Determination of the Michaelis-Menten kinetics and the genes expression involved in phyto-degradation of cyanide and ferri-cyanide.

Science.gov (United States)

Yu, Xiao-Zhang; Zhang, Xue-Hong

2016-07-01

Hydroponic experiments were conducted with different species of plants (rice, maize, soybean and willow) exposed to ferri-cyanide to investigate the half-saturation constant (K M ) and the maximal metabolic capacity (v max ) involved in phyto-assimilation. Three varieties for each testing species were collected from different origins. Measured concentrations show that the uptake rates responded biphasically to ferri-cyanide treatments by showing increases linearly at low and almost constant at high concentrations from all treatments, indicating that phyto-assimilation of ferri-cyanide followed the Michaelis-Menten kinetics. Using non-linear regression, the highest v max was by rice, followed by willows. The lowest v max was found for soybean. All plants, except maize (DY26) and rice (XJ12), had a similar K M value, suggesting the same enzyme was active in phyto-assimilation of ferri-cyanide. Transcript level, by real-time quantitative PCR, of enzymes involved in degradation of cyanides showed that the analyzed genes were differently expressed during different cyanides exposure. The expression of CAS and ST genes responded positively to KCN exposure, suggesting that β-CAS and ST pathways were two possible pathways for cyanide detoxification in rice. The transcript level of NIT and ASPNASE genes also showed a remarkable up-regulation to KCN, implying the contribution to the pool of amino acid aspartate, which is an end product of CN metabolism. Up-regulation of GS genes suggests that acquisition of ammonium released from cyanide degradation may be an additional nitrogen source for plant nutrition. Results also revealed that the expressions of these genes, except for GS, were relatively constant during iron cyanide exposure, suggesting that they are likely metabolized by plants through a non-defined pathway rather than the β-CAS pathway.

Transient competitive complexation in biological kinetic isotope fractionation explains nonsteady isotopic effects: Theory and application to denitrification in soils

Science.gov (United States)

Maggi, Federico; Riley, William J.

2009-12-01

The theoretical formulation of biological kinetic isotope fractionation often assumes first-order or Michaelis-Menten kinetics, the latter solved under the quasi-steady state assumption. Both formulations lead to a constant isotope fractionation factor, therefore they may return incorrect estimations of isotopic effects and misleading interpretations of isotopic signatures when fractionation is not a steady process. We have analyzed the isotopic signature of denitrification in biogeochemical soil systems by Menyailo and Hungate (2006) in which high and variable 15N-N2O enrichment during N2O production and inverse isotope fractionation during N2O consumption could not be explained with first-order kinetics and the Rayleigh equation, or with Michaelis-Menten kinetics. When Michaelis-Menten kinetics were coupled to Monod kinetics to describe biomass and enzyme dynamics, and the quasi-steady state assumption was relaxed, transient Michaelis-Menten-Monod kinetics accurately reproduced the observed concentrations, and variable and inverse isotope fractionations. These results imply a substantial revision in modeling isotopic effects, suggesting that steady state kinetics such as first-order, Rayleigh, and classic Michaelis-Menten kinetics should be superseded by transient kinetics in conjunction with biomass and enzyme dynamics.

Transient competitive complexation in biological kinetic isotope fractionation explains non-steady isotopic effects: Theory and application to denitrification in soils

Energy Technology Data Exchange (ETDEWEB)

Maggi, F.M.; Riley, W.J.

2009-06-01

The theoretical formulation of biological kinetic reactions in isotopic applications often assume first-order or Michaelis-Menten-Monod kinetics under the quasi-steady-state assumption to simplify the system kinetics. However, isotopic e ects have the same order of magnitude as the potential error introduced by these simpli cations. Both formulations lead to a constant fractionation factor which may yield incorrect estimations of the isotopic effect and a misleading interpretation of the isotopic signature of a reaction. We have analyzed the isotopic signature of denitri cation in biogeochemical soil systems by Menyailo and Hungate [2006], where high {sup 15}N{sub 2}O enrichment during N{sub 2}O production and inverse isotope fractionation during N{sub 2}O consumption could not be explained with first-order kinetics and the Rayleigh equation, or with the quasi-steady-state Michaelis-Menten-Monod kinetics. When the quasi-steady-state assumption was relaxed, transient Michaelis-Menten-Monod kinetics accurately reproduced the observations and aided in interpretation of experimental isotopic signatures. These results may imply a substantial revision in using the Rayleigh equation for interpretation of isotopic signatures and in modeling biological kinetic isotope fractionation with first-order kinetics or quasi-steady-state Michaelis-Menten-Monod kinetics.

Microscale Measurements of Michaelis-Menten Constants of Neuraminidase with Nanogel Capillary Electrophoresis for the Determination of the Sialic Acid Linkage.

Science.gov (United States)

Gattu, Srikanth; Crihfield, Cassandra L; Holland, Lisa A

2017-01-03

Phospholipid nanogels enhance the stability and performance of the exoglycosidase enzyme neuraminidase and are used to create a fixed zone of enzyme within a capillary. With nanogels, there is no need to covalently immobilize the enzyme, as it is physically constrained. This enables rapid quantification of Michaelis-Menten constants (K M ) for different substrates and ultimately provides a means to quantify the linkage (i.e., 2-3 versus 2-6) of sialic acids. The fixed zone of enzyme is inexpensive and easily positioned in the capillary to support electrophoresis mediated microanalysis using neuraminidase to analyze sialic acid linkages. To circumvent the limitations of diffusion during static incubation, the incubation period is reproducibly achieved by varying the number of forward and reverse passes the substrate makes through the stationary fixed zone using in-capillary electrophoretic mixing. A K M value of 3.3 ± 0.8 mM (V max , 2100 ± 200 μM/min) was obtained for 3'-sialyllactose labeled with 2-aminobenzoic acid using neuraminidase from Clostridium perfringens that cleaves sialic acid monomers with an α2-3,6,8,9 linkage, which is similar to values reported in the literature that required benchtop analyses. The enzyme cleaves the 2-3 linkage faster than the 2-6, and a K M of 2 ± 1 mM (V max , 400 ± 100 μM/min) was obtained for the 6'-sialyllactose substrate. An alternative neuraminidase selective for 2-3 sialic acid linkages generated a K M value of 3 ± 2 mM (V max , 900 ± 300 μM/min) for 3'-sialyllactose. With a knowledge of V max , the method was applied to a mixture of 2-3 and 2-6 sialyllactose as well as 2-3 and 2-6 sialylated triantennary glycan. Nanogel electrophoresis is an inexpensive, rapid, and simple alternative to current technologies used to distinguish the composition of 3' and 6' sialic acid linkages.

(CSTR) and 1-plug flow reactor (PFR)

African Journals Online (AJOL)

Administrator

2010-12-27

Dec 27, 2010 ... 2Department of Chemical Engineering, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria. ... modeled as PFR and described by Michaelis. Menten equation. Designed equations derived from the two equations are used for the reactor sizing of ... Herbivores make a living on cellulose by possessing.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

International Nuclear Information System (INIS)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-01-01

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Energy Technology Data Exchange (ETDEWEB)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti, E-mail: arti@iitm.ac.in [Department of Chemistry, Indian Institute of Technology, Madras, Chennai 600036 (India)

2016-08-28

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Science.gov (United States)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-08-01

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

A Solution of the Convective-Diffusion Equation for Solute Mass Transfer inside a Capillary Membrane Bioreactor

Directory of Open Access Journals (Sweden)

B. Godongwana

2010-01-01

Full Text Available This paper presents an analytical model of substrate mass transfer through the lumen of a membrane bioreactor. The model is a solution of the convective-diffusion equation in two dimensions using a regular perturbation technique. The analysis accounts for radial-convective flow as well as axial diffusion of the substrate specie. The model is applicable to the different modes of operation of membrane bioreactor (MBR systems (e.g., dead-end, open-shell, or closed-shell mode, as well as the vertical or horizontal orientation. The first-order limit of the Michaelis-Menten equation for substrate consumption was used to test the developed model against available analytical results. The results obtained from the application of this model, along with a biofilm growth kinetic model, will be useful in the derivation of an efficiency expression for enzyme production in an MBR.

A century of enzyme kinetic analysis, 1913 to 2013.

Science.gov (United States)

Johnson, Kenneth A

2013-09-02

This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Wang and Li Afr J Tradit Complement Altern Med. (2016) 13(1):99 ...

African Journals Online (AJOL)

PROF ADEWUNMI

It possesses antiseptic, anti-inflammatory, analgesic, anti-cancer and antioxidant ... All experiments on animals were conducted in accordance with and after approval by the ... With the content of gallic acid control as horizontal coordinate and the ... The kinetic constants were calculated based on Michaelis-Menten equation ...

DETERMINATION OF THE SPECIFIC GROWTH RATE ON ...

African Journals Online (AJOL)

Sewage generation is one of the dense problems Nigerians encounter on daily bases, mostly at the urbanized area where factories and industries are located. This paper is aimed at determining the specific growth rate “K” of biological activities on cassava wastewater during degradation using Michaelis-Menten Equation.

Nonthermal effect of microwave irradiation on nitrite uptake in Chlamydomonas reinhardtii

International Nuclear Information System (INIS)

Pedrajas, C.; Cotrino, J.

1989-01-01

When cells of the unicellular green alga Chlamydomonas reinhardtii were subjected to microwave irradiation at 2.45 GHz, nitrite uptake kinetics still obeyed the Michaelis-Menten equation, the Km of the process remaining constant, whereas V max increased, which indicates an enhanced nonthermal permeability in irradiated cells. (author)

A Finite-Difference Solution of Solute Transport through a Membrane Bioreactor

Directory of Open Access Journals (Sweden)

B. Godongwana

2015-01-01

Full Text Available The current paper presents a theoretical analysis of the transport of solutes through a fixed-film membrane bioreactor (MBR, immobilised with an active biocatalyst. The dimensionless convection-diffusion equation with variable coefficients was solved analytically and numerically for concentration profiles of the solutes through the MBR. The analytical solution makes use of regular perturbation and accounts for radial convective flow as well as axial diffusion of the substrate species. The Michaelis-Menten (or Monod rate equation was assumed for the sink term, and the perturbation was extended up to second-order. In the analytical solution only the first-order limit of the Michaelis-Menten equation was considered; hence the linearized equation was solved. In the numerical solution, however, this restriction was lifted. The solution of the nonlinear, elliptic, partial differential equation was based on an implicit finite-difference method (FDM. An upwind scheme was employed for numerical stability. The resulting algebraic equations were solved simultaneously using the multivariate Newton-Raphson iteration method. The solution allows for the evaluation of the effect on the concentration profiles of (i the radial and axial convective velocity, (ii the convective mass transfer rates, (iii the reaction rates, (iv the fraction retentate, and (v the aspect ratio.

New functions to estimate 305-days milk production of Gir cows : Novas Funções para Estimar a Produção de Leite, em 305 Dias de Lactação, de Vacas da Raça Gir

NARCIS (Netherlands)

Reboucas, G.F.; Moraes Goncalves, de T.; Martines, M.L.; Azevedo Junior, J.; Koops, W.J.

2008-01-01

This study aimed to calculate new accumulated and daily functions based on the Michaelis-Menten equation to estimate the 305-days production of Gir cows using test day milk yields. Data consisted of 7,412 lactation records of 3,416 Gir cows (Bos indicus) collected from 1987 to 2004 in 51 herds

A Biochemist's View of Ecosystem Rates and their Response to Changing Temperature

Science.gov (United States)

Arcus, V. L.

2017-12-01

Enzyme kinetics lie at the heart of biochemistry and the Michaelis-Menten equation that defines the relationship between substrate and rate is over 100 years old. About 80 years ago Eyring and Polyani formulated Transistion State Theory (TST) which describes the temperature-dependence of chemical reaction rates and the precise relationship between activation energy and the rate. TST provided a robust theoretical foundation for the Arrhenius equation and together, these equations are the foundation equations for the biochemist. Can these equations provide any insights into rates at larger scales, such as organism growth rates and those rates that interest ecosystem scientists (e.g. heterotrophic respiration, gross primary production)? Let us begin by considering a microbial cell. Microbial growth (i.e. cell division) requires the coordinated kinetics of thousands of enzymes including DNA/RNA polymerases, ribosomes, biosynthetic enzymes - all under a regime of highly complex regulatory effects. There is no a priori reason to expect that Michaelis-Menten kinetics and TST will adequately describe this vastly complex process. Indeed, Lloyd and Taylor showed 23 years ago that soil respiration is not well described by the Arrhenius function. More recently, Heskel and colleagues showed that leaf respiration is also not well described by the Arrhenius function. It is the same case for rates of photosynthesis. Despite this failure of the basic equations of biochemistry to map to biological rates at greater scales, what insights can biochemistry provide to ecosystem science? As nearly all of biological metabolism is mediated through enzyme kinetics, I will begin with the Michaelis-Menten equation under regimes of low and high substrate concentrations. This simplified view can provide surprising insights into processes at larger scales. I will also consider the relationship between the activation energy and the reaction rate. Many, many ecosystem-rate papers focus on the

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

Science.gov (United States)

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.

Victor Henri: 111 years of his equation.

Science.gov (United States)

Cornish-Bowden, Athel; Mazat, Jean-Pierre; Nicolas, Serge

2014-12-01

Victor Henri's great contribution to the understanding of enzyme kinetics and mechanism is not always given the credit that it deserves. In addition, his earlier work in experimental psychology is totally unknown to biochemists, and his later work in spectroscopy and photobiology almost equally so. Applying great rigour to his analysis he succeeded in obtaining a model of enzyme action that explained all of the observations available to him, and he showed why the considerable amount of work done in the preceding decade had not led to understanding. His view was that only physical chemistry could explain the behaviour of enzymes, and that models should be judged in accordance with their capacity not only to explain previously known facts but also to predict new observations against which they could be tested. The kinetic equation usually attributed to Michaelis and Menten was in reality due to him. His thesis of 1903 is now available in English. Copyright © 2014 Elsevier B.V. and Société française de biochimie et biologie Moléculaire (SFBBM). All rights reserved.

Fock space, symbolic algebra, and analytical solutions for small stochastic systems.

Science.gov (United States)

Santos, Fernando A N; Gadêlha, Hermes; Gaffney, Eamonn A

2015-12-01

Randomness is ubiquitous in nature. From single-molecule biochemical reactions to macroscale biological systems, stochasticity permeates individual interactions and often regulates emergent properties of the system. While such systems are regularly studied from a modeling viewpoint using stochastic simulation algorithms, numerous potential analytical tools can be inherited from statistical and quantum physics, replacing randomness due to quantum fluctuations with low-copy-number stochasticity. Nevertheless, classical studies remained limited to the abstract level, demonstrating a more general applicability and equivalence between systems in physics and biology rather than exploiting the physics tools to study biological systems. Here the Fock space representation, used in quantum mechanics, is combined with the symbolic algebra of creation and annihilation operators to consider explicit solutions for the chemical master equations describing small, well-mixed, biochemical, or biological systems. This is illustrated with an exact solution for a Michaelis-Menten single enzyme interacting with limited substrate, including a consideration of very short time scales, which emphasizes when stiffness is present even for small copy numbers. Furthermore, we present a general matrix representation for Michaelis-Menten kinetics with an arbitrary number of enzymes and substrates that, following diagonalization, leads to the solution of this ubiquitous, nonlinear enzyme kinetics problem. For this, a flexible symbolic maple code is provided, demonstrating the prospective advantages of this framework compared to stochastic simulation algorithms. This further highlights the possibilities for analytically based studies of stochastic systems in biology and chemistry using tools from theoretical quantum physics.

Interpreting experimental data on egg production--applications of dynamic differential equations.

Science.gov (United States)

France, J; Lopez, S; Kebreab, E; Dijkstra, J

2013-09-01

This contribution focuses on applying mathematical models based on systems of ordinary first-order differential equations to synthesize and interpret data from egg production experiments. Models based on linear systems of differential equations are contrasted with those based on nonlinear systems. Regression equations arising from analytical solutions to linear compartmental schemes are considered as candidate functions for describing egg production curves, together with aspects of parameter estimation. Extant candidate functions are reviewed, a role for growth functions such as the Gompertz equation suggested, and a function based on a simple new model outlined. Structurally, the new model comprises a single pool with an inflow and an outflow. Compartmental simulation models based on nonlinear systems of differential equations, and thus requiring numerical solution, are next discussed, and aspects of parameter estimation considered. This type of model is illustrated in relation to development and evaluation of a dynamic model of calcium and phosphorus flows in layers. The model consists of 8 state variables representing calcium and phosphorus pools in the crop, stomachs, plasma, and bone. The flow equations are described by Michaelis-Menten or mass action forms. Experiments that measure Ca and P uptake in layers fed different calcium concentrations during shell-forming days are used to evaluate the model. In addition to providing a useful management tool, such a simulation model also provides a means to evaluate feeding strategies aimed at reducing excretion of potential pollutants in poultry manure to the environment.

Kinetics of Butyrate, Acetate, and Hydrogen Metabolism in a Thermophilic, Anaerobic, Butyrate-Degrading Triculture

OpenAIRE

Ahring, Birgitte K.; Westermann, Peter

1987-01-01

Kinetics of butyrate, acetate, and hydrogen metabolism were determined with butyrate-limited, chemostat-grown tricultures of a thermophilic butyrate-utilizing bacterium together with Methanobacterium thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic rod. Kinetic parameters were determined from progress curves fitted to the integrated form of the Michaelis-Menten equation. The apparent half-saturation constants, Km, for butyrate, acetate, and dissolved hyd...

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

DEFF Research Database (Denmark)

Du, Bin; Zielinski, Daniel C.; Kavvas, Erol S.

2016-01-01

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......Background: 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....... 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...

Steady-state cerebral glucose concentrations and transport in the human brain

OpenAIRE

Gruetter, R.; Ugurbil, K.; Seaquist, E. R.

1998-01-01

Understanding the mechanism of brain glucose transport across the blood- brain barrier is of importance to understanding brain energy metabolism. The specific kinetics of glucose transport nave been generally described using standard Michaelis-Menten kinetics. These models predict that the steady- state glucose concentration approaches an upper limit in the human brain when the plasma glucose level is well above the Michaelis-Menten constant for half-maximal transport, K(t). In experiments wh...

More Nuts and Bolts of Michaelis-Menten Enzyme Kinetics

Science.gov (United States)

Lechner, Joseph H.

2011-01-01

Several additions to a classroom activity are proposed in which an "enzyme" (the student) converts "substrates" (nut-bolt assemblies) into "products" (separated nuts and bolts) by unscrewing them. (Contains 1 table.)

Communication: Limitations of the stochastic quasi-steady-state approximation in open biochemical reaction networks

Science.gov (United States)

Thomas, Philipp; Straube, Arthur V.; Grima, Ramon

2011-11-01

It is commonly believed that, whenever timescale separation holds, the predictions of reduced chemical master equations obtained using the stochastic quasi-steady-state approximation are in very good agreement with the predictions of the full master equations. We use the linear noise approximation to obtain a simple formula for the relative error between the predictions of the two master equations for the Michaelis-Menten reaction with substrate input. The reduced approach is predicted to overestimate the variance of the substrate concentration fluctuations by as much as 30%. The theoretical results are validated by stochastic simulations using experimental parameter values for enzymes involved in proteolysis, gluconeogenesis, and fermentation.

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

Directory of Open Access Journals (Sweden)

Oldiges Marco

2009-01-01

Full Text Available Abstract Background To understand the dynamic behavior of cellular systems, mathematical modeling is often necessary and comprises three steps: (1 experimental measurement of participating molecules, (2 assignment of rate laws to each reaction, and (3 parameter calibration with respect to the measurements. In each of these steps the modeler is confronted with a plethora of alternative approaches, e. g., the selection of approximative rate laws in step two as specific equations are often unknown, or the choice of an estimation procedure with its specific settings in step three. This overall process with its numerous choices and the mutual influence between them makes it hard to single out the best modeling approach for a given problem. Results We investigate the modeling process using multiple kinetic equations together with various parameter optimization methods for a well-characterized example network, the biosynthesis of valine and leucine in C. glutamicum. For this purpose, we derive seven dynamic models based on generalized mass action, Michaelis-Menten and convenience kinetics as well as the stochastic Langevin equation. In addition, we introduce two modeling approaches for feedback inhibition to the mass action kinetics. The parameters of each model are estimated using eight optimization strategies. To determine the most promising modeling approaches together with the best optimization algorithms, we carry out a two-step benchmark: (1 coarse-grained comparison of the algorithms on all models and (2 fine-grained tuning of the best optimization algorithms and models. To analyze the space of the best parameters found for each model, we apply clustering, variance, and correlation analysis. Conclusion A mixed model based on the convenience rate law and the Michaelis-Menten equation, in which all reactions are assumed to be reversible, is the most suitable deterministic modeling approach followed by a reversible generalized mass action kinetics

An Inverse Michaelis–Menten Approach for Interfacial Enzyme Kinetics

DEFF Research Database (Denmark)

Kari, Jeppe; Andersen, Morten; Borch, Kim

2017-01-01

Interfacial enzyme reactions are ubiquitous both in vivo and in technical applications, but analysis of their kinetics remains controversial. In particular, it is unclear whether conventional Michaelis–Menten theory, which requires a large excess of substrate, can be applied. Here, an extensive...... experimental study of the enzymatic hydrolysis of insoluble cellulose indeed showed that the conventional approach had a limited applicability. Instead we argue that, unlike bulk reactions, interfacial enzyme catalysis may reach a steady-state condition in the opposite experimental limit, where...... for kinetic analyses of interfacial enzyme reactions and that its analogy to established theory provides a bridge to the accumulated understanding of steady-state enzyme kinetics. Finally, we show that the ratio of parameters from conventional and inverted Michaelis–Menten analysis reveals the density...

Concentration-dependent interactions of the organophosphates chlorpyrifos oxon and methyl paraoxon with human recombinant acetylcholinesterase

International Nuclear Information System (INIS)

Kaushik, R.; Rosenfeld, Clint A.; Sultatos, L.G.

2007-01-01

For many decades it has been thought that oxygen analogs (oxons) of organophosphorus insecticides phosphorylate the catalytic site of acetylcholinesterase by a mechanism that follows simple Michaelis-Menten kinetics. More recently, the interactions of at least some oxons have been shown to be far more complex and likely involve binding of oxons to a second site on acetylcholinesterase that modulates the inhibitory capacity of other oxon molecules at the catalytic site. The current study has investigated the interactions of chlorpyrifos oxon and methyl paraoxon with human recombinant acetylcholinesterase. Both chlorpyrifos oxon and methyl paraoxon were found to have k i 's that change as a function of oxon concentration. Furthermore, 10 nM chlorpyrifos oxon resulted in a transient increase in acetylthiocholine hydrolysis, followed by inhibition. Moreover, in the presence of 100 nM chlorpyrifos oxon, acetylthiocholine was found to influence both the K d (binding affinity) and k 2 (phosphorylation constant) of this oxon. Collectively, these results demonstrate that the interactions of chlorpyrifos oxon and methyl paraoxon with acetylcholinesterase cannot be described by simple Michaelis-Menten kinetics but instead support the hypothesis that these oxons bind to a secondary site on acetylcholinesterase, leading to activation/inhibition of the catalytic site, depending on the nature of the substrate and inhibitor. Additionally, these data raise questions regarding the adequacy of estimating risk of low levels of insecticide exposure from direct extrapolation of insecticide dose-response curves since the capacity of individual oxon molecules at low oxon levels could be greater than individual oxon molecules in vivo associated with the dose-response curve

At the centennial of Michaelis and Menten, competing Michaelis-Menten steps explain effect of GLP-1 on blood-brain transfer and metabolism of glucose

DEFF Research Database (Denmark)

Jensen, Michael Gejl; Rungby, Jørgen; Brock, Birgitte

2014-01-01

Glucagon-like peptide-1 (GLP-1) is a potent insulinotropic incretin hormone with pancreatic and extrapancreatic effects. Studies reveal significant effects in regions of brain tissue that regulate appetite and satiety. The effects cause that mimetics of GLP-1 serves as treatment of type 2 diabete...

Wave equation of a nonlinear triatomic molecule and the adiabatic correction to the Born--Oppenheimer approximation

International Nuclear Information System (INIS)

Bardo, R.D.; Wolfsberg, M.

1977-01-01

The wave equation for a nonlinear polyatomic molecule is formulated in molecule-fixed coordinates by a method originally due to Hirschfelder and Wigner. Application is made to a triatomic molecule, and the wave equation is explicitly presented in a useful molecule-fixed coordinate system. The formula for the adiabatic correction to the Born--Oppenheimer approximation for a triatomic molecule is obtained. The extension of the present formulation to larger polyatomic molecules is pointed out. Some terms in the triatomic molecule wave equation are discussed in detail

A kinetic model and simulation of starch saccharification and simultaneous ethanol fermentation by amyloglucosidase and Zymomonas mobilis

Energy Technology Data Exchange (ETDEWEB)

Lee, C G [Michigan Univ., Ann Arbor, MI (United States). Dept. of Chemical Engineering; Kim, C H; Rhee, S K [Korea Inst. of Science and Technology, Taejon (Korea, Republic of). Genetic Engineering Research Inst.

1992-07-01

A mathematical model is described for the simultaneous saccharification and ethanol fermentation (SSF) of sago starch using amyloglycosidase (AMG) and Zymomonas mobilis. By introducing the degree of polymerization (DP) of oligosaccharides produced from sago starch treated with {alpha}-amylase, a series of Michaelis-Menten equations was obtained. After determining kinetic parameters from the results of simple experiments and from the subsite mapping theory, this model was adapted to simulate the SSF process. The results of simulation for SSF are in good agreement with experimental results. (orig.).

Michaelis' hundred Questions and the Royal Instructions

DEFF Research Database (Denmark)

Friis, Ib

2017-01-01

Michaelis' 100 questions for the expedition is a remarkable document. It provides insight into the sources and methods of biblical research anno 1762, at the same time as highlighting the challenges the members of the expedition faced. As the scholarly foundation of the expedition, the questions ...

Michaelis' Hundred Questions and the Royal Instruction

DEFF Research Database (Denmark)

Friis, Ib

2015-01-01

Michaelis' 100 questions for the expedition is a remarkable document. It provides insight into the sources and methods of biblical research anno 1762, at the same time as highlighting the challenges the members of the expedition faced. As the scholarly foundation of the expedition, the questions ...

Optimization of enzyme parameters for fermentative production of biorenewable fuels and chemicals

Directory of Open Access Journals (Sweden)

Ping Liu

2012-10-01

Full Text Available Microbial biocatalysts such as Escherichia coli and Saccharomyces cerevisiae have been extensively subjected to Metabolic Engineering for the fermentative production of biorenewable fuels and chemicals. This often entails the introduction of new enzymes, deletion of unwanted enzymes and efforts to fine-tune enzyme abundance in order to attain the desired strain performance. Enzyme performance can be quantitatively described in terms of the Michaelis-Menten type parameters Km, turnover number kcat and Ki, which roughly describe the affinity of an enzyme for its substrate, the speed of a reaction and the enzyme sensitivity to inhibition by regulatory molecules. Here we describe examples of where knowledge of these parameters have been used to select, evolve or engineer enzymes for the desired performance and enabled increased production of biorenewable fuels and chemicals. Examples include production of ethanol, isobutanol, 1-butanol and tyrosine and furfural tolerance. The Michaelis-Menten parameters can also be used to judge the cofactor dependence of enzymes and quantify their preference for NADH or NADPH. Similarly, enzymes can be selected, evolved or engineered for the preferred cofactor preference. Examples of exporter engineering and selection are also discussed in the context of production of malate, valine and limonene.

A novel H(2)O(2) amperometric biosensor based on gold nanoparticles/self-doped polyaniline nanofibers.

Science.gov (United States)

Chen, Xiaojun; Chen, Zixuan; Zhu, Jinwei; Xu, Chenbin; Yan, Wei; Yao, Cheng

2011-10-01

A new kind of gold nanoparticles/self-doped polyaniline nanofibers (Au/SPAN) with grooves has been prepared for the immobilization of horseradish peroxidase (HRP) on the surface of glassy carbon electrode (GCE). The ratio of gold in the composite nanofibers was up to 64%, which could promote the conductivity and biocompatibility of SPAN and increase the immobilized amount of HRP molecules greatly. The electrode exhibits enhanced electrocatalytic activity in the reduction of H(2)O(2) in the presence of the mediator hydroquinone (HQ). The effects of concentration of HQ, solution pH and the working potential on the current response of the modified electrode toward H(2)O(2) were optimized to obtain the maximal sensitivity. The proposed biosensor exhibited a good linear response in the range from 10 to 2000 μM with a detection limit of 1.6 μM (S/N=3) under the optimum conditions. The response showed Michaelis-Menten behavior at larger H(2)O(2) concentrations, and the apparent Michaelis-Menten constant K(m) was estimated to be 2.21 mM. The detection of H(2)O(2) concentration in real sample showed acceptable accuracy with the traditional potassium permanganate titration. Copyright © 2011 Elsevier B.V. All rights reserved.

OPTIMIZATION OF ENZYME PARAMETERS FOR FERMENTATIVE PRODUCTION OF BIORENEWABLE FUELS AND CHEMICALS

Directory of Open Access Journals (Sweden)

Laura R. Jarboe

2012-10-01

Full Text Available Microbial biocatalysts such as Escherichia coli and Saccharomyces cerevisiae have been extensively subjected to Metabolic Engineering for the fermentative production of biorenewable fuels and chemicals. This often entails the introduction of new enzymes, deletion of unwanted enzymes and efforts to fine-tune enzyme abundance in order to attain the desired strain performance. Enzyme performance can be quantitatively described in terms of the Michaelis-Menten type parameters Km, turnover number kcat and Ki, which roughly describe the affinity of an enzyme for its substrate, the speed of a reaction and the enzyme sensitivity to inhibition by regulatory molecules. Here we describe examples of where knowledge of these parameters have been used to select, evolve or engineer enzymes for the desired performance and enabled increased production of biorenewable fuels and chemicals. Examples include production of ethanol, isobutanol, 1-butanol and tyrosine and furfural tolerance. The Michaelis-Menten parameters can also be used to judge the cofactor dependence of enzymes and quantify their preference for NADH or NADPH. Similarly, enzymes can be selected, evolved or engineered for the preferred cofactor preference. Examples of exporter engineering and selection are also discussed in the context of production of malate, valine and limonene.

Phosphotyrosine as a substrate of acid and alkaline phosphatases.

Science.gov (United States)

Apostoł, I; Kuciel, R; Wasylewska, E; Ostrowski, W S

1985-01-01

A new spectrophotometric method for following dephosphorylation of phosphotyrosine has been described. The absorption spectra of phosphotyrosine and tyrosine were plotted over the pH range from 3 to 9. The change in absorbance accompanying the conversion of phosphotyrosine to tyrosine was the greatest at 286 nm. The difference absorption coefficients were calculated for several pH values. Dephosphorylation of phosphotyrosine by acid phosphatases from human prostate gland, from wheat germ and potatoes obeys the Michaelis-Menten equation, whereas alkaline phosphatases calf intestine and E. coli are inhibited by excess of substrate.

Enzyme activity and kinetics in substrate-amended river sediments

Energy Technology Data Exchange (ETDEWEB)

Duddridge, J E; Wainwright, M

1982-01-01

In determining the effects of heavy metals in microbial activity and litter degradation in river sediments, one approach is to determine the effects of these pollutants on sediment enzyme activity and synthesis. Methods to assay amylase, cellulase and urease activity in diverse river sediments are reported. Enzyme activity was low in non-amended sediments, but increased markedly when the appropriate substrate was added, paralleling both athropogenic and natural amendment. Linear relationships between enzyme activity, length of incubation, sample size and substrate concentration were established. Sediment enzyme activity generally obeyed Michaelis-Menton kinetics, but of the three enzymes, urease gave least significant correlation coefficients when the data for substrate concentration versus activity was applied to the Eadie-Hofstee transformation of the Michaelis-Menten equation. K/sub m/ and V/sub max/ for amylase, cellulase and urease in sediments are reported. (JMT)

Characterization of lipase in reversed micelles formulated by Cibacron Blue F-3GA modified Span 85

DEFF Research Database (Denmark)

Zhang, Dong Hao; Guo, Zheng; Sun, Yan

2007-01-01

Sorbitan trioleate (Span 85) modified by Cibacron Blue F-3GA (CB) was prepared and used as an affinity surfactant to formulate a reversed micellar system for Candida rugosa lipase (CRL) solubilization. The system was characterized and evaluated by employing CRL-catalyzed hydrolysis of olive oil...... of the encapsulated lipase remained unchanged, but the apparent activity was significantly higher than that of the native enzyme in bulk solution. Kinetic studies indicated that the encapsulated lipase in the reversed micelles of CB-formulated Span 85 followed the Michaelis-Menten equation. The Michaelis constant...... was found to decrease with increasing surfactant concentration, suggesting an increase of the enzyme affinity for the substrate. Stability of the lipase in the reversed micelles was negatively correlated to W0. Introduction Reversed micelles are nanometer-scale transparent aggregates of water and surfactant...

Determining "small parameters" for quasi-steady state

Science.gov (United States)

Goeke, Alexandra; Walcher, Sebastian; Zerz, Eva

2015-08-01

For a parameter-dependent system of ordinary differential equations we present a systematic approach to the determination of parameter values near which singular perturbation scenarios (in the sense of Tikhonov and Fenichel) arise. We call these special values Tikhonov-Fenichel parameter values. The principal application we intend is to equations that describe chemical reactions, in the context of quasi-steady state (or partial equilibrium) settings. Such equations have rational (or even polynomial) right-hand side. We determine the structure of the set of Tikhonov-Fenichel parameter values as a semi-algebraic set, and present an algorithmic approach to their explicit determination, using Groebner bases. Examples and applications (which include the irreversible and reversible Michaelis-Menten systems) illustrate that the approach is rather easy to implement.

Exploring inductive linearization for pharmacokinetic-pharmacodynamic systems of nonlinear ordinary differential equations.

Science.gov (United States)

Hasegawa, Chihiro; Duffull, Stephen B

2018-02-01

Pharmacokinetic-pharmacodynamic systems are often expressed with nonlinear ordinary differential equations (ODEs). While there are numerous methods to solve such ODEs these methods generally rely on time-stepping solutions (e.g. Runge-Kutta) which need to be matched to the characteristics of the problem at hand. The primary aim of this study was to explore the performance of an inductive approximation which iteratively converts nonlinear ODEs to linear time-varying systems which can then be solved algebraically or numerically. The inductive approximation is applied to three examples, a simple nonlinear pharmacokinetic model with Michaelis-Menten elimination (E1), an integrated glucose-insulin model and an HIV viral load model with recursive feedback systems (E2 and E3, respectively). The secondary aim of this study was to explore the potential advantages of analytically solving linearized ODEs with two examples, again E3 with stiff differential equations and a turnover model of luteinizing hormone with a surge function (E4). The inductive linearization coupled with a matrix exponential solution provided accurate predictions for all examples with comparable solution time to the matched time-stepping solutions for nonlinear ODEs. The time-stepping solutions however did not perform well for E4, particularly when the surge was approximated by a square wave. In circumstances when either a linear ODE is particularly desirable or the uncertainty in matching the integrator to the ODE system is of potential risk, then the inductive approximation method coupled with an analytical integration method would be an appropriate alternative.

Synthetic, structural mimetics of the β-hairpin flap of HIV-1 protease inhibit enzyme function.

Science.gov (United States)

Chauhan, Jay; Chen, Shen-En; Fenstermacher, Katherine J; Naser-Tavakolian, Aurash; Reingewertz, Tali; Salmo, Rosene; Lee, Christian; Williams, Emori; Raje, Mithun; Sundberg, Eric; DeStefano, Jeffrey J; Freire, Ernesto; Fletcher, Steven

2015-11-01

Small-molecule mimetics of the β-hairpin flap of HIV-1 protease (HIV-1 PR) were designed based on a 1,4-benzodiazepine scaffold as a strategy to interfere with the flap-flap protein-protein interaction, which functions as a gated mechanism to control access to the active site. Michaelis-Menten kinetics suggested our small-molecules are competitive inhibitors, which indicates the mode of inhibition is through binding the active site or sterically blocking access to the active site and preventing flap closure, as designed. More generally, a new bioactive scaffold for HIV-1PR inhibition has been discovered, with the most potent compound inhibiting the protease with a modest K(i) of 11 μM. Copyright © 2015 Elsevier Ltd. All rights reserved.

Solvent 1H/2H isotopic effects in the reaction of the L-Tyrosine oxidation catalyzed by Tyrosinase

International Nuclear Information System (INIS)

Kozlowska, M.; Kanska, M.

2006-01-01

Tyrosinase is well known catalyst in the oxidation of L-Tyrosine to L-DOPA and following oxidation of L-DOPA to dopachinone. The aim of communication is to present the results of studies on the solvent isotopic effects (SIE) in the above reactions for the 1 H/ 2 H in the 3',5' and 2',6' substituted tyrosine. Obtained dependence of the reaction rate on the substrate concentration were applied for optimization of the kinetic parameters, k cat and k cat /K m , in the Michaelis-Menten equation. As a result - better understanding of the L-DOPA creation can be achieved

Kinetics of alcoholic fermentation during the culturing of bakers' yeast

Energy Technology Data Exchange (ETDEWEB)

Franz, B

1961-01-01

A synthesis was made of the effects of various factors on the rate of fermentation by Saccharomyces cerevisiae. The rate obeyed the Michaelis-Menten equation, was independent of the concentration of yeast, was maximal at 20/sup 0/ (0.61 ml ethanol/g dry yeast/h), was not significantly affected between pH 6.5 and 3.0 but declined at 3.0, was inhibited by ethanol at a rate proportional to the concentration squared (at ethanol = 12 volume %, the fermentation rate was practically zero), and was enhanced by the addition of phosphorus when a P-poor yeast was employed.

Solution of non-steady-state substrate concentration in the action of biosensor response at mixed enzyme kinetics

Science.gov (United States)

Senthamarai, R.; Jana Ranjani, R.

2018-04-01

In this paper, a mathematical model of an amperometric biosensor at mixed enzyme kinetics and diffusion limitation in the case of substrate inhibition has been developed. The model is based on time dependent reaction diffusion equation containing a non -linear term related to non -Michaelis - Menten kinetics of the enzymatic reaction. Solution for the concentration of the substrate has been derived for all values of parameters using the homotopy perturbation method. All the approximate analytic expressions of substrate concentration are compared with simulation results using Scilab/Matlab program. Finally, we have given a satisfactory agreement between them.

Una carta de doña Carolina Michaelis

Directory of Open Access Journals (Sweden)

José Fradejas Lebrero

2003-06-01

Full Text Available Uno de los tres filólogos o críticos literarios más importantes de la Literatura peninsular del siglo XX es doña Carolina Michaelis de Vasconcellos. Cuando se crea la Gesellschaf für Romanische Literatur (1902, los tres van juntos: el socio num. 4 es don Marcelino Menendez Pelayo, el num. 5 don Ramón Menendez Pidal y el num. 6 doña Carolina Michaelis y conste que era más vieja, pues había nacido en 1851 y aún no era doctora, lo sería en Friburgo en 1904, con una obra monumental y maestra: la edición y estudio del Cancionero de Ajuda. Había ya colaborado en el Homenaje a Menendez Pelayo (1899, con quien se carteaba de cuando en cuando y en 1903 proporcionó el texto más interesante de la Leyenda del abad don Juan de Montemayor a don Ramón Menendez Pidal…

Crude Aloe vera Gel Shows Antioxidant Propensities and Inhibits Pancreatic Lipase and Glucose Movement In Vitro

Science.gov (United States)

Taukoorah, Urmeela; Mahomoodally, M. Fawzi

2016-01-01

Aloe vera gel (AVG) is traditionally used in the management of diabetes, obesity, and infectious diseases. The present study aimed to investigate the inhibitory potential of AVG against α-amylase, α-glucosidase, and pancreatic lipase activity in vitro. Enzyme kinetic studies using Michaelis-Menten (K m) and Lineweaver-Burk equations were used to establish the type of inhibition. The antioxidant capacity of AVG was evaluated for its ferric reducing power, 2-diphenyl-2-picrylhydrazyl hydrate scavenging ability, nitric oxide scavenging power, and xanthine oxidase inhibitory activity. The glucose entrapment ability, antimicrobial activity, and total phenolic, flavonoid, tannin, and anthocyanin content were also determined. AVG showed a significantly higher percentage inhibition (85.56 ± 0.91) of pancreatic lipase compared to Orlistat. AVG was found to increase the Michaelis-Menten constant and decreased the maximal velocity (V max) of lipase, indicating mixed inhibition. AVG considerably inhibits glucose movement across dialysis tubes and was comparable to Arabic gum. AVG was ineffective against the tested microorganisms. Total phenolic and flavonoid contents were 66.06 ± 1.14 (GAE)/mg and 60.95 ± 0.97 (RE)/mg, respectively. AVG also showed interesting antioxidant properties. The biological activity observed in this study tends to validate some of the traditional claims of AVG as a functional food. PMID:26880905

Generic Schemes for Single-Molecule Kinetics. 3: Self-Consistent Pathway Solutions for Nonrenewal Processes.

Science.gov (United States)

Piephoff, D Evan; Cao, Jianshu

2018-04-23

We recently developed a pathway analysis framework (paper 1) for describing single-molecule kinetics for renewal (i.e., memoryless) processes based on the decomposition of a kinetic scheme into generic structures. In our approach, waiting time distribution functions corresponding to such structures are expressed in terms of self-consistent pathway solutions and concatenated to form measurable probability distribution functions (PDFs), affording a simple way to decompose and recombine a network. Here, we extend this framework to nonrenewal processes, which involve correlations between events, and employ it to formulate waiting time PDFs, including the first-passage time PDF, for a general kinetic network model. Our technique does not require the assumption of Poissonian kinetics, permitting a more general kinetic description than the usual rate approach, with minimal topological restrictiveness. To demonstrate the usefulness of this technique, we provide explicit calculations for our general model, which we adapt to two generic schemes for single-enzyme turnover with conformational interconversion. For each generic scheme, wherein the intermediate state(s) need not undergo Poissonian decay, the functional dependence of the mean first-passage time on the concentration of an external substrate is analyzed. When conformational detailed balance is satisfied, the enzyme turnover rate (related to the mean first-passage time) reduces to the celebrated Michaelis-Menten functional form, consistent with our previous work involving a similar scheme with all rate processes, thereby establishing further generality to this intriguing result. Our framework affords a general and intuitive approach for evaluating measurable waiting time PDFs and their moments, making it a potentially useful kinetic tool for a wide variety of single-molecule processes.

Diatomite Modified Immobilized Delftia sp. for the Bio-Abiotic Removal of Antibiotics Amoxicillin in the Aqueous System

Science.gov (United States)

Gao, Lijuan; Sun, Jing; Guan, Kai; Shen, Tingting; Wang, Xikui

2017-05-01

Diatomite modified sodium alginate (Si/SA) immobilized Delftia sp. A2(2011) (STT01) was applied to degrade amoxicillin. The immobilized pellets provided a direct and visual probe for the degradation process due to their intrinsic bright colour. The results demonstrated that 100% of amoxicillin and 68.5% of CODcr removal were achieved after 72 h, comparing with the cases of sodium alginate (SA) system (81.2%, 46.9%) and the free cells system (60.5%, 35.5%). The degradation kinetics was in good agreement with Michaelis-Menten equation. The maximum rate (Vm ) and Michaelis constant (Km ) were calculated as 9.09 mg L-1 h-1 and 228 mg L-1, respectively. The results further revealed that diatomite not only acted as immobilization support to improve the mechanical strength and lifetime of the pellets but also as absorbent to promote the treatment efficiency. Therefore, both enzymatic catalysis and chemisorption were responsible for the removal of amoxicillin.

Quantitative Evaluation of the Mechanism Underlying the Biotransportation of the Active Ingredients in Puerariae lobatae Radix and Chuanxiong rhizoma.

Science.gov (United States)

Liang, Xin-Li; Zhang, Jing; Liao, Zheng-Gen; Zhao, Guo-Wei; Luo, Yun; Li, Zhe; Satterlee, Andrew

2015-06-15

The objective of this study was to establish a quantitative method to evaluate the biotransportation of a drug across the cell membrane. Through the application of the law of mass conservation, the drug transportation rate was calculated based on Fick's law of passive diffusion and the Michaelis-Menten equation. The overall membrane-transportation rate was the sum of the passive diffusion rate and the carrier-mediated diffusion rate, which were calculated as the transportation mass divided by the respective rate. The active ingredients of Puerariae lobatae Radix and Chuanxiong rhizoma, namely, puerarin and ferulic acid, respectively, were used as two model drugs. The transportation rates of puerarin and ferulic acid were obtained by fitting a model that includes both Fick's law of diffusion and the Michaelis-Menten equation. Compared with the overall transportation, the carrier-mediated transport and passive diffusion of 1.59 mmol/L puerarin were -35.07% and 64.93%, respectively, whereas the respective transportation modes of 0.1 mmol/L ferulic acid were -35.40% and 64.60%, respectively. Verapamil and MK-571 increased the overall transport rate and ratio, and MK-571 treatment changed the carrier-mediated transport from negative to positive. However, the transport rate and ratio of ferulic acid did not change significantly. The cell transportation mechanisms of puerarin and ferulic acid primarily involve simple passive diffusion and carrier-mediated transportation. Moreover, P-glycoprotein and multidrug resistance-associated protein efflux proteins, and other transportation proteins were found to be involved in the transportation of puerarin. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

application of ascorbic acid 2-phosphate as a new voltammetric

African Journals Online (AJOL)

a

acid 2-phosphate (AAP) as a new voltammetric substrate has been described in this paper. In the alkaline buffer .... ALP labeled goat anti-rabbit ..... Classical Michaelis-Menten kinetic experiments were carried out to measure the maximum.

Study on kinetics of glucose uptake by some species of plankton

Science.gov (United States)

Li, Wenquan; Wang, Xian; Zhang, Yaohua

1993-03-01

The rates of glucose uptake by some species of plankton were determined by3H-glucose tracer method. Experimental results indicated that the observed glucose uptake at natural seawater concentrations by Platymonas subcordiformis and Brachionus plicatilis was principally a metabolic process fitted with the Michaelis-Menten equation in the range of adaptive temperatures. Heterotrophic uptake by Platymonas subcordiformis was mainly dependent on diffusion at high glucose levels. The uptake by Brachionus plicatilis showed active transport even at high glucose levels, indicating its high heterotrophic activity. The uptake rate by Artemia salina was lower, and its V m/K ratio was lower than those of the other two species of plankton.

Redox-dependent substrate-cofactor interactions in the Michaelis-complex of a flavin-dependent oxidoreductase

Science.gov (United States)

Werther, Tobias; Wahlefeld, Stefan; Salewski, Johannes; Kuhlmann, Uwe; Zebger, Ingo; Hildebrandt, Peter; Dobbek, Holger

2017-07-01

How an enzyme activates its substrate for turnover is fundamental for catalysis but incompletely understood on a structural level. With redox enzymes one typically analyses structures of enzyme-substrate complexes in the unreactive oxidation state of the cofactor, assuming that the interaction between enzyme and substrate is independent of the cofactors oxidation state. Here, we investigate the Michaelis complex of the flavoenzyme xenobiotic reductase A with the reactive reduced cofactor bound to its substrates by X-ray crystallography and resonance Raman spectroscopy and compare it to the non-reactive oxidized Michaelis complex mimics. We find that substrates bind in different orientations to the oxidized and reduced flavin, in both cases flattening its structure. But only authentic Michaelis complexes display an unexpected rich vibrational band pattern uncovering a strong donor-acceptor complex between reduced flavin and substrate. This interaction likely activates the catalytic ground state of the reduced flavin, accelerating the reaction within a compressed cofactor-substrate complex.

Mixed Quantum/Classical Theory for Molecule-Molecule Inelastic Scattering: Derivations of Equations and Application to N2 + H2 System.

Science.gov (United States)

Semenov, Alexander; Babikov, Dmitri

2015-12-17

The mixed quantum classical theory, MQCT, for inelastic scattering of two molecules is developed, in which the internal (rotational, vibrational) motion of both collision partners is treated with quantum mechanics, and the molecule-molecule scattering (translational motion) is described by classical trajectories. The resultant MQCT formalism includes a system of coupled differential equations for quantum probability amplitudes, and the classical equations of motion in the mean-field potential. Numerical tests of this theory are carried out for several most important rotational state-to-state transitions in the N2 + H2 system, in a broad range of collision energies. Besides scattering resonances (at low collision energies) excellent agreement with full-quantum results is obtained, including the excitation thresholds, the maxima of cross sections, and even some smaller features, such as slight oscillations of energy dependencies. Most importantly, at higher energies the results of MQCT are nearly identical to the full quantum results, which makes this approach a good alternative to the full-quantum calculations that become computationally expensive at higher collision energies and for heavier collision partners. Extensions of this theory to include vibrational transitions or general asymmetric-top rotor (polyatomic) molecules are relatively straightforward.

Kinetics and mechanism of oxidation of aliphatic alcohols by ...

Indian Academy of Sciences (India)

TBATB) in aqueous acetic acid leads to the formation of the corresponding aldehydes. The reaction is first order with respect to TBATB. Michaelis-Menten type kinetics is observed with respect to alcohols. The reaction failed to induce the ...

Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation.

Directory of Open Access Journals (Sweden)

Andrea Ciliberto

2007-03-01

Full Text Available In metabolic networks, metabolites are usually present in great excess over the enzymes that catalyze their interconversion, and describing the rates of these reactions by using the Michaelis-Menten rate law is perfectly valid. This rate law assumes that the concentration of enzyme-substrate complex (C is much less than the free substrate concentration (S0. However, in protein interaction networks, the enzymes and substrates are all proteins in comparable concentrations, and neglecting C with respect to S0 is not valid. Borghans, DeBoer, and Segel developed an alternative description of enzyme kinetics that is valid when C is comparable to S0. We extend this description, which Borghans et al. call the total quasi-steady state approximation, to networks of coupled enzymatic reactions. First, we analyze an isolated Goldbeter-Koshland switch when enzymes and substrates are present in comparable concentrations. Then, on the basis of a real example of the molecular network governing cell cycle progression, we couple two and three Goldbeter-Koshland switches together to study the effects of feedback in networks of protein kinases and phosphatases. Our analysis shows that the total quasi-steady state approximation provides an excellent kinetic formalism for protein interaction networks, because (1 it unveils the modular structure of the enzymatic reactions, (2 it suggests a simple algorithm to formulate correct kinetic equations, and (3 contrary to classical Michaelis-Menten kinetics, it succeeds in faithfully reproducing the dynamics of the network both qualitatively and quantitatively.

Cyclodextrin Aldehydes are Oxidase Mimics

DEFF Research Database (Denmark)

Fenger, Thomas Hauch; Bjerre, Jeannette; Bols, Mikael

2009-01-01

Cyclodextrins containing 6-aldehyde groups were found to catalyse oxidation of aminophenols in the presence of hydrogen peroxide. The catalysis followed Michaelis-Menten kinetics and is related to the catalysis previously observed with cyclodextrin ketones. A range of different cyclodextrin aldeh...

Toward a muon-specific electronic structure theory: effective electronic Hartree-Fock equations for muonic molecules.

Science.gov (United States)

Rayka, Milad; Goli, Mohammad; Shahbazian, Shant

2018-02-07

An effective set of Hartree-Fock (HF) equations are derived for electrons of muonic systems, i.e., molecules containing a positively charged muon, conceiving the muon as a quantum oscillator, which are completely equivalent to the usual two-component HF equations used to derive stationary states of the muonic molecules. In these effective equations, a non-Coulombic potential is added to the orthodox coulomb and exchange potential energy terms, which describes the interaction of the muon and the electrons effectively and is optimized during the self-consistent field cycles. While in the two-component HF equations a muon is treated as a quantum particle, in the effective HF equations it is absorbed into the effective potential and practically transformed into an effective potential field experienced by electrons. The explicit form of the effective potential depends on the nature of muon's vibrations and is derivable from the basis set used to expand the muonic spatial orbital. The resulting effective Hartree-Fock equations are implemented computationally and used successfully, as a proof of concept, in a series of muonic molecules containing all atoms from the second and third rows of the Periodic Table. To solve the algebraic version of the equations muon-specific Gaussian basis sets are designed for both muon and surrounding electrons and it is demonstrated that the optimized exponents are quite distinct from those derived for the hydrogen isotopes. The developed effective HF theory is quite general and in principle can be used for any muonic system while it is the starting point for a general effective electronic structure theory that incorporates various types of quantum correlations into the muonic systems beyond the HF equations.

Stability in a diffusive food chain model with Michaelis-Menten functional response

DEFF Research Database (Denmark)

Lin, Zhigui; Pedersen, Michael

2004-01-01

This paper deals with the behavior of positive solutions to a reaction-diffusion system with homogeneous Neumann boundary conditions describing a three species food chain. A sufficient condition for the local asymptotical stability is given by linearization and also a sufficient condition...... for the global asymptotical stability is given by a Lyapunov function. Our result shows that the equilibrium solution is globally asymptotically stable if the net birth rate of the first species is big enough and the net death rate of the third species is neither too big nor too small. (C) 2004 Elsevier Ltd. All...

MODELING OF MIXED CHEMOSTAT CULTURES OF AN AEROBIC BACTERIUM, COMAMONAS-TESTOSTERONI, AND AN ANAEROBIC BACTERIUM, VEILLONELLA-ALCALESCENS - COMPARISON WITH EXPERIMENTAL-DATA

NARCIS (Netherlands)

GERRITSE, J; SCHUT, F; GOTTSCHAL, JC

A mathematical model of mixed chemostat cultures of the obligately aerobic bacterium Comamonas testosteroni and the anaerobic bacterium Veillonella alcalescens grown under dual limitation Of L-lactate and oxygen was constructed. The model was based on Michaelis-Menten-type kinetics for the

Immobilization of urease on copper chelated EC-Tri beads and ...

African Journals Online (AJOL)

Maximum reaction rate (Vmax) and Michaelis-Menten constant (km) were determined for the free and immobilized enzymes. Various characteristics of immobilized urease such as the temperature activity curve, thermal stability, operational stability and storage stability were evaluated. The results demonstrated that triazole ...

Effective electronic-only Kohn–Sham equations for the muonic molecules

Science.gov (United States)

Rayka, Milad; Goli, Mohammad; Shahbazian, Shant

A set of effective electronic-only Kohn-Sham (EKS) equations are derived for the muonic molecules (containing a positively charged muon), which are completely equivalent to the coupled electronic-muonic Kohn-Sham equations derived previously within the framework of the Nuclear-Electronic Orbital density functional theory (NEO-DFT). The EKS equations contain effective non-coulombic external potentials depending on parameters describing muon vibration, which are optimized during the solution of the EKS equations making muon KS orbital reproducible. It is demonstrated that the EKS equations are derivable from a certain class of effective electronic Hamiltonians through applying the usual Hohenberg-Kohn theorems revealing a duality between the NEO-DFT and the effective electronic-only DFT methodologies. The EKS equations are computationally applied to a small set of muoniated organic radicals and it is demonstrated that a mean effective potential maybe derived for this class of muonic species while an electronic basis set is also designed for the muon. These computational ingredients are then applied to muoniated ferrocenyl radicals, which had been previously detected experimentally through adding muonium atom to ferrocene. In line with previous computational studies, from the six possible species the staggered conformer, where the muon is attached to the exo position of the cyclopentadienyl ring, is deduced to be the most stable ferrocenyl radical.

Effective electronic-only Kohn-Sham equations for the muonic molecules.

Science.gov (United States)

Rayka, Milad; Goli, Mohammad; Shahbazian, Shant

2018-03-28

A set of effective electronic-only Kohn-Sham (EKS) equations are derived for the muonic molecules (containing a positively charged muon), which are completely equivalent to the coupled electronic-muonic Kohn-Sham equations derived previously within the framework of the nuclear-electronic orbital density functional theory (NEO-DFT). The EKS equations contain effective non-coulombic external potentials depending on parameters describing the muon's vibration, which are optimized during the solution of the EKS equations making the muon's KS orbital reproducible. It is demonstrated that the EKS equations are derivable from a certain class of effective electronic Hamiltonians through applying the usual Hohenberg-Kohn theorems revealing a "duality" between the NEO-DFT and the effective electronic-only DFT methodologies. The EKS equations are computationally applied to a small set of muoniated organic radicals and it is demonstrated that a mean effective potential may be derived for this class of muonic species while an electronic basis set is also designed for the muon. These computational ingredients are then applied to muoniated ferrocenyl radicals, which had been previously detected experimentally through adding a muonium atom to ferrocene. In line with previous computational studies, from the six possible species, the staggered conformer, where the muon is attached to the exo position of the cyclopentadienyl ring, is deduced to be the most stable ferrocenyl radical.

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

Science.gov (United States)

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.

The effects of carbon nanotube addition and oxyfluorination on the glucose-sensing capabilities of glucose oxidase-coated carbon fiber electrodes

Energy Technology Data Exchange (ETDEWEB)

Im, Ji Sun; Yun, Jumi; Kim, Jong Gu [Department of Fine Chemical Engineering and Applied Chemistry, BK21-E2 M, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Bae, Tae-Sung [Department of Fine Chemical Engineering and Applied Chemistry, BK21-E2 M, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Korea Basic Science Institute (KBSI), Jeonju 561-756 (Korea, Republic of); Lee, Young-Seak, E-mail: youngslee@cnu.ac.kr [Department of Fine Chemical Engineering and Applied Chemistry, BK21-E2 M, Chungnam National University, Daejeon 305-764 (Korea, Republic of)

2012-01-15

Glucose-sensing electrodes were constructed from carbon fibers by electrospinning and heat treatment. By controlling the pore size, the specific surface area and pore volume of the electrospun carbon fibers were increased for efficient immobilization of the glucose oxidase. Carbon nanotubes were embedded as an electrically conductive additive to improve the electrical property of the porous carbon fibers. In addition, the surface of the porous carbon fibers was modified with hydrophilic functional groups by direct oxyfluorination to increase the affinity between the hydrophobic carbon surface and the hydrophilic glucose oxidase molecules. The porosity of the carbon fibers was improved significantly with approximately 28- and 35-fold increases in the specific surface area and pore volume, respectively. The number of chemical bonds between carbon and oxygen were increased with higher oxygen content during oxyfluorination based on the X-ray photoelectron spectroscopy results. Glucose sensing was carried out by current voltagram and amperometric methods. A high-performance glucose sensor was obtained with high sensitivity and rapid response time as a result of carbon nanotube addition, physical activation and surface modification. The mechanism of the highly sensitive prepared glucose sensor was modeled by an enzyme kinetics study using the Michaelis-Menten equation.

Michaelis' hundrede spørgsmål og Den Kongelige Instruks

DEFF Research Database (Denmark)

Friis, Ib

2017-01-01

Michaelis' Fragen med de 100 spørgsmål til rejseselskabet er et forunderligt dokument. Det giver et bredt indblik i bibelforkningens kilder og metoder anno 1762, og tegner samtidig klart de udfordringer, som de rejsende stod overfor. Som ekspeditionens videnskabelige fundament er Fragen afgørende...

Direct numerical solution of the Ornstein-Zernike integral equation and spatial distribution of water around hydrophobic molecules

Science.gov (United States)

Ikeguchi, Mitsunori; Doi, Junta

1995-09-01

The Ornstein-Zernike integral equation (OZ equation) has been used to evaluate the distribution function of solvents around solutes, but its numerical solution is difficult for molecules with a complicated shape. This paper proposes a numerical method to directly solve the OZ equation by introducing the 3D lattice. The method employs no approximation the reference interaction site model (RISM) equation employed. The method enables one to obtain the spatial distribution of spherical solvents around solutes with an arbitrary shape. Numerical accuracy is sufficient when the grid-spacing is less than 0.5 Å for solvent water. The spatial water distribution around a propane molecule is demonstrated as an example of a nonspherical hydrophobic molecule using iso-value surfaces. The water model proposed by Pratt and Chandler is used. The distribution agrees with the molecular dynamics simulation. The distribution increases offshore molecular concavities. The spatial distribution of water around 5α-cholest-2-ene (C27H46) is visualized using computer graphics techniques and a similar trend is observed.

Signaling Cascades: Consequences of Varying Substrate and Phosphatase Levels

DEFF Research Database (Denmark)

Feliu, Elisenda; Knudsen, Michael; Wiuf, Carsten Henrik

2012-01-01

We study signaling cascades with an arbitrary number of layers of one-site phosphorylation cycles. Such cascades are abundant in nature and integrated parts of many pathways. Based on the Michaelis-Menten model of enzyme kinetics and the law of mass-action, we derive explicit analytic expressions...

Cyclodextrin-based artificial oxidases with high rate accelerations and selectivity

DEFF Research Database (Denmark)

Zhou, You; Lindbäck, Emil Anders; Pedersen, Christian Marcus

2014-01-01

Three cyclodextrin derivatives with one to four 2-O-formylmethyl groups attached to the secondary rim were prepared and investigated as catalysts for the oxidation of aminophenols in buffered dilute hydrogen peroxide. The derivatives were found to be Michaelis-Menten catalysts and to give rate ac...

Purification and characterization of a chlorite dismutase from Pseudomonas chloritidismutans

NARCIS (Netherlands)

Mehboob, F.; Wolterink, A.F.W.M.; Vermeulen, A.J.; Jiang, B.; Hagedoorn, P.L.; Stams, A.J.M.; Kengen, S.W.M.

2009-01-01

The chlorite dismutase (Cld) of Pseudomonas chloritidismutans was purified from the periplasmic fraction in one step by hydroxyapatite chromatography. The enzyme has a molecular mass of 110 kDa and consists of four 31-kDa subunits. Enzyme catalysis followed Michaelis-Menten kinetics, with Vmax and

Modelling the extra and intracellular uptake and discharge of heavy metals in Fontinalis antipyretica transplanted along a heavy metal and pH contamination gradient

International Nuclear Information System (INIS)

Fernandez, J.A.; Vazquez, M.D.; Lopez, J.; Carballeira, A.

2006-01-01

Samples of the aquatic bryophyte Fontinalis antipyretica Hedw. were transplanted to different sites with the aim of characterizing the kinetics of the uptake and discharge of heavy metals in the extra and intracellular compartments. The accumulation of metals in extracellular compartments, characterized by an initial rapid accumulation, then a gradual slowing down over time, fitted perfectly to a Michaelis-Menten model. The discharge of metals from the same compartment followed an inverse linear model or an inverse Michaelis-Menten model, depending on the metal. In intracellular sites both uptake and discharge occurred more slowly and progressively, following a linear model. We also observed that the acidity of the environment greatly affected metal accumulation in extracellular sites, even when the metals were present at relatively high concentrations, whereas the uptake of metals within cells was much less affected by pH. - The kinetics of uptake and discharge of heavy metals, in different cellular locations, were studied in transplanted aquatic mosses

A path-independent integral for the characterization of solute concentration and flux at biofilm detachments

Science.gov (United States)

Moran, B.; Kulkarni, S.S.; Reeves, H.W.

2007-01-01

A path-independent (conservation) integral is developed for the characterization of solute concentration and flux in a biofilm in the vicinity of a detachment or other flux limiting boundary condition. Steady state conditions of solute diffusion are considered and biofilm kinetics are described by an uptake term which can be expressed in terms of a potential (Michaelis-Menten kinetics). An asymptotic solution for solute concentration at the tip of the detachment is obtained and shown to be analogous to that of antiplane crack problems in linear elasticity. It is shown that the amplitude of the asymptotic solution can be calculated by evaluating a path-independent integral. The special case of a semi-infinite detachment in an infinite strip is considered and the amplitude of the asymptotic field is related to the boundary conditions and problem parameters in closed form for zeroth and first order kinetics and numerically for Michaelis-Menten kinetics. ?? Springer Science+Business Media, Inc. 2007.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

The oxidation of eleven amino acids by tetrabutylammonium tribromide (TBATB) in aqueous acetic acid results in the formation of the corresponding carbonyl compounds and ammonia. The reaction is first order with respect to TBATB. Michaelis-Menten type kinetics is observed with some of the amino acids while others ...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Kinetics and mechanism of oxidation of formic and oxalic acids by quinolinium fluorochromate (QFC) have been studied in dimethylsulphoxide. The main product of oxidation is carbon dioxide. The reaction is first-order with respect to QFC. Michaelis-Menten type of kinetics were observed with respect to the reductants.

Elimination of intermediate species in multiscale stochastic reaction networks

DEFF Research Database (Denmark)

Cappelletti, Daniele; Wiuf, Carsten

2016-01-01

such as the substrate-enzyme complex in the Michaelis-Menten mechanism. Such species are virtually in all real-world networks, they are typically short-lived, degraded at a fast rate and hard to observe experimentally. We provide conditions under which the Markov process of a multiscale reaction network...

International Meeting on Cholinesterases (5th) Held in Madras, India on 24-28 September, 1994.

Science.gov (United States)

1994-09-01

found that hydrolysis of thioesters deviated from simple Michaelis-Menten model. Kinetics was triphasic , displaying complexities of both BuChE and ACHE...of recombinant human acetylcholinesterase (rHuAChE) produced by human embryonic kidney cell line (293) in a fixed-bed reactor (1) was investigated at

Picolinic acid promoted oxidative decarboxylation of ...

African Journals Online (AJOL)

The kinetics and mechanism of picolinic acid promoted reaction of phenylsulfinylacetic acid (PSAA) with Cr(VI) was carried out in aqueous acetonitrile medium under pseudo first order conditions. The reaction follows Michaelis-Menten type of kinetics with respect to PSAA. The catalytic activity by picolinic acid can be ...

In memory of Professor Leonor Michaelis in Nagoya: great contributions to biochemistry in Japan in the first half of the 20th century.

Science.gov (United States)

Nagatsu, Toshiharu Toshi

2013-09-02

Leonor Michaelis spent the years of 1922-1926 as Professor of Biochemistry of the Aichi Medical College (now Graduate School of Medicine, Nagoya University) in Nagoya, Japan. Michaelis succeeded in gathering many bright young biochemists from all over Japan into his laboratory, and made tremendous contributions to the promotion of biochemistry in Japan. Michaelis was invited to many places in Japan to present lectures over those years. Kunio Yagi, who was Professor of Biochemistry at Nagoya University in the second half of the 20th century, succeeded in crystallizing the "Michaelis" enzyme-substrate complex. Historically, Michelis has had an enormous impact on biochemistry in Japan. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Michaël Jackson, un people précurseur

OpenAIRE

Dubied, Annik; Gorin, Valérie

2009-01-01

En parcourant la presse people parue au moment du décès du King of Pop, on observe à quel point Michaël Jackson a été et restera un personnage people précurseur. La titraille, les photographies et la mise en page d'une série de magazines francophones et anglo-saxons présentent un certain nombre de particularités qui résonnent à l'unisson avec la définition du genre people.

A Qualitative Approach to Enzyme Inhibition

Science.gov (United States)

Waldrop, Grover L.

2009-01-01

Most general biochemistry textbooks present enzyme inhibition by showing how the basic Michaelis-Menten parameters K[subscript m] and V[subscript max] are affected mathematically by a particular type of inhibitor. This approach, while mathematically rigorous, does not lend itself to understanding how inhibition patterns are used to determine the…

Benefits of a clinical pharmacokinetic service in optimising ...

African Journals Online (AJOL)

before the termination of the study (test period). Patients kept a seizure diary throughout the study. The MichaelisMenten model was used to calculate doses and predict steady-state serum concentrations. Setting. ine epilepsy clinics. Subjects. One hundred and ninety-five (113 black and 82 coloured) compliant people with ...

Use of Mushroom Tyrosinase to Introduce Michaelis-Menten Enzyme Kinetics to Biochemistry Students

Science.gov (United States)

Flurkey, William H.; Inlow, Jennifer K.

2017-01-01

An inexpensive enzyme kinetics laboratory exercise for undergraduate biochemistry students is described utilizing tyrosinase from white button mushrooms. The exercise can be completed in one or two three-hour lab sessions. The optimal amounts of enzyme, substrate (catechol), and inhibitor (kojic acid) are first determined, and then kinetic data is…

Michaëlis--Menten kinetics of phenazone elimination in the perfused pig liver

DEFF Research Database (Denmark)

Andreasen, B; Tonnesen, K; Rabol, A

1977-01-01

The purpose of the present study was to define the elimination kinetics of phenazone (NFN) in the isolated perfused pig liver. In five experiments phenazone was administered as constant infusion to obtain steady-state periods over a wide range of concentrations. The elimination of phenazone follo...

Artificial Enzymes, "Chemzymes"

DEFF Research Database (Denmark)

Bjerre, Jeannette; Rousseau, Cyril Andre Raphaël; Pedersen, Lavinia Georgeta M

2008-01-01

Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models that successf......Enzymes have fascinated scientists since their discovery and, over some decades, one aim in organic chemistry has been the creation of molecules that mimic the active sites of enzymes and promote catalysis. Nevertheless, even today, there are relatively few examples of enzyme models...... that successfully perform Michaelis-Menten catalysis under enzymatic conditions (i.e., aqueous medium, neutral pH, ambient temperature) and for those that do, very high rate accelerations are seldomly seen. This review will provide a brief summary of the recent developments in artificial enzymes, so called...... "Chemzymes", based on cyclodextrins and other molecules. Only the chemzymes that have shown enzyme-like activity that has been quantified by different methods will be mentioned. This review will summarize the work done in the field of artificial glycosidases, oxidases, epoxidases, and esterases, as well...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

... behaves as an effective catalyst towards oxidation of 3,5-ditertiarybutyl catechol (3,5-DTBC) in acetonitrile to its corresponding quinone derivative in air. The reaction follows first-order reaction kinetics with rate constant 4.28 × 10−5 min-1. The reaction follows Michaelis-Menten enzymatic kinetics with a turnover number of ...

Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin : In silico predictions and experimental validation

NARCIS (Netherlands)

Julsing, Mattijs K.; Vasilev, Nikolay P.; Schneidman-Duhovny, Dina; Muntendarn, Remco; Woerdenbag, Herman J.; Quax, Wim J.; Wolfson, Haim J.; Ionkova, Iliana; Kayser, Oliver

Deoxypodophyllotoxin is stereoselectively converted into epipodophyllotoxin by recombinant human cytochrome P450 3A4 (CY-P3A4). Further kinetic analysis revealed that the Michaelis-Menten K(m) and V(max) for hydroxylation of deoxypodophyllotoxin by CYP3A4 at C7 position were 1.93 mu M and 1.48

Interactions of NH4+ and L-glutamate with NO3- transport processes of non-mycorrhizal Fagus sylvatica roots

NARCIS (Netherlands)

Kreuzwieser, J; Herschbach, C; Stulen, [No Value; Wiersema, P; Vaalburg, W; Rennenberg, H

The processes of NO3- uptake and transport and the effects of NH4+ or L-glutamate on these processes were investigated with excised non-mycorrhizal beech (Fagus sylvatica L,) roots, NO3- net uptake followed uniphasic Michaelis-Menten kinetics in a concentration range of 10 mu M to 1 mM with an

Free-complement local-Schrödinger-equation method for solving the Schrödinger equation of atoms and molecules: Basic theories and features

Science.gov (United States)

Nakatsuji, Hiroshi; Nakashima, Hiroyuki

2015-02-01

The free-complement (FC) method is a general method for solving the Schrödinger equation (SE): The produced wave function has the potentially exact structure as the solution of the Schrödinger equation. The variables included are determined either by using the variational principle (FC-VP) or by imposing the local Schrödinger equations (FC-LSE) at the chosen set of the sampling points. The latter method, referred to as the local Schrödinger equation (LSE) method, is integral-free and therefore applicable to any atom and molecule. The purpose of this paper is to formulate the basic theories of the LSE method and explain their basic features. First, we formulate three variants of the LSE method, the AB, HS, and HTQ methods, and explain their properties. Then, the natures of the LSE methods are clarified in some detail using the simple examples of the hydrogen atom and the Hooke's atom. Finally, the ideas obtained in this study are applied to solving the SE of the helium atom highly accurately with the FC-LSE method. The results are very encouraging: we could get the world's most accurate energy of the helium atom within the sampling-type methodologies, which is comparable to those obtained with the FC-VP method. Thus, the FC-LSE method is an easy and yet a powerful integral-free method for solving the Schrödinger equation of general atoms and molecules.

Modeling uptake kinetics of cadmium by field-grown lettuce

Energy Technology Data Exchange (ETDEWEB)

Chen Weiping [Department of Environmental Sciences, University of California, 900 University Avenue, Riverside, CA 92521 (United States)], E-mail: chenweip@yahoo.com.cn; Li Lianqing [Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095 (China); Chang, Andrew C.; Wu Laosheng [Department of Environmental Sciences, University of California, 900 University Avenue, Riverside, CA 92521 (United States); Kwon, Soon-Ik [Agricultural Environmental and Ecology Division, National Institute of Agricultural Science and Technology, Suwon 441-707 (Korea, Republic of); Bottoms, Rick [Desert Research and Extension Center, 1004 East Holton Road, El Centro, CA 92243 (United States)

2008-03-15

Cadmium uptake by field grown Romaine lettuce treated with P-fertilizers of different Cd levels was investigated over an entire growing season. Results indicated that the rate of Cd uptake at a given time of the season can be satisfactorily described by the Michaelis-Menten kinetics, that is, plant uptake increases as the Cd concentration in soil solution increases, and it gradually approaches a saturation level. However, the rate constant of the Michaelis-Menten kinetics changes over the growing season. Under a given soil Cd level, the cadmium content in plant tissue decreases exponentially with time. To account for the dynamic nature of Cd uptake, a kinetic model integrating the time factor was developed to simulate Cd plant uptake over the growing season: C{sub Plant} = C{sub Solution} . PUF{sub max} . exp[-b . t], where C{sub Plant} and C{sub Solution} refer to the Cd content in plant tissue and soil solution, respectively, PUF{sub max} and b are kinetic constants. - A kinetic model was developed to evaluate the uptake of Cd under field conditions.

Modeling uptake kinetics of cadmium by field-grown lettuce

International Nuclear Information System (INIS)

Chen Weiping; Li Lianqing; Chang, Andrew C.; Wu Laosheng; Kwon, Soon-Ik; Bottoms, Rick

2008-01-01

Cadmium uptake by field grown Romaine lettuce treated with P-fertilizers of different Cd levels was investigated over an entire growing season. Results indicated that the rate of Cd uptake at a given time of the season can be satisfactorily described by the Michaelis-Menten kinetics, that is, plant uptake increases as the Cd concentration in soil solution increases, and it gradually approaches a saturation level. However, the rate constant of the Michaelis-Menten kinetics changes over the growing season. Under a given soil Cd level, the cadmium content in plant tissue decreases exponentially with time. To account for the dynamic nature of Cd uptake, a kinetic model integrating the time factor was developed to simulate Cd plant uptake over the growing season: C Plant = C Solution . PUF max . exp[-b . t], where C Plant and C Solution refer to the Cd content in plant tissue and soil solution, respectively, PUF max and b are kinetic constants. - A kinetic model was developed to evaluate the uptake of Cd under field conditions

Inhibition of serotonin transport by (+)McN5652 is noncompetitive

Energy Technology Data Exchange (ETDEWEB)

Hummerich, Rene [Biochemical Laboratory, Central Institute of Mental Health, 68159 Mannheim (Germany); Schulze, Oliver [Department of Nuclear Medicine, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg (Germany); Raedler, Thomas [Department of Psychiatry and Psychotherapy, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg (Germany); Mikecz, Pal [Department of Nuclear Medicine, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg (Germany); Reimold, Matthias [Department of Nuclear Medicine, University Hospital Tuebingen, D-72076 Tuebingen (Germany); Brenner, Winfried [Department of Nuclear Medicine, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg (Germany); Clausen, Malte [Department of Nuclear Medicine, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg (Germany); Schloss, Patrick [Biochemical Laboratory, Central Institute of Mental Health, 68159 Mannheim (Germany); Buchert, Ralph [Department of Nuclear Medicine, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg (Germany)]. E-mail: buchert@uke.uni-hamburg.de

2006-04-15

Introduction: Imaging of the serotonergic innervation of the brain using positron emission tomography (PET) with the serotonin transporter (SERT) ligand [{sup 11C}] (+)McN5652 might be affected by serotonin in the synaptic cleft if there is relevant interaction between [{sup 11}C] (+)McN5652 and serotonin at the SERT. The aim of the present study therefore was to pharmacologically characterize the interaction of [{sup 11}C] (+)McN5652 and serotonin at the SERT. Methods: In vitro saturation analyses of [{sup 3}H]serotonin uptake into HEK293 cells stably expressing the human SERT were performed in the absence and presence of unlabelled (+)McN5652. Data were evaluated assuming Michaelis-Menten kinetics. Results: Unlabelled (+)McN5652 significantly reduced the maximal rate of serotonin transport V {sub max} of SERT without affecting the Michaelis-Menten constant K {sub M}. Conclusions: This finding indicates that (+)McN5652 inhibits serotonin transport through the SERT in a noncompetitive manner. This might suggest that [{sup 11}C] (+)McN5652 PET is not significantly affected by endogenous serotonin.

Inhibition of serotonin transport by (+)McN5652 is noncompetitive

International Nuclear Information System (INIS)

Hummerich, Rene; Schulze, Oliver; Raedler, Thomas; Mikecz, Pal; Reimold, Matthias; Brenner, Winfried; Clausen, Malte; Schloss, Patrick; Buchert, Ralph

2006-01-01

Introduction: Imaging of the serotonergic innervation of the brain using positron emission tomography (PET) with the serotonin transporter (SERT) ligand [ 11C ] (+)McN5652 might be affected by serotonin in the synaptic cleft if there is relevant interaction between [ 11 C] (+)McN5652 and serotonin at the SERT. The aim of the present study therefore was to pharmacologically characterize the interaction of [ 11 C] (+)McN5652 and serotonin at the SERT. Methods: In vitro saturation analyses of [ 3 H]serotonin uptake into HEK293 cells stably expressing the human SERT were performed in the absence and presence of unlabelled (+)McN5652. Data were evaluated assuming Michaelis-Menten kinetics. Results: Unlabelled (+)McN5652 significantly reduced the maximal rate of serotonin transport V max of SERT without affecting the Michaelis-Menten constant K M . Conclusions: This finding indicates that (+)McN5652 inhibits serotonin transport through the SERT in a noncompetitive manner. This might suggest that [ 11 C] (+)McN5652 PET is not significantly affected by endogenous serotonin

No-threshold dose-response curves for nongenotoxic chemicals: Findings and applications for risk assessment

International Nuclear Information System (INIS)

Sheehan, Daniel M.

2006-01-01

We tested the hypothesis that no threshold exists when estradiol acts through the same mechanism as an active endogenous estrogen. A Michaelis-Menten (MM) equation accounting for response saturation, background effects, and endogenous estrogen level fit a turtle sex-reversal data set with no threshold and estimated the endogenous dose. Additionally, 31 diverse literature dose-response data sets were analyzed by adding a term for nonhormonal background; good fits were obtained but endogenous dose estimations were not significant due to low resolving power. No thresholds were observed. Data sets were plotted using a normalized MM equation; all 178 data points were accommodated on a single graph. Response rates from ∼1% to >95% were well fit. The findings contradict the threshold assumption and low-dose safety. Calculating risk and assuming additivity of effects from multiple chemicals acting through the same mechanism rather than assuming a safe dose for nonthresholded curves is appropriate

Nitrate transport processes in Fagus-Laccaria-mycorrhizae

NARCIS (Netherlands)

Kreuzwieser, J; Stulen, [No Value; Wiersema, P; Vaalburg, W; Rennenberg, H

2000-01-01

The contribution of influx and efflux of NO3- on NO3- net uptake has been studied in excised mycorrhizae of 18-20 week old beech (Fagus sylvatica L.) trees. Net uptake rates of NO3- followed uniphasic Michaelis-Menten kinetics in the concentration range between 10 mu M and 1.0 mM external NO3-, with

Catalytic Activity of μ-Carbido-Dimeric Iron(IV) Octapropylporphyrazinate in the 3,5,7,2',4'-Pentahydroxyflavone Oxidation Reaction with tert-Butyl Hydroperoxide

Science.gov (United States)

Tyurin, D. V.; Zaitseva, S. V.; Kudrik, E. V.

2018-05-01

It is found for the first time that μ-carbido-dimeric iron(IV) octapropylporphyrazinate displays catalytic activity in the oxidation reaction of natural flavonol morin with tert-butyl hydroperoxide, with the catalyst being stable under conditions of the reaction. The kinetics of this reaction are studied. It is shown the reaction proceeds via tentative formation of a complex between the catalyst and the oxidant, followed by O‒O bond homolytic cleavage. The kinetics of the reaction is described in the coordinates of the Michaelis-Menten equation. A linear dependence of the apparent reaction rate constant on the concentration of the catalyst is observed, testifying to its participation in the limiting reaction step. The equilibrium constants and rates of interaction are found. A mechanism is proposed for the reaction on the basis of the experimental data.

Relationship between soil cellulolytic activity and suppression of seedling blight of barley in arable soils

DEFF Research Database (Denmark)

Rasmussen, Peter Have; Knudsen, I.; Elmholt, S.

2002-01-01

the Hanes-Wolf transformation of the Michaelis-Menten equation. Soil samples from 6 to 13 cm depth were collected in the early spring as undisturbed blocks from 10 arable soils with different physico-chemical properties and cultivation history. Significant correlations were found between soil suppresiveness......The objective was to investigate the relationship between soil suppression of seedling blight of barley caused by Fusarium culmorum (W.G. Smith) Sacc. and the soil cellulolytic activity of beta-glucosidase, cellobiohydrolase and endocellulase. Disease suppression was investigated in bioassays...... with test soils mixed with sand, and barley seeds inoculated with F. culmorum. After 19 days, disease severity was evaluated on the barley seedlings. Soil cellulolytic activities were measured using 4-methylumbelliferyl-labelled fluorogenic substrates, and were expressed as V-max values obtained by using...

Efficient and 'green' microwave-assisted synthesis of haloalkylphosphonates via the Michaelis-Arbuzov reaction

Czech Academy of Sciences Publication Activity Database

Jansa, Petr; Holý, Antonín; Dračínský, Martin; Baszczyňski, Ondřej; Česnek, Michal; Janeba, Zlatko

2011-01-01

Roč. 13, č. 4 (2011), s. 882-888 ISSN 1463-9262 R&D Projects: GA AV ČR KJB400550903; GA MŠk 1M0508 Institutional research plan: CEZ:AV0Z40550506 Keywords : microwave-assisted synthesis * haloalkylphosphonates * Michaelis-Arbuzov reaction Subject RIV: CC - Organic Chemistry Impact factor: 6.320, year: 2011

Carolina Michaëlis o los saberes de la Filología

Directory of Open Access Journals (Sweden)

Joaquín Rubio Tovar

2005-06-01

Full Text Available Two important international conferences (Berlin, Santiago on the work of Carolina Michaëlis have been held in recent years. The papers collected value her work within the historical background when it was carried out. Besides, they review the validity of her approach and analysis and present some modem contributions to the fields which she studied, particularly the Cancioneiro da Ajuda.

'In-Crystallo' Capture of a Michaelis Complex And Product Binding Modes of a Bacterial Phosphotriesterase

Energy Technology Data Exchange (ETDEWEB)

Jackson, C.J.; Foo, J.-L.; Kim, H.-K.; Carr, P.D.; Liu, J.-W.; Salem, G.; Ollis, D.L.

2009-05-18

The mechanism by which the binuclear metallophosphotriesterases (PTEs, E.C. 3.1.8.1) catalyse substrate hydrolysis has been extensively studied. The {mu}-hydroxo bridge between the metal ions has been proposed to be the initiating nucleophile in the hydrolytic reaction. In contrast, analysis of some biomimetic systems has indicated that {mu}-hydroxo bridges are often not themselves nucleophiles, but act as general bases for freely exchangeable nucleophilic water molecules. Herein, we present crystallographic analyses of a bacterial PTE from Agrobacterium radiobacter, OpdA, capturing the enzyme-substrate complex during hydrolysis. This model of the Michaelis complex suggests the alignment of the substrate will favor attack from a solvent molecule terminally coordinated to the {alpha}-metal ion. The bridging of both metal ions by the product, without disruption of the {mu}-hydroxo bridge, is also consistent with nucleophilic attack occurring from the terminal position. When phosphodiesters are soaked into crystals of OpdA, they coordinate bidentately to the {beta}-metal ion, displacing the {mu}-hydroxo bridge. Thus, alternative product-binding modes exist for the PTEs, and it is the bridging mode that appears to result from phosphotriester hydrolysis. Kinetic analysis of the PTE and promiscuous phosphodiesterase activities confirms that the presence of a {mu}-hydroxo bridge during phosphotriester hydrolysis is correlated with a lower pK{sub a} for the nucleophile, consistent with a general base function during catalysis.

Single molecule diffusion and the solution of the spherically symmetric residence time equation.

Science.gov (United States)

Agmon, Noam

2011-06-16

The residence time of a single dye molecule diffusing within a laser spot is propotional to the total number of photons emitted by it. With this application in mind, we solve the spherically symmetric "residence time equation" (RTE) to obtain the solution for the Laplace transform of the mean residence time (MRT) within a d-dimensional ball, as a function of the initial location of the particle and the observation time. The solutions for initial conditions of potential experimental interest, starting in the center, on the surface or uniformly within the ball, are explicitly presented. Special cases for dimensions 1, 2, and 3 are obtained, which can be Laplace inverted analytically for d = 1 and 3. In addition, the analytic short- and long-time asymptotic behaviors of the MRT are derived and compared with the exact solutions for d = 1, 2, and 3. As a demonstration of the simplification afforded by the RTE, the Appendix obtains the residence time distribution by solving the Feynman-Kac equation, from which the MRT is obtained by differentiation. Single-molecule diffusion experiments could be devised to test the results for the MRT presented in this work. © 2011 American Chemical Society

Catalytic monolayer voltammetry and in situ scanning tunneling microscopy of copper nitrite reductase on cysteamine-modified Au(111) electrodes

DEFF Research Database (Denmark)

Zhang, Jingdong; Welinder, A.C.; Hansen, Allan Glargaard

2003-01-01

electrochemical scanning tunneling microscopy (in situ STM) directly in aqueous acetate buffer, pH 6.0 has been used. High-resolution in situ STM shows that cysteamine packs into ordered domains with strip features of a periodic distance of 11.7 +/- 0.3 Angstrom. No voltammetric signals of the nitrite substrate...... on this surface could be detected. A strong cathodic catalytic wave appears in the presence of nitrite. The catalytic current follows a Michaelis-Menten pattern with a Michaelis constant of K-m approximate to 44 muM, which is close to the value for AxCuNiR in homogeneous solution. The apparent catalytic rate...

Langevin equation method for the rotational Brownian motion and orientational relaxation in liquids: II. Symmetrical top molecules

CERN Document Server

Coffey, W T; Titov, S V

2003-01-01

A theory of orientational relaxation for the inertial rotational Brownian motion of a symmetric top molecule is developed using the Langevin equation rather than the Fokker-Planck equation. The infinite hierarchy of differential-recurrence relations for the orientational correlation functions for the relaxation behaviour is derived by averaging the corresponding Euler-Langevin equations. The solution of this hierarchy is obtained using matrix continued fractions allowing the calculation of the correlation times and the spectra of the orientational correlation functions for typical values of the model parameters.

Thermodynamic Activity-Based Progress Curve Analysis in Enzyme Kinetics.

Science.gov (United States)

Pleiss, Jürgen

2018-03-01

Macrokinetic Michaelis-Menten models based on thermodynamic activity provide insights into enzyme kinetics because they separate substrate-enzyme from substrate-solvent interactions. Kinetic parameters are estimated from experimental progress curves of enzyme-catalyzed reactions. Three pitfalls are discussed: deviations between thermodynamic and concentration-based models, product effects on the substrate activity coefficient, and product inhibition. Copyright © 2017 Elsevier Ltd. All rights reserved.

A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths.

Science.gov (United States)

Olariu, Victor; Manesso, Erica; Peterson, Carsten

2017-06-01

Depicting developmental processes as movements in free energy genetic landscapes is an illustrative tool. However, exploring such landscapes to obtain quantitative or even qualitative predictions is hampered by the lack of free energy functions corresponding to the biochemical Michaelis-Menten or Hill rate equations for the dynamics. Being armed with energy landscapes defined by a network and its interactions would open up the possibility of swiftly identifying cell states and computing optimal paths, including those of cell reprogramming, thereby avoiding exhaustive trial-and-error simulations with rate equations for different parameter sets. It turns out that sigmoidal rate equations do have approximate free energy associations. With this replacement of rate equations, we develop a deterministic method for estimating the free energy surfaces of systems of interacting genes at different noise levels or temperatures. Once such free energy landscape estimates have been established, we adapt a shortest path algorithm to determine optimal routes in the landscapes. We explore the method on three circuits for haematopoiesis and embryonic stem cell development for commitment and reprogramming scenarios and illustrate how the method can be used to determine sequential steps for onsets of external factors, essential for efficient reprogramming.

An Assessment of Factors Affecting Reactive Transport of Biodegradable BTEX in an Unconfined Aquifer System, Tehran Oil Refinery, Iran

Directory of Open Access Journals (Sweden)

A. Agah

2012-12-01

Full Text Available Risk-based assessment methods are commonly used at the contaminated sites by hydrocarbon pollutants. This paper presents the results of a two-dimensional finite volume model of reactive transport of biodegradable BTEX which have been developed for the saturated zone of an unconfined aquifer in the Pump station area of Tehran oil refinery, Iran. The model governing equations were numerically solved by modification of a general commercial software called PHOENICS. To reduce costs in general, many input parameters of a model are often approximated based on the used values in the contaminated sites with same conditions. It was not fully recognised the effect of errors in these inputs on modelling outputs. Thus, a sensitivity analysis was carried out to determine the influence of parameters variability on the results of model. For this analysis, the sensitivity of the model to changes in the dispersivity, distribution coefficient, parameters of Monod, Michaelis-Menten, first- and zero- order kinetics modes on the BTEX contaminant plume were examined by performing several simulations. It was found that the model is sensitive to changes in dispersivity and parameters of Michaelis-Menten, first- and zero- order kinetics model. On the other hand, the predictions for plumes assuming Monod kinetics are similar, even if different values for parameterization are chosen. The reason for this insensibility is that degradation is not limited by microbial kinetics in the simulation, but by dispersive mixing. Quantifying the effect of changes in model input parameters on the modelling results is essential when it is desired to recognise which model parameters are more vital on the fate and transport of reactive pollutants. Furthermore, this process can provide an insight into understanding pollutant transportation mechanisms.

Stochastic simulation of biological reactions, and its applications for studying actin polymerization.

Science.gov (United States)

Ichikawa, Kazuhisa; Suzuki, Takashi; Murata, Noboru

2010-11-30

Molecular events in biological cells occur in local subregions, where the molecules tend to be small in number. The cytoskeleton, which is important for both the structural changes of cells and their functions, is also a countable entity because of its long fibrous shape. To simulate the local environment using a computer, stochastic simulations should be run. We herein report a new method of stochastic simulation based on random walk and reaction by the collision of all molecules. The microscopic reaction rate P(r) is calculated from the macroscopic rate constant k. The formula involves only local parameters embedded for each molecule. The results of the stochastic simulations of simple second-order, polymerization, Michaelis-Menten-type and other reactions agreed quite well with those of deterministic simulations when the number of molecules was sufficiently large. An analysis of the theory indicated a relationship between variance and the number of molecules in the system, and results of multiple stochastic simulation runs confirmed this relationship. We simulated Ca²(+) dynamics in a cell by inward flow from a point on the cell surface and the polymerization of G-actin forming F-actin. Our results showed that this theory and method can be used to simulate spatially inhomogeneous events.

Biodegradation of BTEX (Benzene, Toluene, Ethylbenzene and Xylenes) composites present in the petrochemical effluents industries; Biodegradacao dos compostos BTX (Benzeno, Tolueno e Xilenos) presentes em efluentes petroquimicos

Energy Technology Data Exchange (ETDEWEB)

Minatti, Gheise; Mello, Josiane M.M. de; Souza, Selene M.A. Guelli Ulson de; Ulson de, Antonio Augusto [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil)

2008-07-01

The compounds BTX inside of the petrochemical effluent have presented a high potential of pollution, representing a serious risk to the environment and to the human. The great improvements in the field of biological treatment of liquid effluent were reached through the process using biofilm capable of degrading toxic compounds. The objective of this paper is to determine the degradation kinetics of BTX using biofilm. The experimental data were compared with two kinetic models, kinetic of first order and model of Michaelis-Menten. The kinetic parameters of BTX compounds were experimentally obtained in a bioreactor in batch with biomass immobilized in activated-carbon, being fed daily with solution of nutrients and BTX. For the kinetic models studied in this paper, the best performance was achieved with the model of Michaelis-Menten showing a good correlation coefficient for the three compounds. The biomass amount in these bioreactors was 49.18, 28.35 and 5.15 mg of SSV per gram of support for the toluene, benzene and o-xylene, respectively. The experimental tests showed that the biomass inside of bioreactor is capable to degrade all compounds in a time of approximately 300 minutes. (author)

Relationship among reaction rate, release rate and efficiency of nanomachine-based targeted drug delivery.

Science.gov (United States)

Zhao, Qingying; Li, Min; Luo, Jun

2017-12-04

In nanomachine applications towards targeted drug delivery, drug molecules released by nanomachines propagate and chemically react with tumor cells in aqueous environment. If the nanomachines release drug molecules faster than the tumor cells react, it will result in loss and waste of drug molecules. It is a potential issue associated with the relationship among reaction rate, release rate and efficiency. This paper aims to investigate the relationship among reaction rate, release rate and efficiency based on two drug reception models. We expect to pave a way for designing a control method of drug release. We adopted two analytical methods that one is drug reception process based on collision with tumors and another is based on Michaelis Menten enzymatic kinetics. To evaluate the analytical formulations, we used the well-known simulation framework N3Sim to establish simulations. The analytical results of the relationship among reaction rate, release rate and efficiency is obtained, which match well with the numerical simulation results in a 3-D environment. Based upon two drug reception models, the results of this paper would be beneficial for designing a control method of nanomahine-based drug release.

Conservative, unconditionally stable discretization methods for Hamiltonian equations, applied to wave motion in lattice equations modeling protein molecules

Science.gov (United States)

LeMesurier, Brenton

2012-01-01

A new approach is described for generating exactly energy-momentum conserving time discretizations for a wide class of Hamiltonian systems of DEs with quadratic momenta, including mechanical systems with central forces; it is well-suited in particular to the large systems that arise in both spatial discretizations of nonlinear wave equations and lattice equations such as the Davydov System modeling energetic pulse propagation in protein molecules. The method is unconditionally stable, making it well-suited to equations of broadly “Discrete NLS form”, including many arising in nonlinear optics. Key features of the resulting discretizations are exact conservation of both the Hamiltonian and quadratic conserved quantities related to continuous linear symmetries, preservation of time reversal symmetry, unconditional stability, and respecting the linearity of certain terms. The last feature allows a simple, efficient iterative solution of the resulting nonlinear algebraic systems that retain unconditional stability, avoiding the need for full Newton-type solvers. One distinction from earlier work on conservative discretizations is a new and more straightforward nearly canonical procedure for constructing the discretizations, based on a “discrete gradient calculus with product rule” that mimics the essential properties of partial derivatives. This numerical method is then used to study the Davydov system, revealing that previously conjectured continuum limit approximations by NLS do not hold, but that sech-like pulses related to NLS solitons can nevertheless sometimes arise.

A mathematical model of phosphorylation AKT in Acute Myeloid Leukemia

Science.gov (United States)

Adi, Y. A.; Kusumo, F. A.; Aryati, L.; Hardianti, M. S.

2016-04-01

In this paper we consider a mathematical model of PI3K/AKT signaling pathways in phosphorylation AKT. PI3K/AKT pathway is an important mediator of cytokine signaling implicated in regulation of hematopoiesis. Constitutive activation of PI3K/AKT signaling pathway has been observed in Acute Meyloid Leukemia (AML) it caused by the mutation of Fms-like Tyrosine Kinase 3 in internal tandem duplication (FLT3-ITD), the most common molecular abnormality associated with AML. Depending upon its phosphorylation status, protein interaction, substrate availability, and localization, AKT can phosphorylate or inhibite numerous substrates in its downstream pathways that promote protein synthesis, survival, proliferation, and metabolism. Firstly, we present a mass action ordinary differential equation model describing AKT double phosphorylation (AKTpp) in a system with 11 equations. Finally, under the asumtion enzyme catalyst constant and steady state equilibrium, we reduce the system in 4 equation included Michaelis Menten constant. Simulation result suggested that a high concentration of PI3K and/or a low concentration of phospatase increased AKTpp activation. This result also indicates that PI3K is a potential target theraphy in AML.

A mathematical model of phosphorylation AKT in Acute Myeloid Leukemia

Energy Technology Data Exchange (ETDEWEB)

Adi, Y. A., E-mail: yudi.adi@math.uad.ac.id [Department of Mathematic Faculty of MIPA Universitas Ahmad Dahlan (Indonesia); Department of Mathematic Faculty of MIPA Universitas Gadjah Mada (Indonesia); Kusumo, F. A.; Aryati, L. [Department of Mathematic Faculty of MIPA Universitas Gadjah Mada (Indonesia); Hardianti, M. S. [Department of Internal Medicine, Faculty of Medicine, Universitas Gadjah Mada (Indonesia)

2016-04-06

In this paper we consider a mathematical model of PI3K/AKT signaling pathways in phosphorylation AKT. PI3K/AKT pathway is an important mediator of cytokine signaling implicated in regulation of hematopoiesis. Constitutive activation of PI3K/AKT signaling pathway has been observed in Acute Meyloid Leukemia (AML) it caused by the mutation of Fms-like Tyrosine Kinase 3 in internal tandem duplication (FLT3-ITD), the most common molecular abnormality associated with AML. Depending upon its phosphorylation status, protein interaction, substrate availability, and localization, AKT can phosphorylate or inhibite numerous substrates in its downstream pathways that promote protein synthesis, survival, proliferation, and metabolism. Firstly, we present a mass action ordinary differential equation model describing AKT double phosphorylation (AKTpp) in a system with 11 equations. Finally, under the asumtion enzyme catalyst constant and steady state equilibrium, we reduce the system in 4 equation included Michaelis Menten constant. Simulation result suggested that a high concentration of PI3K and/or a low concentration of phospatase increased AKTpp activation. This result also indicates that PI3K is a potential target theraphy in AML.

Statistical identifiability and convergence evaluation for nonlinear pharmacokinetic models with particle swarm optimization.

Science.gov (United States)

Kim, Seongho; Li, Lang

2014-02-01

The statistical identifiability of nonlinear pharmacokinetic (PK) models with the Michaelis-Menten (MM) kinetic equation is considered using a global optimization approach, which is particle swarm optimization (PSO). If a model is statistically non-identifiable, the conventional derivative-based estimation approach is often terminated earlier without converging, due to the singularity. To circumvent this difficulty, we develop a derivative-free global optimization algorithm by combining PSO with a derivative-free local optimization algorithm to improve the rate of convergence of PSO. We further propose an efficient approach to not only checking the convergence of estimation but also detecting the identifiability of nonlinear PK models. PK simulation studies demonstrate that the convergence and identifiability of the PK model can be detected efficiently through the proposed approach. The proposed approach is then applied to clinical PK data along with a two-compartmental model. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Use of an uncertainty analysis for genome-scale models as a prediction tool for microbial growth processes in subsurface environments.

Science.gov (United States)

Klier, Christine

2012-03-06

The integration of genome-scale, constraint-based models of microbial cell function into simulations of contaminant transport and fate in complex groundwater systems is a promising approach to help characterize the metabolic activities of microorganisms in natural environments. In constraint-based modeling, the specific uptake flux rates of external metabolites are usually determined by Michaelis-Menten kinetic theory. However, extensive data sets based on experimentally measured values are not always available. In this study, a genome-scale model of Pseudomonas putida was used to study the key issue of uncertainty arising from the parametrization of the influx of two growth-limiting substrates: oxygen and toluene. The results showed that simulated growth rates are highly sensitive to substrate affinity constants and that uncertainties in specific substrate uptake rates have a significant influence on the variability of simulated microbial growth. Michaelis-Menten kinetic theory does not, therefore, seem to be appropriate for descriptions of substrate uptake processes in the genome-scale model of P. putida. Microbial growth rates of P. putida in subsurface environments can only be accurately predicted if the processes of complex substrate transport and microbial uptake regulation are sufficiently understood in natural environments and if data-driven uptake flux constraints can be applied.

Emergence of a code in the polymerization of amino acids along RNA templates.

Directory of Open Access Journals (Sweden)

Jean Lehmann

2009-06-01

Full Text Available The origin of the genetic code in the context of an RNA world is a major problem in the field of biophysical chemistry. In this paper, we describe how the polymerization of amino acids along RNA templates can be affected by the properties of both molecules. Considering a system without enzymes, in which the tRNAs (the translation adaptors are not loaded selectively with amino acids, we show that an elementary translation governed by a Michaelis-Menten type of kinetics can follow different polymerization regimes: random polymerization, homopolymerization and coded polymerization. The regime under which the system is running is set by the relative concentrations of the amino acids and the kinetic constants involved. We point out that the coding regime can naturally occur under prebiotic conditions. It generates partially coded proteins through a mechanism which is remarkably robust against non-specific interactions (mismatches between the adaptors and the RNA template. Features of the genetic code support the existence of this early translation system.

Kinetic evaluation of an anaerobic fluidised-bed reactor treating slaughterhouse wastewater

Energy Technology Data Exchange (ETDEWEB)

Borja, R. [Consejo Superior de Investigaciones Cientificas, Seville (Spain). Inst. de la Grasa; Banks, C.J.; Zhengjian Wang [Manchester Univ. (United Kingdom). Inst. of Science and Technology

1995-09-01

An anaerobic fluidised-bed reactor for purification of slaughterhouse wastewater was modelled as a continuous-flow, completely-mixed homogeneous microbial system, with the feed COD as the limiting-substrate concentration. The average microbial residence time in the reactor was defined in terms of conventional sludge-retention-time. The experimental data obtained indicated that the Michaelis-Menten expression was applicable to a description of substrate utilisation (i.e. COD removal) in the anaerobic fluidised-bed system. The maximum substrate utilisation rate, k, and the Michaelis constant, K{sub s}, were determined to be 1.2/day and 0.039 g/l. The observed biomass yield in the reactor decreased with increasing sludge-retention-time. The specific methane production rate observed was a linear function of the specific substrate-utilisation rate. (Author)

Low birth rates and reproductive skew limit the viability of Europe’s captive eastern black rhinoceros, Diceros bicornis michaeli

NARCIS (Netherlands)

Edwards, K.L.; Walker, S.L.; Durham, A.E.; Pilgrim, M.; Ouma, B.O.; Shultz, S.

2015-01-01

Ex situ populations play a critical role for the conservation of endangered species, especially where in situ populations face imminent threats. For such populations to act as vital reserves, they must be viable and sustainable. Eastern black rhinoceros (Diceros bicornis michaeli) epitomise the

The steady-state kinetics of the NADH-dependent nitrite reductase from Escherichia coli K 12. Nitrite and hydroxylamine reduction.

OpenAIRE

Jackson, R H; Cole, J A; Cornish-Bowden, A

1981-01-01

The reduction of both NO2- and hydroxylamine by the NADH-dependent nitrite reductase of Escherichia coli K 12 (EC 1.6.6.4) appears to follow Michaelis-Menten kinetics over a wide range of NADH concentrations. Substrate inhibition can, however, be detected at low concentrations of the product NAD+. In addition, NAD+ displays mixed product inhibition with respect to NADH and mixed or uncompetitive inhibition with respect to hydroxylamine. These inhibition characteristics are consistent with a m...

Cooperativity in CYP2E1 Metabolism of Acetaminophen and Styrene Mixtures

OpenAIRE

Hartman, Jessica H.; Letzig, Lynda G.; Robertsc, Dean W.; James, Laura P.; Fifer, E. Kim; Miller, Grover P.

2015-01-01

Risk assessment for exposure to mixtures of drugs and pollutants relies heavily on in vitro characterization of their bioactivation and/or metabolism individually and extrapolation to mixtures assuming no interaction. Herein, we demonstrated that in vitro CYP2E1 metabolic activation of acetaminophen and styrene mixtures could not be explained through the Michaelis-Menten mechanism or any models relying on that premise. As a baseline for mixture studies with styrene, steady-state analysis of a...

Analysis of mathematical modelling on potentiometric biosensors.

Science.gov (United States)

Mehala, N; Rajendran, L

2014-01-01

A mathematical model of potentiometric enzyme electrodes for a nonsteady condition has been developed. The model is based on the system of two coupled nonlinear time-dependent reaction diffusion equations for Michaelis-Menten formalism that describes the concentrations of substrate and product within the enzymatic layer. Analytical expressions for the concentration of substrate and product and the corresponding flux response have been derived for all values of parameters using the new homotopy perturbation method. Furthermore, the complex inversion formula is employed in this work to solve the boundary value problem. The analytical solutions obtained allow a full description of the response curves for only two kinetic parameters (unsaturation/saturation parameter and reaction/diffusion parameter). Theoretical descriptions are given for the two limiting cases (zero and first order kinetics) and relatively simple approaches for general cases are presented. All the analytical results are compared with simulation results using Scilab/Matlab program. The numerical results agree with the appropriate theories.

Collective behaviours: from biochemical kinetics to electronic circuits

Science.gov (United States)

Agliari, Elena; Barra, Adriano; Burioni, Raffaella; di Biasio, Aldo; Uguzzoni, Guido

2013-12-01

In this work we aim to highlight a close analogy between cooperative behaviors in chemical kinetics and cybernetics; this is realized by using a common language for their description, that is mean-field statistical mechanics. First, we perform a one-to-one mapping between paradigmatic behaviors in chemical kinetics (i.e., non-cooperative, cooperative, ultra-sensitive, anti-cooperative) and in mean-field statistical mechanics (i.e., paramagnetic, high and low temperature ferromagnetic, anti-ferromagnetic). Interestingly, the statistical mechanics approach allows a unified, broad theory for all scenarios and, in particular, Michaelis-Menten, Hill and Adair equations are consistently recovered. This framework is then tested against experimental biological data with an overall excellent agreement. One step forward, we consistently read the whole mapping from a cybernetic perspective, highlighting deep structural analogies between the above-mentioned kinetics and fundamental bricks in electronics (i.e. operational amplifiers, flashes, flip-flops), so to build a clear bridge linking biochemical kinetics and cybernetics.

Uptake of oxytetracycline and its phytotoxicity to alfalfa (Medicago sativa L.)

International Nuclear Information System (INIS)

Kong, W.D.; Zhu, Y.G.; Liang, Y.C.; Zhang, J.; Smith, F.A.; Yang, M.

2007-01-01

A series of experiments were conducted in a hydroponic system to investigate the uptake of oxytetracycline (OTC) and its toxicity to alfalfa (Medicago sativa L.). OTC inhibited alfalfa shoot and root growth by up to 61% and 85%, respectively. The kinetics of OTC uptake could be well described by Michaelis-Menten equation with V max of 2.25 μmol g -1 fresh weight h -1 , and K m of 0.036 mM. The uptake of OTC by alfalfa was strongly inhibited by the metabolic inhibitor, 2,4-DNP (2,4-dinitrophenol), at pH 3.5 and 6.0, but not by the aquaporin competitors, glycerol and Ag + . OTC uptake, however, was significantly inhibited by Hg 2+ , suggesting that the inhibition of influx was due to general cellular stress rather than the specific action of Hg 2+ on aquaporins. Results from the present study suggested that OTC uptake into alfalfa is an energy-dependent process. - Plant uptake of antibiotic oxytetracycline is energy-dependent

Modeling of an immobilized lipase tubular reactor for the production of glycerol and fatty acids from oils; Modelado de un reactor tubular de lipasas inmovilizadas para la produccion de glicerol y acidos grasos a partir de aceites

Energy Technology Data Exchange (ETDEWEB)

Oddone, S.; Grasselli, M.; Cuellas, A.

2010-07-01

Advances in the design of a bioreactor in the fats and oils industry have permitted the hydrolysis of triglycerides in mild conditions and improved productivity while avoiding the formation of unwanted byproducts. The present work develops a mathematical model that describes the hydrolytic activity of a tubular reactor with immobilized lipases for the production of glycerol and fatty acids from the oil trade. Runge Kuttas numerical method of high order has been applied, considering that there is no accumulation of the substratum in the surface of the membrane, where the enzyme is. At the same time, different equations based on the kinetic model of Michaelis Mentens and the Ping-Pong bi-bi mechanism were examined. Experimental data in discontinuous systems are the basis for the development of the quantitative mathematical model that was used to simulate the process computationally. The obtained results allow for optimizing both the operative variables and the economic aspects of industrial processes. (Author)

Sufficient conditions for optimality for a mathematical model of drug treatment with pharmacodynamics

Directory of Open Access Journals (Sweden)

Maciej Leszczyński

2017-01-01

Full Text Available We consider an optimal control problem for a general mathematical model of drug treatment with a single agent. The control represents the concentration of the agent and its effect (pharmacodynamics is modelled by a Hill function (i.e., Michaelis-Menten type kinetics. The aim is to minimize a cost functional consisting of a weighted average related to the state of the system (both at the end and during a fixed therapy horizon and to the total amount of drugs given. The latter is an indirect measure for the side effects of treatment. It is shown that optimal controls are continuous functions of time that change between full or no dose segments with connecting pieces that take values in the interior of the control set. Sufficient conditions for the strong local optimality of an extremal controlled trajectory in terms of the existence of a solution to a piecewise defined Riccati differential equation are given.

Practical steady-state enzyme kinetics.

Science.gov (United States)

Lorsch, Jon R

2014-01-01

Enzymes are key components of most biological processes. Characterization of enzymes is therefore frequently required during the study of biological systems. Steady-state kinetics provides a simple and rapid means of assessing the substrate specificity of an enzyme. When combined with site-directed mutagenesis (see Site-Directed Mutagenesis), it can be used to probe the roles of particular amino acids in the enzyme in substrate recognition and catalysis. Effects of interaction partners and posttranslational modifications can also be assessed using steady-state kinetics. This overview explains the general principles of steady-state enzyme kinetics experiments in a practical, rather than theoretical, way. Any biochemistry textbook will have a section on the theory of Michaelis-Menten kinetics, including derivations of the relevant equations. No specific enzymatic assay is described here, although a method for monitoring product formation or substrate consumption over time (an assay) is required to perform the experiments described. © 2014 Elsevier Inc. All rights reserved.

[Kinetics of uptake of phosphates and nitrates by marine multicellular algae Gelidium latifolium (Grev.) Born. et Thur].

Science.gov (United States)

Silkin, V A; Chubchikova, I N

2007-01-01

We studied nonstationary kinetics of the uptake of phosphates and nitrates by the red marine algae Gelidium latifolium (Grev.) Born et Thur. and calculated constants of the Michaelis-Menten equation for these elements. In the area of 0-3 microM, the kinetics of phosphate consumption had the following coefficients: maximum rate of uptake 0.8 micromol/(g x h), constant of half-saturation 1.745 microM. For nitrate nitrogen at 0-30 microM, an adaptive strategy of uptake kinetics was noted with change of the equation parameters with time: after 1 h, the maximum rate of uptake was 5.1 micromol/(g x h) and constant of half-saturation 19 gM, while within 2 h, the maximum rate of uptake significantly increased. This could be related to the synthesis of nitrate reductase. Coupled with the uptake of nitrates, nonstationary kinetics of the release of nitrates in the surrounding medium had a one-peak pattern: the maximum concentration of nitrites in the medium and the time of its achievement increased with the initial concentration of nitrates. The maximum concentration of nitrites was 6 to 14% of the initial concentration in the medium.

Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

Science.gov (United States)

Min, Wei; Xie, X. Sunney; Bagchi, Biman

2009-08-01

Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

Transport and phosphorylation of choline in higher plant cells. Phosphorus-31 nuclear magnetic resonance studies

Energy Technology Data Exchange (ETDEWEB)

Bligny, R.; Foray, M.F.; Roby, C.; Douce, R.

1989-03-25

When sycamore cells were suspended in basal medium containing choline, the latter was taken up by the cells very rapidly. A facilitated diffusion system appertained at low concentrations of choline and exhibited Michaelis-Menten kinetics. At higher choline concentrations simple diffusion appeared to be the principal mode of uptake. Addition of choline to the perfusate of compressed sycamore cells monitored by /sup 31/P NMR spectroscopy resulted in a dramatic accumulation of P-choline in the cytoplasmic compartment containing choline kinase and not in the vacuole. The total accumulation of P-choline over a 10-h period exhibited Michaelis-Menten kinetics. During this period, in the absence of Pi in the perfusion medium there was a marked depletion of glucose-6-P, and the cytoplasmic Pi resonance disappeared almost completely. When a threshold of cytoplasmic Pi was attained, the phosphorylation of choline was sustained by the continuous release of Pi from the vacuole although at a much lower rate. However, when 100 microM inorganic phosphate was present in the perfusion medium, externally added Pi was preferentially used to sustain P-choline synthesis. It is clear, therefore, that cytosolic choline kinase associated with a carrier-mediated transport system for choline uptake appeared as effective systems for continuously trapping cytoplasmic Pi including vacuolar Pi entering the cytoplasm.

Differential potassium influx influences growth of two cotton varieties in hydroponics

International Nuclear Information System (INIS)

Ali, L.; Maqsood, M.A.; Kanwal, S.; Aziz, T.

2010-01-01

Potassium uptake rate of two cotton (Gossypium hirsutum L.) varieties viz., NIBGE-2 and MNH-786 was investigated in nutrient solution culture having deficient K at the rate 0.3 mM and deficient K+ Na at the rate 0.3 +2.7 mM. Depletion of K from solution was monitored over a period of 24 h at regular time intervals after 0, 0.5, 1.0, 1.5, 2, 3, 4, 5, 6, 8, 10, 12 and 24 h to estimate K uptake kinetics of the roots i.e. maximum influx, I/sub max/ and the Michaelis-Menten constant, Km. NIBGE-2 had about 2-fold higher (2.0 mg g rdw-1 hr-1) I/sub max/ value for K uptake rate at deficient K+Na than that (1.207 mg g rdw-1 hr-1) for MNH-786. Higher, Michaelis-Menten constant, Km (12.82 ppm) for K uptake rate was observed in both cultivars NIBGE-2 and MNH-786 at deficient K+Na than that at deficient K. Main effects of treatments and varieties had significant (p< 0.05) effect on shoot dry matter, root dry matter, total dry matter and leaf area per plant. Maximum K influx in NIBGE-2 at deficient K and deficient K +Na was attributed to enhanced growth response as compared to that in MNH-786. (author)

Use of CdSe/ZnS luminescent quantum dots incorporated within sol-gel matrix for urea detection

International Nuclear Information System (INIS)

Duong, Hong Dinh; Rhee, Jong Il

2008-01-01

In this work, urea detection techniques based on the pH sensitivity of CdSe/ZnS QDs were developed using three types of sol-gel membranes: a QD-entrapped membrane, urease-immobilized membrane and double layer consisting of a QD-entrapped membrane and urease-immobilized membrane. The surface morphology of the sol-gel membranes deposited on the wells in a 24-well microtiter plate was investigated. The linear detection range of urea was in the range of 0-10 mM with the three types of sol-gel membranes. The urea detection technique based on the double layer consisting of the QD-entrapped membrane and urease-immobilized membrane resulted in the highest sensitivity to urea due to the Michaelis-Menten kinetic parameters. That is, the Michaelis-Menten constant (K m =2.0745 mM) of the free urease in the QD-entrapped membrane was about 4-fold higher than that (K m =0.549 mM) of the immobilized urease in the urease-immobilized membrane and about 12-fold higher than that (K m =0.1698 mM) of the immobilized urease in the double layer. The good stability of the three sol-gel membranes for urea sensing over 2 months showed that the use of sol-gel membranes immobilized with QDs or an enzyme is suitable for biomedical and environmental applications

Use of CdSe/ZnS luminescent quantum dots incorporated within sol-gel matrix for urea detection.

Science.gov (United States)

Duong, Hong Dinh; Rhee, Jong Il

2008-09-19

In this work, urea detection techniques based on the pH sensitivity of CdSe/ZnS QDs were developed using three types of sol-gel membranes: a QD-entrapped membrane, urease-immobilized membrane and double layer consisting of a QD-entrapped membrane and urease-immobilized membrane. The surface morphology of the sol-gel membranes deposited on the wells in a 24-well microtiter plate was investigated. The linear detection range of urea was in the range of 0-10mM with the three types of sol-gel membranes. The urea detection technique based on the double layer consisting of the QD-entrapped membrane and urease-immobilized membrane resulted in the highest sensitivity to urea due to the Michaelis-Menten kinetic parameters. That is, the Michaelis-Menten constant (K(m)=2.0745mM) of the free urease in the QD-entrapped membrane was about 4-fold higher than that (K(m)=0.549mM) of the immobilized urease in the urease-immobilized membrane and about 12-fold higher than that (K(m)=0.1698mM) of the immobilized urease in the double layer. The good stability of the three sol-gel membranes for urea sensing over 2 months showed that the use of sol-gel membranes immobilized with QDs or an enzyme is suitable for biomedical and environmental applications.

ZnO nanowire-based glucose biosensors with different coupling agents

Energy Technology Data Exchange (ETDEWEB)

Jung, Juneui [Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749 (Korea, Republic of); Lim, Sangwoo, E-mail: swlim@yonsei.ac.kr [Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749 (Korea, Republic of)

2013-01-15

Highlights: Black-Right-Pointing-Pointer Fabrication of ZnO nanowire-based glucose biosensors using different coupling agents. Black-Right-Pointing-Pointer Highest sensitivity for (3-aminopropyl)methyldiethoxysilane-treated biosensor. Black-Right-Pointing-Pointer Larger amount of glucose oxidase and lower electron transfer resistance for (3-aminopropyl)methyldiethoxysilane-treated biosensor. - Abstract: ZnO-nanowire-based glucose biosensors were fabricated by immobilizing glucose oxidase (GOx) onto a linker attached to ZnO nanowires. Different coupling agents were used, namely (3-aminopropyl)trimethoxysilane (APTMS), (3-aminopropyl)triethoxysilane (APTES), and (3-aminopropyl)methyldiethoxysilane (APS), to increase the affinity of GOx binding to ZnO nanowires. The amount of GOx immobilized on the ZnO nanowires, the performance, sensitivity, and Michaelis-Menten constant of each biosensor, and the electron transfer resistance through the biosensor were all measured in order to investigate the effect of the coupling agent on the ZnO nanowire-based biosensor. Among the different biosensors, the APS-treated biosensor had the highest sensitivity (17.72 {mu}A cm{sup -2} mM{sup -1}) and the lowest Michaelis-Menten constant (1.37 mM). Since APS-treated ZnO nanowires showed the largest number of C-N groups and the lowest electron transfer resistance through the biosensor, we concluded that these properties were the key factors in the performance of APS-treated glucose biosensors.

Rethinking fundamentals of enzyme action.

Science.gov (United States)

Northrop, D B

1999-01-01

Despite certain limitations, investigators continue to gainfully employ concepts rooted in steady-state kinetics in efforts to draw mechanistically relevant inferences about enzyme catalysis. By reconsidering steady-state enzyme kinetic behavior, this review develops ideas that allow one to arrive at the following new definitions: (a) V/K, the ratio of the maximal initial velocity divided by the Michaelis-Menten constant, is the apparent rate constant for the capture of substrate into enzyme complexes that are destined to yield product(s) at some later point in time; (b) the maximal velocity V is the apparent rate constant for the release of substrate from captured complexes in the form of free product(s); and (c) the Michaelis-Menten constant K is the ratio of the apparent rate constants for release and capture. The physiologic significance of V/K is also explored to illuminate aspects of antibiotic resistance, the concept of "perfection" in enzyme catalysis, and catalytic proficiency. The conceptual basis of congruent thermodynamic cycles is also considered in an attempt to achieve an unambiguous way for comparing an enzyme-catalyzed reaction with its uncatalyzed reference reaction. Such efforts promise a deeper understanding of the origins of catalytic power, as it relates to stabilization of the reactant ground state, stabilization of the transition state, and reciprocal stabilizations of ground and transition states.

Solving the Schrödinger equation of molecules by relaxing the antisymmetry rule: Inter-exchange theory.

Science.gov (United States)

Nakatsuji, Hiroshi; Nakashima, Hiroyuki

2015-05-21

The Schrödinger equation (SE) and the antisymmetry principle constitute the governing principle of chemistry. A general method of solving the SE was presented before as the free complement (FC) theory, which gave highly accurate solutions for small atoms and molecules. We assume here to use the FC theory starting from the local valence bond wave function. When this theory is applied to larger molecules, antisymmetrizations of electronic wave functions become time-consuming and therefore, an additional breakthrough is necessary concerning the antisymmetry principle. Usually, in molecular calculations, we first construct the wave function to satisfy the antisymmetry rule, "electronic wave functions must be prescribed to be antisymmetric for all exchanges of electrons, otherwise bosonic interference may disturb the basis of the science." Starting from determinantal wave functions is typical. Here, we give an antisymmetrization theory, called inter-exchange (iExg) theory, by dividing molecular antisymmetrizations to those within atoms and between atoms. For the electrons belonging to distant atoms in a molecule, only partial antisymmetrizations or even no antisymmetrizations are necessary, depending on the distance between the atoms. So, the above antisymmetry rule is not necessarily followed strictly to get the results of a desired accuracy. For this and other reasons, the necessary parts of the antisymmetrization operations become very small as molecules become larger, leading finally to the operation counts of lower orders of N, the number of electrons. This theory creates a natural antisymmetrization method that is useful for large molecules.

nitrogen saturation in stream ecosystems

OpenAIRE

Earl, S. R.; Valett, H. M.; Webster, J. R.

2006-01-01

The concept of nitrogen (N) saturation has organized the assessment of N loading in terrestrial ecosystems. Here we extend the concept to lotic ecosystems by coupling Michaelis-Menten kinetics and nutrient spiraling. We propose a series of saturation response types, which may be used to characterize the proximity of streams to N saturation. We conducted a series of short-term N releases using a tracer ((NO3)-N-15-N) to measure uptake. Experiments were conducted in streams spanning a gradient ...

Metabolomics on integrated circuit

OpenAIRE

Cheah, Boon Chong; MacDonald, Alasdair I.; Barrett, Michael P.; Cumming, David R.S.

2017-01-01

We have demonstrated a chip-based diagnostics tool for the quantification of metabolites, using specific enzymes, to study enzyme kinetics and calculate the Michaelis-Menten constant. An array of 256×256 ion-sensitive field effect transistors (ISFETs) fabricated in a complementary metal oxide semiconductor (CMOS) process is used for this prototype. We have used hexokinase enzyme reaction on the ISFET CMOS chip with glucose concentration in the physiological range of 0.05 mM – 231 mM and succe...

Extraction of Crude Chitinase from Higher Plants and their Chitin-Hydrolysis Activities; Kotosyokubutu yurai kichinaze no chusyutu to kichin bunkai kassei

Energy Technology Data Exchange (ETDEWEB)

Kondo, K.; Harada, K.; Shibata, M.; Maeda, R. [Doshisha Univ., Kyoto (Japan). Faculty of Engineering

1997-07-10

To prepare a purified chitinase from higher plants, firstly, crude enzymes were extracted from six higher plants, namely, radish seeds, sunflower seeds, watermelon seeds, bamboo leaves, orange skin, and persimmon skin. Using these crude enzymes, pH dependencies of hydrolysis reaction of colloidal chitin are investigated. For radish seeds and bamboo leaves, which have relatively high activities, the kinetics of enzymatic reaction are studies. It is clear that these reactions obey Michaelis-Menten kinetics. 7 refs., 3 figs., 2 tabs.

Effect and Modeling of Glucose Inhibition and In Situ Glucose Removal During Enzymatic Hydrolysis of Pretreated Wheat Straw

DEFF Research Database (Denmark)

Andric, Pavle; Meyer, Anne S.; Jensen, Peter Arendt

2010-01-01

The enzymatic hydrolysis of lignocellulosic biomass is known to be product-inhibited by glucose. In this study, the effects on cellulolytic glucose yields of glucose inhibition and in situ glucose removal were examined and modeled during extended treatment of heat-pretreated wheat straw......, during 96 h of reaction. When glucose was removed by dialysis during the enzymatic hydrolysis, the cellulose conversion rates and glucose yields increased. In fact, with dialytic in situ glucose removal, the rate of enzyme-catalyzed glucose release during 48-72 h of reaction recovered from 20......-40% to become approximate to 70% of the rate recorded during 6-24 h of reaction. Although Michaelis-Menten kinetics do not suffice to model the kinetics of the complex multi-enzymatic degradation of cellulose, the data for the glucose inhibition were surprisingly well described by simple Michaelis...

Inclusion of exact exchange in the noniterative partial-differential-equation method of electron-molecule scattering - Application to e-N2

Science.gov (United States)

Weatherford, C. A.; Onda, K.; Temkin, A.

1985-01-01

The noniterative partial-differential-equation (PDE) approach to electron-molecule scattering of Onda and Temkin (1983) is modified to account for the effects of exchange explicitly. The exchange equation is reduced to a set of inhomogeneous equations containing no integral terms and solved noniteratively in a difference form; a method for propagating the solution to large values of r is described; the changes in the polarization potential of the original PDE method required by the inclusion of exact static exchange are indicated; and the results of computations for e-N2 scattering in the fixed-nuclei approximation are presented in tables and graphs and compared with previous calculations and experimental data. Better agreement is obtained using the modified PDE method.

The sociology of language in Johann David Michaelis's dissertation of 1760.

Science.gov (United States)

Smith, R N

1976-10-01

In 1759 Johann David Michaelis won a prize from the Prussian Royal Academy for his essay Beantwortung der Frage von dem Einfluss der Meinungen in die Sprache, und der sprache in die Meinungen. The essay was published in the following year and translated into French in 1762, into English in 1769, and into Dutch in 1771. The work has two major themes--linguistic relativity and language change--with ancillary discussions of language in general and of homonymy. Its most significant contribution to the theory of language is its discussion of linguistic relativity, especially in its manifestations in the influence of language on thought. Given the intellectual milieu of the work where inquiry was centered on the origin of language and language universals, it stands as one of the few discussions of this topic and it is also one of the most fruitful discussions of linguistic relativity for any period of history.

Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.

Science.gov (United States)

Burnham, Daniel R; Nijholt, Bas; De Vlaminck, Iwijn; Quan, Jinhua; Yusufzai, Timur; Dekker, Cees

2017-05-05

We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces. The dependence of the closing rate on both ionic strength and HARP concentration indicates that removal of RPA occurs via an association-dissociation mechanism where HARP does not remain associated with the DNA. The enzyme exhibits classical Michaelis-Menten kinetics and acts cooperatively with a Hill coefficient of 3 ± 1. Our work also allows the determination of some important features of RPA-bubble structures at low supercoiling, including the existence of multiple bubbles and that RPA molecules are mis-registered on the two strands. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Purification and characterization of a platelet aggregation inhibitor and anticoagulant Cc 5_NTase, CD 73-like, from Cerastes cerastes venom.

Science.gov (United States)

Saoud, Samah; Chérifi, Fatah; Benhassine, Traki; Laraba-Djebari, Fatima

2017-05-01

The present study is the first attempt to report the characterization of a nucleotidase from Cerastes cerastes venom. A 70 kDa 5'-nucleotidase (Cc-5'NTase) was purified to homogeneity. The amino acid sequence of Cc-5'NTase displayed high homology with many nucleotidases. Its activity was optimal at pH 7 with a specific hydrolytic activity toward mono-, di-, and triphosphate adenylated nucleotides. Cc-5'NTase preferentially hydrolyzed ADP and obeyed Michaelis-Menten kinetics. Among the metals and inhibitors tested, Ni 2+ and Mg 2+ completely potentiated enzyme activity, whereas EGTA, PMSF, iodoacetamide, vanillic acid, vanillyl mandelic acid, and 1,10-phenanthroline partially abolished its activity. Cc-5'NTase was not lethal for mice at 5 mg/kg and exhibited in vivo anticoagulant effect. It also dose-dependently inhibited adenosine diphosphate-induced platelet aggregation by converting adenosine diphosphate to adenosine and prohibited arachidonic acid-induced aggregation but was not effective on fibrinogen-induced aggregation. Cc-5'NTase could be a good tool as pharmacological molecule in thrombosis diagnostic and/or therapy. © 2016 Wiley Periodicals, Inc.

Nitrogen saturation in stream ecosystems.

Science.gov (United States)

Earl, Stevan R; Valett, H Maurice; Webster, Jackson R

2006-12-01

The concept of nitrogen (N) saturation has organized the assessment of N loading in terrestrial ecosystems. Here we extend the concept to lotic ecosystems by coupling Michaelis-Menten kinetics and nutrient spiraling. We propose a series of saturation response types, which may be used to characterize the proximity of streams to N saturation. We conducted a series of short-term N releases using a tracer (15NO3-N) to measure uptake. Experiments were conducted in streams spanning a gradient of background N concentration. Uptake increased in four of six streams as NO3-N was incrementally elevated, indicating that these streams were not saturated. Uptake generally corresponded to Michaelis-Menten kinetics but deviated from the model in two streams where some other growth-critical factor may have been limiting. Proximity to saturation was correlated to background N concentration but was better predicted by the ratio of dissolved inorganic N (DIN) to soluble reactive phosphorus (SRP), suggesting phosphorus limitation in several high-N streams. Uptake velocity, a reflection of uptake efficiency, declined nonlinearly with increasing N amendment in all streams. At the same time, uptake velocity was highest in the low-N streams. Our conceptual model of N transport, uptake, and uptake efficiency suggests that, while streams may be active sites of N uptake on the landscape, N saturation contributes to nonlinear changes in stream N dynamics that correspond to decreased uptake efficiency.

Quantifying stream nutrient uptake from ambient to saturation with instantaneous tracer additions

Science.gov (United States)

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.

A Critical View on In Vitro Analysis of P-glycoprotein (P-gp) Transport Kinetics.

Science.gov (United States)

Saaby, Lasse; Brodin, Birger

2017-09-01

Transport proteins expressed in the different barriers of the human body can have great implications on absorption, distribution, and excretion of drug compounds. Inhibition or saturation of a transporter can potentially alter these absorbtion, distribution, metabolism and elimination properties and thereby also the pharmacokinetic profile and bioavailability of drug compounds. P-glycoprotein (P-gp, ABCB1) is an efflux transporter which is present in most of the barriers of the body, including the small intestine, the blood-brain barrier, the liver, and the kidney. In all these tissues, P-gp may mediate efflux of drug compounds and may also be a potential site for drug-drug interactions. Consequently, there is a need to be able to predict the saturation and inhibition of P-gp and other transporters in vivo. For this purpose, Michaelis-Menten steady-state analysis has been applied to estimate kinetic parameters, such as K m and V max , for carrier-mediated transport, whereas half-maximal inhibitor concentration (IC 50 ) and the disassociation constant for an inhibitor/P-gp complex (K i ) have been determined to estimate P-gp inhibition. This review addresses in vitro methods commonly used to study P-gp transport kinetics and aims at providing a critical evaluation of the application of steady-state Michaelis-Menten analysis of kinetic parameters for substrate/P-gp interactions. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Depuración aerobia de los efluentes resultantes del proceso de biometanización del alpechín

Directory of Open Access Journals (Sweden)

Borja Padilla, R.

1992-02-01

Full Text Available A study of aerobic treatment in batch regime of the effluents produced in the olive mill wastewater biomethanation process was carried out. An 83% of effluents organic substances was removal after the third day of fermentation. The substrate removal rate follows a zero-order kinetic for high concentrations, and a first-order kinetic for low organic matter concentration, during the last days of fermentation. The kinetic parameters (q_máx and K were obtained from Michaelis- Menten model.

Se ha efectuado un estudio del proceso de depuración aerobia, en régimen discontinuo, de los efluentes procedentes del proceso de depuración anaerobia o biometanización del alpechín. Se comprueba que el 83% de la materia orgánica presente en este efluente se elimina a partir del tercer día de fermentación. La eliminación de sustrato sigue una cinética de orden cero para altas concentraciones del mismo y una cinética de primer orden para bajas concentraciones de materia orgánica, es decir, durante los últimos días de fermentación. Se aplica el modelo de Michaelis-Menten de eliminación de sustrato para la obtención de los parámetros cinéticos q_máx y K_s que rigen este proceso.

Comparison of biological H2S removal characteristics between a composite packing material with and without functional microorganisms

Science.gov (United States)

Zhu, Rencheng; Li, Shunyi; Bao, Xiaofeng; Dumont, Éric

2017-02-01

The performances of two identical biofilters, filled with a new composite packing material (named CM-5) embedded with functional microorganisms or sterilized CM-5 without microorganisms, were investigated for H2S treatment. Running parameters in terms of microbial counts, pressure drops, and inlet and outlet H2S concentrations were measured. The results show that the microbial count of the CM-5 was approximately ×105 CFU/g before being filled into the biofilter, while that of the sterilized CM-5 was negligible. The functional microorganisms embedded in CM-5 adapted to the environment containing H2S quickly. In most cases, pressure drops of the CM-5 biofilter were slightly higher than those of the sterilized CM-5 biofilter when the gas flow rate was 0.6-2.5 m3/h. The maximum elimination capacity (EC) of the CM-5 biofilter in treating H2S could reach up to 65 g/(m3·h) when the loading rate (LR) was approximately 80 g/(m3·h). If the LR was much higher, the measured EC showed a slight downward trend. The experimental ECs of biofilters were fitted by two typical dynamic models: the Michaelis-Menten model and the Haldane model. Compared with the Michaelis-Menten model, the Haldane model fit the experimental ECs better for the two biofilters because of the presence of the substrate inhibition behaviour.

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters.

Science.gov (United States)

Bristow, Laura A; Dalsgaard, Tage; Tiano, Laura; Mills, Daniel B; Bertagnolli, Anthony D; Wright, Jody J; Hallam, Steven J; Ulloa, Osvaldo; Canfield, Donald E; Revsbech, Niels Peter; Thamdrup, Bo

2016-09-20

A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core (Chile at manipulated O2 levels between 5 nmol⋅L(-1) and 20 μmol⋅L(-1) Rates of both processes were detectable in the low nanomolar range (5-33 nmol⋅L(-1) O2), but demonstrated a strong dependence on O2 concentrations with apparent half-saturation constants (Kms) of 333 ± 130 nmol⋅L(-1) O2 for ammonium oxidation and 778 ± 168 nmol⋅L(-1) O2 for nitrite oxidation assuming one-component Michaelis-Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis-Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.

Molar mass, radius of gyration and second virial coefficient from new static light scattering equations for dilute solutions: application to 21 (macro)molecules.

Science.gov (United States)

Illien, Bertrand; Ying, Ruifeng

2009-05-11

New static light scattering (SLS) equations for dilute binary solutions are derived. Contrarily to the usual SLS equations [Carr-Zimm (CZ)], the new equations have no need for the experimental absolute Rayleigh ratio of a reference liquid and solely rely on the ratio of scattered intensities of solutions and solvent. The new equations, which are based on polarizability equations, take into account the usual refractive index increment partial differential n/partial differential rho(2) complemented by the solvent specific polarizability and a term proportional to the slope of the solution density rho versus the solute mass concentration rho(2) (density increment). Then all the equations are applied to 21 (macro)molecules with a wide range of molar mass (0.2equations clearly achieve a better agreement with supplier M values. For macromolecules (M>500 kg mol(-1)), for which the scattered intensity is no longer independent of the scattering angle, the new equations give the same value of the radius of gyration as the CZ equation and consistent values of the second virial coefficient.

An equation for the prediction of human skin permeability of neutral molecules, ions and ionic species.

Science.gov (United States)

Zhang, Keda; Abraham, Michael H; Liu, Xiangli

2017-04-15

Experimental values of permeability coefficients, as log K p , of chemical compounds across human skin were collected by carefully screening the literature, and adjusted to 37°C for the effect of temperature. The values of log K p for partially ionized acids and bases were separated into those for their neutral and ionic species, forming a total data set of 247 compounds and species (including 35 ionic species). The obtained log K p values have been regressed against Abraham solute descriptors to yield a correlation equation with R 2 =0.866 and SD=0.432 log units. The equation can provide valid predictions for log K p of neutral molecules, ions and ionic species, with predictive R 2 =0.858 and predictive SD=0.445 log units calculated by the leave-one-out statistics. The predicted log K p values for Na + and Et 4 N + are in good agreement with the observed values. We calculated the values of log K p of ketoprofen as a function of the pH of the donor solution, and found that log K p markedly varies only when ketoprofen is largely ionized. This explains why models that neglect ionization of permeants still yield reasonable statistical results. The effect of skin thickness on log K p was investigated by inclusion of two indicator variables, one for intermediate thickness skin and one for full thickness skin, into the above equation. The newly obtained equations were found to be statistically very close to the above equation. Therefore, the thickness of human skin used makes little difference to the experimental values of log K p . Copyright © 2017 Elsevier B.V. All rights reserved.

General chemistry

International Nuclear Information System (INIS)

2009-01-01

This book explains chemical equilibrium with nature and characteristic of chemical equilibrium, law of mass action and direction of chemical equilibrium, acid-base equilibrium with principle of acid and base and amino acid, solubility and precipitation equilibrium with equilibrium of solubility, complex ion and solubility, electrochemistry on oxidation-reduction reaction, battery and fuel cell, decay and electrolysis, chemical reaction speed and nuclear reaction with Michaelis-Menten mechanism safety of nuclear, transition elements and coordination compound with introduction, name, structure and ligand EDTA and solid structure with categorization of solid and unit cell.

A kinetic model for the penicillin biosynthetic pathway in

DEFF Research Database (Denmark)

Nielsen, Jens; Jørgensen, Henrik

1996-01-01

A kinetic model for the first two steps in the penicillin biosynthetic pathway, i.e. the ACV synthetase (ACVS) and the isopenicillin N synthetase (IPNS) is proposed. The model is based on Michaelis-Menten type kinetics with non-competitive inhibition of the ACVS by ACV, and competitive inhibition...... of the IPNS by glutathione. The model predicted flux through the pathway corresponds well with the measured rate of penicillin biosynthesis. From the kinetic model the elasticity coefficients and the flux control coefficients are calculated throughout a fed-batch cultivation, and it is found...

Boltzmann equation analysis of electron-molecule collision cross sections in water vapor and ammonia

International Nuclear Information System (INIS)

Yousfi, M.; Benabdessadok, M.D.

1996-01-01

Sets of electron-molecule collision cross sections for H 2 O and NH 3 have been determined from a classical technique of electron swarm parameter unfolding. This deconvolution method is based on a simplex algorithm using a powerful multiterm Boltzmann equation analysis established in the framework of the classical hydrodynamic approximation. It is well adapted for the simulation of the different classes of swarm experiments (i.e., time resolved, time of flight, and steady state experiments). The sets of collision cross sections that exist in the literature are reviewed and analyzed. Fitted sets of cross sections are determined for H 2 O and NH 3 which exhibit features characteristic of polar molecules such as high rotational excitation collision cross sections. The hydrodynamic swarm parameters (i.e., drift velocity, longitudinal and transverse diffusion coefficients, ionization and attachment coefficients) calculated from the fitted sets are in excellent agreement with the measured ones. These sets are finally used to calculate the transport and reaction coefficients needed for discharge modeling in two cases of typical gas mixtures for which experimental swarm data are very sparse or nonexistent (i.e., flue gas mixtures and gas mixtures for rf plasma surface treatment). copyright 1996 American Institute of Physics

Electric response of a metal-molecule-metal junction to laser pulse by solving hierarchical equations of motion

Energy Technology Data Exchange (ETDEWEB)

Cao, Hui, E-mail: yccaoh@hotmail.com; Zhang, Mingdao; Tao, Tao; Song, Mingxia; Zhang, Chaozhi, E-mail: chzhzhang@sohu.com [Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, Jiangsu (China)

2015-02-28

We have combined the quantum dissipative theory and the time dependent density functional theory to perform the first principle calculation of laser induced quantum dynamical electron transport through a molecule weak bridged to two electrodes. The formalism of hierarchical equations of motion based on non-equilibrium Green’s function theory has been taken in this work. Numerical simulations of optical absorption spectra of benzene, laser induced transient current without and with bias, charge pumping effect, as well as the spectrum analysis from the current in Au-benzene-Au molecular junction are presented and discussed.

Effect of wine inhibitors on the proteolytic activity of papain from Carica papaya L. latex.

Science.gov (United States)

Benucci, Ilaria; Esti, Marco; Liburdi, Katia

2015-01-01

The influence of potential inhibitors naturally present in wine on the proteolytic activity of papain from Carica papaya latex was investigated to evaluate its applicability in white wine protein haze stabilization. Enzymatic activity was tested against a synthetic tripeptide chromogenic substrate in wine-like acidic medium that consisted of tartaric buffer (pH 3.2) supplemented with ethanol, free sulfur dioxide (SO2 ), grape skin and seed tannins within the average ranges of concentrations that are typical in wine. The diagnosis of inhibition type, performed with the graphical method, demonstrated that all of tested wine constituents were reversible inhibitors of papain. The strongest inhibition was exerted by free SO2 , which acted as a mixed-type inhibitor, similar to grape skin and seed tannins. Finally, when tested in table white wines, the catalytic activity of papain, even when if it was ascribable to the hyperbolic behavior of Michaelis-Menten equation, was determined to be strongly affected by free SO2 and total phenol level. © 2014 American Institute of Chemical Engineers.

Kinetic comparison of microbial assemblages for the anaerobic treatment of wastewater with high sulfate and heavy metal contents.

Science.gov (United States)

Sinbuathong, Nusara; Sirirote, Pramote; Liengcharernsit, Winai; Khaodhiar, Sutha; Watts, Daniel J

2009-01-01

Mixed-microbial assemblages enriched from a septic tank, coastal sediment samples, the digester sludge of a brewery wastewater treatment plant and acidic sulfate soil samples were compared on the basis of growth rate, waste and sulfate reduction rate under sulfate reducing conditions at 30 degrees C. The specific growth rate of various cultures was in the range 0.0013-0.0022 hr(-1). Estimates of waste and sulfate reduction rate were obtained by fitting substrate depletion and sulfate reduction data with the Michaelis-Menten equation. The waste reduction rates were in the range 4x10(-8)-1x10(-7) I mg(-1) hr(-1) and generally increased in the presence of copper, likely by copper sulfide precipitation that reduced sulfide and copper toxicity and thus protected the anaerobic microbes. Anaerobic microorganisms from a brewery digester sludge were found to be the most appropriate culture for the treatment of wastewater with high sulfate and heavy metal content due to their growth rate, and waste and sulfate reduction rate.

Conversion of Cassava Starch to Produce Glucose and Fructose by Enzymatic Process Using Microwave Heating

Directory of Open Access Journals (Sweden)

Sumardiono Siswo

2018-01-01

Full Text Available In this study, variation of glycosidase enzyme concentration and saccharification time on enzymatic hydrolysis using microwave have been investigated. Concentration and kinetic parameters rate of glucose and fructose were analyzed. Cassava starch was liquefied and gelatinized by microwave at 80°C. The gelatinized starch was saccharified at 60°C using (0.2;0.4;0.6;0.8;1% (w/v glycosidase enzyme for 24, 48 and 72 hours. The glucose which has been saccharified with 1% glycosidase enzyme for 72 hours gave highest conversion 66.23 %. The optimization process by multilevel reaction gave the highest conversion at enzyme concentrations 0.88 %and saccharification time 29 hours that 68.82%. The highest conversion of glucose was isomerized to fructose. The fructose which has been isomerized for 180 minutes gave highest conversion 20.05 %. The kinetics enzymatic reaction was approached and determined by Michaelis - Menten equation, Km and Vmax of reaction for glucose 22.94 g/L; 2.70 g/L hours and for fructose 3.39 g/L; 0.38 g/L. min respectively.

Determinação das propriedades catalíticas em meio aquoso e orgânico da lipase de Candida rugosa imobilizada em celulignina quimicamente modificada por carbonildiimidazol Assessment of catalytic properties in aqueous and organic media of lipase from Candida rugosa immobilized on wood cellulignin activated with carbonyldiimidazole

Directory of Open Access Journals (Sweden)

Fabrício M. Gomes

2006-07-01

Full Text Available Microbial lipase from Candida rugosa was immobilized by covalent binding on wood cellulignin (Eucaliptus grandis chemically modified with carbonyldiimidazole. The immobilized system was fully evaluated in aqueous (olive oil hydrolysis and organic (ester synthesis media. A comparative study between free and immobilized lipase was carried out in terms of pH, temperature and thermal stability. A higher pH value (8.0 was found optimal for the immobilized lipase. The optimal reaction temperature shifted from 37 °C for the free lipase to 45 °C for the immobilized lipase. The pattern of heat stability indicated that the immobilization process tends to stabilize the enzyme. Kinetics tests at 37 °C following the hydrolysis of olive oil obeyed the Michaelis-Menten rate equation. Values for Km = 924.9 mM and Vmax = 198.3 U/mg were lower than for free lipase, suggesting that the affinity towards the substrate changed and the activity of the immobilized lipase decreased during the course of immobilization. The immobilized derivative was also tested in the ester synthesis from several alcohols and carboxylic acids.

Enzymatic oxidation of rutin by horseradish peroxidase: kinetic mechanism and identification of a dimeric product by LC-Orbitrap mass spectrometry.

Science.gov (United States)

Savic, Sasa; Vojinovic, Katarina; Milenkovic, Sanja; Smelcerovic, Andrija; Lamshoeft, Marc; Petronijevic, Zivomir

2013-12-15

Flavonoid oxidation is important issue in food processing and quality. The kinetic mechanism of enzymatic oxidation of rutin by horseradish peroxidase (HRP) was studied. Rutin oxidation reaction was followed by recording of spectral changes over the time at 360 nm. The studied oxidation is mostly enzymatic and less part non-enzymatic. The reaction with HRP has a higher rate compared with the reaction without of HRP, whereby is part of non-enzymatic reaction about 10% of the total reaction. Kinetic parameters were determined from graphics of linear Michaelis-Menten equation, and it was found that investigated reactions of rutin oxidation by HRP take place in a ping-pong kinetic mechanism. High resolution HPLC-MS analysis of the mixture of oxidized products of rutin revealed the presence of rutin dimer. Because of widely distribution of rutin as well as presence of peroxidases and hydrogen peroxide in fresh foods identification of this enzymatic modification product can be beneficial for foods quality and safety. Copyright © 2013 Elsevier Ltd. All rights reserved.

Uptake of oxytetracycline and its phytotoxicity to alfalfa (Medicago sativa L.)

Energy Technology Data Exchange (ETDEWEB)

Kong, W D [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Zhu, Y G [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Liang, Y C [Ministry of Agriculture Key Laboratory of Plant Nutrition and Nutrient Cycling, Institute of Soils and Fertilizers, Chinese Academy of Agricultural Sciences, Beijing 100081 (China); Zhang, J [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Smith, F A [Soil and Land Systems, School of Earth and Environmental Sciences, University of Adelaide, DP 636, Adelaide, SA 5005 (Australia); Yang, M [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China)

2007-05-15

A series of experiments were conducted in a hydroponic system to investigate the uptake of oxytetracycline (OTC) and its toxicity to alfalfa (Medicago sativa L.). OTC inhibited alfalfa shoot and root growth by up to 61% and 85%, respectively. The kinetics of OTC uptake could be well described by Michaelis-Menten equation with V {sub max} of 2.25 {mu}mol g{sup -1} fresh weight h{sup -1}, and K {sub m} of 0.036 mM. The uptake of OTC by alfalfa was strongly inhibited by the metabolic inhibitor, 2,4-DNP (2,4-dinitrophenol), at pH 3.5 and 6.0, but not by the aquaporin competitors, glycerol and Ag{sup +}. OTC uptake, however, was significantly inhibited by Hg{sup 2+}, suggesting that the inhibition of influx was due to general cellular stress rather than the specific action of Hg{sup 2+} on aquaporins. Results from the present study suggested that OTC uptake into alfalfa is an energy-dependent process. - Plant uptake of antibiotic oxytetracycline is energy-dependent.

Energetics of glucose metabolism: a phenomenological approach to metabolic network modeling.

Science.gov (United States)

Diederichs, Frank

2010-08-12

A new formalism to describe metabolic fluxes as well as membrane transport processes was developed. The new flux equations are comparable to other phenomenological laws. Michaelis-Menten like expressions, as well as flux equations of nonequilibrium thermodynamics, can be regarded as special cases of these new equations. For metabolic network modeling, variable conductances and driving forces are required to enable pathway control and to allow a rapid response to perturbations. When applied to oxidative phosphorylation, results of simulations show that whole oxidative phosphorylation cannot be described as a two-flux-system according to nonequilibrium thermodynamics, although all coupled reactions per se fulfill the equations of this theory. Simulations show that activation of ATP-coupled load reactions plus glucose oxidation is brought about by an increase of only two different conductances: a [Ca(2+)] dependent increase of cytosolic load conductances, and an increase of phosphofructokinase conductance by [AMP], which in turn becomes increased through [ADP] generation by those load reactions. In ventricular myocytes, this feedback mechanism is sufficient to increase cellular power output and O(2) consumption several fold, without any appreciable impairment of energetic parameters. Glucose oxidation proceeds near maximal power output, since transformed input and output conductances are nearly equal, yielding an efficiency of about 0.5. This conductance matching is fulfilled also by glucose oxidation of β-cells. But, as a price for the metabolic mechanism of glucose recognition, β-cells have only a limited capability to increase their power output.

High-dynamic range imaging techniques based on both color-separation algorithms used in conventional graphic arts and the human visual perception modeling

Science.gov (United States)

Lo, Mei-Chun; Hsieh, Tsung-Hsien; Perng, Ruey-Kuen; Chen, Jiong-Qiao

2010-01-01

The aim of this research is to derive illuminant-independent type of HDR imaging modules which can optimally multispectrally reconstruct of every color concerned in high-dynamic-range of original images for preferable cross-media color reproduction applications. Each module, based on either of broadband and multispectral approach, would be incorporated models of perceptual HDR tone-mapping, device characterization. In this study, an xvYCC format of HDR digital camera was used to capture HDR scene images for test. A tone-mapping module was derived based on a multiscale representation of the human visual system and used equations similar to a photoreceptor adaptation equation, proposed by Michaelis-Menten. Additionally, an adaptive bilateral type of gamut mapping algorithm, using approach of a multiple conversing-points (previously derived), was incorporated with or without adaptive Un-sharp Masking (USM) to carry out the optimization of HDR image rendering. An LCD with standard color space of Adobe RGB (D65) was used as a soft-proofing platform to display/represent HDR original RGB images, and also evaluate both renditionquality and prediction-performance of modules derived. Also, another LCD with standard color space of sRGB was used to test gamut-mapping algorithms, used to be integrated with tone-mapping module derived.

Dynamics of Electronically Excited Species in Gaseous and Condensed Phase

Science.gov (United States)

1989-12-01

evaluate the Jacobian J v we make use of the numerical algorithm developed by Stodden and Micha 16, extending it to the equations of motion in...field of the average potential V(Q). The set of equations, Eq. (57), has been recently derived by Stodden and Micha 17 by evaluating directly the...Swaminathan, C. D. Stodden , and D. A. Micha, J. Chem. Phys 99 5501 (1989). 6 R. A. Marcus, Chem. Phys. Lett. 7, 525 (1970); J. Chem. Phys. 54, 3935 (1971); 56

Stochastic models for surface diffusion of molecules

Energy Technology Data Exchange (ETDEWEB)

Shea, Patrick, E-mail: patrick.shea@dal.ca; Kreuzer, Hans Jürgen [Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia B3H 3J5 (Canada)

2014-07-28

We derive a stochastic model for the surface diffusion of molecules, starting from the classical equations of motion for an N-atom molecule on a surface. The equation of motion becomes a generalized Langevin equation for the center of mass of the molecule, with a non-Markovian friction kernel. In the Markov approximation, a standard Langevin equation is recovered, and the effect of the molecular vibrations on the diffusion is seen to lead to an increase in the friction for center of mass motion. This effective friction has a simple form that depends on the curvature of the lowest energy diffusion path in the 3N-dimensional coordinate space. We also find that so long as the intramolecular forces are sufficiently strong, memory effects are usually not significant and the Markov approximation can be employed, resulting in a simple one-dimensional model that can account for the effect of the dynamics of the molecular vibrations on the diffusive motion.

Synthesis, Surface Modification and Optical Properties of Thioglycolic Acid-Capped ZnS Quantum Dots for Starch Recognition at Ultralow Concentration

Science.gov (United States)

Tayebi, Mahnoush; Tavakkoli Yaraki, Mohammad; Ahmadieh, Mahnaz; Mogharei, Azadeh; Tahriri, Mohammadreza; Vashaee, Daryoosh; Tayebi, Lobat

2016-11-01

In this research, water-soluble thioglycolic acid-capped ZnS quantum dots (QDs) are synthesized by the chemical precipitation method. The prepared QDs are characterized using x-ray diffraction and transmission electron microscopy. Results revealed that ZnS QDs have a 2.73 nm crystallite size, cubic zinc blende structure, and spherical morphology with a diameter less than 10 nm. Photoluminescence (PL) spectroscopy is performed to determine the presence of low concentrations of starch. Four emission peaks are observed at 348 nm, 387 nm, 422 nm, and 486 nm and their intensities are quenched by increasing concentration of starch. PL intensity variations in the studied concentrations range (0-100 ppm) are best described by a Michaelis-Menten model. The Michaelis constant ( K m) for immobilized α-amylase in this system is about 101.07 ppm. This implies a great tendency for the enzyme to hydrolyze the starch as substrate. Finally, the limit of detection is found to be about 6.64 ppm.

Is oral absorption of vigabatrin carrier-mediated?

DEFF Research Database (Denmark)

Nøhr, M. K.; Juul, R. V.; Thale, Z. I.

2015-01-01

by mechanistic non-linear mixed effects modelling, evaluating PAT1-ligands as covariates on the PK parameters with a full covariate modelling approach. The oral absorption of vigabatrin was adequately described by a Michaelis-Menten type saturable absorption. Using a Michaelis constant of 32.8 mM, the model......-mediated and if the proton-coupled amino acid transporter 1 (PAT1) was involved in the absorption processes. Vigabatrin (0.3-300 mg/kg) was administered orally or intravenously to Sprague Dawley rats in the absence or presence of PAT1-ligands l-proline, l-tryptophan or sarcosine. The PK profiles of vigabatrin were described...... estimated a maximal oral absorption rate (Vmax) of 64.6 mmol/min and dose-dependent bioavailability with a maximum of 60.9%. Bioavailability was 58.5-60.8% at 0.3-30 mg/kg doses, but decreased to 46.8% at 300 mg/kg. Changes in oral vigabatrin PK after co-administration with PAT1-ligands was explained...

Quantification of in vivo metabolic kinetics of hyperpolarized pyruvate in rat kidneys using dynamic 13C MRSI.

Science.gov (United States)

Xu, Tao; Mayer, Dirk; Gu, Meng; Yen, Yi-Fen; Josan, Sonal; Tropp, James; Pfefferbaum, Adolf; Hurd, Ralph; Spielman, Daniel

2011-10-01

With signal-to-noise ratio enhancements on the order of 10,000-fold, hyperpolarized MRSI of metabolically active substrates allows the study of both the injected substrate and downstream metabolic products in vivo. Although hyperpolarized [1-(13)C]pyruvate, in particular, has been used to demonstrate metabolic activities in various animal models, robust quantification and metabolic modeling remain important areas of investigation. Enzyme saturation effects are routinely seen with commonly used doses of hyperpolarized [1-(13)C]pyruvate; however, most metrics proposed to date, including metabolite ratios, time-to-peak of metabolic products and single exchange rate constants, fail to capture these saturation effects. In addition, the widely used small-flip-angle excitation approach does not correctly model the inflow of fresh downstream metabolites generated proximal to the target slice, which is often a significant factor in vivo. In this work, we developed an efficient quantification framework employing a spiral-based dynamic spectroscopic imaging approach. The approach overcomes the aforementioned limitations and demonstrates that the in vivo (13)C labeling of lactate and alanine after a bolus injection of [1-(13)C]pyruvate is well approximated by saturatable kinetics, which can be mathematically modeled using a Michaelis-Menten-like formulation, with the resulting estimated apparent maximal reaction velocity V(max) and apparent Michaelis constant K(M) being unbiased with respect to critical experimental parameters, including the substrate dose, bolus shape and duration. Although the proposed saturatable model has a similar mathematical formulation to the original Michaelis-Menten kinetics, it is conceptually different. In this study, we focus on the (13)C labeling of lactate and alanine and do not differentiate the labeling mechanism (net flux or isotopic exchange) or the respective contribution of various factors (organ perfusion rate, substrate transport

Hidrólisis enzimática de residuos de la cosecha de caña de azúcar

Directory of Open Access Journals (Sweden)

Jairo G. Salcedo Mendoza

2012-01-01

Full Text Available Título en inglés: Hydrolysis Enzymatic of crop residues sugar cane Resumen: En esta investigación, se hidrolizó un sustrato deslignificado proveniente de residuos de la cosecha caña de azúcar  (hojas y cogollos usando un  preparado enzimático con 27.53 unidades de papel filtro (FPU, obtenido a partir de enzimas comerciales. La hidrólisis se llevó a cabo a un pH de 4.2 y una temperatura de 50 oC. Fueron analizados  modelos de inhibición por sustrato, glucosa e inhibición total por producto. Los resultados mostraron que los modelos que mejor se ajustan a los datos experimentales, son los modelos de inhibición competitiva por glucosa, con una constante de Michaelis (Km de 20.37 g/L,  velocidad máxima (Vmax 39 g/L h y una constante de inhibición  (ki de 0.442. En el caso que las relaciones  enzima – Sustrato (E/S sean mayores  de 0.5, se puede aplicar el modelo cinético de Michaelis-Menten. Palabras clave: Inhibición; modelos cinéticos; hojas y cogollos; coctel de enzimas Abstract: In this research, a delignified substrate from crops residues sugar cane residues (leaves and top cane was hydrolyzed using an enzyme preparation with 27.53 FPU. This enzyme was obtained from trade. Hydrolysis was carried out to pH of 4.2 and a temperature of 50 oC. Models of inhibition models substrate, glucose and total inhibition product was analyzed. The results showed that models that best fit the data experimental was the models competitive glucose inhibition (Km= 20.37, Vmax=39 and ki= 0.442. In the event that E/S is above 0.5, can applied kinetic models of Michaelis – Menten. Keywords: Inhibition; kinetic models; leaves and tops cane; enzyme cocktail.

A hybrid biocatalyst consisting of silver nanoparticle and naphthalenethiol self-assembled monolayer prepared for anchoring glucose oxidase and its use for an enzymatic biofuel cell

Science.gov (United States)

Christwardana, Marcelinus; Kim, Do-Heyoung; Chung, Yongjin; Kwon, Yongchai

2018-01-01

A novel hybrid biocatalyst is synthesized by the enzyme composite consisting of silver nanoparticle (AgNP), naphthalene-thiol based couplers (Naph-SH) and glucose oxidase (GOx), which is then bonded with the supporter consisting of polyethyleneimine (PEI) and carbon nanotube (CNT) (CNT/PEI/AgNPs/Naph-SH/GOx) to facilitate glucose oxidation reaction (GOR). Here, the AgNPs play a role in obstructing denaturation of the GOx molecules from the supporter because of Ag-thiol bond, while the PEIs have the AgNPs keep their states without getting ionized by hydrogen peroxide produced during anodic reaction. The Naph-SHs also prevent ionization of the AgNP by forming self-assembled monolayer on their surface. Such roles of each component enable the catalyst to form (i) hydrophobic interaction between the GOx molecules and supporter and (ii) π-conjugated electron pathway between the GOx molecules and AgNP, promoting electron transfer. Catalytic nature of the catalyst is characterized by measuring catalytic activity and performance of enzymatic biofuel cell (EBC) using the catalyst. Regarding the catalytic activity, the catalyst leads to high electron transfer rate constant (9.6 ± 0.4 s-1), low Michaelis-Menten constant (0.51 ± 0.04 mM), and low charge transfer resistance (7.3 Ω cm2) and high amount of immobilized GOx (54.6%), while regarding the EBC performance, high maximum power density (1.46 ± 0.07 mW cm-2) with superior long-term stability result are observed.

Modeling the drug transport in the anterior segment of the eye.

Science.gov (United States)

Avtar, Ram; Tandon, Deepti

2008-10-02

The aim of the present work is the development of a simple mathematical model for the time course concentration profile of topically administered drugs in the anterior chamber aqueous humor and investigation of the effects of various model parameters on the aqueous humor concentration of lipophilic and hydrophilic drugs. A simple pharmacokinetic model for the transient drug transport in the anterior segment has been developed by using the conservation of mass in the precorneal tear film, Fick's law of diffusion and Michaelis-Menten kinetics of drug metabolism in cornea, and the conservation of mass in the anterior chamber. An analytical solution describing the drug concentration in the anterior chamber has been obtained. The model predicts that an increase in the drug metabolic (consumption) rate in the corneal epithelium reduces the drug concentration in the anterior chamber for both lipophilic and hydrophilic molecules. A decrease in the clearance rate and distribution volume of the drug in the anterior chamber raises the aqueous humor concentration significantly. It is also observed that decay rate of drug concentration in the anterior chamber is higher for lipophilic molecules than that for hydrophilic molecules. The bioavailability of drugs applied topically to the eye may be improved by a rise in the precorneal tear volume, diffusion coefficient in corneal epithelium and distribution coefficient across the endothelium anterior chamber interface, and by reducing the drug metabolism, drug clearance rate and distribution volume in anterior chamber.

KINETIKA FERMENTASI SELULOSA MURNI OLEH Trichoderma reesi QM 9414 MENJADI GLUKOSA DAN PENERAPANNYA PADA JERAMI PADI BEBAS LIGNIN [Kinetics of Pure Cellulose Fermentation by Trichoderma Reesei QM 9414 to Glucose and Its Application of on Lignin Free Rice Straw

Directory of Open Access Journals (Sweden)

M Iyan Sofyan

2004-12-01

Full Text Available The objectives of this research were: 1 to determine aeration rate and substrate concentration of pure cellulose to produce maximum glucose by Trichoderma reesei QM 9414 at 30 oC, and agitation 150 rpm; 2 to study the kinetics of pure cellulose fermentation by Trichoderma reesei QM 9414 to glucose and its implication upon fermentation of the lignin free rice straw. The experiment was arranged in factorial randomized complete design in three times replication. Treatments consisted of three levels of aeration (1,00 vvm; 1,5 vvm; 2,0 vvm and three levels of substrate concentration (0,75 ; 1,00 ; 1,25 % w/v. The results showed that at the exponential phase the average specific growth of Trichoderma reesei QM 9414 was 0,05374 hour-1, the maximum glucose product concentration of pure cellulose was 0.1644 gL-1,and the oxygen transfer was 0,0328 mg L-1 hour-1. According to t-test, the kinetics of pure cellulose fermentation model just the same as the lignin free rice straw fermentation.The enzymes produced by Trichoderma reesei QM 9414 in pure cellulose fermentation media followed the Michaelis-Menten model. The enzyme kinetic parameters were the maximum growth rate was 37x10-3 hour-1 and Michaelis-Menten constant was ½ maximum μ =17,5x10-3 hour-1. The volumetric oxygen transfer (KLa using rice straw was 0,0337 mg.hour-1. The value of KLa could be used for conversion from bioreactor at laboratory scale to commercial scale design.

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

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Klipp Edda

2006-12-01

Full Text Available Abstract 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.

A highly efficient nano-cluster artificial peroxidase and its direct electrochemistry on a nano complex modified glassy carbon electrode.

Science.gov (United States)

Hong, Jun; Wang, Wei; Huang, Kun; Yang, Wei-Yun; Zhao, Ying-Xue; Xiao, Bao-Lin; Gao, Yun-Fei; Moosavi-Movahedi, Zainab; Ghourchian, Hedayatollah; Moosavi-Movahedi, Ali Akbar

2012-01-01

A nano-cluster with highly efficient peroxide activity was constructed based on nafion (NF) and cytochrome c (Cyt c). UV-Vis spectrometry and transmission electron microscopy (TEM) methods were utilized for characterization of the nano-structured enzyme or artificial peroxidase (AP). The nano-cluster was composed of a Chain-Ball structure, with an average ball size of about 40 nm. The Michaelis-Menten (K(m)) and catalytic rate (k(cat)) constants of the AP were determined to be 2.5 ± 0.4 µM and 0.069 ± 0.001 s(-1), respectively, in 50 mM PBS at pH 7.0. The catalytic efficiency of the AP was evaluated to be 0.028 ± 0.005 µM(-1) s(-1), which was 39 ± 5% as efficient as the native horseradish peroxidase (HRP). The AP was also immobilized on a functional multi-wall carbon nanotube (MWNCTs)-gold colloid nanoparticles (AuNPs) nano-complex modified glassy carbon (GC) electrode. The cyclic voltammetry of AP on the nano complex modified GC electrode showed a pair of well-defined redox peaks with a formal potential (E°') of -45 ± 2 mV (vs. Ag/AgCl) at a scan rate of 0.05 V/s. The heterogeneous electron transfer rate constant (k(s)) was evaluated to be 0.65 s(-1). The surface concentration of electroactive AP on GC electrode (Γ) was 7 × 10(-10) mol cm(-2). The apparent Michaelis-Menten constant (K(m)(app)) was 0.23 nM.

The instability of molecules in laser field and isotope separation

International Nuclear Information System (INIS)

Li, K.

1981-01-01

In the present paper the nonlinear differential equation describing the selective decomposition of a molecule as an unimolecular reaction has be deduced from the usual time dependent semi-classical Schroedinger equation. The selective conditions for the instability of a molecule are discussed. The thresholds of the required laser intensities for ICl and HCl diatomic molecules are estimated respectively, where on type of isotope molecules ought to be decomposed for hundred per cent in a laser pulse for different pulse widths. And possibly selective decomposition of the molecule without permanent dipole moment by Raman process is also discussed briefly. (orig.)

Glucose biosensing using glassy carbon electrode modified with polyhydroxy-C60, glucose oxidase and ionic-liquid.

Science.gov (United States)

Yang, Tian; Yang, Xiao-Lu; Zhang, Yu-Shuai; Xiao, BaoLin; Hong, Jun

2014-01-01

Direct electrochemistry of glucose oxidase (GOD) was achieved when an ionic liquid/GOD-Polyhydroxy-C60 functional membrane was confined on a glassy carbon electrode (GCE). The cyclic voltammograms (CVs) of the modified GCE showed a pair of redox peaks with a formal potential (E°') of - 329 ± 2 mV. The heterogeneous electron transfer constant (k(s)) was 1.43 s-1. The modified GCE response to glucose was linear in the range from 0.02 to 2.0 mM. The detection limit was 1 μM. The apparent Michaelis-Menten constant (K(m)(app)) was 1.45 mM.

Estudio de la cinética de la hidrólisis enzimática del bagazo pretratado

OpenAIRE

Albernas Carvajal, Yailet; Corsano, Gabriela; Mesa Garriga, Leyanis; Santos Herrero, Ronaldo; Gonzalez Suarez, Erenio

2016-01-01

En el estudio se determinan los parámetros fundamentales de la cinética enzimática a partir de un modelo cinético pseudo-homogéneo de Michaelis Menten, previamente estudiado con otros materiales lignocelulósicos, para determinar la velocidad de producción de Azúcares Reductores Totales (ART) en el tiempo. Para ello se emplearon los resultados obtenidos a nivel de laboratorio, en el cual se llevó a cabo la hidrólisis enzimática del bagazo previamente pretratado de forma ácida y básica. Se empl...

Estudo da dissolução oxidativa microbiológica de uma complexa amostra mineral contendo pirita (FeS2, Pirrotita (Fe1-xS e Molibdenita (MoS2 Microbiological oxidative dissolution of a complex mineral sample containing pyrite (FeS2, pyrrotite (Fe1-xS and molybdenite (MoS2

Directory of Open Access Journals (Sweden)

Wilmo E. Francisco Jr

2007-10-01

Full Text Available This work aims to study the oxidation of a complex molybdenite mineral which contains pyrite and pyrrotite, by Acidithiobacillus ferrooxidans. This study was performed by respirometric essays and bioleaching in shake flasks. Respirometric essays yielded the kinetics of mineral oxidation. The findings showed that sulfide oxidation followed classical Michaelis-Menten kinetics. Bioleaching in shake flasks allowed evaluation of chemical and mineralogical changes resulting from sulfide oxidation. The results demonstrated that pyrrotite and pyrite were completely oxidized in A. ferrooxidans cultures whereas molybdenite was not consumed. These data indicated that molybdenite was the most recalcitrant sulfide in the sample.

Microbiological oxidative dissolution of a complex mineral sample containing pyrite (FeS2), pyrrotite (Fe1-xS) and molybdenite (MoS2)

International Nuclear Information System (INIS)

Francisco Junior, Wilmo E.; Bevilaqua, Denise; Garcia Junior, Oswaldo

2007-01-01

This work aims to study the oxidation of a complex molybdenite mineral which contains pyrite and pyrrotite, by Acidithiobacillus ferroxidans. This study was performed by respirometric essays and bioleaching in shake flasks. Respirometric essays yielded the kinetics of mineral oxidation. The findings showed that sulfide oxidation followed classical Michaelis-Menten kinetics. Bioleaching in shake flasks allowed evaluation of chemical and mineralogical changes resulting from sulfide oxidation. The results demonstrated that pyrrotite and pyrite were completely oxidized in A. ferrooxidans cultures whereas molybdenite was not consumed. These data indicated that molybdenite was the most recalcitrant sulfide in the sample. (author)

Covalent immobilization of invertase on PAMAM-dendrimer modified superparamagnetic iron oxide nanoparticles

International Nuclear Information System (INIS)

Uzun, K.; Cevik, E.; Senel, M.; Soezeri, H.; Baykal, A.; Abasiyanik, M. F.; Toprak, M. S.

2010-01-01

In this study, polyamidoamine (PAMAM) dendrimer was synthesized on the surface of superparamagnetite nanoparticles to enhance invertase immobilization. The amount of immobilized enzyme on the surface-hyperbranched magnetite nanoparticle was up to 2.5 times (i.e., 250%) as much as that of magnetite nanoparticle modified with only amino silane. Maximum reaction rate (V max ) and Michaelis-Menten constant (K m ) were determined for the free and immobilized enzymes. Various characteristics of immobilized invertase such as; the temperature activity, thermal stability, operational stability, and storage stability were evaluated and results revealed that stability of the enzyme is improved upon immobilization.

Microbiological oxidative dissolution of a complex mineral sample containing pyrite (FeS{sub 2}), pyrrotite (Fe{sub 1-x}S) and molybdenite (MoS{sub 2}); Estudo da dissolucao oxidativa microbiologica de uma complexa amostra mineral contendo pirita (FeS{sub 2}), Pirrotita (Fe{sub 1-x}S) e Molibdenita (MoS{sub 2})

Energy Technology Data Exchange (ETDEWEB)

Francisco Junior, Wilmo E.; Bevilaqua, Denise; Garcia Junior, Oswaldo [UNESP, Araraquara, SP (Brazil). Inst. de Quimica. Dept. de Bioquimica e Tecnologia Quimica]. E-mail: wilmojr@bol.com.br

2007-09-15

This work aims to study the oxidation of a complex molybdenite mineral which contains pyrite and pyrrotite, by Acidithiobacillus ferroxidans. This study was performed by respirometric essays and bioleaching in shake flasks. Respirometric essays yielded the kinetics of mineral oxidation. The findings showed that sulfide oxidation followed classical Michaelis-Menten kinetics. Bioleaching in shake flasks allowed evaluation of chemical and mineralogical changes resulting from sulfide oxidation. The results demonstrated that pyrrotite and pyrite were completely oxidized in A. ferrooxidans cultures whereas molybdenite was not consumed. These data indicated that molybdenite was the most recalcitrant sulfide in the sample. (author)

Monitoring the enzymatic conversion of urea to ammonium by conventional or microchip capillary electrophoresis with contactless conductivity detection.

Science.gov (United States)

Schuchert-Shi, Aiping; Hauser, Peter C

2008-05-15

Capillary electrophoresis with contactless conductivity detection was used to directly quantify the ammonium produced in the enzymatic conversion of urea with urease. This allowed the characterization of the reaction without having to use more elaborate indirect optical methods for quantification. The maximum rate of reaction, V(max), was determined as 5.1 mmol x mL(-1) x min(-1), and the Michaelis-Menten constant, K(m), was determined as 16 mM. Furthermore, the method was successfully applied to the determination of urea in clinical samples of human blood by using a conventional capillary and a microchip device.

Estudio de la cinética de la hidrólisis enzimática del bagazo pretratado

OpenAIRE

Albernas-Carvajal, Yailet; Corsano, Gabriela; Mesa Garriga, Layanis; Santos Herrero, Ronaldo; González Suárez, Erenio

2015-01-01

En el estudio se determinan los parámetros fundamentales de la cinética enzimática a partir de un modelo cinético pseudo-homogéneo de Michaelis Menten, previamente estudiado con otros materiales lignocelulósicos, para determinar la velocidad de producción de Azúcares Reductores Totales (ART) en el tiempo. Para ello se emplearon los resultados obtenidos a nivel de laboratorio, en el cual se llevó a cabo la hidrólisis enzimática del bagazo previamente pretratado de forma ácida y básica. Se empl...

Direct Visualization of Barrier Crossing Dynamics in a Driven Optical Matter System.

Science.gov (United States)

Figliozzi, Patrick; Peterson, Curtis W; Rice, Stuart A; Scherer, Norbert F

2018-04-25

A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are inferred from ensemble measurements or the position of a transducer ( e. g., an AFM cantilever) as a surrogate variable. Direct visualization is highly desirable. Here, we achieve the direct measurement of barrier crossing trajectories by using optical microscopy to observe position and orientation changes of pairs of Ag nanoparticles, i. e. passing events, in an optical ring trap. A two-step mechanism similar to a bimolecular exchange reaction or the Michaelis-Menten scheme is revealed by analysis that combines detailed knowledge of each trajectory, a statistically significant number of repetitions of the passing events, and the driving force dependence of the process. We find that while the total event rate increases with driving force, this increase is due to an increase in the rate of encounters. There is no drive force dependence on the rate of barrier crossing because the key motion for the process involves a random (thermal) radial fluctuation of one particle allowing the other to pass. This simple experiment can readily be extended to study more complex barrier crossing processes by replacing the spherical metal nanoparticles with anisotropic ones or by creating more intricate optical trapping potentials.

Tracer kinetics: Modelling of tracer behaviour in nonlinear and nonsteady state systems exemplified by the evaluation of protein turnover in plant organs

International Nuclear Information System (INIS)

Winkler, E.

1991-01-01

If nonlinear biological processes are investigated by means of tracer experiments they can be modelled with linear kinetic equations (compartment equations) as long as the total system is in a stationary state. But if nonstationary behaviour is included considerations on the kinetics of the individual processes are necessary. Within the range of biological and agricultural investigations especially first order reactions (constant fraction processes), zero order reactions (constant amount process) and saturation reactions (Michaelis-Menten-kinetics) are to be taken into account. A rigorous treatment of data based on system theory can be preceeded by graphic-algebraic procedure which may be more or less uncertain in its results but which can easily be handled. An example is given of methodological considerations concerning the combination of evaluation procedures and the discrimination between different reaction mechanisms. It treats protein turnover in 2 different parts of growing wheat plants investigated by means of an 15 N-tracer experiment. Whereas in a stationary system (upper stalk section) linear tracer equations were sufficient irrespective of the true reaction mechanism, for protein synthesis in the upper leaf as a nonstationary system it was necessary to decide between the hypotheses of a zero order and a first order reaction. In accordance with statements in the literature the unambiguous result was a combination of protein synthesis as a zero order process and of protein degradation as a first order process. (orig.) [de

Aarne Michaël Tallgren and the International Discussion on the Bronze Age of Russia

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Timo Salminen

2017-04-01

Full Text Available This paper is on international scholarly discussion on the Bronze Age of Russia from 1908 until 1939, and in particular on the related role of the internationally renowned Finnish archaeologist Aarne Michaël Tallgren (1885–1945. How did a social network of researchers produce new interpretations and what were the key factors that distinguished the participants in the discussion? Was it a continuous process or a series of sudden changes? How did different ideological backgrounds influence the interpretations? In Western Europe, Tallgren’s most important interlocutors were Gero von Merhart, V Gordon Childe and Ellis H Minns, and in Russia V A Gorodcov and A A Spicyn. The paper is mainly based on correspondence between Tallgren and his colleagues.

Ultrasound assisted intensification of enzyme activity and its properties: a mini-review.

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Nadar, Shamraja S; Rathod, Virendra K

2017-08-22

Over the last decade, ultrasound technique has emerged as the potential technology which shows large applications in food and biotechnology processes. Earlier, ultrasound has been employed as a method of enzyme inactivation but recently, it has been found that ultrasound does not inactivate all enzymes, particularly, under mild conditions. It has been shown that the use of ultrasonic treatment at appropriate frequencies and intensity levels can lead to enhanced enzyme activity due to favourable conformational changes in protein molecules without altering its structural integrity. The present review article gives an overview of influence of ultrasound irradiation parameters (intensity, duty cycle and frequency) and enzyme related factors (enzyme concentration, temperature and pH) on the catalytic activity of enzyme during ultrasound treatment. Also, it includes the effect of ultrasound on thermal kinetic parameters and Michaelis-Menten kinetic parameters (k m and V max ) of enzymes. Further, in this review, the physical and chemical effects of ultrasound on enzyme have been correlated with thermodynamic parameters (enthalpy and entropy). Various techniques used for investigating the conformation changes in enzyme after sonication have been highlighted. At the end, different techniques of immobilization for ultrasound treated enzyme have been summarized.

Target-mediated drug disposition model and its approximations for antibody-drug conjugates.

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Gibiansky, Leonid; Gibiansky, Ekaterina

2014-02-01

Antibody-drug conjugate (ADC) is a complex structure composed of an antibody linked to several molecules of a biologically active cytotoxic drug. The number of ADC compounds in clinical development now exceeds 30, with two of them already on the market. However, there is no rigorous mechanistic model that describes pharmacokinetic (PK) properties of these compounds. PK modeling of ADCs is even more complicated than that of other biologics as the model should describe distribution, binding, and elimination of antibodies with different toxin load, and also the deconjugation process and PK of the released toxin. This work extends the target-mediated drug disposition (TMDD) model to describe ADCs, derives the rapid binding (quasi-equilibrium), quasi-steady-state, and Michaelis-Menten approximations of the TMDD model as applied to ADCs, derives the TMDD model and its approximations for ADCs with load-independent properties, and discusses further simplifications of the system under various assumptions. The developed models are shown to describe data simulated from the available clinical population PK models of trastuzumab emtansine (T-DM1), one of the two currently approved ADCs. Identifiability of model parameters is also discussed and illustrated on the simulated T-DM1 examples.

On enzyme kinetic parameters modification of gamma irradiation

International Nuclear Information System (INIS)

Ferdes, O.S.; Ferdes, M.; Turcu, G.R.

1993-01-01

To elucidate the molecular mechanisms of gamma-ray action on biomolecules there were investigated the modifications in activity and other kinetic parameters for some enzymes irradiated in pure dry state at relative high doses. There were considered bacterial and fungal α-amylases, glucoamylase and Mucor sp. protease irradiated by a 60 Co gamma-ray source in the dose range 1.0-30.0 kGy, at different dose-rates between 0.5-2.0 kGy/h, at room temperature. Considering the enzyme inactivation in this dose range, the dose-effect relationships have an expected form and depend on the irradiation conditions but not significantly on the dose rate. The catalytic properties of enzymes were modified by irradiation. By usual methods it is evidenced a direct correlation between the enzymatic activities, Michaelis-Menten constant, K m , reaction velocities, v, and the irradiation dose. These experimental findings can support a self-consistent theoretical approach on biophysical radiation action on biological active molecules like enzymes. At the same time, some enzyme behaviour to irradiation could be considered like a good biological indicator of radiation response. (Author) 4 Figs., 19 Refs

A Novel ZnO-Methylene Blue Nanocomposite Matrix for Biosensing Application

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Shibu Saha

2011-01-01

Full Text Available A novel hybrid matrix of zinc oxide-methylene blue (ZnO-MB has been successfully developed for biosensing application. The introduction of methylene blue into the ZnO thin film leads to reduction in the charge transfer resistance and suggests an increase in the electron transfer capacity of the composite. Glucose oxidase (GOx was chosen as the model enzyme and effectively immobilized on the surface of hybrid ZnO-MB nanocomposite matrix. Electrochemical measurements were employed to study biosensing response of the GOx/ZnO-MB/ITO bioelectrode as a function of glucose concentration. The low oxidation potential (−0.23 V of the hybrid bioelectrode, in a mediatorless electrolyte, makes it resistant against interference from other bio-molecules. The low value of Michaelis-Menten constant (2.65 mM indicates that immobilized GOx retains its enzymatic activity significantly on the surface of nanocomposite hybrid matrix that results in an enhanced affinity towards its substrate (glucose. The ZnO-MB nanocomposite hybrid matrix, exhibiting enhanced sensing response (0.2 μAmM−1cm−2 with long shelf-life (>10 weeks, has potential for the realization of an integrated biosensing device.

Calculation of statistic estimates of kinetic parameters from substrate uncompetitive inhibition equation using the median method

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Pedro L. Valencia

2017-04-01

Full Text Available We provide initial rate data from enzymatic reaction experiments and tis processing to estimate the kinetic parameters from the substrate uncompetitive inhibition equation using the median method published by Eisenthal and Cornish-Bowden (Cornish-Bowden and Eisenthal, 1974; Eisenthal and Cornish-Bowden, 1974. The method was denominated the direct linear plot and consists in the calculation of the median from a dataset of kinetic parameters Vmax and Km from the Michaelis–Menten equation. In this opportunity we present the procedure to applicate the direct linear plot to the substrate uncompetitive inhibition equation; a three-parameter equation. The median method is characterized for its robustness and its insensibility to outlier. The calculations are presented in an Excel datasheet and a computational algorithm was developed in the free software Python. The kinetic parameters of the substrate uncompetitive inhibition equation Vmax, Km and Ks were calculated using three experimental points from the dataset formed by 13 experimental points. All the 286 combinations were calculated. The dataset of kinetic parameters resulting from this combinatorial was used to calculate the median which corresponds to the statistic estimator of the real kinetic parameters. A comparative statistical analyses between the median method and the least squares was published in Valencia et al. [3].

Quantifying the relative contributions of different solute carriers to aggregate substrate transport

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Taslimifar, Mehdi; Oparija, Lalita; Verrey, Francois; Kurtcuoglu, Vartan; Olgac, Ufuk; Makrides, Victoria

2017-01-01

Determining the contributions of different transporter species to overall cellular transport is fundamental for understanding the physiological regulation of solutes. We calculated the relative activities of Solute Carrier (SLC) transporters using the Michaelis-Menten equation and global fitting to estimate the normalized maximum transport rate for each transporter (Vmax). Data input were the normalized measured uptake of the essential neutral amino acid (AA) L-leucine (Leu) from concentration-dependence assays performed using Xenopus laevis oocytes. Our methodology was verified by calculating Leu and L-phenylalanine (Phe) data in the presence of competitive substrates and/or inhibitors. Among 9 potentially expressed endogenous X. laevis oocyte Leu transporter species, activities of only the uniporters SLC43A2/LAT4 (and/or SLC43A1/LAT3) and the sodium symporter SLC6A19/B0AT1 were required to account for total uptake. Furthermore, Leu and Phe uptake by heterologously expressed human SLC6A14/ATB0,+ and SLC43A2/LAT4 was accurately calculated. This versatile systems biology approach is useful for analyses where the kinetics of each active protein species can be represented by the Hill equation. Furthermore, its applicable even in the absence of protein expression data. It could potentially be applied, for example, to quantify drug transporter activities in target cells to improve specificity. PMID:28091567

Construction and accuracy of partial differential equation approximations to the chemical master equation.

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Grima, Ramon

2011-11-01

The mesoscopic description of chemical kinetics, the chemical master equation, can be exactly solved in only a few simple cases. The analytical intractability stems from the discrete character of the equation, and hence considerable effort has been invested in the development of Fokker-Planck equations, second-order partial differential equation approximations to the master equation. We here consider two different types of higher-order partial differential approximations, one derived from the system-size expansion and the other from the Kramers-Moyal expansion, and derive the accuracy of their predictions for chemical reactive networks composed of arbitrary numbers of unimolecular and bimolecular reactions. In particular, we show that the partial differential equation approximation of order Q from the Kramers-Moyal expansion leads to estimates of the mean number of molecules accurate to order Ω(-(2Q-3)/2), of the variance of the fluctuations in the number of molecules accurate to order Ω(-(2Q-5)/2), and of skewness accurate to order Ω(-(Q-2)). We also show that for large Q, the accuracy in the estimates can be matched only by a partial differential equation approximation from the system-size expansion of approximate order 2Q. Hence, we conclude that partial differential approximations based on the Kramers-Moyal expansion generally lead to considerably more accurate estimates in the mean, variance, and skewness than approximations of the same order derived from the system-size expansion.

Modeling cereal starch hydrolysis during simultaneous saccharification and lactic acid fermentation; case of a sorghum-based fermented beverage, gowé.

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Mestres, Christian; Bettencourt, Munanga de J C; Loiseau, Gérard; Matignon, Brigitte; Grabulos, Joël; Achir, Nawel

2017-10-01

Gowé is an acidic beverage obtained after simultaneous saccharification and fermentation (SSF) of sorghum. A previous paper focused on modeling the growth of lactic acid bacteria during gowé processing. This paper focuses on modeling starch amylolysis to build an aggregated SSF model. The activity of α-amylase was modeled as a function of temperature and pH, and the hydrolysis rates of both native and soluble starch were modeled via a Michaelis-Menten equation taking into account the maltose and glucose inhibition constants. The robustness of the parameter estimators was ensured by step by step identification in sets of experiments conducted with different proportions of native and gelatinized starch by modifying the pre-cooking temperature. The aggregated model was validated on experimental data and showed that both the pre-cooking and fermentation parameters, particularly temperature, are significant levers for controlling not only acid and sugar contents but also the expected viscosity of the final product. This generic approach could be used as a tool to optimize the sanitary and sensory quality of fermentation of other starchy products. Copyright © 2017 Elsevier Ltd. All rights reserved.

Lipase-catalyzed synthesis of palmitanilide: Kinetic model and antimicrobial activity study.

Science.gov (United States)

Liu, Kuan-Miao; Liu, Kuan-Ju

2016-01-01

Enzymatic syntheses of fatty acid anilides are important owing to their wide range of industrial applications in detergents, shampoo, cosmetics, and surfactant formulations. The amidation reaction of Mucor miehei lipase Lipozyme IM20 was investigated for direct amidation of triacylglycerol in organic solvents. The process parameters (reaction temperature, substrate molar ratio, enzyme amount) were optimized to achieve the highest yield of anilide. The maximum yield of palmitanilide (88.9%) was achieved after 24 h of reaction at 40 °C at an enzyme concentration of 1.4% (70 mg). Kinetics of lipase-catalyzed amidation of aniline with tripalmitin has been investigated. The reaction rate could be described in terms of the Michaelis-Menten equation with a Ping-Pong Bi-Bi mechanism and competitive inhibition by both the substrates. The kinetic constants were estimated by using non-linear regression method using enzyme kinetic modules. The enzyme operational stability study showed that Lipozyme IM20 retained 38.1% of the initial activity for the synthesis of palmitanilide (even after repeated use for 48 h). Palmitanilide, a fatty acid amide, exhibited potent antimicrobial activity toward Bacillus cereus. Copyright © 2015 Elsevier Inc. All rights reserved.

The Non-Linear Child: Ontogeny, Isoniazid Concentration, and NAT2 Genotype Modulate Enzyme Reaction Kinetics and Metabolism

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Zoe Rogers

2016-09-01

Full Text Available N-acetyltransferase 2 (NAT2 catalyzes the acetylation of isoniazid to N-acetylisoniazid. NAT2 polymorphism explains 88% of isoniazid clearance variability in adults. We examined the effects of clinical and genetic factors on Michaelis-Menten reaction kinetic constants of maximum velocity (Vmax and affinity (Km in children 0–10 years old. We measured the rates of isoniazid elimination and N-acetylisoniazid production in the blood of 30 children. Since maturation effects could be non-linear, we utilized a pharmacometric approach and the artificial intelligence method, multivariate adaptive regression splines (MARS, to identify factors predicting NAT2 Vmax and Km by examining clinical, genetic, and laboratory factors in toto. Isoniazid concentration predicted both Vmax and Km and superseded the contribution of NAT2 genotype. Age non-linearly modified the NAT2 genotype contribution until maturation at ≥5.3 years. Thus, enzyme efficiency was constrained by substrate concentration, genes, and age. Since MARS output is in the form of basis functions and equations, it allows multiscale systems modeling from the level of cellular chemical reactions to whole body physiological parameters, by automatic selection of significant predictors by the algorithm.

Estimate of respiration rate and physicochemical changes of fresh-cut apples stored under different temperatures

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Cristiane Fagundes

2013-03-01

Full Text Available In this study, the influence of storage temperature and passive modified packaging (PMP on the respiration rate and physicochemical properties of fresh-cut Gala apples (Malus domestica B. was investigated. The samples were packed in flexible multilayer bags and stored at 2 °C, 5 °C, and 7 °C for eleven days. Respiration rate as a function of CO2 and O2 concentrations was determined using gas chromatography. The inhibition parameters were estimated using a mathematical model based on Michaelis-Menten equation. The following physicochemical properties were evaluated: total soluble solids, pH, titratable acidity, and reducing sugars. At 2 °C, the maximum respiration rate was observed after 150 hours. At 5 °C and 7 °C the maximum respiration rates were observed after 100 and 50 hours of storage, respectively. The inhibition model results obtained showed a clear effect of CO2 on O2 consumption. The soluble solids decreased, although not significantly, during storage at the three temperatures studied. Reducing sugars and titratable acidity decreased during storage and the pH increased. These results indicate that the respiration rate influenced the physicochemical properties.

In vitro modulation of cytochrome P450 reductase supported indoleamine 2,3-dioxygenase activity by allosteric effectors cytochrome b(5) and methylene blue.

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Pearson, Josh T; Siu, Sophia; Meininger, David P; Wienkers, Larry C; Rock, Dan A

2010-03-30

Indoleamine 2,3-dioxygenase (IDO) is a heme-containing dioxygenase involved in the degradation of several indoleamine derivatives and has been indicated as an immunosuppressive. IDO is an attractive target for therapeutic intervention in diseases which are known to capitalize on immune suppression, including cancer, HIV, and inflammatory diseases. Conventionally, IDO activity is measured through chemical reduction by the addition of ascorbate and methylene blue. Identification of potential coenzymes involved in the reduction of IDO in vivo should improve in vitro reconstitution systems used to identify potential IDO inhibitors. In this study we show that NADPH-cytochrome P450 reductase (CPR) is capable of supporting IDO activity in vitro and that oxidation of l-Trp follows substrate inhibition kinetics (k(cat) = 0.89 +/- 0.04 s(-1), K(m) = 0.72 +/- 0.15 microM, and K(i) = 9.4 +/- 2.0 microM). Addition of cytochrome b(5) to CPR-supported l-Trp incubations results in modulation from substrate inhibition to sigmoidal kinetics (k(cat) = 1.7 +/- 0.3 s(-1), K(m) = 1.5 +/- 0.9 microM, and K(i) = 1.9 +/- 0.3). CPR-supported d-Trp oxidations (+/-cytochrome b(5)) exhibit Michaelis-Menten kinetics. Addition of methylene blue (minus ascorbate) to CPR-supported reactions resulted in inhibition of d-Trp turnover and modulation of l-Trp kinetics from allosteric to Michaelis-Menten with a concurrent decrease in substrate affinity for IDO. Our data indicate that CPR is capable of supporting IDO activity in vitro and oxidation of tryptophan by IDO displays substrate stereochemistry dependent atypical kinetics which can be modulated by the addition of cytochrome b(5).

Phenytoin pharmacokinetics in critically ill trauma patients.

Science.gov (United States)

Boucher, B A; Rodman, J H; Jaresko, G S; Rasmussen, S N; Watridge, C B; Fabian, T C

1988-12-01

Preliminary data have suggested that phenytoin systemic clearance may increase during initial therapy in critically ill patients. The objectives for this study were to model the time-variant phenytoin clearance and evaluate concomitant changes in protein binding and urinary metabolite elimination. Phenytoin was given as an intravenous loading dose of 15 mg/kg followed by an initial maintenance dose of 6 mg/kg/day in 10 adult critically ill trauma patients. Phenytoin bound and unbound plasma concentrations were determined in 10 patients and urinary excretion of the metabolite p-hydroxyphenyl phenylhydantoin (p-HPPH) was measured in seven patients for 7 to 14 days. A Michaelis-Menten one-compartment model incorporating a time-variant maximal velocity (Vmax) was sufficient to describe the data and superior to a conventional time-invariant Michaelis-Menten model. Vmax for the time-variant model was defined as V'max + Vmax delta (1 - e(-kindt)). Vmax infinity is the value for Vmax when t is large. The median values (ranges) for the parameters were Km = 4.8 (2.6 to 20) mg/L, Vmax infinity = 1348 (372 to 4741) mg/day, and kind = 0.0115 (0.0045 to 0.132) hr-1. Phenytoin free fraction increased in a majority of patients during the study period, with a binding ratio inversely related to albumin. Measured urinary p-HPPH data were consistent with the proposed model. A loading and constant maintenance dose of phenytoin frequently yielded a substantial, clinically significant fall in plasma concentrations with a pattern of apparently increasing clearance that may be a consequence of changes in protein binding, induction of metabolism, or the influence of stress on hepatic metabolic capacity.

Heterotrophic and mixotrophic growth of Micractinium pusillum Fresenius in the presence of acetate and glucose: effect of light and acetate gradient concentration.

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Bouarab, L; Dauta, A; Loudiki, M

2004-06-01

The main objective of this study was to determine the importance of secondary mechanism of organic carbon utilization (mixotrophic and heterotrophic modes) in addition to CO2 fixation (photoautotrophic mode) in the green alga, Micractinium pusillum Fresenius (chlorophyta), isolated from a waste stabilization pond. The growth was studied in the presence of acetate and glucose. The incorporation rate of 14C- acetate was measured in the light and in the dark at different concentrations. Finally, in order to underline the role of photosynthesis and respiration processes in the acetate assimilation, the effect of two specific metabolic inhibitors, a specific inhibitor of photosystem II (DCMU) and an uncoupler respiratory (DNP), has been studied. The obtained results showed that M. pusillum grows in the presence of organic substrates, i.e., glucose and acetate, in the light (mixotrophic growth) as well as in the dark (Heterotrophic growth). The growth was much more important in the light than in the dark and more in the presence of glucose than of acetate. In the light, the presence of acetate led to a variation of growth parameters mumax, iotaopt, and beta. The effect of acetate gradient on the growth of the microalga was severe as soon as its concentration in the medium was higher. The acetate uptake followed a Michaelis-Menten kinetic in the light as well as in the dark. The capacity of assimilation was slightly higher in the dark. The utilization of DNP and DCMU indicates that acetate incorporation is an active process depending on both anabolic (photosynthesis) and catabolic (respiration) metabolisms, corroborating the model of the Michaelis-Menten kinetic.

An evaluation of the inhibition of human butyrylcholinesterase and acetylcholinesterase by the organophosphate chlorpyrifos oxon

International Nuclear Information System (INIS)

Shenouda, Josephine; Green, Paula; Sultatos, Lester

2009-01-01

Acetylcholinesterase (EC 3.1.1.7) and butyrylcholinesterase (EC 3.1.1.8) are enzymes that belong to the superfamily of α/β-hydrolase fold proteins. While they share many characteristics, they also possess many important differences. For example, whereas they have about 54% amino acid sequence identity, the active site gorge of acetylcholinesterase is considerably smaller than that of butyrylcholinesterase. Moreover, both have been shown to display simple and complex kinetic mechanisms, depending on the particular substrate examined, the substrate concentration, and incubation conditions. In the current study, incubation of butyrylthiocholine in a concentration range of 0.005-3.0 mM, with 317 pM human butyrylcholinesterase in vitro, resulted in rates of production of thiocholine that were accurately described by simple Michaelis-Menten kinetics, with a K m of 0.10 mM. Similarly, the inhibition of butyrylcholinesterase in vitro by the organophosphate chlorpyrifos oxon was described by simple Michaelis-Menten kinetics, with a k i of 3048 nM -1 h -1 , and a K D of 2.02 nM. In contrast to inhibition of butyrylcholinesterase, inhibition of human acetylcholinesterase by chlorpyrifos oxon in vitro followed concentration-dependent inhibition kinetics, with the k i increasing as the inhibitor concentration decreased. Chlorpyrifos oxon concentrations of 10 and 0.3 nM gave k i s of 1.2 and 19.3 nM -1 h -1 , respectively. Although the mechanism of concentration-dependent inhibition kinetics is not known, the much smaller, more restrictive active site gorge of acetylcholinesterase almost certainly plays a role. Similarly, the much larger active site gorge of butyrylcholinesterase likely contributes to its much greater reactivity towards chlorpyrifos oxon, compared to acetylcholinesterase.

The steady-state kinetics of the NADH-dependent nitrite reductase from Escherichia coli K 12. Nitrite and hydroxylamine reduction.

Science.gov (United States)

Jackson, R H; Cole, J A; Cornish-Bowden, A

1981-01-01

The reduction of both NO2- and hydroxylamine by the NADH-dependent nitrite reductase of Escherichia coli K 12 (EC 1.6.6.4) appears to follow Michaelis-Menten kinetics over a wide range of NADH concentrations. Substrate inhibition can, however, be detected at low concentrations of the product NAD+. In addition, NAD+ displays mixed product inhibition with respect to NADH and mixed or uncompetitive inhibition with respect to hydroxylamine. These inhibition characteristics are consistent with a mechanism in which hydroxylamine binds during catalysis to a different enzyme form from that generated when NAD+ is released. The apparent maximum velocity with NADH as varied substrate increases as the NAD+ concentration increases from 0.05 to 0.7 mM with 1 mM-NO2- or 100 mM-hydroxylamine as oxidized substrate. This increase is more marked for hydroxylamine reduction than for NO2- reduction. Models incorporating only one binding site for NAD can account for the variation in the Michaelis-Menten parameters for both NADH and hydroxylamine with [NAD+] for hydroxylamine reduction. According to these models, activation of the reaction occurs by reversal of an over-reduction of the enzyme by NADH. If the observed activation of the enzyme by NAD+ derives both from activation of the generation of the enzyme-hydroxylamine complex from the enzyme-NO2- complex during NO2- reduction and from activation of the reduction of the enzyme-hydroxylamine complex to form NH4+, then the variation of Vapp. for NO2- or hydroxylamine with [NAD+] is consistent with the occurrence of the same enzyme-hydroxylamine complex as an intermediate in both reactions. PMID:6279095

Substrate specificity and copper loading of the manganese-oxidizing multicopper oxidase Mnx from Bacillus sp. PL-12.

Science.gov (United States)

Butterfield, Cristina N; Tebo, Bradley M

2017-02-22

Manganese(ii) oxidation in the environment is thought to be driven by bacteria because enzymatic catalysis is many orders of magnitude faster than the abiotic processes. The heterologously purified Mn oxidase (Mnx) from marine Bacillus sp. PL-12 is made up of the multicopper oxidase (MCO) MnxG and two small Cu and heme-binding proteins of unknown function, MnxE and MnxF. Mnx binds Cu and oxidizes both Mn(ii) and Mn(iii), generating Mn(iv) oxide minerals that resemble those found on the Bacillus spore surface. Spectroscopic techniques have illuminated details about the metallo-cofactors of Mnx, but very little is known about their requirement for catalytic activity, and even less is known about the substrate specificity of Mnx. Here we quantify the canonical MCO Cu and persistent peripheral Cu bound to Mnx, and test Mnx oxidizing ability toward different substrates at varying pH. Mn(ii) appears to be the best substrate in terms of k cat , but its oxidation does not follow Michaelis-Menten kinetics, instead showing a sigmoidal cooperative behavior. Mnx also oxidizes Fe(ii) substrate, but in a Michaelis-Menten manner and with a decreased activity, as well as organic substrates. The reduced metals are more rapidly consumed than the larger organic substrates, suggesting the hypothesis that the Mnx substrate site is small and tuned for metal oxidation. Of biological relevance is the result that Mnx has the highest catalytic efficiency for Mn(ii) at the pH of sea water, especially when the protein is loaded with greater than the requisite four MCO copper atoms, suggesting that the protein has evolved specifically for Mn oxidation.

Ordinary differential equation for local accumulation time.

Science.gov (United States)

Berezhkovskii, Alexander M

2011-08-21

Cell differentiation in a developing tissue is controlled by the concentration fields of signaling molecules called morphogens. Formation of these concentration fields can be described by the reaction-diffusion mechanism in which locally produced molecules diffuse through the patterned tissue and are degraded. The formation kinetics at a given point of the patterned tissue can be characterized by the local accumulation time, defined in terms of the local relaxation function. Here, we show that this time satisfies an ordinary differential equation. Using this equation one can straightforwardly determine the local accumulation time, i.e., without preliminary calculation of the relaxation function by solving the partial differential equation, as was done in previous studies. We derive this ordinary differential equation together with the accompanying boundary conditions and demonstrate that the earlier obtained results for the local accumulation time can be recovered by solving this equation. © 2011 American Institute of Physics

Diatomic Molecules Effective Potential for an Harmonic Oscillator ...

African Journals Online (AJOL)

A model anharmonic potential was considered and was used in the Schrödinger time independent wave equation to describe a carbon monoxide molecule. Central difference scheme was used in approximating the derivative term in the Schrödinger equation leading to a tri-diagonal band system of equation. The method of ...

The repair-fixation model: general aspects and the influence of radiation quality

International Nuclear Information System (INIS)

Kiefer, J.; Loebrich, M.

1992-01-01

To explain the shape of cell survival curves after radiation action it is assumed that initial lesions are transient in nature and subject to repair or fixation. Since the underlying processes are controlled by enzymes, Michaelis-Menten kinetics are assumed. No qualitative differences between repair and fixation are postulated, the only differences being the kinetic parameters. This model yields a mathematical expression which is formally equivalent to the ''lethal-potentially-lethal'' (LPL) model. It is demonstrated that both mammalian as well as microbial survival data can be fitted. The inclusion of linear energy transfer (LET) effects is shown to be possible and is discussed qualitatively. (author)

Oxidation study of the synthetic sulfides molybdenite (MoS2) and covellite (CuS) by acidithiobacillus ferrooxidants using respirometric experiments

International Nuclear Information System (INIS)

Francisco Junior, Wilmo E.; Universidade Estadual Paulista; Bevilaqua, Denise; Garcia Junior, Oswaldo

2009-01-01

This paper analyses the oxidation of covellite and molybdenite by Acidithiobacillus ferrooxidans strain LR using respirometric experiments. The results showed that both sulfides were oxidized by A. ferrooxidans, however, the covellite oxidation was much higher than molybdenite. Regarding the kinetic oxidation, the findings revealed that just molybdenite oxidation followed the classical Michaelis-Menten kinetic. It is probably associated with the pathway which these sulfides react to chemistry-bacterial attack, what is influenced by its electronic structures. Besides, experiments conducted in the presence of Fe 3+ did not indicate alterations in molybdenite oxidation. Thus, ferric ions seem not to be essential to the sulfide oxidations. (author)

Oxidation study of the synthetic sulfides molybdenite (MoS{sub 2}) and covellite (CuS) by acidithiobacillus ferrooxidants using respirometric experiments; Estudo da oxidacao dos sulfetos sinteticos molibdenita (MoS2) e covelita (CuS) por Acidithiobacillus ferrooxidans via respirometria celular

Energy Technology Data Exchange (ETDEWEB)

Francisco Junior, Wilmo E. [Universidade Federal de Rondonia (UFRO), Porto Velho, RO (Brazil). Dept. de Quimica; Universidade Estadual Paulista (UNESP), Araraquara, SP (Brazil). Inst. de Quimica. Dept. de Bioquimica e Tecnologia Quimica], e-mail: wilmojr@bol.com.br; Bevilaqua, Denise; Garcia Junior, Oswaldo [Universidade Estadual Paulista (UNESP), Araraquara, SP (Brazil). Inst. de Quimica. Dept. de Bioquimica e Tecnologia Quimica

2009-07-01

This paper analyses the oxidation of covellite and molybdenite by Acidithiobacillus ferrooxidans strain LR using respirometric experiments. The results showed that both sulfides were oxidized by A. ferrooxidans, however, the covellite oxidation was much higher than molybdenite. Regarding the kinetic oxidation, the findings revealed that just molybdenite oxidation followed the classical Michaelis-Menten kinetic. It is probably associated with the pathway which these sulfides react to chemistry-bacterial attack, what is influenced by its electronic structures. Besides, experiments conducted in the presence of Fe{sup 3+} did not indicate alterations in molybdenite oxidation. Thus, ferric ions seem not to be essential to the sulfide oxidations. (author)

Estudo da oxidação dos sulfetos sintéticos molibdenita (MoS2 e covelita (CuS por Acidithiobacillus ferrooxidans via respirometria celular Oxidation study of the synthetic sulfides molybdenite (MoS2 and covellite (CuS by Acidithiobacillus ferrooxidans using respirometric experiments

Directory of Open Access Journals (Sweden)

Wilmo E. Francisco Junior

2009-01-01

Full Text Available This paper analyses the oxidation of covellite and molybdenite by Acidithiobacillus ferrooxidans strain LR using respirometric experiments. The results showed that both sulfides were oxidized by A. ferrooxidans, however, the covellite oxidation was much higher than molybdenite. Regarding the kinetic oxidation, the findings revealed that just molybdenite oxidation followed the classical Michaelis-Menten kinetic. It is probably associated with the pathway which these sulfides react to chemistry-bacterial attack, what is influenced by its electronic structures. Besides, experiments conducted in the presence of Fe3+ did not indicate alterations in molybdenite oxidation. Thus, ferric ions seem not to be essential to the sulfide oxidations.

Modelling the Effects of Ageing Time of Starch on the Enzymatic Activity of Three Amylolytic Enzymes

Science.gov (United States)

Guerra, Nelson P.; Pastrana Castro, Lorenzo

2012-01-01

The effect of increasing ageing time (t) of starch on the activity of three amylolytic enzymes (Termamyl, San Super, and BAN) was investigated. Although all the enzymatic reactions follow michaelian kinetics, v max decreased significantly (P enzymes and the release of the reaction products to the medium. A similar effect was observed when the enzymatic reactions were carried out with unaged starches supplemented with different concentrations of gelatine [G]. The inhibition in the amylolytic activities was best mathematically described by using three modified forms of the Michaelis-Menten model, which included a term to consider, respectively, the linear, exponential, and hyperbolic inhibitory effects of t and [G]. PMID:22666116

Kinetics of glucose transport in rat muscle

DEFF Research Database (Denmark)

Ploug, Thorkil; Galbo, Henrik; Vinten, Jørgen

1987-01-01

The effects of insulin and prior muscle contractions, respectively, on 3-O-methylglucose (3-O-MG) transport in skeletal muscle were studied in the perfused rat hindquarter. Initial rates of entry of 3-O-MG in red gastrocnemius, soleus, and white gastrocnemius muscles as a function of perfusate 3-O-MG...... concentration exhibited Michaelis-Menten kinetics. Uptake by simple diffusion could not be detected. The maximum 3-O-MG transport velocity (Vmax) was increased more by maximum isometric contractions (10- to 40-fold, depending on fiber type) than by insulin (20,000 microU/ml; 3- to 20-fold) in both red and white...

Fast and General Method To Predict the Physicochemical Properties of Druglike Molecules Using the Integral Equation Theory of Molecular Liquids.

Science.gov (United States)

Palmer, David S; Mišin, Maksim; Fedorov, Maxim V; Llinas, Antonio

2015-09-08

We report a method to predict physicochemical properties of druglike molecules using a classical statistical mechanics based solvent model combined with machine learning. The RISM-MOL-INF method introduced here provides an accurate technique to characterize solvation and desolvation processes based on solute-solvent correlation functions computed by the 1D reference interaction site model of the integral equation theory of molecular liquids. These functions can be obtained in a matter of minutes for most small organic and druglike molecules using existing software (RISM-MOL) (Sergiievskyi, V. P.; Hackbusch, W.; Fedorov, M. V. J. Comput. Chem. 2011, 32, 1982-1992). Predictions of caco-2 cell permeability and hydration free energy obtained using the RISM-MOL-INF method are shown to be more accurate than the state-of-the-art tools for benchmark data sets. Due to the importance of solvation and desolvation effects in biological systems, it is anticipated that the RISM-MOL-INF approach will find many applications in biophysical and biomedical property prediction.

Reformulation of Maxwell's equations to incorporate near-solute solvent structure.

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Yang, Pei-Kun; Lim, Carmay

2008-09-04

Maxwell's equations, which treat electromagnetic interactions between macroscopic charged objects in materials, have explained many phenomena and contributed to many applications in our lives. Derived in 1861 when no methods were available to determine the atomic structure of macromolecules, Maxwell's equations assume the solvent to be a structureless continuum. However, near-solute solvent molecules are highly structured, unlike far-solute bulk solvent molecules. Current methods cannot treat both the near-solute solvent structure and time-dependent electromagnetic interactions in a macroscopic system. Here, we derive "microscopic" electrodynamics equations that can treat macroscopic time-dependent electromagnetic field problems like Maxwell's equations and reproduce the solvent molecular and dipole density distributions observed in molecular dynamics simulations. These equations greatly reduce computational expense by not having to include explicit solvent molecules, yet they treat the solvent electrostatic and van der Waals effects more accurately than continuum models. They provide a foundation to study electromagnetic interactions between molecules in a macroscopic system that are ubiquitous in biology, bioelectromagnetism, and nanotechnology. The general strategy presented herein to incorporate the near-solute solvent structure would enable studies on how complex cellular protein-ligand interactions are affected by electromagnetic radiation, which could help to prevent harmful electromagnetic spectra or find potential therapeutic applications.

Integral equations for free-molecule ow in MEMS: recent advancements

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Fedeli Patrick

2017-03-01

Full Text Available We address a Boundary Integral Equation (BIE approach for the analysis of gas dissipation in near-vacuum for Micro Electro Mechanical Systems (MEMS. Inspired by an analogy with the radiosity equation in computer graphics, we discuss an efficient way to compute the visible domain of integration. Moreover, we tackle the issue of near singular integrals by developing a set of analytical formulas for planar polyhedral domains. Finally a validation with experimental results taken from the literature is presented.

Kinetic equation of heterogeneous catalytic isotope exchange

Energy Technology Data Exchange (ETDEWEB)

Trokhimets, A I [AN Belorusskoj SSR, Minsk. Inst. Fiziko-Organicheskoj Khimii

1979-12-01

A kinetic equation is derived for the bimolecular isotope exchange reaction between AXsub(n)sup(*) and BXsub(m)sup(o), all atoms of element X in each molecule being equivalent. The equation can be generalized for homogeneous and heterogeneous catalytic isotope exchange.

Ordinary differential equations with applications in molecular biology.

Science.gov (United States)

Ilea, M; Turnea, M; Rotariu, M

2012-01-01

Differential equations are of basic importance in molecular biology mathematics because many biological laws and relations appear mathematically in the form of a differential equation. In this article we presented some applications of mathematical models represented by ordinary differential equations in molecular biology. The vast majority of quantitative models in cell and molecular biology are formulated in terms of ordinary differential equations for the time evolution of concentrations of molecular species. Assuming that the diffusion in the cell is high enough to make the spatial distribution of molecules homogenous, these equations describe systems with many participating molecules of each kind. We propose an original mathematical model with small parameter for biological phospholipid pathway. All the equations system includes small parameter epsilon. The smallness of epsilon is relative to the size of the solution domain. If we reduce the size of the solution region the same small epsilon will result in a different condition number. It is clear that the solution for a smaller region is less difficult. We introduce the mathematical technique known as boundary function method for singular perturbation system. In this system, the small parameter is an asymptotic variable, different from the independent variable. In general, the solutions of such equations exhibit multiscale phenomena. Singularly perturbed problems form a special class of problems containing a small parameter which may tend to zero. Many molecular biology processes can be quantitatively characterized by ordinary differential equations. Mathematical cell biology is a very active and fast growing interdisciplinary area in which mathematical concepts, techniques, and models are applied to a variety of problems in developmental medicine and bioengineering. Among the different modeling approaches, ordinary differential equations (ODE) are particularly important and have led to significant advances

Hepatic taurine transport: a Na+-dependent carrier on the basolateral plasma membrane

International Nuclear Information System (INIS)

Bucuvalas, J.C.; Goodrich, A.L.; Suchy, F.J.

1987-01-01

Highly purified rat basolateral liver plasma membrane vesicles were used examine the mechanism and the driving forces for hepatic uptake of the β-amino acid, taurine. An inwardly directed 100 mM NaCl gradient stimulated the initial rate of taurine uptake and energized a transient twofold accumulation of taurine above equilibrium (overshoot). In contrast, uptake was slower and no overshoot was detected in the presence of a KCl gradient. A negative intravesicular electrical potential generated by the presence of permeant anions or an outwardly directed K + gradient with valinomycin increased Na + -stimulated taurine uptake. External Cl - stimulated Na + -dependent taurine uptake independent of effects on the transmembrane electrical potential difference. Na + -dependent taurine uptake showed a sigmoidal dependence on extravesicular Na + concentration, suggesting multiple Na + ions are involved in the translocation of each taurine molecule. Na + -dependent taurine uptake demonstrated Michaelis-Menten kinetics with a maximum velocity of 0.537 nmol x mg protein -1 x min -1 and an apparent K/sub m/ of 174 μM. [ 3 H]taurine uptake was inhibited by the presence of excess unlabeled taurine, β-alanine, or hypotaurine but not by L-glutamine or L-alanine. In summary, using basolateral liver plasma membrane vesicles, the authors have shown that hepatic uptake of taurine occurs by a carrier-mediated, secondary active transport process specific for β-amino acids. Uptake is electrogenic, stimulated by external Cl - , and requires multiple Na + ions for the translocation of each taurine molecule

Comparison of dopamine kinetics in the larval Drosophila ventral nerve cord and protocerebrum with improved optogenetic stimulation.

Science.gov (United States)

Privman, Eve; Venton, B Jill

2015-11-01

Dopamine release and uptake have been studied in the Drosophila larval ventral nerve cord (VNC) using optogenetics to stimulate endogenous release. However, other areas of the central nervous system remain uncharacterized. Here, we compare dopamine release in the VNC and protocerebrum of larval Drosophila. Stimulations were performed with CsChrimson, a new, improved, red light-activated channelrhodopsin. In both regions, dopamine release was observed after only a single, 4 ms duration light pulse. Michaelis-Menten modeling was used to understand release and uptake parameters for dopamine. The amount of dopamine released ([DA]p ) on the first stimulation pulse is higher than the average [DA]p released from subsequent pulses. The initial and average amount of dopamine released per stimulation pulse is smaller in the protocerebrum than in the VNC. The average Vmax of 0.08 μM/s in the protocerebrum was significantly higher than the Vmax of 0.05 μM/s in the VNC. The average Km of 0.11 μM in the protocerebrum was not significantly different from the Km of 0.10 μM in the VNC. When the competitive dopamine transporter (DAT) inhibitor nisoxetine was applied, the Km increased significantly in both regions while Vmax stayed the same. This work demonstrates regional differences in dopamine release and uptake kinetics, indicating important variation in the amount of dopamine available for neurotransmission and neuromodulation. We use a new optogenetic tool, red light activated CsChrimson, to stimulate the release of dopamine in the ventral nerve cord and medial protocerebrum of the larval Drosophila central nervous system. We monitored extracellular dopamine by fast scan cyclic voltammetry and used Michaelis-Menten modeling to probe the regulation of extracellular dopamine, discovering important similarities and differences in these two regions. © 2015 International Society for Neurochemistry.

On the precision of quasi steady state assumptions in stochastic dynamics

Science.gov (United States)

Agarwal, Animesh; Adams, Rhys; Castellani, Gastone C.; Shouval, Harel Z.

2012-07-01

Many biochemical networks have complex multidimensional dynamics and there is a long history of methods that have been used for dimensionality reduction for such reaction networks. Usually a deterministic mass action approach is used; however, in small volumes, there are significant fluctuations from the mean which the mass action approach cannot capture. In such cases stochastic simulation methods should be used. In this paper, we evaluate the applicability of one such dimensionality reduction method, the quasi-steady state approximation (QSSA) [L. Menten and M. Michaelis, "Die kinetik der invertinwirkung," Biochem. Z 49, 333369 (1913)] for dimensionality reduction in case of stochastic dynamics. First, the applicability of QSSA approach is evaluated for a canonical system of enzyme reactions. Application of QSSA to such a reaction system in a deterministic setting leads to Michaelis-Menten reduced kinetics which can be used to derive the equilibrium concentrations of the reaction species. In the case of stochastic simulations, however, the steady state is characterized by fluctuations around the mean equilibrium concentration. Our analysis shows that a QSSA based approach for dimensionality reduction captures well the mean of the distribution as obtained from a full dimensional simulation but fails to accurately capture the distribution around that mean. Moreover, the QSSA approximation is not unique. We have then extended the analysis to a simple bistable biochemical network model proposed to account for the stability of synaptic efficacies; the substrate of learning and memory [J. E. Lisman, "A mechanism of memory storage insensitive to molecular turnover: A bistable autophosphorylating kinase," Proc. Natl. Acad. Sci. U.S.A. 82, 3055-3057 (1985)], 10.1073/pnas.82.9.3055. Our analysis shows that a QSSA based dimensionality reduction method results in errors as big as two orders of magnitude in predicting the residence times in the two stable states.

Direct measurement of catalase activity in living cells and tissue biopsies

International Nuclear Information System (INIS)

Scaglione, Christine N.; Xu, Qijin; Ramanujan, V. Krishnan

2016-01-01

Spatiotemporal regulation of enzyme-substrate interactions governs the decision-making steps in biological systems. Enzymes, being functional units of every living cell, contribute to the macromolecular stability of cell survival, proliferation and hence are vital windows to unraveling the biological complexity. Experimental measurements capturing this dynamics of enzyme-substrate interactions in real time add value to this understanding. Furthermore these measurements, upon validation in realistic biological specimens such as clinical biopsies – can further improve our capability in disease diagnostics and treatment monitoring. Towards this direction, we describe here a novel, high-sensitive measurement system for measuring diffusion-limited enzyme-substrate kinetics in real time. Using catalase (enzyme) and hydrogen peroxide (substrate) as the example pair, we demonstrate that this system is capable of direct measurement of catalase activity in vitro and the measured kinetics follows the classical Michaelis-Menten reaction kinetics. We further demonstrate the system performance by measuring catalase activity in living cells and in very small amounts of liver biopsies (down to 1 μg total protein). Catalase-specific enzyme activity is demonstrated by genetic and pharmacological tools. Finally we show the clinically-relevant diagnostic capability of our system by comparing the catalase activities in liver biopsies from young and old mouse (liver and serum) samples. We discuss the potential applicability of this system in clinical diagnostics as well as in intraoperative surgical settings. - Highlights: • A novel, direct measurement of Catalase enzyme activity via, oxygen sensing method. • Steady-stateprofiles of Catalase activity follow the Michaelis-Menten Kinetics. • Catalase-specific activity demonstrated using genetic and pharmacological tools. • Overcomes limitations of spectroscopic methods and indirect calorimetric approaches. • Clear

Direct measurement of catalase activity in living cells and tissue biopsies

Energy Technology Data Exchange (ETDEWEB)

Scaglione, Christine N.; Xu, Qijin; Ramanujan, V. Krishnan, E-mail: Ramanujanv@csmc.edu

2016-01-29

Spatiotemporal regulation of enzyme-substrate interactions governs the decision-making steps in biological systems. Enzymes, being functional units of every living cell, contribute to the macromolecular stability of cell survival, proliferation and hence are vital windows to unraveling the biological complexity. Experimental measurements capturing this dynamics of enzyme-substrate interactions in real time add value to this understanding. Furthermore these measurements, upon validation in realistic biological specimens such as clinical biopsies – can further improve our capability in disease diagnostics and treatment monitoring. Towards this direction, we describe here a novel, high-sensitive measurement system for measuring diffusion-limited enzyme-substrate kinetics in real time. Using catalase (enzyme) and hydrogen peroxide (substrate) as the example pair, we demonstrate that this system is capable of direct measurement of catalase activity in vitro and the measured kinetics follows the classical Michaelis-Menten reaction kinetics. We further demonstrate the system performance by measuring catalase activity in living cells and in very small amounts of liver biopsies (down to 1 μg total protein). Catalase-specific enzyme activity is demonstrated by genetic and pharmacological tools. Finally we show the clinically-relevant diagnostic capability of our system by comparing the catalase activities in liver biopsies from young and old mouse (liver and serum) samples. We discuss the potential applicability of this system in clinical diagnostics as well as in intraoperative surgical settings. - Highlights: • A novel, direct measurement of Catalase enzyme activity via, oxygen sensing method. • Steady-stateprofiles of Catalase activity follow the Michaelis-Menten Kinetics. • Catalase-specific activity demonstrated using genetic and pharmacological tools. • Overcomes limitations of spectroscopic methods and indirect calorimetric approaches. • Clear

Characterization of the human cytochrome P450 enzymes involved in the metabolism of dihydrocodeine

Science.gov (United States)

Kirkwood, L. C.; Nation, R. L.; Somogyi, A. A.

1997-01-01

Aims Using human liver microsomes from donors of the CYP2D6 poor and extensive metabolizer genotypes, the role of individual cytochromes P-450 in the oxidative metabolism of dihydrocodeine was investigated. Methods The kinetics of formation of N- and O-demethylated metabolites, nordihydrocodeine and dihydromorphine, were determined using microsomes from six extensive and one poor metabolizer and the effects of chemical inhibitors selective for individual P-450 enzymes of the 1A, 2A, 2C, 2D, 2E and 3A families and of LKM1 (anti-CYP2D6) antibodies were studied. Results Nordihydrocodeine was the major metabolite in both poor and extensive metabolizers. Kinetic constants for N-demethylation derived from the single enzyme Michaelis-Menten model did not differ between the two groups. Troleandomycin and erythromycin selectively inhibited N-demethylation in both extensive and poor metabolizers. The CYP3A inducer, α-naphthoflavone, increased N-demethylation rates. The kinetics of formation of dihydromorphine in both groups were best described by a single enzyme Michaelis-Menten model although inhibition studies in extensive metabolizers suggested involvement of two enzymes with similar Km values. The kinetic constants for O-demethylation were significantly different in extensive and poor metabolizers. The extensive metabolizers had a mean intrinsic clearance to dihydromorphine more than ten times greater than the poor metabolizer. The CYP2D6 chemical inhibitors, quinidine and quinine, and LKM1 antibodies inhibited O-demethylation in extensive metabolizers; no effect was observed in microsomes from a poor metabolizer. Conclusions CYP2D6 is the major enzyme mediating O-demethylation of dihydrocodeine to dihydromorphine. In contrast, nordihydrocodeine formation is predominantly catalysed by CYP3A. PMID:9431830

Efecto de la sacarosa en la producción de celulosa por Gluconacetobacter xylinus en cultivo estático

Directory of Open Access Journals (Sweden)

Rubén Jaramillo L.

2012-08-01

Full Text Available Objetivo. Determinar el efecto de sacarosa en la productividad de BC por Gluconacetobacter xylinus IFO 13693 en condición estática. Materiales y métodos. La síntesis de celulosa bacteriana (BC por Gluconacetobacter xylinus se llevo a cabo en un cultivo estático discontinuo a temperatura ambiente, en presencia de sacarosa como la principal fuente de carbono a concentraciones iniciales de 0.8 a 7.6 % (p/v. Las concentraciones remanentes de BC, sacarosa, glucosa y fructosa se determinaron cada semana. Para la cinética de la hidrólisis de la sacarosa y formación de celulosa y el coeficiente de rendimiento del producto se utilizo el software Microcal Origin 6.0®. Resultados. En la cuarta semana los valores de BC se encontraron entre 32.5 a 39.5 g/L para las diferentes concentraciones de sacarosa. La cinética para la hidrólisis de sacarosa se ajusta al modelo de Michaelis-Menten, con una Vmax de 0.0002 mol L-1 h-1 y Km de 0.018 M. La producción de BC se ajusta al modelo propuesto por Marx-Figini y Pion, con un valor de la pendiente (kc, entre 0.0018 y 0.0024 h-1 para las diferentes concentraciones iniciales de sacarosa. Los coeficientes de rendimiento tienen valores de 0.8 a 2.4 g de BC producida/g de sacarosa consumida. Conclusiones. La hidrólisis de sacarosa, el consumo de glucosa y fructosa se refleja en la síntesis de celulosa. La hidrólisis de sacarosa y la producción de BC se ajustan a los modelos de Michaelis-Menten y al propuesto por Marx-Figini y Pion, respectivamente. Finalmente, el rendimiento depende de la concentración de sacarosa.

Hepatic and intestinal glucuronidation of mono(2-ethylhexyl) phthalate, an active metabolite of di(2-ethylhexyl) phthalate, in humans, dogs, rats, and mice: an in vitro analysis using microsomal fractions.

Science.gov (United States)

Hanioka, Nobumitsu; Isobe, Takashi; Kinashi, Yu; Tanaka-Kagawa, Toshiko; Jinno, Hideto

2016-07-01

Mono(2-ethylhexyl) phthalate (MEHP) is an active metabolite of di(2-ethylhexyl) phthalate (DEHP) and has endocrine-disrupting effects. MEHP is metabolized into glucuronide by UDP-glucuronosyltransferase (UGT) enzymes in mammals. In the present study, the hepatic and intestinal glucuronidation of MEHP in humans, dogs, rats, and mice was examined in an in vitro system using microsomal fractions. The kinetics of MEHP glucuronidation by liver microsomes followed the Michaelis-Menten model for humans and dogs, and the biphasic model for rats and mice. The K m and V max values of human liver microsomes were 110 µM and 5.8 nmol/min/mg protein, respectively. The kinetics of intestinal microsomes followed the biphasic model for humans, dogs, and mice, and the Michaelis-Menten model for rats. The K m and V max values of human intestinal microsomes were 5.6 µM and 0.40 nmol/min/mg protein, respectively, for the high-affinity phase, and 430 µM and 0.70 nmol/min/mg protein, respectively, for the low-affinity phase. The relative levels of V max estimated by Eadie-Hofstee plots were dogs (2.0) > mice (1.4) > rats (1.0) ≈ humans (1.0) for liver microsomes, and mice (8.5) > dogs (4.1) > rats (3.1) > humans (1.0) for intestinal microsomes. The percentages of the V max values of intestinal microsomes to liver microsomes were mice (120 %) > rats (57 %) > dogs (39 %) > humans (19 %). These results suggest that the metabolic abilities of UGT enzymes expressed in the liver and intestine toward MEHP markedly differed among species, and imply that these species differences are strongly associated with the toxicity of DEHP.

Threshold for extinction and survival in stochastic tumor immune system

Science.gov (United States)

Li, Dongxi; Cheng, Fangjuan

2017-10-01

This paper mainly investigates the stochastic character of tumor growth and extinction in the presence of immune response of a host organism. Firstly, the mathematical model describing the interaction and competition between the tumor cells and immune system is established based on the Michaelis-Menten enzyme kinetics. Then, the threshold conditions for extinction, weak persistence and stochastic persistence of tumor cells are derived by the rigorous theoretical proofs. Finally, stochastic simulation are taken to substantiate and illustrate the conclusion we have derived. The modeling results will be beneficial to understand to concept of immunoediting, and develop the cancer immunotherapy. Besides, our simple theoretical model can help to obtain new insight into the complexity of tumor growth.

Cholesterol biosensor based on rf sputtered zinc oxide nanoporous thin film

International Nuclear Information System (INIS)

Singh, S. P.; Arya, Sunil K.; Pandey, Pratibha; Malhotra, B. D.; Saha, Shibu; Sreenivas, K.; Gupta, Vinay

2007-01-01

Cholesterol oxidase (ChOx) has been immobilized onto zinc oxide (ZnO) nanoporous thin films grown on gold surface. A preferred c-axis oriented ZnO thin film with porous surface morphology has been fabricated by rf sputtering under high pressure. Optical studies and cyclic voltammetric measurements show that the ChOx/ZnO/Au bioelectrode is sensitive to the detection of cholesterol in 25-400 mg/dl range. A relatively low value of enzyme's kinetic parameter (Michaelis-Menten constant) ∼2.1 mM indicates enhanced enzyme affinity of ChOx to cholesterol. The observed results show promising application of nanoporous ZnO thin film for biosensing application without any functionalization

Lipase-catalyzed ring-opening polymerization of lactones to polyesters and its mechanistic aspects.

Science.gov (United States)

Namekawa, S; Suda, S; Uyama, H; Kobayashi, S

1999-01-01

Lipase catalysis induced a ring-opening polymerization of lactones with different ring-sizes. Small-size (four-membered) and medium-size lactones (six- and seven-membered) as well as macrolides (12-, 13-, 16-, and 17-membered) were subjected to lipase-catalyzed polymerization. The polymerization behaviors depended primarily on the lipase origin and the monomer structure. The macrolides showing much lower anionic polymerizability were enzymatically polymerized faster than epsilon-caprolactone. The granular immobilized lipase derived from Candida antartica showed extremely efficient catalysis in the polymerization of epsilon-caprolactone. Single-step terminal functionalization of the polyester was achieved by initiator and terminator methods. The enzymatic polymerizability of lactones was quantitatively evaluated by Michaelis-Menten kinetics.

Parameter Estimation for Simultaneous Saccharification and Fermentation of Food Waste Into Ethanol Using Matlab Simulink

Science.gov (United States)

Davis, Rebecca Anne

The increase in waste disposal and energy costs has provided an incentive to convert carbohydrate-rich food waste streams into fuel. For example, dining halls and restaurants discard foods that require tipping fees for removal. An effective use of food waste may be the enzymatic hydrolysis of the waste to simple sugars and fermentation of the sugars to ethanol. As these wastes have complex compositions which may change day-to-day, experiments were carried out to test fermentability of two different types of food waste at 27° C using Saccharomyces cerevisiae yeast (ATCC4124) and Genencor's STARGEN™ enzyme in batch simultaneous saccharification and fermentation (SSF) experiments. A mathematical model of SSF based on experimentally matched rate equations for enzyme hydrolysis and yeast fermentation was developed in Matlab Simulink®. Using Simulink® parameter estimation 1.1.3, parameters for hydrolysis and fermentation were estimated through modified Michaelis-Menten and Monod-type equations with the aim of predicting changes in the levels of ethanol and glycerol from different initial concentrations of glucose, fructose, maltose, and starch. The model predictions and experimental observations agree reasonably well for the two food waste streams and a third validation dataset. The approach of using Simulink® as a dynamic visual model for SSF represents a simple method which can be applied to a variety of biological pathways and may be very useful for systems approaches in metabolic engineering in the future.

Effects of multi-frequency power ultrasound on the enzymolysis of corn gluten meal: Kinetics and thermodynamics study.

Science.gov (United States)

Jin, Jian; Ma, Haile; Qu, Wenjuan; Wang, Kai; Zhou, Cunshan; He, Ronghai; Luo, Lin; Owusu, John

2015-11-01

The effects of multi-frequency power ultrasound (MPU) pretreatment on the kinetics and thermodynamics of corn gluten meal (CGM) were investigated in this research. The apparent constant (KM), apparent break-down rate constant (kA), reaction rate constants (k), energy of activation (Ea), enthalpy of activation (ΔH), entropy of activation (ΔS) and Gibbs free energy of activation (ΔG) were determined by means of the Michaelis-Menten equation, first-order kinetics model, Arrhenius equation and transition state theory, respectively. The results showed that MPU pretreatment can accelerate the enzymolysis of CGM under different enzymolysis conditions, viz. substrate concentration, enzyme concentration, pH, and temperature. Kinetics analysis revealed that MPU pretreatment decreased the KM value by 26.1% and increased the kA value by 7.3%, indicating ultrasound pretreatment increased the affinity between enzyme and substrate. In addition, the values of k for ultrasound pretreatment were increased by 84.8%, 41.9%, 28.9%, and 18.8% at the temperature of 293, 303, 313 and 323 K, respectively. For the thermodynamic parameters, ultrasound decreased Ea, ΔH and ΔS by 23.0%, 24.3% and 25.3%, respectively, but ultrasound had little change in ΔG value in the temperature range of 293-323 K. In conclusion, MPU pretreatment could remarkably enhance the enzymolysis of CGM, and this method can be applied to protein proteolysis industry to produce peptides. Copyright © 2015 Elsevier B.V. All rights reserved.

Amperometric biosensor for hydrogen peroxide based on Hemoglobin/DNA/Poly-2,6-pyridinediamine modified gold electrode

International Nuclear Information System (INIS)

Tong Zhongqiang; Yuan Ruo; Chai Yaqin; Chen Shihong; Xie Yi

2007-01-01

An amperometric biosensor for hydrogen peroxide (H 2 O 2 ) was fabricated based on immobilization of hemoglobin (Hb) on DNA/Poly-2,6-pyridinediamine (PPD) modified Au electrode. PPD thin films were firstly electro-deposited on Au electrode surface which provide a template to attach negatively charged DNA molecules by electrostatic attraction. The adsorbed DNA network provides a good microenvironment for the immobilization of biomolecules and promotes electron transfer between the immobilized Hb and the electrode surface. The fabrication process of the biosensor was characterized by electrochemical impedance spectroscopy. Experimental conditions influencing the biosensor performance such as pH, potential and temperature were assessed and optimized. The proposed biosensor displayed a good electrocatalytic response to the reduction of H 2 O 2 , its linear range is 1.7 μM to 3 mM with a detection limit of 1.0 μM based on the signal-to-noise ratio of 3 (S/N = 3) under the optimized conditions. The Michaelis-Menten constant K m app of Hb immobilized on the electrode surface was found to be 0.8 mM. The biosensor shows high sensitivity and stability. Importantly, this deposition methodology could be further developed for the immobilization of other proteins and biocompounds

Wave equations for pulse propagation

International Nuclear Information System (INIS)

Shore, B.W.

1987-01-01

Theoretical discussions of the propagation of pulses of laser radiation through atomic or molecular vapor rely on a number of traditional approximations for idealizing the radiation and the molecules, and for quantifying their mutual interaction by various equations of propagation (for the radiation) and excitation (for the molecules). In treating short-pulse phenomena it is essential to consider coherent excitation phenomena of the sort that is manifest in Rabi oscillations of atomic or molecular populations. Such processes are not adequately treated by rate equations for excitation nor by rate equations for radiation. As part of a more comprehensive treatment of the coupled equations that describe propagation of short pulses, this memo presents background discussion of the equations that describe the field. This memo discusses the origin, in Maxwell's equations, of the wave equation used in the description of pulse propagation. It notes the separation into lamellar and solenoidal (or longitudinal and transverse) and positive and negative frequency parts. It mentions the possibility of separating the polarization field into linear and nonlinear parts, in order to define a susceptibility or index of refraction and, from these, a phase and group velocity. The memo discusses various ways of characterizing the polarization characteristics of plane waves, that is, of parameterizing a transverse unit vector, such as the Jones vector, the Stokes vector, and the Poincare sphere. It discusses the connection between macroscopically defined quantities, such as the intensity or, more generally, the Stokes parameters, and microscopic field amplitudes. The material presented here is a portion of a more extensive treatment of propagation to be presented separately. The equations presented here have been described in various books and articles. They are collected here as a summary and review of theory needed when treating pulse propagation

Some aspects of equations of state

International Nuclear Information System (INIS)

Frisch, H.L.

1979-02-01

Some elementary properties of the equation of state of molecules repulsing each other as point centers of force are developed briefly. An inequality for the Lennard--Jones gas is presented. The scaled particle theory equation of state of hard spheres is also reviewed briefly. Means of possibly applying these concepts to represent thermodynamic data on model detonating gases are suggested

Teaching lasers to control molecules

International Nuclear Information System (INIS)

Judson, R.S.; Rabitz, H.

1992-01-01

We simulate a method to teach a laser pulse sequences to excite specified molecular states. We use a learning procedure to direct the production of pulses based on ''fitness'' information provided by a laboratory measurement device. Over a series of pulses the algorithm learns an optimal sequence. The experimental apparatus, which consists of a laser, a sample of molecules and a measurement device, acts as an analog computer that solves Schroedinger's equation n/Iexactly, in real time. We simulate an apparatus that learns to excite specified rotational states in a diatomic molecule

The on-line synthesis of enzyme functionalized silica nanoparticles in a microfluidic reactor using polyethylenimine polymer and R5 peptide

International Nuclear Information System (INIS)

He Ping; Greenway, Gillian; Haswell, Stephen J

2008-01-01

A simple microfluidic reactor system is described for the effective synthesis of enzyme functionalized nanoparticles which offers many advantages over batch reactions, including excellent enzyme efficiencies. Better control of the process parameters in the microfluidic reactor system over batch based methodology enables the production of silica nanoparticles with the optimum size for efficient enzyme immobilization with long-term stability. The synthetic approach is demonstrated with glucose oxidase (GOD) and two different nucleation catalysts of similar molecular mass: the natural R5 peptide, and polyethylenimine (PEI) polymer. Near-quantitative immobilization of GOD in the nanoparticles is obtained using PEI; the immobilization is attributed to electrostatic interaction between PEI and GOD. This interaction, however, limits the mobility of the immobilized enzyme, producing orientation hindrance of the enzyme's active sites as compared to free GOD in solution. In contrast, when the GOD is immobilized inside the silica nanoparticles using R5, lower enzyme immobilization efficiencies are obtained compared to using PEI polymers; however, similar Michaelis-Menten kinetic parameters (i.e. Michaelis constant and turnover number) to those of free GOD are observed. Reactions were monitored in situ using simple, rapid, separation-free amperometric detection

Real-Time Enzyme Kinetics by Quantitative NMR Spectroscopy and Determination of the Michaelis-Menten Constant Using the Lambert-W Function

Science.gov (United States)

Her, Cheenou; Alonzo, Aaron P.; Vang, Justin Y.; Torres, Ernesto; Krishnan, V. V.

2015-01-01

Enzyme kinetics is an essential part of a chemistry curriculum, especially for students interested in biomedical research or in health care fields. Though the concept is routinely performed in undergraduate chemistry/biochemistry classrooms using other spectroscopic methods, we provide an optimized approach that uses a real-time monitoring of the…

A linear algebraic approach to electron-molecule collisions

International Nuclear Information System (INIS)

Collins, L.A.; Schnieder, B.I.

1982-01-01

The linear algebraic approach to electron-molecule collisions is examined by firstly deriving the general set of coupled integrodifferential equations that describe electron collisional processes and then describing the linear algebraic approach for obtaining a solution to the coupled equations. Application of the linear algebraic method to static-exchange, separable exchange and effective optical potential, is examined. (U.K.)

Subcellular distribution and uptake mechanism of di-n-butyl phthalate in roots of pumpkin (Cucurbita moschata) seedlings.

Science.gov (United States)

Lin, Qingqi; Yang, Xiuhong; Huang, Xiongfei; Wang, Shizhong; Chao, Yuanqing; Qiu, Rongliang

2016-01-01

Phthalate acid esters (PAEs) are of particular concern due to their potential environmental risk to human and nonhuman organisms. Although uptake of PAEs by plants has been reported by several researchers, information about the intracellular distribution and uptake mechanisms of PAEs is still lacking. In this study, a series of hydroponic experiments using intact pumpkin (Cucurbita moschata) seedlings was conducted to investigate how di-n-butyl phthalate (DnBP), one of the most frequently identified PAEs in the environment, enters and is distributed in roots. DnBP was transported into subcellular tissues rapidly in the initial uptake period (<12 h). More than 80% of DnBP was detected in the cell walls and organelles, which suggests that DnBP is primarily accumulated in these two fractions due to their high affinity to DnBP. The kinetics of DnBP uptake were fitted well with the Michaelis-Menten equation, suggesting that a carrier-mediated process was involved. The application of 2,4-dinitrophenol and sodium vanadate reduced the uptake of DnBP by 37 and 26%, respectively, while aquaporin inhibitors, silver and glycerol, had no effect on DnBP uptake. These data demonstrated that the uptake of DnBP included a carrier-mediated and energy-dependent process without the participation of aquaporins.

The Non-Linear Child: Ontogeny, Isoniazid Concentration, and NAT2 Genotype Modulate Enzyme Reaction Kinetics and Metabolism.

Science.gov (United States)

Rogers, Zoe; Hiruy, Hiwot; Pasipanodya, Jotam G; Mbowane, Chris; Adamson, John; Ngotho, Lihle; Karim, Farina; Jeena, Prakash; Bishai, William; Gumbo, Tawanda

2016-09-01

N-acetyltransferase 2 (NAT2) catalyzes the acetylation of isoniazid to N-acetylisoniazid. NAT2 polymorphism explains 88% of isoniazid clearance variability in adults. We examined the effects of clinical and genetic factors on Michaelis-Menten reaction kinetic constants of maximum velocity (V max ) and affinity (K m ) in children 0-10years old. We measured the rates of isoniazid elimination and N-acetylisoniazid production in the blood of 30 children. Since maturation effects could be non-linear, we utilized a pharmacometric approach and the artificial intelligence method, multivariate adaptive regression splines (MARS), to identify factors predicting NAT2 V max and K m by examining clinical, genetic, and laboratory factors in toto. Isoniazid concentration predicted both V max and K m and superseded the contribution of NAT2 genotype. Age non-linearly modified the NAT2 genotype contribution until maturation at ≥5.3years. Thus, enzyme efficiency was constrained by substrate concentration, genes, and age. Since MARS output is in the form of basis functions and equations, it allows multiscale systems modeling from the level of cellular chemical reactions to whole body physiological parameters, by automatic selection of significant predictors by the algorithm. Copyright © 2016 Forschungsgesellschaft für Arbeitsphysiologie und Arbeitschutz e.V. Published by Elsevier B.V. All rights reserved.

Mechanistic kinetic modeling generates system-independent P-glycoprotein mediated transport elementary rate constants for inhibition and, in combination with 3D SIM microscopy, elucidates the importance of microvilli morphology on P-glycoprotein mediated efflux activity.

Science.gov (United States)

Ellens, Harma; Meng, Zhou; Le Marchand, Sylvain J; Bentz, Joe

2018-06-01

In vitro transporter kinetics are typically analyzed by steady-state Michaelis-Menten approximations. However, no clear evidence exists that these approximations, applied to multiple transporters in biological membranes, yield system-independent mechanistic parameters needed for reliable in vivo hypothesis generation and testing. Areas covered: The classical mass action model has been developed for P-glycoprotein (P-gp) mediated transport across confluent polarized cell monolayers. Numerical integration of the mass action equations for transport using a stable global optimization program yields fitted elementary rate constants that are system-independent. The efflux active P-gp was defined by the rate at which P-gp delivers drugs to the apical chamber, since as much as 90% of drugs effluxed by P-gp partition back into nearby microvilli prior to reaching the apical chamber. The efflux active P-gp concentration was 10-fold smaller than the total expressed P-gp for Caco-2 cells, due to their microvilli membrane morphology. The mechanistic insights from this analysis are readily extrapolated to P-gp mediated transport in vivo. Expert opinion: In vitro system-independent elementary rate constants for transporters are essential for the generation and validation of robust mechanistic PBPK models. Our modeling approach and programs have broad application potential. They can be used for any drug transporter with minor adaptations.

Using a simple HPLC approach to identify the enzymatic products of UTL-5g, a small molecule TNF-α inhibitor, from porcine esterase and from rabbit esterase.

Science.gov (United States)

Swartz, Kenneth; Zhang, Yiguan; Valeriote, Frederick; Chen, Ben; Shaw, Jiajiu

2013-12-01

UTL-5g is a novel small-molecule chemoprotector that lowers hepatotoxicity, nephrotoxicity, and myelotoxicity induced by cisplatin through TNF-α inhibition among other factors. As a prelude to investigating the metabolites of UTL-5g, we set out to identify the enzymatic products of UTL-5g under the treatment of both porcine liver esterase (PLE) and rabbit liver esterase (RLE). First, a number of mixtures made by UTL-5g and PLE were incubated at 25°C. At predetermined time points, individual samples were quenched by acetonitrile, vortexed, and centrifuged. The supernatants were then analyzed by reversed-phase HPLC (using a C18 column). The retention times and UV/vis spectra of individual peaks were compared to those of UTL-5g and its two postulated enzymatic products; thus the enzymatic products of UTL-5g were tentatively identified. Secondly, a different HPLC method (providing different retentions times) was used to cross-check and to confirm the identities of the two enzymatic products. Based on the observations, it was concluded that under the treatment of PLE, the major enzymatic products of UTL-5g were 5-methyliosxazole-3-carboxylic acid (ISOX) and 2,4-dichloroaniline (DCA). Treatment of UTL-5g by RLE also provided the same enzymatic products of UTL-5g from esterase. These results indicate that the peptide bond in UTL-5g was cleaved by PLE/RLE. Michaelis-Menten kinetics showed that the Km values of UTL-5g were 2.07mM with PLE and 0.37mM with RLE indicating that UTL-5g had a higher affinity with RLE. In summary, by a simple HPLC approach, we have concluded that the peptide bond in UTL-5g was cleaved by esterase from either porcine liver or rabbit liver in vitro and afforded DCA (at a mole ratio of 1:1) and ISOX. However, further studies are needed in order to determine whether UTL-5g is metabolized by microsomal enzymes to produce ISOX and DCA. Copyright © 2013 Elsevier B.V. All rights reserved.

Calculation of Kinetic Data for Processes Leading to UV Signatures

Science.gov (United States)

1989-03-31

Jv we make use of the numerical algorithm developed by Stodden and Micha 17, extending it to the equations of motion in curvilinear coordinates. To be...in the field of the average potential V(Q). The set of equations (4.13’) have been recently derived by Stodden and Michat 5 in a more tedious.way by...B. Bloom, J. Chem. Phys. 83, 5703 (1985) 5 P. K. Swamninathan, C. D. Stodden , and D. A. Micha, J. Chem. Phys., in press (1989). 6 R. A. Marcus, Chem

Boltzmann equations for a binary one-dimensional ideal gas.

Science.gov (United States)

Boozer, A D

2011-09-01

We consider a time-reversal invariant dynamical model of a binary ideal gas of N molecules in one spatial dimension. By making time-asymmetric assumptions about the behavior of the gas, we derive Boltzmann and anti-Boltzmann equations that describe the evolution of the single-molecule velocity distribution functions for an ensemble of such systems. We show that for a special class of initial states of the ensemble one can obtain an exact expression for the N-molecule velocity distribution function, and we use this expression to rigorously prove that the time-asymmetric assumptions needed to derive the Boltzmann and anti-Boltzmann equations hold in the limit of large N. Our results clarify some subtle issues regarding the origin of the time asymmetry of Boltzmann's H theorem.

Cathepsin B Cleavage of vcMMAE-Based Antibody-Drug Conjugate Is Not Drug Location or Monoclonal Antibody Carrier Specific.

Science.gov (United States)

Gikanga, Benson; Adeniji, Nia S; Patapoff, Thomas W; Chih, Hung-Wei; Yi, Li

2016-04-20

Antibody-drug conjugates (ADCs) require thorough characterization and understanding of product quality attributes. The framework of many ADCs comprises one molecule of antibody that is usually conjugated with multiple drug molecules at various locations. It is unknown whether the drug release rate from the ADC is dependent on drug location, and/or local environment, dictated by the sequence and structure of the antibody carrier. This study addresses these issues with valine-citrulline-monomethylauristatin E (vc-MMAE)-based ADC molecules conjugated at reduced disulfide bonds, by evaluating the cathepsin B catalyzed drug release rate of ADC molecules with different drug distributions or antibody carriers. MMAE drug release rates at different locations on ADC I were compared to evaluate the impact of drug location. No difference in rates was observed for drug released from the V(H), V(L), or C(H)2 domains of ADC I. Furthermore, four vc-MMAE ADC molecules were chosen as substrates for cathepsin B for evaluation of Michaelis-Menten parameters. There was no significant difference in K(M) or k(cat) values, suggesting that different sequences of the antibody carrier do not result in different drug release rates. Comparison between ADCs and small molecules containing vc-MMAE moieties as substrates for cathepsin B suggests that the presence of IgG1 antibody carrier, regardless of its bulkiness, does not impact drug release rate. Finally, a molecular dynamics simulation on ADC II revealed that the val-cit moiety at each of the eight possible conjugation sites was, on average, solvent accessible over 50% of its maximum solvent accessible surface area (SASA) during a 500 ns trajectory. Combined, these results suggest that the cathepsin cleavage sites for conjugated drugs are exposed enough for the enzyme to access and that the drug release rate is rather independent of drug location or monoclonal antibody carrier. Therefore, the distribution of drug conjugation at different

Measurement of Membrane Characteristics Using the Phenomenological Equation and the Overall Mass Transport Equation in Ion-Exchange Membrane Electrodialysis of Saline Water

Directory of Open Access Journals (Sweden)

Yoshinobu Tanaka

2012-01-01

Full Text Available The overall membrane pair characteristics included in the overall mass transport equation are understandable using the phenomenological equations expressed in the irreversible thermodynamics. In this investigation, the overall membrane pair characteristics (overall transport number , overall solute permeability , overall electro-osmotic permeability and overall hydraulic permeability were measured by seawater electrodialysis changing current density, temperature and salt concentration, and it was found that occasionally takes minus value. For understanding the above phenomenon, new concept of the overall concentration reflection coefficient ∗ is introduced from the phenomenological equation. This is the aim of this investigation. ∗ is defined for describing the permselectivity between solutes and water molecules in the electrodialysis system just after an electric current interruption. ∗ is expressed by the function of and . ∗ is generally larger than 1 and is positive, but occasionally ∗ becomes less than 1 and becomes negative. Negative means that ions are transferred with water molecules (solvent from desalting cells toward concentrating cells just after an electric current interruption, indicating up-hill transport or coupled transport between water molecules and solutes.

A Relation Between the Eikonal Equation Associated to a Potential Energy Surface and a Hyperbolic Wave Equation.

Science.gov (United States)

Bofill, Josep Maria; Quapp, Wolfgang; Caballero, Marc

2012-12-11

The potential energy surface (PES) of a molecule can be decomposed into equipotential hypersurfaces. We show in this article that the hypersurfaces are the wave fronts of a certain hyperbolic partial differential equation, a wave equation. It is connected with the gradient lines, or the steepest descent, or the steepest ascent lines of the PES. The energy seen as a reaction coordinate plays the central role in this treatment.

Fabrication of a sulfite biosensor by the use of conducting polymer

International Nuclear Information System (INIS)

Hosseini, M.; Bahmani, B; Moztarzadeh, F.; Rabiee, M.

2008-01-01

In this research, an enzyme modified electrode has been produced during the electro polymerization of aniline through incorporation of Sulfite oxidase into a conducting polymer. Then the bioelectrochemical response of resulted sulfite biosensor was investigated at different experimental conditions. Study of the stability of the resulted sulfite biosensor revealed that formation of a passive film on the aluminum surface causes improved stability of the electro active films formed on the electrode surface. The bioelectrochemical response of the enzyme-modified electrode as a sulfite biosensor was investigated at different experimental conditions. The optimum p H and temperature were 8.5 and 35 d eg C , respectively. The apparent Michaelis-Menten constant and the activation energy of the enzyme catalyzed reaction were calculated

A glassy carbon electrode modified with a composite consisting of reduced graphene oxide, zinc oxide and silver nanoparticles in a chitosan matrix for studying the direct electron transfer of glucose oxidase and for enzymatic sensing of glucose

International Nuclear Information System (INIS)

Li, Zhenjiang; Sheng, Liying; Xie, Cuicui; Meng, Alan; Zhao, Kun

2016-01-01

The authors describe the fabrication of a nanocomposite consisting of reduced graphene oxide, zinc oxide and silver nanoparticles by microwave-assisted synthesis. The composite was further reduced in-situ with hydrazine hydrate and then placed, along with the enzyme glucose oxidase, on a glassy carbon electrode. The synergistic effect of the materials employed in the nanocomposite result in excellent electrocatalytic activity. The Michaelis-Menten constant of the adsorbed GOx is 0.25 mM, implying a remarkable affinity of the GOx for glucose. The amperometric response of the modified GCE is linearly proportional to the concentration of glucose in 0.1 to 12.0 mM concentration range, and the detection limit is 10.6 µM. The biosensor is highly selective, well reproducible and stable. (author)

NUMERICAL SOLUTION OF STEADY STATE DISPERSION FLOW MODEL FOR LACTOSE-LACTASE HYDROLYSIS WITH DIFFERENT KINETICS IN FIXED BED

Directory of Open Access Journals (Sweden)

OLAOSEBIKAN ABIDOYE OLAFADEHAN

2010-06-01

Full Text Available A detailed computational procedure for evaluating lactose hydrolysis with immobilized enzyme in a packed bed tubular reactor under dispersion flow conditions is presented. The dispersion flow model for lactose hydrolysis using different kinetics, taking cognizance of external mass transfer resistances, was solved by the method of orthogonal collocation. The reliability of model simulations was tested using experimental data from a laboratory packed bed column, where the -galactosidase of Kluyveromyces fragilis was immobilized on spherical chitosan beads. Comparison of the simulated results with experimental exit conversion shows that the dispersion flow model and using Michaelis-Menten kinetics with competitive product (galactose inhibition are appropriate to interpret the experimental results and simulate the process of lactose hydrolysis in a fixed bed.

Nanoporous cerium oxide thin film for glucose biosensor.

Science.gov (United States)

Saha, Shibu; Arya, Sunil K; Singh, S P; Sreenivas, K; Malhotra, B D; Gupta, Vinay

2009-03-15

Nanoporous cerium oxide (CeO(2)) thin film deposited onto platinum (Pt) coated glass plate using pulsed laser deposition (PLD) has been utilized for immobilization of glucose oxidase (GOx). Atomic force microscopy studies reveal the formation of nanoporous surface morphology of CeO(2) thin film. Response studies carried out using differential pulsed voltammetry (DPV) and optical measurements show that the GOx/CeO(2)/Pt bio-electrode shows linearity in the range of 25-300 mg/dl of glucose concentration. The low value of Michaelis-Menten constant (1.01 mM) indicates enhanced enzyme affinity of GOx to glucose. The observed results show promising application of the nanoporous CeO(2) thin film for glucose sensing application without any surface functionalization or mediator.

Role of carboxydobacteria in consumption of atmospheric carbon monoxide by soil

Energy Technology Data Exchange (ETDEWEB)

Conrad, R. (Max-Planck-Institut fuer Chemie, Mainz, Germany); Meyer, O.; Seiler, W.

1981-08-01

The carbon monoxide consumption rates of the carboxydobacteria Pseudomonas (Seliberia) carboxydohydrogena, P. carboxydovorans, and P. carboxydoflava were measured at high (50%) and low (0.5 ..mu..l liter/sup -1/) mixing ratios of CO in air. CO was only consumed when the bacteria had been grown under CO-autotrophic conditions. At low cell densities the CO comsumption rates measured at low CO mixing ratios were similar in cell suspensions and in mixtures of bacteria in soil. CO consumption observed in natural soil (loess, eolian sand, chernozem) as well as in suspensions or soil mixtures of carboxydobacteria showed Michaelis-Menten kinetics. Considering the difference of the K/sub m/, values and the observed V/sub max/ values, carboxydobacteria cannot contribute significantly to the consumption of atmospheric CO.

Fluctuations induced extinction and stochastic resonance effect in a model of tumor growth with periodic treatment

Energy Technology Data Exchange (ETDEWEB)

Li Dongxi, E-mail: lidongxi@mail.nwpu.edu.c [Department of Applied Mathematics, Northwestern Polytechnical University, Xi' an 710072 (China); Xu Wei; Guo, Yongfeng; Xu Yong [Department of Applied Mathematics, Northwestern Polytechnical University, Xi' an 710072 (China)

2011-01-31

We investigate a stochastic model of tumor growth derived from the catalytic Michaelis-Menten reaction with positional and environmental fluctuations under subthreshold periodic treatment. Firstly, the influences of environmental fluctuations on the treatable stage are analyzed numerically. Applying the standard theory of stochastic resonance derived from the two-state approach, we derive the signal-to-noise ratio (SNR) analytically, which is used to measure the stochastic resonance phenomenon. It is found that the weak environmental fluctuations could induce the extinction of tumor cells in the subthreshold periodic treatment. The positional stability is better in favor of the treatment of the tumor cells. Besides, the appropriate and feasible treatment intensity and the treatment cycle should be highlighted considered in the treatment of tumor cells.

Fluctuations induced extinction and stochastic resonance effect in a model of tumor growth with periodic treatment

International Nuclear Information System (INIS)

Li Dongxi; Xu Wei; Guo, Yongfeng; Xu Yong

2011-01-01

We investigate a stochastic model of tumor growth derived from the catalytic Michaelis-Menten reaction with positional and environmental fluctuations under subthreshold periodic treatment. Firstly, the influences of environmental fluctuations on the treatable stage are analyzed numerically. Applying the standard theory of stochastic resonance derived from the two-state approach, we derive the signal-to-noise ratio (SNR) analytically, which is used to measure the stochastic resonance phenomenon. It is found that the weak environmental fluctuations could induce the extinction of tumor cells in the subthreshold periodic treatment. The positional stability is better in favor of the treatment of the tumor cells. Besides, the appropriate and feasible treatment intensity and the treatment cycle should be highlighted considered in the treatment of tumor cells.

Generalizations of the Toda molecule

Science.gov (United States)

Van Velthoven, W. P. G.; Bais, F. A.

1986-12-01

Finite-energy monopole solutions are constructed for the self-dual equations with spherical symmetry in an arbitrary integer graded Lie algebra. The constraint of spherical symmetry in a complex noncoordinate basis leads to a dimensional reduction. The resulting two-dimensional ( r, t) equations are of second order and furnish new generalizations of the Toda molecule equations. These are then solved by a technique which is due to Leznov and Saveliev. For time-independent solutions a further reduction is made, leading to an ansatz for all SU(2) embeddings of the Lie algebra. The regularity condition at the origin for the solutions, needed to ensure finite energy, is also solved for a special class of nonmaximal embeddings. Explicit solutions are given for the groups SU(2), SO(4), Sp(4) and SU(4).

A general mixture theory. I. Mixtures of spherical molecules

Science.gov (United States)

Hamad, Esam Z.

1996-08-01

We present a new general theory for obtaining mixture properties from the pure species equations of state. The theory addresses the composition and the unlike interactions dependence of mixture equation of state. The density expansion of the mixture equation gives the exact composition dependence of all virial coefficients. The theory introduces multiple-index parameters that can be calculated from binary unlike interaction parameters. In this first part of the work, details are presented for the first and second levels of approximations for spherical molecules. The second order model is simple and very accurate. It predicts the compressibility factor of additive hard spheres within simulation uncertainty (equimolar with size ratio of three). For nonadditive hard spheres, comparison with compressibility factor simulation data over a wide range of density, composition, and nonadditivity parameter, gave an average error of 2%. For mixtures of Lennard-Jones molecules, the model predictions are better than the Weeks-Chandler-Anderson perturbation theory.

Mathematical description of drug-target interactions: application to biologics that bind to targets with two binding sites.

Science.gov (United States)

Gibiansky, Leonid; Gibiansky, Ekaterina

2018-02-01

The emerging discipline of mathematical pharmacology occupies the space between advanced pharmacometrics and systems biology. A characteristic feature of the approach is application of advance mathematical methods to study the behavior of biological systems as described by mathematical (most often differential) equations. One of the early application of mathematical pharmacology (that was not called this name at the time) was formulation and investigation of the target-mediated drug disposition (TMDD) model and its approximations. The model was shown to be remarkably successful, not only in describing the observed data for drug-target interactions, but also in advancing the qualitative and quantitative understanding of those interactions and their role in pharmacokinetic and pharmacodynamic properties of biologics. The TMDD model in its original formulation describes the interaction of the drug that has one binding site with the target that also has only one binding site. Following the framework developed earlier for drugs with one-to-one binding, this work aims to describe a rigorous approach for working with similar systems and to apply it to drugs that bind to targets with two binding sites. The quasi-steady-state, quasi-equilibrium, irreversible binding, and Michaelis-Menten approximations of the model are also derived. These equations can be used, in particular, to predict concentrations of the partially bound target (RC). This could be clinically important if RC remains active and has slow internalization rate. In this case, introduction of the drug aimed to suppress target activity may lead to the opposite effect due to RC accumulation.

Oleamide synthesizing activity from rat kidney: identification as cytochrome c.

Science.gov (United States)

Driscoll, William J; Chaturvedi, Shalini; Mueller, Gregory P

2007-08-03

Oleamide (cis-9-octadecenamide) is the prototype member of an emerging class of lipid signaling molecules collectively known as the primary fatty acid amides. Current evidence suggests that oleamide participates in the biochemical mechanisms underlying the drive to sleep, thermoregulation, and antinociception. Despite the potential importance of oleamide in these physiologic processes, the biochemical pathway for its synthesis in vivo has not been established. We report here the discovery of an oleamide synthetase found in rat tissues using [(14)C]oleoyl-CoA and ammonium ion. Hydrogen peroxide was subsequently found to be a required cofactor. The enzyme displayed temperature and pH optima in the physiologic range, a remarkable resistance to proteolysis, and specificity for long-chain acyl-CoA substrates. The reaction demonstrated Michaelis-Menten kinetics with a K(m) for oleoyl-CoA of 21 microm. Proteomic, biochemical, and immunologic analyses were used to identify the source of the oleamide synthesizing activity as cytochrome c. This identification was based upon peptide mass fingerprinting of isolated synthase protein, a tight correlation between enzymatic activity and immunoreactivity for cytochrome c, and identical functional properties shared by the tissue-derived synthetase and commercially obtained cytochrome c. The ability of cytochrome c to catalyze the formation of oleamide experimentally raises the possibility that cytochrome c may mediate oleamide biosynthesis in vivo.

Self-dual monopoles and toda molecules

Science.gov (United States)

Ganoulis, N.; Goddard, P.; Olive, D.

1982-07-01

Stable static solutions to a gauge field theory with a Higgs field in the adjoint representation and with vanishing self-coupling are self-dual in the sense of Bogomolny. Leznov and Saveliev showed that a specific form of spherical symmetry reduces these equations to a modified form of the Toda molecule equations associated with the overall gauge symmetry G. Values of the constants of integration are found in terms of the distant Higgs field, guaranteeing regularity of the solution at the origin. The expressions hold for any simple Lie group G, depending on G via its root system.

Pharmacokinetic Modeling of Voriconazole To Develop an Alternative Dosing Regimen in Children.

Science.gov (United States)

Gastine, Silke; Lehrnbecher, Thomas; Müller, Carsten; Farowski, Fedja; Bader, Peter; Ullmann-Moskovits, Judith; Cornely, Oliver A; Groll, Andreas H; Hempel, Georg

2018-01-01

The pharmacokinetic variability of voriconazole (VCZ) in immunocompromised children is high, and adequate exposure, particularly in the first days of therapy, is uncertain. A population pharmacokinetic model was developed to explore VCZ exposure in plasma after alternative dosing regimens. Concentration data were obtained from a pediatric phase II study. Nonlinear mixed effects modeling was used to develop the model. Monte Carlo simulations were performed to test an array of three-times-daily (TID) intravenous dosing regimens in children 2 to 12 years of age. A two-compartment model with first-order absorption, nonlinear Michaelis-Menten elimination, and allometric scaling best described the data (maximal kinetic velocity for nonlinear Michaelis-Menten clearance [ V max ] = 51.5 mg/h/70 kg, central volume of distribution [ V 1 ] = 228 liters/70 kg, intercompartmental clearance [ Q ] = 21.9 liters/h/70 kg, peripheral volume of distribution [ V 2 ] = 1,430 liters/70 kg, bioavailability [ F ] = 59.4%, K m = fixed value of 1.15 mg/liter, absorption rate constant = fixed value of 1.19 h -1 ). Interindividual variabilities for V max , V 1 , Q , and F were 63.6%, 45.4%, 67%, and 1.34% on a logit scale, respectively, and residual variability was 37.8% (proportional error) and 0.0049 mg/liter (additive error). Monte Carlo simulations of a regimen of 9 mg/kg of body weight TID simulated for 24, 48, and 72 h followed by 8 mg/kg two times daily (BID) resulted in improved early target attainment relative to that with the currently recommended BID dosing regimen but no increased rate of accumulation thereafter. Pharmacokinetic modeling suggests that intravenous TID dosing at 9 mg/kg per dose for up to 3 days may result in a substantially higher percentage of children 2 to 12 years of age with adequate exposure to VCZ early during treatment. Before implementation of this regimen in patients, however, validation of exposure, safety, and tolerability in a carefully designed

Exact solutions of the generalized Lane–Emden equations of the ...

Indian Academy of Sciences (India)

the mutual attraction of its molecules and subject to the classical laws of thermodynamics. This equation was proposed ... was investigated for first integrals by Leach [31]. Moreover, transformation properties of a more general Emden–Fowler equation were considered in Mellin et al [5]. A review paper by Wong [32] contains ...

Nonlinear propagation of vector extremely short pulses in a medium of symmetric and asymmetric molecules

Energy Technology Data Exchange (ETDEWEB)

Sazonov, S. V., E-mail: sazonov.sergey@gmail.com [National Research Centre “Kurchatov Institute,” (Russian Federation); Ustinov, N. V., E-mail: n-ustinov@mail.ru [Moscow State University of Railways, Kaliningrad Branch (Russian Federation)

2017-02-15

The nonlinear propagation of extremely short electromagnetic pulses in a medium of symmetric and asymmetric molecules placed in static magnetic and electric fields is theoretically studied. Asymmetric molecules differ in that they have nonzero permanent dipole moments in stationary quantum states. A system of wave equations is derived for the ordinary and extraordinary components of pulses. It is shown that this system can be reduced in some cases to a system of coupled Ostrovsky equations and to the equation intagrable by the method for an inverse scattering transformation, including the vector version of the Ostrovsky–Vakhnenko equation. Different types of solutions of this system are considered. Only solutions representing the superposition of periodic solutions are single-valued, whereas soliton and breather solutions are multivalued.

The Approach to Equilibrium: Detailed Balance and the Master Equation

Science.gov (United States)

Alexander, Millard H.; Hall, Gregory E.; Dagdigian, Paul J.

2011-01-01

The approach to the equilibrium (Boltzmann) distribution of populations of internal states of a molecule is governed by inelastic collisions in the gas phase and with surfaces. The set of differential equations governing the time evolution of the internal state populations is commonly called the master equation. An analytic solution to the master…

Response to a temperature modulation as a signature of chemical mechanisms.

Science.gov (United States)

Berthoumieux, H; Jullien, L; Lemarchand, A

2007-11-01

We consider n reactive species involved in unimolecular reactions and submitted to a temperature modulation of small amplitude. We determine the conditions on the rate constants for which the deviations from the equilibrium concentrations of each species can be optimized and find the analytical expression of the frequency associated with an extremum of concentration shift in the case n=3. We prove that the frequency dependence of the displacement of equilibrium gives access to the number n of species involved in the mechanism. We apply the results to the case of the transformation of a reactant into a product through a possible reactive intermediate and find the order relation obeyed by the activation energies of the different barriers. The results typically apply to enzymatic catalysis with kinetics of Michaelis-Menten type.

Correlation analysis of reactivity in the oxidation of some organic diols by tripropylammonium fluorochromate in non-aqueous media

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S. Sheik Mansoor

2016-09-01

Full Text Available The kinetics of oxidation of some organic diols by tripropylammonium fluorochromate (TriPAFC have been studied in dimethylsulfoxide (DMSO. The main product of oxidation is the corresponding hydroxy aldehydes. The reaction is first order with respect to TriPAFC and exhibited Michaelis-Menten type kinetics with respect to organic diols. The reaction is catalyzed by hydrogen ions. The hydrogen ion dependence has the form: kobs = a + b[H+]. Various thermodynamic parameters for the oxidation have been reported and discussed along with the validity of isokinetic relationship. Oxidation of diols was studied in 18 different organic solvents. The rate data are showing satisfactory correlation with Kamlet–Taft solvotochromic parameters (α, β and π∗. A suitable mechanism of oxidation has been proposed.

Simple method for preparing glucose biosensor based on in-situ polypyrrole cross-linked chitosan/glucose oxidase/gold bionanocomposite film.

Science.gov (United States)

Şenel, Mehmet

2015-03-01

A film of chitosan-polypyrrole-gold nanoparticles was fabricated by in-situ chemical synthesis method and its application in glucose biosensor was investigated. The obtained biosensor exhibited a high and reproducible sensitivity of 0.58μA/mM, response time ~4s, linear dynamic range from 1 to 20mM, correlation coefficient of R(2)=0.9981, and limit of detection (LOD), based on S/N ratio (S/N=3) of 0.068mM. A value of 1.83mM for the apparent Michaelis-Menten constant was obtained. The resulting bio-nanocomposite provided a suitable environment for the enzyme to retain its bioactivity at considerably extreme conditions, and the decorated gold nanoparticles in the bio-nanocomposite offer good affinity to enzyme. Copyright © 2014. Published by Elsevier B.V.

Tomato root growth and phosphorus absorption kinetics by tomato plants as affected by phosphorus concentration in nutrient solution

International Nuclear Information System (INIS)

Fontes, P.C.R.; Barber, S.A.

1984-01-01

To evaluate the effects P concentrations in nutrient solution on root growth and on root physiological characteristics involved in P uptake by tomato Lycopersicon esculentum Mill plants, six seedlings were grown in nutrient solution at initial concentrations of 48.5, 97, 194 and 388 μMP until one day before harvest. They were then transferred to solutions with P at 20 μM and 30 μM, and the depletion curves and Michaelis-Menten parameters were determined. The conclusions were that as P supply increased and as the plant P contents are sufficient for maximum growth, the rate of P uptake tends to be lower. The results also indicate that total P uptake by tomato seedlings depends on the amount of root surface area exposed to P. (M.A.C.) [pt

A novel hydrogen peroxide biosensor based on hemoglobin-collagen-CNTs composite nanofibers.

Science.gov (United States)

Li, J; Mei, H; Zheng, W; Pan, P; Sun, X J; Li, F; Guo, F; Zhou, H M; Ma, J Y; Xu, X X; Zheng, Y F

2014-06-01

In this paper, carbon nanotubes (CNTs) were successfully incorporated in the composite composed of hemoglobin (Hb) and collagen using co-electrospinning technology. The formed Hb-collagen-CNTs composite nanofibers possessed distinct advantage of three-dimensional porous structure, biocompatibility and excellent stability. The Hb immobilized in the electrospun nanofibers retained its natural structure and the heterogeneous electron transfer rate constant (ks) of the direct electron transfer between Hb and electrodes was 5.3s(-1). In addition, the electrospun Hb-collagen-CNTs nanofibers modified electrodes showed good electrocatalytic properties toward H2O2 with a detection limit of 0.91μM (signal-to-noise ratio of 3) and the apparent Michaelis-Menten constant (Km(app)) of 32.6μM. Copyright © 2014 Elsevier B.V. All rights reserved.

Characterization of the anion sensitive ATPase in intact vacuoles of Kalanchoe diagremontiana

Energy Technology Data Exchange (ETDEWEB)

Kobza, J.; Uribe, E.G.

1986-04-01

A method for the isolation of intact vacuoles from K. daigremontiana was developed which produced high yields of relatively pure vacuoles as determined by marker enzyme contamination. Upon isolation, the vacuoles were stabilized by the inclusion of 5% (w/v) ficoll. Enzyme activity was insensitive to vanadate and azide but was strongly inhibited by DCCD. Enzyme activity was strictly dependent on the inclusion of Mg/sup 2 +/ and was stimulated by anions as depicted by the series, NO/sub 3//sup -/ < Br/sup -/ < SO/sub 4//sup -/ < HCO/sub 3//sup -/ < Cl/sup -/. It was found that in intact vacuoles the ATPase activity was stimulated by phosphate to a level equivalent to that found with the chloride. The enzyme exhibited Michaelis-Menten kinetics with a Km for Mg-ATP complex of 0.51 mM.

Biodegradation of Benzene, Toluene, Ethylbenzene, and o-, m-, and p-Xylenes by the Newly Isolated Bacterium Comamonas sp. JB.

Science.gov (United States)

Jiang, Bei; Zhou, Zunchun; Dong, Ying; Tao, Wei; Wang, Bai; Jiang, Jingwei; Guan, Xiaoyan

2015-07-01

A bacterium designated strain JB, able to degrade six benzene, toluene, ethylbenzene, and o-, m-, and p-xylene (BTEX) compounds, was isolated from petroleum-contaminated soil. Taxonomic analyses showed that the isolate belonged to Comamonas, and until now, the genus Comamonas has not included any known BTEX degraders. The BTEX biodegradation rate was slightly low on the mineral salt medium (MSM), but adding a small amount of yeast extract greatly enhanced the biodegradation. The relationship between specific degradation rate and individual BTEX was described well by Michaelis-Menten kinetics. The treatment of petrochemical wastewater containing BTEX mixture and phenol was shown to be highly efficient by BTEX-grown JB. In addition, toxicity assessment indicated the treatment of the petrochemical wastewater by BTEX-grown JB led to less toxicity than untreated wastewater.

Michał Kalecki i problem racjonalnej alokacji zasobów w socjalizmie

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Damian Winczewski

2015-06-01

Full Text Available Celem artykułu jest rekonstrukcja poglądów Michała Kaleckiego i jego zwolenników na temat racjonalnej kalkulacji i alokacji zasobów w gospodarce socjalistycznej, a także próba zestawienia tych poglądów z poglądami zwolenników zarówno kapitalizmu, jak i alternatywnych modeli socjalizmu. Pod tym kątem przeanalizowano artykuły polskiego ekonomisty dotyczące schematu tworzenia się cen w kapitalizmie i socjalizmie, roli klasy robotniczej oraz systemu bodźców i sposobu zarządzania gospodarką. W artykule omówiono też poglądy autorów, którzy bazując na pracach Kaleckiego, podjęli się polemiki z obiegową narracją wyjaśniającą porażkę realnego socjalizmu. Zarówno realny kapitalizm, jak i realny socjalizm zmagają się z problemami niedoskonałej informacji i miękkich budżetów, nie istnieje również doskonały model zarządzania gospodarką, w związku z tym nie są to bezpośrednie przyczyny niepowodzenia projektu socjalistycznego. Oprócz problemu innowacji i optymalnych nakładów inwestycyjnych z perspektywy kaleckiańskiej zasadniczym problemem socjalizmu wydaje się ustanowienie właściwych stosunków produkcji w marksistowskim sensie, rozumianych jako zdemokratyzowanie relacji pomiędzy klasą robotniczą a warstwą zarządzającą produkcją.

Physiological Response of Plants Grown on Porous Ceramic Tubes

Science.gov (United States)

Tsao, David; Okos, Martin

1997-01-01

This research involves the manipulation of the root-zone water potential for the purposes of discriminating the rate limiting step in the inorganic nutrient uptake mechanism utilized by higher plants. This reaction sequence includes the pathways controlled by the root-zone conditions such as water tension and gradient concentrations. Furthermore, plant based control mechanisms dictated by various protein productions are differentiated as well. For the nutrients limited by the environmental availability, the kinetics were modeled using convection and diffusion equations. Alternatively, for the nutrients dependent upon enzyme manipulations, the uptakes are modeled using Michaelis-Menten kinetics. In order to differentiate between these various mechanistic steps, an experimental apparatus known as the Porous Ceramic Tube - Nutrient Delivery System (PCT-NDS) was used. Manipulation of the applied suction pressure circulating a nutrient solution through this system imposes a change in the matric component of the water potential. This compensates for the different osmotic components of water potential dictated by nutrient concentration. By maintaining this control over the root-zone conditions, the rate limiting steps in the uptake of the essential nutrients into tomato plants (Lycopersicon esculentum cv. Cherry Elite) were differentiated. Results showed that the uptake of some nutrients were mass transfer limited while others were limited by the enzyme kinetics. Each of these were adequately modeled with calculations and discussions of the parameter estimations provided.

Hysteresis response of daytime net ecosystem exchange during drought

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N. Pingintha

2010-03-01

Full Text Available Continuous measurements of net ecosystem CO₂ exchange (NEE using the eddy-covariance method were made over an agricultural ecosystem in the southeastern US. During optimum environmental conditions, photosynthetically active radiation (PAR was the primary driver controlling daytime NEE, accounting for as much as 67 to 89% of the variation in NEE. However, soil water content became the dominant factor limiting the NEE-PAR response during the peak growth stage. NEE was significantly depressed when high PAR values coincided with very low soil water content. The presence of a counter-clockwise hysteresis of daytime NEE with PAR was observed during periods of water stress. This is a result of the stomatal closure control of photosynthesis at high vapor pressure deficit and enhanced respiration at high temperature. This result is significant since this hysteresis effect limits the range of applicability of the Michaelis-Menten equation and other related expressions in the determination of daytime NEE as a function of PAR. The systematic presence of hysteresis in the response of NEE to PAR suggests that the gap-filling technique based on a non-linear regression approach should take into account the presence of water-limited field conditions. Including this step is therefore likely to improve current evaluation of ecosystem response to increased precipitation variability arising from climatic changes.

Kinetics of butyrate, acetate, and hydrogen metabolism in a thermophilic, anaerobic, butyrate-degrading triculture.

Science.gov (United States)

Ahring, B K; Westermann, P

1987-02-01

Kinetics of butyrate, acetate, and hydrogen metabolism were determined with butyrate-limited, chemostat-grown tricultures of a thermophilic butyrate-utilizing bacterium together with Methanobacterium thermoautotrophicum and the TAM organism, a thermophilic acetate-utilizing methanogenic rod. Kinetic parameters were determined from progress curves fitted to the integrated form of the Michaelis-Menten equation. The apparent half-saturation constants, K(m), for butyrate, acetate, and dissolved hydrogen were 76 muM, 0.4 mM, and 8.5 muM, respectively. Butyrate and hydrogen were metabolized to a concentration of less than 1 muM, whereas acetate uptake usually ceased at a concentration of 25 to 75 muM, indicating a threshold level for acetate uptake. No significant differences in K(m) values for butyrate degradation were found between chemostat- and batch-grown tricultures, although the maximum growth rate was somewhat higher in the batch cultures in which the medium was supplemented with yeast extract. Acetate utilization was found to be the rate-limiting reaction for complete degradation of butyrate to methane and carbon dioxide in continuous culture. Increasing the dilution rate resulted in a gradual accumulation of acetate. The results explain the low concentrations of butyrate and hydrogen normally found during anaerobic digestion and the observation that acetate is the first volatile fatty acid to accumulate upon a decrease in retention time or increase in organic loading of a digestor.

Approximate Solutions of Schrodinger Equation with Some Diatomic Molecular Interactions Using Nikiforov-Uvarov Method

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Ituen B. Okon

2017-01-01

Full Text Available We used a tool of conventional Nikiforov-Uvarov method to determine bound state solutions of Schrodinger equation with quantum interaction potential called Hulthen-Yukawa inversely quadratic potential (HYIQP. We obtained the energy eigenvalues and the total normalized wave function. We employed Hellmann-Feynman Theorem (HFT to compute expectation values r-2, r-1, T, and p2 for four different diatomic molecules: hydrogen molecule (H2, lithium hydride molecule (LiH, hydrogen chloride molecule (HCl, and carbon (II oxide molecule. The resulting energy equation reduces to three well-known potentials which are as follows: Hulthen potential, Yukawa potential, and inversely quadratic potential. The bound state energies for Hulthen and Yukawa potentials agree with the result reported in existing literature. We obtained the numerical bound state energies of the expectation values by implementing MATLAB algorithm using experimentally determined spectroscopic constant for the different diatomic molecules. We developed mathematica programming to obtain wave function and probability density plots for different orbital angular quantum number.

Michaelis kinetic analysis of extracellular cellulase and amylase excreted by Lactobacillus plantarum during cassava fermentation

Science.gov (United States)

Frediansyah, Andri; Kurniadi, Muhamad

2017-01-01

Our previous study reveal that single culture of Lactobacillus plantarum has ability to ferment cassava tuber in relation to produce modified cassava flour (mocaf). It was used to accelerate a fermentation process. L. plantarum grow well and produce some extracellular enzymes i.e. cellulase to change the structure and breakdown the cell wall of cassava tuber. Then, the starchy materials will be hydrolyzed by i.e. amylase into simple sugar and convert to organic acid. All of these process will give new characteristic of cassava i.e. lower fiber content, good flavor, taste, aroma and texture and the amount of cyanide acid is lower. Therefore this present study was to analyze Michaelis kinetics of extracellular carboxymethyl cellulase and amylase production by L. plantarum during cassava fermentation. The maximum carboxymethyl cellulase and amylase activity of 8.60 U/ml and 14.07 U/ml, respectively, were obtained from filtrate which has been incubated at 37°C for 18 h under stationary conditions. The Vmax and Km of CMCase were 0.8506 × 10-3 U/ml and 0.9594 × 10-3 g/mL, respectively. For amylase were 9.291 × 10-3 U/ml and 0.9163 × 10-3 g/ml, respectively.

LOW-TEMPERATURE EQUATION OF STATE OF SOLID METHANE

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L. N. Yakub

2016-02-01

Full Text Available The theoretical equation of state for solid methane, developed within the framework of perturbation theory, with the crystal consisting of spherical molecules as zero-order approximation, and octupole – octupole interaction of methane molecules as a perturbation, is proposed. Thermodynamic functions are computed on the sublimation line up to the triple point. The contribution of the octupole – octupole interaction to the thermodynamic properties of solid methane is estimated.

Phosphorus Uptake Kinetics of Different Types of Duckweed.%不同品种浮萍磷素吸收动力学特征

Institute of Scientific and Technical Information of China (English)

蔡树美; 刘文桃; 张震; 柏彦超; 钱晓晴

2011-01-01

以长江三角洲地区常见的3种浮萍--稀脉浮萍(Lemna aequinoctialis)、少根紫萍(Spirodela oligorrhiza)和紫萍(Spriodela polyrrhiza)为对象,研究不同品种浮萍对HPO42-的吸收动力学影响.结果表明,3种浮萍对无机磷的吸收动力学特征基本可采用Michaelis-Menten方程描述,3种浮萍无机磷吸收速率V对磷浓度S双倒数曲线的拟合关系均在α=0.01水平上显著.稀脉浮萍对无机磷的亲和力较强,适宜应用于对低磷浓度污水的净化;紫萍对无机磷的最大吸收速率Vmax较高,适宜应用于对高磷浓度污水的净化.%An increasing attention has been paid to the use of duckweed in treating eutrophicated water as a tool of bio-remediation of domestic wastewater.Phosphorus uptake kinetics was studied,of different species of duckweeds, i.e.Lemna aequinoctialis, Spirodela oligorrhiza and Spriodela polyrrhiza, which are common in the Yangtze River Delta area.Results show that the phosphorus uptake kinetics of the duckweeds could be expressed with the Michaelis-Menten equation; and the relation between phosphorus uptake rate (V) of the duckweeds and inorganic phosphorus(Pi) concentration (S), was well fitted with a double-reciprocal curve with at =0.01; the Km value for Pi uptake of Lemna aequinoctialis was lower than that of Spirodela oligorrhiza and Spriodela polyrrhiza, making it a better candidate for treating wastewater low in Pi concentration.The maximum phosphorus uptake rate of Spriodela polyrrhiza was higher than that of the other two species, which allows Spriodela polyrrhiza better performance in purifying wastewater higher in Pi concentration.

Self-scattering cross-section of molecules in a beam

International Nuclear Information System (INIS)

Lou, Y.S.

1974-01-01

Molecular collision cross-section has always been measured by the beam scattering method, or by the measurements of thermal conductivity and/or viscosity coefficient, etc. The cross-section thus obtained has been found to be different, qualitatively, from that of the self-scattering of the molecules moving within a molecular beam. By perturbing the zeroth order solution of the Boltzmann equation with a B-G-K kinetic model for the gas upstream to the orifice, and performing particle scattering calculation for molecules within the beam downstream to the orifice, such self-scattering collision cross-section can be determined from the experimental data of velocity distribution functions of molecules in the beam

Discrete Velocity Models for Polyatomic Molecules Without Nonphysical Collision Invariants

Science.gov (United States)

Bernhoff, Niclas

2018-05-01

An important aspect of constructing discrete velocity models (DVMs) for the Boltzmann equation is to obtain the right number of collision invariants. Unlike for the Boltzmann equation, for DVMs there can appear extra collision invariants, so called spurious collision invariants, in plus to the physical ones. A DVM with only physical collision invariants, and hence, without spurious ones, is called normal. The construction of such normal DVMs has been studied a lot in the literature for single species, but also for binary mixtures and recently extensively for multicomponent mixtures. In this paper, we address ways of constructing normal DVMs for polyatomic molecules (here represented by that each molecule has an internal energy, to account for non-translational energies, which can change during collisions), under the assumption that the set of allowed internal energies are finite. We present general algorithms for constructing such models, but we also give concrete examples of such constructions. This approach can also be combined with similar constructions of multicomponent mixtures to obtain multicomponent mixtures with polyatomic molecules, which is also briefly outlined. Then also, chemical reactions can be added.

Semiclassical theory of resonance inelastic electron-molecule collisions

International Nuclear Information System (INIS)

Kazanskij, A.K.

1986-01-01

Semiclassical approach to the theory of resonance electron-molecule collisions, unlocal with respect to interatomic distance was developed. Two problems were considered: modified adiabatic approach for sigle-pole approximation of R-matrix and Fano-Feshbach-Bardsley theory. It is shown that these problems are similar in semiclassical approximation. A simple equation system with coefficients expressed in quadratures was obtained. It enables to determine amplitudes of all processes (including dissociation adhesion, association ejection, free-free and free-bound transitions) in energetic representation with respect to nucleus vibrations in molecule with allowance for both descrete and continuous spectra of nucleus motion in molecule. Quantitative investigation of the system results to the notion of dynamic energy curve of intermediate state, generalizing the motion of such curve in boomerang theory

Force-balance and differential equation for the ground-state electron density in atoms and molecules

International Nuclear Information System (INIS)

Amovilli, C.; March, N.H.; Gal, T.; Nagy, A.

2000-01-01

Holas and March (1995) established a force-balance equation from the many-electron Schroedinger equation. Here, the authors propose this as a basis for the construction of a (usually approximate) differential equation for the ground-state electron density. By way of example they present the simple case of two-electron systems with different external potentials but with weak electron-electron Coulomb repulsion λe 2 /r 12 . In this case first-order Rayleigh-Schroedinger (RS) perturbation theory of the ground-state wave function is known to lead to a compact expression for the first-order density matrix γ(r,rprime) in terms of its diagonal density ρ(r) and the density corresponding to λ = 0. This result allows the force-balance equation to be written as a third-order linear, differential homogeneous equation for the ground-state electron density ρ(r). The example of the two-electron Hookean atom is treated: For this case one can also transcend the first-order RS perturbation theory and get exact results for discrete choices of force constants (external potential)

Effective inclusion of polarization effects in calculations of the oscillator strengths and transition energies in atoms and molecules using the equation-of-motion method

International Nuclear Information System (INIS)

Glushkov, A.V.; Kol'tsova, N.Yu.

1994-01-01

Equations of motion were solved by a modified method in a quasi-particle representation of the density functional taking into account the most important polarization effects, including the so-called 2p-2h two-particle-two-hole interactions. Based on these calculations, spectroscopic data on energies and oscillator strengths of the helium atom (the test computation), carbon monoxide, nitrogen molecule, and ethylene are presented that refine some previously reported experimental and theoretical results. It is shown that in some cases the inclusion of polarization corrections introduced by 2p-2h effects is of basic importance because it provides up to ∼30% contribution to the energies and oscillator strengths. 23 refs., 5 tabs

Phase space structure of triatomic molecules

International Nuclear Information System (INIS)

Lu, Z.; Kellman, M.E.

1997-01-01

The bifurcation structure is investigated for a Hamiltonian for the three coupled nonlinear vibrations of a highly excited triatomic molecule. The starting point is a quantum Hamiltonian used to fit experimental spectra. This Hamiltonian includes 1:1 Darling endash Dennison resonance coupling between the stretches, and 2:1 Fermi resonance coupling between the stretches and bend. A classical Hamiltonian is obtained using the Heisenberg correspondence principle. Surfaces of section show a pronounced degree of chaos at high energies, with a mixture of chaotic and regular dynamics. The large-scale bifurcation structure is found semianalytically, without recourse to numerical solution of Hamilton close-quote s equations, by taking advantage of the fact that the spectroscopic Hamiltonian has a conserved polyad quantum number, corresponding to an approximate constant of the motion of the molecule. Bifurcation diagrams are analyzed for a number of molecules including H 2 O, D 2 O, NO 2 , ClO 2 , O 3 , and H 2 S. copyright 1997 American Institute of Physics

Dual Schroedinger Equation as Global Optimization Algorithm

International Nuclear Information System (INIS)

Huang Xiaofei; eGain Communications, Mountain View, CA 94043

2011-01-01

The dual Schroedinger equation is defined as replacing the imaginary number i by -1 in the original one. This paper shows that the dual equation shares the same stationary states as the original one. Different from the original one, it explicitly defines a dynamic process for a system to evolve from any state to lower energy states and eventually to the lowest one. Its power as a global optimization algorithm might be used by nature for constructing atoms and molecules. It shall be interesting to verify its existence in nature.

Approximate Treatment of the Dirac Equation with Hyperbolic Potential Function

Science.gov (United States)

Durmus, Aysen

2018-03-01

The time independent Dirac equation is solved analytically for equal scalar and vector hyperbolic potential function in the presence of Greene and Aldrich approximation scheme. The bound state energy equation and spinor wave functions expressed by the hypergeometric function have been obtained in detail with asymptotic iteration approach. In order to indicate the accuracy of this different approach proposed to solve second order linear differential equations, we present that in the non-relativistic limit, analytical solutions of the Dirac equation converge to those of the Schrödinger one. We introduce numerical results of the theoretical analysis for hyperbolic potential function. Bound states corresponding to arbitrary values of n and l are reported for potential parameters covering a wide range of interaction. Also, we investigate relativistic vibrational energy spectra of alkali metal diatomic molecules in the different electronic states. It is observed that theoretical vibrational energy values are consistent with experimental Rydberg-Klein-Rees (RKR) results and vibrational energies of NaK, K_2 and KRb diatomic molecules interacting with hyperbolic potential smoothly converge to the experimental dissociation limit D_e=2508cm^{-1}, 254cm^{-1} and 4221cm^{-1}, respectively.

Chemical Continuous Time Random Walks

Science.gov (United States)

Aquino, T.; Dentz, M.

2017-12-01

Traditional methods for modeling solute transport through heterogeneous media employ Eulerian schemes to solve for solute concentration. More recently, Lagrangian methods have removed the need for spatial discretization through the use of Monte Carlo implementations of Langevin equations for solute particle motions. While there have been recent advances in modeling chemically reactive transport with recourse to Lagrangian methods, these remain less developed than their Eulerian counterparts, and many open problems such as efficient convergence and reconstruction of the concentration field remain. We explore a different avenue and consider the question: In heterogeneous chemically reactive systems, is it possible to describe the evolution of macroscopic reactant concentrations without explicitly resolving the spatial transport? Traditional Kinetic Monte Carlo methods, such as the Gillespie algorithm, model chemical reactions as random walks in particle number space, without the introduction of spatial coordinates. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. In real systems, transport limitations lead to incomplete mixing and decreased reaction efficiency. We introduce an arbitrary inter-reaction time distribution, which may account for the impact of incomplete mixing. This process defines an inhomogeneous continuous time random walk in particle number space, from which we derive a generalized chemical Master equation and formulate a generalized Gillespie algorithm. We then determine the modified chemical rate laws for different inter-reaction time distributions. We trace Michaelis-Menten-type kinetics back to finite-mean delay times, and predict time-nonlocal macroscopic reaction kinetics as a consequence of broadly distributed delays. Non-Markovian kinetics exhibit weak ergodicity breaking and show key features of reactions under local non-equilibrium.

Calculation of a hydrogen molecule in the adiabatic approximation

International Nuclear Information System (INIS)

Vukajlovich, F.R.; Mogilevskij, O.A.; Ponomarev, L.I.

1979-01-01

The adiabatic approximation js used for calculating the energy levels of a hydrogen molecule, i.e. of the simplest four-body system with a Coulomb interaction. The aim of this paper is the investigation of the possible use of the adiabatic method in the molecular problems. The most effective regions of its application are discussed. An infinite system of integro-differential equations is constructed, which describes the hydrogen molecule in the adiabatic approximation with the effective potentials taking into account the corrections to the nuclear motion. The energy of the first three vibrational states of the hydrogen molecule is calculated and compared with the experimental data. The convergence of the method is discussed

The symbolic language of substances and molecules: noise or ...

African Journals Online (AJOL)

Most substances are given names and formulae based upon knowledge of their molecules. However for substances most commonly met in elementary chemistry courses, especially inorganic substances, this is often not the case. The potential noise is amplified further when dealing with chemical reaction equations.

Molecular dynamics studies of transport properties and equation of state of supercritical fluids

Science.gov (United States)

Nwobi, Obika C.

Many chemical propulsion systems operate with one or more of the reactants above the critical point in order to enhance their performance. Most of the computational fluid dynamics (CFD) methods used to predict these flows require accurate information on the transport properties and equation of state at these supercritical conditions. This work involves the determination of transport coefficients and equation of state of supercritical fluids by equilibrium molecular dynamics (MD) simulations on parallel computers using the Green-Kubo formulae and the virial equation of state, respectively. MD involves the solution of equations of motion of a system of molecules that interact with each other through an intermolecular potential. Provided that an accurate potential can be found for the system of interest, MD can be used regardless of the phase and thermodynamic conditions of the substances involved. The MD program uses the effective Lennard-Jones potential, with system sizes of 1000-1200 molecules and, simulations of 2,000,000 time-steps for computing transport coefficients and 200,000 time-steps for pressures. The computer code also uses linked cell lists for efficient sorting of molecules, periodic boundary conditions, and a modified velocity Verlet algorithm for particle displacement. Particle decomposition is used for distributing the molecules to different processors of a parallel computer. Simulations have been carried out on pure argon, nitrogen, oxygen and ethylene at various supercritical conditions, with self-diffusion coefficients, shear viscosity coefficients, thermal conductivity coefficients and pressures computed for most of the conditions. Results compare well with experimental and the National Institute of Standards and Technology (NIST) values. The results show that the number of molecules and the potential cut-off radius have no significant effect on the computed coefficients, while long-time integration is necessary for accurate determination of the

Van der Waals equation of state revisited: importance of the dispersion correction.

Science.gov (United States)

de Visser, Sam P

2011-04-28

One of the most basic equations of state describing nonideal gases and liquids is the van der Waals equation of state, and as a consequence, it is generally taught in most first year undergraduate chemistry courses. In this work, we show that the constants a and b in the van der Waals equation of state are linearly proportional to the polarizability volume of the molecules in a gas or liquid. Using this information, a new thermodynamic one-parameter equation of state is derived that contains experimentally measurable variables and physics constants only. This is the first equation of state apart from the Ideal Gas Law that contains experimentally measurable variables and physics constants only, and as such, it may be a very useful and practical equation for the description of dilute gases and liquids. The modified van der Waals equation of state describes pV as the sum of repulsive and attractive intermolecular interaction energies that are represented by an exponential repulsion function between the electron clouds of the molecules and a London dispersion component, respectively. The newly derived equation of state is tested against experimental data for several gas and liquid examples, and the agreement is satisfactory. The description of the equation of state as a one-parameter function also has implications on other thermodynamic functions, such as critical parameters, virial coefficients, and isothermal compressibilities. Using our modified van der Waals equation of state, we show that all of these properties are a function of the molecular polarizability volume. Correlations of experimental data confirm the derived proportionalities.

Enantiomeric fractioning, degradation and metabolite formation of Mecoprop in subsoils with a phenoxy acid contamination history

DEFF Research Database (Denmark)

Frkova, Zuzana; Johansen, Anders; Karlson, Ulrich G.

2015-01-01

for their ability to degrade mecoprop under natural and amended conditions. Degradation of mecoprop was studied at elevated and environmentally relevant mecoprop concentrations as affected by nitrate and glucose at nitrate-reducing conditions and at a presence of oxygen (mimicking purging the soil with air. Results......As persistence and toxicity of the enantiomers of chiral pesticides are different a more comprehensive understanding of the fate of enantiomers of agrochemicals in the environment is necessary. Subsoils sampled vertically (2.5-6 m) at a site with a history of phenoxy acid contamination were used...... and enantioselectivity. Glucose hinders mecoprop degradation and changes the EF. Changing EF confirmed enzymatic dgradation of mecoprop in soils, which was well interpreted using the Michaelis-Menten kinetic model. The highest mecoprop degradation rate was measured in soils incubated at nitrate-reducing conditions...

Model-Based Optimization of Scaffold Geometry and Operating Conditions of Radial Flow Packed-Bed Bioreactors for Therapeutic Applications

Directory of Open Access Journals (Sweden)

Danilo Donato

2014-01-01

Full Text Available Radial flow perfusion of cell-seeded hollow cylindrical porous scaffolds may overcome the transport limitations of pure diffusion and direct axial perfusion in the realization of bioengineered substitutes of failing or missing tissues. Little has been reported on the optimization criteria of such bioreactors. A steady-state model was developed, combining convective and dispersive transport of dissolved oxygen with Michaelis-Menten cellular consumption kinetics. Dimensional analysis was used to combine more effectively geometric and operational variables in the dimensionless groups determining bioreactor performance. The effectiveness of cell oxygenation was expressed in terms of non-hypoxic fractional construct volume. The model permits the optimization of the geometry of hollow cylindrical constructs, and direction and magnitude of perfusion flow, to ensure cell oxygenation and culture at controlled oxygen concentration profiles. This may help engineer tissues suitable for therapeutic and drug screening purposes.

Transformation frequency of γ irradiated plasmid DNA and the enzymatic double strand break formation by incubation in a protein extract of Escherichia coli

International Nuclear Information System (INIS)

Schulte-Frohlinde, D.; Mark, F.; Ventur, Y.

1994-01-01

It was found that incubation of γ-irradiated or DNaseI-treated plasmid DNA in a protein extract of Escherichia coli leads to enzyme-induced formation of double strand breaks (dsb) in competition with repair of precursors of these dsb. A survival curve of the plasmid DNA (as determined by transformation of E. coli) was calculated on the basis of enzyme-induced dsb as well as those produced by irradiation assuming that they are lethal. The calculated D O value was the same as that measured directly by transformation of irradiated plasmid DNA. Two models are presented that fit the experimental survival data as a function of dose. One is based on damage formation in the plasmid DNA including enzymatic conversion of single strand damage into dsb (U-model), the other is an enzymatic repair saturation model based on Michaelis-Menten kinetics. (Author)

Aza Cope Rearrangement of Propargyl Enammonium Cations Catalyzed By a Self-Assembled `Nanozyme

Energy Technology Data Exchange (ETDEWEB)

Hastings, Courntey J.; Fiedler, Dorothea; Bergman, Robert G.; Raymond, Kenneth N.

2008-02-27

The tetrahedral [Ga{sub 4}L{sub 6}]{sup 12-} assembly (L = N,N-bis(2,3-dihydroxybenzoyl)-1,5-diaminonaphthalene) encapsulates a variety of cations, including propargyl enammonium cations capable of undergoing the aza Cope rearrangement. For propargyl enammonium substrates that are encapsulated in the [Ga{sub 4}L{sub 6}]{sup 12-} assembly, rate accelerations of up to 184 are observed when compared to the background reaction. After rearrangement, the product iminium ion is released into solution and hydrolyzed allowing for catalytic turnover. The activation parameters for the catalyzed and uncatalyzed reaction were determined, revealing that a lowered entropy of activation is responsible for the observed rate enhancements. The catalyzed reaction exhibits saturation kinetics; the rate data obey the Michaelis-Menten model of enzyme kinetics, and competitive inhibition using a non-reactive guest has been demonstrated.

Parallel synthesis of libraries of anodic and cathodic functionalized electrodeposition paints as immobilization matrix for amperometric biosensors.

Science.gov (United States)

Ngounou, Bertrand; Aliyev, Elchin H; Guschin, Dmitrii A; Sultanov, Yusif M; Efendiev, Ayaz A; Schuhmann, Wolfgang

2007-09-01

The integration of flexible anchoring groups bearing imidazolyl or pyridyl substituents into the structure of electrodeposition paints (EDP) is the basis for the parallel synthesis of a library containing 107 members of different cathodic and anodic EDPs with a high variation in polymer properties. The obtained EDPs were used as immobilization matrix for biosensor fabrication using glucose oxidase as a model enzyme. Amperometric glucose sensors based on the different EDPs showed a wide variation in their sensor characteristics with respect to the apparent Michaelis-Menten constant (KM(app)) representing the linear measuring range and the maximum current (Imax(app)). Based on these results first assumptions concerning the impact of different side chains in the EDP on the expected biosensor properties could be obtained allowing for an improved rational optimization of EDPs used as immobilization matrix in amperometric biosensors.

Characteristics of 36C103- influx into nitrate reductase deficient mutant E1 pisum sativum seedlings: evidence for restricted ''induction'' by nitrate compared with wild type

International Nuclear Information System (INIS)

Deane-Drummond, C.E.; Jacobsen, E.

1986-01-01

The characteristics of nitrate uptake into seedlings of Pisum sativum L. cv. Rondo mutant E 1 defective for nitrate reductase (NR) and of its parent variety Rondo have been investigated using 36 C10 3 - as an analogue for nitrate. The apparent Michaelis Menten constants (K m ) for 36 ClO 3 - influx measured over 10 min were similar for mutant E 1 and the wild type (Wt). There was a 28% increase in 36 C10 3 - into Wt seedlings following nitrate pretreatment but this was not found when mutant seedlings were used. N starvation increased 36 C10 3 - influx into both mutant and Wt seedlings, and the rate of cycling E/I was also enhanced to a similar extent. The results are discussed in terms of current ideas on the regulation of nitrate uptake and assimilation. (author)

A Critical View on In Vitro Analysis of P-glycoprotein (P-gp) Transport Kinetics

DEFF Research Database (Denmark)

Saaby, Lasse; Brodin, Birger

2017-01-01

Transport proteins expressed in the different barriers of the human body can have great implications on absorption, distribution, and excretion of drug compounds. Inhibition or saturation of a transporter can potentially alter these absorbtion, distribution, metabolism and elimination properties...... and thereby also the pharmacokinetic profile and bioavailability of drug compounds. P-glycoprotein (P-gp, ABCB1) is an efflux transporter which is present in most of the barriers of the body, including the small intestine, the blood-brain barrier, the liver, and the kidney. In all these tissues, P-gp may...... mediate efflux of drug compounds and may also be a potential site for drug-drug interactions. Consequently, there is a need to be able to predict the saturation and inhibition of P-gp and other transporters in vivo. For this purpose, Michaelis-Menten steady-state analysis has been applied to estimate...

The kinetics of denitrification in permeable sediments

DEFF Research Database (Denmark)

Evrard, Victor; Glud, Ronnie N.; Cook, Perran L. M.

2013-01-01

Permeable sediments comprise the majority of shelf sediments, yet the rates of denitrification remain highly uncertain in these environments. Computational models are increasingly being used to understand the dynamics of denitrification in permeable sediments, which are complex environments...... on sediments taken from six shallow coastal sites in Port Phillip Bay, Victoria, Australia. The results showed that denitrification commenced rapidly (within 30 min) after the onset of anoxia and the kinetics could be well described by Michaelis-Menten kinetics with half saturation constants (apparent K...... in cohesive sediments despite organic carbon contents one order of magnitude lower for the sediments studied here. The ratio of sediment O-2 consumption to V-max was in the range of 0.02-0.09, and was on average much lower than the theoretical ratio of 0.8. As a consequence, models implemented...

Interstellar molecules and masers

International Nuclear Information System (INIS)

Nguyen-Q-Rieu; Guibert, J.

1978-01-01

The study of dense and dark clouds, in which hydrogen is mostly in molecular form, became possible since the discovery of interstellar molecules, emitting in the centimeter and millimeter wavelengths. The molecular lines are generally not in local thermal equilibrium (LTE). Their intensity can often be explained by invoking a population inversion mechanism. Maser emission lines due to OH, H 2 O and SiO molecules are among the most intense molecular lines. The H 2 CO molecule, detected in absorption in front of the cold cosmic background radiation of 2.7 K, illustrates the inverse phenomenon, the antimaser absorption. For a radio transition of frequency v, the inversion rate Δn (relative population difference between the upper and lower level) as well as the maser gain can be determined from the radio observations. In the case of the OH lines in the 2 PIsub(3/2), J=3/2 state, the inversion rates approximately 1 to 2% derived from the observations, are comparable with those obtained in the laboratory. The determination of the excitation mechanisms of the masers, through the statistical equilibrium and radiative transfer equations, implies the knowledge of collisional and radiative transition probabilities. A pumping model, which can satisfactorily explain the radio observations of some interstellar OH clouds, will be discussed [fr

Surface single-molecule dynamics controlled by entropy at low temperatures

Science.gov (United States)

Gehrig, J. C.; Penedo, M.; Parschau, M.; Schwenk, J.; Marioni, M. A.; Hudson, E. W.; Hug, H. J.

2017-02-01

Configuration transitions of individual molecules and atoms on surfaces are traditionally described using an Arrhenius equation with energy barrier and pre-exponential factor (attempt rate) parameters. Characteristic parameters can vary even for identical systems, and pre-exponential factors sometimes differ by orders of magnitude. Using low-temperature scanning tunnelling microscopy (STM) to measure an individual dibutyl sulfide molecule on Au(111), we show that the differences arise when the relative position of tip apex and molecule changes by a fraction of the molecule size. Altering the tip position on that scale modifies the transition's barrier and attempt rate in a highly correlated fashion, which results in a single-molecular enthalpy-entropy compensation. Conversely, appropriately positioning the STM tip allows selecting the operating point on the compensation line and modifying the transition rates. The results highlight the need to consider entropy in transition rates of single molecules, even at low temperatures.

Diffusion-equation representations of landform evolution in the simplest circumstances: Appendix C

Science.gov (United States)

Hanks, Thomas C.

2009-01-01

The diffusion equation is one of the three great partial differential equations of classical physics. It describes the flow or diffusion of heat in the presence of temperature gradients, fluid flow in porous media in the presence of pressure gradients, and the diffusion of molecules in the presence of chemical gradients. [The other two equations are the wave equation, which describes the propagation of electromagnetic waves (including light), acoustic (sound) waves, and elastic (seismic) waves radiated from earthquakes; and LaPlace’s equation, which describes the behavior of electric, gravitational, and fluid potentials, all part of potential field theory. The diffusion equation reduces to LaPlace’s equation at steady state, when the field of interest does not depend on t. Poisson’s equation is LaPlace’s equation with a source term.

Orientation of KRb molecules in a switched electrostatic field

International Nuclear Information System (INIS)

Huang Yun-Xia; Xu Shu-Wu; Yang Xiao-Hua

2013-01-01

We theoretically investigate the orientation of the cold KRb molecules induced in a switched electrostatic field by numerically solving the full time-dependent Schrödinger equation. The results show that the periodic field-free molecular orientation can be realized for the KRb molecules by rapidly switching off the electrostatic field. Meanwhile, by varying the switching times of the electrostatic field, the adiabatic and nonadiabatic interactions of the molecules with the applied field can be realized. Moreover, the influences of the electrostatic field strength and the rotational temperature to the degree of the molecular orientation are studied. The investigations show that increasing the electrostatic field will increase the degree of the molecular orientation, both in the constant-field regime and in the field-free regime, while the increasing of the rotational temperature of the cold molecules will greatly decrease the degree of the molecular orientation. (atomic and molecular physics)

Differential Equations Models to Study Quorum Sensing.

Science.gov (United States)

Pérez-Velázquez, Judith; Hense, Burkhard A

2018-01-01

Mathematical models to study quorum sensing (QS) have become an important tool to explore all aspects of this type of bacterial communication. A wide spectrum of mathematical tools and methods such as dynamical systems, stochastics, and spatial models can be employed. In this chapter, we focus on giving an overview of models consisting of differential equations (DE), which can be used to describe changing quantities, for example, the dynamics of one or more signaling molecule in time and space, often in conjunction with bacterial growth dynamics. The chapter is divided into two sections: ordinary differential equations (ODE) and partial differential equations (PDE) models of QS. Rates of change are represented mathematically by derivatives, i.e., in terms of DE. ODE models allow describing changes in one independent variable, for example, time. PDE models can be used to follow changes in more than one independent variable, for example, time and space. Both types of models often consist of systems (i.e., more than one equation) of equations, such as equations for bacterial growth and autoinducer concentration dynamics. Almost from the onset, mathematical modeling of QS using differential equations has been an interdisciplinary endeavor and many of the works we revised here will be placed into their biological context.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

Energy Technology Data Exchange (ETDEWEB)

Fidiani, Elok [Department of Physics, Parahyangan Catholic University, Bandung-Jawa Barat (Indonesia)

2016-03-11

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H{sub 2} and O{sub 2}. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.

Modeling of diatomic molecule using the Morse potential and the Verlet algorithm

International Nuclear Information System (INIS)

Fidiani, Elok

2016-01-01

Performing molecular modeling usually uses special software for Molecular Dynamics (MD) such as: GROMACS, NAMD, JMOL etc. Molecular dynamics is a computational method to calculate the time dependent behavior of a molecular system. In this work, MATLAB was used as numerical method for a simple modeling of some diatomic molecules: HCl, H_2 and O_2. MATLAB is a matrix based numerical software, in order to do numerical analysis, all the functions and equations describing properties of atoms and molecules must be developed manually in MATLAB. In this work, a Morse potential was generated to describe the bond interaction between the two atoms. In order to analyze the simultaneous motion of molecules, the Verlet Algorithm derived from Newton’s Equations of Motion (classical mechanics) was operated. Both the Morse potential and the Verlet algorithm were integrated using MATLAB to derive physical properties and the trajectory of the molecules. The data computed by MATLAB is always in the form of a matrix. To visualize it, Visualized Molecular Dynamics (VMD) was performed. Such method is useful for development and testing some types of interaction on a molecular scale. Besides, this can be very helpful for describing some basic principles of molecular interaction for educational purposes.

Nutrient flux fuels the summer primary productivity in the oligotrophic waters of the Gulf of Aqaba, Red Sea

Directory of Open Access Journals (Sweden)

Tariq Al-Najjar

2005-03-01

Full Text Available The thermohaline characteristics of the Gulf of Aqaba, Red Sea,depict a well-defined seasonal pattern of winter mixing from December toApril and summer stratification from May to November. This thermohalinestructure is a major controlling factor of the nutrient, chlorophyll aand primary productivity seasonal cycles. The nitrate and chlorophyll aconcentration records generated down to 200 m at a vertical resolution of25 m - weekly during 1994, 1995 and every two weeks from April 1997 throughto December 2000 - are employed to assess the nitrogen flux across the summerthermocline of the Gulf of Aqaba. The flux calculations are based on a simplediffusion model that incorporates the physical stress eddy diffusivity factorKz and a biological stress factor k. Both Kz and k arecalculated using the Michaelis-Menten equation and the nitrate concentrationgradient. The total nitrate flux of the Gulf of Aqaba during the seven summermonths (May-November is estimated at 0.52 mole N m-2. In relation toestablished primary productivity values (75.5 g C m-2 (MayNovember-1 and the generated chlorophyll a records, thisyields an f fraction of new to total primary production of 0.50. Thisrelatively high f value is discussed with respect to the geophysicalcharacteristics of the Gulf of Aqaba and similar oceanic basins. The remaining50% is accounted for by cross-sectional flow from the relativelynutrient-rich coral reef coastal habitat and rapid recycling, triggered byhigh irradiance and water temperature.

The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

Directory of Open Access Journals (Sweden)

Giulio Caravagna

Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

Evaluation of deltamethrin kinetics and dosimetry in the maturing rat using a PBPK model

International Nuclear Information System (INIS)

Tornero-Velez, Rogelio; Mirfazaelian, Ahmad; Kim, Kyu-Bong; Anand, Sathanandam S.; Kim, Hyo J.; Haines, Wendy T.; Bruckner, James V.; Fisher, Jeffrey W.

2010-01-01

Immature rats are more susceptible than adults to the acute neurotoxicity of pyrethroid insecticides like deltamethrin (DLM). A companion kinetics study (Kim et al., in press) revealed that blood and brain levels of the neuroactive parent compound were inversely related to age in rats 10, 21, 40 and 90 days old. The objective of the current study was to modify a physiologically based pharmacokinetic (PBPK) model of DLM disposition in the adult male Sprague-Dawley rat (Mirfazaelian et al., 2006), so blood and target organ dosimetry could be accurately predicted during maturation. Age-specific organ weights and age-dependent changes in the oxidative and hydrolytic clearance of DLM were modeled with a generalized Michaelis-Menten model for growth and the summary equations incorporated into the PBPK model. The model's simulations compared favorably with empirical DLM time-courses in plasma, blood, brain and fat for the four age-groups evaluated (10, 21, 40 and 90 days old). PND 10 pups' area under the 24-h brain concentration time curve (AUC 0-24h ) was 3.8-fold higher than that of the PND 90 adults. Our maturing rat PBPK model allows for updating with age- and chemical-dependent parameters, so pyrethroid dosimetry can be forecast in young and aged individuals. Hence, this model provides a methodology for risk assessors to consider age-specific adjustments to oral Reference Doses on the basis of PK differences.

Determination of esterase activity and characterization of cholinesterases in the reef fish Haemulon plumieri.

Science.gov (United States)

Leticia, Alpuche-Gual; Gerardo, Gold-Bouchot

2008-11-01

White grunt (Haemulon plumieri) has been proposed by the Mesoamerican Barrier Reef System (MBRS) Synoptic Monitoring Program as a bioindicator species. It is in this sense that the present study has a main goal to evaluate this organism's suitability as an indicator species. Individuals were captured during three seasons at the port of Sisal, Yucatan, Mexico which is located in an area that is considered to be weakly impacted by human activities such as agriculture or industry. Both cholinesterase (ChE) and carboxylesterase (CbE) activities were measured in brain, muscle, liver and eye of sampled individuals. Results indicated that ChE and CbE activities were greatest in the brain (256.3 ± 43) and in the liver (191 ± 21), respectively. Furthermore, ChEs detected in brain, liver and muscle were characterized, and results suggested that the acetylcholinesterase (AChE) type was more abundant relative to pseudocholinesterase (BChE) which was rare. In addition, K(m) and V(max) and IC(50) values were calculated from the Michaelis-Menten equation. Finally, an additional experiment in vitro showed a significant decrease in both ChE and CbE activities when different tissues were exposed to model xenobiotics, such as benzo[a]pyrene and Chlorpyrifos. In conclusion, findings from this study confirm the potential suitability of H. plumieri as an organic pollution bioindicator species, and thus of practical use for environmental biomonitoring purposes.

Magnetized poly(STY-co-DVB) as a matrix for immobilizing microbial lipase to be used in biotransformation

Science.gov (United States)

Bento, H. B. S.; de Castro, H. F.; de Oliveira, P. C.; Freitas, L.

2017-03-01

Magnetized hydrophobic polymeric particles were prepared by suspension polymerization of styrene and divinylbenzene with the addition of magnetite (Fe3O4) functionalized with oleic acid (OA). The magnetic poly(STY-co-DVB) particles were characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and scanning electron microscopy (SEM). The results showed that the magnetic polymer particles fulfill the requirements for being used as matrix in the immobilization of microbial lipase from Candida rugosa by physical adsorption. The resulted immobilized derivative presented high catalytic activity in both aqueous and non-aqueous media. A comparative study between free and immobilized lipases showed a similar biochemical behavior, but with better hydrolytic activity at a pH range of 8.0-8.5. The patterns of heat stability indicated that the immobilization process also stabilizes the enzyme by a 50-fold improvement of thermal stability parameters (thermal deactivation and half-life time). Data on olive oil hydrolytic activities indicated that the Michaelis-Menten equation can be used to adjust data so as to calculate Km and Vmax, which attained values of 1766 mM and 5870 μM g-1 min-1, respectively. Such values indicated that the immobilized system was subjected to mass transfer limitations. High operational stability (t ½=1014 h) was achieved under repetitive batch runs in ester synthesis. The results indicated that the magnetized support particles can be very promising carriers for immobilizing enzymes in biotransformation reactions.

The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

Science.gov (United States)

Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto

2013-01-01

After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

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

Science.gov (United States)

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

2001-02-01

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

Kinetic study of enzymatic hydrolysis of acid-pretreated coconut coir

Science.gov (United States)

Fatmawati, Akbarningrum; Agustriyanto, Rudy

2015-12-01

Biomass waste utilization for biofuel production such as bioethanol, has become more prominent currently. Coconut coir is one of lignocellulosic food wastes, which is abundant in Indonesia. Bioethanol production from such materials consists of more than one step. Pretreatment and enzymatic hydrolysis is crucial steps to produce sugar which can then be fermented into bioethanol. In this research, ground coconut coir was pretreated using dilute sulfuric acid at 121°C. This pretreatment had increased the cellulose content and decreased the lignin content of coconut coir. The pretreated coconut coir was hydrolyzed using a mix of two commercial cellulase enzymes at pH of 4.8 and temperature of 50°C. The enzymatic hydrolysis was conducted at several initial coconut coir slurry concentrations (0.1-2 g/100 mL) and reaction times (2-72 hours). The reducing sugar concentration profiles had been produced and can be used to obtain reaction rates. The highest reducing sugar concentration obtained was 1,152.567 mg/L, which was produced at initial slurry concentration of 2 g/100 mL and 72 hours reaction time. In this paper, the reducing sugar concentrations were empirically modeled as a function of reaction time using power equations. Michaelis-Menten kinetic model for enzymatic hydrolysis reaction is adopted. The kinetic parameters of that model for sulfuric acid-pretreated coconut coir enzymatic hydrolysis had been obtained which are Vm of 3.587×104 mg/L.h, and KM of 130.6 mg/L.

Covalent immobilization of α-amylase on magnetic particles as catalyst for hydrolysis of high-amylose starch.

Science.gov (United States)

Guo, Hui; Tang, Yi; Yu, Yang; Xue, Lu; Qian, Jun-Qing

2016-06-01

Enzyme immobilized on magnetic particles can be used as efficient recoverable biocatalysts under strong magnetic response. To enable re-use of enzyme, modified Fe3O4 particles were used as carrier to immobilize α-amylase in this paper. Firstly, the surface of Fe3O4 particles were coated with amino groups by direct using TEOS (tetraethoxysilane) followed by treatment with APTES (3-aminopropyltriethoxysilane) and then carboxylated by reacting it with succinic anhydride. In addition, the effect of the immobilization condition on enzyme activity recovery and immobilization efficiency were investigated. The results showed that the optimal immobilization occurred under following conditions: pH 5.5, 40°C, enzyme concentration of 20mgmL(-1), reaction time for 36h. Using immobilized α-amylase as biocatalyst, the optimum pH and temperature for hydrolysis were observed to be 6.5 and 60°C. The kinetics of hydrolysis reaction were studied using Michaelis-Menten equation. The affinity constant (Km) and maximum reaction rate (vmax) of magnetic particles immobilization α-amylase (MPIA) was 0.543mgmL(-1) and 1.321mgmin(-1) compared to those of 0.377mgmL(-1) and 6.859mgmin(-1) of free enzyme. After immobilization, enzymatic activity, storage stability, thermo-stability, and reusability of MPIA were found superior to those of the free one. MPIA maintained 86% enzyme activity after 30 days and maintained 78% enzyme activity after recycling six times. Copyright © 2016 Elsevier B.V. All rights reserved.

Effect of bio-column composed of aged refuse on methane abatement--a novel configuration of biological oxidation in refuse landfill.

Science.gov (United States)

Han, Dan; Zhao, Youcai; Xue, Binjie; Chai, Xiaoli

2010-01-01

An experimental bio-column composed of aged refuse was installed around the exhaust pipe as a new way to mitigate methane in refuse landfill. One of the objectives of this work was to assess the effect of aged refuse thickness in bio-column on reducing CH4 emissions. Over the study period, methane oxidation was observed at various thicknesses, 5 cm (small size), 10 cm (middle size) and 15 cm (large size), representing one to three times of pipeline diameters. The middle and large size both showed over 90% methane conversion, and the highest methane conversion rate of above 95% occurred in the middle-size column cell. Michaelis-Menten equation addressed the methanotrophs diffusion in different layers of the bio-columns. Maximum methanotrophic activity (Vmax) measured at the three thicknesses ranged from 6.4 x 10(-3) to 15.6 x 10(-3) units, and the half-saturation value (K(M)) ranged from 0.85% to 1.67%. Both the highest Vmax and K(M) were observed at the middle-size of the bio-column, as well as the largest methanotrophs population, suggesting a significant efficiency of methane mitigation happened in the optimum zone with greatest affinity and methanotrophic bacteria activities. Therefore, bio-column is a potential style for methane abatement in landfill, and the aged refuse both naturally formed and artificially placed in the column plays a critical role in CH4 emission.

Laccase immobilized on methylene blue modified mesoporous silica MCM-41/PVA

International Nuclear Information System (INIS)

Xu Xinhua; Lu Ping; Zhou Yumei; Zhao Zhenzhen; Guo Meiqing

2009-01-01

The mesoporous silica sieve MCM-41 containing methylene blue (MB) provides a suitable immobilization of biomolecule matrix due to its uniform pore structure, high surface areas, good biocompatibility and nice conductivity. Based on this, a facilely fabricated amperometric biosensor by entrapping laccase into the MB modified MCM-41/PVA composite film has been developed. Laccase from Trametes versicolor is assembled on a composite film of MCM-41 containing MB/PVA modified Au electrode and the electrode is characterized with respect to transmission electron microscopy (TEM) and scanning electron microscopic (SEM), Cyclic voltammetry (CV), response time, detection limit, linear range and activity of laccase. The laccase modified electrode remains good redox behavior in pH 4.95 acetate buffer solution, at room temperature in present of 0.1 mM catechol. The response time (t 90% ) of the modified electrode is less than 4 s for catechol. The detection limit is 0.331 μM and the linear detect range is about from 4.0 μM to 87.98 μM for catechol with a correlation coefficient of 0.99913(S/N = 3). The apparent Michaelis-Menten (K M app ) is estimated using the Lineweaver-Burk equation and the K M app value is about 0.256 mM. This work demonstrated that the mesoporous silica MCM-41 containing MB provides a novel support for laccase immobilization and the construction of biosensors with a faster response and better bioactivity.

CYP2E1 Metabolism of Styrene Involves Allostery

Science.gov (United States)

Hartman, Jessica H.; Boysen, Gunnar

2012-01-01

We are the first to report allosterism during styrene oxidation by recombinant CYP2E1 and human liver microsomes. At low styrene concentrations, oxidation is inefficient because of weak binding to CYP2E1 (Ks = 830 μM). A second styrene molecule then binds CYP2E1 with higher affinity (Kss = 110 μM) and significantly improves oxidation to achieve a kcat of 6.3 nmol · min−1 · nmol CYP2E1−1. The transition between these metabolic cycles coincides with reported styrene concentrations in blood from exposed workers; thus, this CYP2E1 mechanism may be relevant in vivo. Scaled modeling of the in vitro-positive allosteric mechanism for styrene metabolism to its in vivo clearance led to significant deviations from the traditional model based on Michaelis-Menten kinetics. Low styrene levels were notably much less toxic than generally assumed. We interrogated the allosteric mechanism using the CYP2E1-specific inhibitor and drug 4-methylpyrazole, which we have shown binds two CYP2E1 sites. From the current studies, styrene was a positive allosteric effector on 4-methylpyrazole binding, based on a 10-fold increase in 4-methylpyrazole binding affinity from Ki 0.51 to Ksi 0.043 μM. The inhibitor was a negative allosteric effector on styrene oxidation, because kcat decreased 6-fold to 0.98 nmol · min−1 · nmol CYP2E1−1. Consequently, mixtures of styrene and other molecules can induce allosteric effects on binding and metabolism by CYP2E1 and thus mitigate the efficiency of their metabolism and corresponding effects on human health. Taken together, our elucidation of mechanisms for these allosteric reactions provides a powerful tool for further investigating the complexities of CYP2E1 metabolism of drugs and pollutants. PMID:22807108

Mathematical modelling of tissue formation on the basis of ordinary differential equations

Directory of Open Access Journals (Sweden)

Maxim N. Nazarov

2017-10-01

Full Text Available A mathematical model is proposed for describing the population dynamics of cellular clusters on the basis of systems of the first-order ordinary differential equations. The main requirement for the construction of model equations was to obtain a formal biological justification for their derivation, as well as proof of their correctness. In addition, for all the parameters involved in the model equations, the presence of biological meaning was guaranteed, as well as the possibility of evaluating them either during the experiment or by using models of intracellular biochemistry. In the desired model the intercellular exchange of a special signal molecules was chosen as the main mechanism for coordination of the tissue growth and new types selection during cell division. For simplicity, all signalling molecules that can create cells of the same type were not considered separately in the model, but were instead combined in a single complex of molecules: a ‘generalized signal’. Such an approach allows us to eventually assign signals as a functions of cell types and introduce their effects in the form of matrices in the models, where the rows are responsible for the types of cells receiving the signals, and the columns for the types of cells emitting signals.

Mechanism of pulse discharge production of iodine atoms from CF3I molecules for a chemical oxygen-iodine laser

International Nuclear Information System (INIS)

Kochetov, I V; Napartovich, A P; Vagin, N P; Yuryshev, N N

2009-01-01

The pulsed chemical oxygen-iodine laser (COIL) development is aimed at many new applications. Pulsed electric discharge is most effective in turning COIL operation into the pulse mode by instant production of iodine atoms. A numerical model is developed for simulations of the pulsed COIL initiated by an electric discharge. The model comprises a system of kinetic equations for neutral and charged species, electric circuit equation, gas thermal balance equation and the photon balance equation. Reaction rate coefficients for processes involving electrons are found by solving the electron Boltzmann equation, which is re-calculated in a course of computations when plasma parameters changed. The processes accounted for in the Boltzmann equation include excitation and ionization of atoms and molecules, dissociation of molecules, electron attachment processes, electron-ion recombination, electron-electron collisions, second-kind collisions and stepwise excitation of molecules. The last processes are particularly important because of a high singlet oxygen concentration in gas flow from the singlet oxygen chemical generator. Results of numerical simulations are compared with experimental laser pulse waveforms. It is concluded that there is satisfactory agreement between theory and the experiment. The prevailing mechanism of iodine atom formation from the CF 3 I donor in a very complex kinetic system of the COIL medium under pulse discharge conditions, based on their detailed numerical modelling and by comparing these results both with experimental results of other authors and their own experiments, is established. The dominant iodine atom production mechanism for conditions under study is the electron-impact dissociation of CF 3 I molecules. It was proved that in the conditions of the experiment the secondary chemical reactions with O atoms play an insignificant role.

Collision of hydrogen molecules interacting with two grapheme sheets

Directory of Open Access Journals (Sweden)

Malivuk-Gak Dragana

2017-01-01

Full Text Available It have been performed the computational experiments with two hydrogen molecules and two graphene sheets. Hydrogen - hydrogen and hydrogen - carbon interactions are described by Lennard - Jones potential. Equations of motion of the wave packet centre are solved numerically. The initial molecule velocity was determined by temperature and collisions occur in central point between two sheets. The molecules after collision stay near or get far away of graphene sheets. Then one can find what temperatures, graphene sheet sizes and their distances are favourable for hydrogen storage. It is found that quantum corrections of the molecule classical trajectories are not significant here. Those investigations of possibility of hydrogen storage by physisorption are of interest for improvement of the fuel cell systems. The main disadvantages of computational experiments are: (1 it cannot compute with very large number of C atoms, (2 it is assumed that carbon atoms are placed always in their equilibrium positions and (3 the changes of wave packet width are not considered.

In vivo measurements of brain glucose transport using the reversible michaelis-menten model and simultaneous measurements of cerebral blood flow changes during hypoglycemia

OpenAIRE

Choi, I.-Y.; Lee, S.-P.; Kim, S.-G.; Gruetter, R.

2001-01-01

Glucose is the major substrate that sustains normal brain function. When the brain glucose concentration approaches zero, glucose transport across the blood-brain barrier becomes rate limiting for metabolism during, for example, increased metabolic activity and hypoglycemia. Steady-state brain glucose concentrations in α-chloralose anesthetized rats were measured noninvasively as a function of plasma glucose. The relation between brain and plasma glucose was linear at 4.5 to 30 mmol/L plasma ...

Nonlinear Poisson equation for heterogeneous media.

Science.gov (United States)

Hu, Langhua; Wei, Guo-Wei

2012-08-22

The Poisson equation is a widely accepted model for electrostatic analysis. However, the Poisson equation is derived based on electric polarizations in a linear, isotropic, and homogeneous dielectric medium. This article introduces a nonlinear Poisson equation to take into consideration of hyperpolarization effects due to intensive charges and possible nonlinear, anisotropic, and heterogeneous media. Variational principle is utilized to derive the nonlinear Poisson model from an electrostatic energy functional. To apply the proposed nonlinear Poisson equation for the solvation analysis, we also construct a nonpolar solvation energy functional based on the nonlinear Poisson equation by using the geometric measure theory. At a fixed temperature, the proposed nonlinear Poisson theory is extensively validated by the electrostatic analysis of the Kirkwood model and a set of 20 proteins, and the solvation analysis of a set of 17 small molecules whose experimental measurements are also available for a comparison. Moreover, the nonlinear Poisson equation is further applied to the solvation analysis of 21 compounds at different temperatures. Numerical results are compared to theoretical prediction, experimental measurements, and those obtained from other theoretical methods in the literature. A good agreement between our results and experimental data as well as theoretical results suggests that the proposed nonlinear Poisson model is a potentially useful model for electrostatic analysis involving hyperpolarization effects. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Double ionization of molecule H2 in intense ultrashort laser fields

International Nuclear Information System (INIS)

Le, Thu-Thuy; Nguyen, Ngoc-Ty

2015-01-01

By solving numerically the time-dependent Schrödinger equation (TDSE), we have calculated the double ionization probability when a vibrating hydrogen molecule interacts with intense ultrashort laser pulses. The results show that in the case of vibrating nuclei the double ionization probability is higher than that of the fixed nuclei. Additionally, the double ionization probability is larger if the molecule is vibrating in a higher level. This is due to the decreasing of ionization potential when the inter-nuclei separation increases. (paper)

Theoretical femtosecond physics atoms and molecules in strong laser fields

CERN Document Server

Grossmann, Frank

2013-01-01

Theoretical investigations of atoms and molecules interacting with pulsed or continuous wave lasers up to atomic field strengths on the order of 10^16 W/cm² are leading to an understanding of many challenging experimental discoveries. This book deals with the basics of femtosecond physics and goes up to the latest applications of new phenomena. The book presents an introduction to laser physics with mode-locking and pulsed laser operation. The solution of the time-dependent Schrödinger equation is discussed both analytically and numerically. The basis for the non-perturbative treatment of laser-matter interaction in the book is the numerical solution of the time-dependent Schrödinger equation. The light field is treated classically, and different possible gauges are discussed. Physical phenonema, ranging from Rabi-oscillations in two-level systems to the ionization of atoms, the generation of high harmonics, the ionization and dissociation of molecules as well as the control of chemical reactions are pre...

Seeing diabetes: visual detection of glucose based on the intrinsic peroxidase-like activity of MoS2 nanosheets

Science.gov (United States)

Lin, Tianran; Zhong, Liangshuang; Guo, Liangqia; Fu, Fengfu; Chen, Guonan

2014-09-01

Molybdenum disulfide (MoS2) has attracted increasing research interest recently due to its unique physical, optical and electrical properties, correlated with its 2D ultrathin atomic-layered structure. Until now, however, great efforts have focused on its applications such as lithium ion batteries, transistors, and hydrogen evolution reactions. Herein, for the first time, MoS2 nanosheets are discovered to possess an intrinsic peroxidase-like activity and can catalytically oxidize 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2 to produce a color reaction. The catalytic activity follows the typical Michaelis-Menten kinetics and is dependent on temperature, pH, H2O2 concentration, and reaction time. Based on this finding, a highly sensitive and selective colorimetric method for H2O2 and glucose detection is developed and applied to detect glucose in serum samples. Moreover, a simple, inexpensive, instrument-free and portable test kit for the visual detection of glucose in normal and diabetic serum samples is constructed by utilizing agarose hydrogel as a visual detection platform.Molybdenum disulfide (MoS2) has attracted increasing research interest recently due to its unique physical, optical and electrical properties, correlated with its 2D ultrathin atomic-layered structure. Until now, however, great efforts have focused on its applications such as lithium ion batteries, transistors, and hydrogen evolution reactions. Herein, for the first time, MoS2 nanosheets are discovered to possess an intrinsic peroxidase-like activity and can catalytically oxidize 3,3',5,5'-tetramethylbenzidine (TMB) by H2O2 to produce a color reaction. The catalytic activity follows the typical Michaelis-Menten kinetics and is dependent on temperature, pH, H2O2 concentration, and reaction time. Based on this finding, a highly sensitive and selective colorimetric method for H2O2 and glucose detection is developed and applied to detect glucose in serum samples. Moreover, a simple, inexpensive

Species Differences in the Oxidative Desulfurization of a Thiouracil-Based Irreversible Myeloperoxidase Inactivator by Flavin-Containing Monooxygenase Enzymes.

Science.gov (United States)

Eng, Heather; Sharma, Raman; Wolford, Angela; Di, Li; Ruggeri, Roger B; Buckbinder, Leonard; Conn, Edward L; Dalvie, Deepak K; Kalgutkar, Amit S

2016-08-01

N1-Substituted-6-arylthiouracils, represented by compound 1 [6-(2,4-dimethoxyphenyl)-1-(2-hydroxyethyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one], are a novel class of selective irreversible inhibitors of human myeloperoxidase. The present account is a summary of our in vitro studies on the facile oxidative desulfurization in compound 1 to a cyclic ether metabolite M1 [5-(2,4-dimethoxyphenyl)-2,3-dihydro-7H-oxazolo[3,2-a]pyrimidin-7-one] in NADPH-supplemented rats (t1/2 [half-life = mean ± S.D.] = 8.6 ± 0.4 minutes) and dog liver microsomes (t1/2 = 11.2 ± 0.4 minutes), but not in human liver microsomes (t1/2 > 120 minutes). The in vitro metabolic instability also manifested in moderate-to-high plasma clearances of the parent compound in rats and dogs with significant concentrations of M1 detected in circulation. Mild heat deactivation of liver microsomes or coincubation with the flavin-containing monooxygenase (FMO) inhibitor imipramine significantly diminished M1 formation. In contrast, oxidative metabolism of compound 1 to M1 was not inhibited by the pan cytochrome P450 inactivator 1-aminobenzotriazole. Incubations with recombinant FMO isoforms (FMO1, FMO3, and FMO5) revealed that FMO1 principally catalyzed the conversion of compound 1 to M1. FMO1 is not expressed in adult human liver, which rationalizes the species difference in oxidative desulfurization. Oxidation by FMO1 followed Michaelis-Menten kinetics with Michaelis-Menten constant, maximum rate of oxidative desulfurization, and intrinsic clearance values of 209 μM, 20.4 nmol/min/mg protein, and 82.7 μl/min/mg protein, respectively. Addition of excess glutathione essentially eliminated the conversion of compound 1 to M1 in NADPH-supplemented rat and dog liver microsomes, which suggests that the initial FMO1-mediated S-oxygenation of compound 1 yields a sulfenic acid intermediate capable of redox cycling to the parent compound in a glutathione-dependent fashion or undergoing further oxidation to a more

Theory of Feshbach molecule formation in a dilute gas during a magnetic field ramp

DEFF Research Database (Denmark)

Williams, J. E.; Nygaard, Nicolai; Clark, C. W.

2006-01-01

Starting with coupled atom-molecule Boltzmann equations, we develop a simplified model to understand molecule formation observed in recent experiments. Our theory predicts several key features: (1) the effective adiabatic rate constant is proportional to density; (2) in an adiabatic ramp...... show qualitative agreement with the data from [Hodby et al, Phys. Rev. Lett. 94, 120402 (2005)] without the use of adjustable parameters....

Kohn-Sham potentials for fullerenes and spherical molecules

International Nuclear Information System (INIS)

Pavlyukh, Y.; Berakdar, J.

2010-01-01

We present a procedure for the construction of accurate Kohn-Sham potentials of quasispherical molecules starting from the first-principles valence densities. The method is demonstrated for the case of icosahedral C 20 2+ and C 60 molecules. Provided the density is N representable the Hohenberg-Kohn theorem guarantees the uniqueness of the obtained potentials. The potential is iteratively built following the suggestion of R. van Leeuwen and E. J. Baerends [Phys. Rev. A 49, 2421 (1994)]. The high symmetry of the molecules allows a parametrization of the angular dependence of the densities and the potentials using a small number of symmetry-adapted spherical harmonics. The radial behavior of these quantities is represented on a grid and the density is reconstructed from the approximate potential by numerically solving the coupled-channel Kohn-Sham equations. Subsequently, the potential is updated and the procedure is continued until convergence is achieved.

Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

Science.gov (United States)

Kuo, Tzu-Ling; Garcia-Manyes, Sergi; Li, Jingyuan; Barel, Itay; Lu, Hui; Berne, Bruce J; Urbakh, Michael; Klafter, Joseph; Fernández, Julio M

2010-06-22

The widely used Arrhenius equation describes the kinetics of simple two-state reactions, with the implicit assumption of a single transition state with a well-defined activation energy barrier DeltaE, as the rate-limiting step. However, it has become increasingly clear that the saddle point of the free-energy surface in most reactions is populated by ensembles of conformations, leading to nonexponential kinetics. Here we present a theory that generalizes the Arrhenius equation to include static disorder of conformational degrees of freedom as a function of an external perturbation to fully account for a diverse set of transition states. The effect of a perturbation on static disorder is best examined at the single-molecule level. Here we use force-clamp spectroscopy to study the nonexponential kinetics of single ubiquitin proteins unfolding under force. We find that the measured variance in DeltaE shows both force-dependent and independent components, where the force-dependent component scales with F(2), in excellent agreement with our theory. Our study illustrates a novel adaptation of the classical Arrhenius equation that accounts for the microscopic origins of nonexponential kinetics, which are essential in understanding the rapidly growing body of single-molecule data.

Quantum superposition of the state discrete spectrum of mathematical correlation molecule for small samples of biometric data

Directory of Open Access Journals (Sweden)

Vladimir I. Volchikhin

2017-06-01

Full Text Available Introduction: The study promotes to decrease a number of errors of calculating the correlation coefficient in small test samples. Materials and Methods: We used simulation tool for the distribution functions of the density values of the correlation coefficient in small samples. A method for quantization of the data, allows obtaining a discrete spectrum states of one of the varieties of correlation functional. This allows us to consider the proposed structure as a mathematical correlation molecule, described by some analogue continuous-quantum Schrödinger equation. Results: The chi-squared Pearson’s molecule on small samples allows enhancing power of classical chi-squared test to 20 times. A mathematical correlation molecule described in the article has similar properties. It allows in the future reducing calculation errors of the classical correlation coefficients in small samples. Discussion and Conclusions: The authors suggest that there are infinitely many mathematical molecules are similar in their properties to the actual physical molecules. Schrödinger equations are not unique, their analogues can be constructed for each mathematical molecule. You can expect a mathematical synthesis of molecules for a large number of known statistical tests and statistical moments. All this should make it possible to reduce calculation errors due to quantum effects that occur in small test samples.

Equations for the kinetic modeling of supersonically flowing electrically excited lasers

International Nuclear Information System (INIS)

Lind, R.C.

1973-01-01

The equations for the kinetic modeling of a supersonically flowing electrically excited laser system are presented. The work focuses on the use of diatomic gases, in particular carbon monoxide mixtures. The equations presented include the vibrational rate equation which describes the vibrational population distribution, the electron, ion and electronic level rate equations, the gasdynamic equations for an ionized gas in the presence of an applied electric field, and the free electron Boltzmann equation including flow and gradient coupling terms. The model developed accounts for vibration--vibration collisions, vibration-translation collisions, electron-molecule inelastic excitation and superelastic de-excitation collisions, charge particle collisions, ionization and three body recombination collisions, elastic collisions, and radiative decay, all of which take place in such a system. A simplified form of the free electron Boltzmann equation is developed and discussed with emphasis placed on its coupling with the supersonic flow. A brief description of a possible solution procedure for the set of coupled equations is discussed

Kinetics of the norepinephrine analog [76Br]-meta-bromobenzylguanidine in isolated working rat heart

International Nuclear Information System (INIS)

Raffel, David; Loc'h, Christian; Mardon, Karine; Maziere, Bernard; Syrota, Andre

1998-01-01

A related set of kinetic studies of the norepinephrine analog [ 76 Br]-meta-bromobenzylguanidine (MBBG) were performed with an isolated working rat heart preparation. A series of constant infusion studies over a wide range of MBBG concentrations allowed estimation of the Michaelis-Menten constants for transport by the neuronal norepinephrine transporter (uptake 1 ) and the extraneuronal uptake system (uptake 2 ). Pharmacological blocking studies with inhibitors of uptake 1 , uptake 2 and vesicular uptake were performed to delineate the relative importance of these norepinephrine handling mechanisms on the kinetics of MBBG in the rat heart. Bolus injection studies were done to assess the ability of compartmental modeling techniques to characterize the kinetics of MBBG. These studies demonstrate that MBBG shares many of the same uptake mechanisms as norepinephrine in the rat heart. PET imaging studies with MBBG would be useful for assessing sympathetic nerve status in the living human heart

AIR POLLUTION FROM ANIMAL AND MUNICIPAL WASTEWATER: ASSESSMENT OF PRODUCTION AND RELEASE OF NOXIOUS GASES

DEFF Research Database (Denmark)

Dai, Xiaorong

from animal manure (mixture of urine and feces) by hydrolysis of urinary urea catalyzed by microbial urease present in feces. To better understand the enzymatic process of ammonia formation in manure, experiments based on Michaelis-Menten kinetics were conducted to obtain accurate estimates...... of the kinetic parameters of urease activity of feces and manure from pig and cattle, and to investigate the effects of pH on animal fecal urease by individual ammonium generation rate determination at five pH levels. Investigating the gas production and release mechanisms is important not only for estimating...... characteristics of different types of wastes (e.g., the total nitrogen, total ammoniacal nitrogen, dry matter, and pH) had great influence on the releases of NH3, CO2, H2S, and SO2. The investigation of kinetic parameter showed that the maximum urease activity for pig feces is at around pH 7, while...

Modelling and finite-time stability analysis of psoriasis pathogenesis

Science.gov (United States)

Oza, Harshal B.; Pandey, Rakesh; Roper, Daniel; Al-Nuaimi, Yusur; Spurgeon, Sarah K.; Goodfellow, Marc

2017-08-01

A new systems model of psoriasis is presented and analysed from the perspective of control theory. Cytokines are treated as actuators to the plant model that govern the cell population under the reasonable assumption that cytokine dynamics are faster than the cell population dynamics. The analysis of various equilibria is undertaken based on singular perturbation theory. Finite-time stability and stabilisation have been studied in various engineering applications where the principal paradigm uses non-Lipschitz functions of the states. A comprehensive study of the finite-time stability properties of the proposed psoriasis dynamics is carried out. It is demonstrated that the dynamics are finite-time convergent to certain equilibrium points rather than asymptotically or exponentially convergent. This feature of finite-time convergence motivates the development of a modified version of the Michaelis-Menten function, frequently used in biology. This framework is used to model cytokines as fast finite-time actuators.

Preparation of biosensors by immobilization of polyphenol oxidase in conducting copolymers and their use in determination of phenolic compounds in red wine.

Science.gov (United States)

Böyükbayram, A Elif; Kiralp, Senem; Toppare, Levent; Yağci, Yusuf

2006-10-01

Electrochemically produced graft copolymers of thiophene capped polytetrahydofuran (TPTHF1 and TPTHF2) and pyrrole were achieved by constant potential electrolysis using sodium dodecylsulfate (SDS) as the supporting electrolyte. Characterizations were based on Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). Electrical conductivities were measured by the four-probe technique. Novel biosensors for phenolic compounds were constructed by immobilizing polyphenol oxidase (PPO) into conducting copolymers prepared by electropolymerization of pyrrole with thiophene capped polytetrahydrofuran. Kinetic parameters, maximum reaction rate (V(max)) and Michaelis-Menten constant (K(m)) and optimum conditions regarding temperature and pH were determined for the immobilized enzyme. Operational stability and shelf-life of the enzyme electrodes were investigated. Enzyme electrodes of polyphenol oxidase were used to determine the amount of phenolic compounds in two brands of Turkish red wines and found very useful owing to their high kinetic parameters and wide pH working range.

Kinetic Studies on Trichoderna Viride Cellulase

International Nuclear Information System (INIS)

Saw Aung; Oo Aung; Aung Myint

2002-02-01

Studies on cellulase enzyme (EC 3.2.1.4), which catalyzes the hydrolysis of. cellulose to yield glucose, were made. Cellulase from a fungus source, Trichoderma viride was cultivated on Czapek's agar medium and enzyme production broth medium was employed for parameter tests. The microscopic examination and cellulase hydrolysis test on subcultured fungi were applied to confirm the T. viride species. A calibration curve for standard glucose was plotted by using visible spectroscopy. Dinitrosalicylic acid was used as enzyme reaction inhibitor and the colour intensity was measured in a UV-visible spectrophotometer at a λ max of 570 nm. The parameters such as optimum pH, optimum temperature, effect of substrate concentration, effect, of enzyme concentration, enzyme unit (EU), reaction order (n), maximum velocity (V max ), Michaelis-Menten constant (K m ) using various substrates, viz., carboxy methylcellulose, cotton fibre and filter paper determined. (author)

Evidence of enzymatic catalysis of oxygen reduction on stainless steels under marine biofilm.

Science.gov (United States)

Faimali, Marco; Benedetti, Alessandro; Pavanello, Giovanni; Chelossi, Elisabetta; Wrubl, Federico; Mollica, Alfonso

2011-04-01

Cathodic current trends on stainless steel samples with different surface percentages covered by biofilm and potentiostatically polarized in natural seawater were studied under oxygen concentration changes, temperature increases, and additions of enzymic inhibitors to the solution. The results showed that on each surface fraction covered by biofilm the oxygen reduction kinetics resembled a reaction catalyzed by an immobilised enzyme with high oxygen affinity (apparent Michaelis-Menten dissociation constant close to K(O(2))(M)  ≈ 10 μM) and low activation energy (W ≈ 20 KJ mole(-1)). The proposed enzyme rapidly degraded when the temperature was increased above the ambient (half-life time of ∼1 day at 25°C, and of a few minutes at 50°C). Furthermore, when reversible enzymic inhibitors (eg sodium azide and cyanide) were added, the cathodic current induced by biofilm growth was inhibited.

Dimension reduction for stochastic dynamical systems forced onto a manifold by large drift: a constructive approach with examples from theoretical biology

Science.gov (United States)

Parsons, Todd L.; Rogers, Tim

2017-10-01

Systems composed of large numbers of interacting agents often admit an effective coarse-grained description in terms of a multidimensional stochastic dynamical system, driven by small-amplitude intrinsic noise. In applications to biological, ecological, chemical and social dynamics it is common for these models to posses quantities that are approximately conserved on short timescales, in which case system trajectories are observed to remain close to some lower-dimensional subspace. Here, we derive explicit and general formulae for a reduced-dimension description of such processes that is exact in the limit of small noise and well-separated slow and fast dynamics. The Michaelis-Menten law of enzyme-catalysed reactions, and the link between the Lotka-Volterra and Wright-Fisher processes are explored as a simple worked examples. Extensions of the method are presented for infinite dimensional systems and processes coupled to non-Gaussian noise sources.

Nutrient Removal from Wastewater using Microalgae: A Kinetic Evaluation and Lipid Analysis.

Science.gov (United States)

2017-09-15

The objective of this study was to examine the performance of mixed microalgal bioreactors in treating three differenttypes of wastewaters - kitchen wastewater (KWW), palm oil mill effluent (POME), and pharmaceutical wastewater (PWW) in semi-continuous mode and to analyze the lipid content in the harvested algal biomass. The reactors were monitored for total nitrogen and phosphate removal at eight solid retention times (SRTs) - 2, 4, 6, 8, 10, 12, 14, and 16 days. The nutrient uptake kinetic parameters were quantified using linearized Michaelis-Menten and Monod models at steady-state conditions. The nutrient removal efficiency and lipid production were found to be higher in KWW when compared with the other wastewaters. Saturated fatty acids (C16:0, C18:0, and C18:1) accounted for more than 60% of the algal fatty acids for all the wastewaters. The lipid is, therefore, considered suitable for synthesizing biodiesel.

Flexible single molecule simulation of reaction-diffusion processes

International Nuclear Information System (INIS)

Hellander, Stefan; Loetstedt, Per

2011-01-01

An algorithm is developed for simulation of the motion and reactions of single molecules at a microscopic level. The molecules diffuse in a solvent and react with each other or a polymer and molecules can dissociate. Such simulations are of interest e.g. in molecular biology. The algorithm is similar to the Green's function reaction dynamics (GFRD) algorithm by van Zon and ten Wolde where longer time steps can be taken by computing the probability density functions (PDFs) and then sample from the distribution functions. Our computation of the PDFs is much less complicated than GFRD and more flexible. The solution of the partial differential equation for the PDF is split into two steps to simplify the calculations. The sampling is without splitting error in two of the coordinate directions for a pair of molecules and a molecule-polymer interaction and is approximate in the third direction. The PDF is obtained either from an analytical solution or a numerical discretization. The errors due to the operator splitting, the partitioning of the system, and the numerical approximations are analyzed. The method is applied to three different systems involving up to four reactions. Comparisons with other mesoscopic and macroscopic models show excellent agreement.

Analytic structure of solutions to multiconfiguration equations

Energy Technology Data Exchange (ETDEWEB)

Fournais, Soeren [Department of Mathematical Sciences, University of Aarhus, Ny Munkegade, Building 1530, DK-8000 Arhus C (Denmark); Hoffmann-Ostenhof, Maria [Fakultaet fuer Mathematik, Universitaet Wien, Nordbergstrasse 15, A-1090 Vienna (Austria); Hoffmann-Ostenhof, Thomas [Institut fuer Theoretische Chemie, Waehringerstrasse 17, Universitaet Wien, A-1090 Vienna (Austria); Soerensen, Thomas Oestergaard [Department of Mathematics, Imperial College London, Huxley Building, 180 Queen' s Gate, London SW7 2AZ (United Kingdom)], E-mail: fournais@imf.au.dk, E-mail: Maria.Hoffmann-Ostenhof@univie.ac.at, E-mail: thoffman@esi.ac.at, E-mail: t.sorensen@imperial.ac.uk

2009-08-07

We study the regularity at the positions of the (fixed) nuclei of solutions to (non-relativistic) multiconfiguration equations (including Hartree-Fock) of Coulomb systems. We prove the following: let {l_brace}{psi}{sub 1}, ..., {psi}{sub M}{r_brace} be any solution to the rank-M multiconfiguration equations for a molecule with L fixed nuclei at R{sub 1},...,R{sub L} element of R{sup 3}. Then, for any j in {l_brace}1, ..., M{r_brace}, k in {l_brace}1, ..., L{r_brace}, there exists a neighborhood U{sub j,k} subset or equal R{sup 3} of R{sub k}, and functions {psi}{sup (1)}{sub j,k}, {psi}{sup (2)}{sub j,k}, real analytic in U{sub j,k}, such that {phi}{sub j}(x)={phi}{sub j,k}{sup (1)}(x)+|x-R{sub k}|{phi}{sub j,k}{sup (2)}(x), x element of U{sub j,k}. A similar result holds for the corresponding electron density. The proof uses the Kustaanheimo-Stiefel transformation, as applied in [9] to the study of the eigenfunctions of the Schroedinger operator of atoms and molecules near two-particle coalescence points.

Understanding the sub-cellular dynamics of silicon transportation and synthesis in diatoms using population-level data and computational optimization.

Directory of Open Access Journals (Sweden)

Narjes Javaheri

2014-06-01

Full Text Available Controlled synthesis of silicon is a major challenge in nanotechnology and material science. Diatoms, the unicellular algae, are an inspiring example of silica biosynthesis, producing complex and delicate nano-structures. This happens in several cell compartments, including cytoplasm and silica deposition vesicle (SDV. Considering the low concentration of silicic acid in oceans, cells have developed silicon transporter proteins (SIT. Moreover, cells change the level of active SITs during one cell cycle, likely as a response to the level of external nutrients and internal deposition rates. Despite this topic being of fundamental interest, the intracellular dynamics of nutrients and cell regulation strategies remain poorly understood. One reason is the difficulties in measurements and manipulation of these mechanisms at such small scales, and even when possible, data often contain large errors. Therefore, using computational techniques seems inevitable. We have constructed a mathematical model for silicon dynamics in the diatom Thalassiosira pseudonana in four compartments: external environment, cytoplasm, SDV and deposited silica. The model builds on mass conservation and Michaelis-Menten kinetics as mass transport equations. In order to find the free parameters of the model from sparse, noisy experimental data, an optimization technique (global and local search, together with enzyme related penalty terms, has been applied. We have connected population-level data to individual-cell-level quantities including the effect of early division of non-synchronized cells. Our model is robust, proven by sensitivity and perturbation analysis, and predicts dynamics of intracellular nutrients and enzymes in different compartments. The model produces different uptake regimes, previously recognized as surge, externally-controlled and internally-controlled uptakes. Finally, we imposed a flux of SITs to the model and compared it with previous classical kinetics

A radial distribution function-based open boundary force model for multi-centered molecules

KAUST Repository

Neumann, Philipp

2014-06-01

We derive an expression for radial distribution function (RDF)-based open boundary forcing for molecules with multiple interaction sites. Due to the high-dimensionality of the molecule configuration space and missing rotational invariance, a computationally cheap, 1D approximation of the arising integral expressions as in the single-centered case is not possible anymore. We propose a simple, yet accurate model invoking standard molecule- and site-based RDFs to approximate the respective integral equation. The new open boundary force model is validated for ethane in different scenarios and shows very good agreement with data from periodic simulations. © World Scientific Publishing Company.

Environmental effects on molecules immersed in liquids

International Nuclear Information System (INIS)

Sese, L.M.

1990-01-01

A methodology to study environmental effects is thoroughly discussed. It combines molecular quantum mechanics and classical statistical mechanics of molecular fluids. Pair distribution functions collecting statistical information appear quite naturally in the quantum equations describing a single molecule. As well as allowing the computation of any individual molecular property in a liquid phase, this approach satisfies a number of theoretical requirements (dependence on density and temperature, validity in the thermodynamic limit). In a sense, it can be regarded as a useful alternative to the well-known Monte Carlo averaging processes for calculating molecular properties. Numerical applications studying liquid carbon disulphide and liquid carbon tetrachloride at several state points are given. Results cover typical RHF information (CNDO/2) on molecules, and show the sensitivity of the presented methodology to structural changes in liquids. (orig.)

Influence of orientation averaging on the anisotropy of thermal neutrons scattering on water molecules

International Nuclear Information System (INIS)

Markovic, M. I.; Radunovic, J. B.

1976-01-01

Determination of spatial distribution of neutron flux in water, most frequently used moderator in thermal reactors, demands microscopic scattering kernels dependence on cosine of thermal neutrons scattering angle when solving the Boltzmann equation. Since spatial orientation of water molecules influences this dependence it is necessary to perform orientation averaging or rotation-vibrational intermediate scattering function for water molecules. The calculations described in this paper and the obtained results showed that methods of orientation averaging do not influence the anisotropy of thermal neutrons scattering on water molecules, but do influence the inelastic scattering

Memory effects in single-molecule spectroscopy

International Nuclear Information System (INIS)

Schmitt, Daniel T.; Schulz, Michael; Reineker, Peter

2007-01-01

From the time series of LH2 optical single-molecule fluorescence excitation spectra of Rhodospirillum molischianum the memory function of the Mori-Zwanzig equation for the optical intensity is derived numerically. We show that the time dependence of the excited states is determined by at least three different non-Markovian stochastic processes with decay constants for the Mori-Zwanzig kernel on the order of 1-5min -1 . We suggest that this decay stems from the conformational motion of the protein scaffold of LH2

Gas-evolution oscillators. 10. A model based on a delay equation

Energy Technology Data Exchange (ETDEWEB)

Bar-Eli, K.; Noyes, R.M. [Univ. of Oregon, Eugene, OR (United States)

1992-09-17

This paper develops a simplified method to model the behavior of a gas-evolution oscillator with two differential delay equations in two unknowns consisting of the population of dissolved molecules in solution and the pressure of the gas.

Gas-evolution oscillators. 10. A model based on a delay equation

International Nuclear Information System (INIS)

Bar-Eli, K.; Noyes, R.M.

1992-01-01

This paper develops a simplified method to model the behavior of a gas-evolution oscillator with two differential delay equations in two unknowns consisting of the population of dissolved molecules in solution and the pressure of the gas

Linear-algebraic approach to electron-molecule collisions: General formulation

International Nuclear Information System (INIS)

Collins, L.A.; Schneider, B.I.

1981-01-01

We present a linear-algebraic approach to electron-molecule collisions based on an integral equations form with either logarithmic or asymptotic boundary conditions. The introduction of exchange effects does not alter the basic form or order of the linear-algebraic equations for a local potential. In addition to the standard procedure of directly evaluating the exchange integrals by numerical quadrature, we also incorporate exchange effects through a separable-potential approximation. Efficient schemes are developed for reducing the number of points and channels that must be included. The method is applied at the static-exchange level to a number of molecular systems including H 2 , N 2 , LiH, and CO 2

Multiphoton dissociation of polyatomic molecules

International Nuclear Information System (INIS)

Schulz, P.A.

1979-10-01

The dynamics of infrared multiphoton excitation and dissociation of SF 6 was investigated under collision free conditions by a crossed laser-molecular beam method. In order to understand the excitation mechanism and to elucidate the requirements of laser intensity and energy fluence, a series of experiments were carried out to measure the dissociation yield dependences on energy fluence, vibrational temperature of SF 6 , the pulse duration of the CO 2 laser and the frequency in both one and two laser experiments. Translational energy distributions of the SF 5 dissociation product measured by time of flight and angular distributions and the dissociation lifetime of excited SF 6 as inferred from the observation of secondary dissociation of SF 5 into SF 4 and F during the laser pulse suggest that the dynamics of dissociation of excited molecules is dominated by complete energy randomization and rapid intramolecular energy transfer on a nanosecond timescale, and can be adequately described by RRKM theory. An improved phenomenological model including the initial intensity dependent excitation, a rate equation describing the absorption and stimulated emission of single photons, and the unimolecular dissociation of excited molecules is constructed based on available experimental results. The model shows that the energy fluence of the laser determines the excitation of molecules in the quasi-continuum and the excess energy with which molecules dissociate after the laser pulse. The role played by the laser intensity in multiphoton dissociation is more significant than just that of overcoming the intensity dependent absorption in the lowest levels. 63 references

Improved alternating gradient transport and focusing of neutral molecules

International Nuclear Information System (INIS)

Kalnins, Juris; Lambertson, Glen; Gould, Harvey

2001-01-01

Polar molecules, in strong-field seeking states, can be transported and focused by an alternating sequence of electric field gradients that focus in one transverse direction while defocusing in the other. We show by calculation and numerical simulation, how one may greatly improve the alternating gradient transport and focusing of molecules. We use a new optimized multipole lens design, a FODO lattice beam transport line, and lenses to match the beam transport line to the beam source and the final focus. We derive analytic expressions for the potentials, fields, and gradients that may be used to design these lenses. We describe a simple lens optimization procedure and derive the equations of motion for tracking molecules through a beam transport line. As an example, we model a straight beamline that transports a 560 m/s jet-source beam of methyl fluoride molecules 15 m from its source and focuses it to 2 mm diameter. We calculate the beam transport line acceptance and transmission, for a beam with velocity spread, and estimate the transmitted intensity for specified source conditions. Possible applications are discussed

Catalytic properties of IgMs with amylolytic activity isolated from patients with multiple sclerosis.

Science.gov (United States)

Ivanen, Dina R; Kulminskaya, Anna A; Shabalin, Konstantin A; Isaeva-Ivanova, Luydmila V; Ershova, Nadezhda A; Saveliev, Andrew N; Nevinsky, Gregory A; Neustroev, Kirill N

2004-08-01

Recently, amylolytic activity was detected in IgMs isolated from the sera of the patients with multiple sclerosis. All purified samples of IgM were electrophoretically homogenous and did not contain any co-purified a-amylase and a-glucosidase activities, in accordance with a set of criteria developed for abzymes. The amylolytic activity of abzymes was studied in the hydrolysis of p-nitrophenyl a-D-maltooligosaccharides with different degrees of polymerization from 1 to 8 by TLC and reverse-phase HPLC techniques. All IgM samples isolated from 54 patients with clinically definite multiple sclerosis demonstrated hydrolytic activity towards the above artificial substrates. The Michaelis constant values (Km) in the hydrolysis of p-nitrophenyl a-D-maltoheptaoside were in the range of 10 p-nitrophenyl or p-nitrophenyl a-D-glucosides, thus indicating the presence of an a-D-glucosidase activity. For a number of the investigated samples, specific amylolytic activity increased depending on the length of substrates (from p-nitrophenyl maltopentaoside to p-nitrophenyl maltohexaoside); for other IgMs, the opposite dependence was observed. All IgMs studied did not exhibit any other glycoside hydrolase activities toward p-nitrophenyl glycoside substrates. Abzyme fractions from different donors demonstrated catalytic heterogeneity in Michaelis-Menten parameters and different modes of action in the hydrolysis of p-nitrophenyl maltooligosaccharides. Enzymatic properties of the IgMs tested varied from human a-amylases. All investigated abzyme samples did not show transglycosylating ability.

[Investigations on the physiology of the glands of carnivorous plants : IV. The kinetics of chloride secretion by the gland tissue of Nepenthes].

Science.gov (United States)

Lüttge, U

1966-03-01

The transport of chloride in isolated tissue from Nepenthes pitchers was investigated using (36)Cl(-), an Aminco-Cotlove chloride-titrator for the determinations of Cl(-) concentrations, and KCN and AsO 4 (-) -as metabolic inhibitors.The tissue was brought in contact with different experimental solutions (=medium). The surface corresponding to the outside of the pitchers was cut with a razor blade to remove the cutinized epidermal layer. At this surface the Cl(-) uptake from the medium is a metabolic process which depends on the Cl(-)-concentration of the medium in a manner that corresponds to the MICHAELIS-MENTEN kinetics. The Michaelis-constant of this transport step was 3×10(-2)M. The Cl(-)-efflux into the medium, however, is a passive process.The opposite surface of the tissue slices (corresponding to the inside of the pitchers) carries the glands. The chloride secretion taking place here is also dependent on metabolism. In vitro it occurs even when a high gradient of chloride concentration has been set up between the medium and the solution which is in contact with the glands. In vivo the Cl(-)-concentration of the pitcher fluid and the amount of Cl(-) per gram of tissue water are almost equal.The rôle of chloride in the physiology of Nepenthes is still under investigation, A correlation between the chloride content of the pitcher fluid and its enzymatic activity (Casein-test), however, could already be demonstrated.

THE KINETICS OF THE REACTIONS CATALYZED BY AN ENZYMATIC PREPARATION PRODUCED BY A BACILLUS LICHENIFORMIS STRAIN

Directory of Open Access Journals (Sweden)

MONICA DRAGOMIRESCU

2007-05-01

Full Text Available Robust immobilization techniques that preserve the activity of biomolecules have manypotential applications. In recent years, a number of new bioimobilisation methods in solgel-derived materials were reported. The interactions between the biomolecule and theinorganic material determine the degree to which the biomolecule retains its nativeproperties. The newer technological developments in the field of immobilizedbiocatalysts can offer the possibility of a wider and more economical exploitation ofbiocatalysts in biological applications, food and feed industry, medicine, and in thedevelopment of bioprocess monitoring devices, like the biosensors.The aim of this study was to obtain immobilized enzymatic preparations by methodswhich affect enzyme conformations and kinetic parameters as less as possible. Weimmobilized the enzymatic preparation with protease activity produced by a Bacilluslicheniformis B 40 local strain by physical bonding on ceramics and entrapment into solgel-derived glasses obtained from tetraethyl orthosilicate (TEOS, deposited in thin layeron a ceramic support (entrapment/deposition. Both physically adsorbed andentrapped/deposited enzymes follow Michaelis-Menten kinetics, similar with the solubleenzyme. In the case of immobilized enzymes, the apparent Michaelis constant, Km, wasgreater than that of the native one, as it was expected. The kinetic parameters indicatethat the enzymatic preparations adsorbed on ceramic support and entrapped/depositedshow less affinity for the substrate, Km being 1.3 and 2.1 times higher than that of thenative enzyme, respectively. The maximum velocity increased also by 3.5 and 7.9 timesrespectively, compared with the free counterpart (according to Lineweaver-Burklinearization.

Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance

Science.gov (United States)

Kuzyakov, Yakov; Xu, Xingliang

2014-05-01

Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 15N-labelling studies that investigated 15N redistribution between roots and microorganisms. Calculated Michaelis-Menten kinetics based on Km (Michaelis constant) and Vmax (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower Km values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (Vmax) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms.

Estimate of respiration rate and physicochemical changes of fresh-cut apples stored under different temperatures Estimativa da taxa de respiração e das mudanças físico-químicas de maçãs minimamente processadas e estocadas sob diferentes temperaturas

Directory of Open Access Journals (Sweden)

Cristiane Fagundes

2013-03-01

Full Text Available In this study, the influence of storage temperature and passive modified packaging (PMP on the respiration rate and physicochemical properties of fresh-cut Gala apples (Malus domestica B. was investigated. The samples were packed in flexible multilayer bags and stored at 2 °C, 5 °C, and 7 °C for eleven days. Respiration rate as a function of CO2 and O2 concentrations was determined using gas chromatography. The inhibition parameters were estimated using a mathematical model based on Michaelis-Menten equation. The following physicochemical properties were evaluated: total soluble solids, pH, titratable acidity, and reducing sugars. At 2 °C, the maximum respiration rate was observed after 150 hours. At 5 °C and 7 °C the maximum respiration rates were observed after 100 and 50 hours of storage, respectively. The inhibition model results obtained showed a clear effect of CO2 on O2 consumption. The soluble solids decreased, although not significantly, during storage at the three temperatures studied. Reducing sugars and titratable acidity decreased during storage and the pH increased. These results indicate that the respiration rate influenced the physicochemical properties.Neste estudo, a influência da temperatura de armazenamento e da embalagem com atmosfera modificada passiva (AMP na taxa respiratória e nas propriedades físico-químicas de maçãs da variedade Gala (Malus domestica, B. minimamente processadas foi investigada. As amostras foram acondicionadas em embalagens flexíveis e armazenados a 2 °C, 5 °C e 7 °C, durante 11 dias. A taxa de respiração foi gerada para diferentes concentrações de O2 e CO2, obtidas por cromatografia gasosa. Os parâmetros de inibição foram estimados por um modelo matemático baseado na equação de Michaelis-Menten. Foram avaliadas as seguintes propriedades físico-químicas: sólidos solúveis totais, pH, acidez titulável e açúcares redutores. A 2 °C, a taxa de respiração máxima foi

On the non-stationary generalized Langevin equation

Science.gov (United States)

Meyer, Hugues; Voigtmann, Thomas; Schilling, Tanja

2017-12-01

In molecular dynamics simulations and single molecule experiments, observables are usually measured along dynamic trajectories and then averaged over an ensemble ("bundle") of trajectories. Under stationary conditions, the time-evolution of such averages is described by the generalized Langevin equation. By contrast, if the dynamics is not stationary, it is not a priori clear which form the equation of motion for an averaged observable has. We employ the formalism of time-dependent projection operator techniques to derive the equation of motion for a non-equilibrium trajectory-averaged observable as well as for its non-stationary auto-correlation function. The equation is similar in structure to the generalized Langevin equation but exhibits a time-dependent memory kernel as well as a fluctuating force that implicitly depends on the initial conditions of the process. We also derive a relation between this memory kernel and the autocorrelation function of the fluctuating force that has a structure similar to a fluctuation-dissipation relation. In addition, we show how the choice of the projection operator allows us to relate the Taylor expansion of the memory kernel to data that are accessible in MD simulations and experiments, thus allowing us to construct the equation of motion. As a numerical example, the procedure is applied to Brownian motion initialized in non-equilibrium conditions and is shown to be consistent with direct measurements from simulations.

Generalized empirical equation for the extrapolated range of electrons in elemental and compound materials

International Nuclear Information System (INIS)

Lima, W. de; Poli CR, D. de

1999-01-01

The extrapolated range R ex of electrons is useful for various purposes in research and in the application of electrons, for example, in polymer modification, electron energy determination and estimation of effects associated with deep penetration of electrons. A number of works have used empirical equations to express the extrapolated range for some elements. In this work a generalized empirical equation, very simple and accurate, in the energy region 0.3 keV - 50 MeV is proposed. The extrapolated range for elements, in organic or inorganic molecules and compound materials, can be well expressed as a function of the atomic number Z or two empirical parameters Zm for molecules and Zc for compound materials instead of Z. (author)

The damped wave equation with unbounded damping

Czech Academy of Sciences Publication Activity Database

Freitas, P.; Siegl, Petr; Tretter, C.

2018-01-01

Roč. 264, č. 12 (2018), s. 7023-7054 ISSN 0022-0396 Institutional support: RVO:61389005 Keywords : damped wave equation * unbounded damping * essential spectrum * quadratic operator funciton with unbounded coefficients * Schrodinger operators with complex potentials Subject RIV: BE - Theoretical Physics OBOR OECD: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect) Impact factor: 1.988, year: 2016

An equations of motion approach for open shell systems

International Nuclear Information System (INIS)

Yeager, D.L.; McKoy, V.

1975-01-01

A straightforward scheme is developed for extending the equations of motion formalism to systems with simple open shell ground states. Equations for open shell random phase approximation (RPA) are given for the cases of one electron outside of a closed shell in a nondegenerate molecular orbital and for the triplet ground state with two electrons outside of a closed shell in degenerate molecular orbitals. Applications to other open shells and extension of the open shell EOM to higher orders are both straightforward. Results for the open shell RPA for lithium atom and oxygen molecule are given

Effects of missense mutations in sortase A gene on enzyme activity in Streptococcus mutans.

Science.gov (United States)

Zhuang, P L; Yu, L X; Tao, Y; Zhou, Y; Zhi, Q H; Lin, H C

2016-04-11

Streptococcus mutans (S. mutans) is the major aetiological agent of dental caries, and the transpeptidase Sortase A (SrtA) plays a major role in cariogenicity. The T168G and G470A missense mutations in the srtA gene may be linked to caries susceptibility, as demonstrated in our previous studies. This study aimed to investigate the effects of these missense mutations of the srtA gene on SrtA enzyme activity in S. mutans. The point mutated recombinant S.mutans T168G and G470A sortases were expressed in expression plasmid pET32a. S. mutans UA159 sortase coding gene srtA was used as the template for point mutation. Enzymatic activity was assessed by quantifying increases in the fluorescence intensity generated when a substrate Dabcyl-QALPNTGEE-Edans was cleaved by SrtA. The kinetic constants were calculated based on the curve fit for the Michaelis-Menten equation. SrtA△N40(UA159) and the mutant enzymes, SrtA△N40(D56E) and SrtA△N40(R157H), were expressed and purified. A kinetic analysis showed that the affinity of SrtA△N40(D56E) and SrtA△N40(R157H) remained approximately equal to the affinity of SrtA△N40(UA159), as determined by the Michaelis constant (K m ). However, the catalytic rate constant (k cat ) and catalytic efficiency (k cat /K m ) of SrtA△N40(D56E) were reduced compared with those of SrtA△N40(R157H) and SrtA△N40(UA159), whereas the k cat and k cat /K m values of SrtA△N40(R157H) were slightly lower than those of SrtA△N40(UA159). The findings of this study indicate that the T168G missense mutation of the srtA gene results in a significant reduction in enzymatic activity compared with S. mutans UA159, suggesting that the T168G missense mutation of the srtA gene may be related to low cariogenicity.

Streptococcal 5'-Nucleotidase A (S5nA), a Novel Streptococcus pyogenes Virulence Factor That Facilitates Immune Evasion.

Science.gov (United States)

Zheng, Lisa; Khemlani, Adrina; Lorenz, Natalie; Loh, Jacelyn M S; Langley, Ries J; Proft, Thomas

2015-12-25

Streptococcus pyogenes is an important human pathogen that causes a wide range of diseases. Using bioinformatics analysis of the complete S. pyogenes strain SF370 genome, we have identified a novel S. pyogenes virulence factor, which we termed streptococcal 5'-nucleotidase A (S5nA). A recombinant form of S5nA hydrolyzed AMP and ADP, but not ATP, to generate the immunomodulatory molecule adenosine. Michaelis-Menten kinetics revealed a Km of 169 μm and a Vmax of 7550 nmol/mg/min for the substrate AMP. Furthermore, recombinant S5nA acted synergistically with S. pyogenes nuclease A to generate macrophage-toxic deoxyadenosine from DNA. The enzyme showed optimal activity between pH 5 and pH 6.5 and between 37 and 47 °C. Like other 5'-nucleotidases, S5nA requires divalent cations and was active in the presence of Mg(2+), Ca(2+), or Mn(2+). However, Zn(2+) inhibited the enzymatic activity. Structural modeling combined with mutational analysis revealed a highly conserved catalytic dyad as well as conserved substrate and cation-binding sites. Recombinant S5nA significantly increased the survival of the non-pathogenic bacterium Lactococcus lactis during a human whole blood killing assay in a dose-dependent manner, suggesting a role as an S. pyogenes virulence factor. In conclusion, we have identified a novel S. pyogenes enzyme with 5'-nucleotidase activity and immune evasion properties. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Catalytic versatility of Bacillus pumilus β-xylosidase: glycosyl transfer and hydrolysis promoted with α- and β-D-xylosyl fluoride

International Nuclear Information System (INIS)

Kasumi, T.; Tsumuraya, Y.; Brewer, C.F.; Kersters-Hilderson, H.; Claeyssens, M.; Hehre, E.J.

1987-01-01

Bacillus pumilus β-xylosidase, an enzyme considered restricted to hydrolyzing a narrow range of β-D-xylosidic substrates with inversion of configuration, was found to catalyze different stereochemical, essentially irreversible, glycosylation reactions with α- and β-D-xylopyranosyl fluoride. The enzyme promoted the hydrolysis of β-D-xylopyranosyl fluoride at a high rate, V = 6.25 μmol min -1 mg -1 at 0 0 C, in a reaction that obeyed Michaelis-Menten kinetics. In contrast, its action upon α-D-xylopyranosyl fluoride was slow and characterized by an unusual relation between the rate of fluoride release and the substrate concentration, suggesting the possible need for two substrate molecules to be bound at the active center in order for reaction to occur. Moreover, 1 H NMR spectra of a digest of α-D-xylosyl fluoride showed the substrate to be specifically converted to α-D-xylose by the enzyme. The observed retention of configuration is not consistent with direct hydrolysis by this inverting enzyme but is strongly indicative of the occurrence of two successive inverting reactions: xylosyl transfer from α-D-xylosyl fluoride to form a β-D-xylosidic product, followed by hydrolysis of the latter to produce α-D-xylose. The transient intermediate product formed enzymically from α-D-xylosyl fluoride in the presence of [ 14 C]xylose was isolated and shown by its specific radioactivity and 1 H NMR spectrum as well as by methylatino and enzymic analyses to be 4-O-β-D-xylopyranosyl-D-xylopyranose containing one [ 14 C]xylose residue

Role of N2 molecules in pulse discharge production of I atoms for a pulsed chemical oxygen-iodine laser

International Nuclear Information System (INIS)

Kochetov, I V; Napartovich, A P; Vagin, N P; Yuryshev, N N

2011-01-01

A pulsed electric discharge is the most effective means to turn chemical oxygen-iodine laser (COIL) operation into the pulse mode by fast production of iodine atoms. Experimental studies and numerical simulations are performed on a pulsed COIL initiated by an electric discharge in a mixture CF 3 I : N 2 : O 2 ( 3 X) : O 2 (a 1 Δ g ) flowing out of a chemical singlet oxygen generator. A transverse pulsed discharge is realized at various iodide pressures. The model comprises a system of kinetic equations for neutral and charged species, the electric circuit equation, the gas thermal balance equation and the photon balance equation. Reaction rate coefficients for processes involving electrons are repeatedly re-calculated by the electron Boltzmann equation solver when the plasma parameters are changed. The processes accounted for in the Boltzmann equation include direct and stepwise excitation and ionization of atoms and molecules, dissociation of molecules, electron attachment processes, electron-ion recombination, electron-electron collisions and second-kind collisions. The last processes are particularly important because of a high singlet oxygen concentration in gas flow from the singlet oxygen chemical generator. A conclusion is drawn about satisfactory agreement between the theory and the experiment.

Production and spectroscopy of ultracold YbRb* molecules

International Nuclear Information System (INIS)

Nemitz, Nils

2008-11-01

This thesis describes the formation of electronically excited but translationally cold molecules formed from rubidium atoms and two isotopes of ytterbium ( 176 Yb and 174 Yb) by means of photoassociation. The experiments were performed in a combined MOT with 10 9 rubidium atoms and 2.10 6 ytterbium atoms at temperatures of less than 1 mK. Photoassociation lines were found by trap loss spectroscopy throughout a wavelength range of 2 nm near the 795 nm D1 transition in rubidium. The majority of lines belong to two vibrational series in the excited YbRb * molecule, converging on a system of a ground state ytterbium atom and an excited rubidium atom. The strong variation of line strength between different vibrational lines is explained through the Franck-Condon principle. An improved version of the Leroy-Bernstein equation was used to extract the leading dispersion coefficient of the potential from the vibrational progression. Most of the observed lines show a resolved rotational structure as expected from a basic quantum mechanical model. The series terminates with the third or forth rotational component due to the ground state centrifugal barrier.The measured rotational constants agree very well with calculations based on the C 6 coefficient. The discovery of a splitting of the rotational components into subcomponents indicates an uncommon angular momentum coupling described by Hund's case. Variations in the depth of the subcomponents indicates a similar splitting in the ground state, with the energies of the substates based on the alignment of the rubidium atom's magnetic dipole moment relative to the angular momentum carried by an approaching ytterbium atom. This creates an additional ground state barrier, partially suppressing some of the subcomponents. Using a rate equation model developed for this purpose, a maximum formation rate of 2.5.10 6 molecules per second was calculated over the volume of the entire trap. The work presented here is an important step on

Variance decomposition in stochastic simulators.

Science.gov (United States)

Le Maître, O P; Knio, O M; Moraes, A

2015-06-28

This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

Variance decomposition in stochastic simulators

Science.gov (United States)

Le Maître, O. P.; Knio, O. M.; Moraes, A.

2015-06-01

This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

Nonlinearities and transit times in soil organic matter models: new developments in the SoilR package

Science.gov (United States)

Sierra, Carlos; Müller, Markus

2016-04-01

SoilR is an R package for implementing diverse models representing soil organic matter dynamics. In previous releases of this package, we presented the implementation of linear first-order models with any number of pools as well as radiocarbon dynamics. We present here new improvements of the package regarding the possibility to implement models with nonlinear interactions among state variables and the possibility to calculate ages and transit times for nonlinear models with time dependencies. We show here examples on how to implement model structures with Michaelis-Menten terms for explicit microbial growth and resource use efficiency, and Langmuir isotherms for representing adsorption of organic matter to mineral surfaces. These nonlinear terms can be implemented for any number of organic matter pools, microbial functional groups, or mineralogy, depending on user's requirements. Through a simple example, we also show how transit times of organic matter in soils are controlled by the time-dependencies of the input terms.

Dependence of nitrite oxidation on nitrite and oxygen in low-oxygen seawater

Science.gov (United States)

Sun, Xin; Ji, Qixing; Jayakumar, Amal; Ward, Bess B.

2017-08-01

Nitrite oxidation is an essential step in transformations of fixed nitrogen. The physiology of nitrite oxidizing bacteria (NOB) implies that the rates of nitrite oxidation should be controlled by concentration of their substrate, nitrite, and the terminal electron acceptor, oxygen. The sensitivities of nitrite oxidation to oxygen and nitrite concentrations were investigated using 15N tracer incubations in the Eastern Tropical North Pacific. Nitrite stimulated nitrite oxidation under low in situ nitrite conditions, following Michaelis-Menten kinetics, indicating that nitrite was the limiting substrate. The nitrite half-saturation constant (Ks = 0.254 ± 0.161 μM) was 1-3 orders of magnitude lower than in cultivated NOB, indicating higher affinity of marine NOB for nitrite. The highest rates of nitrite oxidation were measured in the oxygen depleted zone (ODZ), and were partially inhibited by additions of oxygen. This oxygen sensitivity suggests that ODZ specialist NOB, adapted to low-oxygen conditions, are responsible for apparently anaerobic nitrite oxidation.

Passage of delta sleep-inducing peptide (DSIP) across the blood-cerebrospinal fluid barrier

International Nuclear Information System (INIS)

Zlokovic, B.V.; Segal, M.B.; Davson, H.; Jankov, R.M.

1988-01-01

Unidirectional flux of 125 I-labeled DSIP at the blood-tissue interface of the blood-cerebrospinal fluid (CSF) barrier was studied in the perfused in situ choroid plexuses of the lateral ventricles of the sheep. Arterio-venous loss of 125 I-radioactivity suggested a low-to-moderate permeability of the choroid epithelium to the intact peptide from the blood side. A saturable mechanism with Michaelis-Menten type kinetics with high affinity and very low capacity (approximate values: Kt = 5.0 +/- 0.4 nM; Vmax = 272 +/- 10 fmol.min-1) was demonstrated at the blood-tissue interface of the choroid plexus. The clearance of DSIP from the ventricles during ventriculo-cisternal perfusion in the rabbit indicated no significant flux of the intact peptide out of the CSF. The results suggest that DSIP crosses the blood-CSF barrier, while the system lacks the specific mechanisms for removal from the CSF found with most, if not all, amino acids and several peptides

A metabolic and pharmacokinetic comparison of theophylline and aminophylline (theophylline ethylenediamine).

Science.gov (United States)

Monks, T J; Smith, R L; Caldwell, J

1981-02-01

The metabolism and pharmacokinetics of intravenously administered theophylline and aminophylline (theophylline ethylenediamine) have been studied in 3 volunteers, using 14C-labelled theophylline. Both compounds were metabolized extensively and 1,3-dimethyluric acid, 1-methyluric acid, 3-methylxanthine and two unknown minor metabolites were excreted in the urine, in addition to theophylline. The elimination of theophylline, 1,3-dimethyluric acid, 1-methyluric acid and the unknown metabolites followed first-order kinetics, but that of 3-methylxanthine followed Michaelis-Menten kinetics. When given as aminophylline, theophylline was metabolized more rapidly and extensively than when given alone. The recovery of 14C in the urine was significantly higher after aminophylline than after theophylline. Abstention from intake of dietary methylxanthines for 7 days resulted in more rapid and extensive metabolism of aminophylline compared with results from the same subjects on their usual diets. The results indicate that, from a metabolic and pharmacokinetic viewpoint, aminophylline and theophylline are not equivalent.

Measurement and Modeling of Respiration Rate of Tomato (Cultivar Roma) for Modified Atmosphere Storage.

Science.gov (United States)

Kandasamy, Palani; Moitra, Ranabir; Mukherjee, Souti

2015-01-01

Experiments were conducted to determine the respiration rate of tomato at 10, 20 and 30 °C using closed respiration system. Oxygen depletion and carbon dioxide accumulation in the system containing tomato was monitored. Respiration rate was found to decrease with increasing CO2 and decreasing O2 concentration. Michaelis-Menten type model based on enzyme kinetics was evaluated using experimental data generated for predicting the respiration rate. The model parameters that obtained from the respiration rate at different O2 and CO2 concentration levels were used to fit the model against the storage temperatures. The fitting was fair (R2 = 0.923 to 0.970) when the respiration rate was expressed as O2 concentation. Since inhibition constant for CO2 concentration tended towards negetive, the model was modified as a function of O2 concentration only. The modified model was fitted to the experimental data and showed good agreement (R2 = 0.998) with experimentally estimated respiration rate.

Enhancing Activity and Stability of Uricase from Lactobacillus plantarum by Zeolite immobilization

Science.gov (United States)

Iswantini, D.; Nurhidayat, N.; Sarah

2017-03-01

Lactobacillus plantarum has been known be able to produce uricase for uric acid biosensor. Durability and stability of L. plantarum in generating uricase enzyme was low. Hence, we tried to enhance its durability and stability by immobilizing it onto activated 250 mg zeolite at room temperature using 100 μL L.plantarum suspension and 2.87 mM uric acid, while Michaelis-Menten constant (KM) and Vmax were obtained at 6.7431 mM and 0.9171 µA consecutively, and the linearity range was 0.1-3.3 mM (R2 = 0.9667). Limit of detection (LOD) and limit of quantification (LOQ) value of the measurement were 0.4827 mM and 1.6092 mM respectively. Biosensor stability treatment was carried out in two different treatments, using the same electrode and using disposable electrode. The disposable electrode stability showed better result based on repeated measurements, but stability was still need improvement.

Scopadulcic acid B, a new tetracyclic diterpenoid from Scoparia dulcis L. Its structure, H+, K(+)-adenosine triphosphatase inhibitory activity and pharmacokinetic behaviour in rats.

Science.gov (United States)

Hayashi, T; Okamura, K; Kakemi, M; Asano, S; Mizutani, M; Takeguchi, N; Kawasaki, M; Tezuka, Y; Kikuchi, T; Morita, N

1990-10-01

The structure of scopadulcic acid B (2, SDB), a major ingredient of the Paraguayan herb "Typychá kuratũ" (Scoparia dulcis L.), was elucidated mainly by comparison of its spectral data with that of scopadulcic acid A (1). SDB inhibited both the K(+)-dependent adenosine triphosphatase (ATPase) activity of a hog gastric proton pump (H+, K(+)-ATPase) with a value of 20-30 microM for IC50 and proton transport into gastric vesicles. Pharmacokinetic studies of SDB in rats indicated that plasma SDB concentrations after i.v. injection of the sodium salt of SDB (SDB-Na) were described reasonably well by a two-compartment open model with Michaelis-Menten elimination kinetics. Plasma concentrations after oral administration of SDB-Na or SDB showed a much slower decline than what was expected following the i. v. study. It was suggested that the sustained plasma level of SDB after oral administration of SDB-Na or SDB was accounted for by relatively slow but efficient gastro-intestinal absorption in rats.

Electrochemical quantification of the antioxidant capacity of medicinal plants using biosensors.

Science.gov (United States)

Rodríguez-Sevilla, Erika; Ramírez-Silva, María-Teresa; Romero-Romo, Mario; Ibarra-Escutia, Pedro; Palomar-Pardavé, Manuel

2014-08-08

The working area of a screen-printed electrode, SPE, was modified with the enzyme tyrosinase (Tyr) using different immobilization methods, namely entrapment with water-soluble polyvinyl alcohol (PVA), cross-linking using glutaraldehyde (GA), and cross-linking using GA and human serum albumin (HSA); the resulting electrodes were termed SPE/Tyr/PVA, SPE/Tyr/GA and SPE/Tyr/HSA/GA, respectively. These biosensors were characterized by means of amperometry and EIS techniques. From amperometric evaluations, the apparent Michaelis-Menten constant, Km', of each biosensor was evaluated while the respective charge transfer resistance, Rct, was assessed from impedance measurements. It was found that the SPE/Tyr/GA had the smallest Km' (57 ± 7) µM and Rct values. This electrode also displayed both the lowest detection and quantification limits for catechol quantification. Using the SPE/Tyr/GA, the Trolox Equivalent Antioxidant Capacity (TEAC) was determined from infusions prepared with "mirto" (Salvia microphylla), "hHierba dulce" (Lippia dulcis) and "salve real" (Lippia alba), medicinal plants commonly used in Mexico.

Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains.

Science.gov (United States)

Karow, Anne R; Theissen, Bettina; Klostermeier, Dagmar

2007-01-01

RNA helicases mediate structural rearrangements of RNA or RNA-protein complexes at the expense of ATP hydrolysis. Members of the DEAD box helicase family consist of two flexibly connected helicase domains. They share nine conserved sequence motifs that are involved in nucleotide binding and hydrolysis, RNA binding, and helicase activity. Most of these motifs line the cleft between the two helicase domains, and extensive communication between them is required for RNA unwinding. The two helicase domains of the Bacillus subtilis RNA helicase YxiN were produced separately as intein fusions, and a functional RNA helicase was generated by expressed protein ligation. The ligated helicase binds adenine nucleotides with very similar affinities to the wild-type protein. Importantly, its intrinsically low ATPase activity is stimulated by RNA, and the Michaelis-Menten parameters are similar to those of the wild-type. Finally, ligated YxiN unwinds a minimal RNA substrate to an extent comparable to that of the wild-type helicase, confirming authentic interdomain communication.

Thermo-kinetics of lipase-catalyzed synthesis of 6-O-glucosyldecanoate.

Science.gov (United States)

Gumel, A M; Annuar, M S M; Heidelberg, T; Chisti, Y

2011-10-01

Lipase-catalyzed synthesis of 6-O-glucosyldecanoate from d-glucose and decanoic acid was performed in dimethyl sulfoxide (DMSO), a mixture of DMSO and tert-butanol and tert-butanol alone with a decreasing order of polarity. The highest conversion yield (> 65%) of decanoic acid was obtained in the blended solvent of intermediate polarity mainly because it could dissolve relatively large amounts of both the reactants. The reaction obeyed Michaelis-Menten type of kinetics. The affinity of the enzyme towards the limiting substrate (decanoic acid) was not affected by the polarity of the solvent, but increased significantly with temperature. The esterification reaction was endothermic with activation energy in the range of 60-67 kJ mol⁻¹. Based on the Gibbs energy values, in the solvent blend of DMSO and tert-butanol the position of the equilibrium was shifted more towards the products compared to the position in pure solvents. Monoester of glucose was the main product of the reaction. Copyright © 2011 Elsevier Ltd. All rights reserved.

Direct electron transfer of horseradish peroxidase on Nafion-cysteine modified gold electrode

International Nuclear Information System (INIS)

Hong, Jun; Moosavi-Movahedi, Ali Akbar; Ghourchian, Hedayatollah; Rad, Ahmad Molaei; Rezaei-Zarchi, Saeed

2007-01-01

Direct electron transfer of horseradish peroxidase, immobilized on a functional membrane-modified gold electrode, was studied. The electrode showed a quasi-reversible electrochemical redox behavior with a formal potential of 60mV (versus Ag/AgCl) in 20mM potassium phosphate buffer solution at pH 7.0 and temperature 25 o C. The cathodic transfer coefficient was 0.42 and electron transfer rate constant was evaluated to be 1.6s -1 . Furthermore, the modified electrode was used as a biosensor and exhibited a satisfactory stability and sensitivity to H 2 O 2 . The linear range of this biosensor for H 2 O 2 determination was from 5.0x10 -6 to 1.5x10 -4 M while its detection limit, based on a signal-to-noise ratio of 3, was 1.3x10 -6 M. The apparent Michaelis-Menten constant (K m app ) for immobilized HRP was calculated to be 1.6x10 -4 M

Variance decomposition in stochastic simulators

Energy Technology Data Exchange (ETDEWEB)

Le Maître, O. P., E-mail: olm@limsi.fr [LIMSI-CNRS, UPR 3251, Orsay (France); Knio, O. M., E-mail: knio@duke.edu [Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708 (United States); Moraes, A., E-mail: alvaro.moraesgutierrez@kaust.edu.sa [King Abdullah University of Science and Technology, Thuwal (Saudi Arabia)

2015-06-28

This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

Enzyme-like catalysis via ternary complex mechanism: alkoxy-bridged dinuclear cobalt complex mediates chemoselective O-esterification over N-amidation.

Science.gov (United States)

Hayashi, Yukiko; Santoro, Stefano; Azuma, Yuki; Himo, Fahmi; Ohshima, Takashi; Mashima, Kazushi

2013-04-24

Hydroxy group-selective acylation in the presence of more nucleophilic amines was achieved using acetates of first-row late transition metals, such as Mn, Fe, Co, Cu, and Zn. Among them, cobalt(II) acetate was the best catalyst in terms of reactivity and selectivity. The combination of an octanuclear cobalt carboxylate cluster [Co4(OCOR)6O]2 (2a: R = CF3, 2b: R = CH3, 2c: R = (t)Bu) with nitrogen-containing ligands, such as 2,2'-bipyridine, provided an efficient catalytic system for transesterification, in which an alkoxide-bridged dinuclear complex, Co2(OCO(t)Bu)2(bpy)2(μ2-OCH2-C6H4-4-CH3)2 (10), was successfully isolated as a key intermediate. Kinetic studies and density functional theory calculations revealed Michaelis-Menten behavior of the complex 10 through an ordered ternary complex mechanism similar to dinuclear metallo-enzymes, suggesting the formation of alkoxides followed by coordination of the ester.

Comparison of indocyanine green clearance with Child's-Pugh score and hepatic histology: a multivariate analysis.

Science.gov (United States)

Mukherjee, Sandeep; Rogers, Mary A M; Buniak, Borys

2006-01-01

Indocyanine green clearance, measured by percentage disappearance rate, detects alterations in liver function and may be used as a non-invasive determinant of hepatic reserve. The aims of this study were to compare liver histology and Child's-Pugh score with percentage disappearance rate and determine which variables correlated with PDR. Child's-Pugh score, liver function tests, liver biopsies and indocyanine green testing (0.5mg/kg) were performed in 102 consecutive patients with cirrhosis of diverse etiologies. Indocyanine green concentration was determined using spectrophotometric analysis (806nm) and plotted logarithmically with Michaelis-Menten kinetics to calculate the percentage disappearance rate. Liver biopsies were graded using the modified Knodell score to obtain a histological activity index. In bivariable analysis, percentage disappearance rate significantly correlated with Child's-Pugh score, albumin, bilirubin, prothrombin time and histological activity index. Albumin, prothrombin time and histological activity index were independent predictors of percentage disappearance rate in the final model (albumin ptime ptime and histological activity index.

The mechanism distinguishability problem in biochemical kinetics: the single-enzyme, single-substrate reaction as a case study.

Science.gov (United States)

Schnell, Santiago; Chappell, Michael J; Evans, Neil D; Roussel, Marc R

2006-01-01

A theoretical analysis of the distinguishability problem of two rival models of the single enzyme-single substrate reaction, the Michaelis-Menten and Henri mechanisms, is presented. We also outline a general approach for analysing the structural indistinguishability between two mechanisms. The approach involves constructing, if possible, a smooth mapping between the two candidate models. Evans et al. [N.D. Evans, M.J. Chappell, M.J. Chapman, K.R. Godfrey, Structural indistinguishability between uncontrolled (autonomous) nonlinear analytic systems, Automatica 40 (2004) 1947-1953] have shown that if, in addition, either of the mechanisms satisfies a particular criterion then such a transformation always exists when the models are indistinguishable from their experimentally observable outputs. The approach is applied to the single enzyme-single substrate reaction mechanism. In principle, mechanisms can be distinguished using this analysis, but we show that our ability to distinguish mechanistic models depends both on the precise measurements made, and on our knowledge of the system prior to performing the kinetics experiments.

Phenols removal by immobilized tyrosinase reactor in on-line high performance liquid chromatography

International Nuclear Information System (INIS)

Girelli, Anna Maria; Mattei, Enrico; Messina, Antonella

2006-01-01

The development of an immobilized enzyme reactor (IMER) based on tyrosinase immobilized on aminopropyl-controlled pore glass (AP-CPG) for the removal of phenols from model aqueous solutions was reported. To elucidate the influence of the substrate nature, the apparent (V ' max , K ' m ) and the inherent (V max , K m ) Michaelis-Menten constants were determined by Lineweaver-Burk method and the external diffusional contributions on measured enzyme activities were removed by a graphical method. The dephenolization process was realized by recycling the phenol solutions through the bioreactor connected to a chitosan trap in order to remove the colored quinone-type products of the tyrosinase reactions. The results indicated that a complete removal of phenol derivatives in the range of 150-300min, with the exception of 60% removal for phenol reached in 400min, was obtained. The observed sequence: cresol>4-methylcathecol>catechol>4-Cl-phenol-bar phenol was in accordance to the V ' max /K ' m values

Purification and characterization of broccoli (Brassica oleracea var. italica) myrosinase (β-thioglucosidase glucohydrolase).

Science.gov (United States)

Mahn, Andrea; Angulo, Alejandro; Cabañas, Fernanda

2014-12-03

Myrosinase (β-thioglucosidase glucohydrolase, EC 3.2.1.147) from broccoli (Brassica oleracea var. italica) was purified by ammonium sulfate precipitation followed by concanavalin A affinity chromatography, with an intermediate dialysis step, resulting in 88% recovery and 1318-fold purification. These are the highest values reported for the purification of any myrosinase. The subunits of broccoli myrosinase have a molecular mass of 50-55 kDa. The native molecular mass of myrosinase was 157 kDa, and accordingly, it is composed of three subunits. The maximum activity was observed at 40 °C and at pH below 5.0. Kinetic assays demonstrated that broccoli myrosinase is subjected to substrate (sinigrin) inhibition. The Michaelis-Menten model, considering substrate inhibition, gave Vmax equal to 0.246 μmol min(-1), Km equal to 0.086 mM, and K(I) equal to 0.368 mM. This is the first study about purification and characterization of broccoli myrosinase.

Uptake, accumulation and metabolic response of ferricyanide in weeping willows.

Science.gov (United States)

Yu, Xiao-Zhang; Gu, Ji-Dong

2009-01-01

The remediation potential and metabolic responses of plants to ferricyanide were investigated using pre-rooted weeping willows (Salix babylonica L.) grown hydroponically in growth chambers and treated with potassium ferricyanide. Positive responses were observed for the plants exposed to cyanide recovered in plant biomass was constant in all treatments, indicating that transport is a major limiting step for the uptake of ferricyanide by plants. The majority of the ferricyanide taken up from the growth media was possibly assimilated during transport through plants. The velocity of the removal processes can be described by Michaelis-Menten kinetics, and the half-saturation constant (K(M)) and the maximum removal capacity (v(max)) were estimated to be 228.1 mg CN L(-1) and 36.43 mg CN kg(-1) d(-1), respectively, using non-linear regression methods. These results suggest that weeping willows can take up, transport and assimilate ferricyanide; and phytoremediation is an option for cleaning up the environmental sites contaminated with cyanide complexes.

Spectral Quasi-Equilibrium Manifold for Chemical Kinetics.

Science.gov (United States)

Kooshkbaghi, Mahdi; Frouzakis, Christos E; Boulouchos, Konstantinos; Karlin, Iliya V

2016-05-26

The Spectral Quasi-Equilibrium Manifold (SQEM) method is a model reduction technique for chemical kinetics based on entropy maximization under constraints built by the slowest eigenvectors at equilibrium. The method is revisited here and discussed and validated through the Michaelis-Menten kinetic scheme, and the quality of the reduction is related to the temporal evolution and the gap between eigenvalues. SQEM is then applied to detailed reaction mechanisms for the homogeneous combustion of hydrogen, syngas, and methane mixtures with air in adiabatic constant pressure reactors. The system states computed using SQEM are compared with those obtained by direct integration of the detailed mechanism, and good agreement between the reduced and the detailed descriptions is demonstrated. The SQEM reduced model of hydrogen/air combustion is also compared with another similar technique, the Rate-Controlled Constrained-Equilibrium (RCCE). For the same number of representative variables, SQEM is found to provide a more accurate description.

Variance decomposition in stochastic simulators

KAUST Repository

Le Maî tre, O. P.; Knio, O. M.; Moraes, Alvaro

2015-01-01

This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

Kinetics of Oxidation of Metochlopramide withChloramine-T in HClO4 Medium

Directory of Open Access Journals (Sweden)

K. M. Meenakshi

2009-01-01

Full Text Available The kinetics of oxidation of metochlopramide hydrochloride (MCP with sodium N-chloro p-toluenesulfonamide (CAT in perchloric acid solution has been studied at 313K. The reaction rate shows a first order dependence on [CAT], fractional order on [MCP] and inverse fractional order on [H+]. There is a negative effect of dielectric constant of the solvent. The addition of the reduction product of CAT has no significant effect on the rate. The rate remained unchanged with the variation in the ionic strength of the medium. The reaction fails to induce the polymerization of acrylonitrile. Thermodynamic parameters have been computed by Arrhenius plot. The stoichiometry of the reaction was found to be 1:2 and oxidation products were identified. The Michaelis-Menten type of kinetics has been proposed. CH3C6H4SO2NHCl have been assumed to be the reactive oxidizing species. Thermodynamic parameters were computed by studying reactions at different temperatures. A mechanism consistent with observed kinetics is proposed.

New insights into the catalytic mechanism of human glycine N-acyltransferase.

Science.gov (United States)

van der Sluis, Rencia; Ungerer, Vida; Nortje, Carla; A van Dijk, Alberdina; Erasmus, Elardus

2017-11-01

Even though the glycine conjugation pathway was one of the first metabolic pathways to be discovered, this pathway remains very poorly characterized. The bi-substrate kinetic parameters of a recombinant human glycine N-acyltransferase (GLYAT, E.C. 2.3.1.13) were determined using the traditional colorimetric method and a newly developed HPLC-ESI-MS/MS method. Previous studies analyzing the kinetic parameters of GLYAT, indicated a random Bi-Bi and/or ping-pong mechanism. In this study, the hippuric acid concentrations produced by the GLYAT enzyme reaction were analyzed using the allosteric sigmoidal enzyme kinetic module. Analyses of the initial rate (v) against substrate concentration plots, produced a sigmoidal curve (substrate activation) when the benzoyl-CoA concentrations was kept constant, whereas the plot with glycine concentrations kept constant, passed through a maximum (substrate inhibition). Thus, human GLYAT exhibits mechanistic kinetic cooperativity as described by the Ferdinand enzyme mechanism rather than the previously assumed Michaelis-Menten reaction mechanism. © 2017 Wiley Periodicals, Inc.

The Investigation of Electrochemistry Behaviors of Tyrosinase Based on Directly-Electrodeposited Grapheneon Choline-Gold Nanoparticles.

Science.gov (United States)

He, Yaping; Yang, Xiaohui; Han, Quan; Zheng, Jianbin

2017-06-23

A novel catechol (CA) biosensor was developed by embedding tyrosinase (Tyr) onto in situ electrochemical reduction graphene (EGR) on choline-functionalized gold nanoparticle (AuNPs-Ch) film. The results of UV-Vis spectra indicated that Tyr retained its original structure in the film, and an electrochemical investigation of the biosensor showed a pair of well-defined, quasi-reversible redox peaks with E pa = -0.0744 V and E pc = -0.114 V (vs. SCE) in 0.1 M, pH 7.0 sodium phosphate-buffered saline at a scan rate of 100 mV/s. The transfer rate constant k s is 0.66 s -1 . The Tyr-EGR/AuNPs-Ch showed a good electrochemical catalytic response for the reduction of CA, with the linear range from 0.2 to 270 μM and a detection limit of 0.1 μM (S/N = 3). The apparent Michaelis-Menten constant was estimated to be 109 μM.

Equation of state of solid hydrogen at 0 deg K. A bibliography

International Nuclear Information System (INIS)

Masse, J.-L.

1976-02-01

A bibliography on solid hydrogen at 0 deg K and its equation of state is presented. The isotopic derivatives of H 2 , such as D 2 , HD... have been also considered. Both phases of solid hydrogen have been studied: the molecular phase, stable at low pressure, and the hypothetical metallic phase which must be stable at high pressure. The study of the molecular phase is preceded by a study of the (H 2 ,H 2 ) system of two interacting H 2 , molecules, the knowledge of this interaction being necessary for the evaluation of the properties of the molecular solid phase. The three systems: (H 2 ,H 2 ) and molecular solid and metallic hydrogen have been considered from the experimental and theoretical points of view. The properties of these systems, the measurement or the calculation of which are described, have been chosen on account of their usefulness for the research of the equation of state of molecular or metallic solid hydrogen. Different interaction potentials of two hydrogen molecules and different equations of state of molecular solid hydrogen are given. Some theoretical studies are proposed [fr

A KDE-Based Random Walk Method for Modeling Reactive Transport With Complex Kinetics in Porous Media

Science.gov (United States)

Sole-Mari, Guillem; Fernà ndez-Garcia, Daniel; Rodríguez-Escales, Paula; Sanchez-Vila, Xavier

2017-11-01

In recent years, a large body of the literature has been devoted to study reactive transport of solutes in porous media based on pure Lagrangian formulations. Such approaches have also been extended to accommodate second-order bimolecular reactions, in which the reaction rate is proportional to the concentrations of the reactants. Rather, in some cases, chemical reactions involving two reactants follow more complicated rate laws. Some examples are (1) reaction rate laws written in terms of powers of concentrations, (2) redox reactions incorporating a limiting term (e.g., Michaelis-Menten), or (3) any reaction where the activity coefficients vary with the concentration of the reactants, just to name a few. We provide a methodology to account for complex kinetic bimolecular reactions in a fully Lagrangian framework where each particle represents a fraction of the total mass of a specific solute. The method, built as an extension to the second-order case, is based on the concept of optimal Kernel Density Estimator, which allows the concentrations to be written in terms of particle locations, hence transferring the concept of reaction rate to that of particle location distribution. By doing so, we can update the probability of particles reacting without the need to fully reconstruct the concentration maps. The performance and convergence of the method is tested for several illustrative examples that simulate the Advection-Dispersion-Reaction Equation in a 1-D homogeneous column. Finally, a 2-D application example is presented evaluating the need of fully describing non-bilinear chemical kinetics in a randomly heterogeneous porous medium.

The kinetics of phagocytosis of 198Au colloids ''in vitro''

International Nuclear Information System (INIS)

Astorri, N.L.; Bergoc, R.M.; Bianchin, A.M.; Caro, R.A.; Ihlo, J.E.; Rivera, E.S.

1982-01-01

The kinetics of the phagocytosis of 198-Au colloids by macrophages ''in vitro'' was studied by incubating during 5 hours phagocytic cells from the liver and the spleen of Wistar rats with colloidal radiogold particles, in the presence of an adequate culture medium (TC-199 with 10 per cent of Bovine Fetal Serum). In each experiment, the number of colloidal gold particles offered to each phatocytic cell, (Au) 0 and the mean rate of phagocytosis v, were calculated. The latter value was determined by measuring the radioactivity incorporated into the phagocytic cells during the incubation; it was expressed as the number of phagocytized colloidal gold particles per cell per minute. The values of log v = f [log (Au) 0 ] were plotted. The Lineweaver-Burk analysis of the results demonstrates that the kinetics of the phagocytosis of colloidal radiogold particles ''in vitro'' follows a model similar to Michaelis-Menten equations for enzyme reactions. The values of the substratum constant Ks and maximun velocity Vm were obtained by the regression analysis of the 1/v vs. 1/(Au) 0 graph. Vm was equal to 9.44 x 10 and 1.63 x 10 phagocytized colloidal gold particles per cell per minute for liver and spleen macrophages, respectively. Ks was equal to 6.01 x 10 9 and 8.02 x 10 8 colloidal gold particles per cell for liver and spleen macrophages, respectively. The significance of these differences is discussed and attributed mainly to a change of the specific engulfment rate constant. (author) [es

Treatment of ferrous-NTA-based NO x scrubber solution by an up-flow anaerobic packed bed bioreactor.

Science.gov (United States)

Chandrashekhar, B; Sahu, Nidhi; Tabassum, Heena; Pai, Padmaraj; Morone, Amruta; Pandey, R A

2015-06-01

A bench scale system consisting of an up-flow packed bed bioreactor (UAPBR) made of polyurethane foam was used for the treatment and regeneration of aqueous solution of ferrous-NTA scrubbed with nitric oxide (NO). The biomass in the UAPBR was sequentially acclimatized under denitrifying and iron reducing conditions using ethanol as electron donor, after which nitric oxide (NO) gas was loaded continuously to the system by absorption. The system was investigated for different parameters viz. pH, removal efficiency of nitric oxide, biological reduction efficiency of Fe(II)NTA-NO and COD utilization. The Fe(II)NTA-NO reduction efficiency reached 87.8 % at a loading rate of 0.24 mmol L(-1) h(-1), while the scrubber efficiency reached more than 75 % with 250 ppm NO. Stover-Kincannon and a Plug-flow kinetic model based on Michaelis-Menten equation were used to describe the UAPBR performance with respect to Fe(II)NTA-NO and COD removal. The Stover-Kincannon model was found capable of describing the Fe(II)NTA-NO reduction (R m = 8.92 mM h(-1) and K NO = 11.46 mM h(-1)) while plug-flow model provided better fit to the COD utilization (U m = 66.62 mg L(-1) h(-1), K COD = 7.28 mg L(-1)). Analyses for pH, Fe(III)NTA, ammonium, nitrite concentration, and FTIR analysis of the medium samples indicated degradation of NTA, which leads to ammonium and nitrite accumulation in the medium, and affect the regeneration process.

Calculations on isotope separation by laser induced photodissociation of polyatomic molecules. Final report

International Nuclear Information System (INIS)

Lamb, W.E. Jr.

1978-11-01

This report describes research on the theory of isotope separation produced by the illumination of polyatomic molecules by intense infrared laser radiation. Newton's equations of motion were integrated for the atoms of the SF 6 molecule including the laser field interaction. The first year's work has been largely dedicated to obtaining a suitable interatomic potential valid for arbitrary configurations of the seven particles. This potential gives the correct symmetry of the molecule, the equilibrium configuration, the frequencies of the six distinct normal modes of oscillation and the correct (or assumed) value of the total potential energy of the molecule. Other conditions can easily be imposed in order to obtain a more refined potential energy function, for example, by making allowance for anharmonicity data. A suitable expression was also obtained for the interaction energy between a laser field and the polyatomic molecule. The electromagnetic field is treated classically, and it would be easily possible to treat the cases of time dependent pulses, frequency modulation and noise

Molecule Matters van der Waals Molecules

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 12. Molecule Matters van der Waals Molecules - Noble Gas Clusters are London Molecules! E Arunan. Feature Article Volume 14 Issue 12 December 2009 pp 1210-1222 ...

Quantum-mechanical transport equation for atomic systems.

Science.gov (United States)

Berman, P. R.

1972-01-01

A quantum-mechanical transport equation (QMTE) is derived which should be applicable to a wide range of problems involving the interaction of radiation with atoms or molecules which are also subject to collisions with perturber atoms. The equation follows the time evolution of the macroscopic atomic density matrix elements of atoms located at classical position R and moving with classical velocity v. It is quantum mechanical in the sense that all collision kernels or rates which appear have been obtained from a quantum-mechanical theory and, as such, properly take into account the energy-level variations and velocity changes of the active (emitting or absorbing) atom produced in collisions with perturber atoms. The present formulation is better suited to problems involving high-intensity external fields, such as those encountered in laser physics.

CAL3JHH: a Java program to calculate the vicinal coupling constants (3J H,H) of organic molecules.

Science.gov (United States)

Aguirre-Valderrama, Alonso; Dobado, José A

2008-12-01

Here, we present a free web-accessible application, developed in the JAVA programming language for the calculation of vicinal coupling constant (3J(H,H)) of organic molecules with the H-Csp3-Csp3-H fragment. This JAVA applet is oriented to assist chemists in structural and conformational analyses, allowing the user to calculate the averaged 3J(H,H) values among conformers, according to its Boltzmann populations. Thus, the CAL3JHH program uses the Haasnoot-Leeuw-Altona equation, and, by reading the molecule geometry from a protein data bank (PDB) file format or from multiple pdb files, automatically detects all the coupled hydrogens, evaluating the data needed for this equation. Moreover, a "Graphical viewer" menu allows the display of the results on the 3D molecule structure, as well as the plotting of the Newman projection for the couplings.

Complex dynamics in diatomic molecules. Part II: Quantum trajectories

International Nuclear Information System (INIS)

Yang, C.-D.; Weng, H.-J.

2008-01-01

The second part of this paper deals with quantum trajectories in diatomic molecules, which has not been considered before in the literature. Morse potential serves as a more accurate function than a simple harmonic oscillator for illustrating a realistic picture about the vibration of diatomic molecules. However, if we determine molecular dynamics by integrating the classical force equations derived from a Morse potential, we will find that the resulting trajectories do not consist with the probabilistic prediction of quantum mechanics. On the other hand, the quantum trajectory determined by Bohmian mechanics [Bohm D. A suggested interpretation of the quantum theory in terms of hidden variable. Phys. Rev. 1952;85:166-179] leads to the conclusion that a diatomic molecule is motionless in all its vibrational eigen-states, which also contradicts probabilistic prediction of quantum mechanics. In this paper, we point out that the quantum trajectory of a diatomic molecule completely consistent with quantum mechanics does exist and can be solved from the quantum Hamilton equations of motion derived in Part I, which is based on a complex-space formulation of fractal spacetime [El Naschie MS. A review of E-Infinity theory and the mass spectrum of high energy particle physics. Chaos, Solitons and Fractals 2004;19:209-36; El Naschie MS. E-Infinity theory - some recent results and new interpretations. Chaos, Solitons and Fractals 2006;29:845-853; El Naschie MS. The concepts of E-infinity. An elementary introduction to the cantorian-fractal theory of quantum physics. Chaos, Solitons and Fractals 2004;22:495-511; El Naschie MS. SU(5) grand unification in a transfinite form. Chaos, Solitons and Fractals 2007;32:370-374; Nottale L. Fractal space-time and microphysics: towards a theory of scale relativity. Singapore: World Scientific; 1993; Ord G. Fractal space time and the statistical mechanics of random works. Chaos, Soiltons and Fractals 1996;7:821-843] approach to quantum

Structure of deformable diatomic molecules: a modified n-butane liquid

International Nuclear Information System (INIS)

Jang, Seanea; Kim, Soonchul; Lee, Songhi

2005-01-01

The density functional approximation for polyatomic molecules, which is based on the bridge function of the intermolecular interaction, was developed and applied to investigate the thermodynamic and the structural properties of deformable diatomic molecules. The Percus trick was employed to calculate the uniform structure of modified n-butane. The calculated static correlation functions were used to predict the density behaviors of a modified n-butane liquid at liquid-solid interfaces. The theoretical results show that (i) at low densities, the hypernetted-chain (HNC) equation compares with the density functional approximation based on the bridge function and that (ii) the relative population between the gauche and the trans states strongly affects the liquid structure at liquid-solid interfaces.

Unconventional superfluids of fermionic polar molecules in a bilayer system

Energy Technology Data Exchange (ETDEWEB)

Boudjemâa, Abdelâali, E-mail: a.boudjemaa@univhb-chlef.dz

2017-05-25

We study unconventional superfluids of fermionic polar molecules in a two-dimensional bilayer system with dipoles are head-to-tail across the layers. We analyze the critical temperature of several unconventional pairings as a function of different system parameters. The peculiar competition between the d- and the s-wave pairings is discussed. We show that the experimental observation of such unconventional superfluids requires ultralow temperatures, which opens up new possibilities to realize several topological phases. - Highlights: • Investigation of novel superfluids of fermionic polar molecules in a bilayer geometry. • Solving the gap equation and the l-wave interlayer scattering problem. • Calculation of the critical temperature of several competing pairings using the BCS approach.

Diffusion coefficients of Fokker-Planck equation for rotating dust grains in a fusion plasma

Science.gov (United States)

Bakhtiyari-Ramezani, M.; Mahmoodi, J.; Alinejad, N.

2015-11-01

In the fusion devices, ions, H atoms, and H2 molecules collide with dust grains and exert stochastic torques which lead to small variations in angular momentum of the grain. By considering adsorption of the colliding particles, thermal desorption of H atoms and normal H2 molecules, and desorption of the recombined H2 molecules from the surface of an oblate spheroidal grain, we obtain diffusion coefficients of the Fokker-Planck equation for the distribution function of fluctuating angular momentum. Torque coefficients corresponding to the recombination mechanism show that the nonspherical dust grains may rotate with a suprathermal angular velocity.

3D Multi-Level Non-LTE Radiative Transfer for the CO Molecule

Science.gov (United States)

Berkner, A.; Schweitzer, A.; Hauschildt, P. H.

2015-01-01

The photospheres of cool stars are both rich in molecules and an environment where the assumption of LTE can not be upheld under all circumstances. Unfortunately, detailed 3D non-LTE calculations involving molecules are hardly feasible with current computers. For this reason, we present our implementation of the super level technique, in which molecular levels are combined into super levels, to reduce the number of unknowns in the rate equations and, thus, the computational effort and memory requirements involved, and show the results of our first tests against the 1D implementation of the same method.

Numerical calculation of the cross section by the solution of the wave equation

International Nuclear Information System (INIS)

Drewko, J.

1982-01-01

A numerical method of solving of the wave equation is described for chosen vibrational eigenfunctions. A prepared program calculates the total cross sections for the resonant vibrational excitation for diatomic molecules on the basis of introduced molecular data. (author)

Observing electron localization in a dissociating H2+ molecule in real time.

Science.gov (United States)

Xu, H; Li, Zhichao; He, Feng; Wang, X; Atia-Tul-Noor, A; Kielpinski, D; Sang, R T; Litvinyuk, I V

2017-06-16

Dissociation of diatomic molecules with odd number of electrons always causes the unpaired electron to localize on one of the two resulting atomic fragments. In the simplest diatomic molecule H 2 + dissociation yields a hydrogen atom and a proton with the sole electron ending up on one of the two nuclei. That is equivalent to breaking of a chemical bond-the most fundamental chemical process. Here we observe such electron localization in real time by performing a pump-probe experiment. We demonstrate that in H 2 + electron localization is complete in just 15 fs when the molecule's internuclear distance reaches 8 atomic units. The measurement is supported by a theoretical simulation based on numerical solution of the time-dependent Schrödinger equation. This observation advances our understanding of detailed dynamics of molecular dissociation.

Non-equilibrium reaction rates in chemical kinetic equations

Science.gov (United States)

Gorbachev, Yuriy

2018-05-01

Within the recently proposed asymptotic method for solving the Boltzmann equation for chemically reacting gas mixture, the chemical kinetic equations has been derived. Corresponding one-temperature non-equilibrium reaction rates are expressed in terms of specific heat capacities of the species participate in the chemical reactions, bracket integrals connected with the internal energy transfer in inelastic non-reactive collisions and energy transfer coefficients. Reactions of dissociation/recombination of homonuclear and heteronuclear diatomic molecules are considered. It is shown that all reaction rates are the complex functions of the species densities, similarly to the unimolecular reaction rates. For determining the rate coefficients it is recommended to tabulate corresponding bracket integrals, additionally to the equilibrium rate constants. Correlation of the obtained results with the irreversible thermodynamics is established.

Molecule Matters van der Waals Molecules

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Molecule Matters van der Waals Molecules - Rg•••HF Complexes are Debye Molecules! E Arunan. Feature Article Volume 15 Issue 7 July 2010 pp 667-674. Fulltext. Click here to view fulltext PDF. Permanent link:

AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation.

Science.gov (United States)

Koehl, Patrice; Delarue, Marc

2010-02-14

The Poisson-Boltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar Poisson-Boltzmann-Langevin (DPBL) formalism represents the solvent as a collection of orientable dipoles with nonuniform concentration; this leads to a nonlinear permittivity function that depends both on the position and on the local electric field at that position. The differences in the assumptions underlying these two models lead to significant differences in the equations they generate. The PB equation is a second order, elliptic, nonlinear partial differential equation (PDE). Its response coefficients correspond to the dielectric permittivity and are therefore constant within each subdomain of the system considered (i.e., inside and outside of the molecules considered). While the DPBL equation is also a second order, elliptic, nonlinear PDE, its response coefficients are nonlinear functions of the electrostatic potential. Many solvers have been developed for the PB equation; to our knowledge, none of these can be directly applied to the DPBL equation. The methods they use may adapt to the difference; their implementations however are PBE specific. We adapted the PBE solver originally developed by Holst and Saied [J. Comput. Chem. 16, 337 (1995)] to the problem of solving the DPBL equation. This solver uses a truncated Newton method with a multigrid preconditioner. Numerical evidences suggest that it converges for the DPBL equation and that the convergence is superlinear. It is found however to be slow and greedy in memory requirement for problems commonly encountered in computational biology and computational chemistry. To circumvent these problems, we propose two variants, a quasi-Newton solver based on a simplified, inexact Jacobian and an iterative self-consistent solver that is based directly on the PBE

Theoretical study of molecular vibration and Application to linear triatomic molecules: case of OCS

International Nuclear Information System (INIS)

Andrianavalomahefa, A.

2014-01-01

Our aim is to give a theoretical approach to the calculation of vibrational energy levels of polyatomic molecules. By using matrix calculation, we have to solve an eigenvalue equation that gives normal vibration frequencies of the system. A basis change introduces normal coordinates of vibration, which diagonalize the Hamiltonian. The harmonic approximation gives a rough evaluation of parameters which describe the system. Then, we introduce nonlinear terms to take into account the anharmonicity of interatomic bounds. Morse oscillator gives good approximation for diatomic molecules. We consider cubic and quartic potential terms for polyatomic molecules. We treat the problem both in classical and quantum approach. The results thus obtained are applied to study longitudinal vibration of carbonyl sulfide. [fr

Using a Mechanistic Reactive Transport Model to Represent Soil Organic Matter Dynamics and Climate Sensitivity

Science.gov (United States)

Guerry, N.; Riley, W. J.; Maggi, F.; Torn, M. S.; Kleber, M.

2011-12-01

The nature of long term Soil Organic Matter (SOM) dynamics is uncertain and the mechanisms involved are crudely represented in site, regional, and global models. Recent work challenging the paradigm that SOM is stabilized because of its sequential transformations to more intrinsically recalcitrant compounds motivated us to develop a mechanistic modeling framework that can be used to test hypotheses of SOM dynamics. We developed our C cycling model in TOUGHREACT, an established 3-dimensional reactive transport solver that accounts for multiple phases (aqueous, gaseous, sorbed), multiple species, advection and diffusion, and multiple microbial populations. Energy and mass exchange through the soil boundaries are accounted for via ground heat flux, rainfall, C sources (e.g., exudation, woody, leaf, root litter) and C losses (e.g., CO2 emissions and DOC deep percolation). SOM is categorized according to the various types of compounds commonly found in the above mentioned C sources and microbial byproducts, including poly- and monosaccharides, lignin, amino compounds, organic acids, nucleic acids, lipids, and phenols. Each of these compounds is accounted for by one or more representative species in the model. A reaction network was developed to describe the microbially-mediated processes and chemical interactions of these species, including depolymerization, microbial assimilation, respiration and deposition of byproducts, and incorporation of dead biomass into SOM stocks. Enzymatic reactions are characterized by Michaelis-Menten kinetics, with maximum reaction rates determined by the species' O/C ratio. Microbial activity is further regulated by soil moisture content, O2 availability, pH, and temperature. For the initial set of simulations, literature values were used to constrain microbial Monod parameters, Michaelis-Menten parameters, sorption parameters, physical protection, partitioning of microbial byproducts, and partitioning of litter inputs, although there is

Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance.

Science.gov (United States)

Kuzyakov, Yakov; Xu, Xingliang

2013-05-01

Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 (15)N-labelling studies that investigated (15)N redistribution between roots and microorganisms. Calculated Michaelis-Menten kinetics based on K(m) (Michaelis constant) and V(max) (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower K(m) values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (V(max)) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Analytical solutions of the Dirac equation under Hellmann–Frost–Musulin potential

International Nuclear Information System (INIS)

Onate, C.A.; Onyeaju, M.C.; Ikot, A.N.

2016-01-01

The approximate analytical solutions of the Dirac equation with Hellmann–Frost–Musulin potential have been studied by using the generalized parametric Nikiforov–Uvarov (NU) method for arbitrary spin–orbit quantum number k under the spin and pseudospin symmetries. The Hellmann–Frost–Musulin potential is a superposition potential that consists of Yukawa potential, Coulomb potential, and Frost–Musulin potential. As a particular case, we found the energy levels of the non-relativistic limit of the spin symmetry. The energy equation of Yukawa potential, Coulomb potential, Hellmann potential and Frost–Musulin potential are obtained. Energy values are generated for some diatomic molecules.

Analytical solutions of the Dirac equation under Hellmann–Frost–Musulin potential

Energy Technology Data Exchange (ETDEWEB)

Onate, C.A., E-mail: oaclems14@physicist.net [Physics Department, University of Benin (Nigeria); Onyeaju, M.C.; Ikot, A.N. [Theoretical Physics Group, Physics Department, University of Port Harcourt (Nigeria)

2016-12-15

The approximate analytical solutions of the Dirac equation with Hellmann–Frost–Musulin potential have been studied by using the generalized parametric Nikiforov–Uvarov (NU) method for arbitrary spin–orbit quantum number k under the spin and pseudospin symmetries. The Hellmann–Frost–Musulin potential is a superposition potential that consists of Yukawa potential, Coulomb potential, and Frost–Musulin potential. As a particular case, we found the energy levels of the non-relativistic limit of the spin symmetry. The energy equation of Yukawa potential, Coulomb potential, Hellmann potential and Frost–Musulin potential are obtained. Energy values are generated for some diatomic molecules.

Michaël Oustinoff et Christine Raguet-Bouvard, eds. Contraintes syntaxiques et liberté stylistique : le déplacement dans les éléments de la phrase. Palimpsestes n° 14.

Directory of Open Access Journals (Sweden)

Monique DeMattia

2006-04-01

Full Text Available Le numéro 14 de la revue Palimpsestes, comprend sept articles de recherche, suivis d’une table ronde contenant six interventions, ainsi que quelques extraits de débats. Michaël Oustinoff signe l’avant-propos de ce numéro, ainsi que la présentation de la table ronde.Ce volume se propose d’approfondir notre connaissance de ce domaine si vaste et complexe qu’est la traduction. Il aborde les difficultés rencontrées par tout traducteur, qui se doit de naviguer entre deux écueils majeurs, pour repr...

Continuous analog of Newton's method for determination of quasistationary solutions of the Schroedinger equation

International Nuclear Information System (INIS)

Ponomarev, L.I.; Puzynin, I.V.; Puzynina, T.P.

1975-01-01

The paper is a part of further development of investigations in which a numerical solution method of the Schroedinger equation for the case of a discrete spectrum has been developed and applied. The suggested algorithm (CAMEN scheme) is generalized and applied to quasistationary solutions of the Schroedinger equation system. Some specific features of the CAMEN scheme realization (such as establishing boundary conditions are observed while calculating quasistationary levels of hydrogen mesic molecules. The calculations have been carried out for energies and wave functions of quasistationary states of hydrogen mesic molecules. The choice of the initial approximation, the accuracy of calculations and characteristics of the convergence of the method have been investigated. The CAMEN algorithm has been realized in the form of the FORTRAN program packet. The CAMEN scheme can be also used for solving scatering problems

Introducing a Simple Equation to Express Oxidation States as an Alternative to Using Rules Associated with Words Alone

Science.gov (United States)

Minkiewicz, Piotr; Darewicz, Malgorzata; Iwaniak, Anna

2018-01-01

A simple equation to calculate the oxidation states (oxidation numbers) of individual atoms in molecules and ions may be introduced instead of rules associated with words alone. The equation includes two of three categories of bonds, classified as proposed by Goodstein: number of bonds with more electronegative atoms and number of bonds with less…

General formulation of the variational cellular method for molecules and crystals

International Nuclear Information System (INIS)

Ferreira, L.G.; Leite, J.R.

A variational form of the cellular method is proposed as a new model to solve the one-electron Schroedinger equation for molecules and crystals. The model keeps the good features of the traditional cellular method, as the arbitrary partition of space, and eliminates its main drawback, the slow convergency of the cellular expansion series. With the aid of a criterion of precision on the trial wave functions, we discuss the possibilities offered by the method for more accurate calculations of the electronic structures of molecules and solids. As an example of the accuracy and fast convergency of the model, computation of the energy spectrum of the hydrogen molecular ion H 2 + is presented

Effect of the moment of inertia of an electron shell on the rotational g factor of a molecule

International Nuclear Information System (INIS)

Rebane, T.K.

1988-01-01

It is noted that electron currents induced by the rotation of a molecule make a contribution not only to the magnetic moment, but also to the angular momentum of a molecule and to its moment of inertia. An improved equation for the rotational g factor of a molecule, allowing for the contribution of electrons to the moment of inertia, is given. The B 1 summation + /sub u/ excited electronic state of the hydrogen molecule is used as an example to show that the electronic contribution to the moment of inertia amounts to 0.3 to 0.5% (for H 2 and D 2 molecules, respectively) of the value of the nuclear contribution, and its consideration in calculations of g factors is obligatory

Magnetic field modification of ultracold molecule-molecule collisions

International Nuclear Information System (INIS)

Tscherbul, T V; Suleimanov, Yu V; Aquilanti, V; Krems, R V

2009-01-01

We present an accurate quantum mechanical study of molecule-molecule collisions in the presence of a magnetic field. The work focuses on the analysis of elastic scattering and spin relaxation in collisions of O 2 ( 3 Σ g - ) molecules at cold (∼0.1 K) and ultracold (∼10 -6 K) temperatures. Our calculations show that magnetic spin relaxation in molecule-molecule collisions is extremely efficient except at magnetic fields below 1 mT. The rate constant for spin relaxation at T=0.1 K and a magnetic field of 0.1 T is found to be as large as 6.1x10 -11 cm -3 s -1 . The magnetic field dependence of elastic and inelastic scattering cross sections at ultracold temperatures is dominated by a manifold of Feshbach resonances with the density of ∼100 resonances per Tesla for collisions of molecules in the absolute ground state. This suggests that the scattering length of ultracold molecules in the absolute ground state can be effectively tuned in a very wide range of magnetic fields. Our calculations demonstrate that the number and properties of the magnetic Feshbach resonances are dramatically different for molecules in the absolute ground and excited spin states. The density of Feshbach resonances for molecule-molecule scattering in the low-field-seeking Zeeman state is reduced by a factor of 10.

Differential Equations Compatible with KZ Equations

International Nuclear Information System (INIS)

Felder, G.; Markov, Y.; Tarasov, V.; Varchenko, A.

2000-01-01

We define a system of 'dynamical' differential equations compatible with the KZ differential equations. The KZ differential equations are associated to a complex simple Lie algebra g. These are equations on a function of n complex variables z i taking values in the tensor product of n finite dimensional g-modules. The KZ equations depend on the 'dual' variable in the Cartan subalgebra of g. The dynamical differential equations are differential equations with respect to the dual variable. We prove that the standard hypergeometric solutions of the KZ equations also satisfy the dynamical equations. As an application we give a new determinant formula for the coordinates of a basis of hypergeometric solutions

About of the quantum theory of the molecules

International Nuclear Information System (INIS)

Born M; Oppenheimer, R

1998-01-01

It is shown that the parts of molecular spectral terms corresponding to electronic motion, nuclear rotational and nuclear vibration energies mar be obtained systematically as members of a power series development on the fourth root of the ratio between the electron mass and the average nuclear mass. Such procedure leads to rotational equations, which represent a generalization of the Kramers and Pauli hypotheses (about a top with intrinsic angular momentum). Furthermore, justifications of the Franck and Condon considerations about the band intensities are given. This is shown for diatomic molecules

Continuum simulations of water flow past fullerene molecules

DEFF Research Database (Denmark)

Popadic, A.; Praprotnik, M.; Koumoutsakos, P.

2015-01-01

We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow...

An exactly solvable model for multiphoton excitation of polyatomic molecules in the presence of collisions

International Nuclear Information System (INIS)

Strekalov, M L

2013-01-01

A theoretical study has been made on the non-stationary phenomena in the relaxation of highly vibrationally excited molecules under laser radiation giving rise to these molecules. An exact analytical solution to the master equation has been obtained in terms of Meixner polynomials with regard to VV and VT processes. The time-dependent vibrational distribution is used to obtain analytical expressions for the mean number of photons, stored on the vibrational degrees of freedom and transferred to a thermal bath. Using the latter result, an explicit expression is given for the average energy transfer as a function of time. Its dependence on the partial pressure of absorbing molecules has also been established. (paper)

Molecules in strong laser fields. In depth study of H2 molecule

International Nuclear Information System (INIS)

Awasthi, Manohar

2009-01-01

A method for solving the time-dependent Schroedinger equation (TDSE) describing the electronic motion of the molecules exposed to very short intense laser pulses has been developed. The time-dependent electronic wavefunction is expanded in terms of a superposition of field-free eigenstates. The field-free eigenstates are calculated in two ways. In the first approach, which is applicable to two electron systems like H 2 , fully correlated field-free eigenstates are obtained in complete dimensionality using configuration-interaction calculation where the one-electron basis functions are built from B splines. In the second approach, which is even applicable to larger molecules, the field-free eigenstates are calculated within the single-active-electron (SAE) approximation using density functional theory. In general, the method can be divided into two parts, in the first part the field-free eigenstates are calculated and then in the second part a time propagation for the laser pulse parameters is performed. The H 2 molecule is the testing ground for the implementation of both the methods. The reliability of the configuration interaction (CI) based method for the solution of TDSE (CI-TDSE) is tested by comparing results in the low-intensity regime to the prediction of lowest-order perturbation theory. Another test for the CI-TDSE method is in the united atom limit for the H 2 molecule. By selecting a very small value of the internuclear distance close to zero for the H 2 molecule, Helium atom is obtained. Once the functionality and the reliability of the method is established, it is used for obtaining accurate results for molecular hydrogen exposed to intense laser fields. The results for the standard 800 nm Titanium-Sapphire laser and its harmonics at 400 nm and 266 nm are shown. The results for a scan over a wide range of incident photon energies as well as dependence on the internuclear distance are presented. The photoelectron spectra including above

Theoretical aspects of electron transfer reactions of complex molecules

DEFF Research Database (Denmark)

Kuznetsov, A. M.; Ulstrup, Jens

2001-01-01

Features of electron transfer involving complex molecules are discussed. This notion presently refers to molecular reactants where charge transfer is accompanied by large molecular reorganization, and commonly used displaced harmonic oscillator models do not apply. It is shown that comprehensive...... theory of charge transfer in polar media offers convenient tools for the treatment of experimental data for such systems, with due account of large-amplitude strongly anharmonic intramolecular reorganization. Equations for the activation barrier and free energy relationships are provided, incorporating...

Alignment of symmetric top molecules by short laser pulses

DEFF Research Database (Denmark)

Hamilton, Edward; Seideman, Tamar; Ejdrup, Tine

2005-01-01

-resolved photofragment imaging. Using methyliodide and tert-butyliodide as examples, we calculate and measure the alignment dynamics, focusing on the temporal structure and intensity of the revival patterns, including their dependence on the pulse duration, and their behavior at long times, where centrifugal distortion......Nonadiabatic alignment of symmetric top molecules induced by a linearly polarized, moderately intense picosecond laser pulse is studied theoretically and experimentally. Our studies are based on the combination of a nonperturbative solution of the Schrodinger equation with femtosecond time...

Current-induced magnetic switching of a single molecule magnet on a spin valve

International Nuclear Information System (INIS)

Zhang, Xiao; Wang, Zheng-Chuan; Zheng, Qing-Rong; Zhu, Zheng-Gang; Su, Gang

2015-01-01

The current-induced magnetic switching of a single-molecule magnet (SMM) attached on the central region of a spin valve is explored, and the condition for the switching current is derived. Electrons flowing through the spin valve will interact with the SMM via the s–d exchange interaction, producing the spin accumulation that satisfies the spin diffusion equation. We further describe the spin motion of the SMM by a Heisenberg-like equation. Based on the linear stability analysis, we obtain the critical current from two coupled equations. The results of the critical current versus the external magnetic field indicate that one can manipulate the magnetic state of the SMM by an external magnetic field. - Highlights: • We theoretically study the current-induced magnetic switching of the SMM. • We describe the spin motion of the SMM by a Heisenberg-like equation. • We describe the spin accumulation by the spin diffusion equation. • We obtain the critical current by the linear stability analysis. • Our approach can be easily extended to other SMMs

Current-induced magnetic switching of a single molecule magnet on a spin valve

Energy Technology Data Exchange (ETDEWEB)

Zhang, Xiao [Theoretical Condensed Matter Physics and Computational Materials Physics Laboratory, School of Physics, University of Chinese Academy of Sciences, Beijing 100049 (China); Wang, Zheng-Chuan, E-mail: wangzc@ucas.ac.cn [Theoretical Condensed Matter Physics and Computational Materials Physics Laboratory, School of Physics, University of Chinese Academy of Sciences, Beijing 100049 (China); Zheng, Qing-Rong [Theoretical Condensed Matter Physics and Computational Materials Physics Laboratory, School of Physics, University of Chinese Academy of Sciences, Beijing 100049 (China); Zhu, Zheng-Gang [Theoretical Condensed Matter Physics and Computational Materials Physics Laboratory, School of Physics, University of Chinese Academy of Sciences, Beijing 100049 (China); School of Electronics, Electric and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049 (China); Su, Gang, E-mail: gsu@ucas.ac.cn [Theoretical Condensed Matter Physics and Computational Materials Physics Laboratory, School of Physics, University of Chinese Academy of Sciences, Beijing 100049 (China)

2015-04-17

The current-induced magnetic switching of a single-molecule magnet (SMM) attached on the central region of a spin valve is explored, and the condition for the switching current is derived. Electrons flowing through the spin valve will interact with the SMM via the s–d exchange interaction, producing the spin accumulation that satisfies the spin diffusion equation. We further describe the spin motion of the SMM by a Heisenberg-like equation. Based on the linear stability analysis, we obtain the critical current from two coupled equations. The results of the critical current versus the external magnetic field indicate that one can manipulate the magnetic state of the SMM by an external magnetic field. - Highlights: • We theoretically study the current-induced magnetic switching of the SMM. • We describe the spin motion of the SMM by a Heisenberg-like equation. • We describe the spin accumulation by the spin diffusion equation. • We obtain the critical current by the linear stability analysis. • Our approach can be easily extended to other SMMs.

Detecting high-density ultracold molecules using atom–molecule collision

International Nuclear Information System (INIS)

Chen, Jun-Ren; Kao, Cheng-Yang; Chen, Hung-Bin; Liu, Yi-Wei

2013-01-01

Utilizing single-photon photoassociation, we have achieved ultracold rubidium molecules with a high number density that provides a new efficient approach toward molecular quantum degeneracy. A new detection mechanism for ultracold molecules utilizing inelastic atom–molecule collision is demonstrated. The resonant coupling effect on the formation of the X 1 Σ + g ground state 85 Rb 2 allows for a sufficient number of more deeply bound ultracold molecules, which induced an additional trap loss and heating of the co-existing atoms owing to the inelastic atom–molecule collision. Therefore, after the photoassociation process, the ultracold molecules can be investigated using the absorption image of the ultracold rubidium atoms mixed with the molecules in a crossed optical dipole trap. The existence of the ultracold molecules was then verified, and the amount of accumulated molecules was measured. This method detects the final produced ultracold molecules, and hence is distinct from the conventional trap loss experiment, which is used to study the association resonance. It is composed of measurements of the time evolution of an atomic cloud and a decay model, by which the number density of the ultracold 85 Rb 2 molecules in the optical trap was estimated to be >5.2 × 10 11 cm −3 . (paper)

Time-dependent local-to-normal mode transition in triatomic molecules

Science.gov (United States)

Cruz, Hans; Bermúdez-Montaña, Marisol; Lemus, Renato

2018-01-01

Time-evolution of the vibrational states of two interacting harmonic oscillators in the local mode scheme is presented. A local-to-normal mode transition (LNT) is identified and studied from temporal perspective through time-dependent frequencies of the oscillators. The LNT is established as a polyad-breaking phenomenon from the local standpoint for the stretching degrees of freedom in a triatomic molecule. This study is carried out in the algebraic representation of bosonic operators. The dynamics of the states are determined via the solutions of the corresponding nonlinear Ermakov equation and a local time-dependent polyad is obtained as a tool to identify the LNT. Applications of this formalism to H2O, CO2, O3 and NO2 molecules in the adiabatic, sudden and linear regime are considered.

How energetic and environmental constraints of microorganisms determine the carbon turnover in soils

Science.gov (United States)

Don, A.; Rödenbeck, C.; Gleixner, G.

2012-04-01

Microorganisms are the main catalysts driving carbon fluxes from soils. Traditional concepts of soil carbon stabilization failed to account for environmental and energy constraints of microorganisms. The distribution and density of organic carbon in the soil profile maybe a key factor determining the carbon stability and carbon flux. Decomposition is a two-step process following the Michaelis Menten kinetics: In a first step enzyme and substrate form a joint complex and then the decomposition reaction is catalyzed. Thus, biological decomposition relies on the encounter of substrate and the degradation catalyst, the microorganisms. Lower substrate concentration decreases the likelihood of an enzyme to hit a substrate molecule, to form an enzyme-substrate complex, and thus to catalyze the reaction. However, it was unproofen if this concept can be appliued to soils also. A long-term lab experiment revealed that the soil carbon turnover decreased with increasing carbon dilution due to mixture with soil minerals. The ability of microorganisms to move towards substrate in soils seems to be limited. To elucidate the effect of concentration-controlled carbon turnover, we devised the simple simulation model SCAMP based on the two-step kinetic with microorganism and carbon particles been simulated explicitly. The SCAMP model was able to simulate soil carbon profiles and age profiles in a realistic manner. The only carbon stabilization mechanism implemented in the model is the distribution of microorganisms and carbon particles in the soil and thus the availability of carbon for microorganism, which is especially important for subsoil carbon dynamics. The experiments and the model help to explain why large fractions of soil carbon have been stabilized for millennia and decoupled from the global carbon cycle.

Equation-of-motion coupled cluster method for high spin double electron attachment calculations

Energy Technology Data Exchange (ETDEWEB)

Musiał, Monika, E-mail: musial@ich.us.edu.pl; Lupa, Łukasz; Kucharski, Stanisław A. [Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice (Poland)

2014-03-21

The new formulation of the equation-of-motion (EOM) coupled cluster (CC) approach applicable to the calculations of the double electron attachment (DEA) states for the high spin components is proposed. The new EOM equations are derived for the high spin triplet and quintet states. In both cases the new equations are easier to solve but the substantial simplification is observed in the case of quintets. Out of 21 diagrammatic terms contributing to the standard DEA-EOM-CCSDT equations for the R{sub 2} and R{sub 3} amplitudes only four terms survive contributing to the R{sub 3} part. The implemented method has been applied to the calculations of the excited states (singlets, triplets, and quintets) energies of the carbon and silicon atoms and potential energy curves for selected states of the Na{sub 2} (triplets) and B{sub 2} (quintets) molecules.

Electronic excitation of atoms and molecules by electron impact in a linear algebraic, separable potential approach

International Nuclear Information System (INIS)

Collins, L.A.; Schneider, B.I.

1984-01-01

The linear algebraic, separable potential approach is applied to the electronic excitation of atoms and molecules by electron impact. By representing the exchange and off-diagonal direct terms on a basis, the standard set of coupled inelastic equations is reduced to a set of elastic inhomogeneous equations. The procedure greatly simplifies the formulation by allowing a large portion of the problem to be handled by standard bound-state techniques and by greatly reducing the order of the scattering equations that must be solved. Application is made to the excitation of atomic hydrogen in the three-state close-coupling (1s, 2s, 2p) approximation. (author)

Electron collision cross sections and electron swarm parameters for gas molecules

International Nuclear Information System (INIS)

Hayashi, Makoto

1986-01-01

Elastic and inelastic electron collision cross sections for molecules which interest in radiation research have been determined from available electron beam and electron swarm data by utilizing the Boltzmann equation and Monte Carlo simulation method. Electron drift velocity data which interest in radiation Pysics have been discussed and some calculated results of electron drift velocity data for CF 4 and CF 4 -inert gases mixtures will be presented. (author)

Introducing time-dependent molecular fields: a new derivation of the wave equations

Science.gov (United States)

Baer, Michael

2018-02-01

This article is part of a series of articles trying to establish the concept molecular field. The theory that induced us to introduce this novel concept is based on the Born-Huang expansion as applied to the Schroedinger equation that describes the interaction of a molecular system with an external electric field. Assuming the molecular system is made up of two coupled adiabatic states the theory leads from a single spatial curl equation, two space-time curl equations and one single space-time divergent equation to a pair of decoupled wave equations usually encountered within the theory of fields. In the present study, just like in the previous study [see Baer et al., Mol. Phys. 114, 227 (2016)] the wave equations are derived for an electric field having two features: (a) its intensity is high enough; (b) its duration is short enough. Although not all the findings are new the derivation, in the present case, is new, straightforward, fluent and much friendlier as compared to the previous one and therefore should be presented again. For this situation the study reveals that the just described interaction creates two fields that coexist within a molecule: one is a novel vectorial field formed via the interaction of the electric field with the Born-Huang non-adiabatic coupling terms (NACTs) and the other is an ordinary, scalar, electric field essentially identical to the original electric field. Section 4 devoted to the visualization of the outcomes via two intersecting Jahn-Teller cones which contain NACTs that become singular at the intersection point of these cones. Finally, the fact that eventually we are facing a kind of a cosmic situation may bring us to speculate that singular NACTs are a result of cosmic phenomena. Thus, if indeed this singularity is somehow connected to reality then, like other singularities in physics, it is formed at (or immediately after) the Big Bang and consequently, guarantees the formation of molecules.

Production and spectroscopy of ultracold YbRb{sup *} molecules

Energy Technology Data Exchange (ETDEWEB)

Nemitz, Nils

2008-11-15

This thesis describes the formation of electronically excited but translationally cold molecules formed from rubidium atoms and two isotopes of ytterbium ({sup 176}Yb and {sup 174}Yb) by means of photoassociation. The experiments were performed in a combined MOT with 10{sup 9} rubidium atoms and 2.10{sup 6} ytterbium atoms at temperatures of less than 1 mK. Photoassociation lines were found by trap loss spectroscopy throughout a wavelength range of 2 nm near the 795 nm D1 transition in rubidium. The majority of lines belong to two vibrational series in the excited YbRb{sup *} molecule, converging on a system of a ground state ytterbium atom and an excited rubidium atom. The strong variation of line strength between different vibrational lines is explained through the Franck-Condon principle. An improved version of the Leroy-Bernstein equation was used to extract the leading dispersion coefficient of the potential from the vibrational progression. Most of the observed lines show a resolved rotational structure as expected from a basic quantum mechanical model. The series terminates with the third or forth rotational component due to the ground state centrifugal barrier.The measured rotational constants agree very well with calculations based on the C{sub 6} coefficient. The discovery of a splitting of the rotational components into subcomponents indicates an uncommon angular momentum coupling described by Hund's case. Variations in the depth of the subcomponents indicates a similar splitting in the ground state, with the energies of the substates based on the alignment of the rubidium atom's magnetic dipole moment relative to the angular momentum carried by an approaching ytterbium atom. This creates an additional ground state barrier, partially suppressing some of the subcomponents. Using a rate equation model developed for this purpose, a maximum formation rate of 2.5.10{sup 6} molecules per second was calculated over the volume of the entire trap. The

Free molecule flow analysis of the interaction of skimming hardware components and background gas with free jets

International Nuclear Information System (INIS)

Raghuraman, P.; Bossel, U.

1974-01-01

Under conditions typical for the extraction of nozzle beams from free jets the rarefied flow pattern in the expansion chamber containing skimming hardware components and background gas is studied using a free molecule solution to the Boltzmann equation

Molecular Beam Chemistry: Reactions of Oxygen Atoms with Halogen Molecules.

Science.gov (United States)

1982-10-15

nonlinear one has s = 3, r = 1, and n = 3/2. In the "loose" complex the bending modes go over to free rotation of the product diatomit molecule; thus s...contains no adjustable parameters. All observable properties *l of the reaction may be predicted including product velocity and angular dis- tributions...example, P. R. Bevington, Data Reduction and Error Analysis for the Physical Sciences (McGraw-Hill Book Co., New York, 1969). 65. Equation (3) is strictly

Structures and potential energy functions of Pu3 molecule

International Nuclear Information System (INIS)

Meng Daqiao; Jiang Gang; Liu Xiaoya; Luo Deli; Zhu Zhenghe

2001-01-01

Density functional (B3LYP) method with relativistic effective core potential (RECP) has been used to optimize the structures of Pu 2 and Pu 3 molecules. The results show that the ground states of Pu 2 and Pu 3 molecules are of D ∞h and D 3h symmetry, and of 13 and 19 fold, respectively. The spectral constants of Pu 2 , ω e = 52.3845 cm -1 and ω e x e = 0.0201 cm -1 , and the harmonic frequencies of Pu 3 , ν 1 = 56.9007 cm -1 , ν 2 = 57.1816 cm - '1 and ν 3 = 64.0785 cm -1 , have also been obtained on the B3LYP/RECP level. The potential energy functions of Pu 2 and Pu 3 have been derived, for the first time so far as known, from normal equation fitting and the many-body expansion theory

Adsorption Equilibrium Equation of Carboxylic Acids on Anion-Exchange Resins in Water.

Science.gov (United States)

Kanazawa, Nobuhiro; Urano, Kohei; Kokado, Naohiro; Urushigawa, Yoshikuni

2001-06-01

The adsorption of propionic acid and benzoic acid on anion-exchange resins was analyzed, and an adsorption equilibrium equation of carboxylic acids was proposed. The adsorption of carboxylic acids on the anion-exchange resins was considered to be the sum of the physical adsorption of the molecule and the ion-exchange adsorption of the ion, which were independent of each other. For the physical adsorption of carboxylic acids, it was conformed to the Freundlich equation. For the ion-exchange adsorption of carboxylate ions, the equilibrium equation corresponded well with the experimental results for wide ranges of concentration and pH. The equation contains a selectivity coefficient S(A)(Cl) for the chloride ion versus the carboxylate ion, which was considered essentially a constant. The influent of the bicarbonate ion from carbon dioxide in air could also be expressed by the additional equilibrium equation with the selectivity coefficient S(HCO(3))(Cl) for the chloride ion versus the bicarbonate ion. Consequently, an adsorption equilibrium equation can estimate the equilibrium adsorption amounts. Even the effect of a coexisting bicarbonate ion is inconsequential when the parameters of the Freundlich isotherm equation and the selectivity coefficients of the carboxylate ion and the bicarbonate ion in each resin are determined in advance. Copyright 2001 Academic Press.

Quantum chemical approach for positron annihilation spectra of atoms and molecules beyond plane-wave approximation

Science.gov (United States)

Ikabata, Yasuhiro; Aiba, Risa; Iwanade, Toru; Nishizawa, Hiroaki; Wang, Feng; Nakai, Hiromi

2018-05-01

We report theoretical calculations of positron-electron annihilation spectra of noble gas atoms and small molecules using the nuclear orbital plus molecular orbital method. Instead of a nuclear wavefunction, the positronic wavefunction is obtained as the solution of the coupled Hartree-Fock or Kohn-Sham equation for a positron and the electrons. The molecular field is included in the positronic Fock operator, which allows an appropriate treatment of the positron-molecule repulsion. The present treatment succeeds in reproducing the Doppler shift, i.e., full width at half maximum (FWHM) of experimentally measured annihilation (γ-ray) spectra for molecules with a mean absolute error less than 10%. The numerical results indicate that the interpretation of the FWHM in terms of a specific molecular orbital is not appropriate.

Low-lying qq(qq)-bar states in a relativistic model based on the Bethe-Salpeter equation

International Nuclear Information System (INIS)

Ram, B.; Kriss, V.

1985-01-01

Low-lying qq(qq)-bar states are analysed in a previously given relativistic model based on the Bethe-Salpeter equation. It is not got M-diquonia, P-mesonia, or meson molecules, but it is got T-diquonia

Molecules in strong laser fields. In depth study of H{sub 2} molecule

Energy Technology Data Exchange (ETDEWEB)

Awasthi, Manohar

2009-10-29

A method for solving the time-dependent Schroedinger equation (TDSE) describing the electronic motion of the molecules exposed to very short intense laser pulses has been developed. The time-dependent electronic wavefunction is expanded in terms of a superposition of field-free eigenstates. The field-free eigenstates are calculated in two ways. In the first approach, which is applicable to two electron systems like H{sub 2}, fully correlated field-free eigenstates are obtained in complete dimensionality using configuration-interaction calculation where the one-electron basis functions are built from B splines. In the second approach, which is even applicable to larger molecules, the field-free eigenstates are calculated within the single-active-electron (SAE) approximation using density functional theory. In general, the method can be divided into two parts, in the first part the field-free eigenstates are calculated and then in the second part a time propagation for the laser pulse parameters is performed. The H{sub 2} molecule is the testing ground for the implementation of both the methods. The reliability of the configuration interaction (CI) based method for the solution of TDSE (CI-TDSE) is tested by comparing results in the low-intensity regime to the prediction of lowest-order perturbation theory. Another test for the CI-TDSE method is in the united atom limit for the H{sub 2} molecule. By selecting a very small value of the internuclear distance close to zero for the H{sub 2} molecule, Helium atom is obtained. Once the functionality and the reliability of the method is established, it is used for obtaining accurate results for molecular hydrogen exposed to intense laser fields. The results for the standard 800 nm Titanium-Sapphire laser and its harmonics at 400 nm and 266 nm are shown. The results for a scan over a wide range of incident photon energies as well as dependence on the internuclear distance are presented. The photoelectron spectra including

Some applications of the Faddeev-Yakubovsky equations to the cold-atom physics

International Nuclear Information System (INIS)

Carbonell, J.; Deltuva, A.; Lazauskas, R.

2011-01-01

We present some recent applications of the Faddeev-Yakubovsky equations in describing atomic bound and scattering problems. We consider the scattering of a charged particle X by atomic hydrogen with special interest in X = p,e ± , systems of cold bosonic molecules and the bound and scattering properties of N=3 and N=4 atomic 4 He multimers. (authors)

Effect of membranes on oxygen transfer rate and consumption within a newly developed three-compartment bioartificial liver device: Advanced experimental and theoretical studies.

Science.gov (United States)

Hilal-Alnaqbi, Ali; Mourad, Abdel-Hamid I; Yousef, Basem F

2014-01-01

A mathematical model is developed to predict oxygen transfer in the fiber-in-fiber (FIF) bioartificial liver device. The model parameters are taken from the constructed and tested FIF modules. We extended the Krogh cylinder model by including one more zone for oxygen transfer. Cellular oxygen uptake was based on Michaelis-Menten kinetics. The effect of varying a number of important model parameters is investigated, including (1) oxygen partial pressure at the inlet, (2) the hydraulic permeability of compartment B (cell region), (3) the hydraulic permeability of the inner membrane, and (4) the oxygen diffusivity of the outer membrane. The mathematical model is validated by comparing its output against the experimentally acquired values of an oxygen transfer rate and the hydrostatic pressure drop. Three governing simultaneous linear differential equations are derived to predict and validate the experimental measurements, e.g., the flow rate and the hydrostatic pressure drop. The model output simulated the experimental measurements to a high degree of accuracy. The model predictions show that the cells in the annulus can be oxygenated well even at high cell density or at a low level of gas phase PG if the value of the oxygen diffusion coefficient Dm is 16 × 10(-5) . The mathematical model also shows that the performance of the FIF improves by increasing the permeability of polypropylene membrane (inner fiber). Moreover, the model predicted that 60% of plasma has access to the cells in the annulus within the first 10% of the FIF bioreactor axial length for a specific polypropylene membrane permeability and can reach 95% within the first 30% of its axial length. © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Nitrate removal in stream ecosystems measured by 15N addition experiments: Denitrification

Science.gov (United States)

Mulholland, P.J.; Hall, R.O.; Sobota, D.J.; Dodds, W.K.; Findlay, S.E.G.; Grimm, N. B.; Hamilton, S.K.; McDowell, W.H.; O'Brien, J. M.; Tank, J.L.; Ashkenas, L.R.; Cooper, L.W.; Dahm, Clifford N.; Gregory, S.V.; Johnson, S.L.; Meyer, J.L.; Peterson, B.J.; Poole, G.C.; Valett, H.M.; Webster, J.R.; Arango, C.P.; Beaulieu, J.J.; Bernot, M.J.; Burgin, A.J.; Crenshaw, C.L.; Helton, A.M.; Johnson, L.T.; Niederlehner, B.R.; Potter, J.D.; Sheibley, R.W.; Thomasn, S.M.

2009-01-01

We measured denitrification rates using a field 15N-NO- 3 tracer-addition approach in a large, cross-site study of nitrate uptake in reference, agricultural, and suburban-urban streams. We measured denitrification rates in 49 of 72 streams studied. Uptake length due to denitrification (SWden) ranged from 89 m to 184 km (median of 9050 m) and there were no significant differences among regions or land-use categories, likely because of the wide range of conditions within each region and land use. N2 production rates far exceeded N2O production rates in all streams. The fraction of total NO-3 removal from water due to denitrification ranged from 0.5% to 100% among streams (median of 16%), and was related to NHz 4 concentration and ecosystem respiration rate (ER). Multivariate approaches showed that the most important factors controlling SWden were specific discharge (discharge / width) and NO-3 concentration (positive effects), and ER and transient storage zones (negative effects). The relationship between areal denitrification rate (Uden) and NO- 3 concentration indicated a partial saturation effect. A power function with an exponent of 0.5 described this relationship better than a Michaelis-Menten equation. Although Uden increased with increasing NO- 3 concentration, the efficiency of NO-3 removal from water via denitrification declined, resulting in a smaller proportion of streamwater NO-3 load removed over a given length of stream. Regional differences in stream denitrification rates were small relative to the proximate factors of NO-3 concentration and ecosystem respiration rate, and land use was an important but indirect control on denitrification in streams, primarily via its effect on NO-3 concentration. ?? 2009.

Vortex molecule in a nanoscopic square superconducting plate

International Nuclear Information System (INIS)

Suematsu, Hisataka; Kato, Masaru; Ishida, Takekazu; Koyama, Tomio; Machida, Masahiko

2010-01-01

Using the finite element method and solving the Bogoliubov-de Gennes equation, we have investigated magnetic field dependence of the stable vortex structures in a mesoscopic superconducting plate at low temperature (T = 0.1T c ). Because of the compactness of vortex configuration, there is interference between bound states around vortices and such quasi-particle structure affects the vortex configuration. Especially in two-vortices state, vortices form a molecule-like state, where bound states of each vortex form molecular orbital like bonding and anti-bonding states. The vortex configuration is different from that, which is expected from the repulsive interaction between vortices. (author)

Equations of State: From the Ideas of van der Waals to Association Theories

DEFF Research Database (Denmark)

Kontogeorgis, Georgios; Economou, Ioannis G.

2010-01-01

equations of state are sensitive to the mixing and combining rules used. Moreover, it is shown that previously reported deficiencies for size-asymmetric systems are more related to the van der Waals one fluid mixing rules used rather than the functionality of the cubic equation of state itself. Improved...... models for polar systems have been developed using the so-called EoS/GE mixing rules and we illustrate with the same methodology how these mixing rules should best be used for size-asymmetric systems. Despite the significant capabilities of cubic equations of state, their limitations lie especially...... in the description of complex phase behavior, e.g. liquid–liquid equilibria for highly polar and/or hydrogen bonding containing molecules. In these cases, advanced equations of state based on statistical mechanics that incorporate ideas from perturbation (e.g. SAFT and CPA), chemical (e.g. APACT) and lattice (e...

Growing interstellar molecules with ion-molecule reactions

International Nuclear Information System (INIS)

Bohme, D.K.

1989-01-01

Laboratory measurements of gas-phase ion-molecule reactions continue to provide important insights into the chemistry of molecular growth in interstellar environments. It is also true that the measurements are becoming more demanding as larger molecules capture our interest. While some of these measurements are motivated by current developments in chemical models of interstellar environments or by new molecular observations by astronomers, others explore novel chemistry which can lead to predictions of new interstellar molecules. Here the author views the results of some recent measurements, taken in the Ion Chemistry Laboratory at York University with the SIFT technique, which address some of the current needs of modellers and observers and which also provide some new fundamental insight into molecular growth, particularly when it occurs in the presence of large molecules such as PAH molecules which are now thought to have a major influence on the chemistry of interstellar environments in which they are present

Stoichiometry and kinetics of single and mixed substrate uptake in Aspergillus niger.

Science.gov (United States)

Lameiras, Francisca; Ras, Cor; Ten Pierick, Angela; Heijnen, Joseph J; van Gulik, Walter M

2018-02-01

In its natural environment, the filamentous fungus Aspergillus niger grows on decaying fruits and plant material, thereby enzymatically degrading the lignocellulosic constituents (lignin, cellulose, hemicellulose, and pectin) into a mixture of mono- and oligosaccharides. To investigate the kinetics and stoichiometry of growth of this fungus on lignocellulosic sugars, we carried out batch cultivations on six representative monosaccharides (glucose, xylose, mannose, rhamnose, arabinose, and galacturonic acid) and a mixture of these. Growth on these substrates was characterized in terms of biomass yields, oxygen/biomass ratios, and specific conversion rates. Interestingly, in combination, some of the carbon sources were consumed simultaneously and some sequentially. With a previously developed protocol, a sequential chemostat cultivation experiment was performed on a feed mixture of the six substrates. We found that the uptake of glucose, xylose, and mannose could be described with a Michaelis-Menten-type kinetics; however, these carbon sources seem to be competing for the same transport systems, while the uptake of arabinose, galacturonic acid, and rhamnose appeared to be repressed by the presence of other substrates.

ISOLASI DAN KARAKTERISASI BAKTERI DENITRIFIKASI SEBAGAI AGEN BIOREMEDIASI NITROGEN ANORGANIK

Directory of Open Access Journals (Sweden)

Khairul Syahputra

2011-08-01

Full Text Available Denitrifikasi merupakan salah satu proses utama yang mengurangi kandungan senyawa nitrogen anorganik di lingkungan. Proses ini dapat digunakan untuk mengatasi kelebihan senyawa nitrogen anorganik yang tinggi di kolam budidaya perikanan. Penelitian ini bertujuan untuk mengisolasi dan mengkarakterisasi isolat bakteri denitrifikasi sebagai agen bioremediasi senyawa nitrogen anorganik. Sebanyak 21 isolat bakteri pereduksi nitrat berhasil diisolasi dari medium pengkayaan dengan konsentrasi nitrat 100 µM dan 1500 µM. Sebanyak 6 isolat merupakan kelompok bakteri denitrifikasi (fermentatif negatif dan 15 isolat termasuk kelompok bakteri fermentatif. Berdasarkan hasil seleksi didapatkan isolat HNF5 dan LNF mempunyai kemampuan reduksi nitrat yang tinggi. Aktivitas reduksi nitrat terjadi dari awal inkubasi, di mana aktivitas paling cepat terjadi pada fase eksponensial pertumbuhan bakteri. Isolat HNF5 dan LNF memiliki kecepatan maksimum reduksi nitrat (Vmaks 0,17 mM.h-1 dan 0,16 mM.h-1 dengan nilai konstanta Michaelis-Menten (Km 0,40 mM dan 0,28 mM. Identifikasi dengan sekuen 16S-rRNA memperlihatkan bahwa isolat HNF5 dan LNF mempunyai kemiripan dengan Pseudomonas aeruginosa.

The effect of increased caffeine intake on the metabolism and pharmacokinetics of theophylline in man.

Science.gov (United States)

Monks, T J; Lawrie, C A; Caldwell, J

1981-01-01

The metabolism and pharmacokinetics of intravenously administered theophylline (100 mg) have been investigated in three healthy male volunteers who consumed 6 bottles/day of a cola beverage, in addition to their usual intake of methylxanthines, for 7 days prior to and during the study. Five urinary metabolites were detected in addition to unchanged theophylline, that is 3-methylxanthine, 1,3-dimethyluric acid, 1-methyluric acid, and two minor unknown metabolites. The elimination of theophylline, 1,3-dimethyluric acid, 1-methyluric acid, and the two unknowns was described by first-order kinetics, whereas that of 3-methylxanthine was described by Michaelis-Menten kinetics. The results have been compared with those previously obtained in the same volunteers while consuming their usual intake of methylxanthine-containing foods and beverages, and this shows that the addition of extra methylxanthines to the diet does not influence the disposition of theophylline. This is in marked contrast to the effect of deprivation of dietary methylxanthines on theophylline metabolism. The results are discussed in terms of the influence of methylxanthines on theophylline metabolism, and of its possible dose-dependency.

Electrochemical Quantification of the Antioxidant Capacity of Medicinal Plants Using Biosensors

Directory of Open Access Journals (Sweden)

Erika Rodríguez-Sevilla

2014-08-01

Full Text Available The working area of a screen-printed electrode, SPE, was modified with the enzyme tyrosinase (Tyr using different immobilization methods, namely entrapment with water-soluble polyvinyl alcohol (PVA, cross-linking using glutaraldehyde (GA, and cross-linking using GA and human serum albumin (HSA; the resulting electrodes were termed SPE/Tyr/PVA, SPE/Tyr/GA and SPE/Tyr/HSA/GA, respectively. These biosensors were characterized by means of amperometry and EIS techniques. From amperometric evaluations, the apparent Michaelis-Menten constant, Km′, of each biosensor was evaluated while the respective charge transfer resistance, Rct, was assessed from impedance measurements. It was found that the SPE/Tyr/GA had the smallest Km′ (57 ± 7 µM and Rct values. This electrode also displayed both the lowest detection and quantification limits for catechol quantification. Using the SPE/Tyr/GA, the Trolox Equivalent Antioxidant Capacity (TEAC was determined from infusions prepared with “mirto” (Salvia microphylla, “hHierba dulce” (Lippia dulcis and “salve real” (Lippia alba, medicinal plants commonly used in Mexico.

Electrochemical Quantification of the Antioxidant Capacity of Medicinal Plants Using Biosensors

Science.gov (United States)

Rodríguez-Sevilla, Erika; Ramírez-Silva, María-Teresa; Romero-Romo, Mario; Ibarra-Escutia, Pedro; Palomar-Pardavé, Manuel

2014-01-01

The working area of a screen-printed electrode, SPE, was modified with the enzyme tyrosinase (Tyr) using different immobilization methods, namely entrapment with water-soluble polyvinyl alcohol (PVA), cross-linking using glutaraldehyde (GA), and cross-linking using GA and human serum albumin (HSA); the resulting electrodes were termed SPE/Tyr/PVA, SPE/Tyr/GA and SPE/Tyr/HSA/GA, respectively. These biosensors were characterized by means of amperometry and EIS techniques. From amperometric evaluations, the apparent Michaelis-Menten constant, Km′, of each biosensor was evaluated while the respective charge transfer resistance, Rct, was assessed from impedance measurements. It was found that the SPE/Tyr/GA had the smallest Km′ (57 ± 7) μM and Rct values. This electrode also displayed both the lowest detection and quantification limits for catechol quantification. Using the SPE/Tyr/GA, the Trolox Equivalent Antioxidant Capacity (TEAC) was determined from infusions prepared with “mirto” (Salvia microphylla), “hHierba dulce” (Lippia dulcis) and “salve real” (Lippia alba), medicinal plants commonly used in Mexico. PMID:25111237

Permeability, transport, and metabolism of solutes in Caco-2 cell monolayers: a theoretical study.

Science.gov (United States)

Sun, Huadong; Pang, K Sandy

2008-01-01

We explored the properties of a catenary model that includes the basolateral (B), apical (A), and cellular compartments via simulations under linear and nonlinear conditions to understand the asymmetric observations arising from transporters, enzymes, and permeability in Caco-2 cells. The efflux ratio (EfR; P(app,B-->A)/P(app,A-->B)), obtained from the effective permeability from the A-->B and B-->A direction under linear conditions, was unity for passively permeable drugs whose transport does not involve transporters; the value was unaffected by cellular binding or metabolism, but increased with apical efflux. Metabolism was asymmetric, showing lesser metabolite accrual for the B-->A than A-->B direction because of inherent differences in the volumes for A and B. Moreover, the net flux (total - passive permeation) due to saturable apical efflux, absorption, or metabolism showed nonconformity to simple Michaelis-Menten kinetics against C(D,0), the loading donor concentration. EfR values differed with saturable apical efflux and metabolism (>1), as well as apical absorption (EfRs transport and metabolic data in Caco-2 cells.

Lipase from liver of seabass (Lates calcarifer): Characteristics and the use for defatting of fish skin.

Science.gov (United States)

Sae-Leaw, Thanasak; Benjakul, Soottawat

2018-02-01

Lipase from liver of seabass (Lates calcarifer), with a molecular weight of 60kDa, was purified to homogeneity using ammonium sulfate precipitation and a series of chromatographies, including diethylaminoethyl sepharose (DEAE) and Sephadex G-75 size exclusion columns. The optimal pH and temperature were 8.0 and 50°C, respectively. Purified lipase had Michaelis-Menten constant (K m ) and catalytic constant (k cat ) of 0.30mM and 2.16s -1 , respectively, when p-nitrophenyl palmitate (p-NPP) was used as the substrate. When seabass skin was treated with crude lipase from seabass liver at various levels (0.15 and 0.30units/g dry skin) for 1-3h at 30°C, the skin treated with lipase at 0.30 units/g dry skin for 3h had the highest lipid removal (84.57%) with lower lipid distribution in skin. Efficacy in defatting was higher than when isopropanol was used. Thus, lipase from liver of seabass could be used to remove fat in fish skin. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nitrile hydratase of Rhodococcus erythropolis: characterization of the enzyme and the use of whole cells for biotransformation of nitriles.

Science.gov (United States)

Kamble, Ashwini L; Banoth, Linga; Meena, Vachan Singh; Singh, Amit; Chisti, Yusuf; Banerjee, U C

2013-08-01

The intracellular cobalt-type nitrile hydratase was purified from the bacterium Rhodococcuserythropolis. The pure enzyme consisted of two subunits of 29 and 30 kDa. The molecular weight of the native enzyme was estimated to be 65 kDa. At 25 °C the enzyme had a half-life of 25 h. The Michaelis-Menten constants K m and v max for the enzyme were 0.624 mM and 5.12 μmol/min/mg, respectively, using 3-cyanopyridine as the substrate. The enzyme-containing freely-suspended bacterial cells and the cells immobilized within alginate beads were evaluated for converting the various nitriles to amides. In a packed bed reactor, alginate beads (2 % alginate; 3 mm bead diameter) containing 200 mg/mL of cells, achieved a conversion of >90 % for benzonitrile and 4-cyanopyridine in 38 h (25 °C, pH 7.0) at a feed substrate concentration of 100 mM. The beads could be reused for up to six reaction cycles.

HYDROLYSIS OF CHEESEWHEY PROTEINSWITH TRYPSIN, CHYMOTRYPSINAND CARBOXYPEPTIDASEA

Directory of Open Access Journals (Sweden)

M. F. CUSTÓDIO

2009-01-01

Full Text Available

This work presents a method for adding value to cheese whey residues by whey proteins hydrolysis, using trypsin, chymotrypsin and carboxypeptidase A as catalysts. Sweet cheese whey was dialyzed and filtered in kaolin. Lactose and protein contents were analyzed after each step. The activities of bovine pancreas trypsin and chymotrypsin were measured at different pHs and temperatures. The optimal pH for the hydrolysis of whey proteins was 9.0 for both enzymes. Optima temperatures were 60ºC for trypsin, and 50ºC for chymotrypsin. Trypsin exhibited typical Michaelis-Menten behavior, but chymotrypsin did not. Electrophoretic analysis showed that neither trypsin nor chymotrypsin alone hydrolyzed whey proteins in less than three hours. Hydrolysis rates of -lactalbumin by trypsin, and of bovine serum albumin by chymotrypsin were low. When these enzymes were combined, however, all protein fractions were attacked and rates of hydrolysis were enhanced by one order of magnitude. The addition of carboxypeptidase A to the others enzymes did not improve the process yield.

Kinetics and Mechanism of Oxidation of Diethyl Ether by Chloramine-T in Acidic Medium

Directory of Open Access Journals (Sweden)

Y. I. Hassan

2012-01-01

Full Text Available The kinetics of oxidation of diethyl ether (DE with sodium N-chloro-p-toluenesulphonamide (CAT in hydrochloric acid solution has been studied at (313°K.The reaction rate show a first order dependence on [CAT] and fractional order dependence on each [DE] and [H+] .The variation of ionic strength of the medium has no significant effect on the reaction rate , addition of p-toluenesulphonamide (p-TSA affects the reaction rate marginally the rate increased with decreasing dielectric constant of the medium , the stochiometry of the reaction was found to be 1:2 and oxidation products were identified , A Michaelis – Menten type mechanism has been suggested to explain the results.The equilibrium and the decomposition constants of CAT – diethyl ether complex have been evaluated. Thermodynamic parameters were computed by studying reaction at temperatures range ( 308 – 323°K for the rate limiting step and for the observed first order constants by the linear Arrhenius plot. The mechanism proposed and the derived rate law are consistent with observed kinetics.

Study on biofiltration capacity and kinetics of nutrient uptake by Gracilaria cervicornis (Turner J. Agardh (Rhodophyta, Gracilariaceae

Directory of Open Access Journals (Sweden)

Marcella A. A. Carneiro

2011-04-01

Full Text Available The absorption efficiency and kinetic parameters (Vmax, Ks and Vmax:Ks of the seaweed Gracilaria cervicornis for the nutrients NH4+, NO3- and PO4(3- were evaluated. Absorption efficiency was measured by monitoring nutrient concentrations for 5 h in culture media with initial concentrations of 5, 10, 20 and 30µM. Kinetic parameters were determined by using the Michaelis-Menten formula. Absorption efficiencies for this algae were greater in treatments with lower concentrations, as evidenced by a reduction of 85.3, 97.5 and 81.2% for NH4+, NO3- and PO4(3-, respectively. Kinetic parameters show that G. cervicornis exhibits greater ability to take up high concentrations of NH4+ (Vmax=158.5µM g dw-1 h-1 and low concentrations of PO4(3- (Ks=5µM and Vmax:Ks=10.3. These results suggest that this algal species has good absorption capacity for the nutrients tested and may be a promising candidate as a bioremediator of eutrophized environments.

Functional and Structural Characterization of a (+)-Limonene Synthase from Citrus sinensis.

Science.gov (United States)

Morehouse, Benjamin R; Kumar, Ramasamy P; Matos, Jason O; Olsen, Sarah Naomi; Entova, Sonya; Oprian, Daniel D

2017-03-28

Terpenes make up the largest and most diverse class of natural compounds and have important commercial and medical applications. Limonene is a cyclic monoterpene (C 10 ) present in nature as two enantiomers, (+) and (-), which are produced by different enzymes. The mechanism of production of the (-)-enantiomer has been studied in great detail, but to understand how enantiomeric selectivity is achieved in this class of enzymes, it is important to develop a thorough biochemical description of enzymes that generate (+)-limonene, as well. Here we report the first cloning and biochemical characterization of a (+)-limonene synthase from navel orange (Citrus sinensis). The enzyme obeys classical Michaelis-Menten kinetics and produces exclusively the (+)-enantiomer. We have determined the crystal structure of the apoprotein in an "open" conformation at 2.3 Å resolution. Comparison with the structure of (-)-limonene synthase (Mentha spicata), which is representative of a fully closed conformation (Protein Data Bank entry 2ONG ), reveals that the short H-α1 helix moves nearly 5 Å inward upon substrate binding, and a conserved Tyr flips to point its hydroxyl group into the active site.

Recovery of Whey Proteins and Enzymatic Hydrolysis of Lactose Derived from Casein Whey Using a Tangential Flow Ultrafiltration Module

Science.gov (United States)

Das, Bipasha; Bhattacharjee, Sangita; Bhattacharjee, Chiranjib

2013-09-01

In this study, ultrafiltration (UF) of pretreated casein whey was carried out in a cross-flow module fitted with 5 kDa molecular weight cut-off polyethersulfone membrane to recover whey proteins in the retentate and lactose in the permeate. Effects of processing conditions, like transmembrane pressure and pH on permeate flux and rejection were investigated and reported. The polarised layer resistance was found to increase with time during UF even in this high shear device. The lactose concentration in the permeate was measured using dinitro salicylic acid method. Enzymatic kinetic study for lactose hydrolysis was carried out at three different temperatures ranging from 30 to 50 °C using β-galactosidase enzyme. The glucose formed during lactose hydrolysis was analyzed using glucose oxidase-peroxidase method. Kinetics of enzymatic hydrolysis of lactose solution was found to follow Michaelis-Menten model and the model parameters were estimated by Lineweaver-Burk plot. The hydrolysis rate was found to be maximum (with Vmax = 5.5091 mmol/L/min) at 30 °C.

Phenols removal by immobilized tyrosinase reactor in on-line high performance liquid chromatography

Energy Technology Data Exchange (ETDEWEB)

Girelli, Anna Maria [Dipartimento di Chimica, Universita degli Studi di Roma ' La Sapienza' , P.le Aldo Moro 5, 00185 Rome (Italy)]. E-mail: annamaria.girelli@uniroma1.it; Mattei, Enrico [Dipartimento di Chimica, Universita degli Studi di Roma ' La Sapienza' , P.le Aldo Moro 5, 00185 Rome (Italy); Messina, Antonella [Dipartimento di Chimica, Universita degli Studi di Roma ' La Sapienza' , P.le Aldo Moro 5, 00185 Rome (Italy)

2006-11-24

The development of an immobilized enzyme reactor (IMER) based on tyrosinase immobilized on aminopropyl-controlled pore glass (AP-CPG) for the removal of phenols from model aqueous solutions was reported. To elucidate the influence of the substrate nature, the apparent (V{sup '}{sub max}, K{sup '}{sub m}) and the inherent (V{sub max}, K{sub m}) Michaelis-Menten constants were determined by Lineweaver-Burk method and the external diffusional contributions on measured enzyme activities were removed by a graphical method. The dephenolization process was realized by recycling the phenol solutions through the bioreactor connected to a chitosan trap in order to remove the colored quinone-type products of the tyrosinase reactions. The results indicated that a complete removal of phenol derivatives in the range of 150-300min, with the exception of 60% removal for phenol reached in 400min, was obtained. The observed sequence: cresol>4-methylcathecol>catechol>4-Cl-phenol-bar phenol was in accordance to the V{sup '}{sub max}/K{sup '}{sub m} values.

Amperometric bienzyme glucose biosensor based on carbon nanotube modified electrode with electropolymerized poly(toluidine blue O) film

International Nuclear Information System (INIS)

Wang Wenju; Wang Fang; Yao Yanli; Hu Shengshui; Shiu, Kwok-Keung

2010-01-01

The amperometric bienzyme glucose biosensor utilizing horseradish peroxidase (HRP) and glucose oxidase (GOx) immobilized in poly(toluidine blue O) (PTBO) film was constructed on multi-walled carbon nanotube (MWNT) modified glassy carbon electrode. The HRP layer could be used to analyze hydrogen peroxide with toluidine blue O (TBO) mediators, while the bienzyme system (HRP + GOx) could be utilized for glucose determination. Glucose underwent biocatalytic oxidation by GOx in the presence of oxygen to yield H 2 O 2 which was further reduced by HRP at the MWNT-modified electrode with TBO mediators. In the absence of oxygen, glucose oxidation proceeded with electron transfer between GOx and the electrode mediated by TBO moieties without H 2 O 2 production. The bienzyme electrode offered high sensitivity for amperometric determination of glucose at low potential, displaying Michaelis-Menten kinetics. The bienzyme glucose biosensor displayed linear response from 0.1 to 1.2 mM with a sensitivity of 113 mA M -1 cm -2 at an applied potential of -0.10 V in air-saturated electrolytes.

Uptake of acidic and basic sugar derivatives in Lemna gibba G1

International Nuclear Information System (INIS)

Sanz, A.; Ullrich, C.I.

1989-01-01

The uptake of acidic and basic sugar derivatives in Lemna gibba L. was studied. Uronic acids applied to the experimental solution induced a small decrease of the membrane potential. After incubation of the plants in a 0.1 millimolar solution of these substrates, no decrease in the concentration of reducing groups in the external solution was detected. Respiration increased by 31% with 50 millimolar galacturonic acid, whereas no effect was found with the same concentration of glucuronic acid. Glucosamine caused a considerable concentration-dependent membrane depolarization. ( 14 C)glucosamine uptake followed Michaelis-Menten kinetics together with a linear component. Influx of this substrate was inhibited by glucose but the type of competition could not be clearly distinguished. Glucosamine, 50 millimolar, inhibited the respiration rate by 30%. The glucosamine uptake was pH-dependent, with maximum uptake at around pH 7. Lack of enhancement of uptake by low pH as well as the permanent membrane depolarization suggest a uniport mechanism for the charged species of the substrate and an electroneutral diffusion of the uncharged species

Valorisation of food and beverage waste via saccharification for sugars recovery.

Science.gov (United States)

Kwan, Tsz Him; Ong, Khai Lun; Haque, Md Ariful; Kwan, Wing Hei; Kulkarni, Sandeep; Lin, Carol Sze Ki

2018-05-01

Valorisation of mixed food and beverage (F&B) waste was studied for the recovery of sugars via saccharification. Glucoamylase and sucrase were employed to hydrolyse the starch and sucrose present in the mixed F&B waste because of the high cost-effectiveness for such recovery. The Michaelis-Menten kinetics model suggests that preservatives and additives in beverages did not inhibit glucoamylase and sucrase during saccharification. High levels of glucose (228.1 g L -1 ) and fructose (55.7 g L -1 ) were efficiently produced within 12 h at a solid-to-liquid ratio of 37.5% (w/v) in 2.5 L bioreactors. An overall conversion yield of 0.17 g sugars per g of mixed F&B waste was obtained in mass balance analysis. Lastly, possible industrial applications of the sugar-rich hydrolysate and by-products are discussed. This study is believed to cast insights into F&B waste recycling via biotechnology to produce high-value added products to promote the establishment of a circular bio-economy. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Study on Pharmacokinetics of Bosentan with Systems Modeling, Part 2: Prospectively Predicting Systemic and Liver Exposure in Healthy Subjects.

Science.gov (United States)

Li, Rui; Kimoto, Emi; Niosi, Mark; Tess, David A; Lin, Jian; Tremaine, Larry M; Di, Li

2018-04-01

Predicting human pharmacokinetics of novel compounds is a critical step in drug discovery and clinical study design but continues to be a challenging task for hepatic transporter substrates, particularly in predicting their liver exposures. In this study, using bosentan as an example, we prospectively predicted systemic exposure and the (pseudo) steady-state unbound liver-to-unbound plasma ratio ( K p uu ) in healthy subjects using 1) a mechanistic approach solely based on in vitro hepatocyte assays and 2) an approach based on hepatic process rates from monkey in vivo data but Michaelis-Menten constants from in vitro data. Both methods reasonably match the observed human systemic time course data, but the second method leads to better prediction accuracy. In addition, the second method can predict a human K p uu value that is close to the value deduced using clinical data. We also generated rat and monkey liver K p uu values in terminal studies. However, these directly measured animal values are different from the deduced human value. Copyright © 2018 by The American Society for Pharmacology and Experimental Therapeutics.

Application of Littlewood-Paley decomposition to the regularity of Boltzmann type kinetic equations; Application de la decomposition de Littlewood-Paley a la regularite pour des equations cinetiques de type Boltzmann

Energy Technology Data Exchange (ETDEWEB)

EL Safadi, M

2007-03-15

We study the regularity of kinetic equations of Boltzmann type.We use essentially Littlewood-Paley method from harmonic analysis, consisting mainly in working with dyadics annulus. We shall mainly concern with the homogeneous case, where the solution f(t,x,v) depends only on the time t and on the velocities v, while working with realistic and singular cross-sections (non cutoff). In the first part, we study the particular case of Maxwellian molecules. Under this hypothesis, the structure of the Boltzmann operator and his Fourier transform write in a simple form. We show a global C{sup {infinity}} regularity. Then, we deal with the case of general cross-sections with 'hard potential'. We are interested in the Landau equation which is limit equation to the Boltzmann equation, taking in account grazing collisions. We prove that any weak solution belongs to Schwartz space S. We demonstrate also a similar regularity for the case of Boltzmann equation. Let us note that our method applies directly for all dimensions, and proofs are often simpler compared to other previous ones. Finally, we finish with Boltzmann-Dirac equation. In particular, we adapt the result of regularity obtained in Alexandre, Desvillettes, Wennberg and Villani work, using the dissipation rate connected with Boltzmann-Dirac equation. (author)

Current and potential uses of bioactive molecules from marine processing waste.

Science.gov (United States)

Suleria, Hafiz Ansar Rasul; Masci, Paul; Gobe, Glenda; Osborne, Simone

2016-03-15

Food industries produce huge amounts of processing waste that are often disposed of incurring expenses and impacting upon the environment. For these and other reasons, food processing waste streams, in particular marine processing waste streams, are gaining popularity amongst pharmaceutical, cosmetic and nutraceutical industries as sources of bioactive molecules. In the last 30 years, there has been a gradual increase in processed marine products with a concomitant increase in waste streams that include viscera, heads, skins, fins, bones, trimmings and shellfish waste. In 2010, these waste streams equated to approximately 24 million tonnes of mostly unused resources. Marine processing waste streams not only represent an abundant resource, they are also enriched with structurally diverse molecules that possess a broad panel of bioactivities including anti-oxidant, anti-coagulant, anti-thrombotic, anti-cancer and immune-stimulatory activities. Retrieval and characterisation of bioactive molecules from marine processing waste also contributes valuable information to the vast field of marine natural product discovery. This review summarises the current use of bioactive molecules from marine processing waste in different products and industries. Moreover, this review summarises new research into processing waste streams and the potential for adoption by industries in the creation of new products containing marine processing waste bioactives. © 2015 Society of Chemical Industry.

Molecule nanoweaver

Science.gov (United States)

Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL

2009-03-10

A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

The structure of nematic model of liquid crystal with cylindrical and ellipsoidal molecules confined in between walls

Directory of Open Access Journals (Sweden)

M. Moradi

2004-12-01

Full Text Available   The density functional theory analogue of Percus Yevick (PY and Hyper-Netted chain (HNC has been used to write the grand potential of a liquid with cylindrical and ellipsoidal molecules. The integral equations for the density can be obtained by minimizing the grand potential with respect to the density. Some kinds of liquid crystals, can have the cylindrical or ellipsoidal rigid molecules. In this study we have calculated the density profile of this kind of liquids confined between hard walls and we compared the results. As it is seen from the graphs of the density profiles the molecules can be arranged as layers with respect to the walls.

Numerical simulation of dynamic quenching of dual-split fluorescence of molecules with intramolecular hydrogen bonds

International Nuclear Information System (INIS)

Morozov, V.A.; Chuvulkin, N.D.; Smolenskij, E.A.; Dubina, Yu.M.

2014-01-01

The dynamic quenching of intensity pulses of the dual-split fluorescence (DSF) has been simulated using numerical solutions of the equations for the population matrix of five states of the model fluorescent molecule (FM). The state with the highest energy is considered as resonantly excited by irradiation, and two other excited states populated by subsequent relaxation processes are taken as initial states for the FM transitions with emission of the DSF photons. The FM model parameters are selected to fit typical parameters of the molecules with intramolecular proton photo transfer. Quenching is considered as a consequence of non-radiative decay of the FM excited states due to collisions with the quencher molecules. Examples of two types of the DSF quenching of the FM are given. The first type leads to an intramolecular radiationless decay of particular excited states of the FM, and the second one results in radiationless transitions from the same states to the quencher molecule states. (authors)

Electrode redox reactions with polarizable molecules

Science.gov (United States)

Matyushov, Dmitry V.

2018-04-01

A theory of redox reactions involving electron transfer between a metal electrode and a polarizable molecule in solution is formulated. Both the existence of molecular polarizability and its ability to change due to electron transfer distinguish this problem from classical theories of interfacial electrochemistry. When the polarizability is different between the oxidized and reduced states, the statistics of thermal fluctuations driving the reactant over the activation barrier becomes non-Gaussian. The problem of electron transfer is formulated as crossing of two non-parabolic free energy surfaces. An analytical solution for these free energy surfaces is provided and the activation barrier of electrode electron transfer is given in terms of two reorganization energies corresponding to the oxidized and reduced states of the molecule in solution. The new non-Gaussian theory is, therefore, based on two theory parameters in contrast to one-parameter Marcus formulation for electrode reactions. The theory, which is consistent with the Nernst equation, predicts asymmetry between the cathodic and anodic branches of the electrode current. They show different slopes at small electrode overpotentials and become curved at larger overpotentials. However, the curvature of the Tafel plot is reduced compared to the Marcus-Hush model and approaches the empirical Butler-Volmer form with different transfer coefficients for the anodic and cathodic currents.

Small molecule hydration energy and entropy from 3D-RISM

Science.gov (United States)

Johnson, J.; Case, D. A.; Yamazaki, T.; Gusarov, S.; Kovalenko, A.; Luchko, T.

2016-09-01

Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models. Here, we show how to compute temperature derivatives of hydration free energies for the 3D-RISM integral equation approach. We have computed hydration free energies of 1123 small drug-like molecules (both neutral and charged). Temperature derivatives were also used to calculate hydration energies and entropies of 74 of these molecules (both neutral and charged) for which experimental data is available. While direct results have rather poor agreement with experiment, we have found that several previously proposed linear hydration free energy correction schemes give good agreement with experiment. These corrections also provide good agreement for hydration energies and entropies though simple extensions are required in some cases.

Small molecule hydration energy and entropy from 3D-RISM

International Nuclear Information System (INIS)

Johnson, J; Case, D A; Yamazaki, T; Gusarov, S; Kovalenko, A; Luchko, T

2016-01-01

Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models. Here, we show how to compute temperature derivatives of hydration free energies for the 3D-RISM integral equation approach. We have computed hydration free energies of 1123 small drug-like molecules (both neutral and charged). Temperature derivatives were also used to calculate hydration energies and entropies of 74 of these molecules (both neutral and charged) for which experimental data is available. While direct results have rather poor agreement with experiment, we have found that several previously proposed linear hydration free energy correction schemes give good agreement with experiment. These corrections also provide good agreement for hydration energies and entropies though simple extensions are required in some cases. (paper)

Symmetry Adaptation of the Rotation-Vibration Theory for Linear Molecules

Directory of Open Access Journals (Sweden)

Katy L. Chubb

2018-04-01

Full Text Available A numerical application of linear-molecule symmetry properties, described by the D ∞ h point group, is formulated in terms of lower-order symmetry groups D n h with finite n. Character tables and irreducible representation transformation matrices are presented for D n h groups with arbitrary n-values. These groups can subsequently be used in the construction of symmetry-adapted ro-vibrational basis functions for solving the Schrödinger equations of linear molecules. Their implementation into the symmetrisation procedure based on a set of “reduced” vibrational eigenvalue problems with simplified Hamiltonians is used as a practical example. It is shown how the solutions of these eigenvalue problems can also be extended to include the classification of basis-set functions using ℓ, the eigenvalue (in units of ℏ of the vibrational angular momentum operator L ^ z . This facilitates the symmetry adaptation of the basis set functions in terms of the irreducible representations of D n h . 12 C 2 H 2 is used as an example of a linear molecule of D ∞ h point group symmetry to illustrate the symmetrisation procedure of the variational nuclear motion program Theoretical ROVibrational Energies (TROVE.

Application of Littlewood-Paley decomposition to the regularity of Boltzmann type kinetic equations

International Nuclear Information System (INIS)

EL Safadi, M.

2007-03-01

We study the regularity of kinetic equations of Boltzmann type.We use essentially Littlewood-Paley method from harmonic analysis, consisting mainly in working with dyadics annulus. We shall mainly concern with the homogeneous case, where the solution f(t,x,v) depends only on the time t and on the velocities v, while working with realistic and singular cross-sections (non cutoff). In the first part, we study the particular case of Maxwellian molecules. Under this hypothesis, the structure of the Boltzmann operator and his Fourier transform write in a simple form. We show a global C ∞ regularity. Then, we deal with the case of general cross-sections with 'hard potential'. We are interested in the Landau equation which is limit equation to the Boltzmann equation, taking in account grazing collisions. We prove that any weak solution belongs to Schwartz space S. We demonstrate also a similar regularity for the case of Boltzmann equation. Let us note that our method applies directly for all dimensions, and proofs are often simpler compared to other previous ones. Finally, we finish with Boltzmann-Dirac equation. In particular, we adapt the result of regularity obtained in Alexandre, Desvillettes, Wennberg and Villani work, using the dissipation rate connected with Boltzmann-Dirac equation. (author)

The Nernst equation applied to oxidation-reduction reactions in myoglobin and hemoglobin. Evaluation of the parameters.

Science.gov (United States)

Saroff, Harry A

Analyses of the binding of oxygen to monomers such as myoglobin employ the Mass Action equation. The Mass Action equation, as such, is not directly applicable for the analysis of the binding of oxygen to oligomers such as hemoglobin. When the binding of oxygen to hemoglobin is analyzed, models incorporating extensions of mass action are employed. Oxidation-reduction reactions of the heme group in myoglobin and hemoglobin involve the binding and dissociation of electrons. This reaction is described with the Nernst equation. The Nernst equation is applicable only to a monomeric species even if the number of electrons involved is greater than unity. To analyze the oxidation-reduction reaction in a molecule such as hemoglobin a model is required which incorporates extensions of the Nernst equation. This communication develops models employing the Nernst equation for oxidation-reduction reactions analogous to those employed for hemoglobin in the analysis of the oxygenation (binding of oxygen) reaction.

Tunneling anisotropic magnetoresistance in single-molecule magnet junctions

Science.gov (United States)

Xie, Haiqing; Wang, Qiang; Jiao, Hujun; Liang, J.-Q.

2012-08-01

We theoretically investigate quantum transport through single-molecule magnet (SMM) junctions with ferromagnetic and normal-metal leads in the sequential regime. The current obtained by means of the rate-equation gives rise to the tunneling anisotropic magnetoresistance (TAMR), which varies with the angle between the magnetization direction of ferromagnetic lead and the easy axis of SMM. The angular dependence of TAMR can serve as a probe to determine experimentally the easy axis of SMM. Moreover, it is demonstrated that both the magnitude and the sign of TAMR are tunable by the bias voltage, suggesting a new spin-valve device with only one magnetic electrode in molecular spintronics.

[Research on the emission spectrum of NO molecule's γ-band system by corona discharge].

Science.gov (United States)

Zhai, Xiao-dong; Ding, Yan-jun; Peng, Zhi-min; Luo, Rui

2012-05-01

The optical emission spectrum of the gamma-band system of NO molecule, A2 sigma+ --> X2 pi(r), has been analyzed and calculated based on the energy structure of NO molecule' doublet states. By employing the theory of diatomic molecular Spectra, some key parameters of equations for the radiative transition intensity were evaluated theoretically, including the potentials of the doublet states of NO molecule's upper and lower energy levels, the electronic transition moments calculated by using r-centroid approximation method, and the Einstein coefficient of different vibrational and rotational levels. The simulated spectrum of the gamma-band system was calculated as a function of different vibrational and rotational temperature. Compared to the theoretical spectroscopy, the measured results were achieved from corona discharge experiments of NO and N2. The vibrational and rotational temperatures were determined approximately by fitting the measured spectral intensities with the calculated ones.

Continuum Navier-Stokes modelling of water ow past fullerene molecules

DEFF Research Database (Denmark)

Walther, J. H.; Popadic, A.; Koumoutsakos, P.

We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the computational cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently...

Continuum Navier-Stokes modelling of water flow past fullerene molecules

DEFF Research Database (Denmark)

Walther, J. H.; Popadic, A.; Koumoutsakos, P.

We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the computational cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently...

Estudio cinético del proceso de digestión anaerobia de aguas de lavado de aceitunas de almazara en reactores de mezcla completa con microorganismos inmovilizados

Directory of Open Access Journals (Sweden)

Borja, Rafael

1999-04-01

Full Text Available A kinetic study of the continuous anaerobic digestion process of wastewaters from the washing of olives prior to the oil production process was carried out in a completely mixed reactor with sepiolite immobilised biomass at 35° C. Four influent COD concentrations, 4,5, 3,5, 2,5 y 1,5 g COD/I were used as substrate operating for a hydraulic retention time range of 4,5 to 1,25 days. The Michaelis-Menten model has been applied, obtaining the values of the maximum substrate utilization rate, k( (g COD/g VSS day, and the kinetic constant of the process, K_s (g COD/I, for each influent substrate concentration studied. The values of these parameters significantly decreased with decreasing concentration of influent wastewater, showing the highest values for the greatest influent substrate concentration used as feed. The microbial yield coefficient, Y_x, and sludge decay rate coefficient, k_d, were also determined to be 0,14 g VSS/g COD and 0,003 days^-1 respectively.

Se ha efectuado un estudio cinético del proceso de digestión anaerobia en régimen continuo de aguas de lavado de aceitunas de almazara en un reactor de mezcla completa utilizando sepiolita como soporte para la inmovilización de los microorganismos responsables del proceso, a la temperatura de 35° C. Se utilizan cuatro concentraciones de sustrato como alimento, 4,5, 3,5, 2,5 y 1,5g DQO/I, operando con cada una de ellas en un rango de tiempos de retención hidráulicos de 4,5 a 1,25 días. Para ello, se aplica el método cinético de Michaelis-Menten, obteniéndose los valores de la velocidad máxima de utilización de sustrato, k(g DQO/g SSV día, y de la constante cinética del proceso, K_s (g DQO/I, para cada concentración de sustrato objeto de estudio. Se observa que estas constantes cinéticas disminuyen de forma significativa al disminuir la concentración de sustrato en el alimento