-carbon bond dissociation and relate these parameters, in conjunction with molecular properties, to autoignition resistance. Three model reactions were investigated in the present work: dissociation of ethane, ethanol, and ethanal. All studies were conducted at the multiconfigurational level of theory, and the rate coefficients were evaluated from 300 to 2000 K. The comparison of dissociation energies and Arrhenius expressions indicates that autoignition resistance is related to the kinetic control of dissociation reactions and it is possible to relate the higher octane number of ethanol based fuels to the kinetics parameters of carbon-carbon bond fission. Graphical abstract Effect of the functional group in the Arrhenius parameters of the C-C dissociation. Arrhenius curves calculated at NEVPT2(6,6)/6-311G(2df,2pd).

Evaluation of oxygen reduction activity by the thin-film rotating disk electrode methodology: The effects of potentiodynamic parameters

DOE PAGES

Chen, Guangyu; Li, Meng; Kuttiyiel, Kurian A.; ...

2016-04-11

Here, an accurate and efficient assessment of activity is critical for the research and development of electrocatalysts for oxygen reduction reaction (ORR). Currently, the methodology combining the thin-film rotating disk electrode (TF-RDE) and potentiodynamic polarization is the most commonly used to pre-evaluate ORR activity, acquire kinetic data (i.e., kinetic current, Tafel slope, etc.), and gain understanding of the ORR mechanism. However, it is often neglected that appropriate potentiodynamic parameters have to be chosen to obtain reliable results. We first evaluate the potentiodynamic and potentiostatic polarization measurements with TF-RDE to examine the ORR activity of Pt nanoelectrocatalyst. Furthermore, our results demonstratemore » that besides depending on the nature of electrocatalyst, the apparent ORR kinetics also strongly depends on the associated potentiodynamic parameters, such as scan rate and scan region, which have a great effect on the coverage of adsorbed OH ad/O ad on Pt surface, thereby affecting the ORR activities of both nanosized and bulk Pt. However, the apparent Tafel slopes remained nearly the same, indicating that the ORR mechanism in all the measurements was not affected by different potentiodynamic parameters.« less

Derived and thiourea-functionalized silica for cadmium removal: isotherm, kinetic and thermodynamic studies

NASA Astrophysics Data System (ADS)

Omotunde, Iyanu; Okoronkwo, Afamefuna; Oluwashina, Olugbenga

2018-03-01

The present study explored the feasibility of using derived and thiourea-functionalized silica as adsorbent for the removal of cadmium under different experimental conditions. Effects of various parameters such as function of point of zero charge (pHPZC), solution pH, sorbent-sorbate resident time and ratio, concentration and temperature were investigated. The sorption of cadmium followed the pseudo-second-order rate kinetics. Thermodynamic studies revealed that the sorption of cadmium was endothermic and spontaneous, with good affinity toward the sorbent. Various isotherm models, viz. Langmuir, Freundlich, Temkin, Dubinin-Radushkevich, Harkins-Jura, and Halsey isotherms were used to analyze the equilibrium data at different temperatures. The Freundlich, Halsey, Langmuir, and Temkin models were found to be in good agreement with the experimental data with high R 2, low RMSE, and low χ 2 values. The results show that the sorption capacity increases with an increase in solution temperature from 28 to 65 °C. The maximum sorption capacity calculated from Langmuir isotherm was 27.55 and 28.41 mg g-1 for derived and thiourea-functionalized silica, respectively, at optimum condition of pH 5 and contact time of 120 min.

Capabilities of Fully Parallelized MHD Stability Code MARS

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2016-10-01

Results of full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. Parallel version of MARS, named PMARS, has been recently developed at FAR-TECH. Parallelized MARS is an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, implemented in MARS. Parallelization of the code included parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse vector iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the MARS algorithm using parallel libraries and procedures. Parallelized MARS is capable of calculating eigenmodes with significantly increased spatial resolution: up to 5,000 adapted radial grid points with up to 500 poloidal harmonics. Such resolution is sufficient for simulation of kink, tearing and peeling-ballooning instabilities with physically relevant parameters. Work is supported by the U.S. DOE SBIR program.

Kinetics and thermal stability of the Ni62Nb38- x Ta x ( x=5, 10, 15, 20 and 25) bulk metallic glasses

NASA Astrophysics Data System (ADS)

He, MengKe; Zhang, Yi; Xia, Lei; Yu, Peng

2017-07-01

We studied thermal stability and its relationship to the glass-forming ability (GFA) of the Ni62Nb38- x Ta x ( x=5, 10, 15, 20, 25) bulk metallic glasses (BMG) from a kinetic point of view. By fitting the heating-rate dependence of glass transition temperature ( T g onset) and crystallization temperatures ( T x onset and T x peak) of the Ni62Nb38- x Ta x BMG using the Vogel-Fulcher-Tammann (VFT) equation, we obtained the ideal glass transition and crystallization temperatures ( T g 0 and T x 0) and the fragility parameter ( m), and also constructed continuous heating transition (CHT) diagrams for crystallization of the BMG. The CHT diagrams of the BMG indicate enhanced thermal stability by Ta addition; the T g 0 as well as the T x 0 also illustrates this improved stability limit. The compositional dependence of m, which agrees well with that of the reduced glass-transition temperature, indicates a strong correlation between liquid fragility and glass-forming ability in the present alloy system. These results provide new evidence for understanding thermal stability, liquid fragility, and GFA in BMG.

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

Perret, Gregory

The critical decay constant (B/A), delayed neutron fraction (B) and generation time (A) of the Minerve reactor were measured by the Paul Scherrer Institut (PSI) and the Commissariat a l'Energie Atomique (CEA) in September 2014 using the Feynman-alpha and Power Spectral Density neutron noise measurement techniques. Three slightly subcritical configuration were measured using two 1-g {sup 235}U fission chambers. This paper reports on the results obtained by PSI in the near critical configuration (-2g). The most reliable and precise results were obtained with the Cross-Power Spectral Density technique: B = 708.4±9.2 pcm, B/A = 79.0±0.6 s{sup -1} and A 89.7±1.4more » micros. Predictions of the same kinetic parameters were obtained with MCNP5-v1.6 and the JEFF-3.1 and ENDF/B-VII.1 nuclear data libraries. On average the predictions for B and B/A overestimate the experimental results by 5% and 11%, respectively. The discrepancy is suspected to come from either a corruption of the data or from the inadequacy of the point kinetic equations to interpret the measurements in the Minerve driven system. (authors)« less

General dynamical properties of cosmological models with nonminimal kinetic coupling

NASA Astrophysics Data System (ADS)

Matsumoto, Jiro; Sushkov, Sergey V.

2018-01-01

We consider cosmological dynamics in the theory of gravity with the scalar field possessing the nonminimal kinetic coupling to curvature given as η Gμνphi,μphi,ν, where η is an arbitrary coupling parameter, and the scalar potential V(phi) which assumed to be as general as possible. With an appropriate dimensionless parametrization we represent the field equations as an autonomous dynamical system which contains ultimately only one arbitrary function χ (x)= 8 π | η | V(x/√8 π) with x=√8 πphi. Then, assuming the rather general properties of χ(x), we analyze stationary points and their stability, as well as all possible asymptotical regimes of the dynamical system. It has been shown that for a broad class of χ(x) there exist attractors representing three accelerated regimes of the Universe evolution, including de Sitter expansion (or late-time inflation), the Little Rip scenario, and the Big Rip scenario. As the specific examples, we consider a power-law potential V(phi)=M4(phi/phi0)σ, Higgs-like potential V(phi)=λ/4(phi2‑phi02)2, and exponential potential V(phi)=M4 e‑phi/phi0.

Enzyme reactor design under thermal inactivation.

PubMed

Illanes, Andrés; Wilson, Lorena

2003-01-01

Temperature is a very relevant variable for any bioprocess. Temperature optimization of bioreactor operation is a key aspect for process economics. This is especially true for enzyme-catalyzed processes, because enzymes are complex, unstable catalysts whose technological potential relies on their operational stability. Enzyme reactor design is presented with a special emphasis on the effect of thermal inactivation. Enzyme thermal inactivation is a very complex process from a mechanistic point of view. However, for the purpose of enzyme reactor design, it has been oversimplified frequently, considering one-stage first-order kinetics of inactivation and data gathered under nonreactive conditions that poorly represent the actual conditions within the reactor. More complex mechanisms are frequent, especially in the case of immobilized enzymes, and most important is the effect of catalytic modulators (substrates and products) on enzyme stability under operation conditions. This review focuses primarily on reactor design and operation under modulated thermal inactivation. It also presents a scheme for bioreactor temperature optimization, based on validated temperature-explicit functions for all the kinetic and inactivation parameters involved. More conventional enzyme reactor design is presented merely as a background for the purpose of highlighting the need for a deeper insight into enzyme inactivation for proper bioreactor design.

Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity

PubMed Central

2014-01-01

Background One of the distinctive features of biological oscillators such as circadian clocks and cell cycles is robustness which is the ability to resume reliable operation in the face of different types of perturbations. In the previous study, we proposed multiparameter sensitivity (MPS) as an intelligible measure for robustness to fluctuations in kinetic parameters. Analytical solutions directly connect the mechanisms and kinetic parameters to dynamic properties such as period, amplitude and their associated MPSs. Although negative feedback loops are known as common structures to biological oscillators, the analytical solutions have not been presented for a general model of negative feedback oscillators. Results We present the analytical expressions for the period, amplitude and their associated MPSs for a general model of negative feedback oscillators. The analytical solutions are validated by comparing them with numerical solutions. The analytical solutions explicitly show how the dynamic properties depend on the kinetic parameters. The ratio of a threshold to the amplitude has a strong impact on the period MPS. As the ratio approaches to one, the MPS increases, indicating that the period becomes more sensitive to changes in kinetic parameters. We present the first mathematical proof that the distributed time-delay mechanism contributes to making the oscillation period robust to parameter fluctuations. The MPS decreases with an increase in the feedback loop length (i.e., the number of molecular species constituting the feedback loop). Conclusions Since a general model of negative feedback oscillators was employed, the results shown in this paper are expected to be true for many of biological oscillators. This study strongly supports that the hypothesis that phosphorylations of clock proteins contribute to the robustness of circadian rhythms. The analytical solutions give synthetic biologists some clues to design gene oscillators with robust and desired period. PMID:25605374

Quantitative gait analysis in parkin disease: Possible role of dystonia.

PubMed

Castagna, Anna; Frittoli, Serena; Ferrarin, Maurizio; Del Sorbo, Francesca; Romito, Luigi M; Elia, Antonio E; Albanese, Alberto

2016-11-01

Parkin disease (PARK2, OMIM 602544) is an autosomal-recessive early-onset parkinsonism characterized by an early occurrence of lower limb dystonia. The aim of this study was to analyze spatiotemporal, kinematic, and kinetic gait parameters in patients with parkin disease in the OFF and ON conditions compared to healthy age-matched controls. Fifteen patients with parkin disease and 15 healthy age-matched controls were studied in a gait analysis laboratory with an integrated optoelectronic system. Spatiotemporal, kinematic, and kinetic gait parameters at a self-selected speed were recorded in the OFF and ON conditions. A jerk index was computed to quantify the possible reduction of smoothness of joint movements. Compared to controls, parkin patients had, either in the OFF or in the ON conditions, significant reduction of walking velocity, increased step width, and decreased percentage of double support. Kinematic analysis in both conditions showed: increased ankle dorsiflexion and knee flexion at the initial contact; maximal flexion and increased range of motion in mid stance; increased hip flexion and max extension in stance at pelvis; and increased mean tilt antiversion. Kinetics showed increased hip and knee power generation in stance in either condition. The jerk index was increased at all joints both in OFF and ON. There were no correlations between individual gait parameters and clinical ratings. Parkin patients have an abnormal gait pattern that does not vary between the OFF and the ON conditions. Variations recorded with instrumented analysis are more evident for kinematic than kinetic parameters at lower limbs. Severity of dystonia does not correlate with any individual kinematic parameter. © 2016 International Parkinson and Movement Disorder Society. © 2016 International Parkinson and Movement Disorder Society.

Combining in silico evolution and nonlinear dimensionality reduction to redesign responses of signaling networks

NASA Astrophysics Data System (ADS)

Prescott, Aaron M.; Abel, Steven M.

2016-12-01

The rational design of network behavior is a central goal of synthetic biology. Here, we combine in silico evolution with nonlinear dimensionality reduction to redesign the responses of fixed-topology signaling networks and to characterize sets of kinetic parameters that underlie various input-output relations. We first consider the earliest part of the T cell receptor (TCR) signaling network and demonstrate that it can produce a variety of input-output relations (quantified as the level of TCR phosphorylation as a function of the characteristic TCR binding time). We utilize an evolutionary algorithm (EA) to identify sets of kinetic parameters that give rise to: (i) sigmoidal responses with the activation threshold varied over 6 orders of magnitude, (ii) a graded response, and (iii) an inverted response in which short TCR binding times lead to activation. We also consider a network with both positive and negative feedback and use the EA to evolve oscillatory responses with different periods in response to a change in input. For each targeted input-output relation, we conduct many independent runs of the EA and use nonlinear dimensionality reduction to embed the resulting data for each network in two dimensions. We then partition the results into groups and characterize constraints placed on the parameters by the different targeted response curves. Our approach provides a way (i) to guide the design of kinetic parameters of fixed-topology networks to generate novel input-output relations and (ii) to constrain ranges of biological parameters using experimental data. In the cases considered, the network topologies exhibit significant flexibility in generating alternative responses, with distinct patterns of kinetic rates emerging for different targeted responses.

Kinetics of heavy metal adsorption and desorption in soil: Developing a unified model based on chemical speciation

NASA Astrophysics Data System (ADS)

Peng, Lanfang; Liu, Paiyu; Feng, Xionghan; Wang, Zimeng; Cheng, Tao; Liang, Yuzhen; Lin, Zhang; Shi, Zhenqing

2018-03-01

Predicting the kinetics of heavy metal adsorption and desorption in soil requires consideration of multiple heterogeneous soil binding sites and variations of reaction chemistry conditions. Although chemical speciation models have been developed for predicting the equilibrium of metal adsorption on soil organic matter (SOM) and important mineral phases (e.g. Fe and Al (hydr)oxides), there is still a lack of modeling tools for predicting the kinetics of metal adsorption and desorption reactions in soil. In this study, we developed a unified model for the kinetics of heavy metal adsorption and desorption in soil based on the equilibrium models WHAM 7 and CD-MUSIC, which specifically consider metal kinetic reactions with multiple binding sites of SOM and soil minerals simultaneously. For each specific binding site, metal adsorption and desorption rate coefficients were constrained by the local equilibrium partition coefficients predicted by WHAM 7 or CD-MUSIC, and, for each metal, the desorption rate coefficients of various binding sites were constrained by their metal binding constants with those sites. The model had only one fitting parameter for each soil binding phase, and all other parameters were derived from WHAM 7 and CD-MUSIC. A stirred-flow method was used to study the kinetics of Cd, Cu, Ni, Pb, and Zn adsorption and desorption in multiple soils under various pH and metal concentrations, and the model successfully reproduced most of the kinetic data. We quantitatively elucidated the significance of different soil components and important soil binding sites during the adsorption and desorption kinetic processes. Our model has provided a theoretical framework to predict metal adsorption and desorption kinetics, which can be further used to predict the dynamic behavior of heavy metals in soil under various natural conditions by coupling other important soil processes.

Receptor binding kinetics equations: Derivation using the Laplace transform method.

PubMed

Hoare, Sam R J

Measuring unlabeled ligand receptor binding kinetics is valuable in optimizing and understanding drug action. Unfortunately, deriving equations for estimating kinetic parameters is challenging because it involves calculus; integration can be a frustrating barrier to the pharmacologist seeking to measure simple rate parameters. Here, a well-known tool for simplifying the derivation, the Laplace transform, is applied to models of receptor-ligand interaction. The method transforms differential equations to a form in which simple algebra can be applied to solve for the variable of interest, for example the concentration of ligand-bound receptor. The goal is to provide instruction using familiar examples, to enable investigators familiar with handling equilibrium binding equations to derive kinetic equations for receptor-ligand interaction. First, the Laplace transform is used to derive the equations for association and dissociation of labeled ligand binding. Next, its use for unlabeled ligand kinetic equations is exemplified by a full derivation of the kinetics of competitive binding equation. Finally, new unlabeled ligand equations are derived using the Laplace transform. These equations incorporate a pre-incubation step with unlabeled or labeled ligand. Four equations for measuring unlabeled ligand kinetics were compared and the two new equations verified by comparison with numerical solution. Importantly, the equations have not been verified with experimental data because no such experiments are evident in the literature. Equations were formatted for use in the curve-fitting program GraphPad Prism 6.0 and fitted to simulated data. This description of the Laplace transform method will enable pharmacologists to derive kinetic equations for their model or experimental paradigm under study. Application of the transform will expand the set of equations available for the pharmacologist to measure unlabeled ligand binding kinetics, and for other time-dependent pharmacological activities. Copyright © 2017 Elsevier Inc. All rights reserved.

A potential low cost adsorbent for the removal of cationic dyes from aqueous solutions

NASA Astrophysics Data System (ADS)

Uddin, Md. Tamez; Rahman, Md. Arifur; Rukanuzzaman, Md.; Islam, Md. Akhtarul

2017-10-01

This study was aimed at using mango leaf powder (MLP) as a potential adsorbent for the removal of methylene blue (MB) from aqueous solutions. Characterization of the adsorbent was carried out with scanning electron microscopy, Fourier transform infrared spectroscopy, and nitrogen adsorption-desorption analysis. The pH at the point of zero charge of the adsorbent was determined by titration method and was found a value to be 5.6 ± 0.2. Batch studies were performed to evaluate the influence of various experimental parameters like initial solution pH, contact time, initial concentration of dye and adsorbent dosage on the removal of MB. An adsorption-desorption study was carried out resulting the mechanism of adsorption was carried out by electrostatic force of attraction. The adsorption equilibrium time required for the adsorption of MB on MLP was almost 2 h and 85 ± 5% of the total amount of dye uptake was found to occur in the first rapid phase (30 min). The Langmuir and Freundlich isotherm models were used for modeling the adsorption equilibrium. The experimental equilibrium data could be well interpreted by Langmuir isotherm with maximum adsorption capacity of 156 mg/g. To state the sorption kinetics, the fits of pseudo-first-order and pseudo-second-order kinetic models were investigated. It was obtained that the adsorption process followed the pseudo-second-order rate kinetics. The above findings suggest that MLP can be effectively used for decontamination of dye containing wastewater.

Drug release and swelling kinetics of directly compressed glipizide sustained-release matrices: establishment of level A IVIVC.

PubMed

Sankalia, Jolly M; Sankalia, Mayur G; Mashru, Rajashree C

2008-07-02

The purpose of this study was to examine a level A in vitro-in vivo correlation (IVIVC) for glipizide hydrophilic sustained-release matrices, with an acceptable internal predictability, in the presence of a range of formulation/manufacturing changes. The effect of polymeric blends of ethylcellulose, microcrystalline cellulose, hydroxypropylmethylcellulose, xanthan gum, guar gum, Starch 1500, and lactose on in vitro release profiles was studied and fitted to various release kinetics models. Water uptake kinetics with scanning electron microscopy (SEM) was carried out to support the drug release mechanism. An IVIVC was established by comparing the pharmacokinetic parameters of optimized (M-24) and marketed (Glytop-2.5 SR) formulations after single oral dose studies on white albino rabbits. The matrix M-19 (xanthan:MCC PH301 at 70:40) and M-24 (xanthan:HPMC K4M:Starch 1500 at 70:25:15) showed the glipizide release within the predetermined constraints at all time points with Korsmeyer-Peppas' and zero-order release mechanism, respectively. Kopcha model revealed that the xanthan gum is the major excipient responsible for the diffusional release profile and was further supported by SEM and swelling studies. A significant level A IVIVC with acceptable limits of prediction errors (below 15%) enables the prediction of in vivo performance from their in vitro release profile. It was concluded that proper selection of rate-controlling polymers with release rate modifier excipients will determine overall release profile, duration and mechanism from directly compressed matrices.

Kinetics Tuning the Electrochemistry of Lithium Dendrites Formation in Lithium Batteries through Electrolytes

DOE PAGES

Tao, Ran; Bi, Xuanxuan; Li, Shu; ...

2017-02-13

Lithium batteries are one of the most advance energy storage devices in the world and have attracted extensive research interests. However, lithium dendrite growth was a safety issue which handicapped the application of pure lithium metal in the negative electrode. In this paper, two solvents, propylene carbonate (PC) and 2-methyl-tetrahydrofuran (2MeTHF), and four Li + salts, LiPF 6, LiAsF 6, LiBF 4 and LiClO 4 were investigated in terms of their effects on the kinetics of lithium dendrite formation in eight electrolyte solutions. The kinetic parameters of charge transfer step (exchange current density, j 0, transfer coefficient, α) of Limore » +/Li redox system, the mass transfer parameters of Li + (transfer number of Li +, t Li+, diffusion coefficient of Li +, D Li+), and the conductivity (κ) of each electrolyte were studied separately. The results demonstrate that the solvents play a critical role in the measured j 0, t Li+, D Li+, and κ of the electrolyte, while the choice of Li + salts only slightly affect the measured parameters. Finally, the understanding of the kinetics will gain insight into the mechanism of lithium dendrite formation and provide guidelines to the future application of lithium metal.« less

Kinetics Tuning the Electrochemistry of Lithium Dendrites Formation in Lithium Batteries through Electrolytes

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

Tao, Ran; Bi, Xuanxuan; Li, Shu

Lithium batteries are one of the most advance energy storage devices in the world and have attracted extensive research interests. However, lithium dendrite growth was a safety issue which handicapped the application of pure lithium metal in the negative electrode. In this paper, two solvents, propylene carbonate (PC) and 2-methyl-tetrahydrofuran (2MeTHF), and four Li + salts, LiPF 6, LiAsF 6, LiBF 4 and LiClO 4 were investigated in terms of their effects on the kinetics of lithium dendrite formation in eight electrolyte solutions. The kinetic parameters of charge transfer step (exchange current density, j 0, transfer coefficient, α) of Limore » +/Li redox system, the mass transfer parameters of Li + (transfer number of Li +, t Li+, diffusion coefficient of Li +, D Li+), and the conductivity (κ) of each electrolyte were studied separately. The results demonstrate that the solvents play a critical role in the measured j 0, t Li+, D Li+, and κ of the electrolyte, while the choice of Li + salts only slightly affect the measured parameters. Finally, the understanding of the kinetics will gain insight into the mechanism of lithium dendrite formation and provide guidelines to the future application of lithium metal.« less

Effect of gamma-irradiation on thermal decomposition kinetics, X-ray diffraction pattern and spectral properties of tris(1,2-diaminoethane)nickel(II)sulphate

NASA Astrophysics Data System (ADS)

Jayashri, T. A.; Krishnan, G.; Rema Rani, N.

2014-12-01

Tris(1,2-diaminoethane)nickel(II)sulphate was prepared, and characterised by various chemical and spectral techniques. The sample was irradiated with 60Co gamma rays for varying doses. Sulphite ion and ammonia were detected and estimated in the irradiated samples. Non-isothermal decomposition kinetics, X-ray diffraction pattern, Fourier transform infrared spectroscopy, electronic, fast atom bombardment mass spectra, and surface morphology of the complex were studied before and after irradiation. Kinetic parameters were evaluated by integral, differential, and approximation methods. Irradiation enhanced thermal decomposition, lowering thermal and kinetic parameters. The mechanism of decomposition is controlled by R3 function. From X-ray diffraction studies, change in lattice parameters and subsequent changes in unit cell volume and average crystallite size were observed. Both unirradiated and irradiated samples of the complex belong to trigonal crystal system. Decrease in the intensity of the peaks was observed in the infrared spectra of irradiated samples. Electronic spectral studies revealed that the M-L interaction is unaffected by irradiation. Mass spectral studies showed that the fragmentation patterns of the unirradiated and irradiated samples are similar. The additional fragment with m/z 256 found in the irradiated sample is attributed to S8+. Surface morphology of the complex changed upon irradiation.

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.

Esterification of fatty acids using nylon-immobilized lipase in n-hexane: kinetic parameters and chain-length effects.

PubMed

Zaidi, A; Gainer, J L; Carta, G; Mrani, A; Kadiri, T; Belarbi, Y; Mir, A

2002-02-28

The esterification of long-chain fatty acids in n-hexane catalyzed by nylon-immobilized lipase from Candida rugosa has been investigated. Butyl oleate (22 carbon atoms), oleyl butyrate (22 carbon atoms) and oleyl oleate (36 carbon atoms) were produced at maximum reaction rates of approximately equal to 60 mmol h(-1) g(-1) immobilized enzyme when the substrates were present in equimolar proportions at an initial concentration of 0.6 mol l(-1). The observed kinetic behavior of all the esterification reactions is found to follow a ping-pong bi-bi mechanism with competitive inhibition by both substrates. The effect of the chain-length of the fatty acids and the alcohols could be correlated to some mechanistic models, in accordance with the calculated kinetic parameters.

The combination of kinetic and flow cytometric semen parameters as a tool to predict fertility in cryopreserved bull semen.

PubMed

Gliozzi, T M; Turri, F; Manes, S; Cassinelli, C; Pizzi, F

2017-11-01

Within recent years, there has been growing interest in the prediction of bull fertility through in vitro assessment of semen quality. A model for fertility prediction based on early evaluation of semen quality parameters, to exclude sires with potentially low fertility from breeding programs, would therefore be useful. The aim of the present study was to identify the most suitable parameters that would provide reliable prediction of fertility. Frozen semen from 18 Italian Holstein-Friesian proven bulls was analyzed using computer-assisted semen analysis (CASA) (motility and kinetic parameters) and flow cytometry (FCM) (viability, acrosomal integrity, mitochondrial function, lipid peroxidation, plasma membrane stability and DNA integrity). Bulls were divided into two groups (low and high fertility) based on the estimated relative conception rate (ERCR). Significant differences were found between fertility groups for total motility, active cells, straightness, linearity, viability and percentage of DNA fragmented sperm. Correlations were observed between ERCR and some kinetic parameters, and membrane instability and some DNA integrity indicators. In order to define a model with high relation between semen quality parameters and ERCR, backward stepwise multiple regression analysis was applied. Thus, we obtained a prediction model that explained almost half (R 2=0.47, P<0.05) of the variation in the conception rate and included nine variables: five kinetic parameters measured by CASA (total motility, active cells, beat cross frequency, curvilinear velocity and amplitude of lateral head displacement) and four parameters related to DNA integrity evaluated by FCM (degree of chromatin structure abnormality Alpha-T, extent of chromatin structure abnormality (Alpha-T standard deviation), percentage of DNA fragmented sperm and percentage of sperm with high green fluorescence representative of immature cells). A significant relationship (R 2=0.84, P<0.05) was observed between real and predicted fertility. Once the accuracy of fertility prediction has been confirmed, the model developed in the present study could be used by artificial insemination centers for bull selection or for elimination of poor fertility ejaculates.

Dynamic Metabolic Model Building Based on the Ensemble Modeling Approach

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

Liao, James C.

2016-10-01

Ensemble modeling of kinetic systems addresses the challenges of kinetic model construction, with respect to parameter value selection, and still allows for the rich insights possible from kinetic models. This project aimed to show that constructing, implementing, and analyzing such models is a useful tool for the metabolic engineering toolkit, and that they can result in actionable insights from models. Key concepts are developed and deliverable publications and results are presented.

The Kinetics of Dissolution Revisited

NASA Astrophysics Data System (ADS)

Antonel, Paula S.; Hoijemberg, Pablo A.; Maiante, Leandro M.; Lagorio, M. Gabriela

2003-09-01

An experiment analyzing the kinetics of dissolution of a solid with cylindrical geometry in water is presented. The dissolution process is followed by measuring the solid mass and its size parameters (thickness and diameter) as a function of time. It is verified that the dissolution rate follows the Nernst model. Data treatment is compared with the dissolution of a spherical solid previously described. Kinetics, diffusion concepts, and polynomial fitting of experimental data are combined in this simple experiment.

Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics.

PubMed

Vaas, Lea A I; Sikorski, Johannes; Michael, Victoria; Göker, Markus; Klenk, Hans-Peter

2012-01-01

The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed '-omics' techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data.

Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics

PubMed Central

Vaas, Lea A. I.; Sikorski, Johannes; Michael, Victoria; Göker, Markus; Klenk, Hans-Peter

2012-01-01

Background The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed ‘-omics’ techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. Methodology The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. Conclusions We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data. PMID:22536335

FY2014 Parameters for Helions and Gold Ions in Booster, AGS, and RHIC

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

Gardner, C. J.

The nominal parameters for helions (helion is the bound state of two protons and one neutron, the nucleus of a helium-3 atom) and gold ions in Booster, AGS, and RHIC are given for the FY2014 running period. The parameters are found using various formulas to derive mass, helion anomalous g-factor, kinetic parameters, RF parameters, ring parameters, etc..

Modeling hypertrophic IP3 transients in the cardiac myocyte.

PubMed

Cooling, Michael; Hunter, Peter; Crampin, Edmund J

2007-11-15

Cardiac hypertrophy is a known risk factor for heart disease, and at the cellular level is caused by a complex interaction of signal transduction pathways. The IP3-calcineurin pathway plays an important role in stimulating the transcription factor NFAT which binds to DNA cooperatively with other hypertrophic transcription factors. Using available kinetic data, we construct a mathematical model of the IP3 signal production system after stimulation by a hypertrophic alpha-adrenergic agonist (endothelin-1) in the mouse atrial cardiac myocyte. We use a global sensitivity analysis to identify key controlling parameters with respect to the resultant IP3 transient, including the phosphorylation of cell-membrane receptors, the ligand strength and binding kinetics to precoupled (with G(alpha)GDP) receptor, and the kinetics associated with precoupling the receptors. We show that the kinetics associated with the receptor system contribute to the behavior of the system to a great extent, with precoupled receptors driving the response to extracellular ligand. Finally, by reparameterizing for a second hypertrophic alpha-adrenergic agonist, angiotensin-II, we show that differences in key receptor kinetic and membrane density parameters are sufficient to explain different observed IP3 transients in essentially the same pathway.

Kinetic modelling of non-enzymatic browning and changes of physio-chemical parameters of peach juice during storage.

PubMed

Lyu, Jian; Liu, Xuan; Bi, Jinfeng; Wu, Xinye; Zhou, Linyan; Ruan, Weihong; Zhou, Mo; Jiao, Yi

2018-03-01

Kinetics of non-enzymatic browning and loss of free amino acids during different storage temperature (4, 25, 37 °C) were investigated. Changes of browning degree ( A 420 ), color parameters, Vitamin C ( V c ), free amino acids and 5-hydroxymethylfurfural (5-HMF) were analyzed to evaluate the non-enzymatic browning reactions, which were significantly affected by storage temperature. The lower temperature (4 °C) decreased the loss of V c and the generation of 5-HMF, but induce the highest loss of serine. At the end of storage, loss of serine, alanine and aspartic acid were mainly lost. Results showed that zero-order kinetic model ( R 2  > 0.859), the first-order model ( R 2  > 0.926) and the combined kinetic model ( R 2  > 0.916) were the most appropriate to describe the changes of a * and b * values, the degradation of V c and the changes of A 420 , L * and 5-HMF during different storage temperatures. These kinetic models can be applied for predicting and minimizing the non-enzymatic browning of fresh peach juice during storage.

Sorption kinetics of diuron on volcanic ash derived soils.

PubMed

Cáceres-Jensen, Lizethly; Rodríguez-Becerra, Jorge; Parra-Rivero, Joselyn; Escudey, Mauricio; Barrientos, Lorena; Castro-Castillo, Vicente

2013-10-15

Diuron sorption kinetic was studied in Andisols, Inceptisol and Ultisols soils in view of their distinctive physical and chemical properties: acidic pH and variable surface charge. Two types of kinetic models were used to fit the experimental dates: those that allow to establish principal kinetic parameters and modeling of sorption process (pseudo-first-order, pseudo-second-order), and some ones frequently used to describe solute transport mechanisms of organic compounds on different sorbents intended for remediation purposes (Elovich equation, intraparticle diffusion, Boyd, and two-site nonequilibrium models). The best fit was obtained with the pseudo-second-order model. The rate constant and the initial rate constant values obtained through this model demonstrated the behavior of Diuron in each soil, in Andisols were observed the highest values for both parameters. The application of the models to describe solute transport mechanisms allowed establishing that in all soils the mass transfer controls the sorption kinetic across the boundary layer and intraparticle diffusion into macropores and micropores. The slowest sorption rate was observed on Ultisols, behavior which must be taken into account when the leaching potential of Diuron is considered. Copyright © 2013 Elsevier B.V. All rights reserved.

Traveltime-based descriptions of transport and mixing in heterogeneous domains

NASA Astrophysics Data System (ADS)

Luo, Jian; Cirpka, Olaf A.

2008-09-01

Modeling mixing-controlled reactive transport using traditional spatial discretization of the domain requires identifying the spatial distributions of hydraulic and reactive parameters including mixing-related quantities such as dispersivities and kinetic mass transfer coefficients. In most applications, breakthrough curves (BTCs) of conservative and reactive compounds are measured at only a few locations and spatially explicit models are calibrated by matching these BTCs. A common difficulty in such applications is that the individual BTCs differ too strongly to justify the assumption of spatial homogeneity, whereas the number of observation points is too small to identify the spatial distribution of the decisive parameters. The key objective of the current study is to characterize physical transport by the analysis of conservative tracer BTCs and predict the macroscopic BTCs of compounds that react upon mixing from the interpretation of conservative tracer BTCs and reactive parameters determined in the laboratory. We do this in the framework of traveltime-based transport models which do not require spatially explicit, costly aquifer characterization. By considering BTCs of a conservative tracer measured on different scales, one can distinguish between mixing, which is a prerequisite for reactions, and spreading, which per se does not foster reactions. In the traveltime-based framework, the BTC of a solute crossing an observation plane, or ending in a well, is interpreted as the weighted average of concentrations in an ensemble of non-interacting streamtubes, each of which is characterized by a distinct traveltime value. Mixing is described by longitudinal dispersion and/or kinetic mass transfer along individual streamtubes, whereas spreading is characterized by the distribution of traveltimes, which also determines the weights associated with each stream tube. Key issues in using the traveltime-based framework include the description of mixing mechanisms and the estimation of the traveltime distribution. In this work, we account for both apparent longitudinal dispersion and kinetic mass transfer as mixing mechanisms, thus generalizing the stochastic-convective model with or without inter-phase mass transfer and the advective-dispersive streamtube model. We present a nonparametric approach of determining the traveltime distribution, given a BTC integrated over an observation plane and estimated mixing parameters. The latter approach is superior to fitting parametric models in cases wherein the true traveltime distribution exhibits multiple peaks or long tails. It is demonstrated that there is freedom for the combinations of mixing parameters and traveltime distributions to fit conservative BTCs and describe the tailing. A reactive transport case of a dual Michaelis-Menten problem demonstrates that the reactive mixing introduced by local dispersion and mass transfer may be described by apparent mean mass transfer with coefficients evaluated by local BTCs.

A kinetics database and scripts for PHREEQC

NASA Astrophysics Data System (ADS)

Hu, B.; Zhang, Y.; Teng, Y.; Zhu, C.

2017-12-01

Kinetics of geochemical reactions has been increasingly used in numerical models to simulate coupled flow, mass transport, and chemical reactions. However, the kinetic data are scattered in the literature. To assemble a kinetic dataset for a modeling project is an intimidating task for most. In order to facilitate the application of kinetics in geochemical modeling, we assembled kinetics parameters into a database for the geochemical simulation program, PHREEQC (version 3.0). Kinetics data were collected from the literature. Our database includes kinetic data for over 70 minerals. The rate equations are also programmed into scripts with the Basic language. Using the new kinetic database, we simulated reaction path during the albite dissolution process using various rate equations in the literature. The simulation results with three different rate equations gave difference reaction paths at different time scale. Another application involves a coupled reactive transport model simulating the advancement of an acid plume in an acid mine drainage site associated with Bear Creek Uranium tailings pond. Geochemical reactions including calcite, gypsum, and illite were simulated with PHREEQC using the new kinetic database. The simulation results successfully demonstrated the utility of new kinetic database.

Methods for determining the physiological state of a plant

DOEpatents

Kramer, David M.; Sacksteder, Colette

2003-09-23

The present invention provides methods for measuring a photosynthetic parameter. The methods of the invention include the steps of: (a) illuminating a plant leaf until steady-state photosynthesis is achieved; (b) subjecting the illuminated plant leaf to a period of darkness; (c) using a kinetic spectrophotometer or kinetic spectrophotometer/fluorimeter to collect spectral data from the plant leaf treated in accordance with steps (a) and (b); and (d) determining a photosynthetic parameter from the spectral data. In another aspect, the invention provides methods for determining the physiological state of a plant.

Parameterization of annealing kinetics in pharmaceutical glasses.

PubMed

Hodge, Ian M

2013-07-01

Numerical simulations indicate that neglecting the canonical nonlinearity of glassy-state annealing kinetics in pharmaceutical (and other) glasses leads to good KWW fits to the dependence of enthalpy on annealing time, but with spurious KWW parameters that are affected by nonlinearity. A simplified treatment of nonlinearity that uses the Struik shift factor is found to be a useful approximation for these analyses, and can account for previously reported differences between linear and nonlinear KWW parameters (Kawakami K, Pikal MJ. 2005. J Pharm Sci 94:948-965). Copyright © 2013 Wiley Periodicals, Inc.

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

Improving Student Results in the Crystal Violet Chemical Kinetics Experiment

ERIC Educational Resources Information Center

Kazmierczak, Nathanael; Vander Griend, Douglas A.

2017-01-01

Despite widespread use in general chemistry laboratories, the crystal violet chemical kinetics experiment frequently suffers from erroneous student results. Student calculations for the reaction order in hydroxide often contain large asymmetric errors, pointing to the presence of systematic error. Through a combination of "in silico"…

The nonlocal electron kinetics for a low-pressure glow discharge dusty plasma

NASA Astrophysics Data System (ADS)

Liang, Yonggan; Wang, Ying; Li, Hui; Tian, Ruihuan; Yuan, Chengxun; Kudryavtsev, A. A.; Rabadanov, K. M.; Wu, Jian; Zhou, Zhongxiang; Tian, Hao

2018-05-01

The nonlocal electron kinetic model based on the Boltzmann equation is developed in low-pressure argon glow discharge dusty plasmas. The additional electron-dust elastic and inelastic collision processes are considered when solving the kinetic equation numerically. The orbital motion limited theory and collision enhanced collection approximation are employed to calculate the dust surface potential. The electron energy distribution function (EEDF), effective electron temperature Teff, and dust surface potential are investigated under different plasma and dust conditions by solving the Boltzmann and the dust charging current balance equations self-consistently. A comparison of the calculation results obtained from nonlocal and local kinetic models is made. It is shown that the appearance of dust particles leads to a deviation of the EEDF from its original profile for both nonlocal and local kinetic models. With the increase in dust density and size, the effective electron temperature and dust surface potential decrease due to the high-energy electron loss on the dust surface. Meanwhile, the nonlocal and local results differ much from each other under the same calculation condition. It is concluded that, for low-pressure (PR ≤ 1 cm*Torr) glow discharge dusty plasmas, the existence of dust particles will amplify the difference of local and nonlocal EEDFs, which makes the local kinetic model more improper to determine the main parameters of the positive column. The nonlocal kinetic model should be used for the calculation of the EEDFs and dusty plasma parameters.

Clustered Single Cellulosic Fiber Dissolution Kinetics and Mechanisms through Optical Microscopy under Limited Dissolving Conditions.

PubMed

Mäkelä, Valtteri; Wahlström, Ronny; Holopainen-Mantila, Ulla; Kilpeläinen, Ilkka; King, Alistair W T

2018-05-14

Herein, we describe a new method of assessing the kinetics of dissolution of single fibers by dissolution under limited dissolving conditions. The dissolution is followed by optical microscopy under limited dissolving conditions. Videos of the dissolution were processed in ImageJ to yield kinetics for dissolution, based on the disappearance of pixels associated with intact fibers. Data processing was performed using the Python language, utilizing available scientific libraries. The methods of processing the data include clustering of the single fiber data, identifying clusters associated with different fiber types, producing average dissolution traces and also extraction of practical parameters, such as, time taken to dissolve 25, 50, 75, 95, and 99.5% of the clustered fibers. In addition to these simple parameters, exponential fitting was also performed yielding rate constants for fiber dissolution. Fits for sample and cluster averages were variable, although demonstrating first-order kinetics for dissolution overall. To illustrate this process, two reference pulps (a bleached softwood kraft pulp and a bleached hardwood pre-hydrolysis kraft pulp) and their cellulase-treated versions were analyzed. As expected, differences in the kinetics and dissolution mechanisms between these samples were observed. Our initial interpretations are presented, based on the combined mechanistic observations and single fiber dissolution kinetics for these different samples. While the dissolution mechanisms observed were similar to those published previously, the more direct link of mechanistic information with the kinetics improve our understanding of cell wall structure and pre-treatments, toward improved processability.

Heterogeneous kinetics of H2O, HNO3 and HCl on HNO3 hydrates (α-NAT, β-NAT, NAD) in the range 175-200 K

NASA Astrophysics Data System (ADS)

Iannarelli, Riccardo; Rossi, Michel J.

2016-09-01

Experiments on the title compounds have been performed using a multidiagnostic stirred-flow reactor (SFR) in which the gas phase as well as the condensed phase has been simultaneously investigated under stratospheric temperatures in the range 175-200 K. Wall interactions of the title compounds have been taken into account using Langmuir adsorption isotherms in order to close the mass balance between deposited and desorbed (recovered) compounds. Thin solid films at 1 µm typical thickness have been used as a proxy for atmospheric ice particles and have been deposited on a Si window of the cryostat, with the optical element being the only cold point in the deposition chamber. Fourier transform infrared (FTIR) absorption spectroscopy in transmission as well as partial and total pressure measurement using residual gas mass spectrometry (MS) and sensitive pressure gauges have been employed in order to monitor growth and evaporation processes as a function of temperature using both pulsed and continuous gas admission and monitoring under SFR conditions. Thin solid H2O ice films were used as the starting point throughout, with the initial spontaneous formation of α-NAT (nitric acid trihydrate) followed by the gradual transformation of α- to β-NAT at T > 185 K. Nitric acid dihydrate (NAD) was spontaneously formed at somewhat larger partial pressures of HNO3 deposited on pure H2O ice. In contrast to published reports, the formation of α-NAT proceeded without prior formation of an amorphous HNO3 / H2O layer and always resulted in β-NAT. For α- and β-NAT, the temperature-dependent accommodation coefficient α(H2O) and α(HNO3), the evaporation flux Jev(H2O) and Jev(HNO3) and the resulting saturation vapor pressure Peq(H2O) and Peq(HNO3) were measured and compared to binary phase diagrams of HNO3 / H2O in order to afford a thermochemical check of the kinetic parameters. The resulting kinetic and thermodynamic parameters of activation energies for evaporation (Eev) and standard heats of evaporation ΔHev0 of H2O and HNO3 for α- and β-NAT, respectively, led to an estimate for the relative standard enthalpy difference between α- and β-NAT of -6.0 ± 20 kJ mol-1 in favor of β-NAT, as expected, despite a significantly larger value of Eev for HNO3 in α-NAT. This in turn implies a substantial activation energy for HNO3 accommodation in α- compared to β-NAT where Eacc(HNO3) is essentially zero. The kinetic (α(HCl), Jev(HCl)) and thermodynamic (Peq(HCl)) parameters of HCl-doped α- and β-NAT have been determined under the assumption that HCl adsorption did not significantly affect α(H2O) and α(HNO3) as well as the evaporation flux Jev(H2O). Jev(HCl) and Peq(HCl) on both α- and β-NAT are larger than the corresponding values for HNO3 across the investigated temperature range but significantly smaller than the values for pure H2O ice at T < 200 K.

Revisiting Supernova 1987A constraints on dark photons

DOE PAGES

Chang, Jae Hyeok; Essig, Rouven; McDermott, Samuel D.

2017-01-25

We revisit constraints on dark photons with masses below ~ 100 MeV from the observations of Supernova 1987A. If dark photons are produced in sufficient quantity, they reduce the amount of energy emitted in the form of neutrinos, in conflict with observations. For the first time, we include the effects of finite temperature and density on the kinetic-mixing parameter,ϵ, in this environment. This causes the constraints on ϵ to weaken with the dark-photon mass below ~ 15 MeV. For large-enough values of ϵ, it is well known that dark photons can be reabsorbed within the supernova. Since the rates ofmore » reabsorption processes decrease as the dark-photon energy increases, we point out that dark photons with energies above the Wien peak can escape without scattering, contributing more to energy loss than is possible assuming a blackbody spectrum. Furthermore, we estimate the systematic uncertainties on the cooling bounds by deriving constraints assuming one analytic and four different simulated temperature and density profiles of the proto-neutron star. Finally, we estimate also the systematic uncertainty on the bound by varying the distance across which dark photons must propagate from their point of production to be able to affect the star. Finally, this work clarifies the bounds from SN1987A on the dark-photon parameter space.« less

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.

Kinetic Model of Growth of Arthropoda Populations

NASA Astrophysics Data System (ADS)

Ershov, Yu. A.; Kuznetsov, M. A.

2018-05-01

Kinetic equations were derived for calculating the growth of crustacean populations ( Crustacea) based on the biological growth model suggested earlier using shrimp ( Caridea) populations as an example. The development cycle of successive stages for populations can be represented in the form of quasi-chemical equations. The kinetic equations that describe the development cycle of crustaceans allow quantitative prediction of the development of populations depending on conditions. In contrast to extrapolation-simulation models, in the developed kinetic model of biological growth the kinetic parameters are the experimental characteristics of population growth. Verification and parametric identification of the developed model on the basis of the experimental data showed agreement with experiment within the error of the measurement technique.

Drift-free kinetic equations for turbulent dispersion

NASA Astrophysics Data System (ADS)

Bragg, A.; Swailes, D. C.; Skartlien, R.

2012-11-01

The dispersion of passive scalars and inertial particles in a turbulent flow can be described in terms of probability density functions (PDFs) defining the statistical distribution of relevant scalar or particle variables. The construction of transport equations governing the evolution of such PDFs has been the subject of numerous studies, and various authors have presented formulations for this type of equation, usually referred to as a kinetic equation. In the literature it is often stated, and widely assumed, that these PDF kinetic equation formulations are equivalent. In this paper it is shown that this is not the case, and the significance of differences among the various forms is considered. In particular, consideration is given to which form of equation is most appropriate for modeling dispersion in inhomogeneous turbulence and most consistent with the underlying particle equation of motion. In this regard the PDF equations for inertial particles are considered in the limit of zero particle Stokes number and assessed against the fully mixed (zero-drift) condition for fluid points. A long-standing question regarding the validity of kinetic equations in the fluid-point limit is answered; it is demonstrated formally that one version of the kinetic equation (derived using the Furutsu-Novikov method) provides a model that satisfies this zero-drift condition exactly in both homogeneous and inhomogeneous systems. In contrast, other forms of the kinetic equation do not satisfy this limit or apply only in a limited regime.

Drift-free kinetic equations for turbulent dispersion.

PubMed

Bragg, A; Swailes, D C; Skartlien, R

2012-11-01

The dispersion of passive scalars and inertial particles in a turbulent flow can be described in terms of probability density functions (PDFs) defining the statistical distribution of relevant scalar or particle variables. The construction of transport equations governing the evolution of such PDFs has been the subject of numerous studies, and various authors have presented formulations for this type of equation, usually referred to as a kinetic equation. In the literature it is often stated, and widely assumed, that these PDF kinetic equation formulations are equivalent. In this paper it is shown that this is not the case, and the significance of differences among the various forms is considered. In particular, consideration is given to which form of equation is most appropriate for modeling dispersion in inhomogeneous turbulence and most consistent with the underlying particle equation of motion. In this regard the PDF equations for inertial particles are considered in the limit of zero particle Stokes number and assessed against the fully mixed (zero-drift) condition for fluid points. A long-standing question regarding the validity of kinetic equations in the fluid-point limit is answered; it is demonstrated formally that one version of the kinetic equation (derived using the Furutsu-Novikov method) provides a model that satisfies this zero-drift condition exactly in both homogeneous and inhomogeneous systems. In contrast, other forms of the kinetic equation do not satisfy this limit or apply only in a limited regime.

Fundamental properties of Fanaroff-Riley type II radio galaxies investigated via Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Kapińska, A. D.; Uttley, P.; Kaiser, C. R.

2012-08-01

Radio galaxies and quasars are among the largest and most powerful single objects known and are believed to have had a significant impact on the evolving Universe and its large-scale structure. We explore the intrinsic and extrinsic properties of the population of Fanaroff-Riley type II (FR II) objects, i.e. their kinetic luminosities, lifetimes and the central densities of their environments. In particular, the radio and kinetic luminosity functions of these powerful radio sources are investigated using the complete, flux-limited radio catalogues of the Third Cambridge Revised Revised Catalogue (3CRR) and Best et al. We construct multidimensional Monte Carlo simulations using semi-analytical models of FR II source time evolution to create artificial samples of radio galaxies. Unlike previous studies, we compare radio luminosity functions found with both the observed and simulated data to explore the best-fitting fundamental source parameters. The new Monte Carlo method we present here allows us to (i) set better limits on the predicted fundamental parameters of which confidence intervals estimated over broad ranges are presented and (ii) generate the most plausible underlying parent populations of these radio sources. Moreover, as has not been done before, we allow the source physical properties (kinetic luminosities, lifetimes and central densities) to co-evolve with redshift, and we find that all the investigated parameters most likely undergo cosmological evolution. Strikingly, we find that the break in the kinetic luminosity function must undergo redshift evolution of at least (1 + z)3. The fundamental parameters are strongly degenerate, and independent constraints are necessary to draw more precise conclusions. We use the estimated kinetic luminosity functions to set constraints on the duty cycles of these powerful radio sources. A comparison of the duty cycles of powerful FR IIs with those determined from radiative luminosities of active galactic nuclei of comparable black hole mass suggests a transition in behaviour from high to low redshifts, corresponding to either a drop in the typical black hole mass of powerful FR IIs at low redshifts, or a transition to a kinetically dominated, radiatively inefficient FR II population.

Mathematical Modeling of Ammonia Electro-Oxidation on Polycrystalline Pt Deposited Electrodes

NASA Astrophysics Data System (ADS)

Diaz Aldana, Luis A.

The ammonia electrolysis process has been proposed as a feasible way for electrochemical generation of fuel grade hydrogen (H2). Ammonia is identified as one of the most suitable energy carriers due to its high hydrogen density, and its safe and efficient distribution chain. Moreover, the fact that this process can be applied even at low ammonia concentration feedstock opens its application to wastewater treatment along with H 2 co-generation. In the ammonia electrolysis process, ammonia is electro-oxidized in the anode side to produce N2 while H2 is evolved from water reduction in the cathode. A thermodynamic energy requirement of just five percent of the energy used in hydrogen production from water electrolysis is expected from ammonia electrolysis. However, the absence of a complete understanding of the reaction mechanism and kinetics involved in the ammonia electro-oxidation has not yet allowed the full commercialization of this process. For that reason, a kinetic model that can be trusted in the design and scale up of the ammonia electrolyzer needs to be developed. This research focused on the elucidation of the reaction mechanism and kinetic parameters for the ammonia electro-oxidation. The definition of the most relevant elementary reactions steps was obtained through the parallel analysis of experimental data and the development of a mathematical model of the ammonia electro-oxidation in a well defined hydrodynamic system, such as the rotating disk electrode (RDE). Ammonia electro-oxidation to N 2 as final product was concluded to be a slow surface confined process where parallel reactions leading to the deactivation of the catalyst are present. Through the development of this work it was possible to define a reaction mechanism and values for the kinetic parameters for ammonia electro-oxidation that allow an accurate representation of the experimental observations on a RDE system. Additionally, the validity of the reaction mechanism and kinetic parameters were supplemented by means of process scale up, performance evaluation, and hydrodynamic analysis in a flow cell electrolyzer. An adequate simulation of the flow electrolyzer performance was accomplished using the obtained kinetic parameters.

Characteristics of laser-induced plasma as a spectroscopic light emission source

NASA Astrophysics Data System (ADS)

Ma, Q. L.; Motto-Ros, V.; Lei, W. Q.; Wang, X. C.; Boueri, M.; Laye, F.; Zeng, C. Q.; Sausy, M.; Wartelle, A.; Bai, X. S.; Zheng, L. J.; Zeng, H. P.; Baudelet, M.; Yu, J.

2012-05-01

Laser-induced plasma is today a widespread spectroscopic emission source. It can be easily generated using compact and reliable nanosecond pulsed lasers and finds applications in various domains with laser-induced breakdown spectroscopy (LIBS). It is however such a particular medium which is intrinsically a transient and non-point light emitting source. Its timeand space-resolved diagnostics is therefore crucial for its optimized use. In this paper, we review our work on the investigation of the morphology and the evolution of the plasma. Different time scales relevant for the description of the plasma's kinetics and dynamics are covered by suitable techniques. Our results show detailed evolution and transformation of the plasma with high temporal and spatial resolutions. The effects of the laser parameters as well as the background gas are particularly studied.

Biocompatible Polymer Nanoformulation To Improve the Release and Safety of a Drug Mimic Molecule Detectable via ICP-MS.

PubMed

Ferrari, Raffaele; Talamini, Laura; Violatto, Martina Bruna; Giangregorio, Paola; Sponchioni, Mattia; Morbidelli, Massimo; Salmona, Mario; Bigini, Paolo; Moscatelli, Davide

2017-01-03

Fluorescent poly(ε-caprolactone)-based nanoparticles (NPs) have been synthesized and successfully loaded with a titanium organometallic compound as a mimic of a water-insoluble drug. The nature of this nanovector enabled us to combine the quantification of the metal in tissues after systemic administration in healthy immunocompetent mice by inductively coupled plasma mass spectroscopy (ICP-MS) followed by the visualization of NPs in organ sections by confocal microscopy. This innovative method of nanodrug screening has enabled us to elucidate the crucial parameters of their kinetics. The organometallic compound is a good mimic of most anticancer drugs, and this approach is an interesting starting point to design the relevance of a broad range of nanoformulations in terms of safety and targeted delivery of the cargoes.

The Simulator Development for RDE Reactor

NASA Astrophysics Data System (ADS)

Subekti, Muhammad; Bakhri, Syaiful; Sunaryo, Geni Rina

2018-02-01

BATAN is proposing the construction of experimental power reactor (RDE reactor) for increasing the public acceptance on NPP development plan, proofing the safety level of the most advanced reactor by performing safety demonstration on the accidents such as Chernobyl and Fukushima, and owning the generation fourth (G4) reactor technology. For owning the reactor technology, the one of research activities is RDE’s simulator development that employing standard equation. The development utilizes standard point kinetic and thermal equation. The examination of the simulator carried out comparison in which the simulation’s calculation result has good agreement with assumed parameters and ChemCAD calculation results. The transient simulation describes the characteristic of the simulator to respond the variation of power increase of 1.5%/min, 2.5%/min, and 3.5%/min.

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.